diff --git a/data/covid/preprints-summary.csv b/data/covid/preprints-summary.csv index 6773f0d5..296aa0a7 100644 --- a/data/covid/preprints-summary.csv +++ b/data/covid/preprints-summary.csv @@ -1,49 +1,49 @@ -health policy,primary care research,microbiology,cardiovascular medicine,genomics,emergency medicine,ophthalmology,infectious diseases,pathology,month,obstetrics and gynecology,health economics,systems biology,geriatric medicine,neurology,respiratory medicine,orthopedics,immunology,evolutionary biology,dentistry and oral medicine,pediatrics,radiology and imaging,hiv aids,allergy and immunology,intensive care and critical care medicine,dermatology,molecular biology,health informatics,genetic and genomic medicine,occupational and environmental health,pharmacology and therapeutics,biophysics,psychiatry and clinical psychology,public and global health,scientific communication and education,biochemistry,surgery,oncology,epidemiology,Total,health systems and quality improvement,bioinformatics -,,,,,,,,,Jan-24,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,1,, -,,,1,,,,,,Dec-23,,2,,,1,,,,,,,,,,,,,,,1,,,,1,,,,,4,10,, -,,,,,,,1,,Nov-23,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,2,4,, -,,,,,,,1,,Oct-23,,,,,,,,1,,,,,,,,,,1,,,,,,,,,,,1,4,, -,,,,,,,1,,Sep-23,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,, -,1,,,,,,,,Aug-23,,,,,,,,,,,,,,,,,,,,1,,,,1,,,,,4,7,, -,,,,,,,,,Jul-23,,,,,,,,,,,,,,,,,,,1,,,,,,,,,,3,6,2, -,,,,,,,2,,Jun-23,,,,,,,1,,,,,,,,,,,1,,1,,,,,1,,,,1,7,, -,,,,,,,1,,May-23,,,,,,1,,1,,,,,,,,,,,,,,,,1,,,,,2,6,, -,,,,,,,1,,Apr-23,,,,,,,,,,,,,,,,,,,,,,,,2,,,,,,3,, -,,,,,,,3,,Mar-23,,,,,,,,,,,,,,,,,,,,1,,,1,2,,,,,1,8,, -,,,,,,,,,Feb-23,,,,,1,1,,,,,,,,,,,,,,,,,,2,,,,,3,7,, -,,,,,,,1,,Jan-23,,,,,,,,,,,,,,,,,,,,,,,,,,,,,5,6,, -1,,,,,,,4,1,Dec-22,,,,,,2,,,,,,,,,,,,,,,,,,1,,,,,3,12,, -,,,,,,,4,,Nov-22,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,4,, -,,,1,,,,2,,Oct-22,,,,,,,,,,,,,,,,,,,,,,,,2,,,,,1,6,, -,,1,,,,,2,,Sep-22,,,,,,1,,,,,1,,,,,,,,,2,,,,1,,,,,,8,, -,,,,,,,3,,Aug-22,,,,,,,,,,,,,,,,,,,,,,,,2,,,,,4,9,, -,,,,,,,3,,Jul-22,,,,,,,,1,,,1,,,,,,,1,,,,,,,,,,,2,8,, -,,,,,,,4,,Jun-22,,,,,,,,,,,,,,,,,,1,1,,,,5,1,,,,,6,18,, -,1,1,,,,,5,,May-22,,1,,,,,,,,,,,,,,,,,,,,,2,1,,,,,2,14,1, -,,1,1,,,,3,,Apr-22,,1,,,,1,,,,,,,,,,,,,,1,,,,1,,,,,5,16,2, -,1,,,,,,5,,Mar-22,,,,,,1,,,1,,,,,,,,,,,,,,1,,,,,,9,18,, -,,,,,,,3,,Feb-22,,,,,1,,,,,,,,,,,,,,,,,,,1,,,,,6,11,, -,,,1,,,,2,,Jan-22,,,,,,,,,,,,,,,,,,2,,1,,,,1,,,,,5,12,, -,1,1,1,,,,6,,Dec-21,,,,,1,,,,,,1,,,,,,,,,,,,,1,,,,,10,22,, -,1,,,1,,,5,,Nov-21,,,,,1,,,,,,,,,,1,,,,,,,1,1,3,,,,,9,25,2, -,,,,,,,3,,Oct-21,,,,1,,,,,,,1,,,,,,,,,,,,2,,,,,,4,11,, -,,,1,,,,5,,Sep-21,,,,,,,,,,,,,,,1,,,1,,,1,,,2,,,,,6,17,, -,,,1,,,,3,,Aug-21,,,,,,1,,,,,,,,,1,,,1,,1,,,,3,,,,,2,13,, -,,,,,1,,12,,Jul-21,,,,,,2,,,,,1,,,,1,,,,1,,,,,4,,,,1,3,26,, -,1,,,,,,7,,Jun-21,,,,,1,,,1,,,1,,,1,1,,,1,,1,,,1,4,,,,,7,28,1, -,,,,,,,8,,May-21,,,,,,,,,,,,,,,,1,,1,1,,,,1,1,,,,,11,24,, -,1,1,,,,,7,,Apr-21,,,,,,,,,,,,,,1,,,,1,,2,,,1,1,,,,,4,20,1, -,,,,,,,17,,Mar-21,,,,2,1,,,,,,1,1,,,,,,2,1,,,,1,5,,1,1,,6,39,, -,,,1,,,,9,,Feb-21,,1,,,,,,,,,,,,,,,,1,,,,,,1,,,1,,9,24,1, -1,1,,,,,,8,,Jan-21,,,,1,,,,1,,1,,,,,1,,,,,,,,,2,,,,,4,21,1, -,1,1,2,2,,,4,,Dec-20,,,,,,,,,,,,,,,,,,3,,,,,2,2,,,,,4,22,1, -1,,,,,,,13,,Nov-20,,,,,,,,1,,,,,,,,,,1,,,,,,5,,,,,6,28,,1 -1,1,,,,,,11,,Oct-20,,,1,1,,,,1,,,,,,,1,,,1,,,,,3,,,,,1,6,29,,1 -,1,1,,,3,,8,,Sep-20,,,,,,,,,,,,,1,,1,,,,,,,,1,3,,,,,6,25,, -,,,,,2,,12,,Aug-20,1,,,,,,,,,,,,,,,,1,,1,1,,,,2,,,,,6,27,1, -,,,1,1,,,8,,Jul-20,,,,,,1,,,,,,,,,1,,,,,,,,1,4,,,,,8,25,, -1,,,1,,,1,10,,Jun-20,,,,1,,1,,1,,,,,,,3,,,1,,,,,4,3,,,,1,7,37,1,1 -,,,2,,,,10,,May-20,,1,,1,,1,,,,,,,,,1,,,1,,1,,,,9,,,,1,8,37,,1 -,,,,1,,,7,,Apr-20,,,,,,,,,,,,,,,,,,,2,,,,,1,,,,,6,18,1, -,,,,,,,1,,Mar-20,,,,,,,,,,,,,,,,,,,,,,,,3,,,,,4,8,, -,,,,,,,1,,Feb-20,,,,,,,,,,,,,,,,,,,,,,,,2,,,,,4,7,, +genetic and genomic medicine,biophysics,immunology,occupational and environmental health,health informatics,radiology and imaging,bioinformatics,geriatric medicine,epidemiology,respiratory medicine,genomics,health systems and quality improvement,pharmacology and therapeutics,microbiology,biochemistry,surgery,health policy,obstetrics and gynecology,psychiatry and clinical psychology,allergy and immunology,molecular biology,systems biology,hiv aids,oncology,neurology,intensive care and critical care medicine,pediatrics,emergency medicine,Total,scientific communication and education,health economics,infectious diseases,dentistry and oral medicine,orthopedics,public and global health,evolutionary biology,dermatology,primary care research,ophthalmology,pathology,month,cardiovascular medicine +,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,1,,,,,,Jan-24, +,,,1,,,,,3,,,,,,,,,,,,,,,,1,,,,9,,2,,,,1,,,,,,Dec-23,1 +,,,,,,,,2,,,,,,,,,,,,,,,1,,,,,4,,,1,,,,,,,,,Nov-23, +,,,,1,,,,1,1,,,,,,,,,,,,,,,,,,,4,,,1,,,,,,,,,Oct-23, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,1,,,,,,,,,Sep-23, +,,,1,,,,,4,,,,,,,,,,,,,,,,,,,,7,,,,,,1,,,1,,,Aug-23, +1,,,,,,,,3,,,2,,,,,,,,,,,,,,,,,7,,,,,,1,,,,,,Jul-23, +,,,1,1,,,,1,,,,,,,,,,,,,,,,,,,,7,1,,2,,1,,,,,,,Jun-23, +,,1,,,,,,2,1,,,,,,,,,,,,,,,,,,,6,,,1,,,1,,,,,,May-23, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,3,,,1,,,2,,,,,,Apr-23, +,,,,,,,,2,,,,,,,,,,1,,,,,,,,,,8,,,3,,,2,,,,,,Mar-23, +,,,,,,,,4,1,,,,,,,,,,,,,,,1,,,,8,,,,,,2,,,,,,Feb-23, +,,,,,,,,5,,,,,,,,,,,,,,,,,,,,6,,,1,,,,,,,,,Jan-23, +,,,,,,,,3,2,,,,,,,1,,,,,,,,,,,,12,,,4,,,1,,,,,1,Dec-22, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,4,,,4,,,,,,,,,Nov-22, +,,,,,,,,1,,,,,,,,,,,,,,,,,,,,6,,,2,,,2,,,,,,Oct-22,1 +,,,2,,,,,1,1,,,,1,,,,,,,,,,,,,1,,9,,,2,,,1,,,,,,Sep-22, +,,,,,,,,4,,,,,,,,,,,,,,,,,,,,10,,,3,,,3,,,,,,Aug-22, +,,1,,1,,,,2,,,,,,,,,,,,,,,,,,1,,8,,,3,,,,,,,,,Jul-22, +1,,,,1,,,,5,,,,,,,,,,5,,,,,,,,,,17,,,4,,,1,,,,,,Jun-22, +,,,,,,,,2,,,1,,1,,,,,2,,,,,,,,,,12,,1,4,,,,,,1,,,May-22, +,,,1,,,,,5,1,,2,,1,,,,,,,,,,,,,,,15,,1,2,,,1,,,,,,Apr-22,1 +,,,,,,,,9,1,,,,,,,,,1,,,,,,,,,,18,,,5,,,,1,,1,,,Mar-22, +,,,,,,,,6,,,,,,,,,,,,,,,,1,,,,12,,,4,,,1,,,,,,Feb-22, +,,1,1,1,,,,5,,,,,,,,,,,,,,,,,,,,13,,,3,,,1,,,,,,Jan-22,1 +,,,,,,,,10,,,,,1,,,,,,,,,,,1,,1,,24,,,8,,,1,,,1,,,Dec-21,1 +,1,,,,,,,9,,1,2,,,,,,,1,,,,,,1,1,,,25,,,5,,,3,,,1,,,Nov-21, +,,,,,,,1,4,,,,,,,,,,2,,,,,,,,1,,11,,,3,,,,,,,,,Oct-21, +,,,,1,,,,6,,,,1,,,,,,,,,,,,,,,,16,,,5,,,2,,,,,,Sep-21,1 +,,,1,1,,,,2,1,,,,,,,,,,,,,,,,1,,,13,,,3,,,3,,,,,,Aug-21,1 +1,,,,,,,,3,2,,,,,,,,,,,,,,1,,1,1,1,26,,,12,,,4,,,,,,Jul-21, +,,1,1,1,,,,6,,,1,,,,,,,1,1,,,,,1,1,1,,27,,,7,,,4,,,1,,,Jun-21, +,,,,1,,,,10,,,,,,,,,,1,,,,,,,,,,22,,,8,,,1,,1,,,,May-21, +,,,2,1,,,,4,,,1,,1,,,,,1,1,,,,,,,,,20,,,7,,,1,,,1,,,Apr-21, +1,,,,2,1,,2,6,,,,,,1,1,,,1,,,,,,1,,1,,39,,,17,,,5,,,,,,Mar-21, +,,,,1,,,,9,,,1,,,,1,,,,,,,,,,,,,24,,1,9,,,1,,,,,,Feb-21,1 +,,1,,,,,1,4,,,1,,,,,1,,1,,,,,,,1,,,23,,,8,1,,3,,,1,,,Jan-21, +,,,,3,,,,4,,2,1,,1,,,,,2,,,,,,,,,,23,,,4,,,3,,,1,,,Dec-20,2 +,,1,,1,,1,,6,,,,,,,,1,,,,,,,,,,,,27,,,12,,,5,,,,,,Nov-20, +,,1,,1,,1,1,6,,,,,,,,1,,3,,,1,,1,,1,,,30,,,12,,,,,,1,,,Oct-20, +,,,,1,,,,5,,,,,1,,,,,2,,,,1,,,1,,3,26,,,8,,,3,,,1,,,Sep-20, +1,,,1,,,,,6,,,1,,,,,,1,,,1,,,,,,,2,27,,,12,,,2,,,,,,Aug-20, +,,1,,,,,,10,1,1,,,,,,,,1,,,,,,,1,,,28,,,8,,,4,,,,,,Jul-20,1 +,,1,,1,,1,1,7,1,,1,,,,,1,,4,,,,,1,,3,,,36,,,9,,,3,,,,1,,Jun-20,1 +,,,1,1,,1,1,7,1,,,,,,,,,,,,,,1,,1,,,34,,1,9,,,9,,,,,,May-20,1 +2,,,,,,,,7,,1,1,,,,,,,,,,,,,,,,,19,,,7,,,1,,,,,,Apr-20, +,,,,,,,,4,,,,,,,,,,,,,,,,,,,,8,,,1,,,3,,,,,,Mar-20, +,,,,,,,,4,,,,,,,,,,,,,,,,,,,,7,,,1,,,2,,,,,,Feb-20, diff --git a/data/covid/preprints.csv b/data/covid/preprints.csv index 9fe2d7d0..94e5f404 100644 --- a/data/covid/preprints.csv +++ b/data/covid/preprints.csv @@ -88,13 +88,6 @@ OutcomesWe considered eight outcomes: depression, serious mental illness, genera InterpretationIncidence of mental illness is elevated for up to a year following severe COVID-19 in unvaccinated people. Vaccination mitigates the adverse effect of COVID-19 on mental health. FundingMedical Research Council (MC_PC_20059) and NIHR (COV-LT-0009).",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2023.12.04.23299364,2023-12-04,https://medrxiv.org/cgi/content/short/2023.12.04.23299364,Clinical coding of long COVID in primary care 2020-2023 in a cohort of 19 million adults: an OpenSAFELY analysis,Alasdair D Henderson; Ben FC Butler-Cole; John Tazare; Laurie A Tomlinson; Michael Marks; Mark Jit; Andrew Briggs; Liang-Yu Lin; Oliver Carlile; Christopher Bates; John Parry; Sebastian CJ Bacon; Iain Dillingham; William A Dennison; Ruth E Costello; Yinghui Wei; Alex J Walker; William Hulme; Ben Goldacre; Amir Mehrkar; Brian MacKenna; The OpenSAFELY Collaborative; Emily Herrett; Rosalind M Eggo,"London School of Hygiene & Tropical Medicine; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; TPP, TPP House, 129 Low Lane, Horsforth, Leeds; TPP, TPP House, 129 Low Lane, Horsforth, Leeds; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Patient and Public Involvement Steering Committee, London,; London School of Hygiene & Tropical Medicine; Centre for Mathematical Sciences, School of Engineering, Computing and Mathematics, University of Plymouth, Plymouth; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine","BackgroundLong COVID is the patient-coined term for the persistent symptoms of COVID-19 illness for weeks, months or years following the acute infection. There is a large burden of long COVID globally from self-reported data, but the epidemiology, causes and treatments remain poorly understood. Primary care is used to help identify and treat patients with long COVID and therefore Electronic Health Records (EHRs) of past COVID-19 patients could be used to help fill these knowledge gaps. We aimed to describe those with long COVID in primary care records in England. - -MethodsWith the approval of NHS England we used routine clinical data from over 19 million adults in England linked to SARS-COV-2 test result, hospitalisation and vaccination data to describe trends in the recording of 16 clinical codes related to long COVID between November 2020 and January 2023. We calculated rates per 100,000 person-years and plotted how these changed over time. We compared crude and minimally adjusted rates of recorded long COVID in patient records between different key demographic and vaccination characteristics using negative binomial models. - -FindingsWe identified a total of 55,465 people recorded to have long COVID over the study period, with incidence of new long COVID records increasing steadily over 2021, and declining over 2022. The overall rate per 100,000 person-years was 177.5 cases in women (95% CI: 175.5-179) and 100.5 men (99.5-102). In terms of vaccination against COVID-19, the lowest rates were observed in those with 3+ vaccine doses (103.5 [95% CI: 101.5-105]). Finally, the majority of those with a long COVID record did not have a recorded positive SARS-COV-2 test 12 weeks before the long COVID record. - -InterpretationEHR recorded long COVID remains very low compared and incident records of long COVID declined over 2022. We found the lowest rates of recorded long COVID in people with 3 or more vaccine doses. We summarised several sources of possible bias for researchers using EHRs to study long COVID.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.11.30.23299229,2023-12-01,https://medrxiv.org/cgi/content/short/2023.11.30.23299229,Population age as a key factor in the COVID-19 pandemic dynamics,Igor Nesteruk; Matt Keeling,"Institute of Hydromechanics National Academy of sciences of Ukraine; School of Life Sciences & Mathematics Institute, University of Warwick, UK","The population and governments of many countries are losing interest in the SARS-CoV-2 infection, the number of tests and the number of new cases detected is sharply decreasing. To compare the accumulated numbers CC of cases and deaths DC per million and to answer the question why the less vaccinated Africa has accumulated 36 times lower CC values and 15 times lower DC values than Europe, simple statistical analysis have been performed. CC and DC values demonstrated rather strong correlation with the median age of populations. One-year increment in the median year yields 12-18 thousand increase in CC values and 52-83 increase in DC values. Zero-COVID countries succeed to have much lower numbers of deaths per capita and case fatality ratios DC/CC.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.11.28.23299156,2023-11-29,https://medrxiv.org/cgi/content/short/2023.11.28.23299156,Examining the association of live virus neutralisation activity of capillary microsamples and risk of SARS-CoV-2 infections: a nested case control study within the Virus Watch community cohort,Alexei Yavlinsky; Vincent Nguyen; Sarah Beale; Emma Wall; Mary Y Wu; Isobel Braithwaite; Jana Kovar; Madhumita Shrotri; Annalan Mathew Dwight Navaratnam; Wing Lam Erica Fong; Thomas Edward Byrne; Francois Balloux; Ibrahim Abubakar; Benjamin J Cowling; Andrew Hayward; Robert W Aldridge,University College London; University College London; University College London; The Francis Crick Institute; The Francis Crick Institute; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; The University of Hong Kong; University College London; University College London,"Due to the proliferation of new SARS-CoV-2 variants, most COVID-19 cases are now caused by post-vaccine infections and a substantial proportion are reinfections. While prior research on correlates of protection has focused on the role of anti-spike antibodies, the results of the corresponding antibody assays may not accurately predict the risk of infection with new SARS-CoV-2 variants. In this study, we investigated the association between live virus neutralising antibody activity and SARS-CoV-2 infection risk using self-administered capillary microsample blood tests from VirusWatch participants. The study was conducted during the transition between the dominance of the B.1.617.2 (Delta) and B.1.1.529 (Omicron BA.1) SARS-CoV-2 variants, enabling us to investigate the association between variant-specific virus inhibition and subsequent infections within each dominance period. Greater inhibition of Omicron BA.1 live virus was associated with a reduction in infection risk during both the Delta and Omicron BA.1 dominance periods. Delta virus inhibition was associated with infection risk reduction during the Delta dominance period, but we found no association between Delta inhibition and protection against infection during the Omicron BA.1 dominance period. Our results are consistent with earlier findings and suggest that variant-specific serosurveillance of immunity and protection against SARS-CoV-2 infection at the population level could inform public health policy in near-real time using inexpensive and accessible home-based testing.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.11.24.23296021,2023-11-27,https://medrxiv.org/cgi/content/short/2023.11.24.23296021,Severe acute myositis and myocarditis upon initiation of six-weekly Pembrolizumab post-COVID-19 mRNA vaccination,Robert Aerwyn Watson; Weiyu Ye; Chelsea Alice Taylor; Rosalin Anisha Cooper; Orion Tong; Tim James; Brian Shine; Monika Hofer; Damian Jenkins; Robert Pell; Eleni Ieremia; Stephanie Jones; David Maldonado-Perez; Ian Roberts; Nicholas Coupe; Mark Ross Middleton; Miranda Jane Payne; Benjamin Peter Fairfax,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Oxford; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; University of Oxford; Oxford University Hospitals NHS Foundation Trust; University of Oxford,"We describe three cases of critical acute myositis with myocarditis occurring within 22 days of each other at a single institution, all within one month of receiving the initial cycle of the anti-PD-1 drug Pembrolizumab. Analysis of T cell receptor repertoires from peripheral blood and tissues revealed a high degree of clonal expansion and public clones between cases, with several T cell clones expanded within the skeletal muscle putatively recognising viral epitopes. All patients had recently received a COVID-19 mRNA booster vaccine prior to treatment and were positive for SARS-CoV2 Spike antibody. In conclusion, we report a series of unusually severe myositis and myocarditis following PD-1 blockade and the COVID-19 mRNA vaccination.",oncology,fuzzy,100,100 @@ -115,13 +108,6 @@ MethodsConcentrations for black carbon(BC), particulate matter 10(PM10), particu ResultsSingle pollutant analysis showed the direct effect of higher risk of SARS-CoV-2 infection with increased exposure to PM2.5(RR1.11,95%CI 1.08;1.15), PM10(RR1.06,95%CI 1.04;1.09), NO2(RR1.04,95%CI 1.04;1.05) and NOx(RR1.02,95%CI 1.02;1.02) per 1{micro}g/m3 increment with DEFRA 2015-19 data. Sensitivity analyses altering covariates, exposure window and modelled air pollution data source produced similar estimates. Higher risk of SARS-CoV-2 per 10-5m-1 increment of BC (RR1.86, 95%CI 1.62;2.14) was observed using ELAPSE data. ConclusionLong term exposure to higher concentrations of air pollutions increases the risk of SARS-CoV-2 infection, highlighting that adverse health effects of air pollution is not only limited to non-communicable diseases.",epidemiology,fuzzy,100,100 -bioRxiv,10.1101/2023.10.22.563481,2023-10-24,https://biorxiv.org/cgi/content/short/2023.10.22.563481,Microfluidic antibody profiling after repeated SARS-CoV-2 vaccination links antibody affinity and concentration to impaired immunity and variant escape in patients on anti-CD-20 therapy,Ashley Priddey; Michael Xin Hua Chen-Xu; Daniel James Cooper; Serena MacMillan; Georg Meisl; Catherine K Xu; Myra Hosmillo; Ian G Goodfellow; Rafael Kollyfas; Rainer Doffinger; John R Bradley; Irina I Mohorianu; Rachel Jones; Tuomas P.J. Knowles; Rona Smith; Vasilis Kosmoliaptsis,"Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK; Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK; Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK and NIHR Blood and Transplant Research Unit in Organ D","BackgroundPatients with autoimmune/inflammatory conditions on anti-CD20 therapies, such as Rituximab, have suboptimal humoral responses to vaccination and are vulnerable to poorer clinical outcomes following SARS-CoV-2 infection. We aimed to examine how the fundamental parameters of antibody responses, namely affinity and concentration, shape the quality of humoral immunity after vaccination in these patients. - -MethodsWe performed in depth antibody characterisation in sera collected four to six weeks after each of three vaccine doses to wild-type (WT) SARS-CoV-2 in Rituximab-treated primary vasculitis patients (n=14) using Luminex and pseudovirus neutralisation assays, whereas a novel microfluidic-based immunoassay was used to quantify polyclonal antibody affinity and concentration against both WT and Omicron (B.1.1.529) variants. Comparative antibody profiling was performed at equivalent time points in healthy individuals after three antigenic exposures to WT SARS-CoV-2 (one infection and two vaccinations; n=15) and in convalescent patients after WT SARS-CoV-2 infection (n=30). - -ResultsRituximab-treated patients had lower antibody levels and neutralisation titres against both WT and Omicron SARS-CoV-2 variants compared to healthy individuals. Neutralisation capacity was weaker against Omicron versus WT both in Rituximab-treated patients and in healthy individuals. In the Rituximab cohort, this was driven by lower antibody affinity against Omicron versus WT (median [range] KD: 21.6 [9.7-38.8] nM vs 4.6 [2.3-44.8] nM, p=0.0004). By contrast, healthy individuals with hybrid immunity produced a broader antibody response, a subset of which recognised Omicron with higher affinity than antibodies in Rituximab-treated patients (median [range] KD: 1.05 [0.45-1.84] nM vs 20.25 [13.2-38.8] nM, p=0.0002), underpinning the stronger serum neutralisation capacity against Omicron in the former group. Rituximab-treated patients had similar anti-WT antibody levels and neutralisation titres to unvaccinated convalescent individuals, despite two more exposures to SARS-CoV-2 antigen. Temporal profiling of the antibody response showed evidence of affinity maturation in healthy convalescent patients after a single SARS-CoV-2 infection which was not observed in Rituximab-treated patients, despite repeated vaccination. - -DiscussionOur results enrich previous observations of impaired humoral immune responses to SARS-CoV-2 in Rituximab-treated patients and highlight the significance of quantitative assessment of serum antibody affinity and concentration in monitoring anti-viral immunity, viral escape, and the evolution of the humoral response.",immunology,fuzzy,100,100 medRxiv,10.1101/2023.10.12.23296948,2023-10-13,https://medrxiv.org/cgi/content/short/2023.10.12.23296948,"A nationwide study of 331 rare diseases among 58 million individuals: prevalence, demographics, and COVID-19 outcomes",Johan H Thygesen; HUAYU ZHANG; Hanane Issa; Jinge Wu; Tuankasfee Hama; Ana-Catarina Pinho-Gomes; Tudor Groza; Sara Khalid; Richard Lumbers; Mevhibe Hocaoglu; Kamlesh Khunti; Rouven Priedon; Amitava Banerjee; Nikolas Pontikos; Christopher Tomlinson; Ana Torralbo; Paul Taylor; Cathie Sudlow; Spiros Denaxas; Harry Hemingway; Honghan Wu,"Institute of Health Informatics, University College London, London, UK; Advanced Care Research Centre, Usher Institute, University of Edinburgh, Edinburgh, UK.; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, UK; Institute of Health Informatics, University College London, London, UK; Cicely Saunders Institute of Palliative Care, Policy and Rehabilitation, Kings College London, London, UK; College of Life Sciences, University of Leicester, Leicester, UK; Health Data Research UK, London, UK; Institute of Health Informatics, University College London, London, UK; UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Health Data Research UK, London, UK; British Heart Foundation Data Science Centre, London, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edin; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK","BackgroundThe Global Burden of Disease study has provided key evidence to inform clinicians, researchers, and policy makers across common diseases, but no similar effort with single study design exists for hundreds of rare diseases. Consequently, many rare conditions lack population-level evidence including prevalence and clinical vulnerability. This has led to the absence of evidence-based care for rare diseases, prominently in the COVID-19 pandemic. MethodThis study used electronic health records (EHRs) of more than 58 million people in England, linking nine National Health Service datasets spanning healthcare settings for people alive on Jan 23, 2020. Starting with all rare diseases listed in Orphanet, we quality assured and filtered down to analyse 331 conditions with ICD-10 or SNOMED-CT mappings clinically validated in our dataset. We report 1) population prevalence, clinical and demographic details of rare diseases, and 2) investigate differences in mortality with SARs-CoV-2. @@ -137,6 +123,15 @@ Research in contextO_ST_ABSEvidence before the studyC_ST_ABSWe have previously p Added value of this studyIn this study we use national scale EHR data from England to report age and gender adjusted point prevalence for 331 rare diseases, with clinically-validated ICD-10 and/or SNOMED-CT code lists. Among these, 186 (56.2%) diseases did not have existing point prevalence data available in Orphanet. To our knowledge, this is the first time that rare diseases have been examined on a national scale, encompassing a population of over 58 million people. The large sample size provides sufficient statistical power to detect and describe enough carriers of even very rare conditions <1 case per million. Our analysis of COVID-related mortality has demonstrated the clinical relevance of national data for rare diseases. Specifically, we identified eight rare conditions that are associated with a significantly increased risk of mortality from COVID-19, even among fully vaccinated individuals. Implication of all the available evidenceThese findings provide robust reproducible prevalence, gender, and ethnicity estimates for disease that may often have been under prioritised, and where such information in most cases was not previously available. Our COVID-19 mortality findings highlight the need for targeted policy and support addressing the high level of vulnerability of these patients to COVID-19.",health informatics,fuzzy,100,100 +medRxiv,10.1101/2023.10.11.23296866,2023-10-12,https://medrxiv.org/cgi/content/short/2023.10.11.23296866,"SARS-CoV-2, influenza A/B and respiratory syncytial virus positivity and association with influenza-like illness and self-reported symptoms, over the 2022/23 winter season in the UK: a longitudinal surveillance cohort",Elisabeth Dietz; Emma Elizabeth Pritchard; Koen Pouwels; Muhammad Ehsaan; Joshua Blake; Charlotte Gaughan; Eric Haduli; Hugh Boothe; Karina-Doris Vihta; Tim Peto; Nicole Stoesser; Philippa Matthews; Nick Taylor; Ian Diamond; Ruth Studley; Emma Rourke; Paul Birrell; Daniela De Angelis; Tom Fowler; Conall Watson; David W Eyre; Thomas House; Ann Sarah Walker,University of Oxford; University of Oxford; University of Oxford; Berkshire and Surrey Pathology Services; University of Cambridge; Office of National Statistics; Berkshire and Surrey Pathology Services; Berkshire and Surrey Pathology Services; University of Oxford; University of Oxford; University of Oxford; The Francis Crick Institute; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Cambridge; University of Cambridge; UK Health Security Agency; UK Health Security Agency; University of Oxford; University of Manchester; University of Oxford,"BackgroundSyndromic surveillance often relies on patients presenting to healthcare. Community cohorts, although more challenging to recruit, could provide additional population-wide insights, particularly with SARS-CoV-2 co-circulating with other respiratory viruses. + +MethodsWe estimated positivity and incidence of SARS-CoV-2, influenza A/B, and RSV, and trends in self-reported symptoms including influenza-like illness (ILI), over the 2022/23 winter season in a broadly representative UK community cohort (COVID-19 Infection Survey), using negative-binomial generalised additive models. We estimated associations between test positivity and each of symptoms and influenza vaccination, using adjusted logistic and multinomial models. + +FindingsSwabs taken at 32,937/1,352,979 (2.4%) assessments tested positive for SARS-CoV-2, 181/14,939 (1.2%) for RSV and 130/14,939 (0.9%) for influenza A/B, varying by age over time. Positivity and incidence peaks were earliest for RSV, then influenza A/B, then SARS-CoV-2, and were highest for RSV in the youngest and for SARS-CoV-2 in the oldest age-groups. Many test-positives did not report key symptoms: middle-aged participants were generally more symptomatic than older or younger participants, but still only [~]25% reported ILI-WHO and [~]60% ILI-ECDC. Most symptomatic participants did not test positive for any of the three viruses. Influenza A/B-positivity was lower in participants reporting influenza vaccination in the current and previous seasons (odds ratio=0.55 (95% CI 0.32,0.95)) versus neither season. + +InterpretationSymptom profiles varied little by aetiology, making distinguishing SARS-CoV-2, influenza and RSV using symptoms challenging. Most symptoms were not explained by these viruses, indicating the importance of other pathogens in syndromic surveillance. Influenza vaccination was associated with lower rates of community influenza test positivity. + +FundingUK Health Security Agency, Department of Health and Social Care, National Institute for Health Research.",respiratory medicine,fuzzy,100,100 medRxiv,10.1101/2023.10.06.23296657,2023-10-06,https://medrxiv.org/cgi/content/short/2023.10.06.23296657,The macroeconomic and epidemiological impacts of Covid-19 in Pakistan.,Henning Tarp Jensen; Marcus R. Keogh-Brown; Rosalind M Eggo; Carl A. B. Pearson; Sergio Torres-Rueda; Maryam Huda; Muhammad Khalid; Wahaj Sulfiqar; - CMMID COVID-19 Working Group; Richard D. Smith; Mark Jit; Anna Vassall,"London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; Aga Khan University; Ministry of National Health Services, Regulations & Coordination, Islamabad, Pakistan; Ministry of National Health Services, Regulations & Coordination, Islamabad, Pakistan; -; University of Exeter; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine","""Coronavirus Disease 2019"" (C19) is a respiratory illness caused by ""new Coronavirus"" SARS-CoV-2. The C19 pandemic, which engulfed the world in 2021, also caused a national C19 epidemic in Pakistan, who responded with initial forced lockdowns (15-30 March 2020) and a subsequent switch to a smart lockdown strategy, and, by 31 December 2020, Pakistan had managed to limit confirmed cases and case fatalities to 482,506 (456 per 100,000) and 10,176 (4.8 per 100,000). The early switch to a smart lockdown strategy, and successful follow-up move to central coordination and effective communication and enforcement of Standard Operating Procedures, was motivated by a concern over how broad-based forced lockdowns would affect poor households and day-labour. The current study aims to investigate how the national Pakistan C19 epidemic would have unfolded under an uncontrolled baseline scenario and an alternative set of controlled non-pharmaceutical intervention (NPI) policy lockdown scenarios, including health and macroeconomic outcomes. We employ a dynamically-recursive version of the IFPRI Standard Computable General Equilibrium model framework (Lofgren, Lee Harris and Robinson 2002), and a, by now, well-established epidemiological transmission-dynamic model framework (Davies, Klepac et al 2020) using Pakistan-specific 5-year age-group contact matrices on four types of contact rates, including at home, at work, at school, and at other locations (Prem, Cook & Jit 2017), to characterize an uncontrolled spread of disease. Our simulation results indicate that an uncontrolled C19 epidemic, by itself, would have led to a 0.12% reduction in Pakistani GDP (-721mn USD), and a total of 0.65mn critically ill and 1.52mn severely ill C19 patients during 2020-21, while 405,000 Pakistani citizens would have lost their lives. Since the majority of case fatalities and symptomatic cases, respectively 345,000 and 35.9mn, would have occurred in 2020, the case fatality and confirmed case numbers, observed by 31. December 2020 represents an outcome which is far better than the alternative. Case fatalities by 31. December 2020 could possibly have been somewhat improved either via a more prolonged one-off 10 week forced lockdown (66% reduction) or a 1-month forced lockdown/2-months opening intermittent lockdown strategy (33% reduction), but both sets of strategies would have carried significant GDP costs in the order of 2.2%-6.2% of real GDP.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2023.08.30.23294821,2023-09-01,https://medrxiv.org/cgi/content/short/2023.08.30.23294821,Symptom experience before vs. after confirmed SARS-CoV-2 infection: a population and case control study using prospectively recorded symptom data.,Carole Helene Sudre; Michela Antonelli; Nathan J Cheetham; Erika Molteni; Liane S Canas; Vicky Bowyer; Benjamin Murray; Khaled Rjoob; Marc Modat; Joan Capdevia Pujol; Christina Hu; Jonathan Wolf; Timothy D Spector; Alexander Hammers; Claire J Steves; Sebastien Ourselin; Emma L Duncan,University College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; University College London; King's College London; Zoe Ltd; Zoe Ltd; Zoe Ltd; King's College London; King's College London; King's College London; King's College London; King's College London,"BackgroundSome individuals experience prolonged illness after acute COVID-19. We assessed whether pre-infection symptoms affected post-COVID illness duration. @@ -271,6 +266,27 @@ Methods and findingsWe analysed General Practice (GP) consultation and hospital ConclusionsThis analysis provides a comprehensive examination of management and outcomes of community-onset UTI in female patients, considering the changes in GP consultations during the COVID-19 pandemic. Our findings highlighted the importance of appropriate urine testing to support UTI diagnosis in symptomatic patients and initiation of antibiotic treatment with appropriate course duration. Continued monitoring is required to assess the overall impact on patients and health systems from the changed landscape of primary care delivery.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.07.06.23292295,2023-07-07,https://medrxiv.org/cgi/content/short/2023.07.06.23292295,Spatio-temporal surveillance and early detection of SARS-CoV-2 variants of concern,Massimo Cavallaro; Louise Dyson; Michael J Tildesley; Daniel Todkill; Matt J Keeling,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,"The SARS-CoV-2 pandemic has been characterized by the repeated emergence of genetically distinct virus variants of increased transmissibility and immune evasion compared to pre-existing lineages. In many countries, their containment required the intervention of public health authorities and the imposition of control measures. While the primary role of testing is to identify infection, target treatment, and limit spread (through isolation and contact tracing), a secondary benefit is in terms of surveillance and the early detection of new variants. Here we study the spatial invasion and early spread of the Alpha, Delta, and Omicron (BA.1 and BA.2) variants in England from September 2020 to February 2022 using the random neighbourhood covering (RaNCover) method. This is a statistical technique for the detection of aberrations in spatial point processes, which we tailored here to community PCR (polymerase-chain-reaction) test data where the TaqPath kit provides a proxy measure of the switch between variants. Retrospectively, RaNCover detected the earliest signals associated with the four novel variants that led to large infection waves in England. With suitable data our method therefore has the potential to rapidly detect outbreaks of future SARS-CoV-2 variants, thus helping to inform targeted public health interventions.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2023.07.03.23291596,2023-07-05,https://medrxiv.org/cgi/content/short/2023.07.03.23291596,Risk of COVID-19 death in adults who received booster COVID-19 vaccinations: national retrospective cohort study on 14.6 million people in England,Isobel L Ward; Chris Robertson; Utkarsh Agrawal; Lynsey Patterson; Declan T Bradley; Ting Shi; Simon de Lusignan; Richard Hobbs; Aziz Sheikh; Vahe Nafilyan,"Office for National Statistics, Newport, UK; Department of Mathematics and Statistics, Strathclyde University, Glasgow, Scotland and Public Health Scotland, Glasgow, Scotland; Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Centre for Public Health, Queen's University Belfast, Belfast, UK and Public Health Agency, Belfast, UK; Centre for Public Health, Queen's University Belfast, Belfast, UK and Public Health Agency, Belfast, UK; Usher Institute, University of Edinburgh, Edinburgh, UK; Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Usher Institute, University of Edinburgh, Edinburgh, UK; Office for National Statistics, Newport, UK","ImportanceThe emergence of the COVID-19 vaccination has been critical in changing the course of the COVID-19 pandemic, with estimates suggesting vaccinations have prevented millions of deaths worldwide. To ensure protection remains high in vulnerable groups booster vaccinations in the UK have been targeted based on age and clinical vulnerabilities. + +ObjectiveWe sought to identify adults who had received a booster vaccination as part of the autumn 2022 campaign in England yet remained at increased risk of postbooster COVID-19 death and compared to non-COVID-19 risk. + +Design, Setting, and ParticipantsWe undertook a national retrospective cohort study using data from the 2021 Census linked to electronic health records. We fitted cause-specific Cox models to examine the association between health conditions and the risk of COVID-19 death and all-other-cause death for adults aged 50-100-years in England vaccinated with a booster in autumn 2022. Our total population was 14,644,570 people; there were 6,800 COVID-19 deaths and 150,075 non-COVID-19 deaths. + +ExposureSociodemographic characteristics (sex, age, ethnic group, region), disability, body mass index, and diagnosis of a health condition defined from QCovid2. + +Main Outcomes and MeasuresThe primary outcome of this study was COVID-19 death. The secondary outcome was all-cause non-COVID-19 deaths. + +ResultsHaving learning disabilities or Down Syndrome (hazard ratio=5.07;95% confidence interval=3.69-6.98), pulmonary hypertension or fibrosis (2.88;2.43-3.40), motor neuron disease, multiple sclerosis, myasthenia or Huntingtons disease (2.94, 1.82-4.74), cancer of blood and bone marrow (3.11;2.72-3.56), Parkinsons disease (2.74;2.34-3.20), lung or oral cancer (2.57;2.04 to 3.24), dementia (2.64;2.46 to 2.83) or liver cirrhosis (2.65;1.95 to 3.59) was associated with an increased risk of COVID-19 death. Individuals with cancer of the blood or bone marrow, chronic kidney disease, cystic fibrosis, pulmonary hypotension or fibrosis, or rheumatoid arthritis or systemic lupus erythematosus had a significantly higher risk of COVID-19 death relative to other causes of death compared with individuals who did not have diagnoses. + +Conclusions, and RelevanceWe identify groups who are at increased risk of postbooster COVID-19 death relative to non-COVID-19 deaths. Policy makers should continue to priorities vulnerable groups for subsequent COVID-19 booster doses to minimise the risk of COVID-19 death. + +FundingNational Core Studies-Immunity, National Core Studies-Data and Connectivity, Health Data Research UK, and the Medical Research Council. + +Key PointsQuestion: What health conditions are associated with increased risk of postbooster COVID-19 death in adults who received a COVID-19 vaccination in autumn 2022? + +Findings: Certain groups were found to be at overall higher risk of postbooster COVID-19 death (e.g., learning disability or Down Syndrome) and certain groups were found to have significantly higher relative risk of COVID-19 death compared to other non-COVID-19 causes (e.g., cancer of the blood or bone marrow). + +Meaning: This work has implications for prioritisation of vaccination booster doses worldwide. We highlight which groups with health conditions are at elevated risk of postbooster COVID-19 death.",public and global health,fuzzy,100,100 medRxiv,10.1101/2023.06.29.23292056,2023-07-01,https://medrxiv.org/cgi/content/short/2023.06.29.23292056,Genome-wide Association Study of Long COVID,Vilma Lammi; Tomoko Nakanishi; Samuel E Jones; Shea J Andrews; Juha Karjalainen; Beatriz Cortes; Heath E O'Brien; Brian E Fulton-Howard; Hele H Haapaniemi; Axel Schmidt; Ruth E Mitchell; Abdou Mousas; Massimo Mangino; Alicia Huerta-Chagoya; Nasa Sinnott-Armstrong; Elizabeth T Cirulli; Marc Vaudel; Alex SF Kwong; Amit K Maiti; Minttu M Marttila; Chiara Batini; Francesca Minnai; Anna R Dearman; CA Robert Warmerdam; Celia B Sequeros; Thomas W Winkler; Daniel M Jordan; Lindsay Guare; Ekaterina Vergasova; Eirini Marouli; Pasquale Striano; Ummu Afeera Zainulabid; Ashutosh Kumar; Hajar Fauzan Ahmad; Ryuya Edahiro; Shuhei Azekawa; - Long COVID Host Genetics Initiative; - FinnGen; - DBDS Genomic Consortium; - GEN-COVID Multicenter Study; Joseph J Grzymski; Makoto Ishii; Yukinori Okada; Noam D Beckmann; Meena Kumari; Ralf Wagner; Iris M Heid; Catherine John; Patrick J Short; Per Magnus; Karina Banasik; Frank Geller; Lude H Franke; Alexander Rakitko; Emma L Duncan; Alessandra Renieri; Konstantinos K Tsilidis; Rafael de Cid; Ahmadreza Niavarani; Teresa Tusie-Luna; Shefali S Verma; George Davey Smith; Nicholas J Timpson; Mark J Daly; Andrea Ganna; Eva C Schulte; J Brent Richards; Kerstin U Ludwig; Michael Hultstrom; Hugo Zeberg; Hanna M Ollila,Institute for Molecular Medicine Finland (FIMM); Department of Human Genetics; Institute for Molecular Medicine Finland (FIMM); University of California San Francisco; Institute for Molecular Medicine Finland (FIMM); Genomes for Life-GCAT lab; Sano Genetics Limited; Genetics and Genomic Sciences; Institute for Molecular Medicine Finland (FIMM); Institute of Human Genetics; Centre for Clinical Brain Sciences; Department of Hygiene and Epidemiology; Department of Twin Research; Departamento de Medicina Genomica y Toxicologia Ambiental; Herbold Computational Biology Program; Helix; Mohn Center for Diabetes Precision Medicine; University of Bristol; Department of Genetics and Genomics; University of Helsinki; Department of Population Health Sciences; Institute for Biomedical Technologies - National Research Council; Institute for Social and Economic Research; Department of Genetics; Novo Nordisk Foundation Center for Protein Research; Department of Genetic Epidemiology; Charles Bronfman Institute for Personalized Medicine; Department of Pathology and Laboratory Medicine; Genotek Ltd.; William Harvey Research Institute; IRCCS G; Department of Internal Medicine; Department of Anatomy; Faculty of Industrial Sciences and Technology; Department of Statistical Genetics; Division of Pulmonary Medicine; ; ; ; ; Center for Genomic Medicine; Division of Pulmonary Medicine; Department of Statistical Genetics; Charles Bronfman Institute for Personalized Medicine; Institute for Social and Economic Research; Institute of Medical Microbiology & Hygiene; Department of Genetic Epidemiology; Department of Population Health Sciences; Sano Genetics Limited; Centre for Fertility and Health; Novo Nordisk Foundation Center for Protein Research; Statens Serum Institute; Department of Genetics; Genotek Ltd.; Department of Twin Research and Genetic Epidemiology; Medical Genetics; Department of Hygiene and Epidemiology; Genomes for Life-GCAT lab; Digestive Oncology Research Center; Instituto de Investigaciones Biomedicas Unam/ Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran; Department of Pathology and Laboratory Medicine; MRC Integrative Epidemiology Unit at the University of Bristol; MRC Integrative Epidemiology Unit at the University of Bristol; Institute for Molecular Medicine Finland (FIMM); Institute for Molecular Medicine Finland (FIMM); Institute of Psychiatric Phenomics & Genomics; Department of Human Genetics; Institute of Human Genetics; Anaesthesiology and Intensive Care Medicine; Department of Evolutionary Genetics; Institute for Molecular Medicine Finland (FIMM),"Infections can lead to persistent or long-term symptoms and diseases such as shingles after varicella zoster, cancers after human papillomavirus, or rheumatic fever after streptococcal infections1, 2. Similarly, infection by SARS-CoV-2 can result in Long COVID, a condition characterized by symptoms of fatigue and pulmonary and cognitive dysfunction3-5. The biological mechanisms that contribute to the development of Long COVID remain to be clarified. We leveraged the COVID-19 Host Genetics Initiative6, 7 to perform a genome-wide association study for Long COVID including up to 6,450 Long COVID cases and 1,093,995 population controls from 24 studies across 16 countries. We identified the first genome-wide significant association for Long COVID at the FOXP4 locus. FOXP4 has been previously associated with COVID-19 severity6, lung function8, and cancers9, suggesting a broader role for lung function in the pathophysiology of Long COVID. While we identify COVID-19 severity as a causal risk factor for Long COVID, the impact of the genetic risk factor located in the FOXP4 locus could not be solely explained by its association to severe COVID-19. Our findings further support the role of pulmonary dysfunction and COVID-19 severity in the development of Long COVID.",genetic and genomic medicine,fuzzy,100,100 medRxiv,10.1101/2023.06.30.23292079,2023-06-30,https://medrxiv.org/cgi/content/short/2023.06.30.23292079,Synthesis and new evidence from the PROTECT UK National Core Study: Determining occupational risks of SARS-CoV-2 infection and COVID-19 mortality,Sarah Rhodes; Sarah Beale; Mark Cherrie; William Mueller; Fiona Holland; Melissa Matz; Ioannis Basinas; Jack D Wilkinson; Matthew Gittins; Bernardine Farrell; Andrew Hayward; Neil Pearce; Martie van Tongeren,University of Manchester; University College London; Institute of Occupational Medicine; Institute of Occupational Medicine; University of Manchester; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester; University of Manchester; University of Manchester; UCL; London School of Hygiene and Tropical Medicine; University of Manchester,"IntroductionThe PROTECT National Core Study was funded by the UK Health and Safety Executive (HSE) to investigate routes of transmission for SARS-CoV-2 and variation between settings. @@ -358,15 +374,6 @@ MethodsWe included UK COVID-19 Infection Survey participants who tested positive ResultsOverall, Long Covid was reported by those [≥]16 years after 4.0% and 2.4% of first and second infections, respectively; the corresponding estimates among those <16 years were 1.0% and 0.6%. The aOR for Long Covid after second compared to first infections was 0.72 (95% confidence interval: 0.63-0.81) for those [≥]16 years and 0.93 (0.57-1.53) for those <16 years. ConclusionsThe risk of new-onset Long Covid after a second SARS-CoV-2 infection is lower than that after a first infection for those [≥]16 years, though there is no evidence of a difference in risk for those <16 years. However, there remains some risk of new-onset Long Covid after a second infection, with around 1 in 40 of those [≥]16 years and 1 in 165 of those <16 years reporting Long Covid after a second infection.",public and global health,fuzzy,100,100 -medRxiv,10.1101/2023.03.24.23287700,2023-03-26,https://medrxiv.org/cgi/content/short/2023.03.24.23287700,The potential contribution of vaccination uptake to occupational differences in risk of SARS-CoV-2: Analysis of the ONS COVID-19 Infection Survey,Jack D Wilkinson; Evangelia Demou; Mark Cherrie; Rhiannon Edge; Matthew Gittins; Srinivasa Vittal Katikireddi; Theocharis Kromydas; WIll Mueller; Neil Pearce; Martie van Tongeren; Sarah Rhodes,University of Manchester; University of Glasgow; Institute of Occupational Medicine; University of Lancaster; University of Manchester; University of Glasgow; University of Glasgow; Institute for Occupational Medicine; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester,"ObjectivesTo assess variation in vaccination uptake across occupational groups as a potential explanation for variation in risk of SARS-CoV-2 infection. - -DesignWe analysed data from the UK Office of National Statistics COVID-19 Infection Survey linked to vaccination data from the National Immunisation Management System in England from December 1st 2020 to 11th May 2022. We analysed vaccination uptake and SARS-CoV-2 infection risk by occupational group and assessed whether adjustment for vaccination reduced the variation in risk between occupational groups. - -Setting - -ResultsEstimated rates of triple-vaccination were high across all occupational groups (80% or above), but were lowest for food processing (80%), personal care (82%), hospitality (83%), manual occupations (84%), and retail (85%). High rates were observed for individuals working in health (95% for office-based, 92% for those in patient-facing roles) and education (91%) and office-based workers not included in other categories (90%). The impact of adjusting for vaccination when estimating relative risks of infection was generally modest (ratio of hazard ratios reduced from 1.38 to 1.32), but was consistent with the hypothesis that low vaccination rates contribute to elevated risk in some groups. Conversely, estimated relative risk for some occupational groups, such as people working in education, remained high despite high vaccine coverage. - -ConclusionsVariation in vaccination coverage might account for a modest proportion of occupational differences in infection risk. Vaccination rates were uniformly very high in this cohort, which may suggest that the participants are not representative of the general population. Accordingly, these results should be considered tentative pending the accumulation of additional evidence.",occupational and environmental health,fuzzy,100,100 medRxiv,10.1101/2023.03.24.23287666,2023-03-24,https://medrxiv.org/cgi/content/short/2023.03.24.23287666,Occupational differences in the prevalence and severity of long-COVID: Analysis of the ONS Coronavirus (COVID-19) Infection Survey,Theocharis Kromydas; Evangelia Demou; Rhiannon Edge; Matthew Gittins; Srinivasa Vittal Katikireddi; Neil Pearce; Martie van Tongeren; Jack Wilkinson; Sarah Rhodes,University of Glasgow; University of Glasgow; Lancaster University; University of Manchester; University of Glasgow; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester; University of Manchester,"ObjectivesTo establish whether prevalence and severity of long-COVID symptoms vary by industry and occupation. MethodsWe utilised ONS Coronavirus Infection Survey (CIS) data (February 2021-April 2022) of working-age participants (16-65 years). Exposures were industrial sector, occupation and major Standard Occupational Classification (SOC) group. Outcomes were self-reported: (1) long-COVID symptoms; and (2) reduced function due to long-COVID. Binary (outcome 1) and ordered (outcome 2) logistic regression were used to estimate odds ratios (OR) and prevalence (marginal means) for all exposures. @@ -435,6 +442,15 @@ Our analyses indicate that mental health conditions are more common among those The findings have implications for mental health service planning and efforts to reduce barriers to treatment access, especially for individuals who live on their own.",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2023.02.26.23286474,2023-03-06,https://medrxiv.org/cgi/content/short/2023.02.26.23286474,Improving the representativeness of UKs national COVID-19 Infection Survey through spatio-temporal regression and post-stratification,Koen B Pouwels; David W Eyre; Thomas House; Ben Aspey; Philippa C Matthews; Nicole Stoesser; John Newton; Ian Diamond; Ruth Studley; Nick Taylor; John Bell; Jeremy Farrar; Jaison Kolenchery; Brian Marsden; Sarah Hoosdally; Yvonne Jones; David Stuart; Derrick Crook; tim E peto; Ann Sarah Walker; - COVID-19 Infection Survey Team,University of Oxford; University of Oxford; University of Manchester; Office for National Statistics; The Francis Crick Institute; University of Oxford; University of Exeter; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; oxford university; University of Oxford; -,"Population-representative estimates of SARS-CoV-2 infection prevalence and antibody levels in specific geographic areas at different time points are needed to optimise policy responses. However, even population-wide surveys are potentially impacted by biases arising from differences in participation rates across key groups. Here, we use spatio-temporal regression and post-stratification models to UKs national COVID-19 Infection Survey (CIS) to obtain representative estimates of PCR positivity (6,496,052 tests) and antibody prevalence (1,941,333 tests) for different regions, ages and ethnicities (7-December-2020 to 4-May-2022). Not accounting for vaccination status through post-stratification led to small underestimation of PCR positivity, but more substantial overestimations of antibody levels in the population (up to 21%), particularly in groups with low vaccine uptake in the general population. There was marked variation in the relative contribution of different areas and age-groups to each wave. Future analyses of infectious disease surveys should take into account major drivers of outcomes of interest that may also influence participation, with vaccination being an important factor to consider.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2023.03.01.23286627,2023-03-03,https://medrxiv.org/cgi/content/short/2023.03.01.23286627,Effectiveness of successive booster vaccine doses against SARS-CoV-2 related mortality in residents of Long-Term Care Facilities in the VIVALDI study,Oliver Stirrup; Madhumita Shrotri; Natalie L. Adams; Maria Krutikov; Borscha Azmi; Igor Monakhov; Gokhan Tut; Paul Moss; Andrew Hayward; Andrew Copas; Laura Shallcross,University College London; University College London; University College London; University College London; University College London; UK Health Security Agency; University of Birmingham; University of Birmingham; University College London; University College London; University College London,"We evaluated the effectiveness of 1-3 booster vaccinations against SARS-CoV-2 related mortality among a cohort of 13407 older residents of long-term care facilities (LTCFs) participating in the VIVALDI study in England in 2022. Cox regression was used to estimate relative hazards of SARS-CoV-2 related death following booster vaccination relative to 2 doses (after 84+ days), stratified by previous SARS-CoV-2 infection and adjusting for age, sex and LTCF capacity. Each booster provided additional short-term protection relative to primary vaccination, with consistent pattern of waning to 45-75% reduction in risk beyond 112 days.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2023.03.01.23286624,2023-03-03,https://medrxiv.org/cgi/content/short/2023.03.01.23286624,Risk of cardiovascular events following COVID-19 in people with and without pre-existing chronic respiratory disease,Hannah Whittaker; Costantinos Kallis; Angela Wood; Thomas Bolton; Samantha Walker; Aziz Sheikh; Alex Brownrigg; Ashley Akbari; Kamil Sterniczuk; Jennifer K Quint,"Imperial College London; Imperial College London; Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, United Kingdom; Health Data Research UK; Asthm + Lung; The University of Edinburgh College of Medicine and Veterinary Medicine; Health Data Research UK BREATHE; Swansea University; Health Data Research UK BREATHE; Imperial College London","BackgroundCOVID-19 is associated with a higher risk of cardiovascular outcomes in the general population, but it is unknown whether people with pre-existing chronic respiratory disease (CRD) have a higher risk of cardiovascular events post-COVID-19 compared with the general population and, if so, what respiratory-related risk factors may modify this risk in these people. + +MethodsPrimary and secondary care data from the National Health Service and COVID-19-specific linked data were used to define a population of adults in England with COVID-19 (index date) between 01/01/2020-30/11/2021. Adjusted Cox Proportional Hazard regression was used to quantify the association between CRD, asthma-related factors, COPD-related factors, and risk of cardiovascular events. CRD included asthma, COPD, bronchiectasis, cystic fibrosis, or pulmonary fibrosis prior to COVID-19 diagnosis. Asthma-specific factors included baseline asthma control, exacerbations, and inhaled corticosteroid (ICS) dose. COPD-specific risk factors included baseline ICS prescriptions and exacerbations. Secondary objectives quantified the impact of COVID-19 hospitalisation and vaccine dose on cardiovascular outcomes. + +ResultsOf 3,670,455 people, those with CRD had a modest higher risk of cardiovascular events (HRadj 1.11, 95%CI 1.07-1.14), heart failure (HRadj 1.15, 1.09-1.21), and pulmonary emboli (HRadj 1.20, 1.11-1.30) compared with people without CRD. In people with asthma, baseline exacerbations and high-dose ICS were associated with a higher risk of cardiovascular outcomes (HRadj 1.24, 1.15-1.34 and 1.12, 1.01-1.24, respectively). In people with COPD, exacerbations were associated with a higher risk of cardiovascular outcomes (HRadj 1.40, 1.28-1.52). Regardless of CRD, the risk of cardiovascular events was lower with increasing COVID-19 vaccine dose. + +ConclusionsHigher risk of cardiovascular events following COVID-19 might be explained at least in part by the underlying CRD and severity of that condition. In addition, COVID-19 vaccines were beneficial to both people with and without CRD with regards to CV events. + +Key MessagesPre-existing chronic respiratory disease, asthma and COPD severity were associated with a higher risk of various types of cardiovascular outcomes following COVID-19. Regardless of having pre-existing chronic respiratory disease, COVID-19 vaccination reduced the risk of cardiovascular events following COVID-19.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.02.28.23286559,2023-03-01,https://medrxiv.org/cgi/content/short/2023.02.28.23286559,Elevated symptoms of depression and anxiety among family members and friends of critically ill COVID-19 patients - An observational study of five cohorts across four countries,Anikó Lovik; Juan González-Hijón; Asle Hoffart; Chloe Fawns-Ritchie; Ingibjörg Magnúsdóttir; Li Lu; Anna Bára Unnarsdóttir; Anna K. Kähler; Archie Campbell; Arna Hauksdóttir; Charilaos Chourpiliadis; Daniel L McCartney; Edda Björk Thordardóttir; Emily E. Joyce; Emma M. Frans; Jóhanna Jakobsdóttir; Lill Trogstad; Ole A. Andreassen; Per Magnus; Sverre Urnes Johnson; Patrick F. Sullivan; Thor Aspelund; David J. Porteous; Helga Ask; Omid V. Ebrahimi; Unnur Anna Valdimarsdóttir; Fang Fang,Karolinska Institutet and Leiden University; Karolinska Institutet; University of Oslo; University of Edinburgh; University of Iceland; University of Oslo; University of Iceland; Karolinska Institutet; University of Edinburgh; University of Iceland; Karolinska Institutet; University of Edinburgh; University of Iceland; Karolinska Institutet; Karolinska Institutet; University of Iceland; Norwegian Institute of Public Health; University of Oslo; Norwegian Institute of Public Health; University of Oslo; Karolinska Institutet; University of Iceland; University of Edinburgh; University of Oslo; University of Oslo; Karolinska Institutet; Karolinska Institutet,"BackgroundLittle is known regarding the mental health impact of having a significant person (family member and/or close friend) with COVID-19 of different severity. MethodsThe study included five prospective cohorts from four countries (Iceland, Norway, Sweden, and the UK) with self-reported data on COVID-19 and symptoms of depression and anxiety during March 2020-March 2022. We calculated the prevalence ratio (PR) of depression and anxiety in relation to having a significant person with COVID-19 and performed a longitudinal analysis in the Swedish cohort to describe the temporal patterns of the results. @@ -475,6 +491,7 @@ ResultsThere were 737,356 confirmed COVID-19 cases including 9,315 COVID-related ConclusionsObserved associations between long-term outdoor air pollution exposure and COVID-19 mortality in London are strongly confounded by geography, ethnicity and deprivation. SummaryUsing a large individual-level dataset, we found that a positive association between long-term outdoor air pollution and COVID-19 mortality in London did not persist after adjusting for confounders including population density, ethnicity and deprivation.",respiratory medicine,fuzzy,100,100 +medRxiv,10.1101/2023.02.10.23285717,2023-02-14,https://medrxiv.org/cgi/content/short/2023.02.10.23285717,The long COVID evidence gap: comparing self-reporting and clinical coding of long COVID using longitudinal study data linked to healthcare records.,Anika Knuppel; Andy Boyd; John Macleod; Nishi Chaturvedi; Dylan M Williams,"MRC Unit of Lifelong Health and Ageing at UCL, University College London, London W1E 7HB, London, United Kingdom; Institute of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, United Kingdom; Institute of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, United Kingdom; MRC Unit of Lifelong Health and Ageing at UCL, University College London, London W1E 7HB, London, United Kingdom; MRC Unit of Lifelong Health and Ageing at UCL, University College London, London W1E 7HB, London, United Kingdom","The term ""long COVID"" (LC) was coined in spring 2020 by individuals with ongoing symptoms following COVID-19, but it took until December 2020 for clinical codes to be created in order to record persistent post-COVID-19 illness and referrals within electronic health records (EHRs). Analysis of whole-population EHR databases have helped understand the epidemiology of LC; yet concerns exist about the completeness of accessible EHRs for LC. UK longitudinal population studies (LPS) collected self-reported data on COVID-19 and LC from early 2020 and deposited these data in the UK Longitudinal Linkage Collaboration (UK LLC) research database where they are systematically linked to the participants EHRs. Comparisons of LPS reported LC with recorded LC in the EHRs of the same individuals may be helpful in understanding the epidemiology of emerging conditions such as LC. We used data from 10 UK LPS in the UK LLC to investigate whether participants self-reporting LC had a LC diagnosis or referral code in their English EHR after 10 to 22 months of follow up. Of 6412 participants with COVID-19 symptom duration data and linkage to health records, 898 (14.0%) self-reported LC of any severity in LPS surveys. Among these, just 42 (4.7%; 95% CI: 3.5, 6.3) were identified with LC-related codes in EHRs. In individuals reporting debilitating LC, this proportion was only marginally higher (5.6%; 95% CI: 3.7, 8.3). Our data show a striking discrepancy between LC as perceived and reported by participants in LPS and evidence of LC recorded in their EHRs; and that this discrepancy was patterned by ethnicity and possibly by indicators of deprivation. Self-reported symptoms may not be reflected in coded EHRs due to factors including variations in individuals help seeking behaviours, clinician coding practices and the availability of appropriate codes. However, these considerations appear unlikely to provide a complete explanation for the substantial observed reporting discrepancy. These results may indicate substantial unmet clinical need, in keeping with patient reports of difficulties accessing healthcare and sub-optimal recognition of, and response to, their illness when they do. They may also indicate potential shortcomings of epidemiological research on LC based on EHR- or LPS-based ascertainment alone and illustrate the value of triangulation between LPS and EHR data where linked and made available through resources such as the UK LLC.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.02.09.23285649,2023-02-14,https://medrxiv.org/cgi/content/short/2023.02.09.23285649,"Antibody prevalence after 3 or more COVID-19 vaccine doses in 23,000 immunosuppressed individuals: a cross-sectional study from MELODY",Fiona A Pearce; Sean Hua Lim; Mary Bythell; Peter Lanyon; Rachel Hog; Adam Taylor; Gillian Powter; Graham Cooke; Helen Ward; Joseph Chilcot; Helen Thomas; Lisa Mumford; Stephen P McAdoo; Gavin J Pettigrew; Liz Lightstone; Michelle Willicombe,"Lifespan and Population Health, School of Medicine, University of Nottingham, Nottingham, UK; Centre for Cancer Immunology, University of Southampton, Southampton, UK; National Disease Registration Service, NHS Digital; Department of Rheumatology, Nottingham University Hospitals NHS Trust, Nottingham, UK; Statistics and Clinical Research, NHS Blood and Transplant, Bristol, UK; Lifespan and Population Health, School of Medicine, University of Nottingham, Nottingham, UK; NHS Blood and Transplant Clinical Trials Unit, Oxford, UK; Imperial College; Imperial College London; Institute of Psychiatry, Psychology & Neuroscience, King's College London, UK; Statistics and Clinical Research, NHS Blood and Transplant, Bristol, UK; Statistics and Clinical Research, NHS Blood and Transplant, Bristol, UK; Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, Du Cane Road, London, UK.; Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK; Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, Du Cane Road, London, UK.; Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, Du Cane Road, London, UK.","ObjectivesTo investigate the prevalence of spike-protein antibodies following at least 3 COVID-19 vaccine doses in immunocompromised individuals. DesignCross-sectional study using UK national disease registries of individuals with solid organ transplants (SOT), rare autoimmune rheumatic diseases (RAIRD) and lymphoid malignancies (LM). @@ -797,6 +814,17 @@ ResultsOverall, higher risk classifications for the first six domains tended to ConclusionsAn exposure-response relationship exists in the early phase of the COVID-19 pandemic for number of contacts, nature of contacts, contacts via surfaces, indoor or outdoor location, ability to social distance and use of face coverings. These associations appear to have diminished over time.",occupational and environmental health,fuzzy,100,100 medRxiv,10.1101/2022.09.16.22279985,2022-09-17,https://medrxiv.org/cgi/content/short/2022.09.16.22279985,Bayesian Prediction of Severe Outcomes in the LabMarCS: Laboratory Markers of COVID-19 Severity - Bristol Cohort,Brian Sullivan; Edward Barker; Philip Williams; Louis MacGregor; Ranjeet Bhamber; Matt Thomas; Stefan Gurney; Catherine Hyams; Alastair Whiteway; Jennifer A Cooper; Chris McWilliams; Katy Turner; Andrew W Dowsey; Mahableshwar Albur,"University of Bristol; University of Bristol; University Hospitals Bristol and Weston NHS Trust; University of Bristol; University of Bristol; Southmead Hospital, North Bristol NHS Trust; University Hospitals Bristol and Weston NHS Trust; Southmead Hospital, North Bristol NHS Trust; Southmead Hospital, North Bristol NHS Trust; University of Bristol; University of Bristol; University of Bristol; University of Bristol; Southmead Hospital, North Bristol NHS Trust","We describe several regression models to predict severe outcomes in COVID-19 and challenges present in complex observational medical data. We demonstrate best practices for data curation, cross-validated statistical modelling, and variable selection emphasizing recent Bayesian methods. The study follows a retrospective observational cohort design using multicentre records across National Health Service (NHS) trusts in southwest England, UK. Participants included hospitalised adult patients positive for SARS-CoV 2 during March to October 2020, totalling 843 patients (mean age 71, 45% female, 32% died or needed ICU stay), split into training (n=590) and validation groups (n=253). Models were fit to predict severe outcomes (ICU admission or death within 28-days of admission to hospital for COVID-19, or a positive PCR result if already admitted) using demographic data and initial results from 30 biomarker tests collected within 3 days of admission or testing positive if already admitted. Cross-validation results showed standard logistic regression had an internal validation median AUC of 0.74 (95% Interval [0.62,0.83]), and external validation AUC of 0.68 [0.61, 0.71]; a Bayesian logistic regression (with horseshoe prior) internal AUC of 0.79 [0.71, 0.87], and external AUC of 0.70 [0.68, 0.71]. Variable selection performed using Bayesian predictive projection determined a four variable model using Age, Urea, Prothrombin time and Neutrophil-Lymphocyte ratio, with a median internal AUC of 0.79 [0.78, 0.80], and external AUC of 0.67 [0.65, 0.69]. We illustrate best-practices protocol for conventional and Bayesian prediction modelling on complex clinical data and reiterate the predictive value of previously identified biomarkers for COVID-19 severity assessment.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2022.09.14.22279931,2022-09-15,https://medrxiv.org/cgi/content/short/2022.09.14.22279931,Detecting changes in population trends in infection surveillance using community SARS-CoV-2 prevalence as an exemplar,Emma Elizabeth Pritchard; Karina-Doris Vihta; David W Eyre; Susan Hopkins; Tim EA Peto; Philippa C Matthews; Nicole Stoesser; Ruth Studley; Emma Rourke; Ian Diamond; Koen B Pouwels; Ann Sarah Walker,"University of Oxford; University of Oxford; University of Oxford; UK Health Security Agency; University of Oxford; The Francis Crick Institute, London; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; University of Oxford","BackgroundMonitoring infection trends is vital to informing public health strategy. Detecting and quantifying changes in growth rates can inform policymakers rationale for implementing or continuing interventions aimed at reducing impact. Substantial changes in SARS-CoV-2 prevalence with emergence of variants provides opportunity to investigate different methods to do this. + +MethodsWe included PCR results from all participants in the UKs COVID-19 Infection Survey between 1 August 2020-30 June 2022. Change-points for growth rates were identified using iterative sequential regression (ISR) and second derivatives of generalised additive models (GAMs). + +Consistency between methods and timeliness of detection were compared. + +FindingsOf 8,799,079 visits, 147,278 (1{middle dot}7%) were PCR-positive. Over the time period, change-points associated with emergence of major variants were estimated to occur a median 4 days earlier (IQR 0-8) in GAMs versus ISR, with only 2/48 change-points identified by only one method. Estimating recent change-points using successive data periods, four change-points (4/96) identified by GAMs were not found when adding later data or by ISR; 77% (74/96) of change-points identified by successive GAMs were identified by ISR. Change-points were detected 3-5 weeks after they occurred in both methods but could be detected earlier within specific subgroups. + +InterpretationChange-points in growth rates of SARS-CoV-2 can be detected in near real-time using ISR and second derivatives of GAMs. To increase certainty about changes in epidemic trajectories both methods could be run in parallel. Running either method in near real-time on different infection surveillance data streams could provide timely warnings of changing underlying epidemiology. + +FundingUK Health Security Agency, Department of Health and Social Care (UK), Welsh Government, Department of Health (on behalf of the Northern Ireland Government), Scottish Government, National Institute for Health Research.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2022.09.11.22279823,2022-09-12,https://medrxiv.org/cgi/content/short/2022.09.11.22279823,Effects of the COVID-19 pandemic on the mental health of clinically extremely vulnerable children and children living with clinically extremely vulnerable people in Wales: A data linkage study,Laura Elizabeth Cowley; Karen Hodgson; Jiao Song; Tony Whiffen; Jacinta Tan; Ann John; Amrita Bandyopadhyay; Alisha R Davies,Swansea University; Public Health Wales; Public Health Wales; Welsh Government; University of Oxford; Swansea University; Swansea University; Public Health Wales,"ObjectivesTo determine whether clinically extremely vulnerable (CEV) children or children living with a CEV person in Wales were at greater risk of presenting with anxiety or depression in primary or secondary care during the COVID-19 pandemic compared with children in the general population, and to compare patterns of anxiety and depression during the pandemic (23rd March 2020-31st January 2021, referred to as 2020/21) and before the pandemic (March 23rd 2019-January 31st 2020, referred to as 2019/20), between CEV children and the general population. DesignPopulation-based cross-sectional cohort study using anonymised, linked, routinely collected health and administrative data held in the Secure Anonymised Information Linkage Databank. CEV individuals were identified using the COVID-19 Shielded Patient List. @@ -919,6 +947,13 @@ We examine post-illness metabolomic and gut-microbiome profiles, in community-dw We found an atherogenic-dyslipidaemic metabolic profile, and greater biomarker scores, associated with longer illness, both in individuals with and without SARS-CoV-2 infection. We found no association between illness duration and gut microbiome in convalescence. Findings highlight the potential role of cardiometabolic dysfunction to the experience of long illness duration, including after COVID-19.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2022.08.08.22278493,2022-08-09,https://medrxiv.org/cgi/content/short/2022.08.08.22278493,Inequalities in colorectal cancer screening uptake in Wales: examination of the impact of the temporary suspension of the screening programme during the COVID-19 pandemic,Diana Bright; Sharon Hillier; Jiao Song; Dyfed W Huws; Giles Greene; Karen Hodgson; Ashley Akbari; Rowena Griffiths; Alisha R Davies,"Public Health Wales; Public Health Wales; Public Health Wales; Public Health Wales; Population Data Science, Swansea University Medical School, Faculty of Medicine, Health & Life Science, Swansea University, Swansea, Wales; Public Health Wales; Public Health Wales; Population Data Science, Swansea University Medical School, Faculty of Medicine, Health & Life Science, Swansea University, Swansea, Wales; Population Data Science, Swansea University Medical School, Faculty of Medicine, Health & Life Science, Swansea University, Swansea, Wales; Public Health Wales","BackgroundResponse to the early stages of the COVID-19 pandemic resulted in the temporary disruption of cancer screening in the UK, and strong public messaging to stay safe and to protect NHS capacity. Following reintroduction in services, we explored the impact on inequalities in uptake of the Bowel Screening Wales (BSW) programme to identify groups who may benefit from tailored interventions. + +MethodsRecords within the BSW were linked to electronic health records (EHR) and administrative data within the Secured Anonymised Information Linkage (SAIL) Databank. Ethnic group was obtained from a linked data method available within SAIL. We examined uptake for the first 3 months of invitations (August to October) following the reintroduction of BSW programme in 2020, compared to the same period in the preceding 3 years. Uptake was measured across a 6 month follow-up period. Logistic models were conducted to analyse variations in uptake by sex, age group, income deprivation quintile, urban/rural location, ethnic group, and clinically extremely vulnerable (CEV) status in each period; and to compare uptake within sociodemographic groups between different periods. + +ResultsUptake during August to October 2020 (period 2020/21; 60.4%) declined compared to the same period in 2019/20 (62.7%) but remained above the 60% Welsh standard. Variation by sex, age, income deprivation, and ethnic groups was observed in all periods studied. Compared to the pre-pandemic period in 2019/20, uptake declined for most demographic groups, except for older individuals (70-74 years) and those in the most income deprived group. Uptake continues to be lower in males, younger individuals, people living in the most income deprived areas and those of Asian and unknown ethnic backgrounds. + +ConclusionsOur findings are encouraging with overall uptake achieving the 60% Welsh standard during the first three months after the programme restarted in 2020 despite the disruption. Inequalities did not worsen after the programme resumed activities but variations in CRC screening in Wales associated with sex, age, deprivation and ethnicity remain. This needs to be considered in targeting strategies to improve uptake and informed choice in CRC screening to avoid exacerbating disparities in CRC outcomes as screening services recover from the pandemic.",public and global health,fuzzy,100,100 medRxiv,10.1101/2022.07.30.22278161,2022-08-02,https://medrxiv.org/cgi/content/short/2022.07.30.22278161,Changes in COVID-19-related mortality across key demographic and clinical subgroups: an observational cohort study using the OpenSAFELY platform on 18 million adults in England,- The OpenSAFELY Collaborative; Linda Nab; Edward P K Parker; Colm D Andrews; William J Hulme; Louis Fisher; Jessica Morley; Amir Mehrkar; Brian MacKenna; Peter Inglesby; Caroline E Morton; Sebastian CJ Bacon; George Hickman; David Evans; Tom Ward; Rebecca M Smith; Simon Davy; Iain Dillingham; Steven Maude; Ben FC Butler-Cole; Thomas O'Dwyer; Catherine L Stables; Lucy Bridges; Christopher Bates; Jonathan Cockburn; John Parry; Frank Hester; Sam Harper; Bang Zheng; Elizabeth J Williamson; Rosalind M Eggo; Stephen JW Evans; Ben Goldacre; Laurie A Tomlinson; Alex J Walker,"-; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG","ObjectivesTo quantify in absolute and relative terms how population-level COVID-19 death rates have changed in demographic and clinical subgroups. DesignRetrospective cohort study on behalf of NHS England. @@ -1022,7 +1057,6 @@ MethodsCOVIDENCE UK is a longitudinal population-based study that investigates r ResultsThe study was launched on 1st May 2020 and closed to recruitment on 6th October 2021. A total of 19,981 participants enrolled and consented to 5-year follow-up with medical record linkage. Their mean age was 59.1 years (range 16.0 to 94.4 years), 70.2% were female, and 93.7% identified their ethnic origin as White. Analyses conducted to date have provided key insights into risk factors for SARS-CoV-2 infection and COVID-19 disease, determinants of SARS-CoV-2 vaccine immunogenicity and efficacy, and impacts of COVID-19 on health economic outcomes. The cohort has also supported conduct of a Phase 3 randomised trial-within-cohort study (CORONAVIT) evaluating implementation of a test-and-treat approach to correcting sub-optimal vitamin D status on incidence and severity of acute respiratory infections, including COVID-19. ConclusionsThe COVIDENCE UK dataset represents a valuable resource containing granular information on factors influencing susceptibility to, and impacts of, COVID-19 in UK adults. Researchers wishing to access anonymised participant-level data should contacting the corresponding author for further information.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2022.06.20.22275994,2022-06-20,https://medrxiv.org/cgi/content/short/2022.06.20.22275994,Characterising patterns of COVID-19 and long COVID symptoms: Evidence from nine UK longitudinal studies,Ruth C E Bowyer; Charlotte Huggins; Renin Toms; Richard John Shaw; Bo Hou; Ellen J Thompson; Alex Siu Fung Kwong; Dylan M Williams; Milla Kibble; George B Ploubidis; Nicholas J Timpson; Jonathan A C Sterne; Nishi Chaturvedi; Claire J Steves; Kate Tilling; Richard J Silverwood,King's College London; University of Edinburgh; University of Bristol; University of Glasgow; Bradford Institute for Health Research; King's College London; University of Bristol; UCL; King's College London; University College London; University of Bristol; University of Bristol; University College London; King's College London; University of Bristol; University College London,"Multiple studies across global populations have established the primary symptoms characterising COVID-19 (Coronavirus Disease 2019) and long COVID. However, as symptoms may also occur in the absence of COVID-19, a lack of appropriate controls has often meant that specificity of symptoms to acute COVID-19 or long COVID could not be examined. We aimed to characterise patterns of COVID-19 and long COVID symptoms across nine UK longitudinal studies, totalling over 42,000 participants. Conducting latent class analyses separately in three groups ( no COVID-19, COVID-19 in last 12 weeks, COVID-19 > 12 weeks ago), the data did not support the presence of more than two distinct symptom patterns, representing high and low symptom burden, in each group. Comparing the high symptom burden classes between the COVID-19 in last 12 weeks and no COVID-19 groups we identified symptoms characteristic of acute COVID-19, including loss of taste and smell, fatigue, cough, shortness of breath and muscle pains or aches. Comparing the high symptom burden classes between the COVID-19 > 12 weeks ago and no COVID-19 groups we identified symptoms characteristic of long COVID, including fatigue, shortness of breath, muscle pain or aches, difficulty concentrating and chest tightness. The identified symptom patterns among individuals with COVID-19 > 12 weeks ago were strongly associated with self-reported length of time unable to function as normal due to COVID-19 symptoms, suggesting that the symptom pattern identified corresponds to long COVID. Building the evidence base regarding typical long COVID symptoms will improve diagnosis of this condition and the ability to elicit underlying biological mechanisms, leading to better patient access to treatment and services.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2022.06.18.22276437,2022-06-19,https://medrxiv.org/cgi/content/short/2022.06.18.22276437,A patient-centric characterization of systemic recovery from SARS-CoV-2 infection,Hélène Ruffieux; Aimee Hanson; Samantha Lodge; Nathan Lawler; Luke Whiley; Nicola Gray; Tui Nolan; Laura Bergamaschi; Federica Mescia; - CITIID-NIHR COVID BioResource Collaboration; Nathalie Kingston; John Bradley; Elaine Holmes; Julien Wist; Jeremy Nicholson; Paul Lyons; Kenneth Smith; Sylvia Richardson; Glenn Bantug; Christoph Hess,University of Cambridge; University of Cambridge; Murdoch University; Murdoch University; Murdoch University; Murdoch University; University of Cambridge; University of Cambridge; University of Cambridge; ; University of Cambridge; University of Cambridge; Murdoch University; Murdoch University; Murdoch University; University of Cambridge; University of Cambridge; University of Cambridge; University and University Hospital Basel; University of Cambridge,"The biology driving individual patient responses to SARS-CoV-2 infection remains ill understood. Here, we developed a patient-centric framework leveraging detailed longitudinal phenotyping data, covering a year post disease onset, from 215 SARS-CoV-2 infected subjects with differing disease severities. Our analyses revealed distinct ""systemic recovery"" profiles with specific progression and resolution of the inflammatory, immune, metabolic and clinical responses, over weeks to several months after infection. In particular, we found a strong intra-patient temporal covariation of innate immune cell numbers, kynurenine- and host lipid-metabolites, which suggested candidate immunometabolic pathways putatively influencing restoration of homeostasis, the risk of death and of long COVID. Based on these data, we identified a composite signature predictive of systemic recovery on the patient level, using a joint model on cellular and molecular parameters measured soon after disease onset. New predictions can be generated using the online tool http://shiny.mrc-bsu.cam.ac.uk/apps/covid-systemic-recovery-prediction-app, designed to test our findings prospectively. Graphical abstract @@ -1151,7 +1185,6 @@ Main outcome measureCOVID-19 related hospitalisation or COVID-19 related death w ResultsBetween December 16, 2021 and February 10, 2022, 3331 and 2689 patients were treated with sotrovimab and molnupiravir, with no substantial differences in their baseline characteristics. The mean age of all 6020 patients was 52 (SD=16) years; 59% were female, 89% White and 88% had three or more COVID-19 vaccinations. Within 28 days after treatment initiation, 87 (1.4%) COVID-19 related hospitalisations/deaths were observed (32 treated with sotrovimab and 55 with molnupiravir). Cox proportional hazards models stratified by area showed that after adjusting for demographics, high-risk cohort categories, vaccination status, calendar time, body mass index and other comorbidities, treatment with sotrovimab was associated with a substantially lower risk than treatment with molnupiravir (hazard ratio, HR=0.54, 95% CI: 0.33 to 0.88; P=0.014). Consistent results were obtained from propensity score weighted Cox models (HR=0.50, 95% CI: 0.31 to 0.81; P=0.005) and when restricted to fully vaccinated people (HR=0.53, 95% CI: 0.31 to 0.90; P=0.019). No substantial effect modifications by other characteristics were detected (all P values for interaction>0.10). Findings were similar in an exploratory analysis of patients treated between February 16 and May 1, 2022 when the Omicron BA.2 variant was dominant in England. ConclusionIn routine care of non-hospitalised high-risk adult patients with COVID-19 in England, those who received sotrovimab were at lower risk of severe COVID-19 outcomes than those receiving molnupiravir.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2022.05.21.22275368,2022-05-23,https://medrxiv.org/cgi/content/short/2022.05.21.22275368,"Variant-specific symptoms of COVID-19 among 1,542,510 people in England",Matthew Whitaker; Joshua Elliott; Barbara Bodinier; Wendy S Barclay; Helen Ward; Graham Cooke; Christl A Donnelly; Marc Chadeau-Hyam; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health,"Infection with SARS-CoV-2 virus is associated with a wide range of symptoms. The REal-time Assessment of Community Transmission -1 (REACT-1) study has been monitoring the spread and clinical manifestation of SARS-CoV-2 among random samples of the population in England from 1 May 2020 to 31 March 2022. We show changing symptom profiles associated with the different variants over that period, with lower reporting of loss of sense of smell and taste for Omicron compared to previous variants, and higher reporting of cold-like and influenza-like symptoms, controlling for vaccination status. Contrary to the perception that recent variants have become successively milder, Omicron BA.2 was associated with reporting more symptoms, with greater disruption to daily activities, than BA.1. With restrictions lifted and routine testing limited in many countries, monitoring the changing symptom profiles associated with SARS-CoV-2 infection and induced changes in daily activities will become increasingly important.",infectious diseases,fuzzy,96,100 medRxiv,10.1101/2022.05.19.22275214,2022-05-22,https://medrxiv.org/cgi/content/short/2022.05.19.22275214,Antibody levels following vaccination against SARS-CoV-2: associations with post-vaccination infection and risk factors,Nathan J Cheetham; Milla Kibble; Andrew Wong; Richard J Silverwood; Anika Knuppel; Dylan M Williams; Olivia K L Hamilton; Paul H Lee; Charis Bridger Staatz; Giorgio Di Gessa; Jingmin Zhu; Srinivasa Vittal Katikireddi; George B Ploubidis; Ellen J Thompson; Ruth C E Bowyer; Xinyuan Zhang; Golboo Abbasian; Maria Paz Garcia; Deborah Hart; Jeffrew Seow; Carl Graham; Neophytos Kouphou; Sam Acors; Michael H Malim; Ruth E Mitchell; Kate Northstone; Daniel Major-Smith; Sarah Matthews; Thomas Breeze; Michael Crawford; Lynn Molloy; Alex Siu Fung Kwong; Katie J Doores; Nishi Chaturvedi; Emma L Duncan; Nicholas J Timpson; Claire J Steves,King's College London; University of Cambridge; University College London; University College London; University College London; University College London; University of Glasgow; University of Leicester; University College London; University College London; University College London; University of Glasgow; University College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; King's College London; University College London; King's College London; University of Bristol; King's College London,"SARS-CoV-2 antibody levels can be used to assess humoral immune responses following SARS-CoV-2 infection or vaccination, and may predict risk of future infection. From cross-sectional antibody testing of 9,361 individuals from TwinsUK and ALSPAC UK population-based longitudinal studies (jointly in April-May 2021, and TwinsUK only in November 2021-January 2022), we tested associations between antibody levels following vaccination and: (1) SARS-CoV-2 infection following vaccination(s); (2) health, socio-demographic, SARS-CoV-2 infection and SARS-CoV-2 vaccination variables. Within TwinsUK, single-vaccinated individuals with the lowest 20% of anti-Spike antibody levels at initial testing had 3-fold greater odds of SARS-CoV-2 infection over the next six to nine months, compared to the top 20%. In TwinsUK and ALSPAC, individuals identified as at increased risk of COVID-19 complication through the UK ""Shielded Patient List"" had consistently greater odds (2 to 4-fold) of having antibody levels in the lowest 10%. Third vaccination increased absolute antibody levels for almost all individuals, and reduced relative disparities compared with earlier vaccinations. @@ -1168,23 +1201,6 @@ OutcomesPooled estimates of the standardized difference in outcome between those InterpretationSelf-reporting COVID-19 was longitudinally associated with deterioration in mental health and life satisfaction. Our findings have important implications for mental health service provision, given the substantial prevalence of COVID-19 in the UK and worldwide. FundingMRC and NIHR",psychiatry and clinical psychology,fuzzy,100,100 -medRxiv,10.1101/2022.05.09.22274769,2022-05-11,https://medrxiv.org/cgi/content/short/2022.05.09.22274769,"COVID-19 vaccination in pregnancy: views and vaccination uptake rates in pregnancy, a mixed methods analysis from the Born In Wales study",Mohamed Mhereeg; Hope Jones; Jonathan Kennedy; Michael Seaborne; Michael Parker; Natasha Kennedy; Sarah Beeson; Luisa Zuccolo; Alisha Davies; Sinead Brophy,"Swansea University Medical School, Swansea, Wales, UK; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Bristol Medical School, University of Bristol, Bristol, England, UK.; Public Health Wales, UK; Swansea University Medical School, Swansea, Wales, UK","BackgroundVaccine hesitancy amongst pregnant women has been found to be a concern during past epidemics. - -ObjectivesThe aims of this study were to 1) estimate COVID-19 vaccination rates among pregnant women in Wales and their association with age, ethnicity, and area of deprivation, using electronic health records (EHR) linkage, and 2) explore pregnant womens views on receiving the COVID-19 vaccine during pregnancy using data from a survey recruiting via social media (Facebook, Twitter), through midwives, and posters in hospitals (Born in Wales Cohort). - -DesignA mixed methods study utilising routinely collected linked data from the Secure Anonymised Information Linkage (SAIL) (Objective 1) and the Born In Wales Birth Cohort participants (Objective 2). SAIL combines data from general practice, hospital admissions, the national community child health dataset, maternal indicators dataset, and COVID-19 vaccination databases. - -Setting and participantsObjective 1) All women documented as being pregnant on or after 13th April 2021, aged 18 years or older, and eligible for COVID-19 vaccination were identified in routine health care. They were linked to the vaccination data up to and including 31st December 2021. Objective 2) Separately, a cross-section of pregnant women in Wales were invited to complete an online survey via social media advertising. The survey asked what their views were on having the COVID-19 vaccination during pregnancy, and if they had already received, or intended to receive, the COVID-19 vaccination during their pregnancies. They were also asked to give reasons for their decisions. - -Outcomes1 (a). Rate of vaccination uptake per month during pregnancy among women eligible for vaccination. 1 (b). Survival analysis was utilised to examine and compare the length of time to vaccination uptake in pregnancy, and variation in uptake by; age, ethnicity, and deprivation area was examined using hazard ratios (HR) from Cox regression. 2.Expectant mothers views of the COVID-19 vaccination during pregnancy. - -Results - -Population-level data linkage (objective 1)Within the population cohort, 32.7% (n = 8,203) were vaccinated (at least one dose of the vaccine) during pregnancy, 34.1% (n = 8,572) remained unvaccinated throughout follow-up period, and 33.2% (n = 8,336) received the vaccine postpartum. Younger women (<30 years) were less likely to have the vaccine and those living in areas of high deprivation were also less likely to have the vaccine (HR=0.88, 95% CI 0.82 to 0.95). Asian and other ethnic groups were 1.12 and 1.18 times more likely to have the vaccine in pregnancy compared to women of White ethnicity (HR=1.12, 95% CI 1.00 to 1.25) and (HR=1.18, 95% CI 1.03 to 1.37) respectively. - -Survey responses (objective 2)69% of participants stated that they would be happy to have the vaccine during pregnancy (n = 207). The remainder, 31%, indicated that they would not have the vaccine during pregnancy (n = 94). Reasons for having the vaccine related to protecting self and baby, perceived risk level, and receipt of sufficient evidence and advice. Reasons for vaccine refusal included lack of research about long-term outcomes for the baby, anxiety about vaccines, inconsistent advice/information, and preference to wait until after the pregnancy. - -ConclusionPotentially only 1 in 3 pregnant women would have the COVID-19 vaccine during pregnancy, even though 2 in 3 reported they would have the vaccination, thus it is critical to develop tailored strategies to increase its acceptance rate and to decrease vaccine hesitancy. A targeted approach to vaccinations may be required for groups such as younger people and those living in higher deprivation level areas.",public and global health,fuzzy,100,100 bioRxiv,10.1101/2022.05.07.491004,2022-05-10,https://biorxiv.org/cgi/content/short/2022.05.07.491004,SARS-CoV-2 Spike N-Terminal Domain modulates TMPRSS2-dependent viral entry and fusogenicity,Bo Meng; Rawlings Datir; Jinwook Choi; - CITIID-NIHR BioResource COVID-19 Collaboration; John Bradley; Kenneth GC Smith; Joo Hyeon Lee; Ravindra K Gupta,University of Cambridge; University of Cambridge; University of Cambridge; -; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge,"Over 20 mutations have been identified in the N-Terminal Domain (NTD) of SARS-CoV-2 spike and yet few of them are fully characterised. Here we first examined the contribution of the NTD to infection and cell-cell fusion by constructing different VOC-based chimeric spikes bearing B.1617 lineage (Delta and Kappa variants) NTDs and generating spike pseudotyped lentivirus (PV). We found the Delta NTD on a Kappa or WT background increased spike S1/S2 cleavage efficiency and virus entry, specifically in Calu-3 lung cells and airway organoids, through use of TMPRSS2. We have previously shown Delta spike confers rapid cell-cell fusion kinetics; here we show that increased fusogenicity can be conferred to WT and Kappa variant spikes by transfer of the Delta NTD. Moving to contemporary variants, we found that BA.2 had higher entry efficiency in a range of cell types as compared to BA.1. BA.2 showed higher fusogenic activity than BA.1, but the BA.2 NTD could not confer higher fusion to BA.1 spike. There was low efficiency of TMPRSS2 usage by both BA.1 and BA.2, and chimeras of Omicron BA.1 and BA.2 spikes with a Delta NTD did not result in more efficient use of TMRPSS2 or cell-cell fusogenicity. We conclude that the NTD allosterically modulates S1/S2 cleavage and spike-mediated functions such as entry and cell-cell fusion in a spike context dependent manner, and allosteric interactions may be lost when combining regions from more distantly related spike proteins. These data may explain the lack of successful SARS-CoV-2 inter-variant recombinants bearing breakpoints within spike.",microbiology,fuzzy,100,100 medRxiv,10.1101/2022.05.10.22274890,2022-05-10,https://medrxiv.org/cgi/content/short/2022.05.10.22274890,Biopsychosocial response to the COVID-19 lockdown in people with major depressive disorder and multiple sclerosis.,Sara Siddi; Iago Gine Vazquez; Raquel Bailon; Faith Matcham; Femke Lamers; Spyridon Kontaxis; Estela Laporta Puyal; Esther Garcia; Belen Arranz; Gloria Dallacosta; Anna Isabel Guerrero Perez; Anna Zabalza; Mathias Buron; Giancarlo Comi; Letizia Leocani; Peter Annas; Matthew Hotopf; Brenda Penninx; Melinda Magyari; Per Sorensen; Xavier Montalban; Grace Lavalle; Alina Ivan; Carolin Oetzmann; Katie White; Sonia Difrancesco; Patrick Locatelli; Jordi Aguilo; Vaibhav Narayan; Amos Folarin; Richard Dobson; Judith Anne Dineley; Daniel Leightley; Nicholas Cummins; Yarharth Ranjan; Zulqarnain Rashid; Aki Rintala; Giovanni De Girolamo; Antonio Preti; Sara Simblett; Til Wykes; Inez Myin-Germeys; Josep Maria Haro,"Parc Sanitari Sant Joan de Deu Cibersam; Parc Sanitari Sant Joan de Deu Cibersam; Universidad de Zaragoza; King's College London; Amsterdam UMC Locatie AMC, Amsterdam, North Holland, NL; Universidad de Zaragoza; Universidad de Zaragoza; Universitat Autonoma de Barcelona; Parc Sanitari Sant Joan de Deu Cibersam; Istituto di Ricovero e Cura a Carattere Scientifico Ospedale San Raffaele Milano; Vall d'Hebron Institut de Recerca; Vall d'Hebron Institut de Recerca; Copenhagen University Hospital Kobenhavn; Istituto di Ricovero e Cura a Carattere Scientifico Ospedale San Raffaele Milano; Istituto di Ricovero e Cura a Carattere Scientifico Ospedale San Raffaele Milano; H Lundbeck AS Valby; Institute of Psychiatry, Psychological Medicine; Amsterdam UMC Locatie AMC, Amsterdam, North Holland, NL; Copenhagen University Hospital Kobenhavn; Copenhagen University Hospital Kobenhavn; Vall d'Hebron Institut de Recerca; King's College London; King's College London; King's College London; King's College London; Amsterdam UMC Locatie AMC, Amsterdam, North Holland, NL; University of Bergamo; Universitat Autonoma de Barcelona; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Katholieke Universiteit Leuven; Centro San Giovanni di Dio Fatebenefratelli; Universita degli Studi di Torino; King's College London; King's College London; KU Leuven; Parc Sanitari Sant Joan de Deu Cibersam","BackgroundChanges in lifestyle, finances and work status during COVID-19 lockdowns may have led to biopsychosocial changes in people with pre-existing vulnerabilities such as Major Depressive Disorders (MDD) and Multiple Sclerosis (MS). @@ -1307,13 +1323,6 @@ Several reported interventions or factors suggest the potential to mitigate the Approximately one per cent of the global population resides in care homes, while care home residents account for nearly one-third of deaths attributed to COVID-19 in the 25 countries studied. Reducing this ratio requires analysing current care home infrastructures, funding models, and incentives for providing high-quality care. The scale of the problem in care homes requires robust evaluation and coordinated strategies to improve outcomes for those most vulnerable to COVID-19. Failure to address these systemic problems could mean global care home populations will be similarly affected by future crises and pandemics.",public and global health,fuzzy,90,100 medRxiv,10.1101/2022.04.11.22273690,2022-04-17,https://medrxiv.org/cgi/content/short/2022.04.11.22273690,Evaluation of isotype specific salivary antibody assays for detecting previous SARS-CoV-2 infection in children and adults,Amy C Thomas; Elizabeth Oliver; Holly Baum; Kapil Gupter; Kathryn Shelley; Anna Long; Hayley Jones; Joyce Smith; Benjamin Hitchings; Natalie di Bartolo; Kate Vasileiou; Fruzsina Rabi; Hanin Alamir; Malak Eghleilib; Ore Francis; Jennifer Oliver; Begonia Morales-Aza; Ulrike Obst; Debbie Shattock; Rachael Barr; Lucy Collingwood; Kaltun Duale; Niall Grace; Guillaume Gonnage Livera; Lindsay Bishop; Harriet Downing; Fernanda Rodrigues; Nicholas J Timpson; Caroline J Relton; Ashley Mark Toye; Derek N Woolfson; Imre Berger; Anu Goenka; Andrew D. Mark Davidson; Kathleen M Gillespie; Alistair JK Williams; Mick Bailey; Ellen Brooks-Pollock; Adam Finn; Alice Halliday; - CoMMinS Study Team,University of Bristol; University of Bristol; University of Bristol; University of Bristol and Imophoron Ltd.; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; Universidade de Coimbra; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; -,"Saliva is easily obtainable non-invasively and potentially suitable for detecting both current and previous SARS-CoV-2 infection. We established 6 standardised enzyme linked immunosorbent assays (ELISA) capable of detecting IgA and IgG antibodies to whole SARS-CoV-2 spike protein, to its receptor binding domain region and to nucleocapsid protein in saliva. In test accuracy (n=320), we found that spike IgG performed best (ROC AUC: 95.0%, 92.8-97.3%), followed by spike IgA (ROC AUC: 89.9%, 86.5-93.2%) for discriminating between pre-pandemic and post COVID-19 saliva samples. Using machine learning, diagnostic performance was improved when a combination of tests was used. As expected, salivary IgA was poorly correlated with serum, indicating an oral mucosal response whereas salivary IgG responses were predictive of those in serum. When deployed to 20 household outbreaks undergoing Delta and Omicron infection, antibody responses were heterogeneous but remained a reliable indicator of recent infection. Intriguingly, unvaccinated children showed evidence of exposure almost exclusively through specific IgA responses in the absence of evidence of viral infection. We have provided robust standardisation, evaluation, and field-testing of salivary antibody assays as tools for monitoring SARS-CoV-2 immune responses. Future work should focus on investigating salivary antibody responses following infection and vaccination to understand patterns of SARS-CoV-2 transmission and inform ongoing vaccination strategies.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2022.04.14.22272888,2022-04-14,https://medrxiv.org/cgi/content/short/2022.04.14.22272888,Anti-inflammatory therapy with nebulised dornase alfa in patients with severe COVID-19 pneumonia,Joanna Porter; Jamie Inshaw; Vincente Joel Solis; Emma Denneny; Rebecca Evans; Mia I. Temkin; Nathalia De Vasconcelos; Iker Valle Aramburu; Dennis Hoving; Donna Basire; Tracey Crissell; Jesusa Guinto; Alison Webb; Hanif Esmail; Victoria Johnston; Anna Last; Thomas Rampling; Elisa Theresa Helbig; Lena Lippert; Florian Kurth; Bryan Williams; Aiden Flynn; Pauline Lukey; Veronique Birault; Venizelos Papayannopoulos,"UCL Respiratory, University College London, UK; Exploristics, Belfast, N. Ireland; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; UCL Respiratory, University College London, UK; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany; Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany; Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; Exploristics, Belfast, N. Ireland; Target to Treatment Consulting Ltd, Stevenage, UK; Translation, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK","BackgroundCell-free (cf)-DNA, from cellular sources, including Neutrophil Extracellular Traps (NETs), is found in the circulation of COVID-19 patients and may contribute to immune dysregulation. This study determined whether pulmonary administration of the endonuclease, dornase alfa, reduced systemic inflammation by degrading local and systemic cf-DNA. - -MethodsEligible patients were randomized (3:1) to receive twice-daily nebulised dornase alfa in addition to best available care (BAC) or BAC alone for seven days or until discharge. A 2:1 ratio of matched contemporary controls (CC) provided additional comparators. The primary endpoint was improvement in C-reactive protein (CRP) over time, analysed using a repeated-measures mixed model, adjusted for baseline factors. - -ResultsBetween June 2020-October 2021 we recruited 39 evaluable patients: 30 randomised to dornase alfa; 9 randomised to BAC; with 60 CC. Dornase alfa reduced CRP by 33% compared to BAC. Least squares (LS) mean post-dexamethasone CRP fell from 101.9mg/L to 23.23 mg/L in the BAC+ dornase alfa group versus a fall from 99.5mg/L to 34.82 mg/L in the BAC group at 7 days; P=0.01. This effect of dornase alfa on CRP was confirmed with subgroup and sensitivity analyses. Dornase alfa increased the chance of live discharge by 63% (HR 1.63, 95% CI 1.01 to 2.61, P=0.03), increased lymphocyte counts (LSmean 1.08 vs 0.87, P=0.02) and reduced circulating cf-DNA and the coagulopathy marker D-dimer (LS mean: 570.78 vs 1656.96 g/mL, P=0.004). Dornase alfa was well-tolerated. - -ConclusionsWe provide proof-of-concept evidence that dornase alfa reduces pathogenic inflammation in hospitalised patients with COVID-19 pneumonia.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.04.12.22273752,2022-04-13,https://medrxiv.org/cgi/content/short/2022.04.12.22273752,Protection conferred by vaccine plus previous infection (hybrid immunity) with vaccines of three different platforms during the Omicron variant period in Brazil,Thiago Cerqueira-Silva; Vinicius de Araújo Oliveira; Enny S. Paixão; Pilar Florentino; Gerson O. Penna; Neil Pearce; Guilherme L. Werneck; Maurício L. Barreto; Viviane S. Boaventura; Manoel Barral-Netto,"Faculdade de Medicina - Universidade Federal da Bahia; Center of Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, Fiocruz, Salvador, Bahia, Brazil; London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; Nuúcleo de Medicina Tropical, Universidade de Brasiília. Escola Fiocruz de Governo, Fiocruz, DF, Brazil; London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; Universidade Federal do Rio de Janeiro, Rio de Janeiro,Brazil; Instituto de Saúde Coletiva - Universidade Federal da Bahia; Faculdade de Medicina - Universidade Federal da Bahia; Faculdade de Medicina - Universidade Federal da Bahia","Hybrid immunity (infection plus vaccination) provided high protection against infection and severe disease in the periods of delta and gamma variants of concern. However, the protection of hybrid immunity in the Omicron era remains unknown. We performed a test-negative study using Brazilian national databases between January 01 and March 22, 2022, a period of predominant circulation of the Omicron variant in Brazil. Hybrid immunity offered low protection against infection, with rapid waning, compared to unvaccinated with or without previous infection. For severe illness (hospitalisation or death), the protection, although already high for unvaccinated pre-infected increased regardless of the type of vaccine (Ad26.COV2.S, BNT162b2, ChAdOx-1 or CoronaVac). In conclusion, during the Omicron-dominant period in Brazil, hybrid immunity offered high protection against severe illness and low protection against infection.",epidemiology,fuzzy,100,100 @@ -1612,6 +1621,23 @@ ResultsSARS-CoV-2 total antibodies against spike protein were present in 366 (94 ConclusionOur results indicate that the level of SARS-CoV-2 total antibodies against spike protein persists for the vast majority of non-vaccinated PCR-positive persons at least 10 to 12 months after mild COVID-19.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.02.17.22271126,2022-02-18,https://medrxiv.org/cgi/content/short/2022.02.17.22271126,"Serological responses and six-month trajectories to COVID-19 Comirnaty and Spikevax booster vaccine, September 2021 to January 2022, London, United Kingdom",Georgina Ireland; Heather Whitaker; Shamez Ladhani; Frances Baawuah; Sathyvani Subbarao; Suzanne Elgohari; Alexandra Smith; Michelle O'Brien; Corinne Whillock; Oliver Martin; Paul Moss; Mary E Ramsay; Gayatri Amirthalingam; Kevin E Brown,UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; Brondesbury Medical Centre; UK Health Security Agency; UK Health Security Agency; University of Birmingham; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency,"In contrast to the increasing levels of high avidity S antibody measured by the Roche assay in the first 6 months following natural infection, marked waning is seen post 2 or 3 doses of vaccine. Although the kinetics differ between those with vaccine-induced immunity compared to those infected prior to vaccination (hybrid immunity), waning rates appear to be similar following 2 or 3 doses of vaccine. These data should allow countries to optimise the timing of future doses of vaccine.",public and global health,fuzzy,100,100 +medRxiv,10.1101/2022.02.14.22270930,2022-02-15,https://medrxiv.org/cgi/content/short/2022.02.14.22270930,Determinants of antibody responses to two doses of ChAdOx1 nCoV-19 or BNT162b2 and a subsequent booster dose of BNT162b2 or mRNA-1273: population-based cohort study (COVIDENCE UK),David A Jolliffe; Sian E Faustini; Hayley Holt; Natalia Perdek; Sheena Maltby; Mohammad Talaei; Matthew Greenig; Giulia Vivaldi; Florence Tydeman; Jane Symons; Gwyneth A Davies; Ronan Lyons; Frank Kee; Aziz Sheikh; Seif O Shaheen; Alex Richter; Adrian R Martineau,Queen Mary University of London; University of Birmingham; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Jane Symons Media; Swansea University; Swansea University; Queen's University Belfast; Edinburgh University; Queen Mary University of London; University of Birminghan; Queen Mary University of London,"BackgroundAntibody responses to SARS-CoV-2 vaccination vary for reasons that remain poorly understood. + +MethodsWe tested for presence of combined IgG, IgA and IgM (IgGAM) anti-spike antibodies before and after administration of two doses of ChAdOx1 nCoV-19 (ChAdOx1, Oxford-AstraZeneca) or BNT162b2 (Pfizer-BioNTech) in UK adults participating in a population-based longitudinal study who received their first dose of vaccine from December 15, 2020 to July 10, 2021. Information on sixty-six potential sociodemographic, behavioural, clinical, pharmacological and nutritional determinants of serological response to vaccination was captured using serial online questionnaires. We used logistic regression to estimate multivariable-adjusted odds ratios (aORs) for associations between independent variables and risk of seronegativity following two vaccine doses. Participants who were seronegative after receiving two vaccine doses were offered an additional antibody test following subsequent administration of a booster dose of BNT162b2 or mRNA-1273 (Moderna) from September 23 to December 12, 2021. + +FindingsSerology results following two vaccine doses were available for 9,101 participants, of whom 5,770 (63.4%) received ChAdOx1 and 3,331 (36.6%) received BNT162b2. Anti-spike IgGAM was undetectable in 378 (4.2%) participants at a median of 8.6 weeks (IQR 6.4-10.7 weeks) after their second dose of vaccine. Seronegativity following two doses of SARS-CoV-2 vaccination was associated with administration of ChAdOx1 vs BNT162b2 (aOR 7.03, 95% CI 4.39-11.24), shorter interval between first and second vaccine doses (aOR 2.37, 1.06-5.26, for <6 weeks vs >10 weeks; aOR 1.59, 1.18-2.13, for 6-10 weeks vs >10 weeks), poorer self-assessed general health (aOR 3.33, 1.49-7.46, for poor vs excellent), immunodeficiencies (aOR 6.75, 2.63-17.35) and prescription of systemic immunosuppressants (aOR 3.76, 2.44-5.78). By contrast, pre-vaccination SARS-CoV-2 seropositivity (aOR 0.16, 0.04-0.70, for symptomatic seropositives vs seronegatives) and supplemental vitamin D intake (aOR 0.73, 0.53-0.99) were associated with reduced risk of post-vaccination seronegativity. 247/378 (65.3%) of participants who were seronegative after two doses of ChAdOx1 vs BNT162b2 provided a third sample at a median of 7.8 weeks (IQR 5.8-10.4) after receiving a booster dose of BNT162b2 or mRNA-1273: eight (3.2%) of them remained seronegative after three vaccine doses, all of whom either had a primary immunodeficiency or were taking systemic immunosuppressant drugs. + +InterpretationWe identify multiple determinants of antibody responses to two doses of ChAdOx1 or BNT162b2, many of which are potentially modifiable. Booster doses of BNT162b2 or mRNA-1273 were highly effective in achieving seroconversion in those who failed to mount antibody responses following two doses of ChAdOx1 or BNT162b2. + +Study registrationhttps://clinicaltrials.gov/ct2/show/NCT04330599 + +FundingBarts Charity, Fischer Family Trust, The Exilarchs Foundation, DSM Nutritional Products, Health Data Research UK + +Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, medRxiv, and Google Scholar for papers published from January 1, 2020, to February 1, 2022, using the search terms (antibody OR humoral OR serologic* OR immunogenic*) AND (SARS-CoV-2 vaccine OR ChAdOx1 or BNT162b2 coronavirus), with no language restrictions. Population-based studies investigating multiple potential determinants of vaccine immunogenicity in people with known pre-vaccination SARS-CoV-2 serostatus are lacking. + +Added value of this studyThis large population-based study, conducted in a population with known pre-vaccination SARS-CoV-2 serostatus, examines a comprehensive range of potential sociodemographic, behavioural, clinical, pharmacological and nutritional determinants of antibody responses to administration of two major SARS-CoV-2 vaccines (i.e., ChAdOx1 or BNT162b2), many of which have not previously been investigated. It is also the first population-based study to characterise antibody responses to booster doses of SARS-CoV-2 vaccines in adults who were seronegative after their primary course of vaccination. + +Implications of all the available evidenceIncreased risk of seronegativity following two doses of SARS-CoV-2 vaccines was associated with administration of ChAdOx1 vs BNT162b2, shorter interval between first and second vaccine doses, poorer self-assessed general health, immunocompromise and SARS-CoV-2 seronegativity pre-vaccination. Regular intake of vitamin D supplements was associated with reduced risk of post-vaccination seronegativity. Randomised controlled trials are now needed to test for causality. Booster doses of BNT162b2 or mRNA-1273 were highly effective in achieving seroconversion in the majority of people who failed to mount antibody responses following a primary course of vaccination, the few exceptions being a subset of those with primary immunodeficiency or systemic immunosuppressant drugs.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.02.10.22270799,2022-02-13,https://medrxiv.org/cgi/content/short/2022.02.10.22270799,Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study,Oliver Stirrup; James Blackstone; Fiona Mapp; Alyson MacNeil; Monica Panca; Alison Holmes; Nicholas Machin; Gee Yen Shin; Tabitha Mahungu; Kordo Saeed; Tranprit Saluja; Yusri Taha; Nikunj Mahida; Cassie Pope; Anu Chawla; Teresa Cutino-Moguel; Asif Tamuri; Rachel Williams; Alistair Darby; David L Robertson; Flavia Flaviani; Eleni Nastouli; Samuel Robson; Darren Smith; Matthew Loose; Kenneth Laing; Irene Monahan; Beatrix Kele; Sam Haldenby; Ryan George; Matthew Bashton; Adam Witney; Matthew Byott; Francesc Coll; Michael Chapman; Sharon Peacock; - COG-UK HOCI Investigators; - COG-UK Consortium; Joseph Hughes; Gaia Nebbia; David G Partridge; Matthew Parker; James Richard Price; Christine Peters; Sunando Roy; Luke B Snell; Thushan I de Silva; Emma Thomson; Paul Flowers; Andrew Copas; Judith Breuer,"Institute for Global Health, UCL, London, UK; Comprehensive Clinical Trials Unit, UCL, London, UK; Institute for Global Health, UCL, London, UK; Comprehensive Clinical Trials Unit, UCL, London, UK; Comprehensive Clinical Trials Unit, UCL, London, UK; Imperial College Healthcare NHS Trust, London, UK; Manchester University NHS Foundation Trust, Manchester, UK; University College London Hospitals NHS Foundation Trust, London, UK; Royal Free NHS Foundation Trust, London, UK; University Hospital Southampton NHS Foundation Trust, Southampton, UK; Sandwell and West Birmingham NHS Trust, UK; Departments of Virology and Infectious Diseases, Newcastle Hospitals NHS Foundation Trust, Newcastle, UK; Nottingham University Hospitals NHS Trust, Nottingham, UK; St George's University Hospitals NHS Foundation Trust, London, UK; Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Barts Health NHS Trust, London, UK; Research Computing, UCL, London, UK; Department of Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, UCL, London, UK; Centre for Genomic Research, University of Liverpool, Liverpool, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK; University College London Hospitals NHS Foundation Trust, London, UK; Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, UK; Department of Applied Sciences, Northumbria University, Newcastle, UK; School of Life Sciences, University of Nottingham, Nottingham, UK; Institute for Infection and Immunity, St George's University of London, London, UK; Institute for Infection and Immunity, St George's University of London, London, UK; Barts Health NHS Trust, London, UK; Centre for Genomic Research, University of Liverpool, Liverpool, UK; Manchester University NHS Foundation Trust, Manchester, UK; The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University, Newcastle, UK; Institute for Infection and Immunity, St George's University of London, London, UK; University College London Hospitals NHS Foundation Trust, London, UK; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Health Data Research UK Cambridge Hub, Cambridge UK; Department of Medicine, University of Cambridge, Cambridge, UK; ; ; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK; Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK; Imperial College Healthcare NHS Trust, London, UK; NHS Greater Glasgow and Clyde, Glasgow, UK; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, UCL, London, UK; Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, The University of Sheffield, Sheffield, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; School of Psychological Sciences and Health, University of Strathclyde, Glasgow, UK; Institute for Global Health, UCL, London, UK; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, UCL, London, UK","IntroductionViral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. MethodsWe conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data-collection period, followed by intervention periods comprising 8 weeks of rapid (<48h) and 4 weeks of longer-turnaround (5-10 day) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital onset COVID-19 infections (HOCIs; detected [≥]48h from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on incidence of probable/definite hospital-acquired infections (HAIs) was evaluated. @@ -1677,6 +1703,13 @@ MethodsA comprehensive search of multiple databases (WHO COVID-19 database; Medl ResultsFifty-one studies were included. 59% (30/51) were rated as low quality, 29% (15/51) as moderate and 12% (6/51) as high-moderate. Most evidence (84%, 43/51 studies) was from high-income countries. 47% (24/51) of studies reported reductions in presentation frequency, including all 6 rated as high-moderate quality, which reported reductions of 17- 56%. Settings treating higher lethality self-harm were overrepresented among studies reporting increased demand. Two of the 3 higher quality studies including study observation months from 2021 reported reductions in service utilisation. Evidence from 2021 suggested increased use of health services following self-harm among adolescents, particularly girls. ConclusionsSustained reductions in service utilisation were seen into the first half of 2021. However, evidence from low- and middle-income countries is lacking. The increased use of health services among adolescents, particularly girls, into 2021 is of concern. Our findings may reflect changes in thresholds for help seeking, use of alternative sources of support and variable effects of the pandemic across different groups.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2022.01.26.22269540,2022-01-28,https://medrxiv.org/cgi/content/short/2022.01.26.22269540,Impact of voluntary risk-mitigation behaviour on transmission of the Omicron SARS-CoV-2 variant in England,Ellen Brooks-Pollock; Kate Northstone; Lorenzo Pellis; Francesca Scarabel; Amy C Thomas; Emily J Nixon; David A Matthews; Vicky Bower; Maria-Paz Garcia; Claire J Steves; Nicholas J Timpson; Leon Danon,"University of Bristol; University of Bristol; The University of Manchester; University of Manchester; University of Bristol; University of Bristol; University of Bristol; King's College London; King's College London; King's College London; University of Bristol; Department of Engineering Mathematics, University of Bristol, UK.","BackgroundThe Omicron variant of SARS-CoV-2 infection poses substantial challenges to public health. In England, ""plan B"" mitigation measures were introduced in December 2021 including increased home working and face coverings in shops, but stopped short of restrictions on social contacts. The impact of voluntary risk mitigation behaviours on future SARS-CoV-2 burden is unknown. + +MethodsWe developed a rapid online survey of risk mitigation behaviours during the winter 2021 festive period and deployed in two longitudinal cohort studies in the UK (Avon Longitudinal Study of Parents and Children (ALSPAC) and TwinsUK/Covid Symptom Study (CSS) Biobank) in December 2021. Using an individual-based, probabilistic model of COVID-19 transmission between social contacts with SARS-CoV-2 Omicron variant parameters and realistic vaccine coverage in England, we describe the potential impact of the SARS-CoV-2 Omicron wave in England in terms of the effective reproduction number and cumulative infections, hospital admissions and deaths. Using survey results, we estimated in real-time the impact of voluntary risk mitigation behaviours on the Omicron wave in England, if implemented for the entire epidemic wave. + +ResultsOver 95% of survey respondents (NALSPAC=2,686 and NTwins=6,155) reported some risk mitigation behaviours, with vaccination and using home testing kits reported most frequently. Less than half of those respondents reported that their behaviour was due to ""plan B"". We estimate that without risk mitigation behaviours, the Omicron variant is consistent with an effective reproduction number between 2.5 and 3.5. Due to the reduced vaccine effectiveness against infection with the Omicron variant, our modelled estimates suggest that between 55% and 60% of the English population could be infected during the current wave, translating into between 15,000 and 46,000 cumulative deaths, depending on assumptions about vaccine effectiveness. We estimate that voluntary risk reduction measures could reduce the effective reproduction number to between 1.8 and 2.2 and reduce the cumulative number of deaths by up to 24%. + +ConclusionsWe conclude that voluntary measures substantially reduce the projected impact of the SARS-CoV-2 Omicron variant, but that voluntary measures alone would be unlikely to completely control transmission.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.01.26.22269877,2022-01-27,https://medrxiv.org/cgi/content/short/2022.01.26.22269877,The impacts of increased global vaccine sharing on the COVID-19 pandemic; a retrospective modelling study,Sam Moore; Edward M Hill; Louise J Dyson; Michael J Tildesley; Matt J Keeling,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,"BackgroundThe SARS-CoV-2 pandemic has generated considerable morbidity and mortality world-wide. While the protection offered by vaccines (and booster doses) offers a method of mitigating the worst effects, by the end of 2021 the distribution of vaccine was highly heterogeneous with some countries achieving over 90% coverage in adults by the end of 2021, while others have less than 2%. In part, this is due to the availability of sufficient vaccine, although vaccine hesitancy also plays a role. MethodsWe use an age-structured model of SARS-CoV-2 dynamics, matched to national data from 152 countries, to investigate the global impact of different vaccine sharing protocols during 2021. We assume a direct relationship between the emergence of variants with increased transmissibility and the cumulative amount of global infection, such that lower global prevalence leads to a lower reproductive number within each country. We compare five vaccine sharing scenarios, from the current situation, through sharing once a particular within-country threshold is reached (e.g. all over 40s have received 2 doses), to full sharing where all countries achieve equal age-dependent vaccine deployment. @@ -1720,6 +1753,7 @@ C_LIO_LIChild-reported health behaviours were measured before the COVID-19 pande C_LIO_LIHealth behaviours captured through the national-scale HAPPEN survey represent children attending schools that engaged with the HAPPEN Wales primary school network and may not be representative of the whole population of Wales. C_LIO_LIThe period of study for PCR-testing for and testing positive for SARS-CoV-2 includes a time frame with varying prevalence rates, approaches to testing children (targeted and mass testing) and restrictions which were not measured in this study. C_LI",public and global health,fuzzy,100,100 +bioRxiv,10.1101/2022.01.14.475727,2022-01-18,https://biorxiv.org/cgi/content/short/2022.01.14.475727,Obesity associated with attenuated tissue immune cell responses in COVID-19,Shuang Andrew Guo; Georgina S Bowyer; John Robert Ferdinand; Mailis Maes; Zewen K Tuong; Eleanor Gilman; Rik G. H. Lindeboom; Masahiro Yoshida; Kaylee Worlock; Hudaa Gopee; Emily Stephenson; Paul A Lyons; Kenneth G. C. Smith; Muzlifah Haniffa; Kerstin B Meyer; Marko Z Nikolic; Richard G Wunderink; Alexander V Misharin; Gordon Dougan; Vilas Navapurkar; Sarah A Teichmann; Andrew Conway Morris; Menna R Clatworthy,University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; University College London; University College London; Newcastle University; Newcastle University; University of Cambridge; University of Cambridge; Newcastle University; Wellcome Sanger Institute; University College London; Northwestern University; Northwestern University; University of Cambridge; Cambridge University Hospitals NHS Foundation Trust; Wellcome Sanger Institute; University of Cambridge; University of Cambridge,"Obesity is common and associated with more severe COVID-19, proposed to be in part related to an adipokine-driven pro-inflammatory state. Here we analysed single cell transcriptomes from bronchiolar lavage in three adult cohorts, comparing obese (Ob, body mass index (BMI) >30m2) and non-obese (N-Ob, BMI <30m2). Surprisingly, we found that Ob subjects had attenuated lung immune/inflammatory responses in SARS-CoV-2 infection, with decreased expression of interferon (IFN), IFN{gamma} and tumour necrosis factor (TNF) alpha response gene signatures in almost all lung epithelial and immune cell subsets, and lower expression of IFNG and TNF in specific lung immune cells. Analysis of peripheral blood immune cells in an independent adult cohort showed a similar, but less marked, reduction in type I IFN and IFN{gamma} response genes, as well as decreased serum IFN, in Ob patients with SARS-CoV-2. Nasal immune cells from Ob children with COVID-19 also showed reduced enrichment of IFN and IFN{gamma} response genes. Altogether, these findings show blunted tissue immune responses in Ob COVID-19 patients, with clinical implications.",immunology,fuzzy,100,100 medRxiv,10.1101/2022.01.18.22269082,2022-01-18,https://medrxiv.org/cgi/content/short/2022.01.18.22269082,OMICRON-ASSOCIATED CHANGES IN SARS-COV-2 SYMPTOMS IN THE UNITED KINGDOM,Karina-Doris Vihta; Koen B. Pouwels; Tim EA Peto; Emma Pritchard; Thomas House; Ruth Studley; Emma Rourke; Duncan Cook; Ian Diamond; Derrick Crook; David A Clifton; Philippa C. Matthews; Nicole Stoesser; David W. Eyre; Ann Sarah Walker; - COVID-19 Infection Survey team,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Manchester; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistcs; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; ,"BackgroundThe SARS-CoV-2 Delta variant has been replaced by the highly transmissible Omicron BA.1 variant, and subsequently by Omicron BA.2. It is important to understand how these changes in dominant variants affect reported symptoms, while also accounting for symptoms arising from other co-circulating respiratory viruses. MethodsIn a nationally representative UK community study, the COVID-19 Infection Survey, we investigated symptoms in PCR-positive infection episodes vs. PCR-negative study visits over calendar time, by age and vaccination status, comparing periods when the Delta, Omicron BA.1 and BA.2 variants were dominant. @@ -1729,11 +1763,6 @@ ResultsBetween October-2020 and April-2022, 120,995 SARS-CoV-2 PCR-positive epis ConclusionsIncreases in sore throat (also common in the general community), and a marked reduction in loss of taste/smell, make Omicron harder to detect with symptom-based testing algorithms, with implications for institutional and national testing policies. SummaryIn a UK community study, loss of taste/smell was markedly less commonly reported with Omicron BA.1/BA.2 than Delta SARS-CoV-2 infections, with smaller declines in reported shortness of breath, myalgia and fatigue/weakness, but increases in sore throat, challenging symptom-based testing algorithms.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2022.01.16.22269146,2022-01-17,https://medrxiv.org/cgi/content/short/2022.01.16.22269146,Development and validation of the Symptom Burden Questionnaire™ for Long COVID: a Rasch analysis,Sarah E Hughes; Shamil Haroon; Anuradhaa Subramanian; Christel McMullan; Olalekan L Aiyegbusi; Grace M Turner; Louise Jackson; Elin Haf Davies; Chris Frost; Gary McNamara; Gary Price; Karen Matthews; Jennifer Camaradou; Jane Ormerod; Anita Walker; Melanie J Calvert,"University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Aparito Limited; Aparito Limited; Aparito Limited; University of Birmingham; Patient and Public Involvement, Therapies for Long COVID (TLC) study, University of Birmingham; Patient and Public Involvement, Therapies for Long COVID (TLC) study, University of Birmingham; Patient and Public Involvement, Therapies for Long COVID (TLC) study, University of Birmingham; University of Birmingham; University of BIrmingham","ObjectiveTo describe the development and initial validation of a novel patient-reported outcome measure of Long COVID symptom burden, the Symptom-Burden Questionnaire for Long COVID (SBQ-LC). - -Method and FindingsThis multi-phase, prospective mixed-methods study took place between April and August 2021 in the United Kingdom (UK). A conceptual framework and initial item pool were developed from published systematic reviews. Further concept elicitation and content validation was undertaken with adults with lived experience (n = 13) and clinicians (n = 10), and face validity was confirmed by the Therapies for Long COVID Study Patient and Public Involvement group (n = 25). The draft SBQ-LC was field tested by adults with self-reported Long COVID recruited via social media and international Long COVID support groups (n = 274). Thematic analysis of interview and survey transcripts established content validity and informed construction of the draft questionnaire. Rasch analysis of field test data guided item and scale refinement and provided evidence of the final SBQ-LCs measurement properties. The Rasch-derived SBQ-LC is composed of 17 independent scales with promising psychometric properties. Respondents rate symptom burden during the past 7-days using a dichotomous response or 4-point rating scale. Each scale provides coverage of a different symptom domain and returns a summed raw score that may be converted to a linear (0 - 100) score. Higher scores represent higher symptom burden. - -ConclusionsThe SBQ-LC is a comprehensive patient-reported assessment of Long COVID symptom burden developed using modern psychometric methods. It measures symptoms of Long COVID important to individuals with lived experience and may be used to evaluate the impact of interventions and inform best practice in clinical management.",health informatics,fuzzy,100,100 medRxiv,10.1101/2022.01.13.22268948,2022-01-14,https://medrxiv.org/cgi/content/short/2022.01.13.22268948,Algorithmic Fairness and Bias Mitigation for Clinical Machine Learning: Insights from Rapid COVID-19 Diagnosis by Adversarial Learning,Jenny Yang; Andrew AS Soltan; Yang Yang; David A Clifton,The University of Oxford; University of Oxford; The University of Oxford; The University of Oxford,"Machine learning is becoming increasingly prominent in healthcare. Although its benefits are clear, growing attention is being given to how machine learning may exacerbate existing biases and disparities. In this study, we introduce an adversarial training framework that is capable of mitigating biases that may have been acquired through data collection or magnified during model development. For example, if one class is over-presented or errors/inconsistencies in practice are reflected in the training data, then a model can be biased by these. To evaluate our adversarial training framework, we used the statistical definition of equalized odds. We evaluated our model for the task of rapidly predicting COVID-19 for patients presenting to hospital emergency departments, and aimed to mitigate regional (hospital) and ethnic biases present. We trained our framework on a large, real-world COVID-19 dataset and demonstrated that adversarial training demonstrably improves outcome fairness (with respect to equalized odds), while still achieving clinically-effective screening performances (NPV>0.98). We compared our method to the benchmark set by related previous work, and performed prospective and external validation on four independent hospital cohorts. Our method can be generalized to any outcomes, models, and definitions of fairness.",health informatics,fuzzy,100,100 medRxiv,10.1101/2022.01.05.21268323,2022-01-06,https://medrxiv.org/cgi/content/short/2022.01.05.21268323,Lineage replacement and evolution captured by the United Kingdom Covid Infection Survey,Katrina A Lythgoe; Tanya Golubchik; Matthew Hall; Thomas House; Roberto Cahuantzi; George MacIntyre-Cockett; Helen Fryer; Laura Thomson; Anel Nurtay; Mahan Ghafari; David Buck; Angie Green; Amy Trebes; Paolo Piazza; Lorne J Lonie; Ruth Studley; Emma Rourke; Darren Smith; Matthew Bashton; Andrew Nelson; Matthew Crown; Clare McCann; Gregory R Young; Rui Andre Nunes de Santos; Zack Richards; Adnan Tariq; - Wellcome Sanger Institute COVID-19 Surveillance Team; - COVID-19 Infection Survey Group; - The COVID-19 Genomics UK (COG-UK) consortium; Christophe Fraser; Ian Diamond; Jeff Barrett; Ann Sarah Walker; David Bonsall,University of Oxford; University of Oxford; University of Oxford; University of Manchester; University of Manchester; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Wellcome Sanger Institute; Office for National Statistics; ; University of Oxford; Office for National Statistics; Wellcome Sanger Institute; University of Oxford; University of Oxford,"The Office for National Statistics COVID-19 Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in the community, and collected data on the United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing the sequenced samples collected by the ONS-CIS during this period. We observed a series of sweeps or partial sweeps, with each sweeping lineage having a distinct growth advantage compared to their predecessors. The sweeps also generated an alternating pattern in which most samples had either S-gene target failure (SGTF) or non- SGTF over time. Evolution was characterised by steadily increasing divergence and diversity within lineages, but with step increases in divergence associated with each sweeping major lineage. This led to a faster overall rate of evolution when measured at the between-lineage level compared to within lineages, and fluctuating levels of diversity. These observations highlight the value of viral sequencing integrated into community surveillance studies to monitor the viral epidemiology and evolution of SARS-CoV-2, and potentially other pathogens, particularly in the current phase of the pandemic with routine RT-PCR testing now ended in the community.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2022.01.01.21268131,2022-01-05,https://medrxiv.org/cgi/content/short/2022.01.01.21268131,Bayesian Estimation of real-time Epidemic Growth Rates using Gaussian Processes: local dynamics of SARS-CoV-2 in England,Laura Marcela Guzman Rincon; Edward M Hill; Louise Dyson; Michael J Tildesley; Matt J Keeling,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,"Quantitative assessments of the recent state of an epidemic and short-term projections into the near future are key public health tools that have substantial policy impacts, helping to determine if existing control measures are sufficient or need to be strengthened. Key to these quantitative assessments is the ability to rapidly and robustly measure the speed with which the epidemic is growing or decaying. Frequently, epidemiological trends are addressed in terms of the (time-varying) reproductive number R. Here, we take a more parsimonious approach and calculate the exponential growth rate, r, using a Bayesian hierarchical model to fit a Gaussian process to the epidemiological data. We show how the method can be employed when only case data from positive tests are available, and the improvement gained by including the total number of tests as a measure of heterogeneous testing effort. Although the methods are generic, we apply them to SARS-CoV-2 cases and testing in England, making use of the available high-resolution spatio-temporal data to determine long-term patterns of national growth, highlight regional growth and spatial heterogeneity.",epidemiology,fuzzy,100,100 @@ -1818,6 +1847,15 @@ C_LIO_LIImmunological, proteomic, genetic, and wearable data captured in the stu C_LIO_LIA limitation is that a significant proportion of non-hospitalised individuals affected by COVID-19 in the first wave of the pandemic will lack confirmatory testing and will be excluded from recruitment to the study. C_LI",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.12.20.21268113,2021-12-21,https://medrxiv.org/cgi/content/short/2021.12.20.21268113,A nationwide deep learning pipeline to predict stroke and COVID-19 death in atrial fibrillation,Alex Handy; Angela Wood; Cathie Sudlow; Christopher Tomlinson; Frank Kee; Johan H Thygesen; Mohammad Mamouei; Reecha Sofat; Richard Dobson; Hiu Yan (Samantha) Ip; Spiros Denaxas; - CVD-COVID-UK Consortium,"Institute of Health Informatics, University College London, London, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; British Heart Foundation Data Science Centre, Health Data Research UK, London, UK; Institute of Health Informatics, University College London, London, UK; School of Medicine, Dentistry and Biomedical Sciences, Centre for Public Health, Queens University Belfast, UK; Institute of Health Informatics, University College London, London, UK; Deep Medicine, Oxford Martin School, University of Oxford, Oxford, UK; Institute of Health Informatics, University College London, London, UK; Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Institute of Health Informatics, University College London, London, UK; CVD-COVID-UK Consortium","Deep learning (DL) and machine learning (ML) models trained on long-term patient trajectories held as medical codes in electronic health records (EHR) have the potential to improve disease prediction. Anticoagulant prescribing decisions in atrial fibrillation (AF) offer a use case where the benchmark stroke risk prediction tool (CHA2DS2-VASc) could be meaningfully improved by including more information from a patients medical history. In this study, we design and build the first DL and ML pipeline that uses the routinely updated, linked EHR data for 56 million people in England accessed via NHS Digital to predict first ischaemic stroke in people with AF, and as a secondary outcome, COVID-19 death. Our pipeline improves first stroke prediction in AF by 17% compared to CHA2DS2-VASc (0.61 (0.57-0.65) vs 0.52 (0.52-0.52) area under the receiver operating characteristics curves, 95% confidence interval) and provides a generalisable, opensource framework that other researchers and developers can build on.",cardiovascular medicine,fuzzy,100,100 +medRxiv,10.1101/2021.12.16.21267934,2021-12-17,https://medrxiv.org/cgi/content/short/2021.12.16.21267934,Predictors of SARS-CoV-2 infection in a multi-ethnic cohort of United Kingdom healthcare workers: a prospective nationwide cohort study (UK-REACH),Christopher A Martin; Daniel Pan; Carl Melbourne; Lucy Teece; Avinash Aujayeb; Rebecca F Baggaley; Luke Bryant; Sue Carr; Bindu Gregary; Amit Gupta; Anna Louise Guyatt; Catherine John; Chris McManus; Joshua Nazareth; Laura B Nellums; Rubina Reza; Sandra Simpson; Martin D Tobin; Katherine Woolf; Stephen Zingwe; Kamlesh Khunti; Keith R Abrams; Laura J Gray; Manish Pareek; - UK-REACH Study Collaborative Group,University of Leicester; University of Leicester; University of Leicester; University of Leicester; Northumbria Specialist Emergency Care Hospital; University of Leicester; University of Leicester; General Medical Council; Royal Preston Hospital; Oxford University Hospitals NHS Foundation Trust; University of Leicester; University of Leicester; University College London; University of Leicester; University of Nottingham; Derbyshire Healthcare NHS Foundation Trust; Nottinghamshire Healthcare NHS Foundation Trust; University of Leicester; University College London; Berkshire Healthcare NHS Foundation Trust; University of Leicester; University of Warwick; University of Leicester; University of Leicester; ,"IntroductionHealthcare workers (HCWs), particularly those from ethnic minority groups, have been shown to be at disproportionately higher risk of infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) compared to the general population. However, there is insufficient evidence on how demographic and occupational factors influence infection risk among ethnic minority HCWs. + +MethodsWe conducted a cross-sectional analysis using data from the United Kingdom Research study into Ethnicity And COVID-19 Outcomes in Healthcare workers (UK-REACH) cohort study. We used logistic regression to examine associations of demographic, household and occupational predictor variables with SARS-CoV-2 infection (defined by PCR, serology or suspected COVID-19) in a diverse group of HCWs. + +Results2,496 of the 10,772 HCWs (23.2%) who worked during the first UK national lockdown in March 2020 reported previous SARS-CoV-2 infection. In an adjusted model, demographic and household factors associated with increased odds of infection included younger age, living with other key workers and higher religiosity. Important occupational risk factors associated with increased odds of infection included attending to a higher number of COVID-19 positive patients (aOR 2.49, 95%CI 2.03-3.05 for [≥]21 patients per week vs none), working in a nursing or midwifery role (1.35, 1.15- 1.58, compared to doctors), reporting a lack of access to personal protective equipment (1.27, 1.15 - 1.41) and working in an ambulance (1.95, 1.52-2.50) or hospital inpatient setting (1.54, 1.37 - 1.74). Those who worked in Intensive Care Units were less likely to have been infected (0.76, 0.63-0.90) than those who did not. Black HCWs were more likely to have been infected than their White colleagues, an effect which attenuated after adjustment for other known predictors. + +ConclusionsWe identified key sociodemographic and occupational risk factors associated with SARS-CoV-2 infection amongst UK HCWs, and have determined factors that might contribute to a disproportionate odds of infection in HCWs from Black ethnic groups. These findings demonstrate the importance of social and occupational factors in driving ethnic disparities in COVID-19 outcomes, and should inform policies, including targeted vaccination strategies and risk assessments aimed at protecting HCWs in future waves of the COVID-19 pandemic. + +Trial registrationISRCTN 11811602",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.12.16.21267904,2021-12-17,https://medrxiv.org/cgi/content/short/2021.12.16.21267904,Deficits in hospital care among clinically vulnerable children aged 0 to 4 years during the COVID-19 pandemic,David Etoori; Katie Harron; Louise Mc Grath-Lone; Maximiliane Verfeurden; Ruth Gilbert; Ruth Blackburn,University College London; University College London; University College London; University College London; University College London; University College London,"ObjectiveTo quantify deficits in hospital care for clinically vulnerable children during the COVID-19 pandemic. DesignBirth cohort in Hospital Episode Statistics (HES). @@ -1928,6 +1966,7 @@ MethodsWithin an adult subset of the Virus Watch community cohort study, we soug ResultsBased on analysis of 10475 adult participants including 874 infections acquired outside the household, infection was independently associated with: leaving home for work (AOR 1.20 (1.02 - 1.42) p=0.0307, APAF 6.9%); public transport use (AOR for use more than once per week 1.82 (1.49 - 2.23) p<0.0001, APAF for public transport 12.42%); and shopping (AOR for shopping more than once per week 1.69 (1.29 - 2.21) P=0.0003, APAF for shopping 34.56%). Other non-household activities such as use of hospitality and leisure venues were rare due to restrictions and there were no significant associations with infection risk. ConclusionsA high proportion of the second wave of the pandemic was spent under conditions where people were being advised to work from home where possible, and to minimize exposure to shops, and a wide range of other businesses were subject to severe restrictions. Vaccines were being rolled out to high-risk groups. During this time, going to work was an important risk factor for infection but public transport use likely accounted for a lot of this risk. Only a minority of the cohort left home for work or used public or shared transport. By contrast, the majority of participants visited shops and this activity accounted for about one-third of non-household transmission.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2021.12.08.21267353,2021-12-08,https://medrxiv.org/cgi/content/short/2021.12.08.21267353,The challenge of limited vaccine supplies: impact of prior infection on anti-spike IgG antibody trajectories after a single COVID-19 vaccination,Jia Wei; Philippa Matthews; Nicole Stoesser; Ian Diamond; Ruth Studley; Emma Rourke; Duncan Cook; John Bell; John Newton; Jeremy Farrar; Alison Howarth; Brian Marsden; Sarah Hoosdally; Yvonne Jones; David Stuart; Derrick W Crook; tim E peto; Ann Sarah Walker; David W Eyre; Koen B Pouwels; - COVID-19 Infection Survey team,University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; NIHR Oxford Biomedical Research Centre; oxford university; University of Oxford; University of Oxford; University of Oxford; ,"Given high SARS-CoV-2 incidence, coupled with slow and inequitable vaccine roll-out, there is an urgent need for evidence to underpin optimum vaccine deployment, aiming to maximise global population immunity at speed. We evaluate whether a single vaccination in previously infected individuals generates similar initial and subsequent antibody responses to two vaccinations in those without prior infection. We compared anti-spike IgG antibody responses after a single dose of ChAdOx1, BNT162b2, or mRNA-1273 SARS-CoV-2 vaccines in the COVID-19 Infection Survey in the UK general population. In 100,849 adults who received at least one vaccination, 13,404 (13.3%) had serological and/or PCR evidence of prior infection. Prior infection significantly boosted antibody responses for all three vaccines, producing a higher peak level and longer half-life, and a response comparable to those without prior infection receiving two vaccinations. In those with prior infection, median time above the positivity threshold was estimated to last for >1 year after the first dose. Single-dose vaccination targeted to those previously infected may provide protection in populations with high rates of previous infection faced with limited vaccine supply, as an interim measure while vaccine campaigns are scaled up.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.12.03.21266112,2021-12-05,https://medrxiv.org/cgi/content/short/2021.12.03.21266112,Brain Injury in COVID-19 is Associated with Autoinflammation and Autoimmunity,Edward J Needham; Alex L Ren; Richard J Digby; Joanne G Outtrim; Dorothy A Chatfield; Virginia FJ Newcombe; Rainer Doffinger; Gabriela Barcenas-Morales; Claudia Fonseca; Michael J Taussig; Rowan M Burnstein; Cordelia Dunai; Nyarie Sithole; Nicholas J Ashton; Henrik Zetterberg; Magnus Gisslen; Eden Arvid; Emelie Marklund; Michael J Griffiths; Jonathan Cavanagh; Gerome Breen; Sarosh R Irani; Anne Elmer; Nathalie Kingston; John R Bradley; Leonie S Taams; Benedict D michael; Edward T Bullmore; Kenneth GC Smith; Paul A Lyons; Alasdair JC Coles; David K Menon; - Cambridge NeuroCOVID Group; - NIHR Cambridge Covid BioResource; - NIHR Cambridge Clinical Research Facility,"Department of Clinical Neurosciences, University of Cambridge, UK; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK.; Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK.; Cambridge Protein Arrays Ltd, Babraham Research Campus, Cambridge, UK; Cambridge Protein Arrays Ltd, Babraham Research Campus, Cambridge, UK; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; Clinical Infection Microbiology and Neuroimmunology, Institute of Infection, Veterinary and Ecological Science, Liverpool, UK.; Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK.; Department of Psychiatry and Neurochemistry, Institute of Neuroscience & Physiology, the Sahlgrenska Academy at the University of Gothenburg, Molndal, Sweden.; Department of Psychiatry and Neurochemistry, Institute of Neuroscience & Physiology, the Sahlgrenska Academy at the University of Gothenburg, Molndal, Sweden; C; Department of Infectious Diseases, Institute of Biomedicine, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden; Region Vastra Gotaland; Department of Infectious Diseases, Institute of Biomedicine, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden; Region Vastra Gotaland; Department of Infectious Diseases, Institute of Biomnedicine, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden; Region Vastra Gotalan; Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK.; Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, U; Department of Social Genetic and Developmental Psychiatry, King's College London, London, UK.; Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Department of Neurology, Oxford University H; Cambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, UK ; NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge, UK.; NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge, UK; Department of Medicine, University of Cambridge, Ad; Centre for Inflammation Biology and Cancer Immunology and Dept Inflammation Biology, School of Immunology and Microbial Sciences, Kings College London, Guys Cam; Clinical Infection Microbiology and Neuroimmunology, Institute of Infection, Veterinary and Ecological Science, Liverpool, UK.; Department of Psychiatry, University of Cambridge, Herchel Smith Building for Brain and Mind Sciences, Cambridge Biomedical Campus, Cambridge, UK.; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Je; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Je; Department of Clinical Neurosciences, University of Cambridge, UK; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; ; ; ","COVID-19 has been associated with many neurological complications including stroke, delirium and encephalitis. Furthermore, many individuals experience a protracted post-viral syndrome which is dominated by neuropsychiatric symptoms, and is seemingly unrelated to COVID-19 severity. The true frequency and underlying mechanisms of neurological injury are unknown, but exaggerated host inflammatory responses appear to be a key driver of severe COVID-19 more broadly. We sought to investigate the dynamics of, and relationship between, serum markers of brain injury (neurofilament light [NfL], Glial Fibrillary Acidic Protein [GFAP] and total Tau) and markers of dysregulated host response including measures of autoinflammation (proinflammatory cytokines) and autoimmunity. Brain injury biomarkers were measured using the Quanterix Simoa HDx platform, cytokine profiling by Luminex (R&D) and autoantibodies by a custom protein microarray. @@ -2417,11 +2456,6 @@ FindingsOf 4,091,537 RT-PCR results from 482,677 individuals, 29,903 (0{middle d InterpretationPopulation-level demographic and behavioural surveillance can be a valuable tool in identifying the varying characteristics driving current SARS-CoV-2 positivity, allowing monitoring to inform public health policy. FundingDepartment of Health and Social Care (UK), Welsh Government, Department of Health (on behalf of the Northern Ireland Government), Scottish Government, National Institute for Health Research.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2021.09.02.21262965,2021-09-02,https://medrxiv.org/cgi/content/short/2021.09.02.21262965,Whole genome sequencing identifies multiple loci for critical illness caused by COVID-19,Athanasios Kousathanas; Erola Pairo-Castineira; Konrad Rawlik; Alex Stuckey; Christopher A Odhams; Susan Walker; Clark D Russell; Tomas Malinauskas; Jonathan Millar; Katherine S Elliott; Fiona Griffiths; Wilna Oosthuyzen; Kirstie Morrice; Sean Keating; Bo Wang; Daniel Rhodes; Lucija Klaric; Marie Zechner; Nick Parkinson; Andrew D. Bretherick; Afshan Siddiq; Peter Goddard; Sally Donovan; David Maslove; Alistair Nichol; Malcolm G Semple; Tala Zainy; Fiona Maleady-Crowe; Linda Todd; Shahla Salehi; Julian Knight; Greg Elgar; Georgia Chan; Prabhu Arumugam; Tom A Fowler; Augusto Rendon; Manu Shankar-Hari; Charlotte Summers; Charles Hinds; Peter Horby; Danny McAuley; Hugh Montgomery; Peter J.M. Openshaw; Yang Wu; Jian Yang; Paul Elliott; Timothy Walsh; - GenoMICC Investigators; - 23andMe Investigators; - Covid-19 Human Genetics Initiative; Angie Fawkes; Lee Murphy; Kathy Rowan; Chris P Ponting; Veronique Vitart; James F Wilson; Richard H Scott; Sara Clohisey; Loukas Moutsianas; Andy Law; Mark J Caulfield; J. Kenneth Baillie,"Genomics England, London UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK; Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England, London UK; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, ON, Canada.; Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland.; NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, L; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Department of Intensive Care Medicine, Guy's and St. Thomas NHS Foundation Trust, London, UK.; Department of Medicine, University of Cambridge, Cambridge, UK.; William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK.; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.; Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK; UCL Centre for Human Health and Performance, London, W1T 7HA, UK.; National Heart and Lung Institute, Imperial College London, London, UK; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Imperial College, London; Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK.; ; ; ; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; Intensive Care National Audit & Research Centre, London, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK.; Genomics England, London UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England, London UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England, London UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK","Critical illness in COVID-19 is caused by inflammatory lung injury, mediated by the host immune system. We and others have shown that host genetic variation influences the development of illness requiring critical care1 or hospitalisation2;3;4 following SARS-Co-V2 infection. The GenOMICC (Genetics of Mortality in Critical Care) study recruits critically-ill cases and compares their genomes with population controls in order to find underlying disease mechanisms. - -Here, we use whole genome sequencing and statistical fine mapping in 7,491 critically-ill cases compared with 48,400 population controls to discover and replicate 22 independent variants that significantly predispose to life-threatening COVID-19. We identify 15 new independent associations with critical COVID-19, including variants within genes involved in interferon signalling (IL10RB, PLSCR1), leucocyte differentiation (BCL11A), and blood type antigen secretor status (FUT2). Using transcriptome-wide association and colocalisation to infer the effect of gene expression on disease severity, we find evidence implicating expression of multiple genes, including reduced expression of a membrane flippase (ATP11A), and increased mucin expression (MUC1), in critical disease. - -We show that comparison between critically-ill cases and population controls is highly efficient for genetic association analysis and enables detection of therapeutically-relevant mechanisms of disease. Therapeutic predictions arising from these findings require testing in clinical trials.",intensive care and critical care medicine,fuzzy,100,100 medRxiv,10.1101/2021.08.26.21262523,2021-08-28,https://medrxiv.org/cgi/content/short/2021.08.26.21262523,"Association between tocilizumab, sarilumab and all-cause mortality at 28 days in hospitalized patients with COVID-19: A network meta-analysis",Peter J Godolphin; David J Fisher; Lindsay R Berry; Lennie PG Derde; Janet V Diaz; Anthony C Gordon; Elizabeth Lorenzi; John C Marshall; Srinivas Murthy; Manu Shankar-Hari; Jonathan AC Sterne; Jayne F Tierney; Claire L Vale,University College London; University College London; Berry Consultants; University Medical Center Utrecht; World Health Organization; Imperial College London; Berry Consultants; University of Toronto; University of British Columbia; King's College London; University of Bristol; University College London; University College London,"ObjectiveTo estimate pairwise associations between administration of tocilizumab, sarilumab and usual care or placebo with 28-day mortality, in COVID-19 patients receiving concomitant corticosteroids and non-invasive or mechanical ventilation, based on all available direct and indirect evidence. MethodsEligible trials randomized hospitalized patients with COVID-19 that compared either interleukin-6 receptor antagonist with usual care or placebo in a recent prospective meta-analysis (27 trials, 10930 patients) or that directly compared tocilizumab with sarilumab. Data were restricted to patients receiving corticosteroids and either non-invasive or invasive ventilation at randomization. @@ -2904,13 +2938,6 @@ MethodsIsolated neutrophils from 41 hospitalised, non-ICU COVID-19 patients and ResultsCompared to AMC, COVID-19 neutrophils demonstrated elevated transmigration (p=0.0397) and NETosis (p=0.0366), but impaired phagocytosis (p=0.0236) associated with impaired ROS generation (p<0.0001). Surface expression of CD54 (p<0.0001) and CD11c (p=0.0008) was significantly increased and CD11b significantly decreased (p=0.0229) on COVID-19 patient neutrophils. COVID-19 patients showed increased systemic markers of NETosis including increased cfDNA (p=0.0153) and impaired DNAse activity (p<0.0.001). MPO (p<0.0001), VEGF (p<0.0001), TNFRI (p<0.0001) and IL-6 (p=0.009) were elevated in COVID-19, which positively correlated with disease severity by 4C score. ConclusionCOVID-19 is associated with neutrophil dysfunction across all main effector functions, with altered phenotype, elevated migration, impaired antimicrobial responses and elevated NETosis. These changes represent a clear mechanism for tissue damage and highlight that targeting neutrophil function may help modulate COVID-19 severity.",intensive care and critical care medicine,fuzzy,100,92 -medRxiv,10.1101/2021.06.08.21258531,2021-06-08,https://medrxiv.org/cgi/content/short/2021.06.08.21258531,"The UK Coronavirus Job Retention Scheme and changes in diet, physical activity and sleep during the COVID-19 pandemic: Evidence from eight longitudinal studies",Bozena Wielgoszewska; Jane Maddock; Michael J Green; Giorgio Di Gessa; Sam Parsons; Gareth J Griffith; Jazz Croft; Anna J Stevenson; Charlotte Booth; Richard J Silverwood; David Bann; Praveetha Patalay; Alun D Hughes; Nishi Chaturvedi; Laura D Howe; Emla Fitzsimons; Srinivasa Vittal Katikireddi; George B Ploubidis,"Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Unit for Lifelong Health and Ageing, University College London; MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; Institute of Epidemiology and Health Care, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Integrative Epidemiology Unit, University of Bristol; MRC Integrative Epidemiology Unit, University of Bristol; Centre for Genomic and Experimental Medicine, University of Edinburgh; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; UCL; MRC Unit for Lifelong Health and Ageing, University College London; MRC Unit for Lifelong Health and Ageing, University College London; MRC Integrative Epidemiology Unit, University of Bristol; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; Centre for Longitudinal Studies, UCL Social Research Institute, University College London","BackgroundIn March 2020 the UK implemented the Coronavirus Job Retention Scheme (furlough) to minimize job losses. Our aim was to investigate associations between furlough and diet, physical activity, and sleep during the early stages of the COVID-19 pandemic. - -MethodsWe analysed data from 25,092 participants aged 16 to 66 years from eight UK longitudinal studies. Changes in employment (including being furloughed) were defined by comparing employment status pre- and during the first lockdown. Health behaviours included fruit and vegetable consumption, physical activity, and sleeping patterns. Study-specific estimates obtained using modified Poisson regression, adjusting for socio-demographic characteristics and pre-pandemic health and health behaviours, were statistically pooled using random effects meta-analysis. Associations were also stratified by sex, age, and education. - -ResultsAcross studies, between 8 and 25% of participants were furloughed. Compared to those who remained working, furloughed workers were slightly less likely to be physically inactive (RR:0.85, [0.75-0.97], I2=59%) and did not differ in diet and sleep behaviours, although findings for sleep were heterogenous (I2=85%). In stratified analyses, furlough was associated with low fruit and vegetable consumption among males (RR=1.11; 95%CI: 1.01-1.22; I2: 0%) but not females (RR=0.84; 95%CI: 0.68-1.04; I2: 65%). Considering change in these health behaviours, furloughed workers were more likely than those who remained working to report increased fruit and vegetable consumption, exercise, and hours of sleep. - -ConclusionsThose furloughed exhibited broadly similar levels of health behaviours to those who remained in employment during the initial stages of the pandemic. There was little evidence to suggest that such social protection policies if used in the post-pandemic recovery period and during future economic crises would have adverse impacts on population health behaviours.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.06.08.21258132,2021-06-08,https://medrxiv.org/cgi/content/short/2021.06.08.21258132,"Aspirin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial",Peter W Horby; Guilherme Pessoa-Amorim; Natalie Staplin; Jonathan R Emberson; Enti Spata; Mark Campbell; Leon Peto; Nigel Brunskill; Simon Tiberi; Victor Chew; Thomas Brown; Hasan Tahir; Beate Ebert; David R Chadwick; Tony Whitehouse; Rahuldeb Sarkar; Jonathan Clive Graham; J Kenneth Baillie; Buddha Basnyat; Maya H Buch; Lucy C Chappell; Jeremy N Day; Saul N Faust; Raph Hamers; Thomas Jaki; Katie Jeffery; Edmund Juszczak; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Marion Mafham; Richard Haynes; Martin J Landray,"Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; University of Leicester, Leicester, United Kingdom; Barts Health NHS Foundation Trust, London, United Kingdom; North Tees and Hartlepool NHS Foundation Trust, Hartlepool, United Kingdom; Portsmouth Hospitals University NHS Foundation Trust, Portsmouth, United Kingdom; Royal Free London NHS Foundation Trust, London, United Kingdom; North West Anglia NHS Foundation Trust, Peterborough, United Kingdom; James Cook University Hospital, Middlesbrough, United Kingdom; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Medway NHS Foundation Trust, Gillingham, UK; North Cumbria Integrated Care NHS Foundation Trust, Carlisle, UK; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Oxford University Clinical Research Unit, Nepal, Patan Academy of Health Sciences, Kathmandu, Nepal; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; School of Life Sciences, Kings College London, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia and Faculty of Medicine, University of Indonesia, Jakarta, Indonesia, and Centre for Tropical Medicine; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Respiratory Medicine Department, Nottingham University Hospitals NHS Foundation Trust, Nottingham, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit and Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom","BackgroundAspirin has been proposed as a treatment for COVID-19 on the basis of its antithrombotic properties. MethodsIn this randomised, controlled, open-label platform trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19. Eligible and consenting adults were randomly allocated in a 1:1 ratio to either usual standard of care plus 150mg aspirin once daily until discharge or usual standard of care alone using web-based simple (unstratified) randomisation with allocation concealment. The primary outcome was 28-day mortality. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936). @@ -2978,7 +3005,6 @@ Implications of all the available evidenceSome individuals still contract COVID- medRxiv,10.1101/2021.05.25.21257505,2021-05-25,https://medrxiv.org/cgi/content/short/2021.05.25.21257505,Plitidepsin has a positive therapeutic index in adult patients with COVID-19 requiring hospitalization.,Jose F. Varona; Pedro Landete; Jose A Lopez-Martin; Vicente Estrada; Roger Paredes; Pablo Guisado-Vasco; Lucia Fernandez de Orueta; Miguel Torralba; Jesus Fortun; Roberto Vates; Jose Barberan; Bonaventura Clotet; Julio Ancochea; Daniel Carnevali; Noemi Cabello; Lourdes Porras; Paloma Gijon; Alfonso Monereo; Daniel Abad; Sonia Zuñiga; Isabel Sola; Jordi Rodon; Nuria Izquierdo-Useros; Salvador Fudio; Maria Jose Pontes; Beatriz de Rivas; Patricia Giron de Velasco; Belen Sopesen; Antonio Nieto; Javier Gomez; Pablo Aviles; Rubin Lubomirov; Kris M White; Romel Rosales; Soner Yildiz; Ann-Kathrin Reuschl; Lucy G. Thorne; Clare Jolly; Greg J. Towers; Lorena Zuliani-Alvarez; Mehdi Bouhaddou; Kirsten Obernier; Luis Enjuanes; Jose M Fernandez-Sousa; - Plitidepsin COVID Study Group; Nevan J Krogan; Jose M. Jimeno; Adolfo Garcia-Sastre,"Departamento de Medicina Interna, Hospital Universitario HM Monteprincipe, HM Hospitales, Madrid, Spain. Facultad de Medicina, Universidad San Pablo-CEU, Madrid; Hospital Universitario de La Princesa. Madrid, Spain. Universidad Autonoma de Madrid, Madrid, Spain.; PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain.; Hospital Clinico San Carlos, Madrid, Spain. Universidad Complutense de Madrid, Madrid, Spain.; IrsiCaixa AIDS Research Institute; Internal Medicine Department, Hospital Universitario Quironsalud, Madrid, Spain. Universidad Europea, Madrid, Spain.; Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain. European University of Madrid, Madrid, Spain.; Internal Medicine, Guadalajara University Hospital, Guadalajara, Spain. University of Alcala, Madrid, Spain.; Hospital Universitario Ramon y Cajal, Madrid, Spain.; Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain.; Hospital Universitario HM Monteprincipe, Madrid, Spain. Facultad de Medicina San Pablo CEU, Madrid, Spain.; Head of Infectious Diseases Department, Director of the Research Lab, IrsiCaixa, Barcelone, Spain. Professor of the UAB and the UVIC-UCC, Barcelone, Spain.; Hospital Universitario La Princesa, Madrid, Spain. Centro de Investigacion en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII; Hospital Universitario Quironsalud, Madrid, Spain Universidad Europea, Madrid, Spain.; Infectious Diseases Department, San Carlos University Hospital. Madrid Spain.; Internal Medicine, Hospital General de Ciudad Real, Ciudad Real, Spain.; Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañon, Instituto de Investigacion Sanitaria Gregorio Marañon; Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain; Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain. European University of Madrid, Madrid, Spain.; Department of Molecular and Cell Biology, Centro Nacional de Biotecnologia (CNBCSIC), Madrid, Spain.; Department of Molecular and Cell Biology, Centro Nacional de Biotecnologia (CNBCSIC), Madrid, Spain.; IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, Bellaterra, Spain; IrsiCaixa AIDS Research Institute, 08916, Badalona, Spain. Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, 08916, Badalona, Spain.; PharmaMar - Clinical Pharmacology Unit. Colmenar Viejo, Madrid, Spain; PharmaMar - Medical Affairs Unit. Colmenar Viejo. Madrid, Spain.; PharmaMar - Medical Affairs Unit. Colmenar Viejo, Madrid, Spain.; PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain.; PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain. Sylentis, S.A.U., Tres Cantos, Madrid, Spain. Biocross, S.L., Valladolid, Spain.; PharmaMar - Statistics Unit. Colmenar Viejo, Madrid, Spain.; PharmaMar - Statistics Unit. Colmenar Viejo, Madrid, Spain.; PharmaMar - Preclinical Unit. Colmenar Viejo, Madrid, Spain; PharmaMar - Clinical Pharmacology Unit. Colmenar Viejo, Madrid, Spain; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at ; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at ; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at ; Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom.; Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom.; Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom.; Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom; Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. J. David Gladstone Institutes, San Francisco, CA 94158, USA. QBI, Coronavirus Research G; Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. J. David Gladstone Institutes, San Francisco, CA 94158, USA. QBI, Coronavirus Research G; Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. J. David Gladstone Institutes, San Francisco, CA 94158, USA. QBI, Coronavirus Research G; Department of Molecular and Cell Biology, Centro Nacional de Biotecnologia (CNB-CSIC), Madrid, Spain.; PharmaMar, S.A., Colmenar Viejo, Madrid, Spain.; ; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. ; PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain.; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at ","Plitidepsin is a marine-derived cyclic-peptide that inhibits SARS-CoV-2 replication at low nanomolar concentrations by the targeting of host protein eEF1A (eukaryotic translation-elongation-factor-1A). We evaluated a model of intervention with plitidepsin in hospitalized COVID-19 adult patients where three doses were assessed (1.5, 2 and 2.5 mg/day for 3 days, as a 90-minute intravenous infusion) in 45 patients (15 per dose-cohort). Treatment was well tolerated, with only two Grade 3 treatment-related adverse events observed (hypersensitivity and diarrhea). The discharge rates by Days 8 and 15 were 56.8% and 81.8%, respectively, with data sustaining dose-effect. A mean 4.2 log10 viral load reduction was attained by Day 15. Improvement in inflammation markers was also noted in a seemingly dose-dependent manner. These results suggest that plitidepsin impacts the outcome of patients with COVID-19. One-Sentence SummaryPlitidepsin, an inhibitor of SARS-Cov-2 in vitro, is safe and positively influences the outcome of patients hospitalized with COVID-19.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.05.18.21257396,2021-05-23,https://medrxiv.org/cgi/content/short/2021.05.18.21257396,A Phenome-Wide Association Study of genes associated with COVID-19 severity reveals shared genetics with complex diseases in the Million Veteran Program,Anurag Verma; Noah L. Tsao; Lauren O. Thomann; Yuk-Lam Ho; Sudha K. Iyengar; Shiuh-Wen Luoh; Rotonya Carr; Dana C. Crawford; Jimmy T. Efird; Giulio Genovese; Adriana Hung; Kerry L. Ivey; Michael G. Levin; Julie Lynch; Pradeep Natarajan; Saiju Pyarajan; Alexander Bick; Lauren Costa; Giulio Genovese; Richard Hauger; Ravi Madduri; Gita A. Pathak; Renato Polimanti; Benjamin F. Voight; Marijana Vujkovic; Maryam Zekavat; Hongyu Zhao; Marylyn Ritchie; Kyong-Mi Chang; Kelly Cho; Juan P Casas; Philip S Tsao; J. Michael Gaziano; Christopher O?Donnell; Scott M. Damrauer; Katherine P. Liao,"Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Ph; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Phi; VA Boston Healthcare System, Boston, Massachusetts, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Departments of Population and Quantitative Health Sciences, Ophthalmology and Visual Sciences and Genetics and Genome Sciences, Case Western Reserve University,; VA Portland Health Care System, Portland OR, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Ph; Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA; Cooperative Studies Program Epidemiology Center, Health Services Research and Development, DVAHCS (Duke University Affiliate), Durham, North Carolina, USA.; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.; Tennessee Valley Healthcare System (Nashville VA) , Nashville, Tennessee, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, Utah, USA.; Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA.; VA Boston Healthcare System, Boston, Massachusetts, USA;Harvard Medical School, Boston, Massachusetts, USA; VA Boston Healthcare System, Boston, Massachusetts, USA;Vanderbilt University, Nashville, Tennessee, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.; Department of Psychiatry, University of California, San Diego, La Jolla, CA; Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, ; University of Chicago Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois, USA;Data Science and Learning Division, Arg; Department of Psychiatry, Yale School of Medicine, Connecticut, USA; Department of Psychiatry, Yale School of Medicine, Connecticut, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Ph; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Ph; VA Boston Healthcare System, Boston, Massachusetts, USA; VA Connecticut Healthcare System, West Haven, CT, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; VA Palo Alto Health Care System, Palo Alto, California, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; VA Boston Healthcare System, Boston, Massachusetts, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Phi; VA Boston Healthcare System, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA; Brigham and Women's Hospital, Boston, Massachusetts","The study aims to determine the shared genetic architecture between COVID-19 severity with existing medical conditions using electronic health record (EHR) data. We conducted a Phenome-Wide Association Study (PheWAS) of genetic variants associated with critical illness (n=35) or hospitalization (n=42) due to severe COVID-19 using genome-wide association summary from the Host Genetics Initiative. PheWAS analysis was performed using genotype-phenotype data from the Veterans Affairs Million Veteran Program (MVP). Phenotypes were defined by International Classification of Diseases (ICD) codes mapped to clinically relevant groups using published PheWAS methods. Among 658,582 Veterans, variants associated with severe COVID-19 were tested for association across 1,559 phenotypes. Variants at the ABO locus (rs495828, rs505922) associated with the largest number of phenotypes (nrs495828= 53 and nrs505922=59); strongest association with venous embolism, odds ratio (ORrs495828 1.33 (p=1.32 x 10-199), and thrombosis ORrs505922 1.33, p=2.2 x10-265. Among 67 respiratory conditions tested, 11 had significant associations including MUC5B locus (rs35705950) with increased risk of idiopathic fibrosing alveolitis OR 2.83, p=4.12 x 10-191; CRHR1 (rs61667602) associated with reduced risk of pulmonary fibrosis, OR 0.84, p=2.26x 10-12. The TYK2 locus (rs11085727) associated with reduced risk for autoimmune conditions, e.g., psoriasis OR 0.88, p=6.48 x10-23, lupus OR 0.84, p=3.97 x 10-06. PheWAS stratified by genetic ancestry demonstrated differences in genotype-phenotype associations across ancestry. LMNA (rs581342) associated with neutropenia OR 1.29 p=4.1 x 10-13 among Veterans of African ancestry but not European. Overall, we observed a shared genetic architecture between COVID-19 severity and conditions related to underlying risk factors for severe and poor COVID-19 outcomes. Differing associations between genotype-phenotype across ancestries may inform heterogenous outcomes observed with COVID-19. Divergent associations between risk for severe COVID-19 with autoimmune inflammatory conditions both respiratory and non-respiratory highlights the shared pathways and fine balance of immune host response and autoimmunity and caution required when considering treatment targets.",genetic and genomic medicine,fuzzy,91,92 medRxiv,10.1101/2021.05.13.21257161,2021-05-18,https://medrxiv.org/cgi/content/short/2021.05.13.21257161,"Occupation, Work-Related Contact, and SARS-CoV-2 Anti-Nucleocapsid Serological Status: Findings from the Virus Watch prospective cohort study",Sarah Beale; Parth Patel; Alison Rodger; Isobel Braithwaite; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Annalan MD Navaratnam; Vincent Nguyen; Madhumita Shrotri; Robert W Aldridge; Andrew C Hayward; - Virus Watch Collaborative,University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ,"BackgroundWorkers differ in their risk of acquiring SARS-CoV-2 infection according to their occupation; however, few studies have been able to control for multiple confounders or investigate the work-related factors that drive differences in occupational risk. Using data from the Virus Watch community cohort study in England and Wales, we set out to estimate the total effect of occupation on SARS-CoV-2 serological status, whether this is mediated by frequency of close contact within the workplace, and how exposure to poorly ventilated workplaces varied across occupations. MethodsWe used data from a sub-cohort (n =3761) of adults ([≥]18) tested for SARS-CoV-2 anti-nucleocapsid antibodies between 01 February-28 April 2021 and responded to a questionnaire about work during the pandemic. Anti-nucleocapsid antibodies were used as a proxy of prior natural infection with COVID-19. We used logistic decomposition to estimate the total and direct effect of occupation and indirect effect of workplace contact frequency on odds of seropositivity, adjusting for age, sex, household income and region. We investigated the relationship between occupation and exposure to poorly-ventilated workplace environments using ordinal logistic regression. @@ -3040,13 +3066,6 @@ MethodsWe report the most recent findings on community infections from the REal- ResultsBetween rounds 10 and 11, prevalence of swab-positivity dropped by 50% in England from 0.20% (0.17%, 0.23%) to 0.10% (0.08%, 0.13%), with a corresponding R estimate of 0.90 (0.87, 0.94). Rates of swab-positivity fell in the 55 to 64 year old group from 0.17% (0.12%, 0.25%) in round 10 to 0.06% (0.04%, 0.11%) in round 11. Prevalence in round 11 was higher in the 25 to 34 year old group at 0.21% (0.12%, 0.38%) than in the 55 to 64 year olds and also higher in participants of Asian ethnicity at 0.31% (0.16%, 0.60%) compared with white participants at 0.09% (0.07%, 0.11%). Based on sequence data for positive samples for which a lineage could be identified, we estimate that 92.3% (75.9%, 97.9%, n=24) of infections were from the B.1.1.7 lineage compared to 7.7% (2.1%, 24.1%, n=2) from the B.1.617.2 lineage. Both samples from the B.1.617.2 lineage were detected in London from participants not reporting travel in the previous two weeks. Also, allowing for suitable lag periods, the prior close alignment between prevalence of infections and hospitalisations and deaths nationally has diverged. DiscussionWe observed marked reductions in prevalence from March to April and early May 2021 in England reflecting the success of the vaccination programme and despite easing of restrictions during lockdown. However, there is potential upwards pressure on prevalence from the further easing of lockdown regulations and presence of the B.1.617.2 lineage. If prevalence rises in the coming weeks, policy-makers will need to assess the possible impact on hospitalisations and deaths. In addition, consideration should be given to other health and economic impacts if increased levels of community transmission occur.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2021.05.17.21257223,2021-05-17,https://medrxiv.org/cgi/content/short/2021.05.17.21257223,Serial interval of COVID-19 and the effect of Variant B.1.1.7: analyses from a prospective community cohort study (Virus Watch).,Cyril Roman Geismar; Ellen Fragaszy; Vincent Grigori Nguyen; Wing Lam Erica Fong; Madhumita Shrotri; Sarah Beale; Alison Rodger; Vasileios Lampos; Thomas Edward Byrne; Jana Kovar; Annalan Navaratnam; Parth Patel; Robert W Aldridge; Andrew Hayward; - Virus Watch Collaborative,University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ,"IntroductionIncreased transmissibility of B.1.17 variant of concern (VOC) in the UK may explain its rapid emergence and global spread. We analysed data from putative household infector - infectee pairs in the Virus Watch Community cohort study to assess the serial interval of COVID-19 and whether this was affected by emergence of the B.1.17 variant. - -MethodsThe Virus Watch study is an online, prospective, community cohort study following up entire households in England and Wales during the COVID-19 pandemic. Putative household infector-infectee pairs were identified where more than one person in the household had a positive swab matched to an illness episode. Data on whether individual infections were caused by the B.1.1.7 variant were not available. We therefore developed a classification system based on the percentage of cases estimated to be due to B.1.17 in national surveillance data for different English regions and study weeks. - -ResultsOut of 24,887 illnesses reported, 915 tested positive for SARS-CoV-2 and 186 likely infector-infectee pairs in 186 households amongst 372 individuals were identified. The mean COVID-19 serial interval was 3.18 (95%CI: 2.55 - 3.81) days. There was no significant difference (p=0.267) between the mean serial interval for Variants of Concern (VOC) hotspots (mean = 3.64 days, (95%CI: 2.55 - 4.73)) days and non-VOC hotspots, (mean = 2.72 days, (95%CI: 1.48 - 3.96)). - -ConclusionsOur estimates of the average serial interval of COVID-19 are broadly similar to estimates from previous studies and we find no evidence that B.1.1.7 is associated with a change in serial intervals. Alternative explanations such as increased viral load, longer period of viral shedding or improved receptor binding may instead explain the increased transmissibility and rapid spread and should undergo further investigation.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.05.13.21257146,2021-05-17,https://medrxiv.org/cgi/content/short/2021.05.13.21257146,Sociodemographic inequality in COVID-19 vaccination coverage amongst elderly adults in England: a national linked data study,Vahe Nafilyan; Ted Dolby; Cameron Razieh; Charlotte Gaughan; Jasper Morgan; Daniel Ayoubkhani; Ann Sarah Walker; Kamlesh Khunti; Myer Glickman; Thomas Yates,"Office for National Statistics; Office for National Statistics; Diabetes Research Centre, University of Leicester; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Diabetes Research Centre, University of Leicester; Office for National Statistics; Diabetes Research Centre, University of Leicester","ObjectiveTo examine inequalities in COVID-19 vaccination rates amongst elderly adults in England DesignCohort study @@ -4037,7 +4056,41 @@ ResultsAmongst the population of 31,716 patients discharged following hospitalis InterpretationCardiometabolic and pulmonary adverse outcomes are markedly raised following hospitalisation for COVID-19 compared to the general population. However, the excess risks were more comparable to those seen following hospitalisation with pneumonia. Identifying patients at particularly high risk of outcomes would inform targeted preventive measures. FundingWellcome, Royal Society, National Institute for Health Research, National Institute for Health Research Oxford Biomedical Research Centre, UK Medical Research Council, UK Research and Innovation, Health and Safety Executive.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2021.01.22.21249968,2021-01-25,https://medrxiv.org/cgi/content/short/2021.01.22.21249968,An external validation of the QCovid risk prediction algorithm for risk of mortality from COVID-19 in adults: national validation cohort study in England,Vahe Nafilyan; Ben Humberstone; Nisha Metha; Ian Diamond; Luke Lorenzi; Piotr Pawelek; Ryan Schofield; Jasper Morgan; Paul Brown; Ronan Lyons; Aziz Sheikh; Julia Hippisley-Cox,Office for National Statistics; Office for National Statistics; Office of the Chief Medical Officer; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Swansea University; University of Edinburgh; University of Oxford,"BackgroundTo externally validate a risk prediction algorithm (QCovid) to estimate mortality outcomes from COVID-19 in adults in England. + +MethodsPopulation-based cohort study using the ONS Public Health Linked Data Asset, a cohort based on the 2011 Census linked to Hospital Episode Statistics, the General Practice Extraction Service Data for pandemic planning and research, radiotherapy and systemic chemotherapy records. The primary outcome was time to COVID-19 death, defined as confirmed or suspected COVID-19 death as per death certification. Two time periods were used: (a) 24th January to 30th April 2020; and (b) 1st May to 28th July 2020. We evaluated the performance of the QCovid algorithms using measures of discrimination and calibration for each validation time period. + +FindingsThe study comprises 34,897,648 adults aged 19-100 years resident in England. There were 26,985 COVID-19 deaths during the first time-period and 13,177 during the second. The algorithms had good calibration in the validation cohort in both time periods with close correspondence of observed and predicted risks. They explained 77.1% (95% CI: 76.9% to 77.4%) of the variation in time to death in men in the first time-period (R2); the D statistic was 3.76 (95% CI: 3.73 to 3.79); Harrells C was 0.935 (0.933 to 0.937). Similar results were obtained for women, and in the second time-period. In the top 5% of patients with the highest predicted risks of death, the sensitivity for identifying deaths in the first time period was 65.9% for men and 71.7% for women. People in the top 20% of predicted risks of death accounted for 90.8% of all COVID-19 deaths for men and 93.0% for women. + +InterpretationThe QCovid population-based risk algorithm performed well, showing very high levels of discrimination for COVID-19 deaths in men and women for both time periods. It has the potential to be dynamically updated as the pandemic evolves and therefore, has potential use in guiding national policy. + +FundingNational Institute of Health Research + +RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSPublic policy measures and clinical risk assessment relevant to COVID-19 need to be aided by rigorously developed and validated risk prediction models. A recent living systematic review of published risk prediction models for COVID-19 found most models are subject to a high risk of bias with optimistic reported performance, raising concern that these models may be unreliable when applied in practice. A population-based risk prediction model, QCovid risk prediction algorithm, has recently been developed to identify adults at high risk of serious COVID-19 outcomes, which overcome many of the limitations of previous tools. + +Added value of this studyCommissioned by the Chief Medical Officer for England, we validated the novel clinical risk prediction model (QCovid) to identify risks of short-term severe outcomes due to COVID-19. We used national linked datasets from general practice, death registry and hospital episode data for a population-representative sample of over 34 million adults. The risk models have excellent discrimination in men and women (Harrells C statistic>0.9) and are well calibrated. QCovid represents a new, evidence-based opportunity for population risk-stratification. + +Implications of all the available evidenceQCovid has the potential to support public health policy, from enabling shared decision making between clinicians and patients in relation to health and work risks, to targeted recruitment for clinical trials, and prioritisation of vaccination, for example.",public and global health,fuzzy,100,100 bioRxiv,10.1101/2021.01.25.428136,2021-01-25,https://biorxiv.org/cgi/content/short/2021.01.25.428136,mRNA-1273 efficacy in a severe COVID-19 model: attenuated activation of pulmonary immune cells after challenge,Michelle Meyer; Yuan Wang; Darin Edwards; Gregory R Smith; Aliza B Rubenstein; Palaniappan Ramanathan; Chad E Mire; Colette Pietzsch; Xi Chen; Yongchao Ge; Wan Sze Cheng; Carole Henry; Angela Woods; LingZhi Ma; Guillaume B. E. Stewart-Jones; Kevin W Bock; Minai Mahnaz; Bianca M Nagata; Sivakumar Periasamy; Pei-Yong Shi; Barney S Graham; Ian N Moore; Irene Ramos; Olga G. Troyanskaya; Elena Zaslavsky; Andrea Carfi; Stuart C Sealfon; Alexander Bukreyev,"University of Texas Medical Branch; Princeton University; Moderna Inc; Icahn School of Medicine at Mount Sinai; Icahn School of Medicine at Mount Sinai; University of Texas Medical Branch; University of Texas Medical Branch; University of Texas Medical Branch; Flatiron Institute, Simons Foundation; Icahn School of Medicine at Mount Sinai; Icahn School of Medicine at Mount Sinai; Moderna Inc; Moderna Inc; Moderna Inc; Moderna Inc; National Institute of Health; National Institutes of Health; National Institutes of Health; University of Texas Medical Branch; University of Texas Medical Branch; National Institutes of Health; National Institutes of Health; Icahn School of Medicine at Mount Sinai; Princeton University; Icahn School of Medicine at Mount Sinai; Moderna Inc; Icahn School of Medicine at Mount Sinai; University of Texas Medical Branch at Galveston","The mRNA-1273 vaccine was recently determined to be effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from interim Phase 3 results. Human studies, however, cannot provide the controlled response to infection and complex immunological insight that are only possible with preclinical studies. Hamsters are the only model that reliably exhibit more severe SARS-CoV-2 disease similar to hospitalized patients, making them pertinent for vaccine evaluation. We demonstrate that prime or prime-boost administration of mRNA-1273 in hamsters elicited robust neutralizing antibodies, ameliorated weight loss, suppressed SARS-CoV-2 replication in the airways, and better protected against disease at the highest prime-boost dose. Unlike in mice and non-human primates, mRNA-1273- mediated immunity was non-sterilizing and coincided with an anamnestic response. Single-cell RNA sequencing of lung tissue permitted high resolution analysis which is not possible in vaccinated humans. mRNA-1273 prevented inflammatory cell infiltration and the reduction of lymphocyte proportions, but enabled antiviral responses conducive to lung homeostasis. Surprisingly, infection triggered transcriptome programs in some types of immune cells from vaccinated hamsters that were shared, albeit attenuated, with mock-vaccinated hamsters. Our results support the use of mRNA-1273 in a two-dose schedule and provides insight into the potential responses within the lungs of vaccinated humans who are exposed to SARS-CoV-2.",immunology,fuzzy,96,94 +medRxiv,10.1101/2021.01.21.20240887,2021-01-22,https://medrxiv.org/cgi/content/short/2021.01.21.20240887,"The psychosocial impact of the COVID-19 pandemic on 4,378 UK healthcare workers and ancillary staff: initial baseline data from a cohort study collected during the first wave of the pandemic.",Danielle Lamb; Sam Gnanapragasam; Neil Greenberg; Rupa Bhundia; Ewan Carr; Matthew Hotopf; Reza Razavi; Rosalind Raine; Sean Cross; Amy Dewar; Mary Docherty; Sarah Dorrington; Stephani Hatch; Charlotte Wilson-Jones; Daniel Leightley; Ira Madan; Sally Marlow; Isabel McMullen; Anne Marie Rafferty; Martin Parsons; Catherine Polling; Danai Serfioti; Helen Gaunt; Peter Aitken; Joanna Morris-Bone; Chloe Simela; Veronica French; Rachel Harris; Sharon A.M. Stevelink; Simon Wessely,"Department of Applied Health Research, UCL, 1-19 Torrington Place, London, WC1E 7HB; South London and Maudsley NHS Foundation Trust, London, UK; Health Protection Research Unit, King's College London, Weston Education Centre, 10 Cutcombe Road, London, SE5 9RJ; Department of Psychological Medicine, King's College London, London, UK.; Department of Biostatistics and Health Informatics, King's College London, London, UK; National Institute of Health Research Biomedical Research Centre at the South London and Maudsley NHS Foundation Trust.; 1 Lambeth Palace Rd, South Bank, London, SE1 7EU; Dept of Applied Health Research, UCL; Department of Psychological Medicine, King's College Hospital. Denmark Hill. SE5 9RS; Guy's and St Thomas' NHS Foundation Trust; Department of Psychological Medicine, King's College Hospital. Denmark Hill. SE5 9RS; Institute of Psychiatry, Psychology and Neuroscience, King's College London; Institute of Psychiatry, Psychology and Neuroscience, King's College London; Institute of Psychiatry, Psychology and Neuroscience, King's College London; King's Centre for Military Health Research, Department of Psychological Medicine, King's College London, London, UK. AND Department of Psychological Medicine, K; Guy's and St Thomas' NHS Foundation Trust, London; Institute of Psychiatry, Psychology and Neuroscience, King's College London; Department of Psychological Medicine, King's College Hospital, South London and Maudsley NHS Foundation Trust; Adult Nursing, King's College London; Mental Health Liaison Team, King's College Hospital; Institute of Psychiatry, Psychology and Neuroscience, King's College London; King's Centre for Military Health Research, King's College London, Room 307, Weston Education Centre, 10 Cutcombe Road, London SE5 9RJ; University Hospital of Leciester NHS Trust. Groby Road Leciester LE4 9QP; Devon Partnership NHS Trust, Trust HQ, R&D, Dryden Road, Exeter, Devon, EX2 5AF; Avon & Wiltshire Mental Health Partnership NHS Trust, R&D, Fromeside, Blackberry Hill Hospital, Bristol, BS16 1EG; Guy's and St Thomas' NHS Foundation Trust, London; Nottinghamshire Healthcare NHS Foundation Trust; Cornwall Partnership Foundation NHS Trust/ Research and Innovation Team; King's Centre for Military Health Research, Department of Psychological Medicine, King's College London, London, UK. AND Department of Psychological Medicine, K; Department of Psychological Medicine, King's College London, Weston Education, Denmark Hill, London, SE5 9JR","ObjectivesThis study reports preliminary findings on the prevalence of, and factors associated with, mental health and wellbeing outcomes of healthcare workers during the early months (April-June) of the COVID-19 pandemic in the UK. + +MethodsPreliminary cross-sectional data were analysed from a cohort study (n=4,378). Clinical and non-clinical staff of three London-based NHS Trusts (UK), including acute and mental health Trusts, took part in an online baseline survey. The primary outcome measure used is the presence of probable common mental disorders (CMDs), measured by the General Health Questionnaire (GHQ-12). Secondary outcomes are probable anxiety (GAD-7), depression (PHQ-9), Post-Traumatic Stress Disorder (PTSD) (PCL-6), suicidal ideation (CIS-R), and alcohol use (AUDIT). Moral injury is measured using the Moray Injury Event Scale (MIES). + +ResultsAnalyses showed substantial levels of CMDs (58.9%, 95%CI 58.1 to 60.8), and of PTSD (30.2%, 95%CI 28.1 to 32.5) with lower levels of depression (27.3%, 95%CI 25.3 to 29.4), anxiety (23.2%, 95%CI 21.3 to 25.3), and alcohol misuse (10.5%, 95%CI, 9.2 to 11.9). Women, younger staff, and nurses tended to have poorer outcomes than other staff, except for alcohol misuse. Higher reported exposure to moral injury (distress resulting from violation of ones moral code) was strongly associated with increased levels of CMDs, anxiety, depression, PTSD symptoms, and alcohol misuse. + +ConclusionsOur findings suggest that mental health support for healthcare workers should consider those demographics and occupations at highest risk. Rigorous longitudinal data are needed in order to respond to the potential long-term mental health impacts of the pandemic. + +HighlightsO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LILarge-scale population studies report increased prevalence of depression, anxiety, and psychological distress during the COVID-19 pandemic. +C_LIO_LIEvidence from previous epidemics indicates a high and persistent burden of adverse mental health outcomes among healthcare workers. +C_LI + +What are the new findings?O_LISubstantial levels of probable common mental disorders and post-traumatic stress disorder were found among healthcare workers. +C_LIO_LIGroups at increased risk of adverse mental health outcomes included women, nurses, and younger staff, as well as those who reported higher levels of moral injury. +C_LI + +How might this impact on policy or clinical practice in the foreseeable future?O_LIThe mental health offering to healthcare workers must consider the interplay of demographic, social, and occupational factors. +C_LIO_LIAdditional longitudinal research that emphasises methodological rigor, namely with use of standardised diagnostic interviews to establish mental health diagnoses, is necessary to better understand the mental health burden, identify those most at risk, and provide appropriate support without pathologizing ordinary distress responses. +C_LI",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2021.01.20.21250158,2021-01-22,https://medrxiv.org/cgi/content/short/2021.01.20.21250158,REACT-1 round 8 interim report: SARS-CoV-2 prevalence during the initial stages of the third national lockdown in England,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E. Walters; Haowei Wang; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear","BackgroundHigh prevalence of SARS-CoV-2 virus in many northern hemisphere populations is causing extreme pressure on healthcare services and leading to high numbers of fatalities. Even though safe and effective vaccines are being deployed in many populations, the majority of those most at-risk of severe COVID-19 will not be protected until late spring, even in countries already at a more advanced stage of vaccine deployment. MethodsThe REal-time Assessment of Community Transmission study-1 (REACT-1) obtains throat and nose swabs from between 120,000 and 180,000 people in the community in England at approximately monthly intervals. Round 8a of REACT-1 mainly covers a period from 6th January 2021 to 15th January 2021. Swabs are tested for SARS-CoV-2 virus and patterns of swab-positivity are described over time, space and with respect to individual characteristics. We compare swab-positivity prevalence from REACT-1 with mobility data based on the GPS locations of individuals using the Facebook mobile phone app. We also compare results from round 8a with those from round 7 in which swabs were collected from 13th November to 24th November (round 7a) and 25th November to 3rd December 2020 (round 7b). @@ -4161,6 +4214,21 @@ Implications of all the available evidenceVaccination is likely to provide subst medRxiv,10.1101/2020.12.30.20248603,2021-01-01,https://medrxiv.org/cgi/content/short/2020.12.30.20248603,SARS-CoV-2 positivity in asymptomatic-screened dental patients,David I Conway; Shauna Culshaw; Maura Edwards; Claire Clark; Chris Watling; Chris Robertson; Raymond Braid; Emma O'Keefe; Niall McGoldrick; Jacky Burns; Stacey Provan; Harper VanSteenhouse; Jodie Hay; Rory Gunson; - Dental COVID-19 Surveillance Survey Group,University of Glasgow and Public Health Scotland; University of Glasgow; NHS Ayrshire and Arran; Public Health Scotland; Public Health Scotland; Strathclyde University and Public Health Scotland; Public Health Scotland; NHS Fife; NHS Fife; NHS Fife; NHS Greater Glasgow & Clyde; BioClavis Ltd; University of Glasgow; NHS Greater Glasgow & Clyde; ,"Enhanced community surveillance is a key pillar of the public health response to COVID-19. Asymptomatic carriage of SARS-CoV-2 is a potentially significant source of transmission, yet remains relatively poorly understood. Disruption of dental services continues with significantly reduced capacity. Ongoing precautions include pre- and/or at appointment COVID-19 symptom screening and use of enhanced personal protective equipment (PPE). This study aimed to investigate SARS-CoV-2 infection in dental patients to inform community surveillance and improve understanding of risks in the dental setting. Thirty-one dental care centres across Scotland invited asymptomatic screened patients over 5-years-old to participate. Following verbal consent and completion of sociodemographic and symptom history questionnaire, trained dental teams took a combined oropharyngeal and nasal swab sample using standardised VTM-containing testkits. Samples were processed by the Lighthouse Lab and patients informed of their results by SMS/e-mail with appropriate self-isolation guidance in the event of a positive test. Over a 13-week period (from 3August to 31October2020) n=4,032 patients, largely representative of the population, were tested. Of these n=22 (0.5%; 95%CI 0.5%, 0.8%) tested positive for SARS-CoV-2. The positivity rate increased over the period, commensurate with uptick in community prevalence identified across all national testing monitoring data streams. All positive cases were successfully followed up by the national contact tracing program. To the best of our knowledge this is the first report of a COVID-19 testing survey in asymptomatic-screened patients presenting in a dental setting. The positivity rate in this patient group reflects the underlying prevalence in community at the time. These data are a salient reminder, particularly when community infection levels are rising, of the importance of appropriate ongoing Infection Prevention Control and PPE vigilance, which is relevant as healthcare team fatigue increases as the pandemic continues. Dental settings are a valuable location for public health surveillance.",dentistry and oral medicine,fuzzy,100,100 medRxiv,10.1101/2020.12.24.20248822,2020-12-26,https://medrxiv.org/cgi/content/short/2020.12.24.20248822,Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England,Nicholas G Davies; Sam Abbott; Rosanna C. Barnard; Christopher I. Jarvis; Adam J. Kucharski; James D Munday; Carl A. B. Pearson; Timothy Russell; Damien Tully; Alex D. Washburne; Tom Wenseleers; Amy Gimma; William Waites; Kerry L. M. Wong; Kevin van Zandvoort; Justin D. Silverman; - CMMID COVID-19 Working Group; - The COVID-19 Genomics UK (COG-UK) Consortium; Karla Diaz-Ordaz; Ruth H Keogh; Rosalind M Eggo; Sebastian Funk; Mark Jit; Katherine E. Atkins; W. John Edmunds,"London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Selva Analytics LLC; KU Leuven; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; College of Information Science and Technology, Pennsylvania State University; ; ; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine","A novel SARS-CoV-2 variant, VOC 202012/01 (lineage B.1.1.7), emerged in southeast England in November 2020 and is rapidly spreading towards fixation. Using a variety of statistical and dynamic modelling approaches, we estimate that this variant has a 43-90% (range of 95% credible intervals 38-130%) higher reproduction number than preexisting variants. A fitted two-strain dynamic transmission model shows that VOC 202012/01 will lead to large resurgences of COVID-19 cases. Without stringent control measures, including limited closure of educational institutions and a greatly accelerated vaccine roll-out, COVID-19 hospitalisations and deaths across England in 2021 will exceed those in 2020. Concerningly, VOC 202012/01 has spread globally and exhibits a similar transmission increase (59-74%) in Denmark, Switzerland, and the United States.",epidemiology,fuzzy,100,100 bioRxiv,10.1101/2020.12.23.424229,2020-12-25,https://biorxiv.org/cgi/content/short/2020.12.23.424229,Patterns of within-host genetic diversity in SARS-CoV-2,Gerry Tonkin-Hill; Inigo Martincorena; Roberto Amato; Andrew R J Lawson; Moritz Gerstung; Ian Johnston; David K Jackson; Naomi R Park; Stefanie V Lensing; Michael A Quail; Sónia Gonçalves; Cristina Ariani; Michael Spencer Chapman; William L Hamilton; Luke W Meredith; Grant Hall; Aminu S Jahun; Yasmin Chaudhry; Myra Hosmillo; Malte L Pinckert; Iliana Georgana; Anna Yakovleva; Laura G Caller; Sarah L Caddy; Theresa Feltwell; Fahad A Khokhar; Charlotte J Houldcroft; Martin D Curran; Surendra Parmar; - The COVID-19 Genomics UK (COG-UK) Consortium; Alex Alderton; Rachel Nelson; Ewan Harrison; John Sillitoe; Stephen D Bentley; Jeffrey C Barrett; M. Estee Torok; Ian G Goodfellow; Cordelia Langford; Dominic Kwiatkowski; - Wellcome Sanger Institute COVID-19 Surveillance Team,"Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; European Bioinformatics Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge and The Francis Crick Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Medicine, University of Cambridge and Cambridge Institute of Therapeutic Immunology and Infectious Disease; Department of Medicine, University of Cambridge; Public Health England; Public Health England; COG-UK; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute and European Bioinformatics Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute and Oxford University; ","Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1,181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within and between host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.",genomics,fuzzy,100,100 +medRxiv,10.1101/2020.12.21.20248607,2020-12-22,https://medrxiv.org/cgi/content/short/2020.12.21.20248607,Time use and social mixing during and around festive periods: Potential changes in the age distribution of COVID-19 cases from increased intergenerational interactions,Edwin van Leeuwen; Frank G. Sandmann; Rosalind M. Eggo; - PHE Joint modelling group; Peter J. White,Public Health England; Public Health England; London School of Hygiene &Tropical Medicine; London School of Hygiene & Tropical Medicine; ; Public Health England; Imperial College London,"RationaleAmid the ongoing coronavirus disease 2019 (COVID-19) pandemic in which many countries have adopted physical distancing measures, tiered restrictions, and episodic ""lockdowns,"" the impact of potentially increased social mixing during festive holidays on the age distribution of new COVID-19 cases remains unclear. + +ObjectiveWe aimed to gain insights into possible changes in the age distribution of COVID-19 cases in the UK after temporarily increased intergenerational interactions in late December 2020. + +MethodWe modelled changes in time use and social mixing based on age-stratified contact rates using historical nationally-representative surveys and up-to-date Google mobility data from four weeks before and after the festive period. We explored changes in the effective reproduction number and the age distribution of cases, in four scenarios: (1) ""normal"": time use and contact patterns as observed historically, (2) ""pre-lockdown"": patterns as seen before the lockdown in November 2020, (3) ""lockdown"": patterns restricted as in November 2020, and (4) ""festive break"": similar to 3 but with social visits over the holiday period as in 1. + +ResultsAcross ages, the estimated Reff decreases during the festive break in scenarios 1-3 and returns to pre-holiday levels in scenarios 2-3, while remaining relatively stable in scenario 4. Relative incidence is likely to decrease in children aged 0-15 but increase in other ages. Changes in age distribution were large during the holidays, and are likely to start before the holidays for individuals aged 16-24 years in scenarios 1-3. + +ConclusionsOur modelling findings suggest that increased contacts during the festive period may shift the age distribution of COVID-19 cases from children towards adults. Given that COVID-19-related hospitalisations and deaths rise by age, more intergenerational mixing risks an increased burden in the period following the holidays. + +HighlightsO_LIHome visits are associated with increased intergenerational mixing. +C_LIO_LIThe effective reproduction number is likely to remain stable or even reduce slightly due to a reduction in contacts at work and school. +C_LIO_LIRelative incidence is likely to become lower in children, but higher in the +C_LIO_LIolder (more vulnerable) age groups around the holiday period, which could lead to increased health care burden. +C_LI",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.12.21.20248475,2020-12-22,https://medrxiv.org/cgi/content/short/2020.12.21.20248475,Clinical outcomes and risk factors for COVID-19 among migrant populations in high-income countries: a systematic review,Sally E Hayward; Anna Deal; Cherie Cheng; Alison F Crawshaw; Miriam Orcutt; Tushna F Vandrevala; Marrie Norredam; Manuel Carballo; Yusuf Ciftci; Ana Requena-Mendez; Chris Greenaway; Jessica Carter; Felicity Knights; Anushka Mehrotra; Farah Seedat; Kayvan Bozorgmehr; Apostolos Veizis; Ines Campos-Matos; Fatima Wurie; Teymur Noori; Martin McKee; Bernadette Kumar; Sally Hargreaves,"Institute for Infection and Immunity, St George's University of London; Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine; Institute for Infection and Immunity, St George's University of London; Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine; Institute for Infection and Immunity, St George's University of London; Institute for Infection and Immunity, St George's University of London; Institute for Global Health, University College London; Faculty of Business and Social Sciences, Kingston University; Danish Research Centre for Migration, Ethnicity and Health, University of Copenhagen; International Centre for Migration, Health, and Development; Doctors of the World UK; Department of Medicine-Solna, Karolinska Institutet; and Barcelona Institute for Global Health (ISGlobal-University of Barcelona); Department of Medicine, McGill University; Institute for Infection and Immunity, St George's University of London; Institute for Infection and Immunity, St George's University of London; Institute for Infection and Immunity, St George's University of London; Public Health England; Public Health, Bielefeld University; Section for Health Equity Studies & Migration, Heidelberg University Hospital; Medecins Sans Frontieres Greece; Public Health England; and UCL Collaborative Centre for Inclusion Health; Public Health England; and UCL Research Department of Epidemiology and Public Health; European Centre for Disease Prevention and Control (ECDC); Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine; Norwegian Institute of Public Health; Institute for Infection and Immunity, St George's University of London","BackgroundMigrants, including refugees, asylum seekers, labour migrants, and undocumented migrants, now constitute a considerable proportion of most high-income countries populations, including their skilled and unskilled workforces. Migrants may be at increased risk of COVID-19 due to their health and social circumstances, yet the extent to which they are being affected and their predisposing risk factors are not clearly understood. We did a systematic review to assess clinical outcomes of COVID-19 in migrant populations (cases, hospitalisations, deaths), indirect health and social impacts, and to determine key risk factors. MethodsWe did a systematic review following PRISMA guidelines, registered with PROSPERO (CRD42020222135). We searched databases including PubMed, Global Health, Scopus, CINAHL, and pre-print databases (medRxiv) via the WHO Global Research on COVID-19 database to Nov 18, 2020 for peer-reviewed and grey literature pertaining to migrants (defined as foreign born) and COVID-19 in 82 high-income countries. We used our international networks to source national datasets and grey literature. Data were extracted on our primary outcomes (cases, hospitalisations, deaths) and we evaluated secondary outcomes on indirect health and social impacts, and risk factors, using narrative synthesis. @@ -4354,13 +4422,6 @@ C_LIO_LIImplications for COVID-19 vaccine efficacy trials and wider public healt C_LI",health informatics,fuzzy,100,100 medRxiv,10.1101/2020.11.19.20234120,2020-11-23,https://medrxiv.org/cgi/content/short/2020.11.19.20234120,Actionable druggable genome-wide Mendelian randomization identifies repurposingopportunities for COVID-19,Liam Gaziano; Claudia Giambartolomei; Alexandre C Pereira; Anna Gaulton; Daniel C Posner; Sonja A Swanson; Yuk Lam Ho; Sudha K Iyengar; Nicole M Kosik; Marijana Vujkovic; David R Gagnon; A Patricia Bento; Pedro Beltrao; Inigo Barrio Hernandez; Lars Ronnblom; Niklas Hagberg; Christian Lundtoft; Claudia Langenberg; Maik Pietzner; Dennis Valentine; Elias Allara; Praveen Surendran; Stephen Burgess; Jing Hua Zhao; James E Peters; Bram P Prins; John Danesh; Poornima Devineni; Yunling Shi; Kristine E Lynch; Scott L DuVall; Helene Garcon; Lauren Thomann; Jin J Zhou; Bryan R Gorman; Jennifer E Huffman; Christopher J O'Donnell; Philip S Tsao; Jean C Beckham; Saiju Pyarajan; Sumitra Muralidhar; Grant D Huang; Rachel Ramoni; Adriana M Hung; Kyong-Mi Chang; Yan V Sun; Jacob Joseph; Andrew R Leach; Todd L Edwards; Kelly Cho; J Michael Gaziano; Adam S Butterworth; Juan P Casas,"VA Boston Healthcare System, University of Cambridge; Instituto Italiano di Tecnologia, University of California Los Angeles; University of Sao Paulo, Harvard University; European Molecular Biology Laboratory, European Bioinformatics Institute; VA Boston Healthcare System; Erasmus Medical Center; VA Boston Healthcare System; Case Western Reserve University and Louis Stoke Cleveland VAMC; VA Boston Healthcare System; The Corporal Michael J. Crescenz VA Medical Center, the University of Pennsylvania Perelman School of Medicine; Boston University, VA Boston Healthcare System; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; Uppsala University; Uppsala University; Uppsala University; Charite University Medicine Berlin, Universityof Cambridge; Universityof Cambridge; University College London; University of Cambridge; Wellcome Genome Campus and University of Cambridge; University of Cambridge; University of Cambridge; Imperial College London; Wellcome Genome Campus and University of Cambridge; University of Cambridge; VA Boston Healthcare System; VA Boston Healthcare System; VA Salt Lake City Health Care System, University of Utah; VA Salt Lake City Health Care System, University of Utah; VA Boston Healthcare System; VA Boston Healthcare System; University of Arizona, Phoenix VA Health Care System; VA Boston Healthcare System; VA Boston Healthcare System; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Palo Alto Health Care System, Stanford University School of Medicine; Durham VA Medical Center, Duke University School of Medicine; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs, Vanderbilt University; The Corporal Michael J. Crescenz VA Medical Center, University of Pennsylvania; Atlanta VA Health Care System, Emory University Rollins School of Public Health; VA Boston Healthcare System and Brigham & Women's Hospital; European Molecular Biology Laboratory, European Bioinformatics Institute; Department of Veterans Affairs Tennessee Valley Healthcare System, Vanderbilt Genetics Institute Vanderbilt University Medical Center; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; University of Cambridge, Wellcome Genome Campus and University of Cambridge; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School","Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization (MR) analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable proteins that are targeted by approved drugs or in clinical phase of drug development. Using summary statistics from the Host Genetics Initiative and the Million Veteran Program, we studied 7,554 patients hospitalized with COVID-19 and >1 million controls. We found significant Mendelian randomization results for three proteins (ACE2: P=1.6x10-6, IFNAR2: P=9.8x10-11, and IL-10RB: P=1.9x10-14) using cis-eQTL genetic instruments that also had strong evidence for colocalization with COVID-19 hospitalization. To disentangle the shared eQTL signal for IL10RB and IFNAR2, we conducted phenome-wide association scans and pathway enrichment analysis, which suggested that IFNAR2 is more likely to play a role in COVID-19 hospitalization. Our findings prioritize trials of drugs targeting IFNAR2 and ACE2 for early management of COVID-19.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.11.19.20234849,2020-11-22,https://medrxiv.org/cgi/content/short/2020.11.19.20234849,Community factors and excess mortality in first wave of the COVID-19 pandemic.,Bethan Davies; Brandon L Parkes; James Bennett; Daniela Fecht; Marta Blangiardo; Majid Ezzati; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London,"Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2020.11.18.20233932,2020-11-20,https://medrxiv.org/cgi/content/short/2020.11.18.20233932,REACT-1 round 6 updated report: high prevalence of SARS-CoV-2 swab positivity with reduced rate of growth in England at the start of November 2020,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E. Walters; Haowei Wang; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear","BackgroundEngland is now in the midst of its second wave of the COVID-19 pandemic. Multiple regions of the country are at high infection prevalence and all areas experienced rapid recent growth of the epidemic during October 2020. - -MethodsREACT-1 is a series of community surveys of SARS-CoV-2 RT-PCR swab-positivity in England designed to monitor the spread of the epidemic and thus increase situational awareness. Round 6 of REACT-1 commenced swab-collection on 16th October. A prior interim report included data from 16th to 25th October for 85,971 participants. Here, we report data for the entire round on 160,175 participants with swab results obtained up to 2nd November 2020. - -ResultsOverall weighted prevalence of infection in the community in England was 1.3% or 130 people per 10,000 infected, up from 60 people per 10,000 in the round 5 report (18th September to 5th October 2020), doubling every 24 days on average since the prior round. The corresponding R number was estimated to be 1.2. Prevalence of infection was highest in North West (2.4%, up from 1.2%), followed by Yorkshire and The Humber (2.3% up from 0.84%), West Midlands (1.6% up from 0.60%), North East (1.5% up from 1.1%), East Midlands (1.3% up from 0.56%), London (0.97%, up from 0.54%), South West (0.80% up from 0.33%), South East (0.69% up from 0.29%), and East of England (0.69% up from 0.30%). Rapid growth in the South observed in the first half of round 6 was no longer apparent in the second half of round 6. We also observed a decline in prevalence in Yorkshire and The Humber during this period. Comparing the first and second halves of round 6, there was a suggestion of decline in weighted prevalence in participants aged 5 to 12 years and in those aged 25 to 44 years. While prevalence remained high, in the second half of round 6 there was suggestion of a slight fall then rise that was seen nationally and also separately in both the North and the South. - -ConclusionThe impact of the second national lockdown in England is not yet known. We provide here a detailed description of swab-positivity patterns at national, regional and local scales for the period immediately preceding lockdown, against which future trends in prevalence can be evaluated.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.11.18.20230649,2020-11-20,https://medrxiv.org/cgi/content/short/2020.11.18.20230649,A network modelling approach to assess non-pharmaceutical disease controls in a worker population: An application to SARS-CoV-2,Edward M Hill; Benjamin D Atkins; Matt J Keeling; Louise Dyson; Michael J Tildesley,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,"BackgroundAs part of a concerted pandemic response to protect public health, businesses can enact non-pharmaceutical controls to minimise exposure to pathogens in workplaces and premises open to the public. Amendments to working practices can lead to the amount, duration and/or proximity of interactions being changed, ultimately altering the dynamics of disease spread. These modifications could be specific to the type of business being operated. MethodsWe use a data-driven approach to parameterise an individual-based network model for transmission of SARS-CoV-2 amongst the working population, stratified into work sectors. The network is comprised of layered contacts to consider the risk of spread in multiple encounter settings (workplaces, households, social and other). We analyse several interventions targeted towards working practices: mandating a fraction of the population to work from home; using temporally asynchronous work patterns; and introducing measures to create COVID-secure workplaces. We also assess the general role of adherence to (or effectiveness of) isolation and test and trace measures and demonstrate the impact of all these interventions across a variety of relevant metrics. @@ -4529,6 +4590,21 @@ medRxiv,10.1101/2020.10.25.20219048,2020-10-27,https://medrxiv.org/cgi/content/s IMPACT STATEMENTCt values from SARS-CoV-2 RT-PCR tests vary widely and over calendar time. They have the potential to be used more broadly in public testing programmes as an ""early-warning"" system for shifts in infectious load and hence transmission.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.10.25.20219071,2020-10-27,https://medrxiv.org/cgi/content/short/2020.10.25.20219071,"Causes of death in mental health service users during the first wave of the COVID-19 pandemic: South London and Maudsley data from March to June 2020, compared with 2015-2019.",Robert Stewart; Amelia Jewell; Matthew Broadbent; Ioannis Bakolis; Jayati Das-Munshi,"King's College London; South London and Maudsley NHS Foundation Trust, London, UK; South London and Maudsley NHS Foundation Trust, London, UK; King's College London, London, UK; King's College London, London, UK","The COVID-19 pandemic is likely to have had a particularly high impact on the health and wellbeing of people with pre-existing mental disorders. This may include higher than expected mortality rates due to severe infections themselves, due to other comorbidities, or through increased suicide rates during lockdown. However, there has been very little published information to date on causes of death in mental health service users. Taking advantage of a large mental healthcare database linked to death registrations, we describe numbers of deaths within specific underlying-cause-of-death groups for the period from 1st March to 30th June in 2020 and compare these with the same four-month periods in 2015-2019. In past and current service users, there were 2561 deaths in March-June 2020, compared to an average of 1452 for the same months in 2015-19: an excess of 1109. The 708 deaths with COVID-19 as the underlying cause in 2020 accounted for 63.8% of that excess. The remaining excess was accounted for by unnatural/unexplained deaths and by deaths recorded as due to neurodegenerative conditions, with no excess in those attributed to cancer, circulatory disorders, digestive disorders, respiratory disorders, or other disease codes. Of 295 unexplained deaths in 2020 with missing data on cause, 162 (54.9%) were awaiting a formal death notice (i.e. the group that included deaths awaiting a coroners inquest) - an excess of 129 compared to the average of previous years, accounting for 11.6% of the excess in total deaths.",psychiatry and clinical psychology,fuzzy,100,100 +medRxiv,10.1101/2020.10.26.20219428,2020-10-27,https://medrxiv.org/cgi/content/short/2020.10.26.20219428,Community prevalence of SARS-CoV-2 in England during April to September 2020: Results from the ONS Coronavirus Infection Survey,Koen B Pouwels; Thomas House; Emma Pritchard; Julie V Robotham; Paul Birrell; Andrew Gelman; Karina-Doris Vihta; Nikola Bowers; Ian Boreham; Heledd Thomas; James Lewis; Iain Bell; John I Bell; John N Newton; Jeremy Farrar; Ian Diamond; Pete Benton; Ann Sarah Walker,University of Oxford; University of Manchester; University of Oxford; Public Health England; Public Health England; Columbia University; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics; Office for National Statistics; University of Oxford,"BackgroundDecisions regarding the continued need for control measures to contain the spread of SARS-CoV-2 rely on accurate and up-to-date information about the number of people and risk factors for testing positive. Existing surveillance systems are not based on population samples and are generally not longitudinal in design. + +MethodsFrom 26 April to 19 September2020, 514,794 samples from 123,497 individuals were collected from individuals aged 2 years and over from a representative sample of private households from England. Participants completed a questionnaire and nose and throat swab were taken. The percentage of individuals testing positive for SARS-CoV-2 RNA was estimated over time using dynamic multilevel regression and post-stratification, to account for potential residual non-representativeness. Potential changes in risk factors for testing positive over time were also evaluated using multilevel regression models. + +FindingsBetween 26 April and 19 September 2020, in total, results were available from 514,794 samples from 123,497 individuals, of which 489 were positive overall from 398 individuals. The percentage of people testing positive for SARS-CoV-2 changed substantially over time, with an initial decrease between end of April and June, followed by low levels during the summer, before marked increases end of August and September 2020. Having a patient-facing role and working outside your home were important risk factors for testing positive in the first period but not (yet) in the second period of increased positivity rates, and age (young adults) being an important driver of the second period of increased positivity rates. A substantial proportion of infections were in individuals not reporting symptoms (53%-70%, dependent on calendar time). + +InterpretationImportant risk factors for testing positive varied substantially between the initial and second periods of higher positivity rates, and a substantial proportion of infections were in individuals not reporting symptoms, indicating that continued monitoring for SARS-CoV-2 in the community will be important for managing the epidemic moving forwards. + +FundingThis study is funded by the Department of Health and Social Care. KBP, ASW, EP and JVR are supported by the National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford in partnership with Public Health England (PHE) (NIHR200915). AG is supported by U.S. National Institute of Health and Office of Naval Research. ASW is also supported by the NIHR Oxford Biomedical Research Centre and by core support from the Medical Research Council UK to the MRC Clinical Trials Unit [MC_UU_12023/22] and is an NIHR Senior Investigator. The views expressed are those of the authors and not necessarily those of the National Health Service, NIHR, Department of Health, or PHE. + +Research in contextO_ST_ABSEvidence before this studyC_ST_ABSUnprecedented control measures, such as national lockdowns, have been widely implemented to contain the spread of SARS-CoV-2. Decisions regarding the continued need for social distancing measures in the overall population, specific subgroups and geographic areas heavily rely on accurate and up-to-date information about the number of people and risk factors for testing positive. We searched PubMed and medRxiv and bioRxiv preprint servers up to 6 June 2020 for epidemiological studies using the terms ""SARS-CoV-2"" and ""prevalence"" or ""incidence"" without data or language restrictions. Most studies were small or had only information about current presence of the virus for a small subset of patients, or used data not representative of the community, such as hospital admissions, deaths or self-reported symptoms. Large population-based studies, such as the current study, are required to understand risk factors and the dynamics of the epidemic. + +Added value of this studyThis is the first longitudinal community survey of SARS-CoV-2 infection at national and regional levels in the UK. With more than 500,000 swabs from more than 120,000 individuals this study provides robust evidence that the percentage of individuals from the general community in England testing positive for SARS-CoV-2 clearly declined between end of April and June 2020,, followed by consistently low levels during the summer, before marked increases end of August and September 2020. Risk factors for testing positive varied substantially between the initial and second periods of higher positivity rates, with having a patient-facing role and working outside your home being important risk factors in the first period but not (yet) in the second period, and age (young adults) being an important driver of the second period of increased positivity rates. Positive tests commonly occurred without symptoms being reported. + +Implications of all the available evidenceThe observed decline in the percentage of individuals testing positive adds to the increasing body of empirical evidence and theoretical models that suggest that the lockdown imposed on 23 March 2020 in England was associated, at least temporarily, with a decrease in infections. Important risk factors for testing positive varied substantially between the initial and second periods of higher positivity rates, and a substantial proportion of infections were in individuals not reporting symptoms, indicating that continued monitoring for SARS-CoV-2 in the community will be important for managing the epidemic moving forwards.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.10.26.20219659,2020-10-27,https://medrxiv.org/cgi/content/short/2020.10.26.20219659,Detecting COVID-19 infection hotspots in England using large-scale self-reported data from a mobile application,Thomas Varsavsky; Mark S Graham; Liane S Canas; Sajaysurya Ganesh; Joan Capdevila Puyol; Carole H Sudre; Benjamin Murray; Marc Modat; M. Jorge Cardoso; Christina M Astley; David A Drew; Long H Nguyen; Tove Fall; Maria F Gomez; Paul W Franks; Andrew T Chan; Richard Davies; Jonathan Wolf; Claire J Steves; Tim D Spector; Sebastien Ourselin,King's College London; King's College London; King's College London; Zoe Global Limited; Zoe Global Limited; King's College London; King's College London; King's College London; King's College London; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Uppsala University; Lund University; Lund University; Massachusetts General Hospital; Zoe Global Limited; Zoe Global Limited; King's College London; King's College London; King's College London,"BackgroundAs many countries seek to slow the spread of COVID-19 without reimposing national restrictions, it has become important to track the disease at a local level to identify areas in need of targeted intervention. MethodsWe performed modelling on longitudinal, self-reported data from users of the COVID Symptom Study app in England between 24 March and 29 September, 2020. Combining a symptom-based predictive model for COVID-19 positivity and RT-PCR tests provided by the Department of Health we were able to estimate disease incidence, prevalence and effective reproduction number. Geographically granular estimates were used to highlight regions with rapidly increasing case numbers, or hotspots. @@ -4721,6 +4797,7 @@ ResultsOver the 9 days for which data are available, we find 363 positives from ConclusionRapid growth has led to high prevalence of SARS-CoV-2 virus in England among all regions and age groups, including those age groups at highest risk. Although there is evidence of a recent deceleration in the epidemic, current levels of prevalence will inevitably result in additional hospitalisations and mortality in coming weeks. A re-doubling of public health efforts is needed to return to a declining phase of the epidemic.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.09.28.20202929,2020-09-29,https://medrxiv.org/cgi/content/short/2020.09.28.20202929,T cell assays differentiate clinical and subclinical SARS-CoV-2 infections from cross-reactive antiviral responses,Ane Ogbe; Barbara Kronsteiner; Donal T Skelly; Matthew Pace; Anthony Brown; Emily Adland; Kareena Adair; Hossain Delowar Akhter; Mohammad Ali; Serat-E Ali; Adrienn Angyal; M. Azim Ansari; Carolina V Arancibia-Carcamo; Helen Brown; Senthil Chinnakannan; Christopher P Conlon; Catherine de Lara; Thushan de Silva; Christina Dold; Tao Dong Dong; Timothy Donnison; David W Eyre; Amy Flaxman; Helen A Fletcher; Joshua Gardner; James T Grist; Carl-Philipp Hackstein; Kanoot Jaruthamsophon; Katie Jeffrey; Teresa Lambe; Lian Lee; Wenqin Li; Nicholas Lim; Philippa C Matthews; Alexander J Mentzer; Shona C Moore; Dean J Naisbitt; Monday Ogese; Graham Ogg; Peter Openshaw; Munir Pirmohamed; Andrew J Pollard; Narayan Ramamurthy; Patpong Rongkard; Sarah Rowland-Jones; Oliver L Sampson; Gavin Screaton; Alessandro Sette; Lizzie Stafford; Craig Thompson; Paul J Thomson; Ryan Thwaites; Vinicius Vieira; Daniela Weiskopf; Panagiota Zacharopoulou; - Oxford Immunology Network Covid-19 Response T cell Consortium; - Oxford Protective T cell Immunology for COVID-19 (OPTIC) Clinical team; Lance Turtle; Paul Klenerman; Philip Goulder; John Frater; Eleanor Barnes; Susanna Dunachie,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Liverpool; University of Oxford; University of Oxford; University of Liverpool; University of Sheffield; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Sheffield; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Liverpool; University of Oxford; University of Oxford; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Liverpool; University of Liverpool; University of Liverpool; University of Oxford; Imperial College; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; La Jolla Institute for Immunology; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Liverpool; Imperial College; University of Oxford; La Jolla Institute for Immunology; University of Oxford; ; ; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"A major issue in identification of protective T cell responses against SARS-CoV-2 lies in distinguishing people infected with SARS-CoV-2 from those with cross-reactive immunity generated by exposure to other coronaviruses. We characterised SARS-CoV-2 T cell immune responses in 168 PCR-confirmed SARS-CoV-2 infected subjects and 118 seronegative subjects without known SARS-CoV-2 exposure using a range of T cell assays that differentially capture immune cell function. Strong ex vivo ELISpot and proliferation responses to multiple antigens (including M, NP and ORF3) were found in those who had been infected by SARS-CoV-2 but were rare in pre-pandemic and unexposed seronegative subjects. However, seronegative doctors with high occupational exposure and recent COVID-19 compatible illness showed patterns of T cell responses characteristic of infection, indicating that these readouts are highly sensitive. By contrast, over 90% of convalescent or unexposed people showed proliferation and cellular lactate responses to spike subunits S1/S2, indicating pre-existing cross-reactive T cell populations. The detection of T cell responses to SARS-CoV-2 is therefore critically dependent on the choice of assay and antigen. Memory responses to specific non-spike proteins provides a method to distinguish recent infection from pre-existing immunity in exposed populations.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2020.09.26.20202150,2020-09-28,https://medrxiv.org/cgi/content/short/2020.09.26.20202150,Comparison of mental health service activity before and shortly after UK social distancing responses to the COVID-19 pandemic: February-March 2020,Robert Stewart; Evangelia Martin; Ioannis Bakolis; Matthew Broadbent; Nicola Byrne; Sabine Landau,King's College London; South London and Maudsley NHS Foundation Trust; King's College London; King's College London; South London and Maudsley NHS Foundation Trust; King's College London,"This study sought to provide an early description of mental health service activity before and after national implementation of social distancing for COVID-19. A time series analysis was carried out of daily service-level activity on data from a large mental healthcare provider in southeast London, from 01.02.2020 to 31.03.2020, comparing activity before and after 16.03.2020: i) inpatient admissions, discharges and numbers, ii) contact numbers and daily caseloads (Liaison, Home Treatment Teams, Community Mental Health Teams); iii) numbers of deaths for past and present patients. Daily face-to-face contact numbers fell for liaison, home treatment and community services with incomplete compensatory rises in non-face-to-face contacts. Daily caseloads fell for all services, apart from working age and child/adolescent community teams. Inpatient numbers fell 13.6% after 16th March, and daily numbers of deaths increased by 61.8%.",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2020.09.25.20201731,2020-09-27,https://medrxiv.org/cgi/content/short/2020.09.25.20201731,Antihypertensive Medications and COVID-19 Diagnosis and Mortality: Population-based Case-Control Analysis in the United Kingdom,Emma Rezel-Potts; Abdel Douiri; Phil J Chowienczyk; Martin C Gulliford,King's College London; King's College London; King's College London; King's College London,"ObjectivesTo evaluate antihypertensive medications and COVID-19 diagnosis and mortality, accounting for healthcare seeking behaviour. DesignA population-based case control study with additional cohort analysis. @@ -4835,13 +4912,6 @@ At the recommended threshold, PMEWS and the WHO criteria showed good sensitivity ConclusionCURB-65, PMEWS and NEWS2 provide good but not excellent prediction for adverse outcome in suspected COVID-19, and predicted death without organ support better than receipt of organ support. PMEWS, the WHO criteria and NEWS2 (using a lower threshold than usually recommended) provide good sensitivity at the expense of specificity. RegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533",emergency medicine,fuzzy,100,100 -medRxiv,10.1101/2020.09.03.20187377,2020-09-05,https://medrxiv.org/cgi/content/short/2020.09.03.20187377,Impact of baseline cases of cough and fever on UK COVID-19 diagnostic testing rates: estimates from the Bug Watch community cohort study,Max T Eyre; Rachel Burns; Victoria Kirkby; Catherine Smith; Spiros Denaxas; Vincent Nguyen; Andrew Hayward; Laura Shallcross; Ellen Fragaszy; Robert W Aldridge,"Centre of Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster, LA1 4YW, UK; Liverpool School of Tropical Med; Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK; Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK; Institute of Health Informatics, University College London, London, NW1 2DA, UK; Institute of Health Informatics, University College London, London, NW1 2DA, UK; Health Data Research UK, London, NW1 2DA, UK; The Alan Turing Institute, London; Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK; Institute of Epidemiology and Health Care; Institute of Epidemiology and Health Care, University College London, London, WC1E 7HB, UK; Institute of Health Informatics, University College London, London, NW1 2DA, UK; Institute of Health Informatics, University College London, London, NW1 2DA, UK; Faculty of Epidemiology and Population Health, London School of Hygiene and Tro; Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK","BackgroundDiagnostic testing forms a major part of the UKs response to the current COVID-19 pandemic with tests offered to people with a continuous cough, high temperature or anosmia. Testing capacity must be sufficient during the winter respiratory season when levels of cough and fever are high due to non-COVID-19 causes. This study aims to make predictions about the contribution of baseline cough or fever to future testing demand in the UK. - -MethodsIn this analysis of the Bug Watch prospective community cohort study, we estimated the incidence of cough or fever in England in 2018-2019. We then estimated the COVID-19 diagnostic testing rates required in the UK for baseline cough or fever cases for the period July 2020-June 2021. This was explored for different rates of the population requesting tests and four second wave scenarios and then compared to current national capacity. - -ResultsThe baseline incidence of cough or fever in the UK is expected to rise rapidly from 154,554 (95%CI 103,083 - 231,725) cases per day in August 2020 to 250,708 (95%CI 181,095 - 347,080) in September, peaking at 444,660 (95%CI 353,084 - 559,988) in December. If 80% of baseline cough or fever cases request tests, average daily UK testing demand would exceed current capacity for five consecutive months (October 2020 to February 2021), with a peak demand of 147,240 (95%CI 73,978 - 239,502) tests per day above capacity in December 2020. - -ConclusionsOur results show that current national COVID-19 testing capacity is likely to be exceeded by demand due to baseline cough and fever alone. This study highlights that the UKs response to the COVID-19 pandemic must ensure that a high proportion of people with symptoms request tests, and that testing capacity is immediately scaled up to meet this high predicted demand.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.09.01.20185793,2020-09-03,https://medrxiv.org/cgi/content/short/2020.09.01.20185793,Prognostic accuracy of emergency department triage tools for children with suspected COVID-19: The PRIEST observational cohort study,Katie Biggs; Ben Thomas; Steve Goodacre; Ellen Lee; Laura Sutton; Matthew Bursnall; Amanda Loban; Simon Waterhouse; Richard Simmonds; Carl Marincowitz; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter,University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust,"ObjectivesEmergency department clinicians can use triage tools to predict adverse outcome and support management decisions for children presenting with suspected COVID-19. We aimed to estimate the accuracy of triage tools for predicting severe illness in children presenting to the emergency department (ED) with suspected COVID-19 infection. MethodsWe undertook a mixed prospective and retrospective observational cohort study in 44 EDs across the United Kingdom (UK). We collected data from children attending with suspected COVID-19 between 26 March 2020 and 28 May 2020, and used presenting data to determine the results of assessment using the WHO algorithm, swine flu hospital pathway for children (SFHPC), Paediatric Observation Priority Score (POPS) and Childrens Observation and Severity Tool (COAST). We recorded 30-day outcome data (death or receipt of respiratory, cardiovascular or renal support) to determine prognostic accuracy for adverse outcome. @@ -4851,6 +4921,7 @@ ResultsWe collected data from 1530 children, including 26 (1.7%) with an adverse ConclusionExisting triage tools have good but not excellent prediction for adverse outcome in children with suspected COVID-19. POPS and COAST could achieve an appropriate balance of sensitivity and specificity for supporting decisions to discharge home by considering any score above zero to be positive. RegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533",emergency medicine,fuzzy,100,100 +medRxiv,10.1101/2020.09.02.20186502,2020-09-03,https://medrxiv.org/cgi/content/short/2020.09.02.20186502,Real-time monitoring of COVID-19 dynamics using automated trend fitting and anomaly detection,Thibaut Jombart; Stephane Ghozzi; Dirk Schumacher; Quentin Leclerc; Mark Jit; Stefan Flasche; Felix Greaves; Tom Ward; Rosalind M Eggo; Emily Nightingale; Sophie Meakin; Oliver J Brady; - Centre for Mathematical Modelling of Infectious Diseases COVID-19 Working Group; Graham Medley; Michael Hohle; John Edmunds,"London School of Hygiene and Tropical Medicine (LSHTM); Department of Epidemiology, Helmholtz Centre for Infection Research, Brunswick, Lower Saxony, Germany; R Epidemics Consortium; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; LSHTM; Joint Biosecurity Centre; Joint Biosecurity Centre; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; LSHTM; London School of Hygiene and Tropical Medicine; ; LSHTM; Department of Mathematics, Stockholm University, Sweden; LSHTM","As several countries gradually release social distancing measures, rapid detection of new localised COVID-19 hotspots and subsequent intervention will be key to avoiding large-scale resurgence of transmission. We introduce ASMODEE (Automatic Selection of Models and Outlier Detection for Epidemics), a new tool for detecting sudden changes in COVID-19 incidence. Our approach relies on automatically selecting the best (fitting or predicting) model from a range of user-defined time series models, excluding the most recent data points, to characterise the main trend in an incidence. We then derive prediction intervals and classify data points outside this interval as outliers, which provides an objective criterion for identifying departures from previous trends. We also provide a method for selecting the optimal breakpoints, used to define how many recent data points are to be excluded from the trend fitting procedure. The analysis of simulated COVID-19 outbreaks suggest ASMODEE compares favourably with a state-of-art outbreak-detection algorithm while being simpler and more flexible. We illustrate our method using publicly available data of NHS Pathways reporting potential COVID-19 cases in England at a fine spatial scale, for which we provide a template automated analysis pipeline. ASMODEE is implemented in the free R package trendbreaker.",health informatics,fuzzy,100,100 medRxiv,10.1101/2020.09.02.20186817,2020-09-03,https://medrxiv.org/cgi/content/short/2020.09.02.20186817,Revealing the extent of the COVID-19 pandemic in Kenya based on serological and PCR-test data,John Ojal; Samuel PC Brand; Vincent Were; Emelda A Okiro; Ivy Kadzo Kombe; Caroline Mburu; Rabia Aziza; Morris Ogero; Ambrose Agweyu; George M Warimwe; Sophie Uyoga; Ifedayo M. O Adetifa; John Anthony Scott; Edward Otieno; Lynette I Ochola-Oyier; Charles Nyaigoti Agoti; Kadondi Kasera; Patrick Amoth; Mercy Mwangangi; Rashid Aman; Wangari Ng'ang'a; Benjamin Tsofa; Philip Bejon; Edwine Barasa; Matt J Keeling; D James Nokes,"Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya and London School of Hygiene and Tropical Medicine; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK.; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; KEMRI-Wellcome Trust Research Programme; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK.; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; KEMRI-Wellcome Trust Research Programme; KEMRI Wellcome Trust Research Programme; KEMRI-Wellcome Trust Research Programme; London School of Hygiene & Tropical Medicine; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Ministry of Health, Government of Kenya, Kenya; Ministry of Health, Government of Kenya, Kenya; Ministry of Health, Government of Kenya, Kenya; Ministry of Health, Government of Kenya, Kenya; Presidential Policy & Strategy Unit, The Presidency, Government of Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; KEMRI-Wellcome Trust Research Programme; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK; KEMRI-Wellcome Trust Research Programme, Kenya and School of Life Sciences, University of Warwick, UK","Policy makers in Africa need robust estimates of the current and future spread of SARS-CoV-2. Data suitable for this purpose are scant. We used national surveillance PCR test, serological survey and mobility data to develop and fit a county-specific transmission model for Kenya. We estimate that the SARS-CoV-2 pandemic peaked before the end of July 2020 in the major urban counties, with 34 - 41% of residents infected, and will peak elsewhere in the country within 2-3 months. Despite this penetration, reported severe cases and deaths are low. Our analysis suggests the COVID-19 disease burden in Kenya may be far less than initially feared. A similar scenario across sub-Saharan Africa would have implications for balancing the consequences of restrictions with those of COVID-19.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.09.01.20183822,2020-09-02,https://medrxiv.org/cgi/content/short/2020.09.01.20183822,Trust and Transparency in times of Crisis: Results from an Online Survey During the First Wave (April 2020) of the COVID-19 Epidemic in the UK,Luisa Enria; Naomi Waterlow; Nina Trivedy Rogers; Hannah Brindle; Sham Lal; Rosalind M Eggo; Shelley Lees; Chrissy h Roberts,London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; UCL; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine (LSHTM),"BackgroundThe success of a governments COVID-19 control strategy relies on public trust and broad acceptance of response measures. We investigated public perceptions of the UK governments COVID-19 response, focusing on the relationship between trust and transparency, during the first wave (April 2020) of the COVID-19 pandemic in the United Kingdom. @@ -5096,6 +5167,7 @@ MethodsWe accessed national English data on all adult COVID-19 specific critical Results30-day mortality peaked for people admitted to critical care in early April (peak 29.1% for HDU, 41.5% for ICU). There was subsequently a sustained decrease in mortality risk until the end of the study period. As a linear trend from the first week of April, adjusted mortality risk decreased by 11.2% (adjusted HR 0.89 [95% CI 0.87 - 0.91]) per week in HDU, and 9.0% (adjusted HR 0.91 [95% CI 0.88 - 0.94]) in ICU. ConclusionsThere has been a substantial mortality improvement in people admitted to critical care with COVID-19 in England, with markedly lower mortality in people admitted in mid-April and May compared to earlier in the pandemic. This trend remains after adjustment for patient demographics and comorbidities suggesting this improvement is not due to changing patient characteristics. Possible causes include the introduction of effective treatments as part of clinical trials and a falling critical care burden.",health systems and quality improvement,fuzzy,100,100 +medRxiv,10.1101/2020.07.29.20164269,2020-07-30,https://medrxiv.org/cgi/content/short/2020.07.29.20164269,The potential health and economic impact of dexamethasone treatment for patients with COVID-19,RICARDO AGUAS; Adam Mahdi; RIMA SHRETTA; Peter Horby; Martin Landray; Lisa J White,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"Dexamethasone has been shown to reduce mortality in hospitalised COVID-19 patients needing oxygen and ventilation by 18% and 36%, respectively. Here, we estimate the potential number of lives saved and life years gained if this treatment would be rolled out in the UK and globally, as well as its cost-effectiveness of implementing this intervention. We estimate that, for the UK, approximately 12,000 [4,250 - 27,000] lives could be saved by January 2021. Assuming that dexamethasone has a similar effect size in settings where access to oxygen therapies is limited, this would translate into approximately 650,000 [240,000 - 1,400,000] lives saved globally. If dexamethasone acts differently in these settings, the impact could be less than half of this value. To estimate the full potential of dexamethasone in the global fight against COVID-19, it is essential to perform clinical research in settings with limited access to oxygen and/or ventilators, e.g. in low and middle-income countries.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.07.29.20162701,2020-07-30,https://medrxiv.org/cgi/content/short/2020.07.29.20162701,Estimates of the rate of infection and asymptomatic COVID-19 disease in a population sample from SE England,Philippa M Wells; Katie M Doores; Simon Couvreur; Rocio Martin Martinez; Jeffrey Seow; Carl Graham; Sam Acors; Neophytos Kouphou; Stuart Neil; Richard Tedder; Pedro Matos; Kate Poulton; Maria Jose Lista; Ruth Dickenson; Helin Sertkaya; Thomas Maguire; Edward Scourfield; Ruth Bowyer; Deborah Hart; Aoife O'Byrne; Kathryn Steele; Oliver Hemmings; Carolina Rosadas; Myra McClure; Joan Capedevila-Pujol; Jonathan wolf; Sebastien Ourseilin; Matthew Brown; Michael Malim; Timothy Spector; Claire Steves,King's College London; King's College London; KCL; King's College London; KCL; KCL; KCL; KCL; KCL; Imperial; KCL; KCL; KCL; KCL; KCL; KCL; KCL; KCL; KCL; KCL; KCL; KCL; Imperial College London; Imperial College London; KCL; Zoe Global; Zoe Global; KCL; KCL; King's College London; King's College London,"BackgroundUnderstanding of the true asymptomatic rate of infection of SARS-CoV-2 is currently limited, as is understanding of the population-based seroprevalence after the first wave of COVID-19 within the UK. The majority of data thus far come from hospitalised patients, with little focus on general population cases, or their symptoms. MethodsWe undertook enzyme linked immunosorbent assay characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged 19-86 (median age 48; 85% female). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million. @@ -5110,6 +5182,25 @@ medRxiv,10.1101/2020.07.26.20161570,2020-07-28,https://medrxiv.org/cgi/content/s Taken over the entire first phase of the pandemic, there was no detectable rise in all-cause mortality in New Zealand, Bulgaria, Hungary, Norway, Denmark and Finland and for women in Austria and Switzerland (posterior probability of an increase in deaths <90%). Women in Portugal and men in Austria experienced relatively small increases in all-cause mortality, with posterior probabilities of 90-99%. For men in Switzerland and Portugal, and both sexes in the Netherlands, France, Sweden, Belgium, Italy, Scotland, Spain and England and Wales, all-cause mortality increased as a result of the pandemic with a posterior probability >99%. After accounting for population size, England and Wales and Spain experienced the highest death toll, nearly 100 deaths per 100,000 people; they also had the largest relative (percent) increase in deaths (37% (95% credible interval 30-44) in England and Wales; 38% (31-44) in Spain). New Zealand, Bulgaria, Hungary, Norway, Denmark and Finland experienced changes in deaths that ranged from possible slight declines to increases of no more than 5%. The large impact in England and Wales stems partly from having experienced (together with Spain) the highest weekly increases in deaths, more than doubling in some weeks, and having had (together with Sweden) the longest duration when deaths exceeded levels that would be expected in the absence of the pandemic. The heterogeneous magnitude and character of the excess deaths due to the Covid-19 pandemic reflect differences in how well countries have managed the pandemic (e.g., timing, extent and adherence to lockdowns and other social distancing measures; effectiveness of test, trace and isolate mechanisms), and the resilience and preparedness of the health and social care system (e.g., effective facility and community care pathways; minimising spread of infection within hospitals and care homes, and between them and the community).",public and global health,fuzzy,100,100 +medRxiv,10.1101/2020.07.23.20160747,2020-07-27,https://medrxiv.org/cgi/content/short/2020.07.23.20160747,Associations of severe COVID-19 with polypharmacy in the REACT-SCOT case-control study,Paul M McKeigue; Sharon Kennedy; Amanda Weir; Jen Bishop; Stuart J McGurnaghan; David McAllister; Chris Robertson; Rachael Wood; Nazir Lone; Janet Murray; Thomas M Caparrotta; Alison Smith-Palmer; David Goldberg; Jim McMenamin; Colin Ramsay; Bruce Guthrie; Sharon Hutchinson; Helen M Colhoun,University of Edinburgh; Public Health Scotland; Public Health Scotland; Public Health Scotland; University of Edinburgh; University of Glasgow; University of Strathclyde; NHS Information Services Division (Public Health Scotland); University of Edinburgh; Public Health Scotland; University of Edinburgh; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; University of Edinburgh; Glasgow Caledonian University; University of Edinburgh,"ObjectivesTo investigate the relation of severe COVID-19 to prior drug prescribing. + +DesignMatched case-control study (REACT-SCOT) based on record linkage to hospital discharges since June 2015 and dispensed prescriptions issued in primary care during the last 240 days. + +SettingScottish population. + +Main outcome measureSevere COVID-19, defined by entry to critical care or fatal outcome. + +ParticipantsAll 4272 cases of severe COVID-19 in Scotland since the start of the epidemic, with 36948 controls matched for age, sex and primary care practice. + +ResultsSevere COVID-19 was strongly associated with the number of non-cardiovascular drug classes dispensed. This association was strongest in those not resident in care homes, in whom the rate ratio (95% CI) associated with dispensing of 12 or more drug classes versus none was 10.8 (8.7, 13.2), and was not accounted for by treatment of conditions designated as conferring increased risk. Of 17 drug classes postulated at the start of the epidemic to be ""medications compromising COVID"", all were associated with increased risk of severe COVID-19. The largest effect was for antipsychotic agents: rate ratio 4.14 (3.39, 5.07). Other drug classes with large effects included proton pump inhibitors (rate rato 2.19 (1.70, 2.80) for >= 2 defined daily doses/day), opioids (3.62 (2.65, 4.94) for >= 50 mg morphine equivalent/day) and gabapentinoids. These associations persisted after adjusting for covariates, and were stronger with recent than with non-recent exposure. + +ConclusionsSevere COVID-19 is associated with polypharmacy and with drugs that cause sedation, respiratory depression or dyskinesia, have anticholinergic effects or affect the gastrointestinal system. These associations are not easily explained by co-morbidity. Although the evidence for causality is not conclusive, these results support existing guidance on reducing overprescribing of these drug classes and limiting inappropriate polypharmacy as a potential means of reducing COVID-19 risk. + +RegistrationENCEPP number EUPAS35558 + +What is already known on this topicTwo previous studies have examined the relationship of severe COVID-19 to drugs for the cardiovascular system. This is the first systematic study of the relationship of severe COVID-19 to prior drug prescribing. + +What this study addsSevere COVID-19 is associated with polypharmacy and with drugs that cause sedation, respiratory depression or dyskinesia, have anticholinergic effects or affect the gastrointestinal system. These associations are not easily explained by co-morbidity. These results support earlier warnings that these drug classes that these drugs might increase susceptibility to COVID-19, and reinforce existing guidance on reducing overprescribing of these drug classes.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.07.25.20156471,2020-07-27,https://medrxiv.org/cgi/content/short/2020.07.25.20156471,Using social contact data to predict and compare the impact of social distancing policies with implications for school re-opening,Ellen Brooks-Pollock; Jonathan M Read; Angela R McLean; Matt J Keeling; Leon Danon,University of Bristol; Lancaster University; University of Oxford; University of Warwick; University of Exeter,"BackgroundIn the absence of a vaccine, SARS-CoV-2 transmission has been controlled by preventing person-to-person interactions via social distancing measures. In order to re-open parts of society, policy-makers need to consider how combinations of measures will affect transmission and understand the trade-offs between them. MethodsWe use age-specific social contact data, together with epidemiological data, to quantify the components of the COVID-19 reproduction number. We estimate the impact of social distancing policies on the reproduction number by turning contacts on and off based on context and age. We focus on the impact of re-opening schools against a background of wider social distancing measures. @@ -5117,6 +5208,11 @@ MethodsWe use age-specific social contact data, together with epidemiological da ResultsWe demonstrate that pre-collected social contact data can be used to provide a time-varying estimate of the reproduction number (R). We find that following lockdown (when R=0.7 (95% CI 0.6, 0.8)), opening primary schools as a modest impact on transmission (R = 0.89 (95%CI: 0.82 - 0.97)) as long as other social interactions are not increased. Opening secondary and primary schools is predicted to have a larger impact (R = 1.22, 95%CI: 1.02 - 1.53)). Contact tracing and COVID security can be used to mitigate the impact of increased social mixing to some extent, however social distancing measures are still required to control transmission. ConclusionsOur approach has been widely used by policy-makers to project the impact of social distancing measures and assess the trade-offs between them. Effective social distancing, contact tracing and COVID-security are required if all age groups are to return to school while controlling transmission.",infectious diseases,fuzzy,100,100 +bioRxiv,10.1101/2020.07.26.221572,2020-07-26,https://biorxiv.org/cgi/content/short/2020.07.26.221572,COVID-19 and Rheumatoid Arthritis share myeloid pathogenic and resolving pathways,Lucy MacDonald; Thomas Dan Otto; Aziza Elmesmari; Barbara Tolusso; Domenico Somma; Charles McSharry; Elisa Gremese; Iain B McInnes; Stefano Alivernini; Mariola Kurowska-Stolarska,"Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), University of Glasgow, Glasgow, United Kingdom; Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), University of Glasgow, Glasgow, United Kingdom; Research into Inflammatory Arthritis Centre Versus Arthritis (RACE) ,University of Glasgow, Glasgow, United Kingdom; Division of Rheumatology, Universita Cattolica del Sacro Cuore, Rome, Italy; Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, United Kingdom.; Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, United Kingdom.; Division of Rheumatology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.; Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), University of Glasgow, Glasgow, United Kingdom.; Fondazione Policlinico Universitario A. Gemelli IRCCS - Universita Cattolica del Sacro Cuore; Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), University of Glasgow, Glasgow, United Kingdom.","BackgroundWe recently delineated the functional biology of pathogenic and inflammation resolving synovial tissue macrophage clusters in rheumatoid arthritis (RA). Whilst RA is not a viral respiratory syndrome, it represents a pro-inflammatory cytokine-driven chronic articular condition often accompanied by cardiovascular and lung pathologies. We hypothesised that functionally equivalent macrophage clusters in the lung might govern inflammation and resolution of COVID-19 pneumonitis. + +MethodsTo provide insight into the targetable functions of COVID-19 bronchoalveolar lavage (BALF) macrophage clusters, a comparative analysis of BALF macrophage single cell transcriptomics (scRNA-seq) with synovial tissue (ST) macrophage scRNA-seq and functional biology was performed. The function of shared BALF and ST MerTK inflammation-resolving pathway was confirmed with inhibitor in primary macrophage-synovial fibroblast co-cultures. Results. Distinct BALF FCNpos and FCNposSPP1pos macrophage clusters emerging in severe COVID-19 patients were closely related to ST CD48highS100A12pos and CD48posSPP1pos clusters driving synovitis in active RA. They shared transcriptomic profile and pathogenic mechanisms. Healthy lung resident alveolar FABP4pos macrophages shared a regulatory transcriptomic profile, including TAM (Tyro, Axl, MerTK) receptors pathway with synovial tissue TREM2pos macrophages that govern RA remission. This pathway was substantially altered in BALF macrophages of severe COVID-19. In vitro dexamethasone inhibited tissue inflammation via macrophages MerTK function. + +ConclusionPathogenesis and resolution of COVID-19 pneumonitis and RA synovitis might be driven by similar macrophage clusters and pathways. The MerTK-dependent anti-inflammatory mechanisms of dexamethasone, and the homeostatic function of TAM pathways that maintain RA in remission advocate the therapeutic MerTK agonism to ameliorate the cytokine storm and pneumonitis of severe COVID-19.",immunology,fuzzy,100,91 medRxiv,10.1101/2020.07.24.20149815,2020-07-26,https://medrxiv.org/cgi/content/short/2020.07.24.20149815,Systematic evaluation and external validation of 22 prognostic models among hospitalised adults with COVID-19: An observational cohort study,Rishi K Gupta; Michael Marks; Thomas H. A. Samuels; Akish Luintel; Tommy Rampling; Humayra Chowdhury; Matteo Quartagno; Arjun Nair; Marc Lipman; Ibrahim Abubakar; Maarten van Smeden; Wai Keong Wong; Bryan Williams; Mahdad Noursadeghi,"Institute for Global Health, University College London, London, UK; London School of Hygiene and Tropical Medicine; University College London Hospitals NHS Trust; University College London Hospitals NHS Trust; University College London Hospitals NHS Trust; University College London Hospitals NHS Trust; MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, University College London, London, UK; University College London Hospitals NHS Trust; UCL Respiratory, Division of Medicine, University College London, London, UK; Institute for Global Health, University College London, London, UK; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands; University College London Hospitals NHS Trust; NIHR University College London Hospitals Biomedical Research Centre; Division of Infection & Immunity, University College London, UK","BackgroundThe number of proposed prognostic models for COVID-19, which aim to predict disease outcomes, is growing rapidly. It is not known whether any are suitable for widespread clinical implementation. We addressed this question by independent and systematic evaluation of their performance among hospitalised COVID-19 cases. MethodsWe conducted an observational cohort study to assess candidate prognostic models, identified through a living systematic review. We included consecutive adults admitted to a secondary care hospital with PCR-confirmed or clinically diagnosed community-acquired COVID-19 (1st February to 30th April 2020). We reconstructed candidate models as per their original descriptions and evaluated performance for their original intended outcomes (clinical deterioration or mortality) and time horizons. We assessed discrimination using the area under the receiver operating characteristic curve (AUROC), and calibration using calibration plots, slopes and calibration-in-the-large. We calculated net benefit compared to the default strategies of treating all and no patients, and against the most discriminating predictor in univariable analyses, based on a limited subset of a priori candidates. @@ -5410,13 +5506,6 @@ FindingsIn ALSPAC-G1 there was evidence that anxiety and lower wellbeing, but no InterpretationThese results suggest increases in anxiety and lower wellbeing that may be related to the COVID-19 pandemic and/or its management, particularly in young people. This research highlights that specific groups may be disproportionally at risk of elevated levels of depression and anxiety during COVID-19 and supports recent calls for increasing funds for mental health services. FundingThe UK Medical Research Council (MRC), the Wellcome Trust and University of Bristol.",psychiatry and clinical psychology,fuzzy,100,100 -medRxiv,10.1101/2020.06.16.20133157,2020-06-18,https://medrxiv.org/cgi/content/short/2020.06.16.20133157,Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease.,Petra Mlcochova; Dami Collier; Allyson V Ritchie; Sonny M Assennato; Myra Hosmillo; Neha Goel; Bo Meng; Krishna Chatterji; Vivien Mendoza; Nigel Temperton; Leo Kiss; Katarzyna A Ciazyns; Xiaoli Xiong; John AG Briggs; James Nathan; Federica Mescia; Hongyi Zhang; Petros Barmpounakis; Nikos Demeris; Richard Skells; Paul Lyons; John Bradley; Stephen Baker; Jean Pierre Allain; Kenneth GC Smith; Ian Goodfellow; Ravindra K Gupta,"University of Cambridge; UCL; Diagnostics for the Real World Europe Ltd; DRW; University of Cambridge; University of Cambridge; University of Cambridge; NIHR Cambridge Clinical Research Facility; CUH NHS Trust; University of Kent; Medical Research Council Laboratory of Molecular Biology, Cambridge; Medical Research Council Laboratory of Molecular Biology, Cambridge; Medical Research Council Laboratory of Molecular Biology; Medical Research Council Laboratory of Molecular Biology; University of Cambridge; University of Cambridge; CUH NHS Trust; Athens University of Economics and Business; Cambridge Clinical Trials Unit-Cancer Theme; Cambridge Clinical Trials Unit-Cancer Theme; University of Cambridge; University of Cambridge; Cambridge University; Diagnostics for the Real World EU Ltd; University of Cambridge; ig299@cam.ac.uk; University of Cambridge","BackgroundRapid COVID-19 diagnosis in hospital is essential for patient management and identification of infectious patients to limit the potential for nosocomial transmission. The diagnosis of infection is complicated by 30-50% of COVID-19 hospital admissions with nose/throat swabs testing negative for SARS-CoV-2 nucleic acid, frequently after the first week of illness when SARS-CoV-2 antibody responses become detectable. We assessed the diagnostic accuracy of combined rapid antibody point of care (POC) and nucleic acid assays for suspected COVID-19 disease in the emergency department. - -MethodsWe developed (i) an in vitro neutralization assay using a lentivirus expressing a genome encoding luciferase and pseudotyped with spike (S) protein and (ii) an ELISA test to detect IgG antibodies to nucleocapsid (N) and S proteins from SARS-CoV-2. We tested two lateral flow rapid fingerprick tests with bands for IgG and IgM. We then prospectively recruited participants with suspected moderate to severe COVID-19 and tested for SARS-CoV-2 nucleic acid in a combined nasal/throat swab using the standard laboratory RT-PCR and a validated rapid POC nucleic acid amplification (NAAT) test. Additionally, serum collected at admission was retrospectively tested by in vitro neutralisation, ELISA and the candidate POC antibody tests. We evaluated the performance of the individual and combined rapid POC diagnostic tests against a composite reference standard of neutralisation and standard laboratory based RT-PCR. - -Results45 participants had specimens tested for nucleic acid in nose/throat swabs as well as stored sera for antibodies. Using the composite reference standard, prevalence of COVID-19 disease was 53.3% (24/45). Median age was 73.5 (IQR 54.0-86.5) years in those with COVID-19 disease by our reference standard and 63.0 (IQR 41.0-72.0) years in those without disease. The overall detection rate by rapid NAAT was 79.2% (95CI 57.8-92.9%), decreasing from 100% (95% CI 65.3-98.6%) in days 1-4 to 50.0% (95% CI 11.8-88.2) for days 9-28 post symptom onset. Correct identification of COVID-19 with combined rapid POC diagnostic tests was 100% (95CI 85.8-100%) with a false positive rate of 5.3-14.3%, driven by POC LFA antibody tests. - -ConclusionsCombined POC tests have the potential to transform our management of COVID-19, including inflammatory manifestations later in disease where nucleic acid test results are negative. A rapid combined approach will also aid recruitment into clinical trials and in prescribing therapeutics, particularly where potentially harmful immune modulators (including steroids) are used.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.06.15.20131722,2020-06-17,https://medrxiv.org/cgi/content/short/2020.06.15.20131722,"Delirium is a presenting symptom of COVID-19 in frail, older adults: a cohort study of 322 hospitalised and 535 community-based older adults",Maria Beatrice Zazzara; Rose S. Penfold; Amy L. Roberts; Karla Lee; Hannah Dooley; Carole H. Sudre; Carly Welch; Ruth C. E. Bowyer; Alessia Visconti; Massimo Mangino; Maxim B. Freydin; Julia S. El-Sayed Moustafa; Kerrin Small; Benjamin Murray; Marc Modat; Jonathan Wolf; Sebastien Ourselin; Finbarr C. Martin; Claire J. Steves; Mary Ni Lochlainn,"Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Gerontology, Neuroscience and O; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; Institute of Inflammation and Ageing, University of Birmingham, B15 2TT; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; NIHR Biomedical Research Centre at Guy's and ; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; Zoe Global Limited,164 Westminster Bridge Road, London SE1 7RW, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; Population Health Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH","BackgroundFrailty, increased vulnerability to physiological stressors, is associated with adverse outcomes. COVID-19 exhibits a more severe disease course in older, co-morbid adults. Awareness of atypical presentations is critical to facilitate early identification. ObjectiveTo assess how frailty affects presenting COVID-19 symptoms in older adults. @@ -5677,15 +5766,6 @@ C_LI O_LSTHow might this impact on policy or clinical practice in the foreseeable future?C_LSTO_LIOur findings reinforce the need for adequate health and safety arrangements and provision of PPE, particularly in the health and social care sectors, and highlight the need for national and organizational policies and practices that protect and support workers with elevated risk of SARS-CoV-2 infection. C_LI",occupational and environmental health,fuzzy,100,100 -medRxiv,10.1101/2020.05.20.20108183,2020-05-23,https://medrxiv.org/cgi/content/short/2020.05.20.20108183,A Rapid Review of the Asymptomatic Proportion of PCR-Confirmed SARS-CoV-2 Infections in Community Settings,Sarah Beale; Andrew Hayward; Laura Shallcross; Robert W Aldridge; Ellen Fragaszy,University College London; University College London; University College London; University College London; University College London,"BackgroundUp to 80% of active SARS-CoV-2 infections are proposed to be asymptomatic based on cross-sectional studies. However, accurate estimates of the asymptomatic proportion require systematic detection and follow-up to differentiate between truly asymptomatic and pre-symptomatic cases. We conducted a rapid review and meta-analysis of current evidence regarding the asymptomatic proportion of PCR-confirmed SARS-CoV-2 infections based on methodologically-appropriate studies in community settings. - -MethodsWe searched Medline and EMBASE for peer-reviewed articles, and BioRxiv and MedRxiv for pre-prints published prior to 05/05/2020. We included studies based in community settings that involved systematic PCR testing on participants and follow-up symptom monitoring regardless of symptom status. We extracted data on study characteristics, frequencies of PCR-confirmed infections by symptom status, and (if available) cycle threshold values and/or duration of viral shedding by symptom status. We computed estimates of the asymptomatic proportion and 95% confidence intervals for each study and overall using random effect meta-analysis. - -FindingsWe screened 270 studies and included 6. The pooled estimate for the asymptomatic proportion of SARS-CoV-2 infections was 11% (95% CI 4%-18%). Estimates of baseline viral load appeared to be similar for asymptomatic and symptomatic cases based on available data in three studies, though detailed reporting of cycle threshold values and natural history of viral shedding by symptom status was limited. - -InterpretationThe asymptomatic proportion of SARS-CoV-2 infections is relatively low when estimated from methodologically-appropriate studies. Further investigation into the degree and duration of infectiousness for asymptomatic infections is warranted. - -FundingMedical Research Council",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.05.18.20086157,2020-05-22,https://medrxiv.org/cgi/content/short/2020.05.18.20086157,COVID-19 in Great Britain: epidemiological and clinical characteristics of the first few hundred (FF100) cases: a descriptive case series and case control analysis,Nicola L Boddington; Andre Charlett; Suzanne Elgohari; Jemma L Walker; Helen Mcdonald; Chloe Byers; Laura Coughlan; Tatiana Garcia Vilaplana; Rosie Whillock; Mary Sinnathamby; Nikolaos Panagiotopoulos; Louise Letley; Pauline MacDonald; Roberto Vivancos; Obaghe Edeghere; Joseph Shingleton; Emma Bennett; Daniel J Grint; Helen Strongman; Kathryn E Mansfield; Christopher Rentsch; Caroline Minassian; Ian J Douglas; Rohini Mathur; Maria Peppa; Simon Cottrell; Jim McMenamin; Maria Zambon; Mary Ramsay; Gavin Dabrera; Vanessa Saliba; Jamie Lopez Bernal,Public Health England; Public Health England; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health Wales; Public Health Scotland; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England,"ObjectivesFollowing detection of the first virologically-confirmed cases of COVID-19 in Great Britain, an enhanced surveillance study was initiated by Public Health England to describe the clinical presentation, course of disease and underlying health conditions associated with infection of the first few hundred cases. MethodsInformation was collected on the first COVID-19 cases according to the First Few X WHO protocol. Case-control analyses of the sensitivity, specificity and predictive value of symptoms and underlying health conditions associated with infection were conducted. Point prevalences of underlying health conditions among the UK general population were presented. @@ -5778,13 +5858,6 @@ Laura Bergamaschi, Ariana Betancourt, Georgie Bowyer, Aloka De Sa, Maddie Epping Epic team/other computing supportBarrie Bailey, Afzal Chaudhry, Rachel Doughton, Chris Workman Statistics/modellingRichard J. Samworth, Caroline Trotter",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2020.05.10.20096925,2020-05-15,https://medrxiv.org/cgi/content/short/2020.05.10.20096925,"NON-WHITE ETHNICITY, MALE SEX, AND HIGHER BODY MASS INDEX, BUT NOT MEDICATIONS ACTING ON THE RENIN-ANGIOTENSIN SYSTEM ARE ASSOCIATED WITH CORONAVIRUS DISEASE 2019 (COVID-19) HOSPITALISATION: REVIEW OF THE FIRST 669 CASES FROM THE UK BIOBANK",Zahra Raisi-Estabragh; Celeste McCracken; Maddalena Ardissino; Mae S Bethell; Jackie Cooper; Cyrus Cooper; Nicholas C Harvey; Steffen E Petersen,"William Harvey Research Institute; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, London, UK; Sir Alexander Fleming Building, Imperial College London, London, UK; North West Anglia NHS Foundation Trust, Hinchingbrooke Hospital, Huntingdon, UK; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, London, UK; MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK; MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, London, UK","BackgroundCardiometabolic morbidity and medications, specifically Angiotensin Converting Enzyme inhibitors (ACEi) and Angiotensin Receptor Blockers (ARBs), have been linked with adverse outcomes from coronavirus disease 2019 (COVID-19). This study aims to investigate factors associated with COVID-19 positivity for the first 669 UK Biobank participants; compared with individuals who tested negative, and with the untested, presumed negative, rest of the population. - -MethodsWe studied 1,474 participants from the UK Biobank who had been tested for COVID-19. Given UK testing policy, this implies a hospital setting, suggesting at least moderate to severe symptoms. We considered the following exposures: age, sex, ethnicity, body mass index (BMI), diabetes, hypertension, hypercholesterolaemia, ACEi/ARB use, prior myocardial infarction (MI), and smoking. We undertook comparisons between: 1) COVID-19 positive and COVID-19 tested negative participants; and 2) COVID-19 tested positive and the remaining participants (tested negative plus untested, n=501,837). Logistic regression models were used to investigate univariate and mutually adjusted associations. - -ResultsAmong participants tested for COVID-19, non-white ethnicity, male sex, and greater BMI were independently associated with COVID-19 positive result. Non-white ethnicity, male sex, greater BMI, diabetes, hypertension, prior MI, and smoking were independently associated with COVID-19 positivity compared to the remining cohort (test negatives plus untested). However, similar associations were observed when comparing those who tested negative for COVID-19 with the untested cohort; suggesting that these factors associate with general hospitalisation rather than specifically with COVID-19. - -ConclusionsAmong participants tested for COVID-19 with presumed moderate to severe symptoms in a hospital setting, non-white ethnicity, male sex, and higher BMI are associated with a positive result. Other cardiometabolic morbidities confer increased risk of hospitalisation, without specificity for COVID-19. Notably, ACE/ARB use did not associate with COVID-19 status.",cardiovascular medicine,fuzzy,100,100 medRxiv,10.1101/2020.05.11.20096347,2020-05-15,https://medrxiv.org/cgi/content/short/2020.05.11.20096347,"The effects of ARBs, ACEIs and statins on clinical outcomes of COVID-19 infection among nursing home residents",Anton De Spiegeleer; Antoon Bronselaer; James T Teo; Geert Byttebier; Guy De Tre; Luc Belmans; Richard Dobson; Evelien Wynendaele; Christophe Van De Wiele; Filip Vandaele; Diemer Van Dijck; Daniel Bean; David Fedson; Bart De Spiegeleer,"Ghent University, Belgium; Ghent University, Belgium; Kings College Hospital NHS Foundation Trust, UK; Bioconstat BV, Belgium; Ghent University, Belgium; Ghent University, Belgium; Kings College London, UK; Ghent University, Belgium; Ghent University, Belgium; VZW Zorg-Saam Zusters Kindsheid Jesu, Belgium; Corilus Health IT Center, Belgium; King's College London, UK; Former University of Virginia, USA; Ghent University, Belgium","Background.COVID-19 infection has limited preventive or therapeutic drug options at this stage. Some of common existing drugs like angiotensin-converting enzyme inhibitors (ACEi), angiotensin II receptor blockers (ARB) and the HMG-CoA reductase inhibitors ( statins) have been hypothesised to impact on disease severity. However, up till now, no studies investigating this association were conducted in the most vulnerable and affected population groups, i.e. older people residing in nursing homes. The purpose of this study has been to explore the association of ACEi/ARB and/or statins with clinical manifestations in COVID-19 infected older people residing in nursing homes. Methods and Findings.We undertook a retrospective multi-centre cohort study in two Belgian nursing homes that experienced similar COVID-19 outbreaks. COVID-19 diagnoses were based on clinical suspicion and/or viral presence using PCR of nasopharyngeal samples. A total of 154 COVID-19 positive subjects was identified. The outcomes were 1) serious COVID-19 defined as a long-stay hospital admission (length of stay [≥] 7 days) or death (at hospital or nursing home) within 14 days of disease onset, and 2) asymptomatic, i.e. no disease symptoms in the whole study-period while still being PCR diagnosed. Disease symptoms were defined as any COVID-19-related clinical symptom (e.g. coughing, dyspnoea, sore throat) or sign (low oxygen saturation and fever) for [≥] 2 days out of 3 consecutive days. @@ -5958,13 +6031,6 @@ medRxiv,10.1101/2020.04.27.20081810,2020-05-03,https://medrxiv.org/cgi/content/s Highlights- A completely redesigned clinical proteomics platform increases throughput and precision while reducing costs. - 27 biomarkers are differentially expressed between WHO severity grades for COVID-19. - The study highlights potential therapeutic targets that include complement factors, the coagulation system, inflammation modulators as well as pro-inflammatory signalling both upstream and downstream of interleukin 6.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2020.04.27.20081711,2020-05-03,https://medrxiv.org/cgi/content/short/2020.04.27.20081711,Response strategies for COVID-19 epidemics in African settings: a mathematical modelling study,Kevin van Zandvoort; Christopher I Jarvis; Carl Pearson; Nicholas G Davies; CMMID COVID-19 working group; Timothy W Russell; Adam J Kucharski; Mark J Jit; Stefan Flasche; Rosalind M Eggo; Francesco Checchi,London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; ; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; LSHTM; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine,"BackgroundThe health impact of COVID-19 may differ in African settings as compared to countries in Europe or China due to demographic, epidemiological, environmental and socio-economic factors. We evaluated strategies to reduce SARS-CoV-2 burden in African countries, so as to support decisions that balance minimising mortality, protecting health services and safeguarding livelihoods. - -MethodsWe used a Susceptible-Exposed-Infectious-Recovered mathematical model, stratified by age, to predict the evolution of COVID-19 epidemics in three countries representing a range of age distributions in Africa (from oldest to youngest average age: Mauritius, Nigeria and Niger), under various effectiveness assumptions for combinations of different non-pharmaceutical interventions: self-isolation of symptomatic people, physical distancing, and shielding (physical isolation) of the high-risk population. We adapted model parameters to better represent uncertainty about what might be expected in African populations, in particular by shifting the distribution of severity risk towards younger ages and increasing the case-fatality ratio. - -ResultsWe predicted median clinical attack rates over the first 12 months of 17% (Niger) to 39% (Mauritius), peaking at 2-4 months, if epidemics were unmitigated. Self-isolation while symptomatic had a maximum impact of about 30% on reducing severe cases, while the impact of physical distancing varied widely depending on percent contact reduction and R0. The effect of shielding high-risk people, e.g. by rehousing them in physical isolation, was sensitive mainly to residual contact with low-risk people, and to a lesser extent to contact among shielded individuals. Response strategies incorporating self-isolation of symptomatic individuals, moderate physical distancing and high uptake of shielding reduced predicted peak bed demand by 46% to 54% and mortality by 60% to 75%. Lockdowns delayed epidemics by about 3 months. Estimates were sensitive to differences in age-specific social mixing patterns, as published in the literature. - -DiscussionIn African settings, as elsewhere, current evidence suggests large COVID-19 epidemics are expected. However, African countries have fewer means to suppress transmission and manage cases. We found that self-isolation of symptomatic persons and general physical distancing are unlikely to avert very large epidemics, unless distancing takes the form of stringent lockdown measures. However, both interventions help to mitigate the epidemic. Shielding of high-risk individuals can reduce health service demand and, even more markedly, mortality if it features high uptake and low contact of shielded and unshielded people, with no increase in contact among shielded people. Strategies combining self-isolation, moderate physical distancing and shielding will probably achieve substantial reductions in mortality in African countries. Temporary lockdowns, where socioeconomically acceptable, can help gain crucial time for planning and expanding health service capacity.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.04.28.20083295,2020-05-02,https://medrxiv.org/cgi/content/short/2020.04.28.20083295,Modifiable and non-modifiable risk factors for COVID-19: results from UK Biobank,Frederick K Ho; Carlos A Celis-Morales; Stuart R Gray; Srinivasa Vittal Katikireddi; Claire L Niedzwiedz; Claire Hastie; Donald M. Lyall; Lyn D. Ferguson; Colin Berry; Daniel F. Mackay; Jason M.R. Gill; Jill P. Pell; Naveed Sattar; Paul I Welsh,University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University Of Glasgow,"BackgroundInformation on risk factors for COVID-19 is sub-optimal. We investigated demographic, lifestyle, socioeconomic, and clinical risk factors, and compared them to risk factors for pneumonia and influenza in UK Biobank. MethodsUK Biobank recruited 37-70 year olds in 2006-2010 from the general population. The outcome of confirmed COVID-19 infection (positive SARS-CoV-2 test) was linked to baseline UK Biobank data. Incident influenza and pneumonia were obtained from primary care data. Poisson regression was used to study the association of exposure variables with outcomes. @@ -6092,6 +6158,31 @@ medRxiv,10.1101/2020.04.07.20056788,2020-04-11,https://medrxiv.org/cgi/content/s Methods and ResultsWe evaluated this hypothesis in a consecutive cohort of 1200 acute inpatients with COVID19 at two hospitals with a multi-ethnic catchment population in London (UK). The mean age was 68{+/-}17 years (57% male) and 74% of patients had at least 1 comorbidity. 415 patients (34.6%) reached the primary endpoint of death or transfer to a critical care unit for organ support within 21-days of symptom onset. 399 patients (33.3 %) were taking ACEi or ARB. Patients on ACEi/ARB were significantly older and had more comorbidities. The odds ratio (OR) for the primary endpoint in patients on ACEi and ARB, after adjustment for age, sex and co-morbidities, was 0.63 (CI 0.47-0.84, p<0.01). ConclusionsThere was no evidence for increased severity of COVID19 disease in hospitalised patients on chronic treatment with ACEi or ARB. A trend towards a beneficial effect of ACEi/ARB requires further evaluation in larger meta-analyses and randomised clinical trials.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2020.04.05.20048421,2020-04-07,https://medrxiv.org/cgi/content/short/2020.04.05.20048421,Loss of smell and taste in combination with other symptoms is a strong predictor of COVID-19 infection,Cristina Menni; Ana Valdes; Maxim B Freydin; Sajaysurya Ganesh; Julia El-Sayed Moustafa; Alessia Visconti; Pirro Hysi; Ruth C E Bowyer; Massimo Mangino; Mario Falchi; Jonathan Wolf; Claire Steves; Tim Spector,"King's College London; NIHR Nottingham Biomedical Research Centre, School of Medicine, University of Nottingham; King's College London; Zoe Global limited; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; King's College London; King's College London","ImportanceA strategy for preventing further spread of the ongoing COVID-19 epidemic is to detect infections and isolate infected individuals without the need of extensive bio-specimen testing. + +ObjectivesHere we investigate the prevalence of loss of smell and taste among COVID-19 diagnosed individuals and we identify the combination of symptoms, besides loss of smell and taste, most likely to correspond to a positive COVID-19 diagnosis in non-severe cases. + +DesignCommunity survey. + +Setting and ParticipantsSubscribers of RADAR COVID-19, an app that was launched for use among the UK general population asking about COVID-19 symptoms. + +Main ExposureLoss of smell and taste. + +Main Outcome MeasuresCOVID-19. + +ResultsBetween 24 and 29 March 2020, 1,573,103 individuals reported their symptoms via the app; 26% reported suffering from one or more symptoms of COVID-19. Of those, n=1702 reported having had a RT-PCR COVID-19 test and gave full report on symptoms including loss of smell and taste; 579 were positive and 1123 negative. In this subset, we find that loss of smell and taste were present in 59% of COVID-19 positive individuals compared to 18% of those negative to the test, yielding an odds ratio (OR) of COVID-19 diagnosis of OR[95%CI]=6.59[5.25; 8.27], P= 1.90x10-59. We also find that a combination of loss of smell and taste, fever, persistent cough, fatigue, diarrhoea, abdominal pain and loss of appetite is predictive of COVID-19 positive test with sensitivity 0.54[0.44; 0.63], specificity 0.86[0.80; 0.90], ROC-AUC 0.77[0.72; 0.82] in the test set, and cross-validation ROC-AUC 0.75[0.72; 0.77]. When applied to the 410,598 individuals reporting symptoms but not formally tested, our model predicted that 13.06%[12.97%;13.15] of these might have been already infected by the virus. + +Conclusions and RelevanceOur study suggests that loss of taste and smell is a strong predictor of having been infected by the COVID-19 virus. Also, the combination of symptoms that could be used to identify and isolate individuals includes anosmia, fever, persistent cough, diarrhoea, fatigue, abdominal pain and loss of appetite. This is particularly relevant to healthcare and other key workers in constant contact with the public who have not yet been tested for COVID-19. + +Key pointsO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIThe spread of COVID-19 can be reduced by identifying and isolating infected individuals but it is not possible to test everyone and priority has been given in most countries to individuals presenting symptoms of the disease. +C_LIO_LICOVID-19 symptoms, such as fever, cough, aches, fatigue are common in many other viral infections +C_LIO_LIThere is therefore a need to identify symptom combinations that can rightly pinpoint to infected individuals +C_LI + +What this study addsO_LIAmong individuals showing symptoms severe enough to be given a COVID-19 RT-PCR test in the UK the prevalence of loss of smell (anosmia) was 3-fold higher (59%) in those positive to the test than among those negative to the test (18%). +C_LIO_LIWe developed a mathematical model combining symptoms to predict individuals likely to be COVID-19 positive and applied this to over 400,000 individuals in the general population presenting some of the COVID-19 symptoms. +C_LIO_LIWe find that [~]13% of those presenting symptoms are likely to have or have had a COVID-19 infection. The proportion was slightly higher in women than in men but is comparable in all age groups, and corresponds to 3.4% of those who filled the app report. +C_LI",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.04.02.20051334,2020-04-06,https://medrxiv.org/cgi/content/short/2020.04.02.20051334,Rapid implementation of mobile technology for real-time epidemiology of COVID-19,David A. Drew; Long H. Nguyen; Claire J. Steves; Jonathan Wolf; Tim D. Spector; Andrew T. Chan; COPE Consortium,Massachusetts General Hospital; Massachusetts General Hospital; King's College London; Zoe Global Limited; King's College London; Massachusetts General Hospital; ,"The rapid pace of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic (COVID-19) presents challenges to the robust collection of population-scale data to address this global health crisis. We established the COronavirus Pandemic Epidemiology (COPE) consortium to bring together scientists with expertise in big data research and epidemiology to develop a COVID-19 Symptom Tracker mobile application that we launched in the UK on March 24, 2020 and the US on March 29, 2020 garnering more than 2.25 million users to date. This mobile application offers data on risk factors, herald symptoms, clinical outcomes, and geographical hot spots. This initiative offers critical proof-of-concept for the repurposing of existing approaches to enable rapidly scalable epidemiologic data collection and analysis which is critical for a data-driven response to this public health challenge. One Sentence SummaryCOVID-19 symptom tracker for smartphones",epidemiology,fuzzy,100,100 diff --git a/data/covid/preprints.exact.csv b/data/covid/preprints.exact.csv index d9ebc6b4..83962c93 100644 --- a/data/covid/preprints.exact.csv +++ b/data/covid/preprints.exact.csv @@ -81,6 +81,15 @@ MethodsConcentrations for black carbon(BC), particulate matter 10(PM10), particu ResultsSingle pollutant analysis showed the direct effect of higher risk of SARS-CoV-2 infection with increased exposure to PM2.5(RR1.11,95%CI 1.08;1.15), PM10(RR1.06,95%CI 1.04;1.09), NO2(RR1.04,95%CI 1.04;1.05) and NOx(RR1.02,95%CI 1.02;1.02) per 1{micro}g/m3 increment with DEFRA 2015-19 data. Sensitivity analyses altering covariates, exposure window and modelled air pollution data source produced similar estimates. Higher risk of SARS-CoV-2 per 10-5m-1 increment of BC (RR1.86, 95%CI 1.62;2.14) was observed using ELAPSE data. ConclusionLong term exposure to higher concentrations of air pollutions increases the risk of SARS-CoV-2 infection, highlighting that adverse health effects of air pollution is not only limited to non-communicable diseases.",epidemiology,exact,100,100 +medRxiv,10.1101/2023.10.11.23296866,2023-10-12,https://medrxiv.org/cgi/content/short/2023.10.11.23296866,"SARS-CoV-2, influenza A/B and respiratory syncytial virus positivity and association with influenza-like illness and self-reported symptoms, over the 2022/23 winter season in the UK: a longitudinal surveillance cohort",Elisabeth Dietz; Emma Elizabeth Pritchard; Koen Pouwels; Muhammad Ehsaan; Joshua Blake; Charlotte Gaughan; Eric Haduli; Hugh Boothe; Karina-Doris Vihta; Tim Peto; Nicole Stoesser; Philippa Matthews; Nick Taylor; Ian Diamond; Ruth Studley; Emma Rourke; Paul Birrell; Daniela De Angelis; Tom Fowler; Conall Watson; David W Eyre; Thomas House; Ann Sarah Walker,University of Oxford; University of Oxford; University of Oxford; Berkshire and Surrey Pathology Services; University of Cambridge; Office of National Statistics; Berkshire and Surrey Pathology Services; Berkshire and Surrey Pathology Services; University of Oxford; University of Oxford; University of Oxford; The Francis Crick Institute; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Cambridge; University of Cambridge; UK Health Security Agency; UK Health Security Agency; University of Oxford; University of Manchester; University of Oxford,"BackgroundSyndromic surveillance often relies on patients presenting to healthcare. Community cohorts, although more challenging to recruit, could provide additional population-wide insights, particularly with SARS-CoV-2 co-circulating with other respiratory viruses. + +MethodsWe estimated positivity and incidence of SARS-CoV-2, influenza A/B, and RSV, and trends in self-reported symptoms including influenza-like illness (ILI), over the 2022/23 winter season in a broadly representative UK community cohort (COVID-19 Infection Survey), using negative-binomial generalised additive models. We estimated associations between test positivity and each of symptoms and influenza vaccination, using adjusted logistic and multinomial models. + +FindingsSwabs taken at 32,937/1,352,979 (2.4%) assessments tested positive for SARS-CoV-2, 181/14,939 (1.2%) for RSV and 130/14,939 (0.9%) for influenza A/B, varying by age over time. Positivity and incidence peaks were earliest for RSV, then influenza A/B, then SARS-CoV-2, and were highest for RSV in the youngest and for SARS-CoV-2 in the oldest age-groups. Many test-positives did not report key symptoms: middle-aged participants were generally more symptomatic than older or younger participants, but still only [~]25% reported ILI-WHO and [~]60% ILI-ECDC. Most symptomatic participants did not test positive for any of the three viruses. Influenza A/B-positivity was lower in participants reporting influenza vaccination in the current and previous seasons (odds ratio=0.55 (95% CI 0.32,0.95)) versus neither season. + +InterpretationSymptom profiles varied little by aetiology, making distinguishing SARS-CoV-2, influenza and RSV using symptoms challenging. Most symptoms were not explained by these viruses, indicating the importance of other pathogens in syndromic surveillance. Influenza vaccination was associated with lower rates of community influenza test positivity. + +FundingUK Health Security Agency, Department of Health and Social Care, National Institute for Health Research.",respiratory medicine,exact,100,100 medRxiv,10.1101/2023.08.25.23294609,2023-08-25,https://medrxiv.org/cgi/content/short/2023.08.25.23294609,Risk factors for SARS-Cov-2 infection at a United Kingdom electricity-generating company: a test-negative design case-control study,Charlotte E Rutter; Martie J Van Tongeren; Tony Fletcher; Sarah E Rhodes; Yiqun Chen; Ian Hall; Nicholas Warren; Neil Pearce,London School of Hygiene and Tropical Medicine; University of Manchester; London School of Hygiene and Tropical Medicine; University of Manchester; Health and Safety Executive; University of Manchester; Health and Safety Executive; London School of Hygiene and Tropical Medicine,"ObjectivesIdentify workplace risk factors for SARS-Cov-2 infection, using data collected by a United Kingdom electricity-generating company. MethodsUsing a test-negative design case-control study we estimated the odds ratios (OR) of infection by job category, site, test reason, sex, vaccination status, vulnerability, site outage, and site COVID-19 weekly risk rating, adjusting for age, test date and test type. @@ -176,15 +185,6 @@ FindingsOverall, 276,840/800,000 (34.6%) of invited participants completed the q InterpretationAlthough COVID-19 is usually of short duration, some adults experience persistent and burdensome illness. FundingThis work is independent research funded by the National Institute for Health and Care Research (NIHR) (REACT Long COVID (REACT-LC) (COV-LT-0040)). This research is part of the Data and Connectivity National Core Study, led by Health Data Research UK in partnership with the Office for National Statistics and funded by UK Research and Innovation (UKRI) (MC_PC_20029). The views expressed in this publication are those of the author(s) and not necessarily those of NIHR or UKRI.",public and global health,exact,100,100 -medRxiv,10.1101/2023.03.24.23287700,2023-03-26,https://medrxiv.org/cgi/content/short/2023.03.24.23287700,The potential contribution of vaccination uptake to occupational differences in risk of SARS-CoV-2: Analysis of the ONS COVID-19 Infection Survey,Jack D Wilkinson; Evangelia Demou; Mark Cherrie; Rhiannon Edge; Matthew Gittins; Srinivasa Vittal Katikireddi; Theocharis Kromydas; WIll Mueller; Neil Pearce; Martie van Tongeren; Sarah Rhodes,University of Manchester; University of Glasgow; Institute of Occupational Medicine; University of Lancaster; University of Manchester; University of Glasgow; University of Glasgow; Institute for Occupational Medicine; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester,"ObjectivesTo assess variation in vaccination uptake across occupational groups as a potential explanation for variation in risk of SARS-CoV-2 infection. - -DesignWe analysed data from the UK Office of National Statistics COVID-19 Infection Survey linked to vaccination data from the National Immunisation Management System in England from December 1st 2020 to 11th May 2022. We analysed vaccination uptake and SARS-CoV-2 infection risk by occupational group and assessed whether adjustment for vaccination reduced the variation in risk between occupational groups. - -Setting - -ResultsEstimated rates of triple-vaccination were high across all occupational groups (80% or above), but were lowest for food processing (80%), personal care (82%), hospitality (83%), manual occupations (84%), and retail (85%). High rates were observed for individuals working in health (95% for office-based, 92% for those in patient-facing roles) and education (91%) and office-based workers not included in other categories (90%). The impact of adjusting for vaccination when estimating relative risks of infection was generally modest (ratio of hazard ratios reduced from 1.38 to 1.32), but was consistent with the hypothesis that low vaccination rates contribute to elevated risk in some groups. Conversely, estimated relative risk for some occupational groups, such as people working in education, remained high despite high vaccine coverage. - -ConclusionsVariation in vaccination coverage might account for a modest proportion of occupational differences in infection risk. Vaccination rates were uniformly very high in this cohort, which may suggest that the participants are not representative of the general population. Accordingly, these results should be considered tentative pending the accumulation of additional evidence.",occupational and environmental health,exact,100,100 medRxiv,10.1101/2023.03.24.23287666,2023-03-24,https://medrxiv.org/cgi/content/short/2023.03.24.23287666,Occupational differences in the prevalence and severity of long-COVID: Analysis of the ONS Coronavirus (COVID-19) Infection Survey,Theocharis Kromydas; Evangelia Demou; Rhiannon Edge; Matthew Gittins; Srinivasa Vittal Katikireddi; Neil Pearce; Martie van Tongeren; Jack Wilkinson; Sarah Rhodes,University of Glasgow; University of Glasgow; Lancaster University; University of Manchester; University of Glasgow; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester; University of Manchester,"ObjectivesTo establish whether prevalence and severity of long-COVID symptoms vary by industry and occupation. MethodsWe utilised ONS Coronavirus Infection Survey (CIS) data (February 2021-April 2022) of working-age participants (16-65 years). Exposures were industrial sector, occupation and major Standard Occupational Classification (SOC) group. Outcomes were self-reported: (1) long-COVID symptoms; and (2) reduced function due to long-COVID. Binary (outcome 1) and ordered (outcome 2) logistic regression were used to estimate odds ratios (OR) and prevalence (marginal means) for all exposures. @@ -246,6 +246,15 @@ Our analyses indicate that mental health conditions are more common among those The findings have implications for mental health service planning and efforts to reduce barriers to treatment access, especially for individuals who live on their own.",psychiatry and clinical psychology,exact,100,100 medRxiv,10.1101/2023.02.26.23286474,2023-03-06,https://medrxiv.org/cgi/content/short/2023.02.26.23286474,Improving the representativeness of UKs national COVID-19 Infection Survey through spatio-temporal regression and post-stratification,Koen B Pouwels; David W Eyre; Thomas House; Ben Aspey; Philippa C Matthews; Nicole Stoesser; John Newton; Ian Diamond; Ruth Studley; Nick Taylor; John Bell; Jeremy Farrar; Jaison Kolenchery; Brian Marsden; Sarah Hoosdally; Yvonne Jones; David Stuart; Derrick Crook; tim E peto; Ann Sarah Walker; - COVID-19 Infection Survey Team,University of Oxford; University of Oxford; University of Manchester; Office for National Statistics; The Francis Crick Institute; University of Oxford; University of Exeter; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; oxford university; University of Oxford; -,"Population-representative estimates of SARS-CoV-2 infection prevalence and antibody levels in specific geographic areas at different time points are needed to optimise policy responses. However, even population-wide surveys are potentially impacted by biases arising from differences in participation rates across key groups. Here, we use spatio-temporal regression and post-stratification models to UKs national COVID-19 Infection Survey (CIS) to obtain representative estimates of PCR positivity (6,496,052 tests) and antibody prevalence (1,941,333 tests) for different regions, ages and ethnicities (7-December-2020 to 4-May-2022). Not accounting for vaccination status through post-stratification led to small underestimation of PCR positivity, but more substantial overestimations of antibody levels in the population (up to 21%), particularly in groups with low vaccine uptake in the general population. There was marked variation in the relative contribution of different areas and age-groups to each wave. Future analyses of infectious disease surveys should take into account major drivers of outcomes of interest that may also influence participation, with vaccination being an important factor to consider.",infectious diseases,exact,100,100 medRxiv,10.1101/2023.03.01.23286627,2023-03-03,https://medrxiv.org/cgi/content/short/2023.03.01.23286627,Effectiveness of successive booster vaccine doses against SARS-CoV-2 related mortality in residents of Long-Term Care Facilities in the VIVALDI study,Oliver Stirrup; Madhumita Shrotri; Natalie L. Adams; Maria Krutikov; Borscha Azmi; Igor Monakhov; Gokhan Tut; Paul Moss; Andrew Hayward; Andrew Copas; Laura Shallcross,University College London; University College London; University College London; University College London; University College London; UK Health Security Agency; University of Birmingham; University of Birmingham; University College London; University College London; University College London,"We evaluated the effectiveness of 1-3 booster vaccinations against SARS-CoV-2 related mortality among a cohort of 13407 older residents of long-term care facilities (LTCFs) participating in the VIVALDI study in England in 2022. Cox regression was used to estimate relative hazards of SARS-CoV-2 related death following booster vaccination relative to 2 doses (after 84+ days), stratified by previous SARS-CoV-2 infection and adjusting for age, sex and LTCF capacity. Each booster provided additional short-term protection relative to primary vaccination, with consistent pattern of waning to 45-75% reduction in risk beyond 112 days.",infectious diseases,exact,100,100 +medRxiv,10.1101/2023.03.01.23286624,2023-03-03,https://medrxiv.org/cgi/content/short/2023.03.01.23286624,Risk of cardiovascular events following COVID-19 in people with and without pre-existing chronic respiratory disease,Hannah Whittaker; Costantinos Kallis; Angela Wood; Thomas Bolton; Samantha Walker; Aziz Sheikh; Alex Brownrigg; Ashley Akbari; Kamil Sterniczuk; Jennifer K Quint,"Imperial College London; Imperial College London; Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, United Kingdom; Health Data Research UK; Asthm + Lung; The University of Edinburgh College of Medicine and Veterinary Medicine; Health Data Research UK BREATHE; Swansea University; Health Data Research UK BREATHE; Imperial College London","BackgroundCOVID-19 is associated with a higher risk of cardiovascular outcomes in the general population, but it is unknown whether people with pre-existing chronic respiratory disease (CRD) have a higher risk of cardiovascular events post-COVID-19 compared with the general population and, if so, what respiratory-related risk factors may modify this risk in these people. + +MethodsPrimary and secondary care data from the National Health Service and COVID-19-specific linked data were used to define a population of adults in England with COVID-19 (index date) between 01/01/2020-30/11/2021. Adjusted Cox Proportional Hazard regression was used to quantify the association between CRD, asthma-related factors, COPD-related factors, and risk of cardiovascular events. CRD included asthma, COPD, bronchiectasis, cystic fibrosis, or pulmonary fibrosis prior to COVID-19 diagnosis. Asthma-specific factors included baseline asthma control, exacerbations, and inhaled corticosteroid (ICS) dose. COPD-specific risk factors included baseline ICS prescriptions and exacerbations. Secondary objectives quantified the impact of COVID-19 hospitalisation and vaccine dose on cardiovascular outcomes. + +ResultsOf 3,670,455 people, those with CRD had a modest higher risk of cardiovascular events (HRadj 1.11, 95%CI 1.07-1.14), heart failure (HRadj 1.15, 1.09-1.21), and pulmonary emboli (HRadj 1.20, 1.11-1.30) compared with people without CRD. In people with asthma, baseline exacerbations and high-dose ICS were associated with a higher risk of cardiovascular outcomes (HRadj 1.24, 1.15-1.34 and 1.12, 1.01-1.24, respectively). In people with COPD, exacerbations were associated with a higher risk of cardiovascular outcomes (HRadj 1.40, 1.28-1.52). Regardless of CRD, the risk of cardiovascular events was lower with increasing COVID-19 vaccine dose. + +ConclusionsHigher risk of cardiovascular events following COVID-19 might be explained at least in part by the underlying CRD and severity of that condition. In addition, COVID-19 vaccines were beneficial to both people with and without CRD with regards to CV events. + +Key MessagesPre-existing chronic respiratory disease, asthma and COPD severity were associated with a higher risk of various types of cardiovascular outcomes following COVID-19. Regardless of having pre-existing chronic respiratory disease, COVID-19 vaccination reduced the risk of cardiovascular events following COVID-19.",epidemiology,exact,100,100 medRxiv,10.1101/2023.02.17.23286079,2023-02-23,https://medrxiv.org/cgi/content/short/2023.02.17.23286079,"Surface sampling for SARS-CoV-2 in workplace outbreak settings in the UK, 2021-22.",Ian George Nicholls; Antony Spencer; Yiqun Chen; Allan Bennett; Barry Atkinson,UK Health Security Agency; UK Health Security Agency; Health and Safety Executive; UK Health Security Agency; UK Health Security Agency,"AimsTo utilise environmental surface sampling to evaluate areas of SARS-CoV-2 contamination within workplaces to identify trends and improve local COVID-control measures. Methods and ResultsSurface sampling was undertaken at 12 workplaces that experienced a cluster of COVID-19 cases in the workforce between March 2021 and March 2022. 7.4% (61/829) of samples collected were positive for SARS-CoV-2 RNA by qPCR with only 1.8% (15/829) of samples identified with crossing threshold (Ct) values below 35.0. No sample returned whole genome sequence inferring RNA detected was degraded. @@ -480,6 +489,17 @@ MethodsData on 244,470 participants were available from the ONS Coronavirus Infe ResultsOverall, higher risk classifications for the first six domains tended to be associated with an increased risk of infection, with little evidence of a relationship for domains relating to proportion of workers with job insecurity or migrant workers. By time there was a clear exposure-response relationship for these domains in the first period only. Results were largely consistent across the two cohorts. ConclusionsAn exposure-response relationship exists in the early phase of the COVID-19 pandemic for number of contacts, nature of contacts, contacts via surfaces, indoor or outdoor location, ability to social distance and use of face coverings. These associations appear to have diminished over time.",occupational and environmental health,exact,100,100 +medRxiv,10.1101/2022.09.14.22279931,2022-09-15,https://medrxiv.org/cgi/content/short/2022.09.14.22279931,Detecting changes in population trends in infection surveillance using community SARS-CoV-2 prevalence as an exemplar,Emma Elizabeth Pritchard; Karina-Doris Vihta; David W Eyre; Susan Hopkins; Tim EA Peto; Philippa C Matthews; Nicole Stoesser; Ruth Studley; Emma Rourke; Ian Diamond; Koen B Pouwels; Ann Sarah Walker,"University of Oxford; University of Oxford; University of Oxford; UK Health Security Agency; University of Oxford; The Francis Crick Institute, London; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; University of Oxford","BackgroundMonitoring infection trends is vital to informing public health strategy. Detecting and quantifying changes in growth rates can inform policymakers rationale for implementing or continuing interventions aimed at reducing impact. Substantial changes in SARS-CoV-2 prevalence with emergence of variants provides opportunity to investigate different methods to do this. + +MethodsWe included PCR results from all participants in the UKs COVID-19 Infection Survey between 1 August 2020-30 June 2022. Change-points for growth rates were identified using iterative sequential regression (ISR) and second derivatives of generalised additive models (GAMs). + +Consistency between methods and timeliness of detection were compared. + +FindingsOf 8,799,079 visits, 147,278 (1{middle dot}7%) were PCR-positive. Over the time period, change-points associated with emergence of major variants were estimated to occur a median 4 days earlier (IQR 0-8) in GAMs versus ISR, with only 2/48 change-points identified by only one method. Estimating recent change-points using successive data periods, four change-points (4/96) identified by GAMs were not found when adding later data or by ISR; 77% (74/96) of change-points identified by successive GAMs were identified by ISR. Change-points were detected 3-5 weeks after they occurred in both methods but could be detected earlier within specific subgroups. + +InterpretationChange-points in growth rates of SARS-CoV-2 can be detected in near real-time using ISR and second derivatives of GAMs. To increase certainty about changes in epidemic trajectories both methods could be run in parallel. Running either method in near real-time on different infection surveillance data streams could provide timely warnings of changing underlying epidemiology. + +FundingUK Health Security Agency, Department of Health and Social Care (UK), Welsh Government, Department of Health (on behalf of the Northern Ireland Government), Scottish Government, National Institute for Health Research.",epidemiology,exact,100,100 medRxiv,10.1101/2022.09.11.22279823,2022-09-12,https://medrxiv.org/cgi/content/short/2022.09.11.22279823,Effects of the COVID-19 pandemic on the mental health of clinically extremely vulnerable children and children living with clinically extremely vulnerable people in Wales: A data linkage study,Laura Elizabeth Cowley; Karen Hodgson; Jiao Song; Tony Whiffen; Jacinta Tan; Ann John; Amrita Bandyopadhyay; Alisha R Davies,Swansea University; Public Health Wales; Public Health Wales; Welsh Government; University of Oxford; Swansea University; Swansea University; Public Health Wales,"ObjectivesTo determine whether clinically extremely vulnerable (CEV) children or children living with a CEV person in Wales were at greater risk of presenting with anxiety or depression in primary or secondary care during the COVID-19 pandemic compared with children in the general population, and to compare patterns of anxiety and depression during the pandemic (23rd March 2020-31st January 2021, referred to as 2020/21) and before the pandemic (March 23rd 2019-January 31st 2020, referred to as 2019/20), between CEV children and the general population. DesignPopulation-based cross-sectional cohort study using anonymised, linked, routinely collected health and administrative data held in the Secure Anonymised Information Linkage Databank. CEV individuals were identified using the COVID-19 Shielded Patient List. @@ -621,7 +641,6 @@ MethodsCOVIDENCE UK is a longitudinal population-based study that investigates r ResultsThe study was launched on 1st May 2020 and closed to recruitment on 6th October 2021. A total of 19,981 participants enrolled and consented to 5-year follow-up with medical record linkage. Their mean age was 59.1 years (range 16.0 to 94.4 years), 70.2% were female, and 93.7% identified their ethnic origin as White. Analyses conducted to date have provided key insights into risk factors for SARS-CoV-2 infection and COVID-19 disease, determinants of SARS-CoV-2 vaccine immunogenicity and efficacy, and impacts of COVID-19 on health economic outcomes. The cohort has also supported conduct of a Phase 3 randomised trial-within-cohort study (CORONAVIT) evaluating implementation of a test-and-treat approach to correcting sub-optimal vitamin D status on incidence and severity of acute respiratory infections, including COVID-19. ConclusionsThe COVIDENCE UK dataset represents a valuable resource containing granular information on factors influencing susceptibility to, and impacts of, COVID-19 in UK adults. Researchers wishing to access anonymised participant-level data should contacting the corresponding author for further information.",epidemiology,exact,100,100 -medRxiv,10.1101/2022.06.20.22275994,2022-06-20,https://medrxiv.org/cgi/content/short/2022.06.20.22275994,Characterising patterns of COVID-19 and long COVID symptoms: Evidence from nine UK longitudinal studies,Ruth C E Bowyer; Charlotte Huggins; Renin Toms; Richard John Shaw; Bo Hou; Ellen J Thompson; Alex Siu Fung Kwong; Dylan M Williams; Milla Kibble; George B Ploubidis; Nicholas J Timpson; Jonathan A C Sterne; Nishi Chaturvedi; Claire J Steves; Kate Tilling; Richard J Silverwood,King's College London; University of Edinburgh; University of Bristol; University of Glasgow; Bradford Institute for Health Research; King's College London; University of Bristol; UCL; King's College London; University College London; University of Bristol; University of Bristol; University College London; King's College London; University of Bristol; University College London,"Multiple studies across global populations have established the primary symptoms characterising COVID-19 (Coronavirus Disease 2019) and long COVID. However, as symptoms may also occur in the absence of COVID-19, a lack of appropriate controls has often meant that specificity of symptoms to acute COVID-19 or long COVID could not be examined. We aimed to characterise patterns of COVID-19 and long COVID symptoms across nine UK longitudinal studies, totalling over 42,000 participants. Conducting latent class analyses separately in three groups ( no COVID-19, COVID-19 in last 12 weeks, COVID-19 > 12 weeks ago), the data did not support the presence of more than two distinct symptom patterns, representing high and low symptom burden, in each group. Comparing the high symptom burden classes between the COVID-19 in last 12 weeks and no COVID-19 groups we identified symptoms characteristic of acute COVID-19, including loss of taste and smell, fatigue, cough, shortness of breath and muscle pains or aches. Comparing the high symptom burden classes between the COVID-19 > 12 weeks ago and no COVID-19 groups we identified symptoms characteristic of long COVID, including fatigue, shortness of breath, muscle pain or aches, difficulty concentrating and chest tightness. The identified symptom patterns among individuals with COVID-19 > 12 weeks ago were strongly associated with self-reported length of time unable to function as normal due to COVID-19 symptoms, suggesting that the symptom pattern identified corresponds to long COVID. Building the evidence base regarding typical long COVID symptoms will improve diagnosis of this condition and the ability to elicit underlying biological mechanisms, leading to better patient access to treatment and services.",epidemiology,exact,100,100 medRxiv,10.1101/2022.06.18.22276437,2022-06-19,https://medrxiv.org/cgi/content/short/2022.06.18.22276437,A patient-centric characterization of systemic recovery from SARS-CoV-2 infection,Hélène Ruffieux; Aimee Hanson; Samantha Lodge; Nathan Lawler; Luke Whiley; Nicola Gray; Tui Nolan; Laura Bergamaschi; Federica Mescia; - CITIID-NIHR COVID BioResource Collaboration; Nathalie Kingston; John Bradley; Elaine Holmes; Julien Wist; Jeremy Nicholson; Paul Lyons; Kenneth Smith; Sylvia Richardson; Glenn Bantug; Christoph Hess,University of Cambridge; University of Cambridge; Murdoch University; Murdoch University; Murdoch University; Murdoch University; University of Cambridge; University of Cambridge; University of Cambridge; ; University of Cambridge; University of Cambridge; Murdoch University; Murdoch University; Murdoch University; University of Cambridge; University of Cambridge; University of Cambridge; University and University Hospital Basel; University of Cambridge,"The biology driving individual patient responses to SARS-CoV-2 infection remains ill understood. Here, we developed a patient-centric framework leveraging detailed longitudinal phenotyping data, covering a year post disease onset, from 215 SARS-CoV-2 infected subjects with differing disease severities. Our analyses revealed distinct ""systemic recovery"" profiles with specific progression and resolution of the inflammatory, immune, metabolic and clinical responses, over weeks to several months after infection. In particular, we found a strong intra-patient temporal covariation of innate immune cell numbers, kynurenine- and host lipid-metabolites, which suggested candidate immunometabolic pathways putatively influencing restoration of homeostasis, the risk of death and of long COVID. Based on these data, we identified a composite signature predictive of systemic recovery on the patient level, using a joint model on cellular and molecular parameters measured soon after disease onset. New predictions can be generated using the online tool http://shiny.mrc-bsu.cam.ac.uk/apps/covid-systemic-recovery-prediction-app, designed to test our findings prospectively. Graphical abstract @@ -877,6 +896,23 @@ ConclusionsOur results support early work showing the relative reduction in seve What is already known on this topicThe Omicron variant, which refers to the whole lineage (BA.1, BA.2, BA.3) had already been shown to be more transmissible than the Delta variant, but there is emerging evidence suggests that the risk of hospitalisation and risk of death within 28 days after a SARS-COV-2 test is lower. However, with a highly transmissible infection and high levels of population testing, definition of death within 28 days is more likely to be susceptible to misclassification bias due to asymptomatic or co-incidental infection. There is no study so far comparing the risk of COVID-19 death as identified from death certification records, with the cause of death assessed by the physician who attended the patient in the last illness. What this study addsUsing data from a large cohort of COVID-19 infections that occurred in December 2021, we examined the difference in the risk COVID-19 death, as identified from death certification records, between the Delta and Omicron BA.1 variant. Our study shows that risk of death involving COVID-19 was reduced by 67% following infection with the Omicron BA.1 variant relative to the Delta variant after adjusting for a wide range of potential confounders, including vaccination status and comorbidities. Importantly, we found that the relative risk of COVID-19 mortality following Omicron versus Delta infection varied by age and sex, with lower relative risk in younger individuals and for males than females. The reduction in risk of death involving COVID-19 was also most pronounced in individuals who had received a booster.",epidemiology,exact,100,100 +medRxiv,10.1101/2022.02.14.22270930,2022-02-15,https://medrxiv.org/cgi/content/short/2022.02.14.22270930,Determinants of antibody responses to two doses of ChAdOx1 nCoV-19 or BNT162b2 and a subsequent booster dose of BNT162b2 or mRNA-1273: population-based cohort study (COVIDENCE UK),David A Jolliffe; Sian E Faustini; Hayley Holt; Natalia Perdek; Sheena Maltby; Mohammad Talaei; Matthew Greenig; Giulia Vivaldi; Florence Tydeman; Jane Symons; Gwyneth A Davies; Ronan Lyons; Frank Kee; Aziz Sheikh; Seif O Shaheen; Alex Richter; Adrian R Martineau,Queen Mary University of London; University of Birmingham; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Jane Symons Media; Swansea University; Swansea University; Queen's University Belfast; Edinburgh University; Queen Mary University of London; University of Birminghan; Queen Mary University of London,"BackgroundAntibody responses to SARS-CoV-2 vaccination vary for reasons that remain poorly understood. + +MethodsWe tested for presence of combined IgG, IgA and IgM (IgGAM) anti-spike antibodies before and after administration of two doses of ChAdOx1 nCoV-19 (ChAdOx1, Oxford-AstraZeneca) or BNT162b2 (Pfizer-BioNTech) in UK adults participating in a population-based longitudinal study who received their first dose of vaccine from December 15, 2020 to July 10, 2021. Information on sixty-six potential sociodemographic, behavioural, clinical, pharmacological and nutritional determinants of serological response to vaccination was captured using serial online questionnaires. We used logistic regression to estimate multivariable-adjusted odds ratios (aORs) for associations between independent variables and risk of seronegativity following two vaccine doses. Participants who were seronegative after receiving two vaccine doses were offered an additional antibody test following subsequent administration of a booster dose of BNT162b2 or mRNA-1273 (Moderna) from September 23 to December 12, 2021. + +FindingsSerology results following two vaccine doses were available for 9,101 participants, of whom 5,770 (63.4%) received ChAdOx1 and 3,331 (36.6%) received BNT162b2. Anti-spike IgGAM was undetectable in 378 (4.2%) participants at a median of 8.6 weeks (IQR 6.4-10.7 weeks) after their second dose of vaccine. Seronegativity following two doses of SARS-CoV-2 vaccination was associated with administration of ChAdOx1 vs BNT162b2 (aOR 7.03, 95% CI 4.39-11.24), shorter interval between first and second vaccine doses (aOR 2.37, 1.06-5.26, for <6 weeks vs >10 weeks; aOR 1.59, 1.18-2.13, for 6-10 weeks vs >10 weeks), poorer self-assessed general health (aOR 3.33, 1.49-7.46, for poor vs excellent), immunodeficiencies (aOR 6.75, 2.63-17.35) and prescription of systemic immunosuppressants (aOR 3.76, 2.44-5.78). By contrast, pre-vaccination SARS-CoV-2 seropositivity (aOR 0.16, 0.04-0.70, for symptomatic seropositives vs seronegatives) and supplemental vitamin D intake (aOR 0.73, 0.53-0.99) were associated with reduced risk of post-vaccination seronegativity. 247/378 (65.3%) of participants who were seronegative after two doses of ChAdOx1 vs BNT162b2 provided a third sample at a median of 7.8 weeks (IQR 5.8-10.4) after receiving a booster dose of BNT162b2 or mRNA-1273: eight (3.2%) of them remained seronegative after three vaccine doses, all of whom either had a primary immunodeficiency or were taking systemic immunosuppressant drugs. + +InterpretationWe identify multiple determinants of antibody responses to two doses of ChAdOx1 or BNT162b2, many of which are potentially modifiable. Booster doses of BNT162b2 or mRNA-1273 were highly effective in achieving seroconversion in those who failed to mount antibody responses following two doses of ChAdOx1 or BNT162b2. + +Study registrationhttps://clinicaltrials.gov/ct2/show/NCT04330599 + +FundingBarts Charity, Fischer Family Trust, The Exilarchs Foundation, DSM Nutritional Products, Health Data Research UK + +Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, medRxiv, and Google Scholar for papers published from January 1, 2020, to February 1, 2022, using the search terms (antibody OR humoral OR serologic* OR immunogenic*) AND (SARS-CoV-2 vaccine OR ChAdOx1 or BNT162b2 coronavirus), with no language restrictions. Population-based studies investigating multiple potential determinants of vaccine immunogenicity in people with known pre-vaccination SARS-CoV-2 serostatus are lacking. + +Added value of this studyThis large population-based study, conducted in a population with known pre-vaccination SARS-CoV-2 serostatus, examines a comprehensive range of potential sociodemographic, behavioural, clinical, pharmacological and nutritional determinants of antibody responses to administration of two major SARS-CoV-2 vaccines (i.e., ChAdOx1 or BNT162b2), many of which have not previously been investigated. It is also the first population-based study to characterise antibody responses to booster doses of SARS-CoV-2 vaccines in adults who were seronegative after their primary course of vaccination. + +Implications of all the available evidenceIncreased risk of seronegativity following two doses of SARS-CoV-2 vaccines was associated with administration of ChAdOx1 vs BNT162b2, shorter interval between first and second vaccine doses, poorer self-assessed general health, immunocompromise and SARS-CoV-2 seronegativity pre-vaccination. Regular intake of vitamin D supplements was associated with reduced risk of post-vaccination seronegativity. Randomised controlled trials are now needed to test for causality. Booster doses of BNT162b2 or mRNA-1273 were highly effective in achieving seroconversion in the majority of people who failed to mount antibody responses following a primary course of vaccination, the few exceptions being a subset of those with primary immunodeficiency or systemic immunosuppressant drugs.",infectious diseases,exact,100,100 medRxiv,10.1101/2022.02.10.22270799,2022-02-13,https://medrxiv.org/cgi/content/short/2022.02.10.22270799,Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study,Oliver Stirrup; James Blackstone; Fiona Mapp; Alyson MacNeil; Monica Panca; Alison Holmes; Nicholas Machin; Gee Yen Shin; Tabitha Mahungu; Kordo Saeed; Tranprit Saluja; Yusri Taha; Nikunj Mahida; Cassie Pope; Anu Chawla; Teresa Cutino-Moguel; Asif Tamuri; Rachel Williams; Alistair Darby; David L Robertson; Flavia Flaviani; Eleni Nastouli; Samuel Robson; Darren Smith; Matthew Loose; Kenneth Laing; Irene Monahan; Beatrix Kele; Sam Haldenby; Ryan George; Matthew Bashton; Adam Witney; Matthew Byott; Francesc Coll; Michael Chapman; Sharon Peacock; - COG-UK HOCI Investigators; - COG-UK Consortium; Joseph Hughes; Gaia Nebbia; David G Partridge; Matthew Parker; James Richard Price; Christine Peters; Sunando Roy; Luke B Snell; Thushan I de Silva; Emma Thomson; Paul Flowers; Andrew Copas; Judith Breuer,"Institute for Global Health, UCL, London, UK; Comprehensive Clinical Trials Unit, UCL, London, UK; Institute for Global Health, UCL, London, UK; Comprehensive Clinical Trials Unit, UCL, London, UK; Comprehensive Clinical Trials Unit, UCL, London, UK; Imperial College Healthcare NHS Trust, London, UK; Manchester University NHS Foundation Trust, Manchester, UK; University College London Hospitals NHS Foundation Trust, London, UK; Royal Free NHS Foundation Trust, London, UK; University Hospital Southampton NHS Foundation Trust, Southampton, UK; Sandwell and West Birmingham NHS Trust, UK; Departments of Virology and Infectious Diseases, Newcastle Hospitals NHS Foundation Trust, Newcastle, UK; Nottingham University Hospitals NHS Trust, Nottingham, UK; St George's University Hospitals NHS Foundation Trust, London, UK; Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Barts Health NHS Trust, London, UK; Research Computing, UCL, London, UK; Department of Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, UCL, London, UK; Centre for Genomic Research, University of Liverpool, Liverpool, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK; University College London Hospitals NHS Foundation Trust, London, UK; Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, UK; Department of Applied Sciences, Northumbria University, Newcastle, UK; School of Life Sciences, University of Nottingham, Nottingham, UK; Institute for Infection and Immunity, St George's University of London, London, UK; Institute for Infection and Immunity, St George's University of London, London, UK; Barts Health NHS Trust, London, UK; Centre for Genomic Research, University of Liverpool, Liverpool, UK; Manchester University NHS Foundation Trust, Manchester, UK; The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University, Newcastle, UK; Institute for Infection and Immunity, St George's University of London, London, UK; University College London Hospitals NHS Foundation Trust, London, UK; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Health Data Research UK Cambridge Hub, Cambridge UK; Department of Medicine, University of Cambridge, Cambridge, UK; ; ; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK; Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK; Imperial College Healthcare NHS Trust, London, UK; NHS Greater Glasgow and Clyde, Glasgow, UK; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, UCL, London, UK; Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, The University of Sheffield, Sheffield, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; School of Psychological Sciences and Health, University of Strathclyde, Glasgow, UK; Institute for Global Health, UCL, London, UK; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, UCL, London, UK","IntroductionViral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. MethodsWe conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data-collection period, followed by intervention periods comprising 8 weeks of rapid (<48h) and 4 weeks of longer-turnaround (5-10 day) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital onset COVID-19 infections (HOCIs; detected [≥]48h from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on incidence of probable/definite hospital-acquired infections (HAIs) was evaluated. @@ -1077,6 +1113,7 @@ MethodsData from 15,190 employed/self-employed participants in the Virus Watch p FindingsIncreased risk was seen in nurses (aRR=1.44, 1.25-1.65; AF=30%, 20-39%), doctors (aRR=1.33, 1.08-1.65; AF=25%, 7-39%), carers (1.45, 1.19-1.76; AF=31%, 16-43%), primary school teachers (aRR=1.67, 1.42-1.96; AF=40%, 30-49%), secondary school teachers (aRR=1.48, 1.26-1.72; AF=32%, 21-42%), and teaching support occupations (aRR=1.42, 1.23-1.64; AF=29%, 18-39%) compared to office-based professional occupations. Differential risk was apparent in the earlier phases (Feb 2020 - May 2021) and attenuated later (June - October 2021) for most groups, although teachers and teaching support workers demonstrated persistently elevated risk across waves. InterpretationOccupational differentials in SARS-CoV-2 infection risk vary over time and are robust to adjustment for socio-demographic, health-related, and non-workplace activity-related potential confounders. Direct investigation into workplace factors underlying elevated risk and how these change over time is needed to inform occupational health interventions.",epidemiology,exact,100,100 +medRxiv,10.1101/2021.12.08.21267353,2021-12-08,https://medrxiv.org/cgi/content/short/2021.12.08.21267353,The challenge of limited vaccine supplies: impact of prior infection on anti-spike IgG antibody trajectories after a single COVID-19 vaccination,Jia Wei; Philippa Matthews; Nicole Stoesser; Ian Diamond; Ruth Studley; Emma Rourke; Duncan Cook; John Bell; John Newton; Jeremy Farrar; Alison Howarth; Brian Marsden; Sarah Hoosdally; Yvonne Jones; David Stuart; Derrick W Crook; tim E peto; Ann Sarah Walker; David W Eyre; Koen B Pouwels; - COVID-19 Infection Survey team,University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; NIHR Oxford Biomedical Research Centre; oxford university; University of Oxford; University of Oxford; University of Oxford; ,"Given high SARS-CoV-2 incidence, coupled with slow and inequitable vaccine roll-out, there is an urgent need for evidence to underpin optimum vaccine deployment, aiming to maximise global population immunity at speed. We evaluate whether a single vaccination in previously infected individuals generates similar initial and subsequent antibody responses to two vaccinations in those without prior infection. We compared anti-spike IgG antibody responses after a single dose of ChAdOx1, BNT162b2, or mRNA-1273 SARS-CoV-2 vaccines in the COVID-19 Infection Survey in the UK general population. In 100,849 adults who received at least one vaccination, 13,404 (13.3%) had serological and/or PCR evidence of prior infection. Prior infection significantly boosted antibody responses for all three vaccines, producing a higher peak level and longer half-life, and a response comparable to those without prior infection receiving two vaccinations. In those with prior infection, median time above the positivity threshold was estimated to last for >1 year after the first dose. Single-dose vaccination targeted to those previously infected may provide protection in populations with high rates of previous infection faced with limited vaccine supply, as an interim measure while vaccine campaigns are scaled up.",infectious diseases,exact,100,100 medRxiv,10.1101/2021.11.24.21266818,2021-12-01,https://medrxiv.org/cgi/content/short/2021.11.24.21266818,Trends and associated factors for Covid-19 hospitalisation and fatality risk in 2.3 million adults in England,Thomas Beaney; Ana Luisa Neves; Ahmed Alboksmaty; Kelsey Flott; Aidan Fowler; Jonathan R Benger; Paul Aylin; Sarah Elkin; Ara Darzi; Jonathan Clarke,Imperial College London; Imperial College London; Imperial College London; Imperial College London; NHS England and Improvement; NHS Digital; Imperial College London; Imperial College London; Imperial College London; Imperial College London,"BackgroundThe Covid-19 case fatality ratio varies between countries and over time but it is unclear whether variation is explained by the underlying risk in those infected. This study aims to describe the trends and risk factors for admission and mortality rates over time in England. MethodsIn this retrospective cohort study, we included all adults ([≥]18 years) in England with a positive Covid-19 test result between 1st October 2020 and 30th April 2021. Data were linked to primary and secondary care electronic health records and death registrations. Our outcomes were i) one or more emergency hospital admissions and ii) death from any cause, within 28 days of a positive test. Multivariable multilevel logistic regression was used to model each outcome with patient risk factors and time. @@ -1567,13 +1604,6 @@ MethodsWe report the most recent findings on community infections from the REal- ResultsBetween rounds 10 and 11, prevalence of swab-positivity dropped by 50% in England from 0.20% (0.17%, 0.23%) to 0.10% (0.08%, 0.13%), with a corresponding R estimate of 0.90 (0.87, 0.94). Rates of swab-positivity fell in the 55 to 64 year old group from 0.17% (0.12%, 0.25%) in round 10 to 0.06% (0.04%, 0.11%) in round 11. Prevalence in round 11 was higher in the 25 to 34 year old group at 0.21% (0.12%, 0.38%) than in the 55 to 64 year olds and also higher in participants of Asian ethnicity at 0.31% (0.16%, 0.60%) compared with white participants at 0.09% (0.07%, 0.11%). Based on sequence data for positive samples for which a lineage could be identified, we estimate that 92.3% (75.9%, 97.9%, n=24) of infections were from the B.1.1.7 lineage compared to 7.7% (2.1%, 24.1%, n=2) from the B.1.617.2 lineage. Both samples from the B.1.617.2 lineage were detected in London from participants not reporting travel in the previous two weeks. Also, allowing for suitable lag periods, the prior close alignment between prevalence of infections and hospitalisations and deaths nationally has diverged. DiscussionWe observed marked reductions in prevalence from March to April and early May 2021 in England reflecting the success of the vaccination programme and despite easing of restrictions during lockdown. However, there is potential upwards pressure on prevalence from the further easing of lockdown regulations and presence of the B.1.617.2 lineage. If prevalence rises in the coming weeks, policy-makers will need to assess the possible impact on hospitalisations and deaths. In addition, consideration should be given to other health and economic impacts if increased levels of community transmission occur.",epidemiology,exact,100,100 -medRxiv,10.1101/2021.05.17.21257223,2021-05-17,https://medrxiv.org/cgi/content/short/2021.05.17.21257223,Serial interval of COVID-19 and the effect of Variant B.1.1.7: analyses from a prospective community cohort study (Virus Watch).,Cyril Roman Geismar; Ellen Fragaszy; Vincent Grigori Nguyen; Wing Lam Erica Fong; Madhumita Shrotri; Sarah Beale; Alison Rodger; Vasileios Lampos; Thomas Edward Byrne; Jana Kovar; Annalan Navaratnam; Parth Patel; Robert W Aldridge; Andrew Hayward; - Virus Watch Collaborative,University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ,"IntroductionIncreased transmissibility of B.1.17 variant of concern (VOC) in the UK may explain its rapid emergence and global spread. We analysed data from putative household infector - infectee pairs in the Virus Watch Community cohort study to assess the serial interval of COVID-19 and whether this was affected by emergence of the B.1.17 variant. - -MethodsThe Virus Watch study is an online, prospective, community cohort study following up entire households in England and Wales during the COVID-19 pandemic. Putative household infector-infectee pairs were identified where more than one person in the household had a positive swab matched to an illness episode. Data on whether individual infections were caused by the B.1.1.7 variant were not available. We therefore developed a classification system based on the percentage of cases estimated to be due to B.1.17 in national surveillance data for different English regions and study weeks. - -ResultsOut of 24,887 illnesses reported, 915 tested positive for SARS-CoV-2 and 186 likely infector-infectee pairs in 186 households amongst 372 individuals were identified. The mean COVID-19 serial interval was 3.18 (95%CI: 2.55 - 3.81) days. There was no significant difference (p=0.267) between the mean serial interval for Variants of Concern (VOC) hotspots (mean = 3.64 days, (95%CI: 2.55 - 4.73)) days and non-VOC hotspots, (mean = 2.72 days, (95%CI: 1.48 - 3.96)). - -ConclusionsOur estimates of the average serial interval of COVID-19 are broadly similar to estimates from previous studies and we find no evidence that B.1.1.7 is associated with a change in serial intervals. Alternative explanations such as increased viral load, longer period of viral shedding or improved receptor binding may instead explain the increased transmissibility and rapid spread and should undergo further investigation.",epidemiology,exact,100,100 medRxiv,10.1101/2021.05.06.21256757,2021-05-14,https://medrxiv.org/cgi/content/short/2021.05.06.21256757,COVID-19 outbreak rates and infection attack rates associated with the workplace: a descriptive epidemiological study,Yiqun Chen; Timothy Aldridge; - UK COVID-19 National Core Studies Consortium; Claire F Ferraro; Fu-Meng Khaw,"Health and Safety Executive, UK; Health and Safety Executive, UK; ; National Infection Service, Public Health England, UK; Public Health England, UK","BackgroundA large number of COVID-19 outbreaks/clusters have been reported in a variety of workplace settings since the start of the pandemic. However, information on the rate of outbreak occurrences which helps to identify the type of workplaces that are more likely to experience an outbreak, or infection attack rates which estimates the potential extent of the virus transmission in an outbreak, has not yet been available to inform intervention strategies to limit transmission. ObjectivesTo link datasets on workplace settings and COVID-19 workplace outbreaks in England in order to: identify the geographical areas and workplace sectors with a high rate of outbreaks; and compare infection attack rates by workplace size and sector. @@ -1970,6 +2000,21 @@ ResultsAmongst the population of 31,716 patients discharged following hospitalis InterpretationCardiometabolic and pulmonary adverse outcomes are markedly raised following hospitalisation for COVID-19 compared to the general population. However, the excess risks were more comparable to those seen following hospitalisation with pneumonia. Identifying patients at particularly high risk of outcomes would inform targeted preventive measures. FundingWellcome, Royal Society, National Institute for Health Research, National Institute for Health Research Oxford Biomedical Research Centre, UK Medical Research Council, UK Research and Innovation, Health and Safety Executive.",epidemiology,exact,100,100 +medRxiv,10.1101/2021.01.22.21249968,2021-01-25,https://medrxiv.org/cgi/content/short/2021.01.22.21249968,An external validation of the QCovid risk prediction algorithm for risk of mortality from COVID-19 in adults: national validation cohort study in England,Vahe Nafilyan; Ben Humberstone; Nisha Metha; Ian Diamond; Luke Lorenzi; Piotr Pawelek; Ryan Schofield; Jasper Morgan; Paul Brown; Ronan Lyons; Aziz Sheikh; Julia Hippisley-Cox,Office for National Statistics; Office for National Statistics; Office of the Chief Medical Officer; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Swansea University; University of Edinburgh; University of Oxford,"BackgroundTo externally validate a risk prediction algorithm (QCovid) to estimate mortality outcomes from COVID-19 in adults in England. + +MethodsPopulation-based cohort study using the ONS Public Health Linked Data Asset, a cohort based on the 2011 Census linked to Hospital Episode Statistics, the General Practice Extraction Service Data for pandemic planning and research, radiotherapy and systemic chemotherapy records. The primary outcome was time to COVID-19 death, defined as confirmed or suspected COVID-19 death as per death certification. Two time periods were used: (a) 24th January to 30th April 2020; and (b) 1st May to 28th July 2020. We evaluated the performance of the QCovid algorithms using measures of discrimination and calibration for each validation time period. + +FindingsThe study comprises 34,897,648 adults aged 19-100 years resident in England. There were 26,985 COVID-19 deaths during the first time-period and 13,177 during the second. The algorithms had good calibration in the validation cohort in both time periods with close correspondence of observed and predicted risks. They explained 77.1% (95% CI: 76.9% to 77.4%) of the variation in time to death in men in the first time-period (R2); the D statistic was 3.76 (95% CI: 3.73 to 3.79); Harrells C was 0.935 (0.933 to 0.937). Similar results were obtained for women, and in the second time-period. In the top 5% of patients with the highest predicted risks of death, the sensitivity for identifying deaths in the first time period was 65.9% for men and 71.7% for women. People in the top 20% of predicted risks of death accounted for 90.8% of all COVID-19 deaths for men and 93.0% for women. + +InterpretationThe QCovid population-based risk algorithm performed well, showing very high levels of discrimination for COVID-19 deaths in men and women for both time periods. It has the potential to be dynamically updated as the pandemic evolves and therefore, has potential use in guiding national policy. + +FundingNational Institute of Health Research + +RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSPublic policy measures and clinical risk assessment relevant to COVID-19 need to be aided by rigorously developed and validated risk prediction models. A recent living systematic review of published risk prediction models for COVID-19 found most models are subject to a high risk of bias with optimistic reported performance, raising concern that these models may be unreliable when applied in practice. A population-based risk prediction model, QCovid risk prediction algorithm, has recently been developed to identify adults at high risk of serious COVID-19 outcomes, which overcome many of the limitations of previous tools. + +Added value of this studyCommissioned by the Chief Medical Officer for England, we validated the novel clinical risk prediction model (QCovid) to identify risks of short-term severe outcomes due to COVID-19. We used national linked datasets from general practice, death registry and hospital episode data for a population-representative sample of over 34 million adults. The risk models have excellent discrimination in men and women (Harrells C statistic>0.9) and are well calibrated. QCovid represents a new, evidence-based opportunity for population risk-stratification. + +Implications of all the available evidenceQCovid has the potential to support public health policy, from enabling shared decision making between clinicians and patients in relation to health and work risks, to targeted recruitment for clinical trials, and prioritisation of vaccination, for example.",public and global health,exact,100,100 medRxiv,10.1101/2021.01.15.21249756,2021-01-20,https://medrxiv.org/cgi/content/short/2021.01.15.21249756,Factors associated with deaths due to COVID-19 versus other causes: population-based cohort analysis of UK primary care data and linked national death registrations within the OpenSAFELY platform,Krishnan Bhaskaran; Sebastian CJ Bacon; Stephen JW Evans; Chris J Bates; Christopher T Rentsch; MacKenna Brian; Laurie Tomlinson; Alex J Walker; Anna Schultze; Caroline E Morton; Daniel Grint; Amir Mehrkar; Rosalind M Eggo; Peter Inglesby; Ian J Douglas; Helen I McDonald; Jonathan Cockburn; Elizabeth J Williamson; David Evans; Helen J Curtis; William J Hulme; John Parry; Frank Hester; Sam Harper; David Spiegelhalter; Liam Smeeth; Ben Goldacre,"London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene Tropical Medicine; The Phoenix Partnership; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; The Phoenix Partnership; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; The Phoenix Partnership; The Phoenix Partnership; Winton Centre for Risk and Evidence Communication, Centre for Mathematical Sciences, University of Cambridge; London School of Hygiene and Tropical Medicine; University of Oxford","BackgroundMortality from COVID-19 shows a strong relationship with age and pre-existing medical conditions, as does mortality from other causes. However it is unclear how specific factors are differentially associated with COVID-19 mortality as compared to mortality from other causes. MethodsWorking on behalf of NHS England, we carried out a cohort study within the OpenSAFELY platform. Primary care data from England were linked to national death registrations. We included all adults (aged [≥]18 years) in the database on 1st February 2020 and with >1 year of continuous prior registration, the cut-off date for deaths was 9th November 2020. Associations between individual-level characteristics and COVID-19 and non-COVID deaths were estimated by fitting age- and sex-adjusted logistic models for these two outcomes. @@ -2180,6 +2225,21 @@ medRxiv,10.1101/2020.10.25.20219048,2020-10-27,https://medrxiv.org/cgi/content/s IMPACT STATEMENTCt values from SARS-CoV-2 RT-PCR tests vary widely and over calendar time. They have the potential to be used more broadly in public testing programmes as an ""early-warning"" system for shifts in infectious load and hence transmission.",infectious diseases,exact,100,100 medRxiv,10.1101/2020.10.25.20219071,2020-10-27,https://medrxiv.org/cgi/content/short/2020.10.25.20219071,"Causes of death in mental health service users during the first wave of the COVID-19 pandemic: South London and Maudsley data from March to June 2020, compared with 2015-2019.",Robert Stewart; Amelia Jewell; Matthew Broadbent; Ioannis Bakolis; Jayati Das-Munshi,"King's College London; South London and Maudsley NHS Foundation Trust, London, UK; South London and Maudsley NHS Foundation Trust, London, UK; King's College London, London, UK; King's College London, London, UK","The COVID-19 pandemic is likely to have had a particularly high impact on the health and wellbeing of people with pre-existing mental disorders. This may include higher than expected mortality rates due to severe infections themselves, due to other comorbidities, or through increased suicide rates during lockdown. However, there has been very little published information to date on causes of death in mental health service users. Taking advantage of a large mental healthcare database linked to death registrations, we describe numbers of deaths within specific underlying-cause-of-death groups for the period from 1st March to 30th June in 2020 and compare these with the same four-month periods in 2015-2019. In past and current service users, there were 2561 deaths in March-June 2020, compared to an average of 1452 for the same months in 2015-19: an excess of 1109. The 708 deaths with COVID-19 as the underlying cause in 2020 accounted for 63.8% of that excess. The remaining excess was accounted for by unnatural/unexplained deaths and by deaths recorded as due to neurodegenerative conditions, with no excess in those attributed to cancer, circulatory disorders, digestive disorders, respiratory disorders, or other disease codes. Of 295 unexplained deaths in 2020 with missing data on cause, 162 (54.9%) were awaiting a formal death notice (i.e. the group that included deaths awaiting a coroners inquest) - an excess of 129 compared to the average of previous years, accounting for 11.6% of the excess in total deaths.",psychiatry and clinical psychology,exact,100,100 +medRxiv,10.1101/2020.10.26.20219428,2020-10-27,https://medrxiv.org/cgi/content/short/2020.10.26.20219428,Community prevalence of SARS-CoV-2 in England during April to September 2020: Results from the ONS Coronavirus Infection Survey,Koen B Pouwels; Thomas House; Emma Pritchard; Julie V Robotham; Paul Birrell; Andrew Gelman; Karina-Doris Vihta; Nikola Bowers; Ian Boreham; Heledd Thomas; James Lewis; Iain Bell; John I Bell; John N Newton; Jeremy Farrar; Ian Diamond; Pete Benton; Ann Sarah Walker,University of Oxford; University of Manchester; University of Oxford; Public Health England; Public Health England; Columbia University; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics; Office for National Statistics; University of Oxford,"BackgroundDecisions regarding the continued need for control measures to contain the spread of SARS-CoV-2 rely on accurate and up-to-date information about the number of people and risk factors for testing positive. Existing surveillance systems are not based on population samples and are generally not longitudinal in design. + +MethodsFrom 26 April to 19 September2020, 514,794 samples from 123,497 individuals were collected from individuals aged 2 years and over from a representative sample of private households from England. Participants completed a questionnaire and nose and throat swab were taken. The percentage of individuals testing positive for SARS-CoV-2 RNA was estimated over time using dynamic multilevel regression and post-stratification, to account for potential residual non-representativeness. Potential changes in risk factors for testing positive over time were also evaluated using multilevel regression models. + +FindingsBetween 26 April and 19 September 2020, in total, results were available from 514,794 samples from 123,497 individuals, of which 489 were positive overall from 398 individuals. The percentage of people testing positive for SARS-CoV-2 changed substantially over time, with an initial decrease between end of April and June, followed by low levels during the summer, before marked increases end of August and September 2020. Having a patient-facing role and working outside your home were important risk factors for testing positive in the first period but not (yet) in the second period of increased positivity rates, and age (young adults) being an important driver of the second period of increased positivity rates. A substantial proportion of infections were in individuals not reporting symptoms (53%-70%, dependent on calendar time). + +InterpretationImportant risk factors for testing positive varied substantially between the initial and second periods of higher positivity rates, and a substantial proportion of infections were in individuals not reporting symptoms, indicating that continued monitoring for SARS-CoV-2 in the community will be important for managing the epidemic moving forwards. + +FundingThis study is funded by the Department of Health and Social Care. KBP, ASW, EP and JVR are supported by the National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford in partnership with Public Health England (PHE) (NIHR200915). AG is supported by U.S. National Institute of Health and Office of Naval Research. ASW is also supported by the NIHR Oxford Biomedical Research Centre and by core support from the Medical Research Council UK to the MRC Clinical Trials Unit [MC_UU_12023/22] and is an NIHR Senior Investigator. The views expressed are those of the authors and not necessarily those of the National Health Service, NIHR, Department of Health, or PHE. + +Research in contextO_ST_ABSEvidence before this studyC_ST_ABSUnprecedented control measures, such as national lockdowns, have been widely implemented to contain the spread of SARS-CoV-2. Decisions regarding the continued need for social distancing measures in the overall population, specific subgroups and geographic areas heavily rely on accurate and up-to-date information about the number of people and risk factors for testing positive. We searched PubMed and medRxiv and bioRxiv preprint servers up to 6 June 2020 for epidemiological studies using the terms ""SARS-CoV-2"" and ""prevalence"" or ""incidence"" without data or language restrictions. Most studies were small or had only information about current presence of the virus for a small subset of patients, or used data not representative of the community, such as hospital admissions, deaths or self-reported symptoms. Large population-based studies, such as the current study, are required to understand risk factors and the dynamics of the epidemic. + +Added value of this studyThis is the first longitudinal community survey of SARS-CoV-2 infection at national and regional levels in the UK. With more than 500,000 swabs from more than 120,000 individuals this study provides robust evidence that the percentage of individuals from the general community in England testing positive for SARS-CoV-2 clearly declined between end of April and June 2020,, followed by consistently low levels during the summer, before marked increases end of August and September 2020. Risk factors for testing positive varied substantially between the initial and second periods of higher positivity rates, with having a patient-facing role and working outside your home being important risk factors in the first period but not (yet) in the second period, and age (young adults) being an important driver of the second period of increased positivity rates. Positive tests commonly occurred without symptoms being reported. + +Implications of all the available evidenceThe observed decline in the percentage of individuals testing positive adds to the increasing body of empirical evidence and theoretical models that suggest that the lockdown imposed on 23 March 2020 in England was associated, at least temporarily, with a decrease in infections. Important risk factors for testing positive varied substantially between the initial and second periods of higher positivity rates, and a substantial proportion of infections were in individuals not reporting symptoms, indicating that continued monitoring for SARS-CoV-2 in the community will be important for managing the epidemic moving forwards.",infectious diseases,exact,100,100 medRxiv,10.1101/2020.10.26.20219550,2020-10-27,https://medrxiv.org/cgi/content/short/2020.10.26.20219550,Human movement can inform the spatial scale of interventions against COVID-19 transmission,Hamish Gibbs; Emily Nightingale; Yang Liu; James Cheshire; Leon Danon; Liam Smeeth; Carl AB Pearson; Chris Grundy; - LSHTM CMMID COVID-19 Working Group; Adam J Kucharski; Rosalind M Eggo,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University College London; University of Exeter; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; ; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine,"BackgroundIn 2020, the UK enacted an intensive, nationwide lockdown on March 23 to mitigate transmission of COVID-19. As restrictions began to ease, resurgences in transmission were targeted by geographically-limited interventions of various stringencies. Understanding the spatial scale of networks of human interaction, and how these networks change over time, is critical to inform interventions targeted at the most at-risk areas without unnecessarily restricting areas at low risk of resurgence. MethodsWe use detailed human mobility data aggregated from Facebook users to determine how the spatially-explicit network of movements changed before and during the lockdown period, in response to the easing of restrictions, and to the introduction of locally-targeted interventions. We also apply community detection techniques to the weighted, directed network of movements to identify geographically-explicit movement communities and measure the evolution of these community structures through time. @@ -2267,6 +2327,7 @@ ResultsOver the 9 days for which data are available, we find 363 positives from ConclusionRapid growth has led to high prevalence of SARS-CoV-2 virus in England among all regions and age groups, including those age groups at highest risk. Although there is evidence of a recent deceleration in the epidemic, current levels of prevalence will inevitably result in additional hospitalisations and mortality in coming weeks. A re-doubling of public health efforts is needed to return to a declining phase of the epidemic.",infectious diseases,exact,100,100 medRxiv,10.1101/2020.09.28.20202929,2020-09-29,https://medrxiv.org/cgi/content/short/2020.09.28.20202929,T cell assays differentiate clinical and subclinical SARS-CoV-2 infections from cross-reactive antiviral responses,Ane Ogbe; Barbara Kronsteiner; Donal T Skelly; Matthew Pace; Anthony Brown; Emily Adland; Kareena Adair; Hossain Delowar Akhter; Mohammad Ali; Serat-E Ali; Adrienn Angyal; M. Azim Ansari; Carolina V Arancibia-Carcamo; Helen Brown; Senthil Chinnakannan; Christopher P Conlon; Catherine de Lara; Thushan de Silva; Christina Dold; Tao Dong Dong; Timothy Donnison; David W Eyre; Amy Flaxman; Helen A Fletcher; Joshua Gardner; James T Grist; Carl-Philipp Hackstein; Kanoot Jaruthamsophon; Katie Jeffrey; Teresa Lambe; Lian Lee; Wenqin Li; Nicholas Lim; Philippa C Matthews; Alexander J Mentzer; Shona C Moore; Dean J Naisbitt; Monday Ogese; Graham Ogg; Peter Openshaw; Munir Pirmohamed; Andrew J Pollard; Narayan Ramamurthy; Patpong Rongkard; Sarah Rowland-Jones; Oliver L Sampson; Gavin Screaton; Alessandro Sette; Lizzie Stafford; Craig Thompson; Paul J Thomson; Ryan Thwaites; Vinicius Vieira; Daniela Weiskopf; Panagiota Zacharopoulou; - Oxford Immunology Network Covid-19 Response T cell Consortium; - Oxford Protective T cell Immunology for COVID-19 (OPTIC) Clinical team; Lance Turtle; Paul Klenerman; Philip Goulder; John Frater; Eleanor Barnes; Susanna Dunachie,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Liverpool; University of Oxford; University of Oxford; University of Liverpool; University of Sheffield; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Sheffield; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Liverpool; University of Oxford; University of Oxford; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Liverpool; University of Liverpool; University of Liverpool; University of Oxford; Imperial College; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; La Jolla Institute for Immunology; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Liverpool; Imperial College; University of Oxford; La Jolla Institute for Immunology; University of Oxford; ; ; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"A major issue in identification of protective T cell responses against SARS-CoV-2 lies in distinguishing people infected with SARS-CoV-2 from those with cross-reactive immunity generated by exposure to other coronaviruses. We characterised SARS-CoV-2 T cell immune responses in 168 PCR-confirmed SARS-CoV-2 infected subjects and 118 seronegative subjects without known SARS-CoV-2 exposure using a range of T cell assays that differentially capture immune cell function. Strong ex vivo ELISpot and proliferation responses to multiple antigens (including M, NP and ORF3) were found in those who had been infected by SARS-CoV-2 but were rare in pre-pandemic and unexposed seronegative subjects. However, seronegative doctors with high occupational exposure and recent COVID-19 compatible illness showed patterns of T cell responses characteristic of infection, indicating that these readouts are highly sensitive. By contrast, over 90% of convalescent or unexposed people showed proliferation and cellular lactate responses to spike subunits S1/S2, indicating pre-existing cross-reactive T cell populations. The detection of T cell responses to SARS-CoV-2 is therefore critically dependent on the choice of assay and antigen. Memory responses to specific non-spike proteins provides a method to distinguish recent infection from pre-existing immunity in exposed populations.",infectious diseases,exact,100,100 +medRxiv,10.1101/2020.09.26.20202150,2020-09-28,https://medrxiv.org/cgi/content/short/2020.09.26.20202150,Comparison of mental health service activity before and shortly after UK social distancing responses to the COVID-19 pandemic: February-March 2020,Robert Stewart; Evangelia Martin; Ioannis Bakolis; Matthew Broadbent; Nicola Byrne; Sabine Landau,King's College London; South London and Maudsley NHS Foundation Trust; King's College London; King's College London; South London and Maudsley NHS Foundation Trust; King's College London,"This study sought to provide an early description of mental health service activity before and after national implementation of social distancing for COVID-19. A time series analysis was carried out of daily service-level activity on data from a large mental healthcare provider in southeast London, from 01.02.2020 to 31.03.2020, comparing activity before and after 16.03.2020: i) inpatient admissions, discharges and numbers, ii) contact numbers and daily caseloads (Liaison, Home Treatment Teams, Community Mental Health Teams); iii) numbers of deaths for past and present patients. Daily face-to-face contact numbers fell for liaison, home treatment and community services with incomplete compensatory rises in non-face-to-face contacts. Daily caseloads fell for all services, apart from working age and child/adolescent community teams. Inpatient numbers fell 13.6% after 16th March, and daily numbers of deaths increased by 61.8%.",psychiatry and clinical psychology,exact,100,100 medRxiv,10.1101/2020.09.24.20200048,2020-09-25,https://medrxiv.org/cgi/content/short/2020.09.24.20200048,Genetic mechanisms of critical illness in Covid-19,Erola Pairo-Castineira; Sara Clohisey; Lucija Klaric; Andrew Bretherick; Konrad Rawlik; Nicholas Parkinson; Dorota Pasko; Susan Walker; Anne Richmond; Max Head Fourman; Andy Law; James Furniss; Elvina Gountouna; Nicola Wrobel; Clark D Russell; Loukas Moutsianas; Bo Wang; Alison Meynert; Zhijian Yang; Ranran Zhai; Chenqing Zheng; Fiona Griffith; Wilna Oosthuyzen; Barbara Shih; Seán Keating; Marie Zechner; Chris Haley; David J Porteous; Caroline Hayward; Julian Knight; Charlotte Summers; Manu Shankar-Hari; Lance Turtle; Antonia Ho; Charles Hinds; Peter Horby; Alistair Nichol; David Maslove; Lowell Ling; Paul Klenerman; Danny McAuley; Hugh Montgomery; Timothy Walsh; - The GenOMICC Investigators; - The ISARIC4C Investigators; - The Covid-19 Human Genetics Initiative; Xia Shen; Kathy Rowan; Angie Fawkes; Lee Murphy; Chris P Ponting; Albert Tenesa; Mark Caulfield; Richard Scott; Peter JM Openshaw; Malcolm G Semple; Veronique Vitart; James F Wilson; J Kenneth Baillie,"Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; The Roslin Institute; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England; Genomics England; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinb; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; University of Edinburgh Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh, UK; Genomics England; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.; Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.; Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Intenstive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinb; Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinb; Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.; Department of Medicine, University of Cambridge, Cambridge, UK.; Department of Intensive Care Medicine, Guy's and St. Thomas NHS Foundation Trust, London, UK; School of Immunology and Microbial Sciences, King's College London; NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, L; MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Univer; William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK.; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.; Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland; Australian and New Zealand Intensive Care Research Cen; Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, ON, Canada.; Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China.; University of Oxford; Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK; Department of Intensive Care Medicine, Royal Vi; UCL Centre for Human Health and Performance, London, W1T 7HA, UK.; Intenstive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK.; -; -; -; Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.; Intensive Care National Audit & Research Centre, London, UK.; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England; William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK; Genomics England; National Heart & Lung Institute, Imperial College London (St Mary's Campus), Norfolk Place, Paddington, London W2 1PG, UK.; University of Liverpool, Liverpool, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK; Ce; Roslin Institute, University of Edinburgh","The subset of patients who develop critical illness in Covid-19 have extensive inflammation affecting the lungs1 and are strikingly different from other patients: immunosuppressive therapy benefits critically-ill patients, but may harm some non-critical cases.2 Since susceptibility to life-threatening infections and immune-mediated diseases are both strongly heritable traits, we reasoned that host genetic variation may identify mechanistic targets for therapeutic development in Covid-19.3 GenOMICC (Genetics Of Mortality In Critical Care, genomicc.org) is a global collaborative study to understand the genetic basis of critical illness. Here we report the results of a genome-wide association study (GWAS) in 2244 critically-ill Covid-19 patients from 208 UK intensive care units (ICUs), representing >95% of all ICU beds. Ancestry-matched controls were drawn from the UK Biobank population study and results were confirmed in GWAS comparisons with two other population control groups: the 100,000 genomes project and Generation Scotland. @@ -2502,6 +2563,7 @@ MethodsWe accessed national English data on all adult COVID-19 specific critical Results30-day mortality peaked for people admitted to critical care in early April (peak 29.1% for HDU, 41.5% for ICU). There was subsequently a sustained decrease in mortality risk until the end of the study period. As a linear trend from the first week of April, adjusted mortality risk decreased by 11.2% (adjusted HR 0.89 [95% CI 0.87 - 0.91]) per week in HDU, and 9.0% (adjusted HR 0.91 [95% CI 0.88 - 0.94]) in ICU. ConclusionsThere has been a substantial mortality improvement in people admitted to critical care with COVID-19 in England, with markedly lower mortality in people admitted in mid-April and May compared to earlier in the pandemic. This trend remains after adjustment for patient demographics and comorbidities suggesting this improvement is not due to changing patient characteristics. Possible causes include the introduction of effective treatments as part of clinical trials and a falling critical care burden.",health systems and quality improvement,exact,100,100 +medRxiv,10.1101/2020.07.29.20164269,2020-07-30,https://medrxiv.org/cgi/content/short/2020.07.29.20164269,The potential health and economic impact of dexamethasone treatment for patients with COVID-19,RICARDO AGUAS; Adam Mahdi; RIMA SHRETTA; Peter Horby; Martin Landray; Lisa J White,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"Dexamethasone has been shown to reduce mortality in hospitalised COVID-19 patients needing oxygen and ventilation by 18% and 36%, respectively. Here, we estimate the potential number of lives saved and life years gained if this treatment would be rolled out in the UK and globally, as well as its cost-effectiveness of implementing this intervention. We estimate that, for the UK, approximately 12,000 [4,250 - 27,000] lives could be saved by January 2021. Assuming that dexamethasone has a similar effect size in settings where access to oxygen therapies is limited, this would translate into approximately 650,000 [240,000 - 1,400,000] lives saved globally. If dexamethasone acts differently in these settings, the impact could be less than half of this value. To estimate the full potential of dexamethasone in the global fight against COVID-19, it is essential to perform clinical research in settings with limited access to oxygen and/or ventilators, e.g. in low and middle-income countries.",epidemiology,exact,100,100 medRxiv,10.1101/2020.07.26.20161570,2020-07-28,https://medrxiv.org/cgi/content/short/2020.07.26.20161570,"Magnitude, demographics and dynamics of the impact of the first phase of the Covid-19 pandemic on all-cause mortality in 17 industrialised countries",Vasilis Kontis; James E Bennett; Theo Rashid; Robbie M Parks; Jonathan Pearson-Stuttard; Michel Guillot; Perviz Asaria; Bin Zhou; Marco Battaglini; Gianni Corsetti; Martin McKee; Mariachiara Di Cesare; Colin D Mathers; Majid Ezzati,Imperial College London; Imperial College London; Imperial College London; Columbia University; Imperial College London; University of Pennsylvania; Imperial College London; Imperial College London; Italian National Institute of Statistics; Italian National Institute of Statistics; London School of Hygiene & Tropical Medicine; Middlesex University London; Independent Researcher; Imperial College London,"The Covid-19 pandemic affects mortality directly through infection as well as through changes in the social, environmental and healthcare determinants of health1. The impacts on mortality are likely to vary across countries in magnitude, timing, and age and sex composition. Here, we applied an ensemble of 16 Bayesian probabilistic models to vital statistics data, by age group and sex, to consistently and comparably estimate the impacts of the first phase of the pandemic on all-cause mortality for 17 industrialised countries. The models accounted for factors that affect death rates including seasonality, temperature, and public holidays, as well as for medium-long-term secular trends and the dependency of death rates in each week on those in preceding week(s). From mid-February through the end of May 2020, an estimated 202,900 (95% credible interval 179,400-224,900) more people died in these 17 countries than would have had the pandemic not taken place. Nearly three quarters of these excess deaths occurred in England and Wales, Italy and Spain, where less than half of the total population of these countries live. When all-cause mortality is considered, the total number of deaths, deaths per 100,000 people, and relative increase in deaths were similar between men and women in most countries. Further, in many countries, the balance of excess deaths changed from male-dominated early in the pandemic to being equal or female-dominated later on. Taken over the entire first phase of the pandemic, there was no detectable rise in all-cause mortality in New Zealand, Bulgaria, Hungary, Norway, Denmark and Finland and for women in Austria and Switzerland (posterior probability of an increase in deaths <90%). Women in Portugal and men in Austria experienced relatively small increases in all-cause mortality, with posterior probabilities of 90-99%. For men in Switzerland and Portugal, and both sexes in the Netherlands, France, Sweden, Belgium, Italy, Scotland, Spain and England and Wales, all-cause mortality increased as a result of the pandemic with a posterior probability >99%. After accounting for population size, England and Wales and Spain experienced the highest death toll, nearly 100 deaths per 100,000 people; they also had the largest relative (percent) increase in deaths (37% (95% credible interval 30-44) in England and Wales; 38% (31-44) in Spain). New Zealand, Bulgaria, Hungary, Norway, Denmark and Finland experienced changes in deaths that ranged from possible slight declines to increases of no more than 5%. The large impact in England and Wales stems partly from having experienced (together with Spain) the highest weekly increases in deaths, more than doubling in some weeks, and having had (together with Sweden) the longest duration when deaths exceeded levels that would be expected in the absence of the pandemic. @@ -2767,15 +2829,6 @@ Key pointsO_ST_ABSQuestionC_ST_ABSWhat is the evidence on the susceptibility and FindingsIn this systematic review and meta-analysis, children and young people under 18-20 years had an 435 lower odds of secondary infection of with SARS-CoV-2 compared to adults 20 years plus, a significant difference. This finding was most marked in children under 12-14 years. Data were insufficient to conclude whether transmission of SARS-CoV-2 by children is lower than by adults. MeaningWe found preliminary evidence that children have a lower susceptibility for SARS-CoV-2 infection compared with adults, although data for adolescents is less clear. The role that children and young people play in transmission of this pandemic remains unclear.",public and global health,exact,100,100 -medRxiv,10.1101/2020.05.20.20108183,2020-05-23,https://medrxiv.org/cgi/content/short/2020.05.20.20108183,A Rapid Review of the Asymptomatic Proportion of PCR-Confirmed SARS-CoV-2 Infections in Community Settings,Sarah Beale; Andrew Hayward; Laura Shallcross; Robert W Aldridge; Ellen Fragaszy,University College London; University College London; University College London; University College London; University College London,"BackgroundUp to 80% of active SARS-CoV-2 infections are proposed to be asymptomatic based on cross-sectional studies. However, accurate estimates of the asymptomatic proportion require systematic detection and follow-up to differentiate between truly asymptomatic and pre-symptomatic cases. We conducted a rapid review and meta-analysis of current evidence regarding the asymptomatic proportion of PCR-confirmed SARS-CoV-2 infections based on methodologically-appropriate studies in community settings. - -MethodsWe searched Medline and EMBASE for peer-reviewed articles, and BioRxiv and MedRxiv for pre-prints published prior to 05/05/2020. We included studies based in community settings that involved systematic PCR testing on participants and follow-up symptom monitoring regardless of symptom status. We extracted data on study characteristics, frequencies of PCR-confirmed infections by symptom status, and (if available) cycle threshold values and/or duration of viral shedding by symptom status. We computed estimates of the asymptomatic proportion and 95% confidence intervals for each study and overall using random effect meta-analysis. - -FindingsWe screened 270 studies and included 6. The pooled estimate for the asymptomatic proportion of SARS-CoV-2 infections was 11% (95% CI 4%-18%). Estimates of baseline viral load appeared to be similar for asymptomatic and symptomatic cases based on available data in three studies, though detailed reporting of cycle threshold values and natural history of viral shedding by symptom status was limited. - -InterpretationThe asymptomatic proportion of SARS-CoV-2 infections is relatively low when estimated from methodologically-appropriate studies. Further investigation into the degree and duration of infectiousness for asymptomatic infections is warranted. - -FundingMedical Research Council",infectious diseases,exact,100,100 medRxiv,10.1101/2020.05.18.20086157,2020-05-22,https://medrxiv.org/cgi/content/short/2020.05.18.20086157,COVID-19 in Great Britain: epidemiological and clinical characteristics of the first few hundred (FF100) cases: a descriptive case series and case control analysis,Nicola L Boddington; Andre Charlett; Suzanne Elgohari; Jemma L Walker; Helen Mcdonald; Chloe Byers; Laura Coughlan; Tatiana Garcia Vilaplana; Rosie Whillock; Mary Sinnathamby; Nikolaos Panagiotopoulos; Louise Letley; Pauline MacDonald; Roberto Vivancos; Obaghe Edeghere; Joseph Shingleton; Emma Bennett; Daniel J Grint; Helen Strongman; Kathryn E Mansfield; Christopher Rentsch; Caroline Minassian; Ian J Douglas; Rohini Mathur; Maria Peppa; Simon Cottrell; Jim McMenamin; Maria Zambon; Mary Ramsay; Gavin Dabrera; Vanessa Saliba; Jamie Lopez Bernal,Public Health England; Public Health England; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health Wales; Public Health Scotland; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England,"ObjectivesFollowing detection of the first virologically-confirmed cases of COVID-19 in Great Britain, an enhanced surveillance study was initiated by Public Health England to describe the clinical presentation, course of disease and underlying health conditions associated with infection of the first few hundred cases. MethodsInformation was collected on the first COVID-19 cases according to the First Few X WHO protocol. Case-control analyses of the sensitivity, specificity and predictive value of symptoms and underlying health conditions associated with infection were conducted. Point prevalences of underlying health conditions among the UK general population were presented. @@ -2942,6 +2995,31 @@ medRxiv,10.1101/2020.04.07.20056788,2020-04-11,https://medrxiv.org/cgi/content/s Methods and ResultsWe evaluated this hypothesis in a consecutive cohort of 1200 acute inpatients with COVID19 at two hospitals with a multi-ethnic catchment population in London (UK). The mean age was 68{+/-}17 years (57% male) and 74% of patients had at least 1 comorbidity. 415 patients (34.6%) reached the primary endpoint of death or transfer to a critical care unit for organ support within 21-days of symptom onset. 399 patients (33.3 %) were taking ACEi or ARB. Patients on ACEi/ARB were significantly older and had more comorbidities. The odds ratio (OR) for the primary endpoint in patients on ACEi and ARB, after adjustment for age, sex and co-morbidities, was 0.63 (CI 0.47-0.84, p<0.01). ConclusionsThere was no evidence for increased severity of COVID19 disease in hospitalised patients on chronic treatment with ACEi or ARB. A trend towards a beneficial effect of ACEi/ARB requires further evaluation in larger meta-analyses and randomised clinical trials.",infectious diseases,exact,100,100 +medRxiv,10.1101/2020.04.05.20048421,2020-04-07,https://medrxiv.org/cgi/content/short/2020.04.05.20048421,Loss of smell and taste in combination with other symptoms is a strong predictor of COVID-19 infection,Cristina Menni; Ana Valdes; Maxim B Freydin; Sajaysurya Ganesh; Julia El-Sayed Moustafa; Alessia Visconti; Pirro Hysi; Ruth C E Bowyer; Massimo Mangino; Mario Falchi; Jonathan Wolf; Claire Steves; Tim Spector,"King's College London; NIHR Nottingham Biomedical Research Centre, School of Medicine, University of Nottingham; King's College London; Zoe Global limited; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; King's College London; King's College London","ImportanceA strategy for preventing further spread of the ongoing COVID-19 epidemic is to detect infections and isolate infected individuals without the need of extensive bio-specimen testing. + +ObjectivesHere we investigate the prevalence of loss of smell and taste among COVID-19 diagnosed individuals and we identify the combination of symptoms, besides loss of smell and taste, most likely to correspond to a positive COVID-19 diagnosis in non-severe cases. + +DesignCommunity survey. + +Setting and ParticipantsSubscribers of RADAR COVID-19, an app that was launched for use among the UK general population asking about COVID-19 symptoms. + +Main ExposureLoss of smell and taste. + +Main Outcome MeasuresCOVID-19. + +ResultsBetween 24 and 29 March 2020, 1,573,103 individuals reported their symptoms via the app; 26% reported suffering from one or more symptoms of COVID-19. Of those, n=1702 reported having had a RT-PCR COVID-19 test and gave full report on symptoms including loss of smell and taste; 579 were positive and 1123 negative. In this subset, we find that loss of smell and taste were present in 59% of COVID-19 positive individuals compared to 18% of those negative to the test, yielding an odds ratio (OR) of COVID-19 diagnosis of OR[95%CI]=6.59[5.25; 8.27], P= 1.90x10-59. We also find that a combination of loss of smell and taste, fever, persistent cough, fatigue, diarrhoea, abdominal pain and loss of appetite is predictive of COVID-19 positive test with sensitivity 0.54[0.44; 0.63], specificity 0.86[0.80; 0.90], ROC-AUC 0.77[0.72; 0.82] in the test set, and cross-validation ROC-AUC 0.75[0.72; 0.77]. When applied to the 410,598 individuals reporting symptoms but not formally tested, our model predicted that 13.06%[12.97%;13.15] of these might have been already infected by the virus. + +Conclusions and RelevanceOur study suggests that loss of taste and smell is a strong predictor of having been infected by the COVID-19 virus. Also, the combination of symptoms that could be used to identify and isolate individuals includes anosmia, fever, persistent cough, diarrhoea, fatigue, abdominal pain and loss of appetite. This is particularly relevant to healthcare and other key workers in constant contact with the public who have not yet been tested for COVID-19. + +Key pointsO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIThe spread of COVID-19 can be reduced by identifying and isolating infected individuals but it is not possible to test everyone and priority has been given in most countries to individuals presenting symptoms of the disease. +C_LIO_LICOVID-19 symptoms, such as fever, cough, aches, fatigue are common in many other viral infections +C_LIO_LIThere is therefore a need to identify symptom combinations that can rightly pinpoint to infected individuals +C_LI + +What this study addsO_LIAmong individuals showing symptoms severe enough to be given a COVID-19 RT-PCR test in the UK the prevalence of loss of smell (anosmia) was 3-fold higher (59%) in those positive to the test than among those negative to the test (18%). +C_LIO_LIWe developed a mathematical model combining symptoms to predict individuals likely to be COVID-19 positive and applied this to over 400,000 individuals in the general population presenting some of the COVID-19 symptoms. +C_LIO_LIWe find that [~]13% of those presenting symptoms are likely to have or have had a COVID-19 infection. The proportion was slightly higher in women than in men but is comparable in all age groups, and corresponds to 3.4% of those who filled the app report. +C_LI",epidemiology,exact,100,100 medRxiv,10.1101/2020.04.02.20051284,2020-04-06,https://medrxiv.org/cgi/content/short/2020.04.02.20051284,Building an International Consortium for Tracking Coronavirus Health Status,Eran Segal; Feng Zhang; Xihong Lin; Gary King; Ophir Shalem; Smadar Shilo; William E. Allen; Yonatan H. Grad; Casey S. Greene; Faisal Alquaddoomi; Simon Anders; Ran Balicer; Tal Bauman; Ximena Bonilla; Gisel Booman; Andrew T. Chan; Ori Ori Cohen; Silvano Coletti; Natalie Davidson; Yuval Dor; David A. Drew; Olivier Elemento; Georgina Evans; Phil Ewels; Joshua Gale; Amir Gavrieli; Benjamin Geiger; Iman Hajirasouliha; Roman Jerala; Andre Kahles; Olli Kallioniemi; Ayya Keshet; Gregory Landua; Tomer Meir; Aline Muller; Long H. Nguyen; Matej Oresic; Svetlana Ovchinnikova; Hedi Peterson; Jay Rajagopal; Gunnar Ratsch; Hagai Rossman; Johan Rung; Andrea Sboner; Alexandros Sigaras; Tim Spector; Ron Steinherz; Irene Stevens; Jaak Vilo; Paul Wilmes; CCC (Coronavirus Census Collective),"Weizmann Institute of Science; Howard Hughes Medical Institute, Core Member, Broad Institute of MIT and Harvard, United States; Departments of Biostatistics and Statistics, Harvard T.H. Chan School of Public Health; Albert J. Weatherhead III University, Institute for Quantitative Social Science, Harvard University; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Society of Fellows, Harvard University, United States; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, United States; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, United States; ETH Zurich, NEXUS Personalized Health Technologies, Zurich, Switzerland; Center for Molecular Biology (ZMBH), University of Heidelberg, Germany; Clalit Research Institute, Clalit Health Services, Israel; Mapping and Geo-Information Engineering, Civil and Environmental Engineering Faculty, The Technion, Israel; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; Regen Network, Argentina; Massachusetts General Hospital (MGH), United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Chelonia Applied Science, Switzerland; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; School of Medicine-IMRIC-Developmental Biology and Cancer Research, The Hebrew University; Massachusetts General Hospital (MGH), United States; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Institute for Quantitative Social Science, Harvard University; Science for Life Laboratory (SciLifeLab), Department of Biochemistry and Biophysics, Stockholm University, Sweden; symptometrics.org; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Department of immunology, Weizmann Institute of Science, Israel; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Department of Synthetic biology and Immunology, National Institute of Chemistry, Slovenia; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; Science for Life Laboratory (SciLifeLab), Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Regen Network, United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Luxembourg Institute of Socio-Economic Research and University of Luxembourg, Luxembourg; Massachusetts General Hospital (MGH), United States; School of Medical Sciences, Orebro University, Orebro, Sweden, and Turku Bioscience Centre, University of Turku and Abo Akademi University, Turku, Finland; Center for Molecular Biology (ZMBH), University of Heidelberg, Germany; Institute of Computer Science, University of Tartu, Estonia, Estonia; Internal Medicine, Harvard Medical School, Department of Pulmonary Medicine and Critical Care, Massachusetts General Hospital (MGH), United States; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich a; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Science for Life Laboratory (SciLifeLab), Department of Immunology, Genetics and Pathology, Uppsala university, Sweden; Englander Institute for Precision Medicine and Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, USA; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Kings College, United Kingdom; Regen Network, United States; Science for Life Laboratory (SciLifeLab), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Sweden; Institute of Computer Science, University of Tartu, Estonia, Estonia; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg; ","Information is the most potent protective weapon we have to combat a pandemic, at both the individual and global level. For individuals, information can help us make personal decisions and provide a sense of security. For the global community, information can inform policy decisions and offer critical insights into the epidemic of COVID-19 disease. Fully leveraging the power of information, however, requires large amounts of data and access to it. To achieve this, we are making steps to form an international consortium, Coronavirus Census Collective (CCC, coronaviruscensuscollective.org), that will serve as a hub for integrating information from multiple data sources that can be utilized to understand, monitor, predict, and combat global pandemics. These sources may include self-reported health status through surveys (including mobile apps), results of diagnostic laboratory tests, and other static and real-time geospatial data. This collective effort to track and share information will be invaluable in predicting hotspots of disease outbreak, identifying which factors control the rate of spreading, informing immediate policy decisions, evaluating the effectiveness of measures taken by health organizations on pandemic control, and providing critical insight on the etiology of COVID-19. It will also help individuals stay informed on this rapidly evolving situation and contribute to other global efforts to slow the spread of disease. In the past few weeks, several initiatives across the globe have surfaced to use daily self-reported symptoms as a means to track disease spread, predict outbreak locations, guide population measures and help in the allocation of healthcare resources. The aim of this paper is to put out a call to standardize these efforts and spark a collaborative effort to maximize the global gain while protecting participant privacy.",infectious diseases,exact,100,100 diff --git a/data/covid/preprints.exact.json b/data/covid/preprints.exact.json index 93182bc4..c7d3f4ec 100644 --- a/data/covid/preprints.exact.json +++ b/data/covid/preprints.exact.json @@ -139,6 +139,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.10.11.23296866", + "date": "2023-10-12", + "link": "https://medrxiv.org/cgi/content/short/2023.10.11.23296866", + "title": "SARS-CoV-2, influenza A/B and respiratory syncytial virus positivity and association with influenza-like illness and self-reported symptoms, over the 2022/23 winter season in the UK: a longitudinal surveillance cohort", + "authors": "Elisabeth Dietz; Emma Elizabeth Pritchard; Koen Pouwels; Muhammad Ehsaan; Joshua Blake; Charlotte Gaughan; Eric Haduli; Hugh Boothe; Karina-Doris Vihta; Tim Peto; Nicole Stoesser; Philippa Matthews; Nick Taylor; Ian Diamond; Ruth Studley; Emma Rourke; Paul Birrell; Daniela De Angelis; Tom Fowler; Conall Watson; David W Eyre; Thomas House; Ann Sarah Walker", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; Berkshire and Surrey Pathology Services; University of Cambridge; Office of National Statistics; Berkshire and Surrey Pathology Services; Berkshire and Surrey Pathology Services; University of Oxford; University of Oxford; University of Oxford; The Francis Crick Institute; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Cambridge; University of Cambridge; UK Health Security Agency; UK Health Security Agency; University of Oxford; University of Manchester; University of Oxford", + "abstract": "BackgroundSyndromic surveillance often relies on patients presenting to healthcare. Community cohorts, although more challenging to recruit, could provide additional population-wide insights, particularly with SARS-CoV-2 co-circulating with other respiratory viruses.\n\nMethodsWe estimated positivity and incidence of SARS-CoV-2, influenza A/B, and RSV, and trends in self-reported symptoms including influenza-like illness (ILI), over the 2022/23 winter season in a broadly representative UK community cohort (COVID-19 Infection Survey), using negative-binomial generalised additive models. We estimated associations between test positivity and each of symptoms and influenza vaccination, using adjusted logistic and multinomial models.\n\nFindingsSwabs taken at 32,937/1,352,979 (2.4%) assessments tested positive for SARS-CoV-2, 181/14,939 (1.2%) for RSV and 130/14,939 (0.9%) for influenza A/B, varying by age over time. Positivity and incidence peaks were earliest for RSV, then influenza A/B, then SARS-CoV-2, and were highest for RSV in the youngest and for SARS-CoV-2 in the oldest age-groups. Many test-positives did not report key symptoms: middle-aged participants were generally more symptomatic than older or younger participants, but still only [~]25% reported ILI-WHO and [~]60% ILI-ECDC. Most symptomatic participants did not test positive for any of the three viruses. Influenza A/B-positivity was lower in participants reporting influenza vaccination in the current and previous seasons (odds ratio=0.55 (95% CI 0.32,0.95)) versus neither season.\n\nInterpretationSymptom profiles varied little by aetiology, making distinguishing SARS-CoV-2, influenza and RSV using symptoms challenging. Most symptoms were not explained by these viruses, indicating the importance of other pathogens in syndromic surveillance. Influenza vaccination was associated with lower rates of community influenza test positivity.\n\nFundingUK Health Security Agency, Department of Health and Social Care, National Institute for Health Research.", + "category": "respiratory medicine", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.08.25.23294609", @@ -349,20 +363,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.03.24.23287700", - "date": "2023-03-26", - "link": "https://medrxiv.org/cgi/content/short/2023.03.24.23287700", - "title": "The potential contribution of vaccination uptake to occupational differences in risk of SARS-CoV-2: Analysis of the ONS COVID-19 Infection Survey", - "authors": "Jack D Wilkinson; Evangelia Demou; Mark Cherrie; Rhiannon Edge; Matthew Gittins; Srinivasa Vittal Katikireddi; Theocharis Kromydas; WIll Mueller; Neil Pearce; Martie van Tongeren; Sarah Rhodes", - "affiliations": "University of Manchester; University of Glasgow; Institute of Occupational Medicine; University of Lancaster; University of Manchester; University of Glasgow; University of Glasgow; Institute for Occupational Medicine; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester", - "abstract": "ObjectivesTo assess variation in vaccination uptake across occupational groups as a potential explanation for variation in risk of SARS-CoV-2 infection.\n\nDesignWe analysed data from the UK Office of National Statistics COVID-19 Infection Survey linked to vaccination data from the National Immunisation Management System in England from December 1st 2020 to 11th May 2022. We analysed vaccination uptake and SARS-CoV-2 infection risk by occupational group and assessed whether adjustment for vaccination reduced the variation in risk between occupational groups.\n\nSetting\n\nResultsEstimated rates of triple-vaccination were high across all occupational groups (80% or above), but were lowest for food processing (80%), personal care (82%), hospitality (83%), manual occupations (84%), and retail (85%). High rates were observed for individuals working in health (95% for office-based, 92% for those in patient-facing roles) and education (91%) and office-based workers not included in other categories (90%). The impact of adjusting for vaccination when estimating relative risks of infection was generally modest (ratio of hazard ratios reduced from 1.38 to 1.32), but was consistent with the hypothesis that low vaccination rates contribute to elevated risk in some groups. Conversely, estimated relative risk for some occupational groups, such as people working in education, remained high despite high vaccine coverage.\n\nConclusionsVariation in vaccination coverage might account for a modest proportion of occupational differences in infection risk. Vaccination rates were uniformly very high in this cohort, which may suggest that the participants are not representative of the general population. Accordingly, these results should be considered tentative pending the accumulation of additional evidence.", - "category": "occupational and environmental health", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.03.24.23287666", @@ -433,6 +433,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.03.01.23286624", + "date": "2023-03-03", + "link": "https://medrxiv.org/cgi/content/short/2023.03.01.23286624", + "title": "Risk of cardiovascular events following COVID-19 in people with and without pre-existing chronic respiratory disease", + "authors": "Hannah Whittaker; Costantinos Kallis; Angela Wood; Thomas Bolton; Samantha Walker; Aziz Sheikh; Alex Brownrigg; Ashley Akbari; Kamil Sterniczuk; Jennifer K Quint", + "affiliations": "Imperial College London; Imperial College London; Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, United Kingdom; Health Data Research UK; Asthm + Lung; The University of Edinburgh College of Medicine and Veterinary Medicine; Health Data Research UK BREATHE; Swansea University; Health Data Research UK BREATHE; Imperial College London", + "abstract": "BackgroundCOVID-19 is associated with a higher risk of cardiovascular outcomes in the general population, but it is unknown whether people with pre-existing chronic respiratory disease (CRD) have a higher risk of cardiovascular events post-COVID-19 compared with the general population and, if so, what respiratory-related risk factors may modify this risk in these people.\n\nMethodsPrimary and secondary care data from the National Health Service and COVID-19-specific linked data were used to define a population of adults in England with COVID-19 (index date) between 01/01/2020-30/11/2021. Adjusted Cox Proportional Hazard regression was used to quantify the association between CRD, asthma-related factors, COPD-related factors, and risk of cardiovascular events. CRD included asthma, COPD, bronchiectasis, cystic fibrosis, or pulmonary fibrosis prior to COVID-19 diagnosis. Asthma-specific factors included baseline asthma control, exacerbations, and inhaled corticosteroid (ICS) dose. COPD-specific risk factors included baseline ICS prescriptions and exacerbations. Secondary objectives quantified the impact of COVID-19 hospitalisation and vaccine dose on cardiovascular outcomes.\n\nResultsOf 3,670,455 people, those with CRD had a modest higher risk of cardiovascular events (HRadj 1.11, 95%CI 1.07-1.14), heart failure (HRadj 1.15, 1.09-1.21), and pulmonary emboli (HRadj 1.20, 1.11-1.30) compared with people without CRD. In people with asthma, baseline exacerbations and high-dose ICS were associated with a higher risk of cardiovascular outcomes (HRadj 1.24, 1.15-1.34 and 1.12, 1.01-1.24, respectively). In people with COPD, exacerbations were associated with a higher risk of cardiovascular outcomes (HRadj 1.40, 1.28-1.52). Regardless of CRD, the risk of cardiovascular events was lower with increasing COVID-19 vaccine dose.\n\nConclusionsHigher risk of cardiovascular events following COVID-19 might be explained at least in part by the underlying CRD and severity of that condition. In addition, COVID-19 vaccines were beneficial to both people with and without CRD with regards to CV events.\n\nKey MessagesPre-existing chronic respiratory disease, asthma and COPD severity were associated with a higher risk of various types of cardiovascular outcomes following COVID-19. Regardless of having pre-existing chronic respiratory disease, COVID-19 vaccination reduced the risk of cardiovascular events following COVID-19.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.02.17.23286079", @@ -755,6 +769,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.09.14.22279931", + "date": "2022-09-15", + "link": "https://medrxiv.org/cgi/content/short/2022.09.14.22279931", + "title": "Detecting changes in population trends in infection surveillance using community SARS-CoV-2 prevalence as an exemplar", + "authors": "Emma Elizabeth Pritchard; Karina-Doris Vihta; David W Eyre; Susan Hopkins; Tim EA Peto; Philippa C Matthews; Nicole Stoesser; Ruth Studley; Emma Rourke; Ian Diamond; Koen B Pouwels; Ann Sarah Walker", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; UK Health Security Agency; University of Oxford; The Francis Crick Institute, London; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; University of Oxford", + "abstract": "BackgroundMonitoring infection trends is vital to informing public health strategy. Detecting and quantifying changes in growth rates can inform policymakers rationale for implementing or continuing interventions aimed at reducing impact. Substantial changes in SARS-CoV-2 prevalence with emergence of variants provides opportunity to investigate different methods to do this.\n\nMethodsWe included PCR results from all participants in the UKs COVID-19 Infection Survey between 1 August 2020-30 June 2022. Change-points for growth rates were identified using iterative sequential regression (ISR) and second derivatives of generalised additive models (GAMs).\n\nConsistency between methods and timeliness of detection were compared.\n\nFindingsOf 8,799,079 visits, 147,278 (1{middle dot}7%) were PCR-positive. Over the time period, change-points associated with emergence of major variants were estimated to occur a median 4 days earlier (IQR 0-8) in GAMs versus ISR, with only 2/48 change-points identified by only one method. Estimating recent change-points using successive data periods, four change-points (4/96) identified by GAMs were not found when adding later data or by ISR; 77% (74/96) of change-points identified by successive GAMs were identified by ISR. Change-points were detected 3-5 weeks after they occurred in both methods but could be detected earlier within specific subgroups.\n\nInterpretationChange-points in growth rates of SARS-CoV-2 can be detected in near real-time using ISR and second derivatives of GAMs. To increase certainty about changes in epidemic trajectories both methods could be run in parallel. Running either method in near real-time on different infection surveillance data streams could provide timely warnings of changing underlying epidemiology.\n\nFundingUK Health Security Agency, Department of Health and Social Care (UK), Welsh Government, Department of Health (on behalf of the Northern Ireland Government), Scottish Government, National Institute for Health Research.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.09.11.22279823", @@ -923,20 +951,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.06.20.22275994", - "date": "2022-06-20", - "link": "https://medrxiv.org/cgi/content/short/2022.06.20.22275994", - "title": "Characterising patterns of COVID-19 and long COVID symptoms: Evidence from nine UK longitudinal studies", - "authors": "Ruth C E Bowyer; Charlotte Huggins; Renin Toms; Richard John Shaw; Bo Hou; Ellen J Thompson; Alex Siu Fung Kwong; Dylan M Williams; Milla Kibble; George B Ploubidis; Nicholas J Timpson; Jonathan A C Sterne; Nishi Chaturvedi; Claire J Steves; Kate Tilling; Richard J Silverwood", - "affiliations": "King's College London; University of Edinburgh; University of Bristol; University of Glasgow; Bradford Institute for Health Research; King's College London; University of Bristol; UCL; King's College London; University College London; University of Bristol; University of Bristol; University College London; King's College London; University of Bristol; University College London", - "abstract": "Multiple studies across global populations have established the primary symptoms characterising COVID-19 (Coronavirus Disease 2019) and long COVID. However, as symptoms may also occur in the absence of COVID-19, a lack of appropriate controls has often meant that specificity of symptoms to acute COVID-19 or long COVID could not be examined. We aimed to characterise patterns of COVID-19 and long COVID symptoms across nine UK longitudinal studies, totalling over 42,000 participants. Conducting latent class analyses separately in three groups ( no COVID-19, COVID-19 in last 12 weeks, COVID-19 > 12 weeks ago), the data did not support the presence of more than two distinct symptom patterns, representing high and low symptom burden, in each group. Comparing the high symptom burden classes between the COVID-19 in last 12 weeks and no COVID-19 groups we identified symptoms characteristic of acute COVID-19, including loss of taste and smell, fatigue, cough, shortness of breath and muscle pains or aches. Comparing the high symptom burden classes between the COVID-19 > 12 weeks ago and no COVID-19 groups we identified symptoms characteristic of long COVID, including fatigue, shortness of breath, muscle pain or aches, difficulty concentrating and chest tightness. The identified symptom patterns among individuals with COVID-19 > 12 weeks ago were strongly associated with self-reported length of time unable to function as normal due to COVID-19 symptoms, suggesting that the symptom pattern identified corresponds to long COVID. Building the evidence base regarding typical long COVID symptoms will improve diagnosis of this condition and the ability to elicit underlying biological mechanisms, leading to better patient access to treatment and services.", - "category": "epidemiology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.06.18.22276437", @@ -1315,6 +1329,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.02.14.22270930", + "date": "2022-02-15", + "link": "https://medrxiv.org/cgi/content/short/2022.02.14.22270930", + "title": "Determinants of antibody responses to two doses of ChAdOx1 nCoV-19 or BNT162b2 and a subsequent booster dose of BNT162b2 or mRNA-1273: population-based cohort study (COVIDENCE UK)", + "authors": "David A Jolliffe; Sian E Faustini; Hayley Holt; Natalia Perdek; Sheena Maltby; Mohammad Talaei; Matthew Greenig; Giulia Vivaldi; Florence Tydeman; Jane Symons; Gwyneth A Davies; Ronan Lyons; Frank Kee; Aziz Sheikh; Seif O Shaheen; Alex Richter; Adrian R Martineau", + "affiliations": "Queen Mary University of London; University of Birmingham; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Jane Symons Media; Swansea University; Swansea University; Queen's University Belfast; Edinburgh University; Queen Mary University of London; University of Birminghan; Queen Mary University of London", + "abstract": "BackgroundAntibody responses to SARS-CoV-2 vaccination vary for reasons that remain poorly understood.\n\nMethodsWe tested for presence of combined IgG, IgA and IgM (IgGAM) anti-spike antibodies before and after administration of two doses of ChAdOx1 nCoV-19 (ChAdOx1, Oxford-AstraZeneca) or BNT162b2 (Pfizer-BioNTech) in UK adults participating in a population-based longitudinal study who received their first dose of vaccine from December 15, 2020 to July 10, 2021. Information on sixty-six potential sociodemographic, behavioural, clinical, pharmacological and nutritional determinants of serological response to vaccination was captured using serial online questionnaires. We used logistic regression to estimate multivariable-adjusted odds ratios (aORs) for associations between independent variables and risk of seronegativity following two vaccine doses. Participants who were seronegative after receiving two vaccine doses were offered an additional antibody test following subsequent administration of a booster dose of BNT162b2 or mRNA-1273 (Moderna) from September 23 to December 12, 2021.\n\nFindingsSerology results following two vaccine doses were available for 9,101 participants, of whom 5,770 (63.4%) received ChAdOx1 and 3,331 (36.6%) received BNT162b2. Anti-spike IgGAM was undetectable in 378 (4.2%) participants at a median of 8.6 weeks (IQR 6.4-10.7 weeks) after their second dose of vaccine. Seronegativity following two doses of SARS-CoV-2 vaccination was associated with administration of ChAdOx1 vs BNT162b2 (aOR 7.03, 95% CI 4.39-11.24), shorter interval between first and second vaccine doses (aOR 2.37, 1.06-5.26, for <6 weeks vs >10 weeks; aOR 1.59, 1.18-2.13, for 6-10 weeks vs >10 weeks), poorer self-assessed general health (aOR 3.33, 1.49-7.46, for poor vs excellent), immunodeficiencies (aOR 6.75, 2.63-17.35) and prescription of systemic immunosuppressants (aOR 3.76, 2.44-5.78). By contrast, pre-vaccination SARS-CoV-2 seropositivity (aOR 0.16, 0.04-0.70, for symptomatic seropositives vs seronegatives) and supplemental vitamin D intake (aOR 0.73, 0.53-0.99) were associated with reduced risk of post-vaccination seronegativity. 247/378 (65.3%) of participants who were seronegative after two doses of ChAdOx1 vs BNT162b2 provided a third sample at a median of 7.8 weeks (IQR 5.8-10.4) after receiving a booster dose of BNT162b2 or mRNA-1273: eight (3.2%) of them remained seronegative after three vaccine doses, all of whom either had a primary immunodeficiency or were taking systemic immunosuppressant drugs.\n\nInterpretationWe identify multiple determinants of antibody responses to two doses of ChAdOx1 or BNT162b2, many of which are potentially modifiable. Booster doses of BNT162b2 or mRNA-1273 were highly effective in achieving seroconversion in those who failed to mount antibody responses following two doses of ChAdOx1 or BNT162b2.\n\nStudy registrationhttps://clinicaltrials.gov/ct2/show/NCT04330599\n\nFundingBarts Charity, Fischer Family Trust, The Exilarchs Foundation, DSM Nutritional Products, Health Data Research UK\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, medRxiv, and Google Scholar for papers published from January 1, 2020, to February 1, 2022, using the search terms (antibody OR humoral OR serologic* OR immunogenic*) AND (SARS-CoV-2 vaccine OR ChAdOx1 or BNT162b2 coronavirus), with no language restrictions. Population-based studies investigating multiple potential determinants of vaccine immunogenicity in people with known pre-vaccination SARS-CoV-2 serostatus are lacking.\n\nAdded value of this studyThis large population-based study, conducted in a population with known pre-vaccination SARS-CoV-2 serostatus, examines a comprehensive range of potential sociodemographic, behavioural, clinical, pharmacological and nutritional determinants of antibody responses to administration of two major SARS-CoV-2 vaccines (i.e., ChAdOx1 or BNT162b2), many of which have not previously been investigated. It is also the first population-based study to characterise antibody responses to booster doses of SARS-CoV-2 vaccines in adults who were seronegative after their primary course of vaccination.\n\nImplications of all the available evidenceIncreased risk of seronegativity following two doses of SARS-CoV-2 vaccines was associated with administration of ChAdOx1 vs BNT162b2, shorter interval between first and second vaccine doses, poorer self-assessed general health, immunocompromise and SARS-CoV-2 seronegativity pre-vaccination. Regular intake of vitamin D supplements was associated with reduced risk of post-vaccination seronegativity. Randomised controlled trials are now needed to test for causality. Booster doses of BNT162b2 or mRNA-1273 were highly effective in achieving seroconversion in the majority of people who failed to mount antibody responses following a primary course of vaccination, the few exceptions being a subset of those with primary immunodeficiency or systemic immunosuppressant drugs.", + "category": "infectious diseases", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.02.10.22270799", @@ -1623,6 +1651,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.12.08.21267353", + "date": "2021-12-08", + "link": "https://medrxiv.org/cgi/content/short/2021.12.08.21267353", + "title": "The challenge of limited vaccine supplies: impact of prior infection on anti-spike IgG antibody trajectories after a single COVID-19 vaccination", + "authors": "Jia Wei; Philippa Matthews; Nicole Stoesser; Ian Diamond; Ruth Studley; Emma Rourke; Duncan Cook; John Bell; John Newton; Jeremy Farrar; Alison Howarth; Brian Marsden; Sarah Hoosdally; Yvonne Jones; David Stuart; Derrick W Crook; tim E peto; Ann Sarah Walker; David W Eyre; Koen B Pouwels; - COVID-19 Infection Survey team", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; NIHR Oxford Biomedical Research Centre; oxford university; University of Oxford; University of Oxford; University of Oxford; ", + "abstract": "Given high SARS-CoV-2 incidence, coupled with slow and inequitable vaccine roll-out, there is an urgent need for evidence to underpin optimum vaccine deployment, aiming to maximise global population immunity at speed. We evaluate whether a single vaccination in previously infected individuals generates similar initial and subsequent antibody responses to two vaccinations in those without prior infection. We compared anti-spike IgG antibody responses after a single dose of ChAdOx1, BNT162b2, or mRNA-1273 SARS-CoV-2 vaccines in the COVID-19 Infection Survey in the UK general population. In 100,849 adults who received at least one vaccination, 13,404 (13.3%) had serological and/or PCR evidence of prior infection. Prior infection significantly boosted antibody responses for all three vaccines, producing a higher peak level and longer half-life, and a response comparable to those without prior infection receiving two vaccinations. In those with prior infection, median time above the positivity threshold was estimated to last for >1 year after the first dose. Single-dose vaccination targeted to those previously infected may provide protection in populations with high rates of previous infection faced with limited vaccine supply, as an interim measure while vaccine campaigns are scaled up.", + "category": "infectious diseases", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.11.24.21266818", @@ -2463,20 +2505,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.05.17.21257223", - "date": "2021-05-17", - "link": "https://medrxiv.org/cgi/content/short/2021.05.17.21257223", - "title": "Serial interval of COVID-19 and the effect of Variant B.1.1.7: analyses from a prospective community cohort study (Virus Watch).", - "authors": "Cyril Roman Geismar; Ellen Fragaszy; Vincent Grigori Nguyen; Wing Lam Erica Fong; Madhumita Shrotri; Sarah Beale; Alison Rodger; Vasileios Lampos; Thomas Edward Byrne; Jana Kovar; Annalan Navaratnam; Parth Patel; Robert W Aldridge; Andrew Hayward; - Virus Watch Collaborative", - "affiliations": "University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ", - "abstract": "IntroductionIncreased transmissibility of B.1.17 variant of concern (VOC) in the UK may explain its rapid emergence and global spread. We analysed data from putative household infector - infectee pairs in the Virus Watch Community cohort study to assess the serial interval of COVID-19 and whether this was affected by emergence of the B.1.17 variant.\n\nMethodsThe Virus Watch study is an online, prospective, community cohort study following up entire households in England and Wales during the COVID-19 pandemic. Putative household infector-infectee pairs were identified where more than one person in the household had a positive swab matched to an illness episode. Data on whether individual infections were caused by the B.1.1.7 variant were not available. We therefore developed a classification system based on the percentage of cases estimated to be due to B.1.17 in national surveillance data for different English regions and study weeks.\n\nResultsOut of 24,887 illnesses reported, 915 tested positive for SARS-CoV-2 and 186 likely infector-infectee pairs in 186 households amongst 372 individuals were identified. The mean COVID-19 serial interval was 3.18 (95%CI: 2.55 - 3.81) days. There was no significant difference (p=0.267) between the mean serial interval for Variants of Concern (VOC) hotspots (mean = 3.64 days, (95%CI: 2.55 - 4.73)) days and non-VOC hotspots, (mean = 2.72 days, (95%CI: 1.48 - 3.96)).\n\nConclusionsOur estimates of the average serial interval of COVID-19 are broadly similar to estimates from previous studies and we find no evidence that B.1.1.7 is associated with a change in serial intervals. Alternative explanations such as increased viral load, longer period of viral shedding or improved receptor binding may instead explain the increased transmissibility and rapid spread and should undergo further investigation.", - "category": "epidemiology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.05.06.21256757", @@ -3023,6 +3051,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.01.22.21249968", + "date": "2021-01-25", + "link": "https://medrxiv.org/cgi/content/short/2021.01.22.21249968", + "title": "An external validation of the QCovid risk prediction algorithm for risk of mortality from COVID-19 in adults: national validation cohort study in England", + "authors": "Vahe Nafilyan; Ben Humberstone; Nisha Metha; Ian Diamond; Luke Lorenzi; Piotr Pawelek; Ryan Schofield; Jasper Morgan; Paul Brown; Ronan Lyons; Aziz Sheikh; Julia Hippisley-Cox", + "affiliations": "Office for National Statistics; Office for National Statistics; Office of the Chief Medical Officer; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Swansea University; University of Edinburgh; University of Oxford", + "abstract": "BackgroundTo externally validate a risk prediction algorithm (QCovid) to estimate mortality outcomes from COVID-19 in adults in England.\n\nMethodsPopulation-based cohort study using the ONS Public Health Linked Data Asset, a cohort based on the 2011 Census linked to Hospital Episode Statistics, the General Practice Extraction Service Data for pandemic planning and research, radiotherapy and systemic chemotherapy records. The primary outcome was time to COVID-19 death, defined as confirmed or suspected COVID-19 death as per death certification. Two time periods were used: (a) 24th January to 30th April 2020; and (b) 1st May to 28th July 2020. We evaluated the performance of the QCovid algorithms using measures of discrimination and calibration for each validation time period.\n\nFindingsThe study comprises 34,897,648 adults aged 19-100 years resident in England. There were 26,985 COVID-19 deaths during the first time-period and 13,177 during the second. The algorithms had good calibration in the validation cohort in both time periods with close correspondence of observed and predicted risks. They explained 77.1% (95% CI: 76.9% to 77.4%) of the variation in time to death in men in the first time-period (R2); the D statistic was 3.76 (95% CI: 3.73 to 3.79); Harrells C was 0.935 (0.933 to 0.937). Similar results were obtained for women, and in the second time-period. In the top 5% of patients with the highest predicted risks of death, the sensitivity for identifying deaths in the first time period was 65.9% for men and 71.7% for women. People in the top 20% of predicted risks of death accounted for 90.8% of all COVID-19 deaths for men and 93.0% for women.\n\nInterpretationThe QCovid population-based risk algorithm performed well, showing very high levels of discrimination for COVID-19 deaths in men and women for both time periods. It has the potential to be dynamically updated as the pandemic evolves and therefore, has potential use in guiding national policy.\n\nFundingNational Institute of Health Research\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSPublic policy measures and clinical risk assessment relevant to COVID-19 need to be aided by rigorously developed and validated risk prediction models. A recent living systematic review of published risk prediction models for COVID-19 found most models are subject to a high risk of bias with optimistic reported performance, raising concern that these models may be unreliable when applied in practice. A population-based risk prediction model, QCovid risk prediction algorithm, has recently been developed to identify adults at high risk of serious COVID-19 outcomes, which overcome many of the limitations of previous tools.\n\nAdded value of this studyCommissioned by the Chief Medical Officer for England, we validated the novel clinical risk prediction model (QCovid) to identify risks of short-term severe outcomes due to COVID-19. We used national linked datasets from general practice, death registry and hospital episode data for a population-representative sample of over 34 million adults. The risk models have excellent discrimination in men and women (Harrells C statistic>0.9) and are well calibrated. QCovid represents a new, evidence-based opportunity for population risk-stratification.\n\nImplications of all the available evidenceQCovid has the potential to support public health policy, from enabling shared decision making between clinicians and patients in relation to health and work risks, to targeted recruitment for clinical trials, and prioritisation of vaccination, for example.", + "category": "public and global health", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.01.15.21249756", @@ -3415,6 +3457,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.10.26.20219428", + "date": "2020-10-27", + "link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219428", + "title": "Community prevalence of SARS-CoV-2 in England during April to September 2020: Results from the ONS Coronavirus Infection Survey", + "authors": "Koen B Pouwels; Thomas House; Emma Pritchard; Julie V Robotham; Paul Birrell; Andrew Gelman; Karina-Doris Vihta; Nikola Bowers; Ian Boreham; Heledd Thomas; James Lewis; Iain Bell; John I Bell; John N Newton; Jeremy Farrar; Ian Diamond; Pete Benton; Ann Sarah Walker", + "affiliations": "University of Oxford; University of Manchester; University of Oxford; Public Health England; Public Health England; Columbia University; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics; Office for National Statistics; University of Oxford", + "abstract": "BackgroundDecisions regarding the continued need for control measures to contain the spread of SARS-CoV-2 rely on accurate and up-to-date information about the number of people and risk factors for testing positive. Existing surveillance systems are not based on population samples and are generally not longitudinal in design.\n\nMethodsFrom 26 April to 19 September2020, 514,794 samples from 123,497 individuals were collected from individuals aged 2 years and over from a representative sample of private households from England. Participants completed a questionnaire and nose and throat swab were taken. The percentage of individuals testing positive for SARS-CoV-2 RNA was estimated over time using dynamic multilevel regression and post-stratification, to account for potential residual non-representativeness. Potential changes in risk factors for testing positive over time were also evaluated using multilevel regression models.\n\nFindingsBetween 26 April and 19 September 2020, in total, results were available from 514,794 samples from 123,497 individuals, of which 489 were positive overall from 398 individuals. The percentage of people testing positive for SARS-CoV-2 changed substantially over time, with an initial decrease between end of April and June, followed by low levels during the summer, before marked increases end of August and September 2020. Having a patient-facing role and working outside your home were important risk factors for testing positive in the first period but not (yet) in the second period of increased positivity rates, and age (young adults) being an important driver of the second period of increased positivity rates. A substantial proportion of infections were in individuals not reporting symptoms (53%-70%, dependent on calendar time).\n\nInterpretationImportant risk factors for testing positive varied substantially between the initial and second periods of higher positivity rates, and a substantial proportion of infections were in individuals not reporting symptoms, indicating that continued monitoring for SARS-CoV-2 in the community will be important for managing the epidemic moving forwards.\n\nFundingThis study is funded by the Department of Health and Social Care. KBP, ASW, EP and JVR are supported by the National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford in partnership with Public Health England (PHE) (NIHR200915). AG is supported by U.S. National Institute of Health and Office of Naval Research. ASW is also supported by the NIHR Oxford Biomedical Research Centre and by core support from the Medical Research Council UK to the MRC Clinical Trials Unit [MC_UU_12023/22] and is an NIHR Senior Investigator. The views expressed are those of the authors and not necessarily those of the National Health Service, NIHR, Department of Health, or PHE.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSUnprecedented control measures, such as national lockdowns, have been widely implemented to contain the spread of SARS-CoV-2. Decisions regarding the continued need for social distancing measures in the overall population, specific subgroups and geographic areas heavily rely on accurate and up-to-date information about the number of people and risk factors for testing positive. We searched PubMed and medRxiv and bioRxiv preprint servers up to 6 June 2020 for epidemiological studies using the terms \"SARS-CoV-2\" and \"prevalence\" or \"incidence\" without data or language restrictions. Most studies were small or had only information about current presence of the virus for a small subset of patients, or used data not representative of the community, such as hospital admissions, deaths or self-reported symptoms. Large population-based studies, such as the current study, are required to understand risk factors and the dynamics of the epidemic.\n\nAdded value of this studyThis is the first longitudinal community survey of SARS-CoV-2 infection at national and regional levels in the UK. With more than 500,000 swabs from more than 120,000 individuals this study provides robust evidence that the percentage of individuals from the general community in England testing positive for SARS-CoV-2 clearly declined between end of April and June 2020,, followed by consistently low levels during the summer, before marked increases end of August and September 2020. Risk factors for testing positive varied substantially between the initial and second periods of higher positivity rates, with having a patient-facing role and working outside your home being important risk factors in the first period but not (yet) in the second period, and age (young adults) being an important driver of the second period of increased positivity rates. Positive tests commonly occurred without symptoms being reported.\n\nImplications of all the available evidenceThe observed decline in the percentage of individuals testing positive adds to the increasing body of empirical evidence and theoretical models that suggest that the lockdown imposed on 23 March 2020 in England was associated, at least temporarily, with a decrease in infections. Important risk factors for testing positive varied substantially between the initial and second periods of higher positivity rates, and a substantial proportion of infections were in individuals not reporting symptoms, indicating that continued monitoring for SARS-CoV-2 in the community will be important for managing the epidemic moving forwards.", + "category": "infectious diseases", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.10.26.20219550", @@ -3569,6 +3625,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.09.26.20202150", + "date": "2020-09-28", + "link": "https://medrxiv.org/cgi/content/short/2020.09.26.20202150", + "title": "Comparison of mental health service activity before and shortly after UK social distancing responses to the COVID-19 pandemic: February-March 2020", + "authors": "Robert Stewart; Evangelia Martin; Ioannis Bakolis; Matthew Broadbent; Nicola Byrne; Sabine Landau", + "affiliations": "King's College London; South London and Maudsley NHS Foundation Trust; King's College London; King's College London; South London and Maudsley NHS Foundation Trust; King's College London", + "abstract": "This study sought to provide an early description of mental health service activity before and after national implementation of social distancing for COVID-19. A time series analysis was carried out of daily service-level activity on data from a large mental healthcare provider in southeast London, from 01.02.2020 to 31.03.2020, comparing activity before and after 16.03.2020: i) inpatient admissions, discharges and numbers, ii) contact numbers and daily caseloads (Liaison, Home Treatment Teams, Community Mental Health Teams); iii) numbers of deaths for past and present patients. Daily face-to-face contact numbers fell for liaison, home treatment and community services with incomplete compensatory rises in non-face-to-face contacts. Daily caseloads fell for all services, apart from working age and child/adolescent community teams. Inpatient numbers fell 13.6% after 16th March, and daily numbers of deaths increased by 61.8%.", + "category": "psychiatry and clinical psychology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.09.24.20200048", @@ -3975,6 +4045,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.07.29.20164269", + "date": "2020-07-30", + "link": "https://medrxiv.org/cgi/content/short/2020.07.29.20164269", + "title": "The potential health and economic impact of dexamethasone treatment for patients with COVID-19", + "authors": "RICARDO AGUAS; Adam Mahdi; RIMA SHRETTA; Peter Horby; Martin Landray; Lisa J White", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford", + "abstract": "Dexamethasone has been shown to reduce mortality in hospitalised COVID-19 patients needing oxygen and ventilation by 18% and 36%, respectively. Here, we estimate the potential number of lives saved and life years gained if this treatment would be rolled out in the UK and globally, as well as its cost-effectiveness of implementing this intervention. We estimate that, for the UK, approximately 12,000 [4,250 - 27,000] lives could be saved by January 2021. Assuming that dexamethasone has a similar effect size in settings where access to oxygen therapies is limited, this would translate into approximately 650,000 [240,000 - 1,400,000] lives saved globally. If dexamethasone acts differently in these settings, the impact could be less than half of this value. To estimate the full potential of dexamethasone in the global fight against COVID-19, it is essential to perform clinical research in settings with limited access to oxygen and/or ventilators, e.g. in low and middle-income countries.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.07.26.20161570", @@ -4409,20 +4493,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.05.20.20108183", - "date": "2020-05-23", - "link": "https://medrxiv.org/cgi/content/short/2020.05.20.20108183", - "title": "A Rapid Review of the Asymptomatic Proportion of PCR-Confirmed SARS-CoV-2 Infections in Community Settings", - "authors": "Sarah Beale; Andrew Hayward; Laura Shallcross; Robert W Aldridge; Ellen Fragaszy", - "affiliations": "University College London; University College London; University College London; University College London; University College London", - "abstract": "BackgroundUp to 80% of active SARS-CoV-2 infections are proposed to be asymptomatic based on cross-sectional studies. However, accurate estimates of the asymptomatic proportion require systematic detection and follow-up to differentiate between truly asymptomatic and pre-symptomatic cases. We conducted a rapid review and meta-analysis of current evidence regarding the asymptomatic proportion of PCR-confirmed SARS-CoV-2 infections based on methodologically-appropriate studies in community settings.\n\nMethodsWe searched Medline and EMBASE for peer-reviewed articles, and BioRxiv and MedRxiv for pre-prints published prior to 05/05/2020. We included studies based in community settings that involved systematic PCR testing on participants and follow-up symptom monitoring regardless of symptom status. We extracted data on study characteristics, frequencies of PCR-confirmed infections by symptom status, and (if available) cycle threshold values and/or duration of viral shedding by symptom status. We computed estimates of the asymptomatic proportion and 95% confidence intervals for each study and overall using random effect meta-analysis.\n\nFindingsWe screened 270 studies and included 6. The pooled estimate for the asymptomatic proportion of SARS-CoV-2 infections was 11% (95% CI 4%-18%). Estimates of baseline viral load appeared to be similar for asymptomatic and symptomatic cases based on available data in three studies, though detailed reporting of cycle threshold values and natural history of viral shedding by symptom status was limited.\n\nInterpretationThe asymptomatic proportion of SARS-CoV-2 infections is relatively low when estimated from methodologically-appropriate studies. Further investigation into the degree and duration of infectiousness for asymptomatic infections is warranted.\n\nFundingMedical Research Council", - "category": "infectious diseases", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.05.18.20086157", @@ -4675,6 +4745,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.04.05.20048421", + "date": "2020-04-07", + "link": "https://medrxiv.org/cgi/content/short/2020.04.05.20048421", + "title": "Loss of smell and taste in combination with other symptoms is a strong predictor of COVID-19 infection", + "authors": "Cristina Menni; Ana Valdes; Maxim B Freydin; Sajaysurya Ganesh; Julia El-Sayed Moustafa; Alessia Visconti; Pirro Hysi; Ruth C E Bowyer; Massimo Mangino; Mario Falchi; Jonathan Wolf; Claire Steves; Tim Spector", + "affiliations": "King's College London; NIHR Nottingham Biomedical Research Centre, School of Medicine, University of Nottingham; King's College London; Zoe Global limited; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; King's College London; King's College London", + "abstract": "ImportanceA strategy for preventing further spread of the ongoing COVID-19 epidemic is to detect infections and isolate infected individuals without the need of extensive bio-specimen testing.\n\nObjectivesHere we investigate the prevalence of loss of smell and taste among COVID-19 diagnosed individuals and we identify the combination of symptoms, besides loss of smell and taste, most likely to correspond to a positive COVID-19 diagnosis in non-severe cases.\n\nDesignCommunity survey.\n\nSetting and ParticipantsSubscribers of RADAR COVID-19, an app that was launched for use among the UK general population asking about COVID-19 symptoms.\n\nMain ExposureLoss of smell and taste.\n\nMain Outcome MeasuresCOVID-19.\n\nResultsBetween 24 and 29 March 2020, 1,573,103 individuals reported their symptoms via the app; 26% reported suffering from one or more symptoms of COVID-19. Of those, n=1702 reported having had a RT-PCR COVID-19 test and gave full report on symptoms including loss of smell and taste; 579 were positive and 1123 negative. In this subset, we find that loss of smell and taste were present in 59% of COVID-19 positive individuals compared to 18% of those negative to the test, yielding an odds ratio (OR) of COVID-19 diagnosis of OR[95%CI]=6.59[5.25; 8.27], P= 1.90x10-59. We also find that a combination of loss of smell and taste, fever, persistent cough, fatigue, diarrhoea, abdominal pain and loss of appetite is predictive of COVID-19 positive test with sensitivity 0.54[0.44; 0.63], specificity 0.86[0.80; 0.90], ROC-AUC 0.77[0.72; 0.82] in the test set, and cross-validation ROC-AUC 0.75[0.72; 0.77]. When applied to the 410,598 individuals reporting symptoms but not formally tested, our model predicted that 13.06%[12.97%;13.15] of these might have been already infected by the virus.\n\nConclusions and RelevanceOur study suggests that loss of taste and smell is a strong predictor of having been infected by the COVID-19 virus. Also, the combination of symptoms that could be used to identify and isolate individuals includes anosmia, fever, persistent cough, diarrhoea, fatigue, abdominal pain and loss of appetite. This is particularly relevant to healthcare and other key workers in constant contact with the public who have not yet been tested for COVID-19.\n\nKey pointsO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIThe spread of COVID-19 can be reduced by identifying and isolating infected individuals but it is not possible to test everyone and priority has been given in most countries to individuals presenting symptoms of the disease.\nC_LIO_LICOVID-19 symptoms, such as fever, cough, aches, fatigue are common in many other viral infections\nC_LIO_LIThere is therefore a need to identify symptom combinations that can rightly pinpoint to infected individuals\nC_LI\n\nWhat this study addsO_LIAmong individuals showing symptoms severe enough to be given a COVID-19 RT-PCR test in the UK the prevalence of loss of smell (anosmia) was 3-fold higher (59%) in those positive to the test than among those negative to the test (18%).\nC_LIO_LIWe developed a mathematical model combining symptoms to predict individuals likely to be COVID-19 positive and applied this to over 400,000 individuals in the general population presenting some of the COVID-19 symptoms.\nC_LIO_LIWe find that [~]13% of those presenting symptoms are likely to have or have had a COVID-19 infection. The proportion was slightly higher in women than in men but is comparable in all age groups, and corresponds to 3.4% of those who filled the app report.\nC_LI", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.04.02.20051284", diff --git a/data/covid/preprints.json b/data/covid/preprints.json index 024ee407..145a849d 100644 --- a/data/covid/preprints.json +++ b/data/covid/preprints.json @@ -125,20 +125,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.12.04.23299364", - "date": "2023-12-04", - "link": "https://medrxiv.org/cgi/content/short/2023.12.04.23299364", - "title": "Clinical coding of long COVID in primary care 2020-2023 in a cohort of 19 million adults: an OpenSAFELY analysis", - "authors": "Alasdair D Henderson; Ben FC Butler-Cole; John Tazare; Laurie A Tomlinson; Michael Marks; Mark Jit; Andrew Briggs; Liang-Yu Lin; Oliver Carlile; Christopher Bates; John Parry; Sebastian CJ Bacon; Iain Dillingham; William A Dennison; Ruth E Costello; Yinghui Wei; Alex J Walker; William Hulme; Ben Goldacre; Amir Mehrkar; Brian MacKenna; The OpenSAFELY Collaborative; Emily Herrett; Rosalind M Eggo", - "affiliations": "London School of Hygiene & Tropical Medicine; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; TPP, TPP House, 129 Low Lane, Horsforth, Leeds; TPP, TPP House, 129 Low Lane, Horsforth, Leeds; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Patient and Public Involvement Steering Committee, London,; London School of Hygiene & Tropical Medicine; Centre for Mathematical Sciences, School of Engineering, Computing and Mathematics, University of Plymouth, Plymouth; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine", - "abstract": "BackgroundLong COVID is the patient-coined term for the persistent symptoms of COVID-19 illness for weeks, months or years following the acute infection. There is a large burden of long COVID globally from self-reported data, but the epidemiology, causes and treatments remain poorly understood. Primary care is used to help identify and treat patients with long COVID and therefore Electronic Health Records (EHRs) of past COVID-19 patients could be used to help fill these knowledge gaps. We aimed to describe those with long COVID in primary care records in England.\n\nMethodsWith the approval of NHS England we used routine clinical data from over 19 million adults in England linked to SARS-COV-2 test result, hospitalisation and vaccination data to describe trends in the recording of 16 clinical codes related to long COVID between November 2020 and January 2023. We calculated rates per 100,000 person-years and plotted how these changed over time. We compared crude and minimally adjusted rates of recorded long COVID in patient records between different key demographic and vaccination characteristics using negative binomial models.\n\nFindingsWe identified a total of 55,465 people recorded to have long COVID over the study period, with incidence of new long COVID records increasing steadily over 2021, and declining over 2022. The overall rate per 100,000 person-years was 177.5 cases in women (95% CI: 175.5-179) and 100.5 men (99.5-102). In terms of vaccination against COVID-19, the lowest rates were observed in those with 3+ vaccine doses (103.5 [95% CI: 101.5-105]). Finally, the majority of those with a long COVID record did not have a recorded positive SARS-COV-2 test 12 weeks before the long COVID record.\n\nInterpretationEHR recorded long COVID remains very low compared and incident records of long COVID declined over 2022. We found the lowest rates of recorded long COVID in people with 3 or more vaccine doses. We summarised several sources of possible bias for researchers using EHRs to study long COVID.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.11.30.23299229", @@ -223,20 +209,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "bioRxiv", - "doi": "10.1101/2023.10.22.563481", - "date": "2023-10-24", - "link": "https://biorxiv.org/cgi/content/short/2023.10.22.563481", - "title": "Microfluidic antibody profiling after repeated SARS-CoV-2 vaccination links antibody affinity and concentration to impaired immunity and variant escape in patients on anti-CD-20 therapy", - "authors": "Ashley Priddey; Michael Xin Hua Chen-Xu; Daniel James Cooper; Serena MacMillan; Georg Meisl; Catherine K Xu; Myra Hosmillo; Ian G Goodfellow; Rafael Kollyfas; Rainer Doffinger; John R Bradley; Irina I Mohorianu; Rachel Jones; Tuomas P.J. Knowles; Rona Smith; Vasilis Kosmoliaptsis", - "affiliations": "Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK; Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK; Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK and NIHR Blood and Transplant Research Unit in Organ D", - "abstract": "BackgroundPatients with autoimmune/inflammatory conditions on anti-CD20 therapies, such as Rituximab, have suboptimal humoral responses to vaccination and are vulnerable to poorer clinical outcomes following SARS-CoV-2 infection. We aimed to examine how the fundamental parameters of antibody responses, namely affinity and concentration, shape the quality of humoral immunity after vaccination in these patients.\n\nMethodsWe performed in depth antibody characterisation in sera collected four to six weeks after each of three vaccine doses to wild-type (WT) SARS-CoV-2 in Rituximab-treated primary vasculitis patients (n=14) using Luminex and pseudovirus neutralisation assays, whereas a novel microfluidic-based immunoassay was used to quantify polyclonal antibody affinity and concentration against both WT and Omicron (B.1.1.529) variants. Comparative antibody profiling was performed at equivalent time points in healthy individuals after three antigenic exposures to WT SARS-CoV-2 (one infection and two vaccinations; n=15) and in convalescent patients after WT SARS-CoV-2 infection (n=30).\n\nResultsRituximab-treated patients had lower antibody levels and neutralisation titres against both WT and Omicron SARS-CoV-2 variants compared to healthy individuals. Neutralisation capacity was weaker against Omicron versus WT both in Rituximab-treated patients and in healthy individuals. In the Rituximab cohort, this was driven by lower antibody affinity against Omicron versus WT (median [range] KD: 21.6 [9.7-38.8] nM vs 4.6 [2.3-44.8] nM, p=0.0004). By contrast, healthy individuals with hybrid immunity produced a broader antibody response, a subset of which recognised Omicron with higher affinity than antibodies in Rituximab-treated patients (median [range] KD: 1.05 [0.45-1.84] nM vs 20.25 [13.2-38.8] nM, p=0.0002), underpinning the stronger serum neutralisation capacity against Omicron in the former group. Rituximab-treated patients had similar anti-WT antibody levels and neutralisation titres to unvaccinated convalescent individuals, despite two more exposures to SARS-CoV-2 antigen. Temporal profiling of the antibody response showed evidence of affinity maturation in healthy convalescent patients after a single SARS-CoV-2 infection which was not observed in Rituximab-treated patients, despite repeated vaccination.\n\nDiscussionOur results enrich previous observations of impaired humoral immune responses to SARS-CoV-2 in Rituximab-treated patients and highlight the significance of quantitative assessment of serum antibody affinity and concentration in monitoring anti-viral immunity, viral escape, and the evolution of the humoral response.", - "category": "immunology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.10.12.23296948", @@ -251,6 +223,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.10.11.23296866", + "date": "2023-10-12", + "link": "https://medrxiv.org/cgi/content/short/2023.10.11.23296866", + "title": "SARS-CoV-2, influenza A/B and respiratory syncytial virus positivity and association with influenza-like illness and self-reported symptoms, over the 2022/23 winter season in the UK: a longitudinal surveillance cohort", + "authors": "Elisabeth Dietz; Emma Elizabeth Pritchard; Koen Pouwels; Muhammad Ehsaan; Joshua Blake; Charlotte Gaughan; Eric Haduli; Hugh Boothe; Karina-Doris Vihta; Tim Peto; Nicole Stoesser; Philippa Matthews; Nick Taylor; Ian Diamond; Ruth Studley; Emma Rourke; Paul Birrell; Daniela De Angelis; Tom Fowler; Conall Watson; David W Eyre; Thomas House; Ann Sarah Walker", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; Berkshire and Surrey Pathology Services; University of Cambridge; Office of National Statistics; Berkshire and Surrey Pathology Services; Berkshire and Surrey Pathology Services; University of Oxford; University of Oxford; University of Oxford; The Francis Crick Institute; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Cambridge; University of Cambridge; UK Health Security Agency; UK Health Security Agency; University of Oxford; University of Manchester; University of Oxford", + "abstract": "BackgroundSyndromic surveillance often relies on patients presenting to healthcare. Community cohorts, although more challenging to recruit, could provide additional population-wide insights, particularly with SARS-CoV-2 co-circulating with other respiratory viruses.\n\nMethodsWe estimated positivity and incidence of SARS-CoV-2, influenza A/B, and RSV, and trends in self-reported symptoms including influenza-like illness (ILI), over the 2022/23 winter season in a broadly representative UK community cohort (COVID-19 Infection Survey), using negative-binomial generalised additive models. We estimated associations between test positivity and each of symptoms and influenza vaccination, using adjusted logistic and multinomial models.\n\nFindingsSwabs taken at 32,937/1,352,979 (2.4%) assessments tested positive for SARS-CoV-2, 181/14,939 (1.2%) for RSV and 130/14,939 (0.9%) for influenza A/B, varying by age over time. Positivity and incidence peaks were earliest for RSV, then influenza A/B, then SARS-CoV-2, and were highest for RSV in the youngest and for SARS-CoV-2 in the oldest age-groups. Many test-positives did not report key symptoms: middle-aged participants were generally more symptomatic than older or younger participants, but still only [~]25% reported ILI-WHO and [~]60% ILI-ECDC. Most symptomatic participants did not test positive for any of the three viruses. Influenza A/B-positivity was lower in participants reporting influenza vaccination in the current and previous seasons (odds ratio=0.55 (95% CI 0.32,0.95)) versus neither season.\n\nInterpretationSymptom profiles varied little by aetiology, making distinguishing SARS-CoV-2, influenza and RSV using symptoms challenging. Most symptoms were not explained by these viruses, indicating the importance of other pathogens in syndromic surveillance. Influenza vaccination was associated with lower rates of community influenza test positivity.\n\nFundingUK Health Security Agency, Department of Health and Social Care, National Institute for Health Research.", + "category": "respiratory medicine", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.10.06.23296657", @@ -447,6 +433,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.07.03.23291596", + "date": "2023-07-05", + "link": "https://medrxiv.org/cgi/content/short/2023.07.03.23291596", + "title": "Risk of COVID-19 death in adults who received booster COVID-19 vaccinations: national retrospective cohort study on 14.6 million people in England", + "authors": "Isobel L Ward; Chris Robertson; Utkarsh Agrawal; Lynsey Patterson; Declan T Bradley; Ting Shi; Simon de Lusignan; Richard Hobbs; Aziz Sheikh; Vahe Nafilyan", + "affiliations": "Office for National Statistics, Newport, UK; Department of Mathematics and Statistics, Strathclyde University, Glasgow, Scotland and Public Health Scotland, Glasgow, Scotland; Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Centre for Public Health, Queen's University Belfast, Belfast, UK and Public Health Agency, Belfast, UK; Centre for Public Health, Queen's University Belfast, Belfast, UK and Public Health Agency, Belfast, UK; Usher Institute, University of Edinburgh, Edinburgh, UK; Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Usher Institute, University of Edinburgh, Edinburgh, UK; Office for National Statistics, Newport, UK", + "abstract": "ImportanceThe emergence of the COVID-19 vaccination has been critical in changing the course of the COVID-19 pandemic, with estimates suggesting vaccinations have prevented millions of deaths worldwide. To ensure protection remains high in vulnerable groups booster vaccinations in the UK have been targeted based on age and clinical vulnerabilities.\n\nObjectiveWe sought to identify adults who had received a booster vaccination as part of the autumn 2022 campaign in England yet remained at increased risk of postbooster COVID-19 death and compared to non-COVID-19 risk.\n\nDesign, Setting, and ParticipantsWe undertook a national retrospective cohort study using data from the 2021 Census linked to electronic health records. We fitted cause-specific Cox models to examine the association between health conditions and the risk of COVID-19 death and all-other-cause death for adults aged 50-100-years in England vaccinated with a booster in autumn 2022. Our total population was 14,644,570 people; there were 6,800 COVID-19 deaths and 150,075 non-COVID-19 deaths.\n\nExposureSociodemographic characteristics (sex, age, ethnic group, region), disability, body mass index, and diagnosis of a health condition defined from QCovid2.\n\nMain Outcomes and MeasuresThe primary outcome of this study was COVID-19 death. The secondary outcome was all-cause non-COVID-19 deaths.\n\nResultsHaving learning disabilities or Down Syndrome (hazard ratio=5.07;95% confidence interval=3.69-6.98), pulmonary hypertension or fibrosis (2.88;2.43-3.40), motor neuron disease, multiple sclerosis, myasthenia or Huntingtons disease (2.94, 1.82-4.74), cancer of blood and bone marrow (3.11;2.72-3.56), Parkinsons disease (2.74;2.34-3.20), lung or oral cancer (2.57;2.04 to 3.24), dementia (2.64;2.46 to 2.83) or liver cirrhosis (2.65;1.95 to 3.59) was associated with an increased risk of COVID-19 death. Individuals with cancer of the blood or bone marrow, chronic kidney disease, cystic fibrosis, pulmonary hypotension or fibrosis, or rheumatoid arthritis or systemic lupus erythematosus had a significantly higher risk of COVID-19 death relative to other causes of death compared with individuals who did not have diagnoses.\n\nConclusions, and RelevanceWe identify groups who are at increased risk of postbooster COVID-19 death relative to non-COVID-19 deaths. Policy makers should continue to priorities vulnerable groups for subsequent COVID-19 booster doses to minimise the risk of COVID-19 death.\n\nFundingNational Core Studies-Immunity, National Core Studies-Data and Connectivity, Health Data Research UK, and the Medical Research Council.\n\nKey PointsQuestion: What health conditions are associated with increased risk of postbooster COVID-19 death in adults who received a COVID-19 vaccination in autumn 2022?\n\nFindings: Certain groups were found to be at overall higher risk of postbooster COVID-19 death (e.g., learning disability or Down Syndrome) and certain groups were found to have significantly higher relative risk of COVID-19 death compared to other non-COVID-19 causes (e.g., cancer of the blood or bone marrow).\n\nMeaning: This work has implications for prioritisation of vaccination booster doses worldwide. We highlight which groups with health conditions are at elevated risk of postbooster COVID-19 death.", + "category": "public and global health", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.06.29.23292056", @@ -685,20 +685,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.03.24.23287700", - "date": "2023-03-26", - "link": "https://medrxiv.org/cgi/content/short/2023.03.24.23287700", - "title": "The potential contribution of vaccination uptake to occupational differences in risk of SARS-CoV-2: Analysis of the ONS COVID-19 Infection Survey", - "authors": "Jack D Wilkinson; Evangelia Demou; Mark Cherrie; Rhiannon Edge; Matthew Gittins; Srinivasa Vittal Katikireddi; Theocharis Kromydas; WIll Mueller; Neil Pearce; Martie van Tongeren; Sarah Rhodes", - "affiliations": "University of Manchester; University of Glasgow; Institute of Occupational Medicine; University of Lancaster; University of Manchester; University of Glasgow; University of Glasgow; Institute for Occupational Medicine; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester", - "abstract": "ObjectivesTo assess variation in vaccination uptake across occupational groups as a potential explanation for variation in risk of SARS-CoV-2 infection.\n\nDesignWe analysed data from the UK Office of National Statistics COVID-19 Infection Survey linked to vaccination data from the National Immunisation Management System in England from December 1st 2020 to 11th May 2022. We analysed vaccination uptake and SARS-CoV-2 infection risk by occupational group and assessed whether adjustment for vaccination reduced the variation in risk between occupational groups.\n\nSetting\n\nResultsEstimated rates of triple-vaccination were high across all occupational groups (80% or above), but were lowest for food processing (80%), personal care (82%), hospitality (83%), manual occupations (84%), and retail (85%). High rates were observed for individuals working in health (95% for office-based, 92% for those in patient-facing roles) and education (91%) and office-based workers not included in other categories (90%). The impact of adjusting for vaccination when estimating relative risks of infection was generally modest (ratio of hazard ratios reduced from 1.38 to 1.32), but was consistent with the hypothesis that low vaccination rates contribute to elevated risk in some groups. Conversely, estimated relative risk for some occupational groups, such as people working in education, remained high despite high vaccine coverage.\n\nConclusionsVariation in vaccination coverage might account for a modest proportion of occupational differences in infection risk. Vaccination rates were uniformly very high in this cohort, which may suggest that the participants are not representative of the general population. Accordingly, these results should be considered tentative pending the accumulation of additional evidence.", - "category": "occupational and environmental health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.03.24.23287666", @@ -783,6 +769,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.03.01.23286624", + "date": "2023-03-03", + "link": "https://medrxiv.org/cgi/content/short/2023.03.01.23286624", + "title": "Risk of cardiovascular events following COVID-19 in people with and without pre-existing chronic respiratory disease", + "authors": "Hannah Whittaker; Costantinos Kallis; Angela Wood; Thomas Bolton; Samantha Walker; Aziz Sheikh; Alex Brownrigg; Ashley Akbari; Kamil Sterniczuk; Jennifer K Quint", + "affiliations": "Imperial College London; Imperial College London; Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, United Kingdom; Health Data Research UK; Asthm + Lung; The University of Edinburgh College of Medicine and Veterinary Medicine; Health Data Research UK BREATHE; Swansea University; Health Data Research UK BREATHE; Imperial College London", + "abstract": "BackgroundCOVID-19 is associated with a higher risk of cardiovascular outcomes in the general population, but it is unknown whether people with pre-existing chronic respiratory disease (CRD) have a higher risk of cardiovascular events post-COVID-19 compared with the general population and, if so, what respiratory-related risk factors may modify this risk in these people.\n\nMethodsPrimary and secondary care data from the National Health Service and COVID-19-specific linked data were used to define a population of adults in England with COVID-19 (index date) between 01/01/2020-30/11/2021. Adjusted Cox Proportional Hazard regression was used to quantify the association between CRD, asthma-related factors, COPD-related factors, and risk of cardiovascular events. CRD included asthma, COPD, bronchiectasis, cystic fibrosis, or pulmonary fibrosis prior to COVID-19 diagnosis. Asthma-specific factors included baseline asthma control, exacerbations, and inhaled corticosteroid (ICS) dose. COPD-specific risk factors included baseline ICS prescriptions and exacerbations. Secondary objectives quantified the impact of COVID-19 hospitalisation and vaccine dose on cardiovascular outcomes.\n\nResultsOf 3,670,455 people, those with CRD had a modest higher risk of cardiovascular events (HRadj 1.11, 95%CI 1.07-1.14), heart failure (HRadj 1.15, 1.09-1.21), and pulmonary emboli (HRadj 1.20, 1.11-1.30) compared with people without CRD. In people with asthma, baseline exacerbations and high-dose ICS were associated with a higher risk of cardiovascular outcomes (HRadj 1.24, 1.15-1.34 and 1.12, 1.01-1.24, respectively). In people with COPD, exacerbations were associated with a higher risk of cardiovascular outcomes (HRadj 1.40, 1.28-1.52). Regardless of CRD, the risk of cardiovascular events was lower with increasing COVID-19 vaccine dose.\n\nConclusionsHigher risk of cardiovascular events following COVID-19 might be explained at least in part by the underlying CRD and severity of that condition. In addition, COVID-19 vaccines were beneficial to both people with and without CRD with regards to CV events.\n\nKey MessagesPre-existing chronic respiratory disease, asthma and COPD severity were associated with a higher risk of various types of cardiovascular outcomes following COVID-19. Regardless of having pre-existing chronic respiratory disease, COVID-19 vaccination reduced the risk of cardiovascular events following COVID-19.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.02.28.23286559", @@ -839,6 +839,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.02.10.23285717", + "date": "2023-02-14", + "link": "https://medrxiv.org/cgi/content/short/2023.02.10.23285717", + "title": "The long COVID evidence gap: comparing self-reporting and clinical coding of long COVID using longitudinal study data linked to healthcare records.", + "authors": "Anika Knuppel; Andy Boyd; John Macleod; Nishi Chaturvedi; Dylan M Williams", + "affiliations": "MRC Unit of Lifelong Health and Ageing at UCL, University College London, London W1E 7HB, London, United Kingdom; Institute of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, United Kingdom; Institute of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, United Kingdom; MRC Unit of Lifelong Health and Ageing at UCL, University College London, London W1E 7HB, London, United Kingdom; MRC Unit of Lifelong Health and Ageing at UCL, University College London, London W1E 7HB, London, United Kingdom", + "abstract": "The term \"long COVID\" (LC) was coined in spring 2020 by individuals with ongoing symptoms following COVID-19, but it took until December 2020 for clinical codes to be created in order to record persistent post-COVID-19 illness and referrals within electronic health records (EHRs). Analysis of whole-population EHR databases have helped understand the epidemiology of LC; yet concerns exist about the completeness of accessible EHRs for LC. UK longitudinal population studies (LPS) collected self-reported data on COVID-19 and LC from early 2020 and deposited these data in the UK Longitudinal Linkage Collaboration (UK LLC) research database where they are systematically linked to the participants EHRs. Comparisons of LPS reported LC with recorded LC in the EHRs of the same individuals may be helpful in understanding the epidemiology of emerging conditions such as LC. We used data from 10 UK LPS in the UK LLC to investigate whether participants self-reporting LC had a LC diagnosis or referral code in their English EHR after 10 to 22 months of follow up. Of 6412 participants with COVID-19 symptom duration data and linkage to health records, 898 (14.0%) self-reported LC of any severity in LPS surveys. Among these, just 42 (4.7%; 95% CI: 3.5, 6.3) were identified with LC-related codes in EHRs. In individuals reporting debilitating LC, this proportion was only marginally higher (5.6%; 95% CI: 3.7, 8.3). Our data show a striking discrepancy between LC as perceived and reported by participants in LPS and evidence of LC recorded in their EHRs; and that this discrepancy was patterned by ethnicity and possibly by indicators of deprivation. Self-reported symptoms may not be reflected in coded EHRs due to factors including variations in individuals help seeking behaviours, clinician coding practices and the availability of appropriate codes. However, these considerations appear unlikely to provide a complete explanation for the substantial observed reporting discrepancy. These results may indicate substantial unmet clinical need, in keeping with patient reports of difficulties accessing healthcare and sub-optimal recognition of, and response to, their illness when they do. They may also indicate potential shortcomings of epidemiological research on LC based on EHR- or LPS-based ascertainment alone and illustrate the value of triangulation between LPS and EHR data where linked and made available through resources such as the UK LLC.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.02.09.23285649", @@ -1357,6 +1371,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.09.14.22279931", + "date": "2022-09-15", + "link": "https://medrxiv.org/cgi/content/short/2022.09.14.22279931", + "title": "Detecting changes in population trends in infection surveillance using community SARS-CoV-2 prevalence as an exemplar", + "authors": "Emma Elizabeth Pritchard; Karina-Doris Vihta; David W Eyre; Susan Hopkins; Tim EA Peto; Philippa C Matthews; Nicole Stoesser; Ruth Studley; Emma Rourke; Ian Diamond; Koen B Pouwels; Ann Sarah Walker", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; UK Health Security Agency; University of Oxford; The Francis Crick Institute, London; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; University of Oxford", + "abstract": "BackgroundMonitoring infection trends is vital to informing public health strategy. Detecting and quantifying changes in growth rates can inform policymakers rationale for implementing or continuing interventions aimed at reducing impact. Substantial changes in SARS-CoV-2 prevalence with emergence of variants provides opportunity to investigate different methods to do this.\n\nMethodsWe included PCR results from all participants in the UKs COVID-19 Infection Survey between 1 August 2020-30 June 2022. Change-points for growth rates were identified using iterative sequential regression (ISR) and second derivatives of generalised additive models (GAMs).\n\nConsistency between methods and timeliness of detection were compared.\n\nFindingsOf 8,799,079 visits, 147,278 (1{middle dot}7%) were PCR-positive. Over the time period, change-points associated with emergence of major variants were estimated to occur a median 4 days earlier (IQR 0-8) in GAMs versus ISR, with only 2/48 change-points identified by only one method. Estimating recent change-points using successive data periods, four change-points (4/96) identified by GAMs were not found when adding later data or by ISR; 77% (74/96) of change-points identified by successive GAMs were identified by ISR. Change-points were detected 3-5 weeks after they occurred in both methods but could be detected earlier within specific subgroups.\n\nInterpretationChange-points in growth rates of SARS-CoV-2 can be detected in near real-time using ISR and second derivatives of GAMs. To increase certainty about changes in epidemic trajectories both methods could be run in parallel. Running either method in near real-time on different infection surveillance data streams could provide timely warnings of changing underlying epidemiology.\n\nFundingUK Health Security Agency, Department of Health and Social Care (UK), Welsh Government, Department of Health (on behalf of the Northern Ireland Government), Scottish Government, National Institute for Health Research.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.09.11.22279823", @@ -1511,6 +1539,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.08.08.22278493", + "date": "2022-08-09", + "link": "https://medrxiv.org/cgi/content/short/2022.08.08.22278493", + "title": "Inequalities in colorectal cancer screening uptake in Wales: examination of the impact of the temporary suspension of the screening programme during the COVID-19 pandemic", + "authors": "Diana Bright; Sharon Hillier; Jiao Song; Dyfed W Huws; Giles Greene; Karen Hodgson; Ashley Akbari; Rowena Griffiths; Alisha R Davies", + "affiliations": "Public Health Wales; Public Health Wales; Public Health Wales; Public Health Wales; Population Data Science, Swansea University Medical School, Faculty of Medicine, Health & Life Science, Swansea University, Swansea, Wales; Public Health Wales; Public Health Wales; Population Data Science, Swansea University Medical School, Faculty of Medicine, Health & Life Science, Swansea University, Swansea, Wales; Population Data Science, Swansea University Medical School, Faculty of Medicine, Health & Life Science, Swansea University, Swansea, Wales; Public Health Wales", + "abstract": "BackgroundResponse to the early stages of the COVID-19 pandemic resulted in the temporary disruption of cancer screening in the UK, and strong public messaging to stay safe and to protect NHS capacity. Following reintroduction in services, we explored the impact on inequalities in uptake of the Bowel Screening Wales (BSW) programme to identify groups who may benefit from tailored interventions.\n\nMethodsRecords within the BSW were linked to electronic health records (EHR) and administrative data within the Secured Anonymised Information Linkage (SAIL) Databank. Ethnic group was obtained from a linked data method available within SAIL. We examined uptake for the first 3 months of invitations (August to October) following the reintroduction of BSW programme in 2020, compared to the same period in the preceding 3 years. Uptake was measured across a 6 month follow-up period. Logistic models were conducted to analyse variations in uptake by sex, age group, income deprivation quintile, urban/rural location, ethnic group, and clinically extremely vulnerable (CEV) status in each period; and to compare uptake within sociodemographic groups between different periods.\n\nResultsUptake during August to October 2020 (period 2020/21; 60.4%) declined compared to the same period in 2019/20 (62.7%) but remained above the 60% Welsh standard. Variation by sex, age, income deprivation, and ethnic groups was observed in all periods studied. Compared to the pre-pandemic period in 2019/20, uptake declined for most demographic groups, except for older individuals (70-74 years) and those in the most income deprived group. Uptake continues to be lower in males, younger individuals, people living in the most income deprived areas and those of Asian and unknown ethnic backgrounds.\n\nConclusionsOur findings are encouraging with overall uptake achieving the 60% Welsh standard during the first three months after the programme restarted in 2020 despite the disruption. Inequalities did not worsen after the programme resumed activities but variations in CRC screening in Wales associated with sex, age, deprivation and ethnicity remain. This needs to be considered in targeting strategies to improve uptake and informed choice in CRC screening to avoid exacerbating disparities in CRC outcomes as screening services recover from the pandemic.", + "category": "public and global health", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.07.30.22278161", @@ -1665,20 +1707,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.06.20.22275994", - "date": "2022-06-20", - "link": "https://medrxiv.org/cgi/content/short/2022.06.20.22275994", - "title": "Characterising patterns of COVID-19 and long COVID symptoms: Evidence from nine UK longitudinal studies", - "authors": "Ruth C E Bowyer; Charlotte Huggins; Renin Toms; Richard John Shaw; Bo Hou; Ellen J Thompson; Alex Siu Fung Kwong; Dylan M Williams; Milla Kibble; George B Ploubidis; Nicholas J Timpson; Jonathan A C Sterne; Nishi Chaturvedi; Claire J Steves; Kate Tilling; Richard J Silverwood", - "affiliations": "King's College London; University of Edinburgh; University of Bristol; University of Glasgow; Bradford Institute for Health Research; King's College London; University of Bristol; UCL; King's College London; University College London; University of Bristol; University of Bristol; University College London; King's College London; University of Bristol; University College London", - "abstract": "Multiple studies across global populations have established the primary symptoms characterising COVID-19 (Coronavirus Disease 2019) and long COVID. However, as symptoms may also occur in the absence of COVID-19, a lack of appropriate controls has often meant that specificity of symptoms to acute COVID-19 or long COVID could not be examined. We aimed to characterise patterns of COVID-19 and long COVID symptoms across nine UK longitudinal studies, totalling over 42,000 participants. Conducting latent class analyses separately in three groups ( no COVID-19, COVID-19 in last 12 weeks, COVID-19 > 12 weeks ago), the data did not support the presence of more than two distinct symptom patterns, representing high and low symptom burden, in each group. Comparing the high symptom burden classes between the COVID-19 in last 12 weeks and no COVID-19 groups we identified symptoms characteristic of acute COVID-19, including loss of taste and smell, fatigue, cough, shortness of breath and muscle pains or aches. Comparing the high symptom burden classes between the COVID-19 > 12 weeks ago and no COVID-19 groups we identified symptoms characteristic of long COVID, including fatigue, shortness of breath, muscle pain or aches, difficulty concentrating and chest tightness. The identified symptom patterns among individuals with COVID-19 > 12 weeks ago were strongly associated with self-reported length of time unable to function as normal due to COVID-19 symptoms, suggesting that the symptom pattern identified corresponds to long COVID. Building the evidence base regarding typical long COVID symptoms will improve diagnosis of this condition and the ability to elicit underlying biological mechanisms, leading to better patient access to treatment and services.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.06.18.22276437", @@ -1917,20 +1945,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.05.21.22275368", - "date": "2022-05-23", - "link": "https://medrxiv.org/cgi/content/short/2022.05.21.22275368", - "title": "Variant-specific symptoms of COVID-19 among 1,542,510 people in England", - "authors": "Matthew Whitaker; Joshua Elliott; Barbara Bodinier; Wendy S Barclay; Helen Ward; Graham Cooke; Christl A Donnelly; Marc Chadeau-Hyam; Paul Elliott", - "affiliations": "Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health", - "abstract": "Infection with SARS-CoV-2 virus is associated with a wide range of symptoms. The REal-time Assessment of Community Transmission -1 (REACT-1) study has been monitoring the spread and clinical manifestation of SARS-CoV-2 among random samples of the population in England from 1 May 2020 to 31 March 2022. We show changing symptom profiles associated with the different variants over that period, with lower reporting of loss of sense of smell and taste for Omicron compared to previous variants, and higher reporting of cold-like and influenza-like symptoms, controlling for vaccination status. Contrary to the perception that recent variants have become successively milder, Omicron BA.2 was associated with reporting more symptoms, with greater disruption to daily activities, than BA.1. With restrictions lifted and routine testing limited in many countries, monitoring the changing symptom profiles associated with SARS-CoV-2 infection and induced changes in daily activities will become increasingly important.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 96, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.05.19.22275214", @@ -1959,20 +1973,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.05.09.22274769", - "date": "2022-05-11", - "link": "https://medrxiv.org/cgi/content/short/2022.05.09.22274769", - "title": "COVID-19 vaccination in pregnancy: views and vaccination uptake rates in pregnancy, a mixed methods analysis from the Born In Wales study", - "authors": "Mohamed Mhereeg; Hope Jones; Jonathan Kennedy; Michael Seaborne; Michael Parker; Natasha Kennedy; Sarah Beeson; Luisa Zuccolo; Alisha Davies; Sinead Brophy", - "affiliations": "Swansea University Medical School, Swansea, Wales, UK; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Bristol Medical School, University of Bristol, Bristol, England, UK.; Public Health Wales, UK; Swansea University Medical School, Swansea, Wales, UK", - "abstract": "BackgroundVaccine hesitancy amongst pregnant women has been found to be a concern during past epidemics.\n\nObjectivesThe aims of this study were to 1) estimate COVID-19 vaccination rates among pregnant women in Wales and their association with age, ethnicity, and area of deprivation, using electronic health records (EHR) linkage, and 2) explore pregnant womens views on receiving the COVID-19 vaccine during pregnancy using data from a survey recruiting via social media (Facebook, Twitter), through midwives, and posters in hospitals (Born in Wales Cohort).\n\nDesignA mixed methods study utilising routinely collected linked data from the Secure Anonymised Information Linkage (SAIL) (Objective 1) and the Born In Wales Birth Cohort participants (Objective 2). SAIL combines data from general practice, hospital admissions, the national community child health dataset, maternal indicators dataset, and COVID-19 vaccination databases.\n\nSetting and participantsObjective 1) All women documented as being pregnant on or after 13th April 2021, aged 18 years or older, and eligible for COVID-19 vaccination were identified in routine health care. They were linked to the vaccination data up to and including 31st December 2021. Objective 2) Separately, a cross-section of pregnant women in Wales were invited to complete an online survey via social media advertising. The survey asked what their views were on having the COVID-19 vaccination during pregnancy, and if they had already received, or intended to receive, the COVID-19 vaccination during their pregnancies. They were also asked to give reasons for their decisions.\n\nOutcomes1 (a). Rate of vaccination uptake per month during pregnancy among women eligible for vaccination. 1 (b). Survival analysis was utilised to examine and compare the length of time to vaccination uptake in pregnancy, and variation in uptake by; age, ethnicity, and deprivation area was examined using hazard ratios (HR) from Cox regression. 2.Expectant mothers views of the COVID-19 vaccination during pregnancy.\n\nResults\n\nPopulation-level data linkage (objective 1)Within the population cohort, 32.7% (n = 8,203) were vaccinated (at least one dose of the vaccine) during pregnancy, 34.1% (n = 8,572) remained unvaccinated throughout follow-up period, and 33.2% (n = 8,336) received the vaccine postpartum. Younger women (<30 years) were less likely to have the vaccine and those living in areas of high deprivation were also less likely to have the vaccine (HR=0.88, 95% CI 0.82 to 0.95). Asian and other ethnic groups were 1.12 and 1.18 times more likely to have the vaccine in pregnancy compared to women of White ethnicity (HR=1.12, 95% CI 1.00 to 1.25) and (HR=1.18, 95% CI 1.03 to 1.37) respectively.\n\nSurvey responses (objective 2)69% of participants stated that they would be happy to have the vaccine during pregnancy (n = 207). The remainder, 31%, indicated that they would not have the vaccine during pregnancy (n = 94). Reasons for having the vaccine related to protecting self and baby, perceived risk level, and receipt of sufficient evidence and advice. Reasons for vaccine refusal included lack of research about long-term outcomes for the baby, anxiety about vaccines, inconsistent advice/information, and preference to wait until after the pregnancy.\n\nConclusionPotentially only 1 in 3 pregnant women would have the COVID-19 vaccine during pregnancy, even though 2 in 3 reported they would have the vaccination, thus it is critical to develop tailored strategies to increase its acceptance rate and to decrease vaccine hesitancy. A targeted approach to vaccinations may be required for groups such as younger people and those living in higher deprivation level areas.", - "category": "public and global health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "bioRxiv", "doi": "10.1101/2022.05.07.491004", @@ -2197,20 +2197,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.04.14.22272888", - "date": "2022-04-14", - "link": "https://medrxiv.org/cgi/content/short/2022.04.14.22272888", - "title": "Anti-inflammatory therapy with nebulised dornase alfa in patients with severe COVID-19 pneumonia", - "authors": "Joanna Porter; Jamie Inshaw; Vincente Joel Solis; Emma Denneny; Rebecca Evans; Mia I. Temkin; Nathalia De Vasconcelos; Iker Valle Aramburu; Dennis Hoving; Donna Basire; Tracey Crissell; Jesusa Guinto; Alison Webb; Hanif Esmail; Victoria Johnston; Anna Last; Thomas Rampling; Elisa Theresa Helbig; Lena Lippert; Florian Kurth; Bryan Williams; Aiden Flynn; Pauline Lukey; Veronique Birault; Venizelos Papayannopoulos", - "affiliations": "UCL Respiratory, University College London, UK; Exploristics, Belfast, N. Ireland; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; UCL Respiratory, University College London, UK; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany; Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany; Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; Exploristics, Belfast, N. Ireland; Target to Treatment Consulting Ltd, Stevenage, UK; Translation, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK", - "abstract": "BackgroundCell-free (cf)-DNA, from cellular sources, including Neutrophil Extracellular Traps (NETs), is found in the circulation of COVID-19 patients and may contribute to immune dysregulation. This study determined whether pulmonary administration of the endonuclease, dornase alfa, reduced systemic inflammation by degrading local and systemic cf-DNA.\n\nMethodsEligible patients were randomized (3:1) to receive twice-daily nebulised dornase alfa in addition to best available care (BAC) or BAC alone for seven days or until discharge. A 2:1 ratio of matched contemporary controls (CC) provided additional comparators. The primary endpoint was improvement in C-reactive protein (CRP) over time, analysed using a repeated-measures mixed model, adjusted for baseline factors.\n\nResultsBetween June 2020-October 2021 we recruited 39 evaluable patients: 30 randomised to dornase alfa; 9 randomised to BAC; with 60 CC. Dornase alfa reduced CRP by 33% compared to BAC. Least squares (LS) mean post-dexamethasone CRP fell from 101.9mg/L to 23.23 mg/L in the BAC+ dornase alfa group versus a fall from 99.5mg/L to 34.82 mg/L in the BAC group at 7 days; P=0.01. This effect of dornase alfa on CRP was confirmed with subgroup and sensitivity analyses. Dornase alfa increased the chance of live discharge by 63% (HR 1.63, 95% CI 1.01 to 2.61, P=0.03), increased lymphocyte counts (LSmean 1.08 vs 0.87, P=0.02) and reduced circulating cf-DNA and the coagulopathy marker D-dimer (LS mean: 570.78 vs 1656.96 g/mL, P=0.004). Dornase alfa was well-tolerated.\n\nConclusionsWe provide proof-of-concept evidence that dornase alfa reduces pathogenic inflammation in hospitalised patients with COVID-19 pneumonia.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.04.12.22273752", @@ -2617,6 +2603,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.02.14.22270930", + "date": "2022-02-15", + "link": "https://medrxiv.org/cgi/content/short/2022.02.14.22270930", + "title": "Determinants of antibody responses to two doses of ChAdOx1 nCoV-19 or BNT162b2 and a subsequent booster dose of BNT162b2 or mRNA-1273: population-based cohort study (COVIDENCE UK)", + "authors": "David A Jolliffe; Sian E Faustini; Hayley Holt; Natalia Perdek; Sheena Maltby; Mohammad Talaei; Matthew Greenig; Giulia Vivaldi; Florence Tydeman; Jane Symons; Gwyneth A Davies; Ronan Lyons; Frank Kee; Aziz Sheikh; Seif O Shaheen; Alex Richter; Adrian R Martineau", + "affiliations": "Queen Mary University of London; University of Birmingham; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Jane Symons Media; Swansea University; Swansea University; Queen's University Belfast; Edinburgh University; Queen Mary University of London; University of Birminghan; Queen Mary University of London", + "abstract": "BackgroundAntibody responses to SARS-CoV-2 vaccination vary for reasons that remain poorly understood.\n\nMethodsWe tested for presence of combined IgG, IgA and IgM (IgGAM) anti-spike antibodies before and after administration of two doses of ChAdOx1 nCoV-19 (ChAdOx1, Oxford-AstraZeneca) or BNT162b2 (Pfizer-BioNTech) in UK adults participating in a population-based longitudinal study who received their first dose of vaccine from December 15, 2020 to July 10, 2021. Information on sixty-six potential sociodemographic, behavioural, clinical, pharmacological and nutritional determinants of serological response to vaccination was captured using serial online questionnaires. We used logistic regression to estimate multivariable-adjusted odds ratios (aORs) for associations between independent variables and risk of seronegativity following two vaccine doses. Participants who were seronegative after receiving two vaccine doses were offered an additional antibody test following subsequent administration of a booster dose of BNT162b2 or mRNA-1273 (Moderna) from September 23 to December 12, 2021.\n\nFindingsSerology results following two vaccine doses were available for 9,101 participants, of whom 5,770 (63.4%) received ChAdOx1 and 3,331 (36.6%) received BNT162b2. Anti-spike IgGAM was undetectable in 378 (4.2%) participants at a median of 8.6 weeks (IQR 6.4-10.7 weeks) after their second dose of vaccine. Seronegativity following two doses of SARS-CoV-2 vaccination was associated with administration of ChAdOx1 vs BNT162b2 (aOR 7.03, 95% CI 4.39-11.24), shorter interval between first and second vaccine doses (aOR 2.37, 1.06-5.26, for <6 weeks vs >10 weeks; aOR 1.59, 1.18-2.13, for 6-10 weeks vs >10 weeks), poorer self-assessed general health (aOR 3.33, 1.49-7.46, for poor vs excellent), immunodeficiencies (aOR 6.75, 2.63-17.35) and prescription of systemic immunosuppressants (aOR 3.76, 2.44-5.78). By contrast, pre-vaccination SARS-CoV-2 seropositivity (aOR 0.16, 0.04-0.70, for symptomatic seropositives vs seronegatives) and supplemental vitamin D intake (aOR 0.73, 0.53-0.99) were associated with reduced risk of post-vaccination seronegativity. 247/378 (65.3%) of participants who were seronegative after two doses of ChAdOx1 vs BNT162b2 provided a third sample at a median of 7.8 weeks (IQR 5.8-10.4) after receiving a booster dose of BNT162b2 or mRNA-1273: eight (3.2%) of them remained seronegative after three vaccine doses, all of whom either had a primary immunodeficiency or were taking systemic immunosuppressant drugs.\n\nInterpretationWe identify multiple determinants of antibody responses to two doses of ChAdOx1 or BNT162b2, many of which are potentially modifiable. Booster doses of BNT162b2 or mRNA-1273 were highly effective in achieving seroconversion in those who failed to mount antibody responses following two doses of ChAdOx1 or BNT162b2.\n\nStudy registrationhttps://clinicaltrials.gov/ct2/show/NCT04330599\n\nFundingBarts Charity, Fischer Family Trust, The Exilarchs Foundation, DSM Nutritional Products, Health Data Research UK\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, medRxiv, and Google Scholar for papers published from January 1, 2020, to February 1, 2022, using the search terms (antibody OR humoral OR serologic* OR immunogenic*) AND (SARS-CoV-2 vaccine OR ChAdOx1 or BNT162b2 coronavirus), with no language restrictions. Population-based studies investigating multiple potential determinants of vaccine immunogenicity in people with known pre-vaccination SARS-CoV-2 serostatus are lacking.\n\nAdded value of this studyThis large population-based study, conducted in a population with known pre-vaccination SARS-CoV-2 serostatus, examines a comprehensive range of potential sociodemographic, behavioural, clinical, pharmacological and nutritional determinants of antibody responses to administration of two major SARS-CoV-2 vaccines (i.e., ChAdOx1 or BNT162b2), many of which have not previously been investigated. It is also the first population-based study to characterise antibody responses to booster doses of SARS-CoV-2 vaccines in adults who were seronegative after their primary course of vaccination.\n\nImplications of all the available evidenceIncreased risk of seronegativity following two doses of SARS-CoV-2 vaccines was associated with administration of ChAdOx1 vs BNT162b2, shorter interval between first and second vaccine doses, poorer self-assessed general health, immunocompromise and SARS-CoV-2 seronegativity pre-vaccination. Regular intake of vitamin D supplements was associated with reduced risk of post-vaccination seronegativity. Randomised controlled trials are now needed to test for causality. Booster doses of BNT162b2 or mRNA-1273 were highly effective in achieving seroconversion in the majority of people who failed to mount antibody responses following a primary course of vaccination, the few exceptions being a subset of those with primary immunodeficiency or systemic immunosuppressant drugs.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.02.10.22270799", @@ -2743,6 +2743,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.01.26.22269540", + "date": "2022-01-28", + "link": "https://medrxiv.org/cgi/content/short/2022.01.26.22269540", + "title": "Impact of voluntary risk-mitigation behaviour on transmission of the Omicron SARS-CoV-2 variant in England", + "authors": "Ellen Brooks-Pollock; Kate Northstone; Lorenzo Pellis; Francesca Scarabel; Amy C Thomas; Emily J Nixon; David A Matthews; Vicky Bower; Maria-Paz Garcia; Claire J Steves; Nicholas J Timpson; Leon Danon", + "affiliations": "University of Bristol; University of Bristol; The University of Manchester; University of Manchester; University of Bristol; University of Bristol; University of Bristol; King's College London; King's College London; King's College London; University of Bristol; Department of Engineering Mathematics, University of Bristol, UK.", + "abstract": "BackgroundThe Omicron variant of SARS-CoV-2 infection poses substantial challenges to public health. In England, \"plan B\" mitigation measures were introduced in December 2021 including increased home working and face coverings in shops, but stopped short of restrictions on social contacts. The impact of voluntary risk mitigation behaviours on future SARS-CoV-2 burden is unknown.\n\nMethodsWe developed a rapid online survey of risk mitigation behaviours during the winter 2021 festive period and deployed in two longitudinal cohort studies in the UK (Avon Longitudinal Study of Parents and Children (ALSPAC) and TwinsUK/Covid Symptom Study (CSS) Biobank) in December 2021. Using an individual-based, probabilistic model of COVID-19 transmission between social contacts with SARS-CoV-2 Omicron variant parameters and realistic vaccine coverage in England, we describe the potential impact of the SARS-CoV-2 Omicron wave in England in terms of the effective reproduction number and cumulative infections, hospital admissions and deaths. Using survey results, we estimated in real-time the impact of voluntary risk mitigation behaviours on the Omicron wave in England, if implemented for the entire epidemic wave.\n\nResultsOver 95% of survey respondents (NALSPAC=2,686 and NTwins=6,155) reported some risk mitigation behaviours, with vaccination and using home testing kits reported most frequently. Less than half of those respondents reported that their behaviour was due to \"plan B\". We estimate that without risk mitigation behaviours, the Omicron variant is consistent with an effective reproduction number between 2.5 and 3.5. Due to the reduced vaccine effectiveness against infection with the Omicron variant, our modelled estimates suggest that between 55% and 60% of the English population could be infected during the current wave, translating into between 15,000 and 46,000 cumulative deaths, depending on assumptions about vaccine effectiveness. We estimate that voluntary risk reduction measures could reduce the effective reproduction number to between 1.8 and 2.2 and reduce the cumulative number of deaths by up to 24%.\n\nConclusionsWe conclude that voluntary measures substantially reduce the projected impact of the SARS-CoV-2 Omicron variant, but that voluntary measures alone would be unlikely to completely control transmission.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.01.26.22269877", @@ -2799,6 +2813,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "bioRxiv", + "doi": "10.1101/2022.01.14.475727", + "date": "2022-01-18", + "link": "https://biorxiv.org/cgi/content/short/2022.01.14.475727", + "title": "Obesity associated with attenuated tissue immune cell responses in COVID-19", + "authors": "Shuang Andrew Guo; Georgina S Bowyer; John Robert Ferdinand; Mailis Maes; Zewen K Tuong; Eleanor Gilman; Rik G. H. Lindeboom; Masahiro Yoshida; Kaylee Worlock; Hudaa Gopee; Emily Stephenson; Paul A Lyons; Kenneth G. C. Smith; Muzlifah Haniffa; Kerstin B Meyer; Marko Z Nikolic; Richard G Wunderink; Alexander V Misharin; Gordon Dougan; Vilas Navapurkar; Sarah A Teichmann; Andrew Conway Morris; Menna R Clatworthy", + "affiliations": "University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; University College London; University College London; Newcastle University; Newcastle University; University of Cambridge; University of Cambridge; Newcastle University; Wellcome Sanger Institute; University College London; Northwestern University; Northwestern University; University of Cambridge; Cambridge University Hospitals NHS Foundation Trust; Wellcome Sanger Institute; University of Cambridge; University of Cambridge", + "abstract": "Obesity is common and associated with more severe COVID-19, proposed to be in part related to an adipokine-driven pro-inflammatory state. Here we analysed single cell transcriptomes from bronchiolar lavage in three adult cohorts, comparing obese (Ob, body mass index (BMI) >30m2) and non-obese (N-Ob, BMI <30m2). Surprisingly, we found that Ob subjects had attenuated lung immune/inflammatory responses in SARS-CoV-2 infection, with decreased expression of interferon (IFN), IFN{gamma} and tumour necrosis factor (TNF) alpha response gene signatures in almost all lung epithelial and immune cell subsets, and lower expression of IFNG and TNF in specific lung immune cells. Analysis of peripheral blood immune cells in an independent adult cohort showed a similar, but less marked, reduction in type I IFN and IFN{gamma} response genes, as well as decreased serum IFN, in Ob patients with SARS-CoV-2. Nasal immune cells from Ob children with COVID-19 also showed reduced enrichment of IFN and IFN{gamma} response genes. Altogether, these findings show blunted tissue immune responses in Ob COVID-19 patients, with clinical implications.", + "category": "immunology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.01.18.22269082", @@ -2813,20 +2841,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.01.16.22269146", - "date": "2022-01-17", - "link": "https://medrxiv.org/cgi/content/short/2022.01.16.22269146", - "title": "Development and validation of the Symptom Burden Questionnaire\u2122 for Long COVID: a Rasch analysis", - "authors": "Sarah E Hughes; Shamil Haroon; Anuradhaa Subramanian; Christel McMullan; Olalekan L Aiyegbusi; Grace M Turner; Louise Jackson; Elin Haf Davies; Chris Frost; Gary McNamara; Gary Price; Karen Matthews; Jennifer Camaradou; Jane Ormerod; Anita Walker; Melanie J Calvert", - "affiliations": "University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Aparito Limited; Aparito Limited; Aparito Limited; University of Birmingham; Patient and Public Involvement, Therapies for Long COVID (TLC) study, University of Birmingham; Patient and Public Involvement, Therapies for Long COVID (TLC) study, University of Birmingham; Patient and Public Involvement, Therapies for Long COVID (TLC) study, University of Birmingham; University of Birmingham; University of BIrmingham", - "abstract": "ObjectiveTo describe the development and initial validation of a novel patient-reported outcome measure of Long COVID symptom burden, the Symptom-Burden Questionnaire for Long COVID (SBQ-LC).\n\nMethod and FindingsThis multi-phase, prospective mixed-methods study took place between April and August 2021 in the United Kingdom (UK). A conceptual framework and initial item pool were developed from published systematic reviews. Further concept elicitation and content validation was undertaken with adults with lived experience (n = 13) and clinicians (n = 10), and face validity was confirmed by the Therapies for Long COVID Study Patient and Public Involvement group (n = 25). The draft SBQ-LC was field tested by adults with self-reported Long COVID recruited via social media and international Long COVID support groups (n = 274). Thematic analysis of interview and survey transcripts established content validity and informed construction of the draft questionnaire. Rasch analysis of field test data guided item and scale refinement and provided evidence of the final SBQ-LCs measurement properties. The Rasch-derived SBQ-LC is composed of 17 independent scales with promising psychometric properties. Respondents rate symptom burden during the past 7-days using a dichotomous response or 4-point rating scale. Each scale provides coverage of a different symptom domain and returns a summed raw score that may be converted to a linear (0 - 100) score. Higher scores represent higher symptom burden.\n\nConclusionsThe SBQ-LC is a comprehensive patient-reported assessment of Long COVID symptom burden developed using modern psychometric methods. It measures symptoms of Long COVID important to individuals with lived experience and may be used to evaluate the impact of interventions and inform best practice in clinical management.", - "category": "health informatics", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.01.13.22268948", @@ -3009,6 +3023,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.12.16.21267934", + "date": "2021-12-17", + "link": "https://medrxiv.org/cgi/content/short/2021.12.16.21267934", + "title": "Predictors of SARS-CoV-2 infection in a multi-ethnic cohort of United Kingdom healthcare workers: a prospective nationwide cohort study (UK-REACH)", + "authors": "Christopher A Martin; Daniel Pan; Carl Melbourne; Lucy Teece; Avinash Aujayeb; Rebecca F Baggaley; Luke Bryant; Sue Carr; Bindu Gregary; Amit Gupta; Anna Louise Guyatt; Catherine John; Chris McManus; Joshua Nazareth; Laura B Nellums; Rubina Reza; Sandra Simpson; Martin D Tobin; Katherine Woolf; Stephen Zingwe; Kamlesh Khunti; Keith R Abrams; Laura J Gray; Manish Pareek; - UK-REACH Study Collaborative Group", + "affiliations": "University of Leicester; University of Leicester; University of Leicester; University of Leicester; Northumbria Specialist Emergency Care Hospital; University of Leicester; University of Leicester; General Medical Council; Royal Preston Hospital; Oxford University Hospitals NHS Foundation Trust; University of Leicester; University of Leicester; University College London; University of Leicester; University of Nottingham; Derbyshire Healthcare NHS Foundation Trust; Nottinghamshire Healthcare NHS Foundation Trust; University of Leicester; University College London; Berkshire Healthcare NHS Foundation Trust; University of Leicester; University of Warwick; University of Leicester; University of Leicester; ", + "abstract": "IntroductionHealthcare workers (HCWs), particularly those from ethnic minority groups, have been shown to be at disproportionately higher risk of infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) compared to the general population. However, there is insufficient evidence on how demographic and occupational factors influence infection risk among ethnic minority HCWs.\n\nMethodsWe conducted a cross-sectional analysis using data from the United Kingdom Research study into Ethnicity And COVID-19 Outcomes in Healthcare workers (UK-REACH) cohort study. We used logistic regression to examine associations of demographic, household and occupational predictor variables with SARS-CoV-2 infection (defined by PCR, serology or suspected COVID-19) in a diverse group of HCWs.\n\nResults2,496 of the 10,772 HCWs (23.2%) who worked during the first UK national lockdown in March 2020 reported previous SARS-CoV-2 infection. In an adjusted model, demographic and household factors associated with increased odds of infection included younger age, living with other key workers and higher religiosity. Important occupational risk factors associated with increased odds of infection included attending to a higher number of COVID-19 positive patients (aOR 2.49, 95%CI 2.03-3.05 for [≥]21 patients per week vs none), working in a nursing or midwifery role (1.35, 1.15- 1.58, compared to doctors), reporting a lack of access to personal protective equipment (1.27, 1.15 - 1.41) and working in an ambulance (1.95, 1.52-2.50) or hospital inpatient setting (1.54, 1.37 - 1.74). Those who worked in Intensive Care Units were less likely to have been infected (0.76, 0.63-0.90) than those who did not. Black HCWs were more likely to have been infected than their White colleagues, an effect which attenuated after adjustment for other known predictors.\n\nConclusionsWe identified key sociodemographic and occupational risk factors associated with SARS-CoV-2 infection amongst UK HCWs, and have determined factors that might contribute to a disproportionate odds of infection in HCWs from Black ethnic groups. These findings demonstrate the importance of social and occupational factors in driving ethnic disparities in COVID-19 outcomes, and should inform policies, including targeted vaccination strategies and risk assessments aimed at protecting HCWs in future waves of the COVID-19 pandemic.\n\nTrial registrationISRCTN 11811602", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.12.16.21267904", @@ -3163,6 +3191,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.12.08.21267353", + "date": "2021-12-08", + "link": "https://medrxiv.org/cgi/content/short/2021.12.08.21267353", + "title": "The challenge of limited vaccine supplies: impact of prior infection on anti-spike IgG antibody trajectories after a single COVID-19 vaccination", + "authors": "Jia Wei; Philippa Matthews; Nicole Stoesser; Ian Diamond; Ruth Studley; Emma Rourke; Duncan Cook; John Bell; John Newton; Jeremy Farrar; Alison Howarth; Brian Marsden; Sarah Hoosdally; Yvonne Jones; David Stuart; Derrick W Crook; tim E peto; Ann Sarah Walker; David W Eyre; Koen B Pouwels; - COVID-19 Infection Survey team", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; NIHR Oxford Biomedical Research Centre; oxford university; University of Oxford; University of Oxford; University of Oxford; ", + "abstract": "Given high SARS-CoV-2 incidence, coupled with slow and inequitable vaccine roll-out, there is an urgent need for evidence to underpin optimum vaccine deployment, aiming to maximise global population immunity at speed. We evaluate whether a single vaccination in previously infected individuals generates similar initial and subsequent antibody responses to two vaccinations in those without prior infection. We compared anti-spike IgG antibody responses after a single dose of ChAdOx1, BNT162b2, or mRNA-1273 SARS-CoV-2 vaccines in the COVID-19 Infection Survey in the UK general population. In 100,849 adults who received at least one vaccination, 13,404 (13.3%) had serological and/or PCR evidence of prior infection. Prior infection significantly boosted antibody responses for all three vaccines, producing a higher peak level and longer half-life, and a response comparable to those without prior infection receiving two vaccinations. In those with prior infection, median time above the positivity threshold was estimated to last for >1 year after the first dose. Single-dose vaccination targeted to those previously infected may provide protection in populations with high rates of previous infection faced with limited vaccine supply, as an interim measure while vaccine campaigns are scaled up.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.12.03.21266112", @@ -3919,20 +3961,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.09.02.21262965", - "date": "2021-09-02", - "link": "https://medrxiv.org/cgi/content/short/2021.09.02.21262965", - "title": "Whole genome sequencing identifies multiple loci for critical illness caused by COVID-19", - "authors": "Athanasios Kousathanas; Erola Pairo-Castineira; Konrad Rawlik; Alex Stuckey; Christopher A Odhams; Susan Walker; Clark D Russell; Tomas Malinauskas; Jonathan Millar; Katherine S Elliott; Fiona Griffiths; Wilna Oosthuyzen; Kirstie Morrice; Sean Keating; Bo Wang; Daniel Rhodes; Lucija Klaric; Marie Zechner; Nick Parkinson; Andrew D. Bretherick; Afshan Siddiq; Peter Goddard; Sally Donovan; David Maslove; Alistair Nichol; Malcolm G Semple; Tala Zainy; Fiona Maleady-Crowe; Linda Todd; Shahla Salehi; Julian Knight; Greg Elgar; Georgia Chan; Prabhu Arumugam; Tom A Fowler; Augusto Rendon; Manu Shankar-Hari; Charlotte Summers; Charles Hinds; Peter Horby; Danny McAuley; Hugh Montgomery; Peter J.M. Openshaw; Yang Wu; Jian Yang; Paul Elliott; Timothy Walsh; - GenoMICC Investigators; - 23andMe Investigators; - Covid-19 Human Genetics Initiative; Angie Fawkes; Lee Murphy; Kathy Rowan; Chris P Ponting; Veronique Vitart; James F Wilson; Richard H Scott; Sara Clohisey; Loukas Moutsianas; Andy Law; Mark J Caulfield; J. Kenneth Baillie", - "affiliations": "Genomics England, London UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK; Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England, London UK; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, ON, Canada.; Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland.; NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, L; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Department of Intensive Care Medicine, Guy's and St. Thomas NHS Foundation Trust, London, UK.; Department of Medicine, University of Cambridge, Cambridge, UK.; William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK.; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.; Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK; UCL Centre for Human Health and Performance, London, W1T 7HA, UK.; National Heart and Lung Institute, Imperial College London, London, UK; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Imperial College, London; Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK.; ; ; ; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; Intensive Care National Audit & Research Centre, London, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK.; Genomics England, London UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England, London UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England, London UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK", - "abstract": "Critical illness in COVID-19 is caused by inflammatory lung injury, mediated by the host immune system. We and others have shown that host genetic variation influences the development of illness requiring critical care1 or hospitalisation2;3;4 following SARS-Co-V2 infection. The GenOMICC (Genetics of Mortality in Critical Care) study recruits critically-ill cases and compares their genomes with population controls in order to find underlying disease mechanisms.\n\nHere, we use whole genome sequencing and statistical fine mapping in 7,491 critically-ill cases compared with 48,400 population controls to discover and replicate 22 independent variants that significantly predispose to life-threatening COVID-19. We identify 15 new independent associations with critical COVID-19, including variants within genes involved in interferon signalling (IL10RB, PLSCR1), leucocyte differentiation (BCL11A), and blood type antigen secretor status (FUT2). Using transcriptome-wide association and colocalisation to infer the effect of gene expression on disease severity, we find evidence implicating expression of multiple genes, including reduced expression of a membrane flippase (ATP11A), and increased mucin expression (MUC1), in critical disease.\n\nWe show that comparison between critically-ill cases and population controls is highly efficient for genetic association analysis and enables detection of therapeutically-relevant mechanisms of disease. Therapeutic predictions arising from these findings require testing in clinical trials.", - "category": "intensive care and critical care medicine", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.08.26.21262523", @@ -4801,20 +4829,6 @@ "author_similarity": 100, "affiliation_similarity": 92 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.06.08.21258531", - "date": "2021-06-08", - "link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258531", - "title": "The UK Coronavirus Job Retention Scheme and changes in diet, physical activity and sleep during the COVID-19 pandemic: Evidence from eight longitudinal studies", - "authors": "Bozena Wielgoszewska; Jane Maddock; Michael J Green; Giorgio Di Gessa; Sam Parsons; Gareth J Griffith; Jazz Croft; Anna J Stevenson; Charlotte Booth; Richard J Silverwood; David Bann; Praveetha Patalay; Alun D Hughes; Nishi Chaturvedi; Laura D Howe; Emla Fitzsimons; Srinivasa Vittal Katikireddi; George B Ploubidis", - "affiliations": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Unit for Lifelong Health and Ageing, University College London; MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; Institute of Epidemiology and Health Care, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Integrative Epidemiology Unit, University of Bristol; MRC Integrative Epidemiology Unit, University of Bristol; Centre for Genomic and Experimental Medicine, University of Edinburgh; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; UCL; MRC Unit for Lifelong Health and Ageing, University College London; MRC Unit for Lifelong Health and Ageing, University College London; MRC Integrative Epidemiology Unit, University of Bristol; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; Centre for Longitudinal Studies, UCL Social Research Institute, University College London", - "abstract": "BackgroundIn March 2020 the UK implemented the Coronavirus Job Retention Scheme (furlough) to minimize job losses. Our aim was to investigate associations between furlough and diet, physical activity, and sleep during the early stages of the COVID-19 pandemic.\n\nMethodsWe analysed data from 25,092 participants aged 16 to 66 years from eight UK longitudinal studies. Changes in employment (including being furloughed) were defined by comparing employment status pre- and during the first lockdown. Health behaviours included fruit and vegetable consumption, physical activity, and sleeping patterns. Study-specific estimates obtained using modified Poisson regression, adjusting for socio-demographic characteristics and pre-pandemic health and health behaviours, were statistically pooled using random effects meta-analysis. Associations were also stratified by sex, age, and education.\n\nResultsAcross studies, between 8 and 25% of participants were furloughed. Compared to those who remained working, furloughed workers were slightly less likely to be physically inactive (RR:0.85, [0.75-0.97], I2=59%) and did not differ in diet and sleep behaviours, although findings for sleep were heterogenous (I2=85%). In stratified analyses, furlough was associated with low fruit and vegetable consumption among males (RR=1.11; 95%CI: 1.01-1.22; I2: 0%) but not females (RR=0.84; 95%CI: 0.68-1.04; I2: 65%). Considering change in these health behaviours, furloughed workers were more likely than those who remained working to report increased fruit and vegetable consumption, exercise, and hours of sleep.\n\nConclusionsThose furloughed exhibited broadly similar levels of health behaviours to those who remained in employment during the initial stages of the pandemic. There was little evidence to suggest that such social protection policies if used in the post-pandemic recovery period and during future economic crises would have adverse impacts on population health behaviours.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.06.08.21258132", @@ -4927,20 +4941,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.05.18.21257396", - "date": "2021-05-23", - "link": "https://medrxiv.org/cgi/content/short/2021.05.18.21257396", - "title": "A Phenome-Wide Association Study of genes associated with COVID-19 severity reveals shared genetics with complex diseases in the Million Veteran Program", - "authors": "Anurag Verma; Noah L. Tsao; Lauren O. Thomann; Yuk-Lam Ho; Sudha K. Iyengar; Shiuh-Wen Luoh; Rotonya Carr; Dana C. Crawford; Jimmy T. Efird; Giulio Genovese; Adriana Hung; Kerry L. Ivey; Michael G. Levin; Julie Lynch; Pradeep Natarajan; Saiju Pyarajan; Alexander Bick; Lauren Costa; Giulio Genovese; Richard Hauger; Ravi Madduri; Gita A. Pathak; Renato Polimanti; Benjamin F. Voight; Marijana Vujkovic; Maryam Zekavat; Hongyu Zhao; Marylyn Ritchie; Kyong-Mi Chang; Kelly Cho; Juan P Casas; Philip S Tsao; J. Michael Gaziano; Christopher O?Donnell; Scott M. Damrauer; Katherine P. Liao", - "affiliations": "Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Ph; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Phi; VA Boston Healthcare System, Boston, Massachusetts, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Departments of Population and Quantitative Health Sciences, Ophthalmology and Visual Sciences and Genetics and Genome Sciences, Case Western Reserve University,; VA Portland Health Care System, Portland OR, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Ph; Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA; Cooperative Studies Program Epidemiology Center, Health Services Research and Development, DVAHCS (Duke University Affiliate), Durham, North Carolina, USA.; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.; Tennessee Valley Healthcare System (Nashville VA) , Nashville, Tennessee, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, Utah, USA.; Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA.; VA Boston Healthcare System, Boston, Massachusetts, USA;Harvard Medical School, Boston, Massachusetts, USA; VA Boston Healthcare System, Boston, Massachusetts, USA;Vanderbilt University, Nashville, Tennessee, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.; Department of Psychiatry, University of California, San Diego, La Jolla, CA; Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, ; University of Chicago Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois, USA;Data Science and Learning Division, Arg; Department of Psychiatry, Yale School of Medicine, Connecticut, USA; Department of Psychiatry, Yale School of Medicine, Connecticut, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Ph; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Ph; VA Boston Healthcare System, Boston, Massachusetts, USA; VA Connecticut Healthcare System, West Haven, CT, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; VA Palo Alto Health Care System, Palo Alto, California, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; VA Boston Healthcare System, Boston, Massachusetts, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Phi; VA Boston Healthcare System, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA; Brigham and Women's Hospital, Boston, Massachusetts", - "abstract": "The study aims to determine the shared genetic architecture between COVID-19 severity with existing medical conditions using electronic health record (EHR) data. We conducted a Phenome-Wide Association Study (PheWAS) of genetic variants associated with critical illness (n=35) or hospitalization (n=42) due to severe COVID-19 using genome-wide association summary from the Host Genetics Initiative. PheWAS analysis was performed using genotype-phenotype data from the Veterans Affairs Million Veteran Program (MVP). Phenotypes were defined by International Classification of Diseases (ICD) codes mapped to clinically relevant groups using published PheWAS methods. Among 658,582 Veterans, variants associated with severe COVID-19 were tested for association across 1,559 phenotypes. Variants at the ABO locus (rs495828, rs505922) associated with the largest number of phenotypes (nrs495828= 53 and nrs505922=59); strongest association with venous embolism, odds ratio (ORrs495828 1.33 (p=1.32 x 10-199), and thrombosis ORrs505922 1.33, p=2.2 x10-265. Among 67 respiratory conditions tested, 11 had significant associations including MUC5B locus (rs35705950) with increased risk of idiopathic fibrosing alveolitis OR 2.83, p=4.12 x 10-191; CRHR1 (rs61667602) associated with reduced risk of pulmonary fibrosis, OR 0.84, p=2.26x 10-12. The TYK2 locus (rs11085727) associated with reduced risk for autoimmune conditions, e.g., psoriasis OR 0.88, p=6.48 x10-23, lupus OR 0.84, p=3.97 x 10-06. PheWAS stratified by genetic ancestry demonstrated differences in genotype-phenotype associations across ancestry. LMNA (rs581342) associated with neutropenia OR 1.29 p=4.1 x 10-13 among Veterans of African ancestry but not European. Overall, we observed a shared genetic architecture between COVID-19 severity and conditions related to underlying risk factors for severe and poor COVID-19 outcomes. Differing associations between genotype-phenotype across ancestries may inform heterogenous outcomes observed with COVID-19. Divergent associations between risk for severe COVID-19 with autoimmune inflammatory conditions both respiratory and non-respiratory highlights the shared pathways and fine balance of immune host response and autoimmunity and caution required when considering treatment targets.", - "category": "genetic and genomic medicine", - "match_type": "fuzzy", - "author_similarity": 91, - "affiliation_similarity": 92 - }, { "site": "medRxiv", "doi": "10.1101/2021.05.13.21257161", @@ -5039,20 +5039,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.05.17.21257223", - "date": "2021-05-17", - "link": "https://medrxiv.org/cgi/content/short/2021.05.17.21257223", - "title": "Serial interval of COVID-19 and the effect of Variant B.1.1.7: analyses from a prospective community cohort study (Virus Watch).", - "authors": "Cyril Roman Geismar; Ellen Fragaszy; Vincent Grigori Nguyen; Wing Lam Erica Fong; Madhumita Shrotri; Sarah Beale; Alison Rodger; Vasileios Lampos; Thomas Edward Byrne; Jana Kovar; Annalan Navaratnam; Parth Patel; Robert W Aldridge; Andrew Hayward; - Virus Watch Collaborative", - "affiliations": "University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ", - "abstract": "IntroductionIncreased transmissibility of B.1.17 variant of concern (VOC) in the UK may explain its rapid emergence and global spread. We analysed data from putative household infector - infectee pairs in the Virus Watch Community cohort study to assess the serial interval of COVID-19 and whether this was affected by emergence of the B.1.17 variant.\n\nMethodsThe Virus Watch study is an online, prospective, community cohort study following up entire households in England and Wales during the COVID-19 pandemic. Putative household infector-infectee pairs were identified where more than one person in the household had a positive swab matched to an illness episode. Data on whether individual infections were caused by the B.1.1.7 variant were not available. We therefore developed a classification system based on the percentage of cases estimated to be due to B.1.17 in national surveillance data for different English regions and study weeks.\n\nResultsOut of 24,887 illnesses reported, 915 tested positive for SARS-CoV-2 and 186 likely infector-infectee pairs in 186 households amongst 372 individuals were identified. The mean COVID-19 serial interval was 3.18 (95%CI: 2.55 - 3.81) days. There was no significant difference (p=0.267) between the mean serial interval for Variants of Concern (VOC) hotspots (mean = 3.64 days, (95%CI: 2.55 - 4.73)) days and non-VOC hotspots, (mean = 2.72 days, (95%CI: 1.48 - 3.96)).\n\nConclusionsOur estimates of the average serial interval of COVID-19 are broadly similar to estimates from previous studies and we find no evidence that B.1.1.7 is associated with a change in serial intervals. Alternative explanations such as increased viral load, longer period of viral shedding or improved receptor binding may instead explain the increased transmissibility and rapid spread and should undergo further investigation.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.05.13.21257146", @@ -6467,6 +6453,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.01.22.21249968", + "date": "2021-01-25", + "link": "https://medrxiv.org/cgi/content/short/2021.01.22.21249968", + "title": "An external validation of the QCovid risk prediction algorithm for risk of mortality from COVID-19 in adults: national validation cohort study in England", + "authors": "Vahe Nafilyan; Ben Humberstone; Nisha Metha; Ian Diamond; Luke Lorenzi; Piotr Pawelek; Ryan Schofield; Jasper Morgan; Paul Brown; Ronan Lyons; Aziz Sheikh; Julia Hippisley-Cox", + "affiliations": "Office for National Statistics; Office for National Statistics; Office of the Chief Medical Officer; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Swansea University; University of Edinburgh; University of Oxford", + "abstract": "BackgroundTo externally validate a risk prediction algorithm (QCovid) to estimate mortality outcomes from COVID-19 in adults in England.\n\nMethodsPopulation-based cohort study using the ONS Public Health Linked Data Asset, a cohort based on the 2011 Census linked to Hospital Episode Statistics, the General Practice Extraction Service Data for pandemic planning and research, radiotherapy and systemic chemotherapy records. The primary outcome was time to COVID-19 death, defined as confirmed or suspected COVID-19 death as per death certification. Two time periods were used: (a) 24th January to 30th April 2020; and (b) 1st May to 28th July 2020. We evaluated the performance of the QCovid algorithms using measures of discrimination and calibration for each validation time period.\n\nFindingsThe study comprises 34,897,648 adults aged 19-100 years resident in England. There were 26,985 COVID-19 deaths during the first time-period and 13,177 during the second. The algorithms had good calibration in the validation cohort in both time periods with close correspondence of observed and predicted risks. They explained 77.1% (95% CI: 76.9% to 77.4%) of the variation in time to death in men in the first time-period (R2); the D statistic was 3.76 (95% CI: 3.73 to 3.79); Harrells C was 0.935 (0.933 to 0.937). Similar results were obtained for women, and in the second time-period. In the top 5% of patients with the highest predicted risks of death, the sensitivity for identifying deaths in the first time period was 65.9% for men and 71.7% for women. People in the top 20% of predicted risks of death accounted for 90.8% of all COVID-19 deaths for men and 93.0% for women.\n\nInterpretationThe QCovid population-based risk algorithm performed well, showing very high levels of discrimination for COVID-19 deaths in men and women for both time periods. It has the potential to be dynamically updated as the pandemic evolves and therefore, has potential use in guiding national policy.\n\nFundingNational Institute of Health Research\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSPublic policy measures and clinical risk assessment relevant to COVID-19 need to be aided by rigorously developed and validated risk prediction models. A recent living systematic review of published risk prediction models for COVID-19 found most models are subject to a high risk of bias with optimistic reported performance, raising concern that these models may be unreliable when applied in practice. A population-based risk prediction model, QCovid risk prediction algorithm, has recently been developed to identify adults at high risk of serious COVID-19 outcomes, which overcome many of the limitations of previous tools.\n\nAdded value of this studyCommissioned by the Chief Medical Officer for England, we validated the novel clinical risk prediction model (QCovid) to identify risks of short-term severe outcomes due to COVID-19. We used national linked datasets from general practice, death registry and hospital episode data for a population-representative sample of over 34 million adults. The risk models have excellent discrimination in men and women (Harrells C statistic>0.9) and are well calibrated. QCovid represents a new, evidence-based opportunity for population risk-stratification.\n\nImplications of all the available evidenceQCovid has the potential to support public health policy, from enabling shared decision making between clinicians and patients in relation to health and work risks, to targeted recruitment for clinical trials, and prioritisation of vaccination, for example.", + "category": "public and global health", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "bioRxiv", "doi": "10.1101/2021.01.25.428136", @@ -6481,6 +6481,20 @@ "author_similarity": 96, "affiliation_similarity": 94 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.01.21.20240887", + "date": "2021-01-22", + "link": "https://medrxiv.org/cgi/content/short/2021.01.21.20240887", + "title": "The psychosocial impact of the COVID-19 pandemic on 4,378 UK healthcare workers and ancillary staff: initial baseline data from a cohort study collected during the first wave of the pandemic.", + "authors": "Danielle Lamb; Sam Gnanapragasam; Neil Greenberg; Rupa Bhundia; Ewan Carr; Matthew Hotopf; Reza Razavi; Rosalind Raine; Sean Cross; Amy Dewar; Mary Docherty; Sarah Dorrington; Stephani Hatch; Charlotte Wilson-Jones; Daniel Leightley; Ira Madan; Sally Marlow; Isabel McMullen; Anne Marie Rafferty; Martin Parsons; Catherine Polling; Danai Serfioti; Helen Gaunt; Peter Aitken; Joanna Morris-Bone; Chloe Simela; Veronica French; Rachel Harris; Sharon A.M. Stevelink; Simon Wessely", + "affiliations": "Department of Applied Health Research, UCL, 1-19 Torrington Place, London, WC1E 7HB; South London and Maudsley NHS Foundation Trust, London, UK; Health Protection Research Unit, King's College London, Weston Education Centre, 10 Cutcombe Road, London, SE5 9RJ; Department of Psychological Medicine, King's College London, London, UK.; Department of Biostatistics and Health Informatics, King's College London, London, UK; National Institute of Health Research Biomedical Research Centre at the South London and Maudsley NHS Foundation Trust.; 1 Lambeth Palace Rd, South Bank, London, SE1 7EU; Dept of Applied Health Research, UCL; Department of Psychological Medicine, King's College Hospital. Denmark Hill. SE5 9RS; Guy's and St Thomas' NHS Foundation Trust; Department of Psychological Medicine, King's College Hospital. Denmark Hill. SE5 9RS; Institute of Psychiatry, Psychology and Neuroscience, King's College London; Institute of Psychiatry, Psychology and Neuroscience, King's College London; Institute of Psychiatry, Psychology and Neuroscience, King's College London; King's Centre for Military Health Research, Department of Psychological Medicine, King's College London, London, UK. AND Department of Psychological Medicine, K; Guy's and St Thomas' NHS Foundation Trust, London; Institute of Psychiatry, Psychology and Neuroscience, King's College London; Department of Psychological Medicine, King's College Hospital, South London and Maudsley NHS Foundation Trust; Adult Nursing, King's College London; Mental Health Liaison Team, King's College Hospital; Institute of Psychiatry, Psychology and Neuroscience, King's College London; King's Centre for Military Health Research, King's College London, Room 307, Weston Education Centre, 10 Cutcombe Road, London SE5 9RJ; University Hospital of Leciester NHS Trust. Groby Road Leciester LE4 9QP; Devon Partnership NHS Trust, Trust HQ, R&D, Dryden Road, Exeter, Devon, EX2 5AF; Avon & Wiltshire Mental Health Partnership NHS Trust, R&D, Fromeside, Blackberry Hill Hospital, Bristol, BS16 1EG; Guy's and St Thomas' NHS Foundation Trust, London; Nottinghamshire Healthcare NHS Foundation Trust; Cornwall Partnership Foundation NHS Trust/ Research and Innovation Team; King's Centre for Military Health Research, Department of Psychological Medicine, King's College London, London, UK. AND Department of Psychological Medicine, K; Department of Psychological Medicine, King's College London, Weston Education, Denmark Hill, London, SE5 9JR", + "abstract": "ObjectivesThis study reports preliminary findings on the prevalence of, and factors associated with, mental health and wellbeing outcomes of healthcare workers during the early months (April-June) of the COVID-19 pandemic in the UK.\n\nMethodsPreliminary cross-sectional data were analysed from a cohort study (n=4,378). Clinical and non-clinical staff of three London-based NHS Trusts (UK), including acute and mental health Trusts, took part in an online baseline survey. The primary outcome measure used is the presence of probable common mental disorders (CMDs), measured by the General Health Questionnaire (GHQ-12). Secondary outcomes are probable anxiety (GAD-7), depression (PHQ-9), Post-Traumatic Stress Disorder (PTSD) (PCL-6), suicidal ideation (CIS-R), and alcohol use (AUDIT). Moral injury is measured using the Moray Injury Event Scale (MIES).\n\nResultsAnalyses showed substantial levels of CMDs (58.9%, 95%CI 58.1 to 60.8), and of PTSD (30.2%, 95%CI 28.1 to 32.5) with lower levels of depression (27.3%, 95%CI 25.3 to 29.4), anxiety (23.2%, 95%CI 21.3 to 25.3), and alcohol misuse (10.5%, 95%CI, 9.2 to 11.9). Women, younger staff, and nurses tended to have poorer outcomes than other staff, except for alcohol misuse. Higher reported exposure to moral injury (distress resulting from violation of ones moral code) was strongly associated with increased levels of CMDs, anxiety, depression, PTSD symptoms, and alcohol misuse.\n\nConclusionsOur findings suggest that mental health support for healthcare workers should consider those demographics and occupations at highest risk. Rigorous longitudinal data are needed in order to respond to the potential long-term mental health impacts of the pandemic.\n\nHighlightsO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LILarge-scale population studies report increased prevalence of depression, anxiety, and psychological distress during the COVID-19 pandemic.\nC_LIO_LIEvidence from previous epidemics indicates a high and persistent burden of adverse mental health outcomes among healthcare workers.\nC_LI\n\nWhat are the new findings?O_LISubstantial levels of probable common mental disorders and post-traumatic stress disorder were found among healthcare workers.\nC_LIO_LIGroups at increased risk of adverse mental health outcomes included women, nurses, and younger staff, as well as those who reported higher levels of moral injury.\nC_LI\n\nHow might this impact on policy or clinical practice in the foreseeable future?O_LIThe mental health offering to healthcare workers must consider the interplay of demographic, social, and occupational factors.\nC_LIO_LIAdditional longitudinal research that emphasises methodological rigor, namely with use of standardised diagnostic interviews to establish mental health diagnoses, is necessary to better understand the mental health burden, identify those most at risk, and provide appropriate support without pathologizing ordinary distress responses.\nC_LI", + "category": "psychiatry and clinical psychology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.01.20.21250158", @@ -6691,6 +6705,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.12.21.20248607", + "date": "2020-12-22", + "link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248607", + "title": "Time use and social mixing during and around festive periods: Potential changes in the age distribution of COVID-19 cases from increased intergenerational interactions", + "authors": "Edwin van Leeuwen; Frank G. Sandmann; Rosalind M. Eggo; - PHE Joint modelling group; Peter J. White", + "affiliations": "Public Health England; Public Health England; London School of Hygiene &Tropical Medicine; London School of Hygiene & Tropical Medicine; ; Public Health England; Imperial College London", + "abstract": "RationaleAmid the ongoing coronavirus disease 2019 (COVID-19) pandemic in which many countries have adopted physical distancing measures, tiered restrictions, and episodic \"lockdowns,\" the impact of potentially increased social mixing during festive holidays on the age distribution of new COVID-19 cases remains unclear.\n\nObjectiveWe aimed to gain insights into possible changes in the age distribution of COVID-19 cases in the UK after temporarily increased intergenerational interactions in late December 2020.\n\nMethodWe modelled changes in time use and social mixing based on age-stratified contact rates using historical nationally-representative surveys and up-to-date Google mobility data from four weeks before and after the festive period. We explored changes in the effective reproduction number and the age distribution of cases, in four scenarios: (1) \"normal\": time use and contact patterns as observed historically, (2) \"pre-lockdown\": patterns as seen before the lockdown in November 2020, (3) \"lockdown\": patterns restricted as in November 2020, and (4) \"festive break\": similar to 3 but with social visits over the holiday period as in 1.\n\nResultsAcross ages, the estimated Reff decreases during the festive break in scenarios 1-3 and returns to pre-holiday levels in scenarios 2-3, while remaining relatively stable in scenario 4. Relative incidence is likely to decrease in children aged 0-15 but increase in other ages. Changes in age distribution were large during the holidays, and are likely to start before the holidays for individuals aged 16-24 years in scenarios 1-3.\n\nConclusionsOur modelling findings suggest that increased contacts during the festive period may shift the age distribution of COVID-19 cases from children towards adults. Given that COVID-19-related hospitalisations and deaths rise by age, more intergenerational mixing risks an increased burden in the period following the holidays.\n\nHighlightsO_LIHome visits are associated with increased intergenerational mixing.\nC_LIO_LIThe effective reproduction number is likely to remain stable or even reduce slightly due to a reduction in contacts at work and school.\nC_LIO_LIRelative incidence is likely to become lower in children, but higher in the\nC_LIO_LIolder (more vulnerable) age groups around the holiday period, which could lead to increased health care burden.\nC_LI", + "category": "public and global health", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.12.21.20248475", @@ -7041,20 +7069,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.11.18.20233932", - "date": "2020-11-20", - "link": "https://medrxiv.org/cgi/content/short/2020.11.18.20233932", - "title": "REACT-1 round 6 updated report: high prevalence of SARS-CoV-2 swab positivity with reduced rate of growth in England at the start of November 2020", - "authors": "Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E. Walters; Haowei Wang; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott", - "affiliations": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear", - "abstract": "BackgroundEngland is now in the midst of its second wave of the COVID-19 pandemic. Multiple regions of the country are at high infection prevalence and all areas experienced rapid recent growth of the epidemic during October 2020.\n\nMethodsREACT-1 is a series of community surveys of SARS-CoV-2 RT-PCR swab-positivity in England designed to monitor the spread of the epidemic and thus increase situational awareness. Round 6 of REACT-1 commenced swab-collection on 16th October. A prior interim report included data from 16th to 25th October for 85,971 participants. Here, we report data for the entire round on 160,175 participants with swab results obtained up to 2nd November 2020.\n\nResultsOverall weighted prevalence of infection in the community in England was 1.3% or 130 people per 10,000 infected, up from 60 people per 10,000 in the round 5 report (18th September to 5th October 2020), doubling every 24 days on average since the prior round. The corresponding R number was estimated to be 1.2. Prevalence of infection was highest in North West (2.4%, up from 1.2%), followed by Yorkshire and The Humber (2.3% up from 0.84%), West Midlands (1.6% up from 0.60%), North East (1.5% up from 1.1%), East Midlands (1.3% up from 0.56%), London (0.97%, up from 0.54%), South West (0.80% up from 0.33%), South East (0.69% up from 0.29%), and East of England (0.69% up from 0.30%). Rapid growth in the South observed in the first half of round 6 was no longer apparent in the second half of round 6. We also observed a decline in prevalence in Yorkshire and The Humber during this period. Comparing the first and second halves of round 6, there was a suggestion of decline in weighted prevalence in participants aged 5 to 12 years and in those aged 25 to 44 years. While prevalence remained high, in the second half of round 6 there was suggestion of a slight fall then rise that was seen nationally and also separately in both the North and the South.\n\nConclusionThe impact of the second national lockdown in England is not yet known. We provide here a detailed description of swab-positivity patterns at national, regional and local scales for the period immediately preceding lockdown, against which future trends in prevalence can be evaluated.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.11.18.20230649", @@ -7419,6 +7433,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.10.26.20219428", + "date": "2020-10-27", + "link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219428", + "title": "Community prevalence of SARS-CoV-2 in England during April to September 2020: Results from the ONS Coronavirus Infection Survey", + "authors": "Koen B Pouwels; Thomas House; Emma Pritchard; Julie V Robotham; Paul Birrell; Andrew Gelman; Karina-Doris Vihta; Nikola Bowers; Ian Boreham; Heledd Thomas; James Lewis; Iain Bell; John I Bell; John N Newton; Jeremy Farrar; Ian Diamond; Pete Benton; Ann Sarah Walker", + "affiliations": "University of Oxford; University of Manchester; University of Oxford; Public Health England; Public Health England; Columbia University; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics; Office for National Statistics; University of Oxford", + "abstract": "BackgroundDecisions regarding the continued need for control measures to contain the spread of SARS-CoV-2 rely on accurate and up-to-date information about the number of people and risk factors for testing positive. Existing surveillance systems are not based on population samples and are generally not longitudinal in design.\n\nMethodsFrom 26 April to 19 September2020, 514,794 samples from 123,497 individuals were collected from individuals aged 2 years and over from a representative sample of private households from England. Participants completed a questionnaire and nose and throat swab were taken. The percentage of individuals testing positive for SARS-CoV-2 RNA was estimated over time using dynamic multilevel regression and post-stratification, to account for potential residual non-representativeness. Potential changes in risk factors for testing positive over time were also evaluated using multilevel regression models.\n\nFindingsBetween 26 April and 19 September 2020, in total, results were available from 514,794 samples from 123,497 individuals, of which 489 were positive overall from 398 individuals. The percentage of people testing positive for SARS-CoV-2 changed substantially over time, with an initial decrease between end of April and June, followed by low levels during the summer, before marked increases end of August and September 2020. Having a patient-facing role and working outside your home were important risk factors for testing positive in the first period but not (yet) in the second period of increased positivity rates, and age (young adults) being an important driver of the second period of increased positivity rates. A substantial proportion of infections were in individuals not reporting symptoms (53%-70%, dependent on calendar time).\n\nInterpretationImportant risk factors for testing positive varied substantially between the initial and second periods of higher positivity rates, and a substantial proportion of infections were in individuals not reporting symptoms, indicating that continued monitoring for SARS-CoV-2 in the community will be important for managing the epidemic moving forwards.\n\nFundingThis study is funded by the Department of Health and Social Care. KBP, ASW, EP and JVR are supported by the National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford in partnership with Public Health England (PHE) (NIHR200915). AG is supported by U.S. National Institute of Health and Office of Naval Research. ASW is also supported by the NIHR Oxford Biomedical Research Centre and by core support from the Medical Research Council UK to the MRC Clinical Trials Unit [MC_UU_12023/22] and is an NIHR Senior Investigator. The views expressed are those of the authors and not necessarily those of the National Health Service, NIHR, Department of Health, or PHE.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSUnprecedented control measures, such as national lockdowns, have been widely implemented to contain the spread of SARS-CoV-2. Decisions regarding the continued need for social distancing measures in the overall population, specific subgroups and geographic areas heavily rely on accurate and up-to-date information about the number of people and risk factors for testing positive. We searched PubMed and medRxiv and bioRxiv preprint servers up to 6 June 2020 for epidemiological studies using the terms \"SARS-CoV-2\" and \"prevalence\" or \"incidence\" without data or language restrictions. Most studies were small or had only information about current presence of the virus for a small subset of patients, or used data not representative of the community, such as hospital admissions, deaths or self-reported symptoms. Large population-based studies, such as the current study, are required to understand risk factors and the dynamics of the epidemic.\n\nAdded value of this studyThis is the first longitudinal community survey of SARS-CoV-2 infection at national and regional levels in the UK. With more than 500,000 swabs from more than 120,000 individuals this study provides robust evidence that the percentage of individuals from the general community in England testing positive for SARS-CoV-2 clearly declined between end of April and June 2020,, followed by consistently low levels during the summer, before marked increases end of August and September 2020. Risk factors for testing positive varied substantially between the initial and second periods of higher positivity rates, with having a patient-facing role and working outside your home being important risk factors in the first period but not (yet) in the second period, and age (young adults) being an important driver of the second period of increased positivity rates. Positive tests commonly occurred without symptoms being reported.\n\nImplications of all the available evidenceThe observed decline in the percentage of individuals testing positive adds to the increasing body of empirical evidence and theoretical models that suggest that the lockdown imposed on 23 March 2020 in England was associated, at least temporarily, with a decrease in infections. Important risk factors for testing positive varied substantially between the initial and second periods of higher positivity rates, and a substantial proportion of infections were in individuals not reporting symptoms, indicating that continued monitoring for SARS-CoV-2 in the community will be important for managing the epidemic moving forwards.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.10.26.20219659", @@ -7783,6 +7811,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.09.26.20202150", + "date": "2020-09-28", + "link": "https://medrxiv.org/cgi/content/short/2020.09.26.20202150", + "title": "Comparison of mental health service activity before and shortly after UK social distancing responses to the COVID-19 pandemic: February-March 2020", + "authors": "Robert Stewart; Evangelia Martin; Ioannis Bakolis; Matthew Broadbent; Nicola Byrne; Sabine Landau", + "affiliations": "King's College London; South London and Maudsley NHS Foundation Trust; King's College London; King's College London; South London and Maudsley NHS Foundation Trust; King's College London", + "abstract": "This study sought to provide an early description of mental health service activity before and after national implementation of social distancing for COVID-19. A time series analysis was carried out of daily service-level activity on data from a large mental healthcare provider in southeast London, from 01.02.2020 to 31.03.2020, comparing activity before and after 16.03.2020: i) inpatient admissions, discharges and numbers, ii) contact numbers and daily caseloads (Liaison, Home Treatment Teams, Community Mental Health Teams); iii) numbers of deaths for past and present patients. Daily face-to-face contact numbers fell for liaison, home treatment and community services with incomplete compensatory rises in non-face-to-face contacts. Daily caseloads fell for all services, apart from working age and child/adolescent community teams. Inpatient numbers fell 13.6% after 16th March, and daily numbers of deaths increased by 61.8%.", + "category": "psychiatry and clinical psychology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.09.25.20201731", @@ -8035,20 +8077,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.09.03.20187377", - "date": "2020-09-05", - "link": "https://medrxiv.org/cgi/content/short/2020.09.03.20187377", - "title": "Impact of baseline cases of cough and fever on UK COVID-19 diagnostic testing rates: estimates from the Bug Watch community cohort study", - "authors": "Max T Eyre; Rachel Burns; Victoria Kirkby; Catherine Smith; Spiros Denaxas; Vincent Nguyen; Andrew Hayward; Laura Shallcross; Ellen Fragaszy; Robert W Aldridge", - "affiliations": "Centre of Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster, LA1 4YW, UK; Liverpool School of Tropical Med; Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK; Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK; Institute of Health Informatics, University College London, London, NW1 2DA, UK; Institute of Health Informatics, University College London, London, NW1 2DA, UK; Health Data Research UK, London, NW1 2DA, UK; The Alan Turing Institute, London; Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK; Institute of Epidemiology and Health Care; Institute of Epidemiology and Health Care, University College London, London, WC1E 7HB, UK; Institute of Health Informatics, University College London, London, NW1 2DA, UK; Institute of Health Informatics, University College London, London, NW1 2DA, UK; Faculty of Epidemiology and Population Health, London School of Hygiene and Tro; Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK", - "abstract": "BackgroundDiagnostic testing forms a major part of the UKs response to the current COVID-19 pandemic with tests offered to people with a continuous cough, high temperature or anosmia. Testing capacity must be sufficient during the winter respiratory season when levels of cough and fever are high due to non-COVID-19 causes. This study aims to make predictions about the contribution of baseline cough or fever to future testing demand in the UK.\n\nMethodsIn this analysis of the Bug Watch prospective community cohort study, we estimated the incidence of cough or fever in England in 2018-2019. We then estimated the COVID-19 diagnostic testing rates required in the UK for baseline cough or fever cases for the period July 2020-June 2021. This was explored for different rates of the population requesting tests and four second wave scenarios and then compared to current national capacity.\n\nResultsThe baseline incidence of cough or fever in the UK is expected to rise rapidly from 154,554 (95%CI 103,083 - 231,725) cases per day in August 2020 to 250,708 (95%CI 181,095 - 347,080) in September, peaking at 444,660 (95%CI 353,084 - 559,988) in December. If 80% of baseline cough or fever cases request tests, average daily UK testing demand would exceed current capacity for five consecutive months (October 2020 to February 2021), with a peak demand of 147,240 (95%CI 73,978 - 239,502) tests per day above capacity in December 2020.\n\nConclusionsOur results show that current national COVID-19 testing capacity is likely to be exceeded by demand due to baseline cough and fever alone. This study highlights that the UKs response to the COVID-19 pandemic must ensure that a high proportion of people with symptoms request tests, and that testing capacity is immediately scaled up to meet this high predicted demand.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.09.01.20185793", @@ -8063,6 +8091,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.09.02.20186502", + "date": "2020-09-03", + "link": "https://medrxiv.org/cgi/content/short/2020.09.02.20186502", + "title": "Real-time monitoring of COVID-19 dynamics using automated trend fitting and anomaly detection", + "authors": "Thibaut Jombart; Stephane Ghozzi; Dirk Schumacher; Quentin Leclerc; Mark Jit; Stefan Flasche; Felix Greaves; Tom Ward; Rosalind M Eggo; Emily Nightingale; Sophie Meakin; Oliver J Brady; - Centre for Mathematical Modelling of Infectious Diseases COVID-19 Working Group; Graham Medley; Michael Hohle; John Edmunds", + "affiliations": "London School of Hygiene and Tropical Medicine (LSHTM); Department of Epidemiology, Helmholtz Centre for Infection Research, Brunswick, Lower Saxony, Germany; R Epidemics Consortium; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; LSHTM; Joint Biosecurity Centre; Joint Biosecurity Centre; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; LSHTM; London School of Hygiene and Tropical Medicine; ; LSHTM; Department of Mathematics, Stockholm University, Sweden; LSHTM", + "abstract": "As several countries gradually release social distancing measures, rapid detection of new localised COVID-19 hotspots and subsequent intervention will be key to avoiding large-scale resurgence of transmission. We introduce ASMODEE (Automatic Selection of Models and Outlier Detection for Epidemics), a new tool for detecting sudden changes in COVID-19 incidence. Our approach relies on automatically selecting the best (fitting or predicting) model from a range of user-defined time series models, excluding the most recent data points, to characterise the main trend in an incidence. We then derive prediction intervals and classify data points outside this interval as outliers, which provides an objective criterion for identifying departures from previous trends. We also provide a method for selecting the optimal breakpoints, used to define how many recent data points are to be excluded from the trend fitting procedure. The analysis of simulated COVID-19 outbreaks suggest ASMODEE compares favourably with a state-of-art outbreak-detection algorithm while being simpler and more flexible. We illustrate our method using publicly available data of NHS Pathways reporting potential COVID-19 cases in England at a fine spatial scale, for which we provide a template automated analysis pipeline. ASMODEE is implemented in the free R package trendbreaker.", + "category": "health informatics", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.09.02.20186817", @@ -8497,6 +8539,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.07.29.20164269", + "date": "2020-07-30", + "link": "https://medrxiv.org/cgi/content/short/2020.07.29.20164269", + "title": "The potential health and economic impact of dexamethasone treatment for patients with COVID-19", + "authors": "RICARDO AGUAS; Adam Mahdi; RIMA SHRETTA; Peter Horby; Martin Landray; Lisa J White", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford", + "abstract": "Dexamethasone has been shown to reduce mortality in hospitalised COVID-19 patients needing oxygen and ventilation by 18% and 36%, respectively. Here, we estimate the potential number of lives saved and life years gained if this treatment would be rolled out in the UK and globally, as well as its cost-effectiveness of implementing this intervention. We estimate that, for the UK, approximately 12,000 [4,250 - 27,000] lives could be saved by January 2021. Assuming that dexamethasone has a similar effect size in settings where access to oxygen therapies is limited, this would translate into approximately 650,000 [240,000 - 1,400,000] lives saved globally. If dexamethasone acts differently in these settings, the impact could be less than half of this value. To estimate the full potential of dexamethasone in the global fight against COVID-19, it is essential to perform clinical research in settings with limited access to oxygen and/or ventilators, e.g. in low and middle-income countries.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.07.29.20162701", @@ -8525,6 +8581,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.07.23.20160747", + "date": "2020-07-27", + "link": "https://medrxiv.org/cgi/content/short/2020.07.23.20160747", + "title": "Associations of severe COVID-19 with polypharmacy in the REACT-SCOT case-control study", + "authors": "Paul M McKeigue; Sharon Kennedy; Amanda Weir; Jen Bishop; Stuart J McGurnaghan; David McAllister; Chris Robertson; Rachael Wood; Nazir Lone; Janet Murray; Thomas M Caparrotta; Alison Smith-Palmer; David Goldberg; Jim McMenamin; Colin Ramsay; Bruce Guthrie; Sharon Hutchinson; Helen M Colhoun", + "affiliations": "University of Edinburgh; Public Health Scotland; Public Health Scotland; Public Health Scotland; University of Edinburgh; University of Glasgow; University of Strathclyde; NHS Information Services Division (Public Health Scotland); University of Edinburgh; Public Health Scotland; University of Edinburgh; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; University of Edinburgh; Glasgow Caledonian University; University of Edinburgh", + "abstract": "ObjectivesTo investigate the relation of severe COVID-19 to prior drug prescribing.\n\nDesignMatched case-control study (REACT-SCOT) based on record linkage to hospital discharges since June 2015 and dispensed prescriptions issued in primary care during the last 240 days.\n\nSettingScottish population.\n\nMain outcome measureSevere COVID-19, defined by entry to critical care or fatal outcome.\n\nParticipantsAll 4272 cases of severe COVID-19 in Scotland since the start of the epidemic, with 36948 controls matched for age, sex and primary care practice.\n\nResultsSevere COVID-19 was strongly associated with the number of non-cardiovascular drug classes dispensed. This association was strongest in those not resident in care homes, in whom the rate ratio (95% CI) associated with dispensing of 12 or more drug classes versus none was 10.8 (8.7, 13.2), and was not accounted for by treatment of conditions designated as conferring increased risk. Of 17 drug classes postulated at the start of the epidemic to be \"medications compromising COVID\", all were associated with increased risk of severe COVID-19. The largest effect was for antipsychotic agents: rate ratio 4.14 (3.39, 5.07). Other drug classes with large effects included proton pump inhibitors (rate rato 2.19 (1.70, 2.80) for >= 2 defined daily doses/day), opioids (3.62 (2.65, 4.94) for >= 50 mg morphine equivalent/day) and gabapentinoids. These associations persisted after adjusting for covariates, and were stronger with recent than with non-recent exposure.\n\nConclusionsSevere COVID-19 is associated with polypharmacy and with drugs that cause sedation, respiratory depression or dyskinesia, have anticholinergic effects or affect the gastrointestinal system. These associations are not easily explained by co-morbidity. Although the evidence for causality is not conclusive, these results support existing guidance on reducing overprescribing of these drug classes and limiting inappropriate polypharmacy as a potential means of reducing COVID-19 risk.\n\nRegistrationENCEPP number EUPAS35558\n\nWhat is already known on this topicTwo previous studies have examined the relationship of severe COVID-19 to drugs for the cardiovascular system. This is the first systematic study of the relationship of severe COVID-19 to prior drug prescribing.\n\nWhat this study addsSevere COVID-19 is associated with polypharmacy and with drugs that cause sedation, respiratory depression or dyskinesia, have anticholinergic effects or affect the gastrointestinal system. These associations are not easily explained by co-morbidity. These results support earlier warnings that these drug classes that these drugs might increase susceptibility to COVID-19, and reinforce existing guidance on reducing overprescribing of these drug classes.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.07.25.20156471", @@ -8539,6 +8609,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "bioRxiv", + "doi": "10.1101/2020.07.26.221572", + "date": "2020-07-26", + "link": "https://biorxiv.org/cgi/content/short/2020.07.26.221572", + "title": "COVID-19 and Rheumatoid Arthritis share myeloid pathogenic and resolving pathways", + "authors": "Lucy MacDonald; Thomas Dan Otto; Aziza Elmesmari; Barbara Tolusso; Domenico Somma; Charles McSharry; Elisa Gremese; Iain B McInnes; Stefano Alivernini; Mariola Kurowska-Stolarska", + "affiliations": "Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), University of Glasgow, Glasgow, United Kingdom; Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), University of Glasgow, Glasgow, United Kingdom; Research into Inflammatory Arthritis Centre Versus Arthritis (RACE) ,University of Glasgow, Glasgow, United Kingdom; Division of Rheumatology, Universita Cattolica del Sacro Cuore, Rome, Italy; Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, United Kingdom.; Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, United Kingdom.; Division of Rheumatology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.; Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), University of Glasgow, Glasgow, United Kingdom.; Fondazione Policlinico Universitario A. Gemelli IRCCS - Universita Cattolica del Sacro Cuore; Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), University of Glasgow, Glasgow, United Kingdom.", + "abstract": "BackgroundWe recently delineated the functional biology of pathogenic and inflammation resolving synovial tissue macrophage clusters in rheumatoid arthritis (RA). Whilst RA is not a viral respiratory syndrome, it represents a pro-inflammatory cytokine-driven chronic articular condition often accompanied by cardiovascular and lung pathologies. We hypothesised that functionally equivalent macrophage clusters in the lung might govern inflammation and resolution of COVID-19 pneumonitis.\n\nMethodsTo provide insight into the targetable functions of COVID-19 bronchoalveolar lavage (BALF) macrophage clusters, a comparative analysis of BALF macrophage single cell transcriptomics (scRNA-seq) with synovial tissue (ST) macrophage scRNA-seq and functional biology was performed. The function of shared BALF and ST MerTK inflammation-resolving pathway was confirmed with inhibitor in primary macrophage-synovial fibroblast co-cultures. Results. Distinct BALF FCNpos and FCNposSPP1pos macrophage clusters emerging in severe COVID-19 patients were closely related to ST CD48highS100A12pos and CD48posSPP1pos clusters driving synovitis in active RA. They shared transcriptomic profile and pathogenic mechanisms. Healthy lung resident alveolar FABP4pos macrophages shared a regulatory transcriptomic profile, including TAM (Tyro, Axl, MerTK) receptors pathway with synovial tissue TREM2pos macrophages that govern RA remission. This pathway was substantially altered in BALF macrophages of severe COVID-19. In vitro dexamethasone inhibited tissue inflammation via macrophages MerTK function.\n\nConclusionPathogenesis and resolution of COVID-19 pneumonitis and RA synovitis might be driven by similar macrophage clusters and pathways. The MerTK-dependent anti-inflammatory mechanisms of dexamethasone, and the homeostatic function of TAM pathways that maintain RA in remission advocate the therapeutic MerTK agonism to ameliorate the cytokine storm and pneumonitis of severe COVID-19.", + "category": "immunology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 91 + }, { "site": "medRxiv", "doi": "10.1101/2020.07.24.20149815", @@ -9029,20 +9113,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.06.16.20133157", - "date": "2020-06-18", - "link": "https://medrxiv.org/cgi/content/short/2020.06.16.20133157", - "title": "Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease.", - "authors": "Petra Mlcochova; Dami Collier; Allyson V Ritchie; Sonny M Assennato; Myra Hosmillo; Neha Goel; Bo Meng; Krishna Chatterji; Vivien Mendoza; Nigel Temperton; Leo Kiss; Katarzyna A Ciazyns; Xiaoli Xiong; John AG Briggs; James Nathan; Federica Mescia; Hongyi Zhang; Petros Barmpounakis; Nikos Demeris; Richard Skells; Paul Lyons; John Bradley; Stephen Baker; Jean Pierre Allain; Kenneth GC Smith; Ian Goodfellow; Ravindra K Gupta", - "affiliations": "University of Cambridge; UCL; Diagnostics for the Real World Europe Ltd; DRW; University of Cambridge; University of Cambridge; University of Cambridge; NIHR Cambridge Clinical Research Facility; CUH NHS Trust; University of Kent; Medical Research Council Laboratory of Molecular Biology, Cambridge; Medical Research Council Laboratory of Molecular Biology, Cambridge; Medical Research Council Laboratory of Molecular Biology; Medical Research Council Laboratory of Molecular Biology; University of Cambridge; University of Cambridge; CUH NHS Trust; Athens University of Economics and Business; Cambridge Clinical Trials Unit-Cancer Theme; Cambridge Clinical Trials Unit-Cancer Theme; University of Cambridge; University of Cambridge; Cambridge University; Diagnostics for the Real World EU Ltd; University of Cambridge; ig299@cam.ac.uk; University of Cambridge", - "abstract": "BackgroundRapid COVID-19 diagnosis in hospital is essential for patient management and identification of infectious patients to limit the potential for nosocomial transmission. The diagnosis of infection is complicated by 30-50% of COVID-19 hospital admissions with nose/throat swabs testing negative for SARS-CoV-2 nucleic acid, frequently after the first week of illness when SARS-CoV-2 antibody responses become detectable. We assessed the diagnostic accuracy of combined rapid antibody point of care (POC) and nucleic acid assays for suspected COVID-19 disease in the emergency department.\n\nMethodsWe developed (i) an in vitro neutralization assay using a lentivirus expressing a genome encoding luciferase and pseudotyped with spike (S) protein and (ii) an ELISA test to detect IgG antibodies to nucleocapsid (N) and S proteins from SARS-CoV-2. We tested two lateral flow rapid fingerprick tests with bands for IgG and IgM. We then prospectively recruited participants with suspected moderate to severe COVID-19 and tested for SARS-CoV-2 nucleic acid in a combined nasal/throat swab using the standard laboratory RT-PCR and a validated rapid POC nucleic acid amplification (NAAT) test. Additionally, serum collected at admission was retrospectively tested by in vitro neutralisation, ELISA and the candidate POC antibody tests. We evaluated the performance of the individual and combined rapid POC diagnostic tests against a composite reference standard of neutralisation and standard laboratory based RT-PCR.\n\nResults45 participants had specimens tested for nucleic acid in nose/throat swabs as well as stored sera for antibodies. Using the composite reference standard, prevalence of COVID-19 disease was 53.3% (24/45). Median age was 73.5 (IQR 54.0-86.5) years in those with COVID-19 disease by our reference standard and 63.0 (IQR 41.0-72.0) years in those without disease. The overall detection rate by rapid NAAT was 79.2% (95CI 57.8-92.9%), decreasing from 100% (95% CI 65.3-98.6%) in days 1-4 to 50.0% (95% CI 11.8-88.2) for days 9-28 post symptom onset. Correct identification of COVID-19 with combined rapid POC diagnostic tests was 100% (95CI 85.8-100%) with a false positive rate of 5.3-14.3%, driven by POC LFA antibody tests.\n\nConclusionsCombined POC tests have the potential to transform our management of COVID-19, including inflammatory manifestations later in disease where nucleic acid test results are negative. A rapid combined approach will also aid recruitment into clinical trials and in prescribing therapeutics, particularly where potentially harmful immune modulators (including steroids) are used.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.06.15.20131722", @@ -9477,20 +9547,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.05.20.20108183", - "date": "2020-05-23", - "link": "https://medrxiv.org/cgi/content/short/2020.05.20.20108183", - "title": "A Rapid Review of the Asymptomatic Proportion of PCR-Confirmed SARS-CoV-2 Infections in Community Settings", - "authors": "Sarah Beale; Andrew Hayward; Laura Shallcross; Robert W Aldridge; Ellen Fragaszy", - "affiliations": "University College London; University College London; University College London; University College London; University College London", - "abstract": "BackgroundUp to 80% of active SARS-CoV-2 infections are proposed to be asymptomatic based on cross-sectional studies. However, accurate estimates of the asymptomatic proportion require systematic detection and follow-up to differentiate between truly asymptomatic and pre-symptomatic cases. We conducted a rapid review and meta-analysis of current evidence regarding the asymptomatic proportion of PCR-confirmed SARS-CoV-2 infections based on methodologically-appropriate studies in community settings.\n\nMethodsWe searched Medline and EMBASE for peer-reviewed articles, and BioRxiv and MedRxiv for pre-prints published prior to 05/05/2020. We included studies based in community settings that involved systematic PCR testing on participants and follow-up symptom monitoring regardless of symptom status. We extracted data on study characteristics, frequencies of PCR-confirmed infections by symptom status, and (if available) cycle threshold values and/or duration of viral shedding by symptom status. We computed estimates of the asymptomatic proportion and 95% confidence intervals for each study and overall using random effect meta-analysis.\n\nFindingsWe screened 270 studies and included 6. The pooled estimate for the asymptomatic proportion of SARS-CoV-2 infections was 11% (95% CI 4%-18%). Estimates of baseline viral load appeared to be similar for asymptomatic and symptomatic cases based on available data in three studies, though detailed reporting of cycle threshold values and natural history of viral shedding by symptom status was limited.\n\nInterpretationThe asymptomatic proportion of SARS-CoV-2 infections is relatively low when estimated from methodologically-appropriate studies. Further investigation into the degree and duration of infectiousness for asymptomatic infections is warranted.\n\nFundingMedical Research Council", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.05.18.20086157", @@ -9575,20 +9631,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.05.10.20096925", - "date": "2020-05-15", - "link": "https://medrxiv.org/cgi/content/short/2020.05.10.20096925", - "title": "NON-WHITE ETHNICITY, MALE SEX, AND HIGHER BODY MASS INDEX, BUT NOT MEDICATIONS ACTING ON THE RENIN-ANGIOTENSIN SYSTEM ARE ASSOCIATED WITH CORONAVIRUS DISEASE 2019 (COVID-19) HOSPITALISATION: REVIEW OF THE FIRST 669 CASES FROM THE UK BIOBANK", - "authors": "Zahra Raisi-Estabragh; Celeste McCracken; Maddalena Ardissino; Mae S Bethell; Jackie Cooper; Cyrus Cooper; Nicholas C Harvey; Steffen E Petersen", - "affiliations": "William Harvey Research Institute; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, London, UK; Sir Alexander Fleming Building, Imperial College London, London, UK; North West Anglia NHS Foundation Trust, Hinchingbrooke Hospital, Huntingdon, UK; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, London, UK; MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK; MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, London, UK", - "abstract": "BackgroundCardiometabolic morbidity and medications, specifically Angiotensin Converting Enzyme inhibitors (ACEi) and Angiotensin Receptor Blockers (ARBs), have been linked with adverse outcomes from coronavirus disease 2019 (COVID-19). This study aims to investigate factors associated with COVID-19 positivity for the first 669 UK Biobank participants; compared with individuals who tested negative, and with the untested, presumed negative, rest of the population.\n\nMethodsWe studied 1,474 participants from the UK Biobank who had been tested for COVID-19. Given UK testing policy, this implies a hospital setting, suggesting at least moderate to severe symptoms. We considered the following exposures: age, sex, ethnicity, body mass index (BMI), diabetes, hypertension, hypercholesterolaemia, ACEi/ARB use, prior myocardial infarction (MI), and smoking. We undertook comparisons between: 1) COVID-19 positive and COVID-19 tested negative participants; and 2) COVID-19 tested positive and the remaining participants (tested negative plus untested, n=501,837). Logistic regression models were used to investigate univariate and mutually adjusted associations.\n\nResultsAmong participants tested for COVID-19, non-white ethnicity, male sex, and greater BMI were independently associated with COVID-19 positive result. Non-white ethnicity, male sex, greater BMI, diabetes, hypertension, prior MI, and smoking were independently associated with COVID-19 positivity compared to the remining cohort (test negatives plus untested). However, similar associations were observed when comparing those who tested negative for COVID-19 with the untested cohort; suggesting that these factors associate with general hospitalisation rather than specifically with COVID-19.\n\nConclusionsAmong participants tested for COVID-19 with presumed moderate to severe symptoms in a hospital setting, non-white ethnicity, male sex, and higher BMI are associated with a positive result. Other cardiometabolic morbidities confer increased risk of hospitalisation, without specificity for COVID-19. Notably, ACE/ARB use did not associate with COVID-19 status.", - "category": "cardiovascular medicine", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.05.11.20096347", @@ -9855,20 +9897,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.04.27.20081711", - "date": "2020-05-03", - "link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081711", - "title": "Response strategies for COVID-19 epidemics in African settings: a mathematical modelling study", - "authors": "Kevin van Zandvoort; Christopher I Jarvis; Carl Pearson; Nicholas G Davies; CMMID COVID-19 working group; Timothy W Russell; Adam J Kucharski; Mark J Jit; Stefan Flasche; Rosalind M Eggo; Francesco Checchi", - "affiliations": "London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; ; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; LSHTM; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine", - "abstract": "BackgroundThe health impact of COVID-19 may differ in African settings as compared to countries in Europe or China due to demographic, epidemiological, environmental and socio-economic factors. We evaluated strategies to reduce SARS-CoV-2 burden in African countries, so as to support decisions that balance minimising mortality, protecting health services and safeguarding livelihoods.\n\nMethodsWe used a Susceptible-Exposed-Infectious-Recovered mathematical model, stratified by age, to predict the evolution of COVID-19 epidemics in three countries representing a range of age distributions in Africa (from oldest to youngest average age: Mauritius, Nigeria and Niger), under various effectiveness assumptions for combinations of different non-pharmaceutical interventions: self-isolation of symptomatic people, physical distancing, and shielding (physical isolation) of the high-risk population. We adapted model parameters to better represent uncertainty about what might be expected in African populations, in particular by shifting the distribution of severity risk towards younger ages and increasing the case-fatality ratio.\n\nResultsWe predicted median clinical attack rates over the first 12 months of 17% (Niger) to 39% (Mauritius), peaking at 2-4 months, if epidemics were unmitigated. Self-isolation while symptomatic had a maximum impact of about 30% on reducing severe cases, while the impact of physical distancing varied widely depending on percent contact reduction and R0. The effect of shielding high-risk people, e.g. by rehousing them in physical isolation, was sensitive mainly to residual contact with low-risk people, and to a lesser extent to contact among shielded individuals. Response strategies incorporating self-isolation of symptomatic individuals, moderate physical distancing and high uptake of shielding reduced predicted peak bed demand by 46% to 54% and mortality by 60% to 75%. Lockdowns delayed epidemics by about 3 months. Estimates were sensitive to differences in age-specific social mixing patterns, as published in the literature.\n\nDiscussionIn African settings, as elsewhere, current evidence suggests large COVID-19 epidemics are expected. However, African countries have fewer means to suppress transmission and manage cases. We found that self-isolation of symptomatic persons and general physical distancing are unlikely to avert very large epidemics, unless distancing takes the form of stringent lockdown measures. However, both interventions help to mitigate the epidemic. Shielding of high-risk individuals can reduce health service demand and, even more markedly, mortality if it features high uptake and low contact of shielded and unshielded people, with no increase in contact among shielded people. Strategies combining self-isolation, moderate physical distancing and shielding will probably achieve substantial reductions in mortality in African countries. Temporary lockdowns, where socioeconomically acceptable, can help gain crucial time for planning and expanding health service capacity.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.04.28.20083295", @@ -10079,6 +10107,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.04.05.20048421", + "date": "2020-04-07", + "link": "https://medrxiv.org/cgi/content/short/2020.04.05.20048421", + "title": "Loss of smell and taste in combination with other symptoms is a strong predictor of COVID-19 infection", + "authors": "Cristina Menni; Ana Valdes; Maxim B Freydin; Sajaysurya Ganesh; Julia El-Sayed Moustafa; Alessia Visconti; Pirro Hysi; Ruth C E Bowyer; Massimo Mangino; Mario Falchi; Jonathan Wolf; Claire Steves; Tim Spector", + "affiliations": "King's College London; NIHR Nottingham Biomedical Research Centre, School of Medicine, University of Nottingham; King's College London; Zoe Global limited; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; King's College London; King's College London", + "abstract": "ImportanceA strategy for preventing further spread of the ongoing COVID-19 epidemic is to detect infections and isolate infected individuals without the need of extensive bio-specimen testing.\n\nObjectivesHere we investigate the prevalence of loss of smell and taste among COVID-19 diagnosed individuals and we identify the combination of symptoms, besides loss of smell and taste, most likely to correspond to a positive COVID-19 diagnosis in non-severe cases.\n\nDesignCommunity survey.\n\nSetting and ParticipantsSubscribers of RADAR COVID-19, an app that was launched for use among the UK general population asking about COVID-19 symptoms.\n\nMain ExposureLoss of smell and taste.\n\nMain Outcome MeasuresCOVID-19.\n\nResultsBetween 24 and 29 March 2020, 1,573,103 individuals reported their symptoms via the app; 26% reported suffering from one or more symptoms of COVID-19. Of those, n=1702 reported having had a RT-PCR COVID-19 test and gave full report on symptoms including loss of smell and taste; 579 were positive and 1123 negative. In this subset, we find that loss of smell and taste were present in 59% of COVID-19 positive individuals compared to 18% of those negative to the test, yielding an odds ratio (OR) of COVID-19 diagnosis of OR[95%CI]=6.59[5.25; 8.27], P= 1.90x10-59. We also find that a combination of loss of smell and taste, fever, persistent cough, fatigue, diarrhoea, abdominal pain and loss of appetite is predictive of COVID-19 positive test with sensitivity 0.54[0.44; 0.63], specificity 0.86[0.80; 0.90], ROC-AUC 0.77[0.72; 0.82] in the test set, and cross-validation ROC-AUC 0.75[0.72; 0.77]. When applied to the 410,598 individuals reporting symptoms but not formally tested, our model predicted that 13.06%[12.97%;13.15] of these might have been already infected by the virus.\n\nConclusions and RelevanceOur study suggests that loss of taste and smell is a strong predictor of having been infected by the COVID-19 virus. Also, the combination of symptoms that could be used to identify and isolate individuals includes anosmia, fever, persistent cough, diarrhoea, fatigue, abdominal pain and loss of appetite. This is particularly relevant to healthcare and other key workers in constant contact with the public who have not yet been tested for COVID-19.\n\nKey pointsO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIThe spread of COVID-19 can be reduced by identifying and isolating infected individuals but it is not possible to test everyone and priority has been given in most countries to individuals presenting symptoms of the disease.\nC_LIO_LICOVID-19 symptoms, such as fever, cough, aches, fatigue are common in many other viral infections\nC_LIO_LIThere is therefore a need to identify symptom combinations that can rightly pinpoint to infected individuals\nC_LI\n\nWhat this study addsO_LIAmong individuals showing symptoms severe enough to be given a COVID-19 RT-PCR test in the UK the prevalence of loss of smell (anosmia) was 3-fold higher (59%) in those positive to the test than among those negative to the test (18%).\nC_LIO_LIWe developed a mathematical model combining symptoms to predict individuals likely to be COVID-19 positive and applied this to over 400,000 individuals in the general population presenting some of the COVID-19 symptoms.\nC_LIO_LIWe find that [~]13% of those presenting symptoms are likely to have or have had a COVID-19 infection. The proportion was slightly higher in women than in men but is comparable in all age groups, and corresponds to 3.4% of those who filled the app report.\nC_LI", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.04.02.20051334", diff --git a/data/covid/raw-preprints.json b/data/covid/raw-preprints.json index ca907f2a..0827c1b2 100644 --- a/data/covid/raw-preprints.json +++ b/data/covid/raw-preprints.json @@ -1,4 +1,395 @@ [ + { + "rel_doi": "10.1101/2024.01.10.575114", + "rel_title": "SARS-CoV-2 papain-like protease activates nociceptors to drive sneeze and pain", + "rel_date": "2024-01-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.10.575114", + "rel_abs": "SARS-CoV-2, the virus responsible for COVID-19, triggers symptoms such as sneezing, aches and pain. These symptoms are mediated by a subset of sensory neurons, known as nociceptors, that detect noxious stimuli, densely innervate the airway epithelium, and interact with airway resident epithelial and immune cells. However, the mechanisms by which viral infection activates these neurons to trigger pain and airway reflexes are unknown. Here, we show that the coronavirus papain-like protease (PLpro) directly activates airway-innervating trigeminal and vagal nociceptors in mice and human iPSC-derived nociceptors. PLpro elicits sneezing and acute pain in mice and triggers the release of neuropeptide calcitonin gene-related peptide (CGRP) from airway afferents. We find that PLpro-induced sneeze and pain requires the host TRPA1 ion channel that has been previously demonstrated to mediate pain, cough, and airway inflammation. Our findings are the first demonstration of a viral product that directly activates sensory neurons to trigger pain and airway reflexes and highlight a new role for PLpro and nociceptors in COVID-19.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Sonali S Mali", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Ricardo Silva", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Zhongyan Gong", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Michael Cronce", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Uyen Vo", + "author_inst": "HHMI/UC Berkeley" + }, + { + "author_name": "Cliff Vuong", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Yalda Moayedi", + "author_inst": "New York University College of Dentistry" + }, + { + "author_name": "Jeffery S Cox", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Diana M Bautista", + "author_inst": "HHMI/University of California, Berkeley" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "neuroscience" + }, + { + "rel_doi": "10.1101/2024.01.10.575003", + "rel_title": "Neuropsychiatric sequelae in an experimental model of post-COVID syndrome in mice", + "rel_date": "2024-01-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.10.575003", + "rel_abs": "The global impact of the COVID-19 pandemic has been unprecedented, and presently, the world is facing a new challenge known as Post-COVID syndrome (PCS). Current estimates suggest that more than 65 million people are grappling with PCS, encompassing several manifestations, including pulmonary, musculoskeletal, metabolic, and neuropsychiatric sequelae (cognitive and behavioral). The mechanisms underlying PCS remain unclear. The present study aimed to: (i) comprehensively characterize the acute effects of pulmonary inoculation of the betacoronavirus MHV-A59 in immunocompetent mice at clinical, cellular, and molecular levels; (ii) examine potential acute and long-term pulmonary, musculoskeletal, and neuropsychiatric sequelae induced by the betacoronavirus MHV-A59; and to (iii) assess sex-specific differences. Male and female C57Bl/6 mice were initially inoculated with varying viral titers (3x10^3 to 3x105 PFU/30 uL) of the betacoronavirus MHV-A59 via the intranasal route to define the highest inoculum capable of inducing disease without causing mortality. Further experiments were conducted with the 3x10^4 PFU inoculum. Mice exhibited an altered neutrophil/lymphocyte ratio in the blood in the 2nd and 5th day post-infection (dpi). Marked lung lesions were characterized by hyperplasia of the alveolar walls, infiltration of polymorphonuclear leukocytes (PMN) and mononuclear leukocytes, hemorrhage, increased concentrations of CCL2, CCL3, CCL5, and CXCL1 chemokines, as well as high viral titers until the 5th dpi. While these lung inflammatory signs resolved, other manifestations were observed up to the 60 dpi, including mild brain lesions with gliosis and hyperemic blood vessels, neuromuscular dysfunctions, anhedonic-like behavior, deficits in spatial working memory, and short-term aversive memory. These musculoskeletal and neuropsychiatric complications were exclusive to female mice and were prevented after ovariectomy. In summary, our study describes for the first time a novel sex-dependent model of PCS focused on neuropsychiatric and musculoskeletal disorders. This model provides a unique platform for future investigations regarding the effects of acute therapeutic interventions on the long-term sequelae unleashed by betacoronavirus infection.", + "rel_num_authors": 35, + "rel_authors": [ + { + "author_name": "Jordane Clarisse Pimenta", + "author_inst": "UFMG" + }, + { + "author_name": "Vinicius Amorim Beltrami", + "author_inst": "UFMG" + }, + { + "author_name": "Bruna Da Silva Oliveira", + "author_inst": "UFMG" + }, + { + "author_name": "Celso Martins Queiroz-Junior", + "author_inst": "Universidade Federal de Minas Gerais" + }, + { + "author_name": "Jessica Barsalini", + "author_inst": "UFMG" + }, + { + "author_name": "Danielle Cunha Teixeira", + "author_inst": "UFMG" + }, + { + "author_name": "Luiz Pedro Souza-Costa", + "author_inst": "UFMG" + }, + { + "author_name": "Anna Luiza Diniz Lima", + "author_inst": "UFMG" + }, + { + "author_name": "Caroline Amaral Machado", + "author_inst": "UFMG" + }, + { + "author_name": "Barbara Zuccolotto Schneider Guimaraes Parreira", + "author_inst": "UFMG" + }, + { + "author_name": "Felipe Rocha da Silva Santos", + "author_inst": "UFMG" + }, + { + "author_name": "Pedro Augusto Carvalho Costa", + "author_inst": "Instituto Rene Rachou" + }, + { + "author_name": "Larisse De Souza Barbosa Lacerda", + "author_inst": "UFMG" + }, + { + "author_name": "Mateus Rodrigues Goncalves", + "author_inst": "Universidade Federal de Minas Gerais" + }, + { + "author_name": "Ian de Meira Chaves", + "author_inst": "UFMG" + }, + { + "author_name": "Manoela Gonzaga Gontijo Couto", + "author_inst": "UFMG" + }, + { + "author_name": "Victor Rodrigues de Melo Costa", + "author_inst": "Universidade Federal de Minas Gerais" + }, + { + "author_name": "Natalia Ribeiro Cabacinha Nobrega", + "author_inst": "UFMG" + }, + { + "author_name": "Barbara Luisa Silva", + "author_inst": "UFMG" + }, + { + "author_name": "Talita Fonseca", + "author_inst": "UFMG" + }, + { + "author_name": "Filipe Resende", + "author_inst": "UFMG" + }, + { + "author_name": "Natalia Teixeira Wnuk", + "author_inst": "UFMG" + }, + { + "author_name": "Hanna L Umezu", + "author_inst": "UFMG" + }, + { + "author_name": "Gabriel Campolina-Silva", + "author_inst": "UFMG" + }, + { + "author_name": "Ana Claudia Andrade", + "author_inst": "UFMG" + }, + { + "author_name": "Renato Santana de Aguiar", + "author_inst": "Federal University of Rio de Janeiro" + }, + { + "author_name": "Guilherme Mattos Jardim Costa", + "author_inst": "UFMG" + }, + { + "author_name": "Pedro Pires Guimaraes", + "author_inst": "Universidade Federal de Minas Gerais" + }, + { + "author_name": "Glauber Santos Ferreira Silva", + "author_inst": "UFMG" + }, + { + "author_name": "Luciene Bruno Vieira", + "author_inst": "UFMG" + }, + { + "author_name": "Vanessa Pinho", + "author_inst": "UFMG" + }, + { + "author_name": "Antonio Lucio Teixeira", + "author_inst": "Hospital das Clinicas da Universidade Federal de Minas Gerais" + }, + { + "author_name": "Mauro Martins Teixeira", + "author_inst": "UFMG" + }, + { + "author_name": "Aline Silva Miranda", + "author_inst": "UFMG" + }, + { + "author_name": "Vivian Vasconcelos Costa", + "author_inst": "Universidade Federal de Minas Gerais" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "neuroscience" + }, + { + "rel_doi": "10.1101/2024.01.10.574975", + "rel_title": "Effective assessment of CD4+ T cell Immunodominance patterns: impact of antigen processing and HLA restriction", + "rel_date": "2024-01-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.10.574975", + "rel_abs": "Identifying T cell epitopes is essential for studying and potentially tuning immune responses to pathogens. The polymorphic nature of major histocompatibility complex of class II (MHCII)-genes, and the complexity of the antigen processing mechanisms hinders the effective prediction of immunodominant patterns in humans, specially at the population level. Here, we combined the output of a reconstituted antigen processing system and of in silico prediction tools for SARS-CoV-2 antigens considering a broad-population coverage DRB1* panel to gain insights on immunodominance patterns. The two methods complement each other, and the resulting model improves upon single positive predictive values (PPV) from each of them to explain known epitopes. This model was used to design a minimalistic peptide pool (59 peptides) matching the performance reported for large overlapping peptide pools (> 500 peptides). Furthermore, almost 70 % of the candidates (23 peptides) selected for a frequent HLA background (DRB1*03:01/*07:01) feature immunodominant responses ex vivo, validating our platform for accessing T cell epitopes at the population level. The analysis of the impact of processing constraints reveals distinct impact of proteolysis and solvent accessible surface area on epitope selection depending on the antigen. Thus, considering these properties for antigens in question should improve available epitope prediction tools.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Miguel Alvaro-Benito", + "author_inst": "Freie Universitaet Berlin" + }, + { + "author_name": "Esam T Abualrous", + "author_inst": "Freie Universitaet Berlin" + }, + { + "author_name": "Holger Lingel", + "author_inst": "Otto-von-Gericke-University" + }, + { + "author_name": "Stefan Meltendorf", + "author_inst": "Otto-von-Gericke-University" + }, + { + "author_name": "Jakob Holzapfel", + "author_inst": "Freie Universitaet Berlin" + }, + { + "author_name": "Jana Sticht", + "author_inst": "Freie Universitaet Berlin" + }, + { + "author_name": "Benno Kuropka", + "author_inst": "Freie Universitaet Berlin" + }, + { + "author_name": "Cecilia Clementi", + "author_inst": "Freie Universitaet Berlin" + }, + { + "author_name": "Frank Kuppler", + "author_inst": "Freie Universitaet Berlin" + }, + { + "author_name": "Monika C Brunner-Weinzierl", + "author_inst": "Otto-von-Gericke-University" + }, + { + "author_name": "Christian Freund", + "author_inst": "Freie Universitaet Berlin" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, + { + "rel_doi": "10.1101/2024.01.10.574981", + "rel_title": "Variant-specific interactions at the plasma membrane: Heparan sulfate's impact on SARS-CoV-2 binding kinetics", + "rel_date": "2024-01-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.10.574981", + "rel_abs": "The worldwide spread of SARS-CoV-2 has been characterised by the emergence of several variants of concern (VOCs) presenting an increasing number of mutations in the viral genome. The spike glycoprotein, responsible for engaging the viral receptor ACE2, exhibits the highest density of mutations, suggesting an ongoing evolution to optimize viral entry. However, previous studies focussed on isolated molecular interactions, neglecting the intricate composition of the plasma membrane and the interplay between viral attachment factors. Our study explores the role of avidity and of the complexity of the plasma membrane composition in modulating the virus-host binding kinetics during the early stages of viral entry for the original Wuhan strain and three VOCs: Omicron BA.1, Delta, and Alpha. We employ fluorescent liposomes decorated with spike from several VOCs as virion mimics in single-particle tracking studies on native supported lipid bilayers derived from pulmonary Calu-3 cells. Our findings reveal an increase in the affinity of the multivalent bond to the cell surface for Omicron driven by an increased association rate. We show that heparan sulfate (HS), a sulfated glycosaminoglycan commonly expressed on cells' plasma membrane, plays a central role in modulating the interaction with the cell surface and we observe a shift in its role from screening the interaction with ACE2 in early VOCs to an important binding factor for Omicron. This is caused by a ~10-fold increase in Omicron's affinity to HS compared to the original Wuhan strain, as shown using atomic force microscopy-based single-molecule force spectroscopy. Our results show the importance of coreceptors, particularly HS, and membrane complexity in the modulation of the attachment in SARS-CoV-2 VOCs. We highlight a transition in the variants' attachment strategy towards the use of HS as an initial docking site, which likely plays a role in shaping Omicron's tropism towards infection of the upper airways, milder symptoms, and higher transmissibility.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Dario Valter Conca", + "author_inst": "Department of Clinical Microbiology, Ume\u00e5 University, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Ume\u00e5 University, Sweden; Ume\u00e5 Centre for Microbia" + }, + { + "author_name": "Fouzia Bano", + "author_inst": "Department of Clinical Microbiology, Ume\u00e5 University, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Ume\u00e5 University, Sweden; Ume\u00e5 Centre for Microbi" + }, + { + "author_name": "Julius von Wir\u00e9n", + "author_inst": "Department of Clinical Microbiology, Ume\u00e5 University, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Ume\u00e5 University, Sweden; Ume\u00e5 Centre for Microbi" + }, + { + "author_name": "Lauriane Scherrer", + "author_inst": "Department of Clinical Microbiology, Ume\u00e5 University, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Ume\u00e5 University, Sweden; Ume\u00e5 Centre for Microbi" + }, + { + "author_name": "Justas Svirelis", + "author_inst": "Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Sweden" + }, + { + "author_name": "Konrad Thorsteinsson", + "author_inst": "Department of Clinical Microbiology, Ume\u00e5 University, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Ume\u00e5 University, Sweden; Ume\u00e5 Centre for Microbi" + }, + { + "author_name": "Andreas Dahlin", + "author_inst": "Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Sweden" + }, + { + "author_name": "Marta Bally", + "author_inst": "Department of Clinical Microbiology, Ume\u00e5 University, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Ume\u00e5 University, Sweden; Ume\u00e5 Centre for Microbi" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, + { + "rel_doi": "10.1101/2024.01.10.574801", + "rel_title": "scRNA-seq reveals persistent aberrant differentiation of nasal epithelium driven by TNF\u03b1 and TGF\u03b2 in post-COVID syndrome", + "rel_date": "2024-01-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.10.574801", + "rel_abs": "Post-COVID syndrome (PCS) currently affects approximately 3-17% of people following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and has the potential to become a significant global health burden. PCS presents with various symptoms, and methods for improved PCS assessment are presently developed to guide therapy. Nevertheless, there are few mechanistic insights and treatment options. Here, we performed single-cell RNA transcriptomics on nasal biopsies from 33 patients suffering from PCS with mild, moderate, or severe symptoms. We identified 17 different cell clusters representing 12 unique cell populations, including all major epithelial cell types of the conducting airways and basal, secretory, and ciliated cells. Severe PCS was associated with decreased numbers of ciliated cells and the presence of immune cells. Ensuing inflammatory signaling upregulated TGF{beta} and induced an epithelial-mesenchymal transition, which led to the high abundance of basal cells and a mis-stratified epithelium. We confirmed the results in vitro using an air-liquid interface culture and validated TNF as the causal inflammatory cytokine. In summary, our results show that one mechanism for sustained PCS is not through continued viral load, but through the presence of immune cells in nasal tissue leading to impaired mucosal barrier function and repeated infections. These findings could be further explored as a therapeutic option akin to other chronic inflammatory diseases by inhibiting the TNF-TGF{beta} axis, restoring the nasal epithelium, and reducing respiratory tract-related infections.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Anke Faehnrich", + "author_inst": "Institute of Experimental Dermatology, University of Luebeck" + }, + { + "author_name": "Karosham Reddy", + "author_inst": "Department of Pediatric Pneumology and Allergology, The University of Luebeck" + }, + { + "author_name": "Fabian Ott", + "author_inst": "Institute of Experimental Dermatology, University of Luebeck" + }, + { + "author_name": "Yamil Maluje", + "author_inst": "Institute of Experimental Dermatology, University of Luebeck" + }, + { + "author_name": "Rochi Saurabh", + "author_inst": "Institute of Experimental Dermatology, University of Luebeck" + }, + { + "author_name": "Ann-Cathrin Schaaf", + "author_inst": "Department of Pediatric Pneumology and Allergology, The University of Luebeck" + }, + { + "author_name": "Sanja Winkelmann", + "author_inst": "Department of Otorhinolaryngology, Head and Neck Surgery, Christian-Albrechts-University Kiel" + }, + { + "author_name": "Bettina Voss", + "author_inst": "Department of Otorhinolaryngology, Head and Neck Surgery, Christian-Albrechts-University Kiel" + }, + { + "author_name": "Martin Laudien", + "author_inst": "Department of Otorhinolaryngology, Head and Neck Surgery, Christian-Albrechts-University Kiel" + }, + { + "author_name": "Thomas Bahmer", + "author_inst": "Internal Medicine Department I, University Hospital Schleswig-Holstein Campus Kiel" + }, + { + "author_name": "Jan Heyckendorf", + "author_inst": "Internal Medicine Department I, University Hospital Schleswig-Holstein Campus Kiel" + }, + { + "author_name": "Folke Brinkmann", + "author_inst": "Department of Pediatric Pneumology and Allergology, The University of Luebeck" + }, + { + "author_name": "Stefan Schreiber", + "author_inst": "Internal Medicine Department I, University Hospital Schleswig-Holstein Campus Kiel" + }, + { + "author_name": "Wolfgang Lieb", + "author_inst": "Institute of Epidemiology, Kiel University" + }, + { + "author_name": "Markus Weckmann", + "author_inst": "Department of Pediatric Pneumology and Allergology, The University of Luebeck, Epigenetics of Chronic Lung Disease, Priority Research Area Chronic Lung Diseases" + }, + { + "author_name": "Hauke Busch", + "author_inst": "Institute of Experimental Dermatology, University of Luebeck" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2024.01.08.574531", "rel_title": "Efficient overexpression and purification of SARS-CoV-2 Nucleocapsid proteins in Escherichia coli", @@ -107,7 +498,7 @@ "rel_date": "2024-01-09", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2024.01.08.24300980", - "rel_abs": "Background: During times of environmental challenges, adaptive coping strategies are essential to maintain mental health. Coping relies on executive control, which is often impaired in individuals with psychiatric disorders. Furthermore, emotional reactivity may interfere with executive control. Studying the association between cognitive skills and adaptive coping strategies, as well as the potential impact of emotional reactivity, could inform how we can provide mental support during large-scale adversity. In this study we examined coping strategies in a thoroughly phenotyped psychiatric cohort, the MIND-Set cohort, during the early COVID-19 pandemic stage. Methods: We studied 1) the association between coping and both subjective and objective executive control before the pandemic, and three different coping strategies used during the pandemic, 2) the mediating role of emotional reactivity, indexed by amygdala reactivity, and 3) the moderating role of the presence of a psychiatric diagnosis in these associations. After finding no specific impact of patient or control status in this association, we decided to post-hoc study the transdiagnostic impact of depression severity in these associations. Results: showed 1) only a significant association between subjective executive control and a self-reported positive reappraisal style and corona-related reappraisal. However, after controlling for depression severity, this association was no longer significant. Additionally, objective executive control was only directly associated with right amygdala reactivity, while amygdala reactivity in neither of the hemispheres mediated the association between executive control and any of the coping styles. Furthermore, the type of diagnosis did not moderate the association between executive control and coping. Conclusion: Our findings firstly underline the difference between self-reported and performance based executive control. While both deficits in subjective and performance based EC may play a role in the persistence of psychiatric symptomatology, this finding emphasizes how depressive symptoms or negative affect can impact reappraisal ability. As this ability is fundamental to staying resilient, treatments focused on reducing negative affect and thereby training reappraisal are pivotal in the maintenance of mental health in the entire population during environmental challenges.", + "rel_abs": "BackgroundDuring times of environmental challenges, adaptive coping strategies are essential to maintain mental health. Coping relies on executive control, which is often impaired in individuals with psychiatric disorders. Furthermore, emotional reactivity may interfere with executive control. Studying the association between cognitive skills and adaptive coping strategies, as well as the potential impact of emotional reactivity, could inform how we can provide mental support during large-scale adversity. In this study we examined coping strategies in a thoroughly phenotyped psychiatric cohort, the MIND-Set cohort, during the early COVID-19 pandemic stage.\n\nMethodsWe studied 1) the association between coping and both subjective and objective executive control before the pandemic, and three different coping strategies used during the pandemic, 2) the mediating role of emotional reactivity, indexed by amygdala reactivity, and 3) the moderating role of the presence of a psychiatric diagnosis in these associations. After finding no specific impact of patient or control status in this association, we decided to post-hoc study the transdiagnostic impact of depression severity in these associations.\n\nResultsshowed 1) only a significant association between subjective executive control and a self-reported positive reappraisal style and corona-related reappraisal. However, after controlling for depression severity, this association was no longer significant. Additionally, objective executive control was only directly associated with right amygdala reactivity, while amygdala reactivity in neither of the hemispheres mediated the association between executive control and any of the coping styles. Furthermore, the type of diagnosis did not moderate the association between executive control and coping.\n\nConclusionOur findings firstly underline the difference between self-reported and performance based executive control. While both deficits in subjective and performance based EC may play a role in the persistence of psychiatric symptomatology, this finding emphasizes how depressive symptoms or negative affect can impact reappraisal ability. As this ability is fundamental to staying resilient, treatments focused on reducing negative affect and thereby training reappraisal are pivotal in the maintenance of mental health in the entire population during environmental challenges.\n\nCompeting Interest StatementThe authors have declared no competing interest.", "rel_num_authors": 8, "rel_authors": [ { @@ -154,7 +545,7 @@ "rel_date": "2024-01-09", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2024.01.07.23300006", - "rel_abs": "Symptoms experienced by children and adolescents with SARS-CoV-2 infections in the alpha, delta and omicron variant dominated phases were investigated using an online survey, and the frequencies of reported symptoms and changes over time were analyzed. The most prevalent symptoms were fever above 38 degrees Celsius, tiredness, headache, runny or blocked nose, sneezing and dry cough. Lethargy and nausea were reported significantly more frequently in the omicron variant dominated phase than in the earlier phases of the pandemic. Compared to symptoms reported by adults, fever and gastrointestinal symptoms were reported more frequently for children, especially in the omicron variant dominated phase, whereas the frequency of loss of smell and loss of taste was significantly lower in children than in adults.", + "rel_abs": "Symptoms experienced by children and adolescents with SARS-CoV-2 infections in the alpha, delta and omicron variant dominated phases were investigated using an online survey, and the frequencies of reported symptoms and changes over time were analyzed. The most prevalent symptoms were fever above 38 {degrees}C, tiredness, headache, runny or blocked nose, sneezing and dry cough. Lethargy and nausea were reported significantly more frequently in the omicron variant dominated phase than in the earlier phases of the pandemic. Compared to symptoms reported by adults, fever and gastrointestinal symptoms were reported more frequently for children, especially in the omicron variant dominated phase, whereas the frequency of loss of smell and loss of taste was significantly lower in children than in adults.", "rel_num_authors": 2, "rel_authors": [ { @@ -220,7 +611,7 @@ "rel_date": "2024-01-09", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2024.01.07.24300910", - "rel_abs": "Objective: To evaluate the durability of protection provided by original monovalent and bivalent COVID-19 vaccination against COVID-19-associated hospitalization and severe in-hospital outcomes Design: Multicenter case-control design with prospective enrollment Setting: 26 hospitals in 20 US states Participants: Adults aged [≥]18 years admitted to hospital with COVID-19-like illness from 8 September 2022 to 31 August 2023 Main outcome measures: The main outcomes were absolute and relative vaccine effectiveness of original monovalent and bivalent COVID-19 vaccines against COVID-19-associated hospitalization and severe in-hospital outcomes, including advanced respiratory support (defined as receipt of high-flow nasal cannula, non-invasive ventilation, or invasive mechanical ventilation [IMV]) and IMV or death. Vaccine effectiveness was estimated using multivariable logistic regression, in which the odds of vaccination (versus being unvaccinated or receiving original monovalent vaccination only) were compared between COVID-19 case patients and control-patients. Bivalent vaccine effectiveness analyses were stratified by time since dose receipt. Results: Among 7028 adults without immunocompromising conditions, 2924 (41.6%) were COVID-19 case patients and 4104 (58.4%) were control patients. Compared to unvaccinated patients, absolute vaccine effectiveness against COVID-19-associated hospitalization was 6% (-7% to 17%) for original monovalent doses only (median time since last dose [IQR] = 421 days [304-571]), 52% (39% to 61%) for a bivalent dose received 7-89 days earlier, and 13% (-10% to 31%) for a bivalent dose received 90-179 days earlier. Absolute vaccine effectiveness against COVID-19-associated advanced respiratory support was 31% (15% to 45%) for original monovalent doses only, 66% (47% to 78%) for a bivalent dose received 7-89 days earlier, and 33% (-1% to 55%) for a bivalent dose received 90-179 days earlier. Absolute vaccine effectiveness against COVID-19-associated IMV or death was 51% (34% to 63%) for original monovalent doses only, 61% (35% to 77%) for a bivalent dose received 7-89 days earlier, and 50% (11% to 71%) for a bivalent dose received 90-179 days earlier. Conclusion: When compared to original monovalent vaccination only, bivalent COVID-19 vaccination provided additional protection against COVID-19-associated hospitalization and certain severe in-hospital outcomes within 3 months of dose receipt. By 3-6 months, protection from a bivalent dose declined to a level similar to that remaining from original monovalent vaccination only. Although no protection remained from original monovalent vaccination against COVID-19-associated hospitalization, it provided durable protection against severe in-hospital outcomes >1 year after receipt of the last dose, particularly against IMV or death.", + "rel_abs": "ObjectiveTo evaluate the durability of protection provided by original monovalent and bivalent COVID-19 vaccination against COVID-19-associated hospitalization and severe in-hospital outcomes.\n\nDesignMulticenter case-control design with prospective enrollment\n\nSetting26 hospitals in 20 US states\n\nParticipantsAdults aged [≥]18 years admitted to hospital with COVID-19-like illness from 8 September 2022 to 31 August 2023\n\nMain outcome measuresThe main outcomes were absolute and relative vaccine effectiveness of original monovalent and bivalent COVID-19 vaccines against COVID-19-associated hospitalization and severe in-hospital outcomes, including advanced respiratory support (defined as receipt of high-flow nasal cannula, non-invasive ventilation, or invasive mechanical ventilation [IMV]) and IMV or death. Vaccine effectiveness was estimated using multivariable logistic regression, in which the odds of vaccination (versus being unvaccinated or receiving original monovalent vaccination only) were compared between COVID-19 case patients and control-patients. Bivalent vaccine effectiveness analyses were stratified by time since dose receipt.\n\nResultsAmong 7028 adults without immunocompromising conditions, 2924 (41.6%) were COVID-19 case patients and 4104 (58.4%) were control patients. Compared to unvaccinated patients, absolute vaccine effectiveness against COVID-19-associated hospitalization was 6% (-7% to 17%) for original monovalent doses only (median time since last dose [IQR] = 421 days [304-571]), 52% (39% to 61%) for a bivalent dose received 7-89 days earlier, and 13% (-10% to 31%) for a bivalent dose received 90-179 days earlier. Absolute vaccine effectiveness against COVID-19-associated advanced respiratory support was 31% (15% to 45%) for original monovalent doses only, 66% (47% to 78%) for a bivalent dose received 7-89 days earlier, and 33% (-1% to 55%) for a bivalent dose received 90-179 days earlier. Absolute vaccine effectiveness against COVID-19-associated IMV or death was 51% (34% to 63%) for original monovalent doses only, 61% (35% to 77%) for a bivalent dose received 7-89 days earlier, and 50% (11% to 71%) for a bivalent dose received 90-179 days earlier.\n\nConclusionWhen compared to original monovalent vaccination only, bivalent COVID-19 vaccination provided additional protection against COVID-19-associated hospitalization and certain severe in-hospital outcomes within 3 months of dose receipt. By 3-6 months, protection from a bivalent dose declined to a level similar to that remaining from original monovalent vaccination only. Although no protection remained from original monovalent vaccination against COVID-19-associated hospitalization, it provided durable protection against severe in-hospital outcomes >1 year after receipt of the last dose, particularly against IMV or death.\n\nSUMMARY BOX What is already known on this topic- On September 1, 2022, bivalent mRNA COVID-19 vaccination was recommended for US adults who had completed at least an original monovalent COVID-19 primary series.\n- Early estimates of bivalent vaccine effectiveness are available for the period soon after dose receipt; however fewer data exist on their durability of protection and effectiveness against severe outcomes.\n\n\nWhat this study adds- When compared to original monovalent vaccination only, bivalent mRNA COVID-19 vaccination provided additional protection against COVID-19-associated hospitalization and certain severe in-hospital outcomes within 3 months of dose receipt. By 3-6 months, protection from a bivalent dose declined to a level similar to that remaining from original monovalent vaccination only.\n- Although no protection remained from original monovalent vaccination against COVID-19-associated hospitalization, it provided durable protection against severe in-hospital outcomes >1 year after receipt of the last dose, particularly against invasive mechanical ventilation or death.", "rel_num_authors": 52, "rel_authors": [ { @@ -443,7 +834,7 @@ "rel_date": "2024-01-09", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2024.01.08.24301002", - "rel_abs": "The spike glycoprotein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to accumulate substitutions, leading to breakthrough infections of vaccinated individuals and prompting the development of updated booster vaccines. Here, we determined the specificity and functionality of antibody and B cell responses following exposure to BA.5 and XBB variants in individuals who received ancestral SARS-CoV-2 mRNA vaccines. BA.5 exposures elicited antibody responses that primarily targeted epitopes conserved between the BA.5 and ancestral spike, with poor reactivity to the XBB.1.5 variant. XBB exposures also elicited antibody responses that targeted epitopes conserved between the XBB.1.5 and ancestral spike. However, unlike BA.5, a single XBB exposure elicited low levels of XBB.1.5-specific antibodies and B cells in some individuals. Pre-existing cross-reactive B cells and antibodies were correlated with stronger overall responses to XBB but weaker XBB-specific responses, suggesting that baseline immunity influences the activation of variant-specific SARS-CoV-2 responses.", + "rel_abs": "The spike glycoprotein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to accumulate substitutions, leading to breakthrough infections of vaccinated individuals and prompting the development of updated booster vaccines. Here, we determined the specificity and functionality of antibody and B cell responses following exposure to BA.5 and XBB variants in individuals who received ancestral SARS-CoV-2 mRNA vaccines. BA.5 exposures elicited antibody responses that primarily targeted epitopes conserved between the BA.5 and ancestral spike, with poor reactivity to the XBB.1.5 variant. XBB exposures also elicited antibody responses that targeted epitopes conserved between the XBB.1.5 and ancestral spike. However, unlike BA.5, a single XBB exposure elicited low levels of XBB.1.5-specific antibodies and B cells in some individuals. Pre-existing cross-reactive B cells and antibodies were correlated with stronger overall responses to XBB but weaker XBB-specific responses, suggesting that baseline immunity influences the activation of variant-specific SARS-CoV-2 responses.\n\nHighlightsO_LIVariant breakthrough infections boost ancestral cross-reactive antibodies and B cells\nC_LIO_LIFirst and second BA.5 exposures fail to elicit variant-specific antibodies and B cells\nC_LIO_LIXBB infections and monovalent vaccinations elicit XBB.1.5-specific responses in some individuals\nC_LIO_LIXBB.1.5-specific responses correlate with low levels of pre-existing humoral immunity\nC_LI", "rel_num_authors": 9, "rel_authors": [ { @@ -1554,37 +1945,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2024.01.03.24300755", - "rel_title": "Quantifying the impact of social activities on SARS-CoV-2 transmission using Google mobility reports", - "rel_date": "2024-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2024.01.03.24300755", - "rel_abs": "We developed a state-space model to investigate which social behaviours had biggest impact on the spread of SARS-CoV-2. The analyses were based on reported hospitalizations, together with information on vaccinations, weather data, virus strains and, most importantly, Google mobility reports on 4 different types of social activities. While our new approach is general, we studied Sweden and Norway on a regional level over 75 weeks, and the major regions of Berlin and Bavaria in Germany over 10 months. Most results are shared for all three countries: Activity in four social settings explain between 40-60% of all infections; Public transport appears as an important setting for infections in all countries; and the transmission potential drops by 40-50% during the summer as compared to the winter peak. However, the analyses for Germany differ in that Retail and recreation is the other setting dominating transmission whereas it is contacts at the Workplace in Norway and Sweden, showing how our model is able to adapt to specific cases. Transmissions not captured by the Google data may happen in other settings, in particular in households. The statistical model has a deterministic time and region specific transmission rate with an additive component for the four Google settings, and a multiplicative part taking seasonality and circulating virus strains into account. Inference is performed in a Bayesian setting using Stan.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Felix G\u00fcnther", - "author_inst": "Department of Mathematics, Stockholm University" - }, - { - "author_name": "Hilde Kjelgaard Brustad", - "author_inst": "Oslo Centre for Biostatistics and Epidemiology, University of Oslo, Oslo University Hospital" - }, - { - "author_name": "Arnoldo Frigessi", - "author_inst": "Oslo Centre for Biostatistics and Epidemiology, University of Oslo, Oslo University Hospital" - }, - { - "author_name": "Tom Britton", - "author_inst": "Department of Mathematics, Stockholm University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2024.01.03.574018", "rel_title": "Prototype mRNA vaccines imprint broadly neutralizing human serum antibodies after Omicron variant-matched boosting", @@ -1861,6 +2221,41 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2024.01.04.574161", + "rel_title": "Antiviral action of different molecules obtained from invertebrates against coronavirus", + "rel_date": "2024-01-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.04.574161", + "rel_abs": "The few availability of antivirals for new strains of highly pathogenic viruses has become a serious public health problem that leads to the death of thousands of people annually. For this reason, the search for new products against these agents has become an urgent need. Many studies have been carried out with this aim. Among the multiple sources of research for new antibiotics and antivirals, bioprospecting for molecules obtained from invertebrates, or their products, has become an increasingly frequent option. Arthropods appeared on the planet around 350 million years ago and have been one of the beings with the greatest adaptability and resistance. Invertebrates have been found in all known ecosystems. Their survival for so long, in such different environments, is an indication that they have a very efficient protection system against environmental infections, despite not having a developed immune system like mammals. Historically, products obtained mainly from bees, such as honey and propolis, have been shown to be of great pharmacologica l importance, being used as antimicrobials, anti-inflammatory, antitumor, healing and several other functions. However, these molecules have also been obtained from other invertebra tes, such as caterpillars and spiders. Previous studies by our group have demonstrated an intense antiviral and antimicrobial activity of these materials. In this study, we identified, isolated and characterized compounds with potent antiviral effect against avian Coronavirus in propolis from Scaptotrigona aff postica, hemolymph of Lonomia obliqua and from mygalin, an acylpolyamine, isolated from hemocytes of spider Acanthoscurria gomesiana. The antiviral assay was carried out by reducing infectious foci in cultures of infected cells and treated with these differents substances obtained from invertebrates. Propolis and crude hemolymph reduced avian coronavirus by an average of 256 x when used at a concentration of 5% v/v and an average reduction of 8x when 160{micro}M of Mygalin was used. Propolis purified and sinthetic hemolymph reduced the virus titer by an average 64 fold. The virus reduction with synthetic mygalin, at a concentration of 26 uM, was average of 16 times. The antiviral responses of the 3 substances were dose dependent. By the other hand, the virus titer reduction was 2 times more intense when the substances were added 1 hour before cell infection with the virus. The chemical characterization of the elements present in the extracts was carried out by liquid chromatography.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ronaldo Z Mendonca", + "author_inst": "Instituto Butantan" + }, + { + "author_name": "Roberto M Nascimento", + "author_inst": "Instituto Butantan" + }, + { + "author_name": "Ana C.O Fernandes", + "author_inst": "Instituto Butantan" + }, + { + "author_name": "Maria I.P de Almeida", + "author_inst": "Instituto Butantan" + }, + { + "author_name": "Pedro I.S Junior", + "author_inst": "Instituto Butantan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2024.01.03.574082", "rel_title": "Mutation of highly conserved residues in loop 2 of the coronavirus macrodomain demonstrates that enhanced ADP-ribose binding is detrimental to infection", @@ -3400,25 +3795,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2023.12.26.572282", - "rel_title": "Synthesis and Assembly of mRNA-Bifunctional Lipid Nanoparticle (BLNP) for Selective Delivery of mRNA Vaccines to Dendritic Cells", - "rel_date": "2023-12-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.12.26.572282", - "rel_abs": "The fight against COVID-19 pandemic has gained a strong consensus about the importance of developing mRNA vaccines to rapidly respond to an outbreak. Several studies have shown that mRNA vaccines formulated as mRNA-lipid nanoparticles (LNPs) for vaccination can elicit a robust and efficient immune response. In this study, we report the preparation of mRNA-bifunctional lipid nanoparticles (mRNA-BLNPs) as vaccines for targeted delivery to dendritic cells (DCs) to improve safety and enhance immune response. Using this DC-targeted delivery system, mice immunized with SARS-CoV-2 spike mRNA-BLNP vaccine elicited a stronger immune response with higher titer of neutralizing IgG antibody response than the LNPformulated vaccine against SARS-CoV-2. In addition, the spike mRNA-BLNP vaccine with deletion of glycosites in the stem elicited a broadly protective immune response against SARS-CoV2 and variants. These findings suggest the importance and potential of developing DC-targeted mRNA vaccines to elicit broadly protective immune responses against human viruses.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Chi-Huey Wong", - "author_inst": "Department of Chemistry, The Scripps Research Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.12.22.23300471", "rel_title": "Nowcasting Reported COVID-19 Hospitalizations Using De-Identified, Aggregated Medical Insurance Claims Data", @@ -3615,6 +3991,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.12.21.23300125", + "rel_title": "Social determinants of recovery from ongoing symptoms following COVID-19 in two UK longitudinal studies: a prospective cohort study", + "rel_date": "2023-12-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.21.23300125", + "rel_abs": "BackgroundSocial gradients in COVID-19 exposure, illness severity, and mortality have been observed in multiple international contexts. Whether pre-existing social factors affect recovery from ongoing symptoms following COVID-19 and long COVID is less well understood.\n\nMethodsWe analysed data on self-perceived recovery following self-reported COVID-19 illness in two United Kingdom community-based cohorts, COVID Symptom Study Biobank (CSSB) (N = 2548) and TwinsUK (N = 1334). Composite variables quantifying socio-demographic advantage and disadvantage prior to the COVID-19 pandemic were generated from sex, ethnic group, education, local area deprivation and employment status. Associations between self-perceived recovery and composite variables were tested with multivariable logistic regression models weighted for inverse probability of study participation, adjusting for potential confounding by age, region and pre- pandemic health factors, and potential mediation by COVID-19 illness characteristics and adverse experiences during the pandemic. Further analyses tested associations between recovery and individual socio-demographic variables reflecting status prior to and during the COVID-19 pandemic.\n\nFindingsSocio-demographic gradients in recovery were observed, with unadjusted recovery rate varying between 50% and 80% in CSSB and 70% and 90% in TwinsUK based on composite socio-demographic variables. Likelihood of recovery was lower for individuals with more indicators of pre-pandemic social disadvantage in both cohorts (CSSB: odds ratio, OR = 0.74, 95% confidence interval, CI: 0.62-0.88, TwinsUK: OR = 0.79, 95% CI: 0.64-0.98 per disadvantage) and higher with more social advantages (CSSB: OR = 1.26, 95% CI: 1.08-1.47, TwinsUK: OR = 1.36, 95% CI: 1.09-1.70 per advantage). Associations were neither explained by differences in COVID-19 illness severity or timing, nor adverse social experiences during the pandemic, which were themselves inversely associated with recovery.\n\nInterpretationStrong social inequalities in the likelihood of recovery from COVID-19 were observed, with ongoing symptoms several months after coronavirus infection more likely for individuals with multiple indicators of social disadvantage. Work is needed to identify modifiable biopsychosocial factors to enable interventions that address inequalities.\n\nFundingChronic Disease Research Foundation, National Institute for Health and Care Research, Medical Research Council, Wellcome LEAP, Wellcome Trust, Engineering & Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council, Versus Arthritis, European Commission, Zoe Ltd.\n\nPlain language summaryAcross the world acute COVID-19 illness has affected the most disadvantaged in society the most. However, we have not looked in detail whether peoples social circumstances affect their recovery from COVID-19. In our study, we asked people from two UK-based health studies if they still had symptoms after having COVID-19. We looked at how advantaged or disadvantaged they were at the start of the pandemic, based on information about their sex, ethnic group, education level, local area, and employment. In both studies, people who were more disadvantaged were more likely to still have symptoms long after having COVID-19. In contrast, more advantaged people were more likely to have fully recovered. We also saw that people who had negative experiences during the pandemic such as losing their job, being unable to afford their bills or not being able to access health & social care services were less likely to recover. More work is needed to understand how and why recovery was so different for people with different circumstances.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSTo search for previous reports on associations between recovery from COVID-19 and socio-demographic factors, we screened abstracts identified from the PubMed search query on December 21, 2023: \"((COVID-19) AND ((recovery) OR (convalescence) OR (\" ongoing symptoms\")) AND ((socioeconomic) OR (sociodemographic) OR (social) OR (gradient))) AND LitCLONGCOVID[filter]\", where LitCLONGCOVID is a filter for articles relating to long COVID (https://pubmed.ncbi.nlm.nih.gov/help/#covid19-article-filters), which returned 210 results published between July, 2020 and December, 2023.\n\nA small number (N = 11) of studies contained direct measures of recovery from COVID-19 in terms of presence/absence of ongoing symptoms relating to COVID-19 illness, either as perceived by the individual or inferred from current symptom reports. Of these, most focused on associations with COVID-19 illness factors such as severity and symptomatology, and prior health indicators. Socio-demographics were mostly used for sample description and adjustments in models rather than as exposures of interest. Of the few studies (N = 8) that tested associations with socio-demographic variables, the range of socio-demographics tested was limited and/or follow-up time typically restricted to 6-12 months since symptom onset. In these studies, associations with recovery were reported for age (N = 4), sex (N = 7), race/ethnicity (N = 2), local area deprivation (N = 1), and education level (N = 1). Associations between long-term symptoms and education or income have been reported in single separate studies. Monthly bulletins up to March 2023 from the UK Coronavirus Infection Survey highlighted prevalence of individuals reporting current effects on daily activities due to long COVID was associated with age, sex, race/ethnicity, local area deprivation and economic activity. No studies were identified that tested for associations of multiple socio-demographics in combination with the likelihood of recovery following COVID-19.\n\nAdded value of this studyThis is the first study to testing the effects of multiple socio-demographics on self-perceived recovery in combination. Measures that attempt to quantify social advantage and disadvantage were generated from multiple known social determinants of health. We tested a wider range of socio-demographic factors than previous studies, including UK geographic region, educational qualification level, employment status and income. Our study has a longer follow-up time than previous comparable reports, with most participants assessed more than one year after infection onset. Detailed data on health before the coronavirus pandemic and COVID-19 illness allowed models to be adjusted extensively and mediation effects to be tested.\n\nImplications of all the available evidenceThe likelihood of full recovery following COVID-19 appears to follow a social gradient, higher for individuals with multiple indicators of social advantages and fewer disadvantages, and lower for those with multiple social disadvantages and fewer advantages prior to the coronavirus pandemic. This reflects and reaffirms the established cycle of social inequalities in health, between individuals status within social hierarchies and ill-health. More work is needed to understand the pathways through which this inequality operates so that interventions can be made.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Nathan J Cheetham", + "author_inst": "King's College London" + }, + { + "author_name": "Vicky Bowyer", + "author_inst": "King's College London" + }, + { + "author_name": "Maria Paz Garcia", + "author_inst": "King's College London" + }, + { + "author_name": "Ruth C E Bowyer", + "author_inst": "King's College London" + }, + { + "author_name": "J D Carpentieri", + "author_inst": "University College London" + }, + { + "author_name": "Andrew Guise", + "author_inst": "King's College London" + }, + { + "author_name": "Ellen J Thompson", + "author_inst": "King's College London" + }, + { + "author_name": "Carole H Sudre", + "author_inst": "University College London" + }, + { + "author_name": "Erika Molteni", + "author_inst": "King's College London" + }, + { + "author_name": "Michela Antonelli", + "author_inst": "King's College London" + }, + { + "author_name": "Rose S Penfold", + "author_inst": "Edinburgh University" + }, + { + "author_name": "Nicholas R Harvey", + "author_inst": "King's College London" + }, + { + "author_name": "Liane S Canas", + "author_inst": "King's College London" + }, + { + "author_name": "Khaled Rjoob", + "author_inst": "University College London" + }, + { + "author_name": "Benjamin Murray", + "author_inst": "King's College London" + }, + { + "author_name": "Eric Kerfoot", + "author_inst": "King's College London" + }, + { + "author_name": "- The COVID Symptom Study Biobank Consortium", + "author_inst": "" + }, + { + "author_name": "Alexander Hammers", + "author_inst": "King's College London" + }, + { + "author_name": "Emma L Duncan", + "author_inst": "King's College London" + }, + { + "author_name": "Claire J Steves", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.12.21.23300355", "rel_title": "Assessing Sociodemographic Factors Associated with Household Hardships during the COVID-19 Pandemic in Manhica, Mozambique using Data Collected between April 2021 and February 2022", @@ -5058,53 +5529,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.12.20.572504", - "rel_title": "Cell type-specific adaptation of the SARS-CoV-2 spike", - "rel_date": "2023-12-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.12.20.572504", - "rel_abs": "SARS-CoV-2 can infect various human tissues and cell types, principally via interaction with its cognate receptor ACE2. However, how the virus evolves in different cellular environments is poorly understood. Here, we used experimental evolution to study the adaptation of the SARS-CoV-2 spike to four human cell lines expressing different levels of key entry factors. After 20 passages, cell type-specific phenotypic changes were observed. Selected spike mutations were identified and functionally characterized in terms of entry efficiency, ACE2 affinity, spike processing, TMPRSS2 usage, entry pathway and syncytia formation. We found that the effects of these mutations varied across cell types. Interestingly, two spike mutations (L48S and A372T) that emerged in cells expressing low ACE2 levels increased receptor affinity, syncytia induction, and entry efficiency under low-ACE2 conditions. Our results demonstrate specific adaptation of the SARS-CoV-2 spike to different cell types and have implications for understanding SARS-CoV-2 tissue tropism and evolution.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Marc Carrascosa-Saez", - "author_inst": "Instituto de Biologia Integrativa de Sistemas" - }, - { - "author_name": "Maria-Carmen Marques", - "author_inst": "Instituto de Biologia Integrativa de Sistemas" - }, - { - "author_name": "- The IBV-COVID19-Pipeline", - "author_inst": "-" - }, - { - "author_name": "Ron Geller", - "author_inst": "Instituto de Biologia Integrativa de Sistemas" - }, - { - "author_name": "Santiago F. Elena", - "author_inst": "Instituto de Biologia Integrativa de Sistemas" - }, - { - "author_name": "Amal Rahmeh", - "author_inst": "Universitat Pompeu Fabra" - }, - { - "author_name": "Jeremy Dufloo", - "author_inst": "Instituto de Biologia Integrativa de Sistemas" - }, - { - "author_name": "Rafael Sanjuan", - "author_inst": "Instituto de Biologia Integrativa de Sistemas" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.12.20.572494", "rel_title": "Integrated histopathology, spatial and single cell transcriptomics resolve cellular drivers of early and late alveolar damage in COVID-19", @@ -5445,6 +5869,65 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2023.12.19.572363", + "rel_title": "Comparison of mitochondrial response to SARS-CoV-2 spike protein receptor binding domain in human lung microvascular, coronary artery endothelial and bronchial epithelial cells", + "rel_date": "2023-12-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.12.19.572363", + "rel_abs": "Recent evidence indicate that SARS-CoV-2 spike protein affects mitochondria with a cell type-dependent outcome. We elucidate the effect of SARS-CoV-2 receptor binding domain (RBD) on the mitochondrial network and cristae morphology, oxygen consumption, mitoROS production, and inflammatory cytokine expression in cultured human lung microvascular (HLMVEC) and coronary artery endothelial (HCAEC) and bronchial epithelial cells (HBEC). Live Mito Orange staining, STED microscopy and Fiji MiNa analysis were used for mitochondrial cristae and network morphometry, Agilent XFp analyser for mitochondrial/glycolytic activity, MitoSOX fluorescence for mitochondrial ROS, and qRT-PCR plus Luminex for cytokines. In HLMVEC, SARS-CoV-2 RBD fragmented the mitochondrial network, decreased cristae density, mitochondrial oxygen consumption and glycolysis and induced mitoROS-mediated GM-CSF and IL-1{beta} expression in all three investigated cell types and IL-8 - in both endothelial cell types. Mitochondrial ROS control SARS-CoV-2 RBD-induced inflammation in HLMVEC, HCAEC and HBEC, with the mitochondria of HLMVEC being more sensitive to SARS-CoV-2 RBD.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Gabriele Kulkoviene", + "author_inst": "Department of Medicinal Chemistry, Pharmacy Faculty, Lithuanian University of Health Sciences" + }, + { + "author_name": "Deimante Narauskaite", + "author_inst": "Preclinical Research Laboratory for Medicinal Products, Institute of Cardiology, Lithuanian University of Health Sciences" + }, + { + "author_name": "Agile Tunaityte", + "author_inst": "Preclinical Research Laboratory for Medicinal Products, Institute of Cardiology, Lithuanian University of Health Sciences" + }, + { + "author_name": "Augusta Volkeviciute", + "author_inst": "Preclinical Research Laboratory for Medicinal Products, Institute of Cardiology, Lithuanian University of Health Sciences" + }, + { + "author_name": "Zbigniev Balion", + "author_inst": "Preclinical Research Laboratory for Medicinal Products, Institute of Cardiology, Lithuanian University of Health Sciences" + }, + { + "author_name": "Olena Kutakh", + "author_inst": "Preclinical Research Laboratory for Medicinal Products, Institute of Cardiology, Lithuanian University of Health Sciences" + }, + { + "author_name": "Dovydas Gecys", + "author_inst": "Institute of Pharmaceutical Technologies, Faculty of Pharmacy, Lithuanian University of Health Sciences" + }, + { + "author_name": "Milda Kairyte", + "author_inst": "Preclinical Research Laboratory for Medicinal Products, Institute of Cardiology, Lithuanian University of Health Sciences" + }, + { + "author_name": "Martyna Uldukyte", + "author_inst": "Preclinical Research Laboratory for Medicinal Products, Institute of Cardiology, Lithuanian University of Health Sciences" + }, + { + "author_name": "Edgaras Stankevicius", + "author_inst": "Preclinical Research Laboratory for Medicinal Products, Institute of Cardiology, Lithuanian University of Health Sciences" + }, + { + "author_name": "Aiste Jekabsone", + "author_inst": "Preclinical Research Laboratory for Medicinal Products, Institute of Cardiology, Lithuanian University of Health Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.12.18.572126", "rel_title": "Multi-target mode of action of Sulfodyne(R), a stabilized Sulforaphane, against pathogenic effects of SARS-CoV-2 infection", @@ -7084,37 +7567,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.12.10.23299100", - "rel_title": "Protect or prevent? A practicable framework for the dilemmas of COVID-19 vaccine prioritization", - "rel_date": "2023-12-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.10.23299100", - "rel_abs": "Determining COVID-19 vaccination strategies presents many challenges in light of limited vaccination capacity and the heterogeneity of affected communities. Who should be prioritized for early vaccination when different groups manifest different levels of risks and contact rates? Answering such questions often becomes computationally intractable given that network size can exceed millions. We obtain a framework to compute the optimal vaccination strategy within seconds to minutes from among all strategies, including highly dynamic ones that adjust vaccine allocation as often as required, and even with modest computation resources. We then determine the optimal strategy for a large range of parameter values representative of various US states, countries, and case studies including retirement homes and prisons. The optimal is almost always one of a few candidate strategies, and, even when not, the suboptimality of the best among these candidates is minimal. Further, we find that many commonly deployed vaccination strategies, such as vaccinating the high risk group first, or administering second doses without delay, can often incur higher death rates, hospitalizations, and symptomatic counts. Our framework can be easily adapted to future variants or pandemics through appropriate choice of the compartments of the disease and parameters.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Raghu Arghal", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Harvey Rubin", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Shirin Saeedi Bidokhti", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Saswati Sarkar", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.12.14.23299967", "rel_title": "Diagnostic Accuracy of the Abbot BinaxNOW COVID-19 Antigen Card Test, Puerto Rico", @@ -7367,6 +7819,177 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2023.12.12.23299822", + "rel_title": "Comparative transcriptomic analyses of peripheral blood mononuclear cells of patients with non-pneumonia and severe pneumonia at 1 year-Long-COVID-19", + "rel_date": "2023-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.12.23299822", + "rel_abs": "Long-COVID-19 manifests as a multisystemic condition with varied symptoms lingering beyond three weeks of acute SARS-CoV-2 infection, though its underlying mechanisms remain elusive. Aiming to decipher the long-term molecular impacts of COVID-19, we conducted a transcriptomic analysis on PBMCs from 1-year post-covid patients, including individuals without pneumonia (NP, n=10), those with severe pneumonia (SP, n=11), and healthy controls (C, n=13). Our extensive RNA sequencing revealed 4843 differentially expressed genes (DEGs) and 1056 differentially expressed long non-coding RNAs (DElncRNAs) in \"C vs NP,\" 1651 DEGs and 577 DElncRNAs in \"C vs SP,\" 954 DEGs and 148 DElncRNAs in \"NP vs SP,\" with 291 DEGs and 70 DElncRNAs shared across all groups. We identified 14 hub genes from 291 DEGs, with functional enrichment analysis showing upregulated DEGs mainly linked to inflammation and osteoclast differentiation, and downregulated DEGs to viral infections and immune responses. These hub genes play central roles in inflammatory and immune processes and are significantly associated with pneumonitis and diverse lung diseases. Investigations revealed unique immune cell signatures across DEG categories, associating upregulated DEGs with neutrophils and monocytes, and downregulated DEGs with CD4 memory effector T cells. Analysis of 14 hub genes showed notable upregulation in the no pneumonia group versus healthy controls, displaying complex patterns in the severe pneumonia group. Our study uncovered potential idiopathic pulmonary fibrosis signals in Long-COVID-19 patients PBMC transcriptome, highlighting the urgency for thorough monitoring and extended research to understand COVID-19s lasting effects. This study sheds light on COVID-19s transcriptomic changes and potential lasting effects, guiding future research and therapeutic approaches for Long-COVID-19.", + "rel_num_authors": 39, + "rel_authors": [ + { + "author_name": "Ozgecan Kayalar", + "author_inst": "Koc University Research Center for Translational Medicine (KUTTAM), Koc University, School of Medicine, Istanbul, Turkey" + }, + { + "author_name": "Pelin Duru Cetinkaya", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Cukurova University, Adana, Turkey" + }, + { + "author_name": "Vahap Eldem", + "author_inst": "Istanbul University, Science Faculty, Department of Biology, Istanbul, Turkey" + }, + { + "author_name": "Serap Argun Baris", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey" + }, + { + "author_name": "Nurdan Kokturk", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Gazi University, Ankara, Turkey" + }, + { + "author_name": "Selim Can Kuralay", + "author_inst": "Istanbul University, Science Faculty, Department of Biology, Istanbul, Turkey" + }, + { + "author_name": "Hadi Rajabi", + "author_inst": "Koc University Research Center for Translational Medicine (KUTTAM), Koc University, School of Medicine, Istanbul, Turkey" + }, + { + "author_name": "Nur Konyalilar", + "author_inst": "Koc University Research Center for Translational Medicine (KUTTAM), Koc University, School of Medicine, Istanbul, Turkey" + }, + { + "author_name": "Deniz Mortazavi", + "author_inst": "Koc University Research Center for Translational Medicine (KUTTAM), Koc University, School of Medicine, Istanbul, Turkey" + }, + { + "author_name": "Seval Kubra Korkunc", + "author_inst": "Koc University Research Center for Translational Medicine (KUTTAM), Koc University, School of Medicine, Istanbul, Turkey" + }, + { + "author_name": "Sinem Erkan", + "author_inst": "Koc University Research Center for Translational Medicine (KUTTAM), Koc University, School of Medicine, Istanbul, Turkey" + }, + { + "author_name": "Gizem Tuse Aksoy", + "author_inst": "Koc University Research Center for Translational Medicine (KUTTAM), Koc University, School of Medicine, Istanbul, Turkey" + }, + { + "author_name": "Gul Eyikudamaci", + "author_inst": "Koc University Research Center for Translational Medicine (KUTTAM), Koc University, School of Medicine, Istanbul, Turkey" + }, + { + "author_name": "Pelin Pinar Deniz", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Cukurova University, Adana, Turkey" + }, + { + "author_name": "Oya Baydar Toprak", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Cukurova University, Adana, Turkey" + }, + { + "author_name": "Pinar Yildiz Gulhan", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Duzce University, Duzce, Turkey" + }, + { + "author_name": "Gulseren Sagcan", + "author_inst": "Department of Pulmonary Medicine, Altunizade Acibadem Hospital, Istanbul, Turkey" + }, + { + "author_name": "Neslihan Kose", + "author_inst": "Department of Pulmonary Medicine, Bilecik Training and Research Hospital, Bilecik, Turkey" + }, + { + "author_name": "Aysegul Tomruk Erdem", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Zonguldak Bulent Ecevit University, Zonguldak, Turkey" + }, + { + "author_name": "Fusun Fakili", + "author_inst": "Department of Biostatistics, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey" + }, + { + "author_name": "Onder Ozturk", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Suleyman Demirel University, Isparta, Turkey" + }, + { + "author_name": "Ilknur Basyigit", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey" + }, + { + "author_name": "Hasim Boyaci", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey" + }, + { + "author_name": "Emel Azak", + "author_inst": "Department of Infectious Disease and Clinical Microbiology, Faculty of Medicine, Kocaeli University, Kocaeli Turkey" + }, + { + "author_name": "Tansu Ulukavak Ciftci", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Gazi University, Ankara, Turkey" + }, + { + "author_name": "Ipek Kivilcim Oguzulgen", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Gazi University, Ankara, Turkey" + }, + { + "author_name": "Hasan Selcuk Ozger", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Gazi University, Ankara, Turkey" + }, + { + "author_name": "Pinar Aysert Yildiz", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Gazi University, Ankara, Turkey" + }, + { + "author_name": "Ismail Hanta", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Cukurova University, Adana, Turkey" + }, + { + "author_name": "Ozlem Ataoglu", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Duzce University, Duzce, Turkey" + }, + { + "author_name": "Merve Ercelik", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Duzce University, Duzce, Turkey" + }, + { + "author_name": "Caglar Cuhadaroglu", + "author_inst": "Department of Pulmonary Medicine, Altunizade Acibadem Hospital, Istanbul, Turkey" + }, + { + "author_name": "Hacer Kuzu Okur", + "author_inst": "Department of Pulmonary Medicine, Altunizade Acibadem Hospital, Istanbul, Turkey" + }, + { + "author_name": "Muge Meltem Tor", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Zonguldak Bulent Ecevit University, Zonguldak, Turkey" + }, + { + "author_name": "Esra Nurlu Temel", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Suleyman Demirel University, Isparta, Turkey" + }, + { + "author_name": "Seval Kul", + "author_inst": "Department of Biostatistics, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey" + }, + { + "author_name": "Yildiz Tutuncu", + "author_inst": "Department of Immunology, Koc University Research Center for Translational Medicine (KUTTAM), Koc University School of Medicine, Istanbul, Turkey" + }, + { + "author_name": "Oya Itil", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey" + }, + { + "author_name": "Hasan Bayram", + "author_inst": "Department of Pulmonary Medicine, Koc University School of Medicine, Istanbul, Turkey" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2023.12.13.23299903", "rel_title": "Expected and observed deaths in France from 2020 to 2022: accurately assessing the excess mortality during the COVID-19 pandemic period.", @@ -8682,45 +9305,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2023.12.08.23299736", - "rel_title": "Spatial and Temporal Patterns of SARS-CoV-2 transmission in uMgungundlovu, Kwa-Zulu Natal, South Africa", - "rel_date": "2023-12-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.08.23299736", - "rel_abs": "BackgroundInvestigating the spatial distribution of SARS-CoV-2 at a local level and describing the pattern of disease occurrence can be used as the basis for efficient prevention and control measures. This research project aims to utilize geospatial analysis to understand the distribution patterns of SARS-CoV-2 and its relationship with certain co-existing factors.\n\nMethodsSpatial characteristics of SARS-CoV-2 were investigated over the first four waves of transmission using ESRI ArcGISPro v2.0, including Local Indicators of Spatial Association (LISA) with Morans \"I\" as the measure of spatial autocorrelation; and Kernel Density Estimation (KDE). In implementing temporal analysis, time series analysis using the Python Seaborn library was used, with separate modelling carried out for each wave.\n\nResultsStatistically significant SARS-CoV-2 incidences were noted across age groups with p-values consistently < 0.001. The central region of the district experienced a higher level of clusters indicated by the LISA (Morans I: wave 1 - 0.22, wave 2 - 0.2, wave 3 - 0.11, wave 4 - 0.13) and the KDE (Highest density of cases: wave 1: 25.1-50, wave 2: 101-150, wave 3: 101-150, wave 4: 50.1-100). Temporal analysis showed more fluctuation at the beginning of each wave with less fluctuation in identified cases within the middle to end of each wave.\n\nConclusionA Geospatial approach of analysing infectious disease transmission is proposed to guide control efforts (e.g., testing/tracing and vaccine rollout) for populations at higher vulnerability. Additionally, the nature and configuration of the social and built environment may be associated with increased transmission. However, locally specific empirical research is required to assess other relevant factors associated with increased transmission.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Radiya Gangat", - "author_inst": "Stellenbosch University" - }, - { - "author_name": "Veranyuy Ngah", - "author_inst": "Stellenbosch University Faculty of Medicine and Health Sciences" - }, - { - "author_name": "Justine Blanford", - "author_inst": "University of Twente Faculty of Geo-Information Science and Earth Observation: Universiteit Twente Faculteit Geo-Informatie Wetenschappen en Aardobservatie" - }, - { - "author_name": "Rushambwa Tawonga", - "author_inst": "University of KwaZulu-Natal School of Development Studies: University of KwaZulu-Natal School of Built Environment and Development Studies" - }, - { - "author_name": "Jabulani Ronnie Ncayiyana", - "author_inst": "University of Kwazulu-Natal" - }, - { - "author_name": "Peter S. Nyasulu", - "author_inst": "Stellenbosch University - Tygerberg Campus: Stellenbosch University Faculty of Medicine and Health Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.12.07.23299429", "rel_title": "Mechanisms underlying exercise intolerance in Long COVID: an accumulation of multi-system dysfunction", @@ -8985,6 +9569,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.12.07.23298951", + "rel_title": "Fungal pleural infection due to Microascus gracilis with pulmonary aspergillosis after COVID-19 pneumonia", + "rel_date": "2023-12-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.07.23298951", + "rel_abs": "AbstractO_ST_ABSBackgroundC_ST_ABSScopulariopsis/Microascus is a rare but devastating pathogen due to its intrinsic resistance to nearly all available antifungal agents. Microascus gracilis, an ascomycetous mould in the order Microascales, family Microascaceae, has recently emerged as a significant invasive pathogen causing opportunistic infections.\n\nObjectives and MethodsWe present a case of pleural infection caused by M. gracilis with pulmonary aspergillosis in an immunocompromised man after COVID-19 pneumonia. To further understand the characteristics of the pathogen isolated from the patient, we identified the strain through mycological characteristics, matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MALDI-TOF MS) and internal transcribed spacer (ITS)-based sequencing, and performed in vitro drug susceptibility testing against common antifungal agents. Moreover, we assessed lymphocyte subsets and programmed cell death protein 1 (PD-1) expression in peripheral blood and pleural effusion to monitor the efficacy of therapy with thymosin--1 and intravenous immunoglobulin.\n\nResultsFilamentous fungi isolated from pleural fluid were identified as M. gracilis based on classical morphology, mass spectrometry and molecular biology methods. The susceptibility results in vitro revealed that multiple antifungal agents were inactive against the strain. Adjuvant immunomodulatory treatment successfully increased the levels of CD3+ T and CD4+ T cells while decreasing the levels of CD3+PD-1+ and CD4+PD-1+ T cells in both peripheral blood and pleural effusion.\n\nConclusionsThe immunocompromised host with opportunistic M. gracilis infection, rapid and accurate recognition through direct microscopic testing with calcofluor white and MOLDI-TOF MS, is the key to achieving a definite diagnosis, and a combination of antifungal therapy with immunomodulatory therapy is vital for improving survival.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Zhimin Hu", + "author_inst": "Wuhan No.1 Hospital" + }, + { + "author_name": "Lina Mao", + "author_inst": "Department of Pulmonary and Critical care medicine, Wuhan No.1 Hospital, Wuhan, China" + }, + { + "author_name": "Tiying Deng", + "author_inst": "Department of Pharmacy, Wuhan No.1 Hospital, Wuhan, China" + }, + { + "author_name": "Bintao Su", + "author_inst": "Department of Laboratory Medicine, Wuhan No.1 Hospital, Wuhan, China" + }, + { + "author_name": "Yi Yang", + "author_inst": "Department of Radiology, Wuhan No.1 Hospital, Wuhan, China" + }, + { + "author_name": "Bilin Dong", + "author_inst": "Hubei Key Laboratory for Infectious and Immune of Dermatosis, Wuhan, China" + }, + { + "author_name": "Qing Xu", + "author_inst": "Department of Pulmonary and Critical Care Medicine, Wuhan No.1 Hospital, Wuhan, China" + }, + { + "author_name": "Shuo Yang", + "author_inst": "Department of Pulmonary and Critical care medicine, Wuhan No.1 Hospital, Wuhan, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.12.06.23299623", "rel_title": "Lack of association between HLA and asymptomatic SARS-CoV-2 infection", @@ -10480,117 +11111,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.12.04.23299364", - "rel_title": "Clinical coding of long COVID in primary care 2020-2023 in a cohort of 19 million adults: an OpenSAFELY analysis", - "rel_date": "2023-12-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.04.23299364", - "rel_abs": "BackgroundLong COVID is the patient-coined term for the persistent symptoms of COVID-19 illness for weeks, months or years following the acute infection. There is a large burden of long COVID globally from self-reported data, but the epidemiology, causes and treatments remain poorly understood. Primary care is used to help identify and treat patients with long COVID and therefore Electronic Health Records (EHRs) of past COVID-19 patients could be used to help fill these knowledge gaps. We aimed to describe those with long COVID in primary care records in England.\n\nMethodsWith the approval of NHS England we used routine clinical data from over 19 million adults in England linked to SARS-COV-2 test result, hospitalisation and vaccination data to describe trends in the recording of 16 clinical codes related to long COVID between November 2020 and January 2023. We calculated rates per 100,000 person-years and plotted how these changed over time. We compared crude and minimally adjusted rates of recorded long COVID in patient records between different key demographic and vaccination characteristics using negative binomial models.\n\nFindingsWe identified a total of 55,465 people recorded to have long COVID over the study period, with incidence of new long COVID records increasing steadily over 2021, and declining over 2022. The overall rate per 100,000 person-years was 177.5 cases in women (95% CI: 175.5-179) and 100.5 men (99.5-102). In terms of vaccination against COVID-19, the lowest rates were observed in those with 3+ vaccine doses (103.5 [95% CI: 101.5-105]). Finally, the majority of those with a long COVID record did not have a recorded positive SARS-COV-2 test 12 weeks before the long COVID record.\n\nInterpretationEHR recorded long COVID remains very low compared and incident records of long COVID declined over 2022. We found the lowest rates of recorded long COVID in people with 3 or more vaccine doses. We summarised several sources of possible bias for researchers using EHRs to study long COVID.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Alasdair D Henderson", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Ben FC Butler-Cole", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "John Tazare", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Laurie A Tomlinson", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Michael Marks", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Mark Jit", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Andrew Briggs", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Liang-Yu Lin", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Oliver Carlile", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Christopher Bates", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds" - }, - { - "author_name": "John Parry", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds" - }, - { - "author_name": "Sebastian CJ Bacon", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Iain Dillingham", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "William A Dennison", - "author_inst": "Patient and Public Involvement Steering Committee, London," - }, - { - "author_name": "Ruth E Costello", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Yinghui Wei", - "author_inst": "Centre for Mathematical Sciences, School of Engineering, Computing and Mathematics, University of Plymouth, Plymouth" - }, - { - "author_name": "Alex J Walker", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "William Hulme", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "The OpenSAFELY Collaborative", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Emily Herrett", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Rosalind M Eggo", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.12.04.23299370", "rel_title": "Real-world effectiveness of sotrovimab for the treatment of SARS-CoV-2 infection during Omicron BA.2 and BA.5 subvariant predominance: a systematic literature review", @@ -10791,6 +11311,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2023.12.03.23299331", + "rel_title": "Long COVID is associated with severe cognitive slowing", + "rel_date": "2023-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.03.23299331", + "rel_abs": "BackgroundCOVID-19 survivors may suffer from a wide range of chronic cognitive symptoms for months or years as part of post-COVID-19 conditions (PCC). To date, there is no definitive objective cognitive marker for PCC. We hypothesised that a key common deficit in people with PCC might be generalised cognitive slowing.\n\nMethodsTo examine cognitive slowing, PCC patients completed two short web-based cognitive tasks, Simple Reaction Time (SRT) and Number Vigilance Test (NVT). 270 patients diagnosed with PCC at two different clinics in UK and Germany were compared to two control groups: individuals who contracted COVID-19 before but did not experience PCC after recovery (No-PCC group) and uninfected individuals (No-COVID group).\n\nFindingsWe identified pronounced cognitive slowing in PCC patients, which distinguished them from age-matched healthy individuals who previously had symptomatic COVID-19 but did not manifest PCC. Cognitive slowing was evident even on a 30-second task measuring simple reaction time (SRT), with PCC patients responding to stimuli [~]3 standard deviations slower than healthy controls. This finding was replicated across two clinic samples in Germany and the UK. Comorbidities such as fatigue, depression, anxiety, sleep disturbance, and post-traumatic stress disorder did not account for the extent of cognitive slowing in PCC patients. Furthermore, cognitive slowing on the SRT was highly correlated with the poor performance of PCC patients on the NVT measure of sustained attention.\n\nInterpretationTogether, these results robustly demonstrate pronounced cognitive slowing in people with PCC, which distinguishes them from age-matched healthy individuals who previously had symptomatic COVID-19 but did not manifest PCC. This might be an important factor contributing to some of the cognitive impairments reported in PCC patients.\n\nFundingWellcome Trust (206330/Z/17/Z), NIHR Oxford Health Biomedical Research Centre, the Thuringer Aufbaubank (2021 FGI 0060), German Forschungsgemeinschaft (DFG, FI 1424/2-1) and the Horizon 2020 Framework Programme of the European Union (ITN SmartAge, H2020-MSCA-ITN-2019-859890).\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched Google Scholar and PubMed for original research or review articles about the cognitive impairment after COVID-19, published up to 3 December 2023. We used terms relating to COVID-19 (SARS-CoV-2, influenza), post-acute symptoms (long COVID, post-COVID conditions, Post-Acute COVID Syndrome) and cognitive impairment (brain fog, cognitive deficit). Previous studies have shown that some people who recovered from the acute symptoms of COVID-19 might nevertheless experience deficits across an array of cognitive functions, including sustained attention, cognitive flexibility, and memory. However, most reports lacked consensus on the precise definition of post-COVID conditions and a common cognitive signature of post-COVID conditions remains unknown.\n\nAdded value of this studyIn this investigation, we identified moderate to severe cognitive slowing in most patients with PCC, but not in most people who previously suffered COVID without developing PCC. This was replicated across two post-COVID clinics in Germany and the UK. To our knowledge, this is the first robust demonstration of cognitive slowing as a cognitive signature of post-COVID conditions.\n\nImplications of all the available evidenceUsing a 30-second web-based, self-administered psychomotor task, cognitive slowing in PCC can be reliably and easily measured as part of diagnostic work-up, and has potential to be a biomarker to track the progress of rehabilitation of PCC. To encourage researchers and clinicians to employ this task, we have ensured that it is available online with online feedback and all of our code is publicly accessible.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Sijia Zhao PhD", + "author_inst": "University of Oxford" + }, + { + "author_name": "Eva Maria Martin", + "author_inst": "Jena University Hospital" + }, + { + "author_name": "Philipp A. Reuken MD", + "author_inst": "Jena University Hospital" + }, + { + "author_name": "Anna Scholcz", + "author_inst": "University of Oxford" + }, + { + "author_name": "Akke Ganse-Dumrath", + "author_inst": "University of Oxford" + }, + { + "author_name": "Annie Srowig", + "author_inst": "Jena University Hospital" + }, + { + "author_name": "Isabelle Utech", + "author_inst": "Jena University Hospital" + }, + { + "author_name": "Valeska Kozik", + "author_inst": "Jena University Hospital" + }, + { + "author_name": "Monique Radscheidt MD", + "author_inst": "Jena University Hospital" + }, + { + "author_name": "Stefan Brodoehl MD", + "author_inst": "Jena University Hospital" + }, + { + "author_name": "Andreas Stallmach MD", + "author_inst": "Jena University Hospital" + }, + { + "author_name": "Matthias Schwab MD", + "author_inst": "Jena University Hospital" + }, + { + "author_name": "Emily Fraser PhD", + "author_inst": "Oxford University Hospitals Foundation NHS Trust" + }, + { + "author_name": "Kathrin Finke PhD", + "author_inst": "Jena University Hospital" + }, + { + "author_name": "Masud Husain FMedSci", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2023.12.03.23299339", "rel_title": "Expression profile analysis of COVID-19 patients", @@ -12166,53 +12761,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.11.29.23299183", - "rel_title": "Diagnostic Performance of Rapid Antigen Testing for SARS-CoV-2: The COVid-19 AntiGen (COVAG) Extension study", - "rel_date": "2023-11-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.29.23299183", - "rel_abs": "BackgroundRapid antigen tests (RATs) for SARS-CoV-2 have been used to combat the still ongoing Covid-19 pandemic. This study is the extension of the COVAG study originally performed from February 1 to March 31, 2021. We compared two RATs, the Panbio COVID-19 Ag Rapid Test (Abbott) and the SD Biosensor Q SARS-CoV-2 Rapid Antigen Test (Roche), against RT-PCR on the foil of new variants.\n\nMethodsWe included 888 all-comers at a diagnostic center between October 20, 2021, and March 18, 2022. RT-PCR-positive samples with a Ct value [≤] 32 were examined for SARS-CoV-2 variants.\n\nFindingsThe sensitivity of the Abbott-RAT and Roche-RAT were 65% and 67%, respectively. For both RATs, lower Ct values were significantly correlated with higher sensitivity. For samples with Ct values [≤] 25, the sensitivities of the Roche-RAT and of the Abbott-RAT were 96% and 95%, for Ct values 25-30 both were 19%, and for Ct values [≥] 30 they were 6% and 2%, respectively. The RATs had substantially higher sensitivities in symptomatic than asymptomatic participants (76, 77%, vs. 29, 31%, for Abbott-RAT, Roche-RAT, respectively) and in participants referred to testing by their primary care physician (84%, 85%) compared to participants who sought testing due to referral by the health department (55%, 58%) or a warning by the Corona-Warn-App (49%, 49%). In persons with self-reported previous Covid-19 sensitivities were markedly lower than in patients without previous Covid-19: 27% vs. 75% for Roche-RAT and 27% vs. 73% for Abbott-RAT. Depending on the vaccination status, the sensitivity of the RATs is 67.6%, 61.5% and 70.6% for non-vaccinated, vaccinated and boostered participants, respectively. For the considered subpopulation of 888 participants, we find no significant correlation between vaccination status and sensitivity.\n\nThe Omicron variant was detected with a sensitivity of 94% and 92%, the delta variant with a sensitivity of 80% and 80% for Abbott-RAT and Roche-RAT, respectively. This difference is attributable to the lower Ct values of the Omicron samples compared to the Delta samples. When adjusted for the Ct value, a multivariate logistic regression did not show a significant difference between Omicron and Delta. In terms of sensitivity, we found no significant difference between the wild-type and the Omicron and Delta variants, but a significantly lower sensitivity to the alpha variant compared to the other variants.\n\nFor a Ct value [≤] 25 the sensitivities were 95.2% and 96.0% for the Abbott-RAT and the Roche-RAT, respectively (Table 4). For a Ct value of 25-30 both RATs had a sensitivity of 18.8%. For a Ct value of 30-32, the sensitivities were 0.0% and 7.1% respectively, for Ct values [≥]32 the sensitivities were 3.0% and 6.0% for Abbott-RAT and Roche-RAT, respectively.\n\nThe specificities were >99% overall.\n\nInterpretation: The sensitivity of the RATs for asymptomatic carriers is unsatisfactory questioning their use for screening. When used in symptomatic patients or when requested by a primary care physician the sensitivities were higher. Our study does not suggest that the vaccination status influences the sensitivity of RATs.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Christoph Wertenauer", - "author_inst": "Medical Clinic V, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany" - }, - { - "author_name": "Alexander Dressel", - "author_inst": "Dr. Dressel Consulting, Mannheim, Germany" - }, - { - "author_name": "Eberhard Wieland", - "author_inst": "SYNLAB Medical Care Center Leinfelden-Echterdingen GmbH, Leinfelden-Echterdingen, Germany" - }, - { - "author_name": "Hans-Joerg Wertenauer", - "author_inst": "Hausaerzte am Schillerplatz, Stuttgart, Germany" - }, - { - "author_name": "Helmine Braitmaier", - "author_inst": "SYNLAB Medical Care Center Leinfelden-Echterdingen GmbH, Leinfelden-Echterdingen, Germany" - }, - { - "author_name": "Anna Straub", - "author_inst": "SYNLAB Medical Care Center Leinfelden-Echterdingen GmbH, Leinfelden-Echterdingen, Germany" - }, - { - "author_name": "Nicolas Luetzner", - "author_inst": "SYNLAB Medical Care Center Leinfelden-Echterdingen GmbH, Leinfelden-Echterdingen, Germany" - }, - { - "author_name": "Winfried Maerz", - "author_inst": "SYNLAB Academy, SYNLAB Holding Deutschland GmbH, Mannheim, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.11.28.23298927", "rel_title": "Social determinants of adult COVID-19 vaccine acceptance and uptake in a Brazilian urban informal community: a longitudinal time-to-event study", @@ -12369,6 +12917,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.11.25.568685", + "rel_title": "The antiviral potential of the antiandrogen enzalutamide and the viral-androgen interplay in seasonal coronaviruses", + "rel_date": "2023-11-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.25.568685", + "rel_abs": "The sex disparity in COVID-19 outcomes with males generally faring worse than females has been associated with the androgen-regulated expression of the protease TMPRSS2 and the cell receptor ACE2 in the lung and fueled interest in antiandrogens as potential antivirals. In this study, we explored enzalutamide, an antiandrogen used commonly against prostate cancer, as a potential antiviral against the human coronaviruses which cause seasonal respiratory infections (HCoV-NL63, -229E, and -OC43). Using lentivirus-pseudotyped and authentic HCoV, we report that enzalutamide reduced 229E and NL63 entry and replication in both TMPRSS2- and non-expressing immortalised cells, suggesting a TMPRSS2-independent mechanism. However, no effect was observed against OC43. To decipher this distinction, we performed RNA-sequencing analysis on 229E-and OC43- infected primary human airway cells. Our results show a significant induction of androgen-responsive genes by 229E compared to OC43 at 24 and 72h post-infection. The virus-mediated effect to AR signaling was further confirmed with a consensus androgen response element (ARE)-driven luciferase assay in androgen-depleted MRC-5 cells. Specifically, 229E induced luciferase reporter activity in the presence and absence of the synthetic androgen mibolerone, while OC43 inhibited induction. These findings highlight a complex interplay between viral infections and androgen signaling, offering insights for potential antiviral interventions.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Oluwadamilola D Ogunjinmi", + "author_inst": "University of Essex" + }, + { + "author_name": "Tukur Abdullahi", + "author_inst": "University of Essex" + }, + { + "author_name": "Riaz-Ali Somji", + "author_inst": "University of Essex" + }, + { + "author_name": "Charlotte L Bevan", + "author_inst": "Imperial College London" + }, + { + "author_name": "Wendy S Barclay", + "author_inst": "Imperial College London" + }, + { + "author_name": "Nigel James Temperton", + "author_inst": "University of Kent" + }, + { + "author_name": "Greg N Brooke", + "author_inst": "University of Essex" + }, + { + "author_name": "Efstathios S Giotis", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.11.25.568642", "rel_title": "Safe plant Hsp90 adjuvants elicit an effective immune response against SARS-CoV2 derived RBD antigen", @@ -14048,25 +14643,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.11.22.23298917", - "rel_title": "Assessment of the effectiveness of required weekly COVID-19 surveillance antigen testing at a university", - "rel_date": "2023-11-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.22.23298917", - "rel_abs": "ObjectivesTo mitigate the COVID-19 pandemic, many institutions implemented a regimen of periodic required testing, irrespective of symptoms. The effectiveness of this\"surveillance testing\" requires assessment.\n\nMethodsI fit a zero-inflated negative binomial model to COVID-19 testing and case investigation data between 1 November 2020 and 15 May 2021, from young adult subjects in one community. I compared the duration of symptoms at time of specimen collection in those diagnosed via (1) surveillance testing at a university, (2) the same universitys student health services, and (3) all other testing venues.\n\nResultsThe data comprised 2926 records: 393 from surveillance testing, 493 from student health service, and 2040 from other venues. About 65% of people with COVID-19 detected via surveillance testing were already symptomatic at time of specimen collection.\n\nPredicted mean duration of pre-testing symptoms was 1.7 days (95% CI 1.59 to 1.84) for the community, 1.81 days (95% CI 1.62 to 1.99) for surveillance, and 2 days (95% CI 1.83 to 2.16) for student health service. The modelled \"inflated\" proportions of asymptomatic subjects from the surveillance stream and the other/community stream were comparable (odds ratio 0.95, p = 0.7709). Comparing surveillance testing with the student health service, the proportion of \"excess\" zero symptom durations was signficantly higher in the former (Chi-square = 12.08, p = 0.0005)\n\nConclusionsSurveillance testing at a university detected 393 people with COVID-19, but no earlier in their trajectory than similar-aged people detected in the broader community. This casts some doubt on the public health value of such programs, which tend to be labor-intensive and expensive.\n\n2 Three-question summary boxO_ST_ABSWhat is the current understanding of this subject?C_ST_ABSAssessments of long-term operational effectiveness of COVID-19 \"surveillance testing\" have not been published.\n\nWhat does this report add to the literature?During the 2020-2021 academic year at one university, people with COVID-19 detected via compulsory weekly surveillance antigen testing were equally likely to be symptomatic at time of detection, and for just as long, as similar-aged people detected via testing venues in the community.\n\nWhat are the implications for public health practice?Surveillance testing programs during the pandemic consumed a large amount of time, money, and effort. In future respiratory pandemics, resources might be better devoted to other mitigation measures.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Christopher W Ryan", - "author_inst": "SUNY Upstate Medical University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.11.22.23298899", "rel_title": "Quantitative susceptibility mapping at 7 Tesla in COVID-19: mechanistic and outcome associations", @@ -14331,6 +14907,57 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2023.11.21.568132", + "rel_title": "SARS-CoV-2 infects neurons, astrocytes, choroid plexus epithelial cells and pericytes of the human central nervous system", + "rel_date": "2023-11-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.21.568132", + "rel_abs": "SARS-CoV-2, the coronavirus responsible for the COVID-19 pandemic, is associated with a range of neurological manifestations including haemorrhage, thrombosis and ischaemic necrosis and encephalitits. However, the mechanism by which this occurs is unclear. Neurological disease associated with SARS-CoV-2 infection has been proposed to occur following direct infection of the central nervous system and/or indirect sequelae as a result of peripheral inflammation. We profiled ACE2 and TMPRSS2 in brain tissue from five healthy human donors, and observed expression of these proteins in astrocytes, neurons and choroid plexus epithelium within frontal cortex and medulla. Primary human astrocytes, neurons and choroid plexus epithelial cells supported productive SARS-CoV-2 infection in an ACE2- dependent manner. Infected cells supported the full viral lifecycle, releasing infectious virus particles. In contrast, primary brain microvascular endothelial cells, pericytes and microglia were refractory to SARS-CoV-2 infection. These data support a model whereby SARS-CoV-2 is neurotropic, and this may in part explain the neurological sequelae of infection.\n\nImportanceA subset of patients with COVID-19 develop neurological symptoms, but the underlying cause is poorly understood. We observed that cells within normal human brain express the SARS-CoV-2 entry factors ACE-2 and TMPRRS2, with expression mainly observed within astrocytes, neurons and choroid plexus epithelium. Primary human astrocytes, neurons and choroid plexus epithelial cells cultured in vitro supported the full SARS-CoV-2 life cycle with a range of SARS-CoV-2 variants. This study demonstrates that cells of the human central nervous system express SARS-CoV-2 entry factors in vivo and support viral infection in vitro, thus supporting a model where neurological symptoms seen in some COVID-19 patients may be as a result of direct viral infection of the central nervous system. Furthermore, these data highlight the importance of investigating the ability of therapeutics to clear virus from this potential reservoir of infection.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ruth Haverty", + "author_inst": "University College Dublin" + }, + { + "author_name": "Janet McCormack", + "author_inst": "University College Dublin" + }, + { + "author_name": "Christopher Evans", + "author_inst": "University College Dublin" + }, + { + "author_name": "Kevin Purves", + "author_inst": "University College Dublin" + }, + { + "author_name": "Sophie O'Reilly", + "author_inst": "University College Dublin" + }, + { + "author_name": "Virginie Wilhelmine Gautier", + "author_inst": "University College Dublin" + }, + { + "author_name": "Keith Rochfort", + "author_inst": "Dublin City University" + }, + { + "author_name": "Aurelie Fabre", + "author_inst": "St Vincent's University Hospital" + }, + { + "author_name": "Nicola Fletcher", + "author_inst": "University College Dublin" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.11.22.23298846", "rel_title": "Recovery of Neurophysiological Measures in Post-COVID Fatigue - a 12-month Longitudinal Follow-up Study", @@ -15830,65 +16457,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.11.20.23298784", - "rel_title": "Assessment of the Usability of SARS-CoV-2 Self Tests in a Peer-Assisted Model among Factory Workers in Bengaluru, India", - "rel_date": "2023-11-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.20.23298784", - "rel_abs": "In order to mitigate the inequities in health outcomes and healthcare access for vulnerable populations during the COVID-19 pandemic, the government of India introduced antigen-based SARS-CoV-2 self-testing kits for self-administered use. In this study, we aimed to determine the usability of these nasal-sampling-based self-tests in a peer-assisted model among factory workers in Bengaluru. The mixed-method cross-sectional study was conducted with 106 factory workers, spanning two sites from February to March 2022 in Bengaluru, India. Panbio COVID-19 Antigen Self-Test kit and the mobile application NAVICA for self-reporting results were used. A peer assistant distributed test kits, guided participants on conducting tests and using the app, and offered demonstrations with their own kit, ensuring no contact with the participants kits. Findings were encapsulated by an observer, who used standardized product-specific usability checklists and pictures of contrived results to assess the usability of the kit and mobile application, result interpretation, and the efficiency of peer instruction/demonstration. Additionally, a post-test survey and focus group discussions with selected participants and peer assistants were conducted to understand user perceptions of the facilitators and barriers to usability. Study findings show that the overall usability score of the test kit with peer assistance was 75.9%, rising to 80.7% for critical steps and 33.8% for all critical steps in uploading results through NAVICA. Additionally, it was seen that peer assistants provided accurate instructions and support for 93.4% of the tests. Among the critical steps in test kit use, maximum errors were made in sample collection and using the correct amount of buffer solution. Concordance between the participant and observer/NAVICA was 97.9%. 62.0% and 56.6% of the participants reported confidence in a) performing and interpreting the test and b) capturing and uploading their results using the mobile application with the assistance of a peer, respectively. Less than half the participants reported confidence in performing these steps independently. The study indicates that the COVID-19 nasal self-testing kit has good usability in factories peer-assisted workplace testing model. Such models can empower vulnerable worker groups to access early detection and self-care tools equitably.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Meghana Ratna Pydi", - "author_inst": "Swasti - The Health Catalyst" - }, - { - "author_name": "Petra Stankard", - "author_inst": "Foundation for Innovative New Diagnostics: FIND" - }, - { - "author_name": "Neha Parikh", - "author_inst": "Swasti - The Health Catalyst" - }, - { - "author_name": "Purnima Ranawat", - "author_inst": "Swasti - The Health Catalyst" - }, - { - "author_name": "Ravneet Kaur", - "author_inst": "Swasti - The Health Catalyst" - }, - { - "author_name": "Shankar AG", - "author_inst": "Swasti - The Health Catalyst" - }, - { - "author_name": "Angela Chaudhuri", - "author_inst": "Swasti - The Health Catalyst" - }, - { - "author_name": "Sonjelle Shilton", - "author_inst": "Foundation for Innovative New Diagnostics: FIND" - }, - { - "author_name": "Aditi Srinivasan", - "author_inst": "Foundation for Innovative New Diagnostics: FIND" - }, - { - "author_name": "Joyita Chowdhury", - "author_inst": "Foundation for Innovative New Diagnostics: FIND" - }, - { - "author_name": "Elena Ivanova Reipold", - "author_inst": "Foundation for Innovative New Diagnostics: FIND" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.11.20.23298741", "rel_title": "Increased Severity of New-onset Type 1 Diabetes in Children and Adolescents during the COVID-19 Pandemic: Experience from a Tertiary Care Center in Serbia", @@ -16109,6 +16677,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.11.16.23298658", + "rel_title": "Impact of State Telehealth Parity Laws for Private Payers on Hypertension Management before and during the COVID-19 Pandemic", + "rel_date": "2023-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.16.23298658", + "rel_abs": "BACKGROUNDTelehealth has emerged as an effective tool for managing common chronic conditions such as hypertension, especially during the COVID-19 pandemic. However, the impact of state telehealth payment and coverage parity laws on hypertension management remains uncertain.\n\nMETHODSData from the MerativeTM MarketScan(R) Commercial Claims and Encounters Database from January 1, 2016 to December 31, 2021 were used to construct the study cohort. The sample included non-pregnant individuals aged 25-64 years with hypertension. We reviewed and coded telehealth parity laws related to hypertension management in all 50 states and the District of Columbia, distinguishing between payment parity laws and coverage parity laws. The primary outcomes were antihypertension medication use, measured by the average medication possession ratio (MPR), medication adherence (MPR [≥]80%), and average number of days of drug supply. We used a generalized difference-in-difference (DID) design to examine the impact of these laws. Results were presented as marginal effects and 95% confidence intervals (CI).\n\nRESULTSAmong 353,220 individuals, states with payment parity laws were significantly linked to increased average MPR by 0.43 percentage point (95% CI: 0.07 - 0.79), and an increase of 0.46 percentage point (95% CI: 0.06 - 0.92) in the probability of medication adherence. Payment parity laws also led to an average increase of 2.14 days (95% CI: 0.11 - 4.17) in antihypertensive drug supply, after controlling for state-fixed effects, year-fixed effects, individual sociodemographic characteristics and state time-varying covariates including unemployment rates, GDP per capita, and poverty rates. In contrast, coverage parity laws were associated with a 2.13-day increase (95% CI: 0.19 - 4.07) in days of drug supply, but did not significantly increase the average MPR or probability of medication adherence. In addition, telehealth payment or coverage parity laws were positively associated with the number of hypertension-related telehealth visits, but this effect did not reach statistical significance. These findings were consistent in sensitivity analyses.\n\nCONCLUSIONSState telehealth payment parity laws were significantly associated with greater medication adherence, whereas coverage parity laws were not. With the increasing adoption of telehealth parity laws across states, these findings may support policymakers in understanding potential implications on management of hypertension.\n\nClinical Perspective What Is New?Telehealth is an effective tool to manage hypertension and state-level telehealth parity laws can influence its application. Prior studies have not clearly differentiated between the impacts of payment parity and coverage parity. Using a quasi-experimental generalized difference-in-differences design, we assessed the effects of telehealth payment parity and coverage parity laws on hypertension management.\n\nOur study found that state telehealth payment parity laws were significantly associated with increased hypertension medication adherence, while coverage parity laws were not.\n\nWhat Are the Clinical Implications?The widespread adoption of telehealth payment parity laws may significantly impact hypertension management, during emergencies like the COVID-19 pandemic and beyond.\n\nConsidering that hypertension impacts approximately half of the adult population, our study provides valuable insights into the potential benefits of telehealth parity laws for private payers in enhancing the management of hypertension.\n\nWith the increasing adoption of telehealth parity laws across states, integrating telehealth into hypertension management holds significant implications for the evolving U.S. healthcare system in the digital age.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Donglan Zhang", + "author_inst": "New York University Long Island School of Medicine" + }, + { + "author_name": "Jun Soo Lee", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Adebola Popoola", + "author_inst": "CDC" + }, + { + "author_name": "Sarah Lee", + "author_inst": "New York University Grossman Long Island School of Medicine" + }, + { + "author_name": "Sandra L. Jackson", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Lisa M Pollack", + "author_inst": "CDC" + }, + { + "author_name": "Xiaobei Dong", + "author_inst": "University of Wisconsin-Milwaukee" + }, + { + "author_name": "Feijun Luo", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Nicole Leigh Therrien", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2023.11.17.23298700", "rel_title": "Antibody response to symptomatic infection with SARS-CoV-2 Omicron variant viruses, December 2021 to June 2022", @@ -17672,49 +18291,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.11.13.23298480", - "rel_title": "Integrating stimulus-organism-response model and theory of planned behavior to explore athletes intention to receive the COVID-19 vaccine booster - A moderated mediation model", - "rel_date": "2023-11-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.13.23298480", - "rel_abs": "This study aims to investigate the factors influencing athletes intention to receive the COVID-19 vaccine booster in Mainland China by integrating the stimulus-organization-response (SOR) model and theory of planned behavior (TPB) as the theoretical framework. Purposive sampling was used to select respondents from the National Games of the Peoples Republic of China. Hard-copy questionnaires were utilized to collect data, resulting in 981 valid responses. Descriptive analysis and partial least squares structural equation modeling were used to analyze the data. The findings reveal that athletes subjective norm and knowledge significantly influence attitude, commitment, and perceived behavioral control. Attitude, commitment, and perceived behavioral control are verified as full mediators between subjective norm, knowledge, and intention to receive the COVID-19 vaccine booster. Knowledge to commitment is the most powerful path to predict athletes intention to receive the COVID-19 vaccine booster. Motivation moderates the relationships between knowledge, attitude, commitment, and perceived behavioral control. The integrating models explanatory power is 83.2%. Athletes knowledge is crucial in shaping a positive attitude, commitment, and perceived control, enhancing their intention to get the COVID-19 vaccine booster.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Wenpeng Zhan", - "author_inst": "Lingnan Normal University" - }, - { - "author_name": "Qianting Deng", - "author_inst": "South China Normal University" - }, - { - "author_name": "Van Bac Nguyen", - "author_inst": "National Taiwan University of Sport" - }, - { - "author_name": "Tran Phan Duc Anh", - "author_inst": "National Taiwan University of Sport" - }, - { - "author_name": "Phan Danh Na", - "author_inst": "National Taiwan University of Sport" - }, - { - "author_name": "An-Shin Shia", - "author_inst": "Lingnan Normal University" - }, - { - "author_name": "Gordon Chih Ming Ku", - "author_inst": "National Taiwan University of Sport" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.11.13.23298463", "rel_title": "A SOLUTION TO THE KERMACK AND MCKENDRICK INTEGRO-DIFFERENTIAL EQUATIONS WHICH ACCURATELY PROJECTS COVID-19 CASE DATA USING GOOGLE MOBILITY DATA AS AN INPUT", @@ -17855,6 +18431,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.11.11.566634", + "rel_title": "Recreating the Biological Steps of Viral Infection on a Bioelectronic Platform to Profile Viral Variants of Concern", + "rel_date": "2023-11-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.11.566634", + "rel_abs": "Viral mutation rates frequently outpace the development of technologies used to detect and identify harmful variants; for SARS Coronavirus-2 (SARS-CoV-2), these are called variants of concern (VOC). Given the continual emergence of VOC, there is a critical need to develop platforms that can identify the presence of a virus and readily identify its propensity for infection. We present an electronic biomembrane sensing platform that recreates the multifaceted and sequential biological cues that give rise to distinct SARS-CoV-2 virus host cell entry pathways and reports the progression of entry steps of these pathways as electrical signals. Within these electrical signals, two necessary entry processes mediated by the viral Spike protein, virus binding and membrane fusion, can be distinguished. Remarkably, we find that closely related VOC exhibit distinct fusion signatures that correlate with trends reported in cell-based infectivity assays, allowing us to report quantitative differences in fusion characteristics among them that inform their infectivity potentials. This cell-free biomimetic infection platform also has a virus-free option that equally reports infectivity potential of the Spike proteins. We used SARS-CoV-2 as our prototype, but we anticipate that this platform will extend to other enveloped viruses and cell lines to quantifiably explore virus/host interactions. This advance should aid in faster determination of entry characteristics and fusogenicities of future VOC, necessary for rapid response.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Zhongmou Chao", + "author_inst": "Cornell University" + }, + { + "author_name": "Ekaterina Selivanovitch", + "author_inst": "Cornell University" + }, + { + "author_name": "Konstantinos Kallitsis", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Zixuan Lu", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Ambika Pachaury", + "author_inst": "Cornell University" + }, + { + "author_name": "R\u00f3is\u00edn Owens", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Susan Daniel", + "author_inst": "Cornell University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2023.11.10.566497", "rel_title": "Single Nucleus RNA Sequencing of Remnant Kidney Biopsies and Urine Cell RNA Sequencing Reveal Cell Specific Markers of Covid-19 Acute Kidney Injury", @@ -19670,81 +20289,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.11.06.565781", - "rel_title": "The \u03b1-dystroglycan N-terminus is a broad-spectrum antiviral agent against SARS-CoV-2 and enveloped viruses", - "rel_date": "2023-11-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.06.565781", - "rel_abs": "The COVID-19 pandemic has shown the need to develop effective therapeutics in preparedness for further epidemics of virus infections that pose a significant threat to human health. As a natural compound antiviral candidate, we focused on -dystroglycan, a highly glycosylated basement membrane protein that links the extracellular matrix to the intracellular cytoskeleton. Here we show that the N-terminal fragment of -dystroglycan (-DGN), as produced in E. coli in the absence of post-translational modifications, blocks infection of SARS-CoV-2 in cell culture, human primary gut organoids and the lungs of transgenic mice expressing the human receptor angiotensin I-converting enzyme 2 (hACE2). Prophylactic and therapeutic administration of -DGN reduced SARS-CoV-2 lung titres and protected the mice from respiratory symptoms and death. Recombinant -DGN also blocked infection of a wide range of enveloped viruses including the four Dengue virus serotypes, influenza A virus, respiratory syncytial virus, tick-borne encephalitis virus, but not human adenovirus, a non-enveloped virus in vitro. This study establishes soluble recombinant -DGN as a broad-band, natural compound candidate therapeutic against enveloped viruses.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Martia Giulia Bigotti", - "author_inst": "University of Bristol" - }, - { - "author_name": "Katja Klein", - "author_inst": "University of Bristol" - }, - { - "author_name": "Esther S Gan", - "author_inst": "Duke-NUS Medical School" - }, - { - "author_name": "Maria Anastasina", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Simon Andersson", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Olli Vapalahti", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Pekka Katajisto", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Maximilian Erdmann", - "author_inst": "University of Bristol" - }, - { - "author_name": "Andrew D. Davidson", - "author_inst": "University of Bristol" - }, - { - "author_name": "Sarah Jane Butcher", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Ian Collinson", - "author_inst": "University of Bristol" - }, - { - "author_name": "Eng Eong Ooi", - "author_inst": "Duke-NUS Medical School" - }, - { - "author_name": "Giuseppe Balistreri", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Andrea Brancaccio", - "author_inst": "CNR Rome and University of Bristol" - }, - { - "author_name": "Yohei Yamauchi", - "author_inst": "ETH Zurich" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.11.06.565757", "rel_title": "Allosteric modulation by the fatty acid site in the glycosylated SARS-CoV-2 spike", @@ -19993,6 +20537,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.11.06.23298151", + "rel_title": "Text Augmentations with R-drop for Classification of Tweets Self-Reporting Covid-19", + "rel_date": "2023-11-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.06.23298151", + "rel_abs": "This paper presents models created for the Social Media Mining for Health 2023 shared task. Our team addressed the first task, classifying tweets that self-report Covid-19 diagnosis. Our approach involves a classification model that incorporates diverse textual augmentations and utilizes R-drop to augment data and mitigate overfitting, boosting model efficacy. Our leading model, enhanced with R-drop and augmentations like synonym substitution, reserved words, and back translations, outperforms the task mean and median scores. Our system achieves an impressive F1 score of 0.877 on the test set.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Sumam Francis", + "author_inst": "KU Leuven, Belgium" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2023.11.06.23298096", "rel_title": "Exploring the perceptions and experiences of community rehabilitation for Long COVID from the perspectives of Scottish General Practitioners and people living with Long COVID: a qualitative study", @@ -21572,53 +22135,6 @@ "type": "new results", "category": "developmental biology" }, - { - "rel_doi": "10.1101/2023.10.30.564067", - "rel_title": "Pervasive aggregation and depletion of host and viral proteins in response to cysteine-reactive electrophilic compounds", - "rel_date": "2023-11-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.30.564067", - "rel_abs": "Protein homeostasis is tightly regulated, with damaged or misfolded proteins quickly eliminated by the proteasome and autophagosome pathways. By co-opting these processes, targeted protein degradation technologies enable pharmacological manipulation of protein abundance. Recently, cysteine-reactive molecules have been added to the degrader toolbox, which offer the benefit of unlocking the therapeutic potential of undruggable protein targets. The proteome-wide impact of these molecules remains to be fully understood and given the general reactivity of many classes of cysteine-reactive electrophiles, on- and off-target effects are likely. Using chemical proteomics, we identified a cysteine-reactive small molecule degrader of the SARS-CoV-2 non- structural protein 14 (nsp14), which effects degradation through direct modification of cysteines in both nsp14 and in host chaperones together with activation of global cell stress response pathways. We find that cysteine-reactive electrophiles increase global protein ubiquitylation, trigger proteasome activation, and result in widespread aggregation and depletion of host proteins, including components of the nuclear pore complex. Formation of stress granules was also found to be a remarkably ubiquitous cellular response to nearly all cysteine-reactive compounds and degraders. Collectively, our study sheds light on complexities of covalent target protein degradation and highlights untapped opportunities in manipulating and characterizing proteostasis processes via deciphering the cysteine-centric regulation of stress response pathways.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ashley R Julio", - "author_inst": "UNIVERSITY OF CALIFORNIA LOS ANGELES" - }, - { - "author_name": "Flowreen Shikwana", - "author_inst": "UNIVERSITY OF CALIFORNIA LOS ANGELES" - }, - { - "author_name": "Cindy Truong", - "author_inst": "UCLA" - }, - { - "author_name": "Nikolas R Burton", - "author_inst": "UNIVERSITY OF CALIFORNIA LOS ANGELES" - }, - { - "author_name": "Emil Dominguez", - "author_inst": "UCLA" - }, - { - "author_name": "Alexandra Turmon", - "author_inst": "UCLA" - }, - { - "author_name": "Jian Cao", - "author_inst": "UCLA" - }, - { - "author_name": "Keriann Backus", - "author_inst": "UNIVERSITY OF CALIFORNIA LOS ANGELES" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.10.31.565042", "rel_title": "SARS-CoV-2 infection leads to sustained testicular injury and functional impairments in K18 hACE2 mice", @@ -21839,6 +22355,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.10.27.23297682", + "rel_title": "Influenza vaccine effectiveness against hospitalized SARS-CoV-2 infection", + "rel_date": "2023-10-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.27.23297682", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackgroundC_ST_ABSSome studies conducted before the Delta and Omicron variant-dominant periods have indicated that influenza vaccination provided protection against COVID-19 infection or hospitalization, but these results were limited by small study cohorts and a lack of comprehensive data on patient characteristics. No studies have examined this question during the Delta and Omicron periods (08/01/2021 to 2/22/2022).\n\nMethodsWe conducted a retrospective cohort study of influenza-vaccinated and unvaccinated patients in the Corewell Health East(CHE, formerly known as Beaumont Health), Corewell Health West(CHW, formerly known as Spectrum Health) and Michigan Medicine (MM) healthcare system during the Delta-dominant and Omicron-dominant periods. We used a test-negative, case-control analysis to assess the effectiveness of the influenza vaccine against hospitalized SARS-CoV-2 outcome in adults, while controlling for individual characteristics as well as pandameic severity and waning immunity of COVID-19 vaccine.\n\nResultsThe influenza vaccination has shown to provided some protection against SARS-CoV-2 hospitalized outcome across three main healthcare systems. CHE site (odds ratio [OR]=0.73, vaccine effectiveness [VE]=27%, 95% confidence interval [CI]: [18-35], p<0.001), CHW site (OR=0.85, VE=15%, 95% CI: [6-24], p<0.001), MM (OR=0.50, VE=50%, 95% CI: [40-58], p <0.001) and overall (OR=0.75, VE=25%, 95% CI: [20-30], p <0.001).\n\nConclusionThe influenza vaccine provides a small degree of protection against SARS-CoV-2 infection across our study sites.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Yung-Chun Lee", + "author_inst": "Division of Biostatistics & Health Informatics, Beaumont Research Institute, Corewell Health East" + }, + { + "author_name": "Lufeiya Liu", + "author_inst": "University of Michigan, Department of Biostatistics" + }, + { + "author_name": "Liyang Yuan", + "author_inst": "University of Michigan, Department of Biostatistics" + }, + { + "author_name": "Malcolm Risk", + "author_inst": "University of Michigan, Department of Biostatistics" + }, + { + "author_name": "Kevin Heinrich", + "author_inst": "Quire Data" + }, + { + "author_name": "Martin Witteveen-Lane", + "author_inst": "Bioinformatics Core, Corewell Health West" + }, + { + "author_name": "Salim Hayek", + "author_inst": "Division of Cardiology, Department of Medicine, University of Michigan" + }, + { + "author_name": "Ryan Malosh", + "author_inst": "Division of Immunization, MDHHS" + }, + { + "author_name": "Rodica Pop-Busui", + "author_inst": "Department of Internal Medicine, University of Michigan" + }, + { + "author_name": "Bian Jiang", + "author_inst": "College of Medicine Division of Health Outcome & Bioinformatic, University of Florida Health" + }, + { + "author_name": "Chen Shen", + "author_inst": "Division of Biostatistics & Health Informatics, Beaumont Research Institute, Corewell Health East" + }, + { + "author_name": "Dave Chesla", + "author_inst": "Bioinformatics Core, Corewell Health West" + }, + { + "author_name": "Richard Kennedy", + "author_inst": "Beaumont Research Institute, Corewell Health East" + }, + { + "author_name": "Xu Shi", + "author_inst": "University of Michigan" + }, + { + "author_name": "Matthew Sims", + "author_inst": "Department of Infectious Disease, Corewell Health East" + }, + { + "author_name": "Ramin Homayouni", + "author_inst": "OUWB school of medicine" + }, + { + "author_name": "Lili Zhao", + "author_inst": "Division of Biostatistics & Health Informatics, Beaumont Research Institute, Corewell Health East" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.10.30.23297772", "rel_title": "Two-years mothering into the pandemic: Impact of the three COVID-19 waves in the Argentinian postpartum womens mental health", @@ -23130,33 +23729,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2023.10.25.23297548", - "rel_title": "The experiences and impact of the COVID-19 pandemic on Young Carers: practice implications and planning for future health emergencies", - "rel_date": "2023-10-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.25.23297548", - "rel_abs": "BackgroundYoung Carers faced significant challenges brought on by the COVID-19 pandemic. We explored the impact of the pandemic and associated restrictions on mental health, wellbeing and access to support in Young Carers in the United Kingdom (UK) to understand how to improve services, as well as support this population in future health emergencies.\n\nMethodWe conducted 22 qualitative semi-structured interviews from May to November 2021, with 14 Young Carers and 8 staff working in organisations that supported them. Interviews took place remotely over video or telephone call, discussing topics such as experiences of the pandemic on their health, wellbeing and caring responsibilities. We used reflexive thematic analysis to analyse interview transcripts.\n\nResultsWe identified 4 overarching themes pertaining to the impact of the pandemic and associated restrictions on mental health, wellbeing, and access to support in Young Carers in the UK: 1) challenges to following the guidelines, 2) changes to and loss of routine, 3) changes in provision of informal and formal support and 4) better understanding of inner resilience and goals. Many participants struggled with their mental health and wellbeing as a result of pandemic related restrictions, impacting on support structures for themselves, as well as the individual cared for. However, positive impacts pertained to additional support from local authority and third sector organisations.\n\nConclusionsOur findings highlight some of the changes that affected Young Carers during the COVID-19 pandemic. The impact of changes to routine and a reduction in pre-pandemic support were the greatest concerns reported by participants in this study. The additional support provided by local authority and third sector organisations during social restrictions suggests such organisations could play a greater role in supporting this population going forward, and that schools and Governments may wish to put in additional strategies and provisions to protect this population in the future.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Dan Hayes", - "author_inst": "University College London" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - }, - { - "author_name": "Alexandra Burton", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2023.10.25.563967", "rel_title": "Discovery of a novel inhibitor of macropinocytosis with antiviral activity", @@ -23465,6 +24037,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.10.25.564079", + "rel_title": "Integrating population-level and cell-based signatures for drug repositioning", + "rel_date": "2023-10-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.25.564079", + "rel_abs": "Drug repositioning presents a streamlined and cost-efficient way to expand the range of therapeutic possibilities. Furthermore, drugs with genetic evidence are more likely to progress successfully through clinical trials towards FDA approval. Exploiting these developments, single gene-based drug repositioning methods have been implemented, but approaches leveraging the entire spectrum of molecular signatures are critically underexplored. Most multi-gene-based approaches rely on differential gene expression (DGE) analysis, which is prone to identify the molecular consequence of disease and renders causal inference challenging. We propose a framework TReD (Transcriptome-informed Reversal Distance) that integrates population-level disease signatures robust to reverse causality and cell-based drug-induced transcriptome response profiles. TReD embeds the disease signature and drug profile in a high-dimensional normed space, quantifying the reversal potential of candidate drugs in a disease-related cell screen assay. The robustness is ensured by evaluation in additional cell screens. For an application, we implement the framework to identify potential drugs against COVID-19. Taking transcriptome-wide association study (TWAS) results from four relevant tissues and three DGE results as disease features, we identify 37 drugs showing potential reversal roles in at least four of the seven disease signatures. Notably, over 70% (27/37) of the drugs have been linked to COVID-19 from other studies, and among them, eight drugs are supported by ongoing/completed clinical trials. For example, TReD identifies the well-studied JAK1/JAK2 inhibitor baricitinib, the first FDA-approved immunomodulatory treatment for COVID-19. Novel potential candidates, including enzastaurin, a selective inhibitor of PKC-beta which can be activated by SARS-CoV-2, are also identified. In summary, we propose a comprehensive genetics-anchored framework integrating population-level signatures and cell-based screens that can accelerate the search for new therapeutic strategies.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Chunfeng He", + "author_inst": "School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China;The Key Laboratory of Intelligent Preventive" + }, + { + "author_name": "Yue Xu", + "author_inst": "School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; The Key Laboratory of Intelligent Preventiv" + }, + { + "author_name": "Yuan Zhou", + "author_inst": "Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA;" + }, + { + "author_name": "Jiayao Fan", + "author_inst": "School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; The Key Laboratory of Intelligent Preventiv" + }, + { + "author_name": "Chunxiao Cheng", + "author_inst": "School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China" + }, + { + "author_name": "Ran Meng", + "author_inst": "School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China" + }, + { + "author_name": "Eric R. Gamazon", + "author_inst": "Vanderbit Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA; Data Science Institute, Vanderbilt University Medical Center, Nashville," + }, + { + "author_name": "Dan Zhou", + "author_inst": "School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; The Key Laboratory of Intelligent Preventiv" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.10.26.23297635", "rel_title": "Online trend estimation and detection of trend deviations in sub-sewershed time series of SARS-CoV-2 RNA measured in wastewater.", @@ -25288,85 +25907,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.10.22.563481", - "rel_title": "Microfluidic antibody profiling after repeated SARS-CoV-2 vaccination links antibody affinity and concentration to impaired immunity and variant escape in patients on anti-CD-20 therapy", - "rel_date": "2023-10-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.22.563481", - "rel_abs": "BackgroundPatients with autoimmune/inflammatory conditions on anti-CD20 therapies, such as Rituximab, have suboptimal humoral responses to vaccination and are vulnerable to poorer clinical outcomes following SARS-CoV-2 infection. We aimed to examine how the fundamental parameters of antibody responses, namely affinity and concentration, shape the quality of humoral immunity after vaccination in these patients.\n\nMethodsWe performed in depth antibody characterisation in sera collected four to six weeks after each of three vaccine doses to wild-type (WT) SARS-CoV-2 in Rituximab-treated primary vasculitis patients (n=14) using Luminex and pseudovirus neutralisation assays, whereas a novel microfluidic-based immunoassay was used to quantify polyclonal antibody affinity and concentration against both WT and Omicron (B.1.1.529) variants. Comparative antibody profiling was performed at equivalent time points in healthy individuals after three antigenic exposures to WT SARS-CoV-2 (one infection and two vaccinations; n=15) and in convalescent patients after WT SARS-CoV-2 infection (n=30).\n\nResultsRituximab-treated patients had lower antibody levels and neutralisation titres against both WT and Omicron SARS-CoV-2 variants compared to healthy individuals. Neutralisation capacity was weaker against Omicron versus WT both in Rituximab-treated patients and in healthy individuals. In the Rituximab cohort, this was driven by lower antibody affinity against Omicron versus WT (median [range] KD: 21.6 [9.7-38.8] nM vs 4.6 [2.3-44.8] nM, p=0.0004). By contrast, healthy individuals with hybrid immunity produced a broader antibody response, a subset of which recognised Omicron with higher affinity than antibodies in Rituximab-treated patients (median [range] KD: 1.05 [0.45-1.84] nM vs 20.25 [13.2-38.8] nM, p=0.0002), underpinning the stronger serum neutralisation capacity against Omicron in the former group. Rituximab-treated patients had similar anti-WT antibody levels and neutralisation titres to unvaccinated convalescent individuals, despite two more exposures to SARS-CoV-2 antigen. Temporal profiling of the antibody response showed evidence of affinity maturation in healthy convalescent patients after a single SARS-CoV-2 infection which was not observed in Rituximab-treated patients, despite repeated vaccination.\n\nDiscussionOur results enrich previous observations of impaired humoral immune responses to SARS-CoV-2 in Rituximab-treated patients and highlight the significance of quantitative assessment of serum antibody affinity and concentration in monitoring anti-viral immunity, viral escape, and the evolution of the humoral response.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Ashley Priddey", - "author_inst": "Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK" - }, - { - "author_name": "Michael Xin Hua Chen-Xu", - "author_inst": "Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U" - }, - { - "author_name": "Daniel James Cooper", - "author_inst": "Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U" - }, - { - "author_name": "Serena MacMillan", - "author_inst": "Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK" - }, - { - "author_name": "Georg Meisl", - "author_inst": "Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK" - }, - { - "author_name": "Catherine K Xu", - "author_inst": "Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK" - }, - { - "author_name": "Myra Hosmillo", - "author_inst": "Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK" - }, - { - "author_name": "Ian G Goodfellow", - "author_inst": "Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK" - }, - { - "author_name": "Rafael Kollyfas", - "author_inst": "Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK" - }, - { - "author_name": "Rainer Doffinger", - "author_inst": "Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK" - }, - { - "author_name": "John R Bradley", - "author_inst": "Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U" - }, - { - "author_name": "Irina I Mohorianu", - "author_inst": "Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK" - }, - { - "author_name": "Rachel Jones", - "author_inst": "Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U" - }, - { - "author_name": "Tuomas P.J. Knowles", - "author_inst": "Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK" - }, - { - "author_name": "Rona Smith", - "author_inst": "Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U" - }, - { - "author_name": "Vasilis Kosmoliaptsis", - "author_inst": "Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK and NIHR Blood and Transplant Research Unit in Organ D" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.10.23.563088", "rel_title": "Nonspecific membrane bilayer perturbations by ivermectin underlie SARS-CoV-2 in vitro activity", @@ -25603,6 +26143,45 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2023.10.22.563490", + "rel_title": "Screening Peptide Drug Candidates to Neutralize Whole Viral Agents : A Case study with SARS-CoV-2 Virus", + "rel_date": "2023-10-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.22.563490", + "rel_abs": "Covid19 pandemic revealed the reality for the need of therapeutic and pharmaceutical molecule development in a short time with different approaches. Although the enhancement of immunological memory by vaccination was the quicker and robust strategy, still medication is required for immediate treatment for a patient. For this purpose, one of the approaches is developing new therapeutic molecule development like peptide-based drugs. Also, peptides can be used developing other molecules like nanobodies. Here, M13 phage display library was used for selecting SARS-CoV-2 interacting peptides for developing a neutralizing molecule for further use. Biopanning was applied with four iterative cycles to select phages displaying different 12-amino acid-long peptides. Then, the M13 phage genomic region where peptide sequences expressed were analyzed and sequences were obtained. Randomly selected peptide sequences were synthesized by solid-state peptide synthesis method. These peptides were analyzed by quartz crystal microbalance method in terms or peptide interaction capacity with specifically wild-type S protein. Next, QCM data was further validated by enzyme-linked immunosorbent assay (ELISA) in order to check peptides according to their neutralizing capacity rather than binding to S1 protein. The results showed that, phage display served an opportunity for selecting peptides which can be used and developed further as pharmaceutical molecules. More specifically, scpep3, scpep8 and scpep10 had both binding and neutralizing capacity for S1 protein as a candidate for therapeutic molecule.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Cemile Elif Ozcelik", + "author_inst": "Bilkent University" + }, + { + "author_name": "Cemre Zekiye Araz", + "author_inst": "Synbiotik Biotechnology and Biomedical Technology Bilkent Kumeevler, Cankaya, Ankara, 06800, Turkey." + }, + { + "author_name": "Ozgur Yilmaz", + "author_inst": "Material Technologies, Marmara Research Center, TUBITAK, Gebze, Kocaeli, 41470, Turkey." + }, + { + "author_name": "Sevgi Gulyuz", + "author_inst": "Material Technologies, Marmara Research Center, TUBITAK, Gebze, Kocaeli, 41470, Turkey." + }, + { + "author_name": "Aykut Ozkul", + "author_inst": "School of Veterinaty Medicine, Ankara University" + }, + { + "author_name": "Urartu Ozgur Safak Seker", + "author_inst": "BILKENT UNIVERSITY" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2023.10.21.563433", "rel_title": "Changes in total charge on spike protein of SARS-CoV-2 in emerging lineages", @@ -27158,41 +27737,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.10.18.23297204", - "rel_title": "Excess deaths in China during SARS-CoV-2 viral waves in 2022-2023", - "rel_date": "2023-10-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.18.23297204", - "rel_abs": "BackgroundThe extent to which the Omicron variant of SARS-CoV-2 raised death rates in China during its viral wave of December 2022-January 2023 remains undocumented.\n\nMethodsWe worked with an established national survey organization to survey 8,004 adults in all 31 administrative areas of China to ask about deaths in families since January 2020. We examined agespecific death rates, focusing on deaths above age 60 years, and at 15-59 years. We compared these to the United Nations (UN) estimates of age-specific mortality in 2019.\n\nFindingsThe survey participants were broadly similar to the 2020 census and other national surveys in age, sex, region, and smoking status, but had lower SARS-CoV-2 vaccination rates and higher education levels. There were no differences between reporting of deaths during the Omicron period versus earlier. The survey captured 456 deaths, of which 329 occurred at ages 60+ years and 212 were women. At ages 60+ years, death rates per 1000 rose 242% (95%CI 128-398%) during December 2022-January 2023. Deaths at ages 15-59 years did not rise appreciably. The UN estimates approximately 675,000 deaths per month at ages 60+ years in 2019. If rates doubled nationally as in our survey, China had approximately 1{middle dot}35 million excess deaths over the two months.\n\nInterpretationChina experienced a sharp but short increase in excess deaths among its elderly during the Omicron wave. If death registry data corroborate our estimates of substantial excess deaths in China, the worldwide estimates of excess deaths to 2023 may need upward adjustment.\n\nFundingCanadian Institutes of Health Research", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Prabhat Jha", - "author_inst": "University of Toronto" - }, - { - "author_name": "Patrick E Brown", - "author_inst": "University of Toronto" - }, - { - "author_name": "Teresa Lam", - "author_inst": "Angus Reid Institute" - }, - { - "author_name": "Ed Morawski", - "author_inst": "Angus Reid Institute" - }, - { - "author_name": "Angus Reid", - "author_inst": "Angus Reid Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.10.17.23297174", "rel_title": "Persistent high mortality rates for Diabetes Mellitus and Hypertension after excluding deaths associated with COVID-19 in Brazil, 2020-2022", @@ -27397,6 +27941,29 @@ "type": "new results", "category": "ecology" }, + { + "rel_doi": "10.1101/2023.10.17.562739", + "rel_title": "Single cell transcriptomics-level Cytokine Activity Prediction and Estimation (SCAPE)", + "rel_date": "2023-10-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.17.562739", + "rel_abs": "Cytokine interaction activity modeling is a pressing problem since uncontrolled cytokine influx is at fault in a variety of medical conditions, including viral infections like COVID19, and cancer. Accurate knowledge of cytokine activity levels can be leveraged to provide tailored treatment recommendations based on individual patients transcriptomics data. Here, we describe a novel method named Single cell transcriptomics-level Cytokine Activity Prediction and Estimation (SCAPE) that can predict cell-level cytokine activity from scRNA-seq data. SCAPE generates activity estimates using cytokine-specific gene sets constructed using information from the CytoSig and Reactome databases and scored with a modified version of the Variance-adjusted Mahalanobis (VAM) method adjusted for negative weights. We validate SCAPE using both simulated and real single cell RNA-sequencing (scRNA-seq) data. For the simulation study, we perturb real scRNA-seq data to reflect the expected stimulation signature of up to 41 cytokines, including chemokines, interleukins and growth factors. For the real data evaluation, we use publicly accessible scRNA-seq data that captures cytokine stimulation and blockade experiment conditions and a COVID19 transcriptomics data. As demonstrated by these evaluations, our approach can accurately estimate cell-level cytokine activity from scRNA-seq data. Our model has the potential to be incorporated in clinical settings as a way to estimate cytokine signaling for different cell populations within an impacted tissue sample.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Azka Javaid", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Hildreth R Frost", + "author_inst": "Dartmouth College" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.10.17.23297138", "rel_title": "Forecasting regional-level COVID-19 hospitalisation in England as an ordinal variable using the machine learning method", @@ -29004,37 +29571,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2023.10.12.23296938", - "rel_title": "The impact of COVID-19 on non-communicable disease patients in sub-Saharan African countries: systematic review", - "rel_date": "2023-10-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.12.23296938", - "rel_abs": "BackgroundCOVID-19 and its prevention measures have had a significant impact on patients with non-communicable diseases (NCDs) by disrupting routine healthcare service and increasing risk factors. These challenges were expected to be more severe in sub-Saharan Africa due to the lack of physical infrastructure and inadequate resources. The quantity of studies conducted was limited, and there was a lack of published systematic reviews in the specified region. This systematic review aimed to comprehensively assess the impact of COVID-19 on NCD patients in sub-Saharan Countries.\n\nMethodThis systematic review adheres to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines and is registered with PROSPERO (ID CRD42023387755). Extensive searches were conducted in MEDLINE, EMBASE, and CINAHL databases in November 2022, supplemented by a manual search of references, grey literature, and the WHO COVID-19 database. Inclusion criteria encompassed studies that reported on the impact of COVID-19 on NCD patients in sub-Saharan African countries, focusing on access to care, health outcomes, and factors related to NCDs. Critical appraisal of study quality was performed using the Joanna Briggs Institute (JBI) analytical cross-sectional studies critical appraisal tool. Data were extracted and synthesized, highlighting the main findings and relevant limitations.\n\nFindingsThis review included 26 primary studies with a cumulative sample size of 15,722 participants, conducted in six sub-Saharan African countries. Findings of these studies identified that the COVID-19 pandemic caused a disruption of 76% to 80% of regular NCDs patient care provision. The studies also identified a reduction in patient health-seeking behavior and reduced medication adherence (39.0%-63%), leading to poor treatment outcome (35.66%-55.8%). Furthermore, the pandemic and related lockdowns have been implicated in the increased prevalence of substance use, decreased physical exercise, and increased mental health problems.\n\nConclusionThis systematic review identified the complex challenges faced by NCD patients in sub-Saharan Africa during the COVID-19 pandemic. It also underlines the need to consider the indirect impact on vulnerable populations while developing pandemic prevention and control strategies for the future. The current NCD management strategies should prioritize the restoration of access to essential healthcare services while considering the multifaceted risks posed by decreased physical activity, poor dietary practices, and increased substance use.\n\nThe main limitation of this review was the study design and setting. All of the studies included in this review employed a cross-sectional design, which may result in a low quality of evidence. This study identified research conducted in only six countries among the 46 UN-classified sub-Saharan nations, which may impair the generalizability of the result.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Muluken Bafa Basa", - "author_inst": "Trinity College Dublin: The University of Dublin Trinity College" - }, - { - "author_name": "Jan De Vries", - "author_inst": "Trinity College Dublin: The University of Dublin Trinity College" - }, - { - "author_name": "David McDonagh", - "author_inst": "Trinity College Dublin: The University of Dublin Trinity College" - }, - { - "author_name": "Catherine Comiskey", - "author_inst": "Trinity College Dublin: The University of Dublin Trinity College" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.10.11.23296808", "rel_title": "Safety of SARS-CoV-2 test-to-stay in daycare: a regression discontinuity in time analysis", @@ -29279,6 +29815,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.10.11.23296866", + "rel_title": "SARS-CoV-2, influenza A/B and respiratory syncytial virus positivity and association with influenza-like illness and self-reported symptoms, over the 2022/23 winter season in the UK: a longitudinal surveillance cohort", + "rel_date": "2023-10-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.11.23296866", + "rel_abs": "BackgroundSyndromic surveillance often relies on patients presenting to healthcare. Community cohorts, although more challenging to recruit, could provide additional population-wide insights, particularly with SARS-CoV-2 co-circulating with other respiratory viruses.\n\nMethodsWe estimated positivity and incidence of SARS-CoV-2, influenza A/B, and RSV, and trends in self-reported symptoms including influenza-like illness (ILI), over the 2022/23 winter season in a broadly representative UK community cohort (COVID-19 Infection Survey), using negative-binomial generalised additive models. We estimated associations between test positivity and each of symptoms and influenza vaccination, using adjusted logistic and multinomial models.\n\nFindingsSwabs taken at 32,937/1,352,979 (2.4%) assessments tested positive for SARS-CoV-2, 181/14,939 (1.2%) for RSV and 130/14,939 (0.9%) for influenza A/B, varying by age over time. Positivity and incidence peaks were earliest for RSV, then influenza A/B, then SARS-CoV-2, and were highest for RSV in the youngest and for SARS-CoV-2 in the oldest age-groups. Many test-positives did not report key symptoms: middle-aged participants were generally more symptomatic than older or younger participants, but still only [~]25% reported ILI-WHO and [~]60% ILI-ECDC. Most symptomatic participants did not test positive for any of the three viruses. Influenza A/B-positivity was lower in participants reporting influenza vaccination in the current and previous seasons (odds ratio=0.55 (95% CI 0.32,0.95)) versus neither season.\n\nInterpretationSymptom profiles varied little by aetiology, making distinguishing SARS-CoV-2, influenza and RSV using symptoms challenging. Most symptoms were not explained by these viruses, indicating the importance of other pathogens in syndromic surveillance. Influenza vaccination was associated with lower rates of community influenza test positivity.\n\nFundingUK Health Security Agency, Department of Health and Social Care, National Institute for Health Research.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Elisabeth Dietz", + "author_inst": "University of Oxford" + }, + { + "author_name": "Emma Elizabeth Pritchard", + "author_inst": "University of Oxford" + }, + { + "author_name": "Koen Pouwels", + "author_inst": "University of Oxford" + }, + { + "author_name": "Muhammad Ehsaan", + "author_inst": "Berkshire and Surrey Pathology Services" + }, + { + "author_name": "Joshua Blake", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Charlotte Gaughan", + "author_inst": "Office of National Statistics" + }, + { + "author_name": "Eric Haduli", + "author_inst": "Berkshire and Surrey Pathology Services" + }, + { + "author_name": "Hugh Boothe", + "author_inst": "Berkshire and Surrey Pathology Services" + }, + { + "author_name": "Karina-Doris Vihta", + "author_inst": "University of Oxford" + }, + { + "author_name": "Tim Peto", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nicole Stoesser", + "author_inst": "University of Oxford" + }, + { + "author_name": "Philippa Matthews", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Nick Taylor", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Ian Diamond", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Ruth Studley", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Emma Rourke", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Paul Birrell", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Daniela De Angelis", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Tom Fowler", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Conall Watson", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "David W Eyre", + "author_inst": "University of Oxford" + }, + { + "author_name": "Thomas House", + "author_inst": "University of Manchester" + }, + { + "author_name": "Ann Sarah Walker", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2023.10.10.561643", "rel_title": "Snapshots from Cryo-ET of active SARS-CoV-2 virions", @@ -30910,105 +31553,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.10.04.560875", - "rel_title": "Unveiling the antiviral capabilities of targeting Human Dihydroorotate Dehydrogenase against SARS-CoV-2", - "rel_date": "2023-10-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.04.560875", - "rel_abs": "The urgent need for effective treatments against emerging viral diseases, driven by drug-resistant strains and new viral variants, remains critical. We focus on inhibiting the human dihydroorotate dehydrogenase (HsDHODH), one of the enzymes in charge of pyrimidine nucleotide synthesis. This strategy could impede viral replication without provoking resistance. We evaluated quinone-based compounds, discovering potent HsDHODH inhibition (low nanomolar IC50) and promising in vitro anti-SARS-CoV-2 activity (low micromolar EC50). These compounds exhibited low toxicity, indicating potential for further development. Additionally, we employed computational tools like molecular docking and QSAR models to analyze protein-ligand interactions. These findings represent a significant step forward in the search for effective antiviral treatments and have great potential to impact the development of new broad-spectrum antiviral drugs.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Aline Purificacao", - "author_inst": "(a) Protein Crystallography Laboratory, Department of Biomolecular Sciences, School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao Paulo, Ribei" - }, - { - "author_name": "Sabrina Silva-Mendonca", - "author_inst": "(b) Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao P" - }, - { - "author_name": "Luiza Cruz", - "author_inst": "(b) Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao P" - }, - { - "author_name": "Carolina Sacramento", - "author_inst": "(d) Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil (e) National Institute for Science and Technology on Innovatio" - }, - { - "author_name": "Jairo Temerozo", - "author_inst": "(d) Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil (e) National Institute for Science and Technology on Innovatio" - }, - { - "author_name": "Natalia Fintelman-Rodrigues", - "author_inst": "(d) Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil (e) National Institute for Science and Technology on Innovatio" - }, - { - "author_name": "Caroline Freitas", - "author_inst": "(d) Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil (e) National Institute for Science and Technology on Innovatio" - }, - { - "author_name": "Bruna Godoi", - "author_inst": "(b) Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao P" - }, - { - "author_name": "Miguel Vaidergorn", - "author_inst": "(b) Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao P" - }, - { - "author_name": "Juliana Leite", - "author_inst": "(h) Laboratory of Tropical Diseases, Dep. Genetics, Evolution, Microbiology and Immunology, Institute of Biology, Unicamp, Campinas, SP, Brazil." - }, - { - "author_name": "Luis Alvarez", - "author_inst": "(h) Laboratory of Tropical Diseases, Dep. Genetics, Evolution, Microbiology and Immunology, Institute of Biology, Unicamp, Campinas, SP, Brazil." - }, - { - "author_name": "Murillo Freitas", - "author_inst": "(c) Laboratory for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goias, Goiania, 74605-170, GO, Brazil." - }, - { - "author_name": "Meryck Silva", - "author_inst": "(c) Laboratory for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goias, Goiania, 74605-170, GO, Brazil." - }, - { - "author_name": "Bianca Martin", - "author_inst": "(i) Innovation Center in nanostructured systems and topical administration (NanoTop), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao Pau" - }, - { - "author_name": "Renata Lopez", - "author_inst": "(i) Innovation Center in nanostructured systems and topical administration (NanoTop), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao Pau" - }, - { - "author_name": "Bruno Neves", - "author_inst": "(c) Laboratory for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goias, Goiania, 74605-170, GO, Brazil." - }, - { - "author_name": "Fabio Costa", - "author_inst": "h) Laboratory of Tropical Diseases, Dep. Genetics, Evolution, Microbiology and Immunology, Institute of Biology, Unicamp, Campinas, SP, Brazil." - }, - { - "author_name": "Thiago Souza", - "author_inst": "(d) Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil (e) National Institute for Science and Technology on Innovatio" - }, - { - "author_name": "Flavio Emery", - "author_inst": "(b) Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao P" - }, - { - "author_name": "Carolina Andrade", - "author_inst": "(b) Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao P" - }, - { - "author_name": "Cristina Nonato", - "author_inst": "(a) Protein Crystallography Laboratory, Department of Biomolecular Sciences, School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao Paulo, Ribei" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.10.05.561047", "rel_title": "Fourth dose of Microneedle Array Patch of SARS-CoV-2 S1 Protein Subunit Vaccine Elicits Robust Long-lasting Humoral Responses in mice", @@ -31217,6 +31761,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2023.10.04.23296537", + "rel_title": "Development and validation of automated methods for COVID-19 PCR MasterMix preparation.", + "rel_date": "2023-10-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.04.23296537", + "rel_abs": "Polymerase Chain Reaction (PCR)-based assays were widely deployed during the SARS-CoV-2 pandemic for population-scale testing. High-throughput molecular diagnostic labora-tories required a high degree of process automation to cope with huge testing demand, fast turn-around times and quality requirements. However, the critical step of preparing a PCR MasterMix has often been neglected by process developers and optimisers, and is largely dependent upon operator skill for the manual pipetting of reagents to construct the PCR MasterMix. Dependence on manual procedures introduces variation, inconsistency, wastage and potentially risks data integrity. To address this issue, we developed a liquid-handler based solution for automated, traceable and compliant PCR MasterMix preparation. Here, we show that a fully automated PCR MasterMix protocol can substitute manual pipetting, without affecting clinical calling, accuracy or precision. Ultimately, this method reduced cost-per-test at a high-throughput laboratory by eliminating operator-induced wastage while improving the quality of results.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Giorgio Fedele", + "author_inst": "University of Calabria, Arcavacata, Italy" + }, + { + "author_name": "Graham Hill", + "author_inst": "Animal and Plant Health Agency, Weybridge, United Kingdom" + }, + { + "author_name": "Amelia Sweetford", + "author_inst": "Michael Sharma Group, Coventry, United Kingdom" + }, + { + "author_name": "Suki Lee", + "author_inst": "Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands" + }, + { + "author_name": "Bobby Yau", + "author_inst": "University of Huddersfield, Huddersfield, United Kingdom" + }, + { + "author_name": "Domenico R. Caputo", + "author_inst": "Unaffiliated" + }, + { + "author_name": "Denise Grovewood", + "author_inst": "SPT Labtech, Melbourn Science Park, United Kingdom" + }, + { + "author_name": "Rowda Dahir", + "author_inst": "University of Cambridge, Cambridge, United Kingdom" + }, + { + "author_name": "Paula Esquivias Ruiz-Dana", + "author_inst": "Por que no, Zaragoza, Spain" + }, + { + "author_name": "Anika Wisniewska", + "author_inst": "Unaffiliated" + }, + { + "author_name": "Anna Di Biase", + "author_inst": "Unaffiliated" + }, + { + "author_name": "Miles Gibson", + "author_inst": "Health Protection Operations, UKHSA, United Kingdom" + }, + { + "author_name": "Benita Percival", + "author_inst": "Omix Ltd, Birmingham, United Kingdom" + }, + { + "author_name": "Stefan Grujic", + "author_inst": "Omix Ltd, Birmingham, United Kingdom" + }, + { + "author_name": "Donald Peter Fraser", + "author_inst": "Omix Ltd, Birmingham, United Kingdom" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pathology" + }, { "rel_doi": "10.1101/2023.10.05.23296586", "rel_title": "Modelling the impact of population mobility, post-infection immunity and vaccination on SARS-CoV-2 transmission in the Dominican Republic", @@ -32744,33 +33363,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.10.01.560357", - "rel_title": "The TMPRSS2 non-protease domains regulating SARS-CoV-2 Spike in mediated virus entry", - "rel_date": "2023-10-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.01.560357", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters cells by binding to the angiotensin-converting enzyme 2 (hACE2) receptor. This process is aided by the transmembrane protease serine 2 (TMPRSS2), which enhances entry efficiency and infectiousness by cleaving the SARS-CoV-2 surface glycoprotein (Spike). The cleavage primes the Spike protein, promoting membrane fusion instead of receptor-mediated endocytosis. Despite the pivotal role played by TMPRSS2, our understanding of its non-protease distinct domains remains limited. In this report, we present evidence indicating the potential phosphorylation of a minimum of six tyrosine residues within the cytosolic tail (CT) of TMPRSS2. Through the use of TMPRSS2 CT phospho-mimetic mutants, we observed a reduction in TMPRSS2 protease activity, accompanied by a decrease in SARS-CoV-2 pseudovirus infection, which was found to occur mainly via the endosomal pathway. We expanded our investigation beyond TMPRSS2 CT and discovered the involvement of other non-protease domains in regulating infection. Our co-immunoprecipitation experiments demonstrated a strong interaction between TMPRSS2 and Spike. We revealed a 21 amino acid long TMPRSS2-Spike-binding region (TSBR) within the TMPRSS2 scavenger receptor cysteine-rich (SRCR) domain that contributes to this interaction. Our study sheds light on novel functionalities associated with TMPRSS2s cytosolic tail and SRCR region. Both of these regions have the capability to regulate SARS-CoV-2 entry pathways. These findings contribute to a deeper understanding of the complex interplay between viral entry and host factors, opening new avenues for potential therapeutic interventions.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Romano Strobelt", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Julia Adler", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Yosef Shaul", - "author_inst": "Weizmann Institute of Science" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.10.01.560365", "rel_title": "Neutralisation of SARS-CoV-2 Omicron subvariants BA.2.86 and EG.5.1 by antibodies induced by earlier infection or vaccination", @@ -33011,6 +33603,45 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.09.29.560110", + "rel_title": "Network-based integrative multi-omics approach reveals biosignatures specific to COVID-19 disease phases.", + "rel_date": "2023-09-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.29.560110", + "rel_abs": "BackgroundCOVID-19 disease is characterized by a spectrum of disease phases (mild, moderate, and severe). Each disease phase is marked by changes in omics profiles with corresponding changes in the expression of features (biosignatures). However, integrative analysis of multiple omics data from different experiments across studies to investigate biosignatures at various disease phases is limited. Exploring an integrative multi-omics profile analysis through a network approach could be used to determine biosignatures associated with specific disease phases and enable the examination of the relationships between the biosignatures.\n\nAimTo identify and characterize biosignatures underlying various COVID-19 disease phases in an integrative multi-omics data analysis.\n\nMethodWe leveraged the correlation network approach to integrate transcriptomics, metabolomics, proteomics, and lipidomics data. The World Health Organization (WHO) Ordinal Scale (WOS) was used as a disease severity reference to harmonize COVID-19 patient metadata across two studies with independent data. A unified COVID-19 knowledge graph was constructed by assembling a disease-specific interactome from the literature and databases. Disease-state omics-specific graphs were constructed by integrating multi-omics data with the unified COVID-19 knowledge graph. We expanded on the network layers of multiXrank, a random walk with restart on multilayer network algorithm, to explore disease state omics-specific graphs and perform enrichment analysis.\n\nResultsNetwork analysis revealed the biosignatures involved in inducing chemokines and inflammatory responses as hubs in the severe and moderate disease phases. We observed more shared biosignatures between severe and moderate disease phases as compared to mild-moderate and mild-severe disease phases. We further identified both biosignatures that discriminate between the disease states and interactions between biosignatures that are either common between or associated with COVID-19 disease phases. Interestingly, cross-layer interactions between different omics profiles increased with disease severity.\n\nConclusionThis study identified both biosignatures of different omics types enriched in disease-related pathways and their associated interactions that are either common between or unique to mild, moderate, and severe COVID-19. These biosignatures include molecular features that underlie the observed clinical heterogeneity of COVID-19 and emphasize the need for disease-phase-specific treatment strategies. In addition, the approach implemented here can be used for other diseases.\n\nKey findings Integrative multi-omics analysis revealed biosignatures and biosignature interactions associated with COVID-19 disease states.\n Disease severity increases with biosignature interactions across different multi-omics data.\n The harmonization approach proposed and implemented here can be applied to other diseases", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Francis E. Agamah", + "author_inst": "Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Science" + }, + { + "author_name": "Thomas H.A. Ederveen", + "author_inst": "Medical BioSciences department, Radboud University Medical Center Nijmegen, The Netherlands" + }, + { + "author_name": "Michelle Skelton", + "author_inst": "Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Science" + }, + { + "author_name": "Darren P. Martin", + "author_inst": "Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Science" + }, + { + "author_name": "Emile R. Chimusa", + "author_inst": "Department of Applied Science, Faculty of Health and Life Sciences, Northumbria University, Newcastle, Tyne and Wear, NE1 8ST, UK." + }, + { + "author_name": "Peter A.C. 't Hoen", + "author_inst": "Medical BioSciences department, Radboud University Medical Center Nijmegen, The Netherlands." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.09.29.560163", "rel_title": "Discovery of First-in-Class PROTAC Degraders of SARS-CoV-2 Main Protease", @@ -34354,29 +34985,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2023.09.26.23295911", - "rel_title": "Analysis of Potential Risk Factors of COVID-19 Based on Variants: Omicron, Delta, and Alpha", - "rel_date": "2023-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.26.23295911", - "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic has changed which affects the risk of COVID-19 infection for specific subgroups. We focused on the subgroups based on the factors (sex, age, and vaccination) and COVID-19 strains (Alpha, Delta, and Omicron). Past studies focused on analyzing these factors based on one geographic region or one COVID-19 strain. Therefore, there is a need to understand these factors association with risk of COVID-19 infection through analyzing data from various geographic regions and strains. The association between COVID-19 strains and the factors was assessed through chi-square test and odds ratio tests. Sex, vaccination, age had a significant association with testing positive for the COVID-19 strains of interest in most geographies. The biggest difference was unvaccinated individuals have 3.14 higher odds of getting Alpha than vaccinated individuals in Canada. These findings provide insights into the groups that are more susceptible to contracting specific strains of COVID-19.\n\nSummaryThis manuscript offers a broad examination of key factors that may impact the risk of COVID-19 infection across various geographic regions. Results provide evidence about potential risk factors for COVID-19 infection around the world for certain sub-groups as COVID-19 mutates.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Dharshini Kannan", - "author_inst": "Innovation Academy" - }, - { - "author_name": "Sreenidhi Muppiri", - "author_inst": "Cambridge High School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.09.25.23289158", "rel_title": "Recruitment, Consent and DNA Sample Acquisition in a U.S. Precision Health Cohort During the COVID-19 Pandemic", @@ -34681,6 +35289,69 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2023.09.24.558358", + "rel_title": "RCoV19: A One-stop Hub for SARS-CoV-2 Genome Data Integration, Variants Monitoring, and Risk Pre-warning", + "rel_date": "2023-09-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.24.558358", + "rel_abs": "The Resource for Coronavirus 2019 (RCoV19, https://ngdc.cncb.ac.cn/ncov/) is an open-access information resource dedicated to providing valuable data on the genomes, mutations, and variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this updated implementation of RCoV19, we have made significant improvements and advancements over the previous version. Firstly, we have implemented a highly refined genome data curation model. This model now features an automated integration pipeline and optimized curation rules, enabling efficient daily updates of data in RCoV19. Secondly, we have developed a global and regional lineage evolution monitoring platform, alongside an outbreak risk pre-warning system. These additions provide a comprehensive understanding of SARS-CoV-2 evolution and transmission patterns, enabling better preparedness and response strategies. Thirdly, we have developed a powerful interactive mutation spectrum comparison module. This module allows users to compare and analyze mutation patterns, assisting in the detection of potential new lineages. Furthermore, we have incorporated a comprehensive knowledgebase on mutation effects. This knowledgebase serves as a valuable resource for retrieving information on the functional implications of specific mutations. In summary, RCoV19 serves as a vital scientific resource, providing access to valuable data, relevant information, and technical support in the global fight against COVID-19.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Cuiping Li", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (National Center for Bioinformation)" + }, + { + "author_name": "Lina Ma", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (National Center for Bioinformation)" + }, + { + "author_name": "Dong Zou", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (National Center for Bioinformation)" + }, + { + "author_name": "Rongqin Zhang", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (National Center for Bioinformation)" + }, + { + "author_name": "Xue Bai", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (National Center for Bioinformation)" + }, + { + "author_name": "Lun Li", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (National Center for Bioinformation)" + }, + { + "author_name": "Gangao Wu", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (National Center for Bioinformation)" + }, + { + "author_name": "Tianhao Huang", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (National Center for Bioinformation)" + }, + { + "author_name": "Wei Zhao", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (National Center for Bioinformation)" + }, + { + "author_name": "Enhui Jin", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (National Center for Bioinformation)" + }, + { + "author_name": "Yiming Bao", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (National Center for Bioinformation)" + }, + { + "author_name": "Shuhui Song", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (National Center for Bioinformation)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.09.25.558837", "rel_title": "Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN Domain", @@ -35508,7 +36179,7 @@ "rel_date": "2023-09-25", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.22.23295541", - "rel_abs": "Our understanding of the quality of cellular and humoral immunity conferred by COVID-19 vaccination alone versus vaccination plus SARS-CoV-2 breakthrough (BT) infection remains incomplete. While the current (2023) SARS-CoV-2 immune landscape of Canadians is complex, in late 2021 most Canadians had either just received a third dose of COVID-19 vaccine, or had received their two dose primary series and then experienced an Omicron BT. Herein we took advantage of this coincident timing to contrast cellular and humoral immunity conferred by three doses of vaccine versus two doses plus BT. Our results show that mild BT infection induces cell-mediated immune responses to variants comparable to an intramuscular vaccine booster dose. In contrast, BT subjects had higher salivary IgG and IgA levels against the Omicron Spike and enhanced reactivity to the ancestral Spike for the IgA isotype, which also reacted with SARS-CoV-1. Serum neutralizing antibody levels against the ancestral strain and the variants were also higher after BT infection. Our results support the need for mucosal vaccines to emulate the enhanced mucosal and humoral immunity induced by Omicron without exposing individuals to the risks associated with SARS-CoV-2 infection.\n\nONE SENTENCE SUMMARYOmicron breakthrough elicits cross-reactive systemic and mucosal immune responses in fully vaccinated adults.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC=\"FIGDIR/small/23295541v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@f3e2a0org.highwire.dtl.DTLVardef@1a3a81aorg.highwire.dtl.DTLVardef@1715958org.highwire.dtl.DTLVardef@a0a332_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_abs": "Our understanding of the quality of cellular and humoral immunity conferred by COVID-19 vaccination alone versus vaccination plus SARS-CoV-2 breakthrough (BT) infection remains incomplete. While the current (2023) SARS-CoV-2 immune landscape of Canadians is complex, in late 2021 most Canadians had either just received a third dose of COVID-19 vaccine, or had received their two dose primary series and then experienced an Omicron BT. Herein we took advantage of this coincident timing to contrast cellular and humoral immunity conferred by three doses of vaccine versus two doses plus BT. Our results show that mild BT infection induces cell-mediated immune responses to variants comparable to an intramuscular vaccine booster dose. In contrast, BT subjects had higher salivary IgG and IgA levels against the Omicron Spike and enhanced reactivity to the ancestral Spike for the IgA isotype, which also reacted with SARS-CoV-1. Serum neutralizing antibody levels against the ancestral strain and the variants were also higher after BT infection. Our results support the need for mucosal vaccines to emulate the enhanced mucosal and humoral immunity induced by Omicron without exposing individuals to the risks associated with SARS-CoV-2 infection.\n\nONE SENTENCE SUMMARYOmicron breakthrough elicits cross-reactive systemic and mucosal immune responses in fully vaccinated adults.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC=\"FIGDIR/small/23295541v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@f1a445org.highwire.dtl.DTLVardef@57b4a6org.highwire.dtl.DTLVardef@152572org.highwire.dtl.DTLVardef@4d68a4_HPS_FORMAT_FIGEXP M_FIG C_FIG", "rel_num_authors": 22, "rel_authors": [ { @@ -36220,61 +36891,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.09.20.23295832", - "rel_title": "Targeted MRM-analysis of plasma proteins in frozen whole blood samples from patients with COVID-19", - "rel_date": "2023-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.20.23295832", - "rel_abs": "The COVID-19 pandemic has exposed a number of key challenges that need to be urgently addressed. In particular, rapid identification and validation of prognostic markers is required. Mass spectrometric studies of blood plasma proteomics provide a deep understanding of the relationship between the severe course of infection and activation of specific pathophysiological pathways. Analysis of plasma proteins in whole blood may also be relevant for the pandemic as it requires minimal sample preparation. Here, for the first time, frozen whole blood samples were used to analyze 189 plasma proteins using multiple reaction monitoring (MRM) mass spectrometry and stable isotope-labeled peptide standards (SIS). A total of 128 samples (FRCC, Russia) from patients with mild (n=40), moderate (n=36) and severe (n=19) COVID-19 infection and healthy controls (n=33) were analyzed. Levels of 114 proteins were quantified and compared. Significant differences between all of the groups were revealed for 61 proteins. Changes in the levels of 30 reproducible COVID-19 markers (SERPING1, CRP, C9, ORM1, APOA1, SAA1/SAA2, LBP, AFM, IGFALS, etc.) were consistent with studies performed with serum/plasma samples. Levels of 70 proteins correlated between whole blood and plasma samples. The best-performing classifier built with 13 significantly different proteins achieved the best combination of ROC-AUC (0.93-0.95) and accuracy (0.87-0.93) metrics and distinguished patients from controls, as well as patients by severity and risk of mortality. Overall, the results support the use of frozen whole blood for MRM analysis of plasma proteins and assessment of the status of patients with COVID-19.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Anna E. Bugrova", - "author_inst": "Emanuel Institute of Biochemical Physics, Russian Academy of Science, 119334 Moscow, Russia" - }, - { - "author_name": "Polina A. Strelnikova", - "author_inst": "Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia" - }, - { - "author_name": "Alexey S. Kononikhin", - "author_inst": "Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia" - }, - { - "author_name": "Natalia V. Zakharova", - "author_inst": "Emanuel Institute of Biochemical Physics, Russian Academy of Science, 119334 Moscow, Russia" - }, - { - "author_name": "Elizaveta O. Diyachkova", - "author_inst": "Pulmonology Scientific and Research Institute, Federal Medical and Biological Agency, 115682 Moscow, Russia" - }, - { - "author_name": "Alexander G. Brzhozovskiy", - "author_inst": "Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia" - }, - { - "author_name": "Maria I. Indeykina", - "author_inst": "Emanuel Institute of Biochemical Physics, Russian Academy of Science, 119334 Moscow, Russia" - }, - { - "author_name": "Ilya N. Kurochkin", - "author_inst": "Emanuel Institute of Biochemical Physics, Russian Academy of Science, 119334 Moscow, Russia" - }, - { - "author_name": "Alexander V. Averyanov", - "author_inst": "Pulmonology Scientific and Research Institute, Federal Medical and Biological Agency, 115682 Moscow, Russia" - }, - { - "author_name": "Evgeny N. Nikolaev", - "author_inst": "Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.09.19.23295768", "rel_title": "COVID-19 VACCINE ACCEPTANCE AND HESITANCY IN GHANA: A SYSTEMATIC REVIEW", @@ -36447,6 +37063,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.09.19.23295776", + "rel_title": "Analysis of SARS-CoV-2 Ig seroprevalence in Northern Ireland", + "rel_date": "2023-09-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.19.23295776", + "rel_abs": "BackgroundWith the impact of SARS-CoV-2 upon public health directly and socioeconomically, further information was required to inform policy decisions designed to limit virus spread. This study sought to contribute to serosurveillance work within Northern Ireland to track SARS-CoV-2 progression and guide health strategy.\n\nMethodsSera/plasma samples from clinical biochemistry laboratories were analysed for anti-SARS-CoV-2 immunoglobulins (Ig). Samples were assessed using an Elecsys anti-SARS-CoV-2 or anti-SARS-CoV-2 S ECLIA (Roche) on an automated Cobas-e-analyser. Samples were also assessed via ELISA (Euroimmun). A subset of samples assessed via Roche Elecsys anti-SARS-CoV-2 IgG assay were subsequently analysed in an ACE2 pseudoneutralisation assay using a V-PLEX SARS-CoV-2 Panel 7 for IgG and ACE2 by MesoScale Diagnostics Inc.\n\nResultsAcross three testing rounds (June-July 2020, November-December 2020 and June-July 2021 (rounds 1-3 respectively)), 4844 residual sera/plasma specimens were assayed for SARS-CoV-2 Ig. Seropositivity rates increased across the study, peaking at 11.6% during round 3. Varying trends in SARS-CoV-2 seropositivity were noted based on demographic factors. For instance, highest rates of seropositivity shifted from older to younger demographics across the study period. In round 3, alpha (B.1.1.7) variant neutralising antibodies were most frequently detected across age groups, with median concentration of anti-spike protein antibodies elevated in 50-69 year olds and anti-S1 RBD antibodies elevated in over 70s, relative to other age groups.\n\nConclusionsWith seropositivity rates of <15% across the assessment period, it can be concluded that the significant proportion of the Northern Ireland population had not yet naturally contracted the virus by mid-2021.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Michelle K Greene", + "author_inst": "QUB" + }, + { + "author_name": "Peter Smyth", + "author_inst": "QUB" + }, + { + "author_name": "Andrew English", + "author_inst": "Ulster University" + }, + { + "author_name": "Joseph McLaughlin", + "author_inst": "Ulster University" + }, + { + "author_name": "Magda Bucholc", + "author_inst": "Ulster University" + }, + { + "author_name": "Janice Bailie", + "author_inst": "HSC RandD Division, Public Health Agency" + }, + { + "author_name": "Julie McCarroll", + "author_inst": "HSC RandD Division, Public Health Agency" + }, + { + "author_name": "Margaret McDonnell", + "author_inst": "Belfast Health and Social Care Trust" + }, + { + "author_name": "Alison Watt", + "author_inst": "Belfast Health and Social Care Trust" + }, + { + "author_name": "George Barnes", + "author_inst": "South-Eastern Health and Social Care Trust" + }, + { + "author_name": "Mark Lynch", + "author_inst": "Western Health and Social Care Trust" + }, + { + "author_name": "Kevan Duffin", + "author_inst": "Southern Health and Social Care Trust" + }, + { + "author_name": "Gerard Duffy", + "author_inst": "Northern Health and Social Care Trust" + }, + { + "author_name": "Claire Lewis", + "author_inst": "QUB" + }, + { + "author_name": "Jacqueline A James", + "author_inst": "QUB" + }, + { + "author_name": "Tom Ford", + "author_inst": "AFBI" + }, + { + "author_name": "Maurice O'Kane", + "author_inst": "Western Health and Social Care Trust" + }, + { + "author_name": "Taranjit Singh Rai", + "author_inst": "Ulster University" + }, + { + "author_name": "Anthony J Bjourson", + "author_inst": "Ulster University" + }, + { + "author_name": "Christopher Cardwell", + "author_inst": "QUB" + }, + { + "author_name": "J Stuart Elborn", + "author_inst": "QUB" + }, + { + "author_name": "David S Gibson", + "author_inst": "Ulster University" + }, + { + "author_name": "Christopher J Scott", + "author_inst": "QUB" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.09.19.23295797", "rel_title": "Automatic Population of the Case Report Forms for an International Multifactorial Adaptive Platform Trial Amid the COVID-19 Pandemic", @@ -37926,61 +38649,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.09.13.23295114", - "rel_title": "Assessing the impact of the Gamma variant on COVID-19 Patient admissions in a Southern Brazilian tertiary hospital - A comparison of dual pandemic phases", - "rel_date": "2023-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.13.23295114", - "rel_abs": "Since the first case of COVID-19, Brazil has undergone infection waves with distinct characteristics. The description of new variants has alerted the emergence of more contagious or virulent viruses. The variant of concern Gamma emerged in Brazil and caused an epidemic wave, but its spread outside the country was limited. We report the clinical-epidemiological profile of hospitalized patients with COVID-19 by comparing two periods. A retrospective cohort study was performed. The primary outcome was to assess individuals with COVID-19 admitted in wards and intensive care units at CHC-UFPR between March 2020 and July 2021, correlating demographic, clinical-epidemiologic, and survival data with the most prevalent viral variant found in each period. We used Kaplan-Meier analysis to estimate the probability of survival and receiver operating characteristic curves to evaluate laboratory tests to find a cutoff point for poor outcomes. Data from 2,887 individuals were analyzed, 1,495 and 1,392 from the first and second periods, respectively. Hospitalization predominated among males in both periods, and the median age was significantly lower in the second one. The frequency of comorbidities was similar. Various demographic factors, clinical assessments, and laboratory tests were examined in relation to greater severity. When comparing the two studied periods, we observed predominance of the Wild virus during the first wave and the Gamma variant during the second, with no significant difference in outcomes. The findings suggest that despite the association of many factors with increased severity, the temporal variation between the two periods did not result in a notable divergence in the measured outcomes. The COVID-19 pandemic has lasted for a long time, with periods marked by peaks of cases, often caused by the emergence of viral variants, resulting in higher infection rates and rapid dissemination but, for variant Gamma, no apparent greater virulence.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Natalia R Domino", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Bruna A Lapinscki", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Felipe Zhen", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Guilherme Yamaguto", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Emmanueli C S Costa", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Vitor L Moriya", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Luciane A Pereira", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Ricardo Petterle", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Meri B Nogueira", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Sonia M Raboni", - "author_inst": "Universidade Federal do Parana Setor de Ciencias da Saude" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.09.12.23294140", "rel_title": "Effectiveness of Canadian travel restrictions in reducing burden of SARS-CoV-2 variants of concern", @@ -38233,6 +38901,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, + { + "rel_doi": "10.1101/2023.09.14.23295542", + "rel_title": "How COVID-19 continues to affect contraception in Scotland: a retrospective analysis of Scottish prescribing data between 2016 and 2023.", + "rel_date": "2023-09-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.14.23295542", + "rel_abs": "BackgroundIn Scotland, the effects of the COVID-19 pandemic on womens access to contraception are unknown. Globally, COVID-19 restrictions have led to a shift to telehealth service delivery alongside a reduction in contraceptive provision. Research into whether the effects of COVID-19 on contraception have abated after restrictions have been lifted is lacking.\n\nMethodsThis is a retrospective longitudinal study of prescribing data from the Scottish Health and Social Care Open Data repository (https://www.opendata.nhs.scot) between January 2016 and January 2023. Contraceptives were extracted and categorised using truncated British National Formulary codes and analysed using R. Contraceptive provision was compared across four periods: pre-COVID-19 (01/01/2016-23/03/2020), lockdown (24/03/2020-29/05/2020 & 05/01/2021-26/04/2021), restrictions (30/05/2020-04/01/2021 & 27/04/2021-30/04/2022), and post-COVID-19 (01/05/2022-01/01/2023).\n\nResultsDuring lockdowns, contraceptive prescribing in Scotland decreased by 82.90% of pre-COVID-19 levels. This trend was more severe for long-acting reversible contraception which fell to 11.80% of pre-COVID-19 prescriptions. After COVID-19, the level of contraceptive prescribing has risen to 108.23% of its pre-pandemic level. Large increases in subcutaneous medroxyprogesterone acetate (499.05%), progestogen-only pills (125.07%), the patch (165.09%), levonorgestrel-IUS (112.54%), and ulipristal acetate emergency contraception prescribing (357.97%). Conversely, combined oral contraceptive pills (75.04%), Cu-IUD (83.63%), the implant (81.10%), and levonorgestrel emergency contraception (67.42%) prescribing has decreased.\n\nConclusionsCOVID-19 vastly decreased contraceptive prescribing during lockdowns in Scotland. Post-COVID-19, changes in contraceptive prescribing within Scottish general practices are reported, with implications for health policy and service delivery planning.\n\nAvailability of Data & CodeAll code and data used are fully available from Zenodo (doi:10.5281/zenodo.8310085)\n\nThe raw dataset used is also publicly available from the Scottish Health and Social Care Open Data repository (opendata.nhs.scot).", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Elliot Johnson-Hall", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "sexual and reproductive health" + }, { "rel_doi": "10.1101/2023.09.14.23295425", "rel_title": "Estimating the population effectiveness of interventions against COVID-19 in France: a modelling study", @@ -39368,89 +40055,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.09.12.23295441", - "rel_title": "Validation of Real-World Case Definitions for COVID-19 Diagnosis and Severe COVID-19 Illness Among Patients Infected with SARS-CoV-2: Translation of Clinical Trial Definitions to Real-World Settings", - "rel_date": "2023-09-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.12.23295441", - "rel_abs": "PurposeThis study assessed the performance of International Classification of Diseases 10th Revision, Clinical Modification (ICD-10-CM) coronavirus disease 2019 (COVID-19) diagnostic code U07.1 against polymerase chain reaction (PCR) test results (Objective 1), and electronic medical record (EMR)-based codified algorithm for severe COVID-19 illness based on endpoints used in the Pfizer-BioNTech COVID-19 vaccine trial against chart review (Objective 2).\n\nMethodsThis retrospective, longitudinal cohort study used EMR data from the Mass General Brigham COVID-19 Data Mart (3/1/2020-11/19/2020) for adult patients with [≥]1 PCR test, antigen test, or code U07.1 (Objective 1) and adult patients with a positive PCR test hospitalized with COVID-19 (Objective 2).\n\nResultsAmong 354,124 patients in Objective 1, 96% had [≥]1 PCR test (including 6% with [≥]1 positive PCR test; 11% with [≥]1 code U07.1). Code U07.1 had low sensitivity (54%) and positive predictive value (PPV; 63%) but high specificity (97%) against the PCR test. Among 300 patients hospitalized for COVID-19 randomly sampled for chart review in Objective 2, the EMR-based case definition for severe COVID-19 illness had high PPV (>95%), showing better performance than severe/critical COVID-19 endpoints defined by the World Health Organization (PPV: 79%).\n\nConclusionsCOVID-19 diagnosis based on ICD-10-CM code U07.1 had inadequate sensitivity and requires confirmation by PCR testing. The EMR-based case definition showed high PPV and can be used to identify cases of severe COVID-19 illness in real-world datasets. These findings highlight the importance of validating outcomes in real-world data, and can guide researchers analyzing COVID-19 data when PCR tests are not readily available.\n\nKEY POINTSO_LIThis study evaluated the performance of International Classification of Diseases 10th Revision, Clinical Modification (ICD-10-CM) codes and an electronic medical record (EMR)-based algorithm for identifying coronavirus disease 2019 (COVID-19) diagnosis and severe COVID-19 illness in real-world data.\nC_LIO_LIICD-10-CM code U07.1 for COVID-19 had low sensitivity and positive predictive value (PPV) against PCR tests.\nC_LIO_LIThe EMR-based algorithm for severe COVID-19 illness developed from the Pfizer- BioNTech COVID-19 vaccine trial had high PPV against chart review, and may be used to identify severe cases in real-world data.\nC_LIO_LIThese results highlight the importance of validating outcomes when conducting analyses of real-world datasets.\nC_LI\n\nPLAIN LANGUAGE SUMMARYAs polymerase chain reaction (PCR) tests for coronavirus disease 2019 (COVID-19) diagnosis are becoming less frequently used and there is no standard definition of severe COVID-19 illness, it is important to have a way of correctly identifying COVID-19 diagnosis or severe COVID-19 illness in real-world data (e.g., electronic medical records [EMRs]). This study examined: 1) how a diagnosis code for COVID-19 used in EMRs (i.e., U07.1) compares to PCR test results in terms of accurately identifying patients with COVID-19; and 2) whether a definition for severe COVID-19 illness developed based on the Pfizer-BioNTech COVID-19 vaccine trial and a definition used by the World Health Organization [WHO]) can be used to accurately identify patients with severe COVID-19 illness in EMRs. The results showed that code U07.1 was not very accurate in identifying patients with COVID-19. On the other hand, the developed definition for severe COVID-19 illness was more accurate than the WHO definition and was able to identify most patients with severe COVID-19 illness in real-world data.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Mei Sheng Duh", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Catherine Nguyen", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Heather Rubino", - "author_inst": "Pfizer, Inc." - }, - { - "author_name": "Christopher Herrick", - "author_inst": "Mass General Brigham" - }, - { - "author_name": "Rose Chang", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Maral DerSarkissian", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Yichuan Grace Hsieh", - "author_inst": "Mass General Brigham" - }, - { - "author_name": "Azeem Banatwala", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Louise H. Yu", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Gregory Belsky", - "author_inst": "Mass General Brigham" - }, - { - "author_name": "Marykate E. Murphy", - "author_inst": "Mass General Brigham" - }, - { - "author_name": "Janet Boyle-Kelly", - "author_inst": "Mass General Brigham" - }, - { - "author_name": "Andrew Cagan", - "author_inst": "Mass General Brigham" - }, - { - "author_name": "Bruce E. Stangle", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Pierre Y. Cremieux", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Francesca Kolitsopoulos", - "author_inst": "Pfizer, Inc." - }, - { - "author_name": "Shawn N. Murphy", - "author_inst": "Mass General Brigham" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.09.12.23295384", "rel_title": "Determinants of de novo B cell responses to drifted epitopes in post-vaccination SARS-CoV-2 infections", @@ -39747,6 +40351,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2023.09.11.23295259", + "rel_title": "Finding Long-COVID: Temporal Topic Modeling of Electronic Health Records from the N3C and RECOVER Programs", + "rel_date": "2023-09-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.11.23295259", + "rel_abs": "Post-Acute Sequelae of SARS-CoV-2 infection (PASC), also known as Long-COVID, encompasses a variety of complex and varied outcomes following COVID-19 infection that are still poorly understood. We clustered over 600 million condition diagnoses from 14 million patients available through the National COVID Cohort Collaborative (N3C), generating hundreds of highly detailed clinical phenotypes. Assessing patient clinical trajectories using these clusters allowed us to identify individual conditions and phenotypes strongly increased after acute infection. We found many conditions increased in COVID-19 patients compared to controls, and using a novel method to predict patient/cluster assignment over time, we additionally found phenotypes specific to patient sex, age, wave of infection, and PASC diagnosis status. While many of these results reflect known PASC symptoms, the resolution provided by this unprecedented data scale suggests avenues for improved diagnostics and mechanistic understanding of this multifaceted disease.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Shawn T O'Neil", + "author_inst": "University of Colorado Anschutz School of Medicine" + }, + { + "author_name": "Charisse Madlock-Brown", + "author_inst": "University of Tennessee Health Science Center" + }, + { + "author_name": "Kenneth J Wilkins", + "author_inst": "NIDDK, National Institutes of Health" + }, + { + "author_name": "Brenda M McGrath", + "author_inst": "OCHIN, Inc." + }, + { + "author_name": "Hannah E Davis", + "author_inst": "Patient-Led Research Collaborative" + }, + { + "author_name": "Gina S Assaf", + "author_inst": "Patient-Led Research Collaborative" + }, + { + "author_name": "Hannah Wei", + "author_inst": "Patient-Led Research Collaborative" + }, + { + "author_name": "Parya Zareie", + "author_inst": "University of California Davis Health" + }, + { + "author_name": "Evan T French", + "author_inst": "Virginia Commonwealth University" + }, + { + "author_name": "Johanna Loomba", + "author_inst": "University of Virginia" + }, + { + "author_name": "Julie A McMurry", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Andrea Zhou", + "author_inst": "University of Virginia" + }, + { + "author_name": "Christopher G Chute", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Richard A Moffitt", + "author_inst": "Emory University" + }, + { + "author_name": "Emily R Pfaff", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Yun Jae Yoo", + "author_inst": "Emory University" + }, + { + "author_name": "Peter Leese", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Robert F Chew", + "author_inst": "RTI International" + }, + { + "author_name": "Michael Lieberman", + "author_inst": "OCHIN, Inc." + }, + { + "author_name": "Melissa A Haendel", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "- N3C Consortium", + "author_inst": "" + }, + { + "author_name": "- RECOVER Consortium", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.09.11.23295344", "rel_title": "Safety and immunogenicity of SW-BIC-213, a modified COVID-19 Lipo-Polyplex mRNA vaccine, in Laotian healthy adults aged 18 years and above: a Phase 1/2 trial", @@ -41418,105 +42125,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2023.09.06.23294696", - "rel_title": "Predictors of SARS-CoV-2 anti-Spike IgG antibody levels following two COVID-19 vaccine doses among children and adults in the Canadian CHILD Cohort", - "rel_date": "2023-09-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.06.23294696", - "rel_abs": "BackgroundVaccination helps prevent SARS-CoV-2 infection and severe COVID-19. However, vaccine-induced humoral immune responses vary among individuals and wane over time. We aimed to describe the SARS-CoV-2 anti-spike IgG antibody response to vaccination and identify health and demographic factors associated with this response among children and adults.\n\nMethodsWe studied a subset of double-vaccinated children (n= 151; mean age: 12 {+/-}1.5 years, 46% female) and adults (n= 995; 44 {+/-}6.0 years, 60% female) from the Canadian CHILD Cohort. Dried blood spots were collected over two time periods (March 2021 to September 2021; October 2021 to January 2022). Antibody levels were quantified using automated chemiluminescent ELISAs. Demographic, vaccination, and health data were collected via online questionnaires. Associations were determined using multivariable regression.\n\nResultsOur cohort had SARS-CoV-2 anti-spike seropositivity rate of 97% following two COVID-19 vaccine doses. In both children and adults, the highest antibody levels were observed around three months post-vaccination and did not differ by biological sex. Higher antibody levels were associated with: prior SARS-CoV-2 infection ({beta}=0.15 scaled luminescence units, 95%CI, 0.06-0.24), age <18 years ({beta}=0.15, 95%CI 0.05-0.26) and receiving the Moderna mRNA ({beta}=0.23, 95%CI 0.11-0.34) or Pfizer-BioNTech mRNA vaccines ({beta}= 0.10, 95%CI, 0.02-0.18) vs. a combination of mRNA and Oxford-AstraZeneca viral vector vaccines. There were no differences in antibody levels when comparing a 3-8 vs. 9-16-week interval between vaccine doses.\n\nInterpretationWe identified key factors associated with post-vaccination antibody responses in children and adults, which could help improve future vaccine development and deployment among different population subgroups.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Rilwan Azeez", - "author_inst": "Department of Immunology, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Larisa Lotoski", - "author_inst": "Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Geoffery L. Winsor", - "author_inst": "Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada" - }, - { - "author_name": "Corey R. Arnold", - "author_inst": "Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada" - }, - { - "author_name": "Yannick Galipeau", - "author_inst": "Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada" - }, - { - "author_name": "Martin Pelchat", - "author_inst": "Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada" - }, - { - "author_name": "Stephanie Goguen", - "author_inst": "Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Elinor Simons", - "author_inst": "Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Theo J. Moraes", - "author_inst": "Division of Respiratory Medicine, Department of Pediatrics and Program in Translational Medicine, SickKids Research Institute, The Hospital for Sick Children, O" - }, - { - "author_name": "Piush J. Mandhane", - "author_inst": "Department of Pediatrics, University of Alberta, Edmonton, AB, Canada" - }, - { - "author_name": "Stuart E. Turvey", - "author_inst": "Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada" - }, - { - "author_name": "Shelly Bolotin", - "author_inst": "Centre for Vaccine Preventable Diseases, University of Toronto: Dalla Lana School of Public Health, University of Toronto" - }, - { - "author_name": "David M. Patrick", - "author_inst": "School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada" - }, - { - "author_name": "Jared Bullard", - "author_inst": "Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Lisa M. Lix", - "author_inst": "Department of Community Health Sciences, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Natasha Doucas", - "author_inst": "CHILD Cohort Study National Parent Engagement Committee" - }, - { - "author_name": "Natalie Rodriguez", - "author_inst": "Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Fiona S.L. Brinkman", - "author_inst": "Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada" - }, - { - "author_name": "Padmaja Subbarao", - "author_inst": "Division of Respiratory Medicine, Department of Pediatrics and Program in Translational Medicine, SickKids Research Institute, The Hospital for Sick Children, O" - }, - { - "author_name": "Marc-Andr\u00e9 Langlois", - "author_inst": "Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada" - }, - { - "author_name": "Meghan Azad", - "author_inst": "Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.09.08.23295177", "rel_title": "Systematical assessment of the impact of single spike mutations of SARS-CoV-2 Omicron sub-variants on the neutralization capacity of post-vaccination sera", @@ -41817,6 +42425,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.09.06.23295138", + "rel_title": "Quantity of SARS-CoV-2 RNA copies exhaled per minute during natural breathing over the course of COVID-19 infection", + "rel_date": "2023-09-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.06.23295138", + "rel_abs": "SARS-CoV-2 is spread through exhaled breath of infected individuals. A fundamental question in understanding transmission of SARS-CoV-2 is how much virus an individual is exhaling into the environment while they breathe, over the course of their infection. Research on viral load dynamics during COVID-19 infection has focused on internal swab specimens, which provide a measure of viral loads inside the respiratory tract, but not on breath. Therefore, the dynamics of viral shedding on exhaled breath over the course of infection are poorly understood. Here, we collected exhaled breath specimens from COVID-19 patients and used RTq-PCR to show that numbers of exhaled SARS-CoV-2 RNA copies during COVID-19 infection do not decrease significantly until day 8 from symptom-onset. COVID-19-positive participants exhaled an average of 80 SARS-CoV-2 viral RNA copies per minute during the first 8 days of infection, with significant variability both between and within individuals, including spikes over 800 copies a minute in some patients. After day 8, there was a steep drop to levels nearing the limit of detection, persisting for up to 20 days. We further found that levels of exhaled viral RNA increased with self-rated symptom-severity, though individual variation was high. Levels of exhaled viral RNA did not differ across age, sex, time of day, vaccination status or viral variant. Our data provide a fine-grained, direct measure of the number of SARS-CoV-2 viral copies exhaled per minute during natural breathing--including 312 breath specimens collected multiple times daily over the course of infection--in order to fill an important gap in our understanding of the time course of exhaled viral loads in COVID-19.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Gregory Lane", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Guangyu Zhou", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Judd F. Hultquist", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Lacy M Simons", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Ramon Lorenzo-Redondo", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Egon A Ozer", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Danielle M McCarthy", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Michael G Ison", + "author_inst": "Division of Microbiology and Infectious Diseases (DMID/NIAID/NIH)" + }, + { + "author_name": "Chad J Achenbach", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Xinkun Wang", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Ching Man Wai", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Eugene Wyatt", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Alan Aalsburg", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Qiaohan Yang", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Torben Noto", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Arghavan Alisoltani", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Daniel Ysselstein", + "author_inst": "Vanqua Bio" + }, + { + "author_name": "Rajeshwar Awatramani", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Robert Murphy", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Grant Theron", + "author_inst": "Stellenbosch University" + }, + { + "author_name": "Christina Zelano", + "author_inst": "Northwestern University Feinberg School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.09.06.556620", "rel_title": "Immunogenicity and tolerability of a SARS-CoV-2 TNX-1800, a live recombinant poxvirus vaccine candidate, in Syrian Hamsters and New Zealand White Rabbits.", @@ -43144,105 +43851,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2023.09.01.555815", - "rel_title": "Antigenicity and infectivity characterization of SARS-CoV-2 BA.2.86", - "rel_date": "2023-09-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.01.555815", - "rel_abs": "The recently identified SARS-CoV-2 variant, BA.2.86, which carries a substantial number of Spike mutations, has raised a global alarm. An immediate assessment of its antigenic properties and infectivity is necessary. Here, we reveal the distinct antigenicity of BA.2.86 compared with previous variants including XBB.1.5. BA.2.86 significantly evades convalescent plasma from XBB breakthrough infection (BTI) and reinfections. Key mutations that mediate the enhanced resistance include N450D, K356T, L452W, A484K, V483del, and V445H on the RBD, while BA.2.86s NTD mutations and E554K on SD1 also largely contribute. However, we found that BA.2.86 pseudovirus exhibits compromised efficiency of infecting HEK293T-hACE2 cells compared to XBB.1.5 and EG.5, which may be caused by K356T, V483del, and E554K, and could potentially limit BA.2.86s transmissibility. In sum, it appears that BA.2.86 has traded its infectivity for higher immune evasion during long-term host-viral evolution. Close attention should be paid to monitoring additional mutations that could improve BA.2.86s infectivity.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Sijie Yang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Yuanling Yu", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Fanchong Jian", - "author_inst": "Peking University" - }, - { - "author_name": "Weiliang Song", - "author_inst": "Peking University" - }, - { - "author_name": "Ayijiang Yisimayi", - "author_inst": "Peking University" - }, - { - "author_name": "Xiaosu Chen", - "author_inst": "Nankai University" - }, - { - "author_name": "Yanli Xu", - "author_inst": "Beijing Ditan Hospital" - }, - { - "author_name": "Peng Wang", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Lingling Yu", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Jing Wang", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Xiao Niu", - "author_inst": "Peking University" - }, - { - "author_name": "Jing Wang", - "author_inst": "Peking University" - }, - { - "author_name": "Tianhe Xiao", - "author_inst": "Peking University" - }, - { - "author_name": "Ran An", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Yao Wang", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Qingqing Gu", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Fei Shao", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Ronghua Jin", - "author_inst": "Beijing Ditan Hospital" - }, - { - "author_name": "Zhongyang Shen", - "author_inst": "Nankai University" - }, - { - "author_name": "Youchun Wang", - "author_inst": "Chinese Academy of Medical Science & Peking Union Medical College" - }, - { - "author_name": "Yunlong Richard Cao", - "author_inst": "Peking University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.09.02.556038", "rel_title": "Neutralization of SARS-CoV-2 EG.5/EG.5.1 by sera from ZF2001 RBD-dimer and its next-generation vaccines", @@ -43431,6 +44039,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.08.31.23294891", + "rel_title": "Application of MALDI-MS and Machine Learning to Detection of SARS-CoV-2 and non-SARS-CoV-2 Respiratory Infections.", + "rel_date": "2023-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.31.23294891", + "rel_abs": "BackgroundMatrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) could aid the diagnosis of acute respiratory infections (ARI) owing to its affordability and high-throughput capacity. MALDI-MS has been proposed for use on commonly available respiratory samples, without specialized sample preparation, making this technology especially attractive for implementation in low-resource regions. Here, we assessed the utility of MALDI-MS in differentiating SARS-CoV-2 versus non-COVID acute respiratory infections (NCARI) in a clinical lab setting of Kazakhstan.\n\nMethodsNasopharyngeal swabs were collected from in- and outpatients with respiratory symptoms and from asymptomatic controls (AC) in 2020-2022. PCR was used to differentiate SARS-CoV-2+ and NCARI cases. MALDI-MS spectra were obtained for a total of 252 samples (115 SARS-CoV-2+, 98 NCARI and 39 AC) without specialized sample preparation. In our first sub-analysis, we followed a published protocol for peak preprocessing and Machine Learning (ML), trained on publicly available spectra from South American SARS-CoV-2+ and NCARI samples. In our second sub-analysis, we trained ML models on a peak intensity matrix representative of both South American (SA) and Kazakhstan (Kaz) samples.\n\nResultsApplying the established MALDI-MS pipeline \"as is\" resulted in a high detection rate for SARS-CoV-2+ samples (91.0%), but low accuracy for NCARI (48.0%) and AC (67.0%) by the top-performing random forest model. After re-training of the ML algorithms on the SA-Kaz peak intensity matrix, the accuracy of detection by the top-performing Support Vector Machine with radial basis function kernel model was at 88.0, 95.0 and 78% for the Kazakhstan SARS-CoV-2+, NCARI, and AC subjects, respectively with a SARS-CoV-2 vs. rest ROC AUC of 0.983 [0.958, 0.987]; a high differentiation accuracy was maintained for the South American SARS-CoV-2 and NCARI.\n\nConclusionsMALDI-MS/ML is a feasible approach for the differentiation of ARI without a specialized sample preparation. The implementation of MALDI-MS/ML in a real clinical lab setting will necessitate continuous optimization to keep up with the rapidly evolving landscape of ARI.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Sergey Yegorov", + "author_inst": "McMaster University Faculty of Health Sciences" + }, + { + "author_name": "Irina Kadyrova", + "author_inst": "Karaganda Medical University" + }, + { + "author_name": "Ilya Korshukov", + "author_inst": "Karaganda Medical University" + }, + { + "author_name": "Aidana Sultanbekova", + "author_inst": "Karaganda Medical University" + }, + { + "author_name": "Valentina Barkhanskaya", + "author_inst": "Nazarbayev University" + }, + { + "author_name": "Tatyana Bashirova", + "author_inst": "Karaganda Medical University" + }, + { + "author_name": "Yerzhan Zhunusov", + "author_inst": "Karaganda Medical University" + }, + { + "author_name": "Yevgeniya Li", + "author_inst": "Karaganda Medical University" + }, + { + "author_name": "Viktoriya Parakhina", + "author_inst": "Karaganda Medical University" + }, + { + "author_name": "Svetlana Kolesnichenko", + "author_inst": "Karaganda Medical University" + }, + { + "author_name": "Yeldar Baiken", + "author_inst": "Nazarbayev University" + }, + { + "author_name": "Bakhyt Matkarimov", + "author_inst": "Nazarbayev University" + }, + { + "author_name": "Dmitriy Vazenmiller", + "author_inst": "Karaganda Medical University" + }, + { + "author_name": "Matthew S. Miller", + "author_inst": "McMaster University" + }, + { + "author_name": "Gonzalo H. Hortelano", + "author_inst": "Nazarbayev University" + }, + { + "author_name": "Anar Turmuhambetova", + "author_inst": "Karaganda Medical University" + }, + { + "author_name": "Antonella E. Chesca", + "author_inst": "Transilvania University of Brasov: Universitatea Transilvania din Brasov" + }, + { + "author_name": "Dmitriy Babenko", + "author_inst": "Karaganda Medical University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.08.31.23294738", "rel_title": "COVID-19-related school closures, United States, July 27, 2020 - June 30, 2022", @@ -44866,53 +45561,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.08.30.23294839", - "rel_title": "Vaccination status and re-infection among COVID patients admitted in COVID High Dependency Unit (HDU) of a tertiary hospital in Eastern Nepal: A cross-sectional study", - "rel_date": "2023-08-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.30.23294839", - "rel_abs": "IntroductionThe relationship between COVID-19 vaccination and Coronavirus disease severity and outcomes remain topics of significant interest. This cross-sectional study done among COVID-19 patients admitted to the High-dependency unit of a tertiary hospital in Eastern Nepal aimed to assess the association between vaccination status, prior infection, and disease outcomes, and the modification of these associations by the presence or absence of comorbidities.\n\nMethodologyDemographic and clinical data were collected from 102 COVID-19 patients admitted to the High-Dependency Unit of Mechi Zonal Hospital, including information on vaccination status, comorbidities, disease severity, and outcomes. Statistical analysis, including chi-square tests and Fishers exact tests, was performed to examine the associations.\n\nResultsAmong the study participants, 49% had received at least one dose of COVID-19 vaccine. Vaccinated individuals had a significantly lower rate of severe disease compared to non-vaccinated individuals ({chi}{superscript 2}=10.05, p=0.002). Recovery and mortality rates did not differ significantly between the two groups ({chi}{superscript 2}=1.008, p=0.315). However, when stratified by comorbidities, vaccinated individuals with comorbidities had higher recovery rates compared to non-vaccinated individuals (85.29% vaccinated vs. 25.00% non-vaccinated, Fishers exact test p=0.024). Vaccinated individuals, both with and without comorbidities, had lower rates of severe disease compared to non-vaccinated individuals. However, the association was found to be significant only in individuals with comorbidities (12.50% vaccinated without comorbidities vs. 47.92% non-vaccinated, p=0.017; 23.53% vaccinated with comorbidities vs. 75.00% non-vaccinated, p=0.065).\n\nConclusionOur findings suggest that COVID-19 vaccination is associated with a reduced risk of severe disease among individuals with or without comorbidities and decreased risk of mortality among those with comorbidities. However, larger studies are needed to validate these findings and further explore the impact of vaccination on disease outcomes. These findings support the ongoing efforts to promote COVID-19 vaccination as a crucial public health intervention.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Sujan Kafle", - "author_inst": "Provincial Hospital Bhadrapur" - }, - { - "author_name": "Varsha Chhetri", - "author_inst": "BP Koirala Institute of Health Sciences" - }, - { - "author_name": "Joshan Lal Bajracharya", - "author_inst": "BP Koirala Institute of Health Sciences" - }, - { - "author_name": "Lenish Pokharel", - "author_inst": "BP Koirala Institute of Health Sciences" - }, - { - "author_name": "Suyash Dawadi", - "author_inst": "BP Koirala Institute of Health Sciences" - }, - { - "author_name": "Ujwal Basnet", - "author_inst": "BP Koirala Institute of Health Sciences" - }, - { - "author_name": "Shreya Dhungana", - "author_inst": "BP Koirala Institute of Health Sciences" - }, - { - "author_name": "Durga Neupane", - "author_inst": "BP Koirala Institute of Health Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.08.29.23293790", "rel_title": "Outpatient treatment with concomitant vaccine-boosted convalescent plasma for patients with immunosuppression and COVID-19", @@ -45333,6 +45981,57 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.08.29.555356", + "rel_title": "Robust acidic pH and digestive enzyme stability of anti-SarsCov2 IgY antibodies: Implications for treatment of viral transmission thru gastrointestinal, ocular, nasal and skin tissues", + "rel_date": "2023-08-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.29.555356", + "rel_abs": "There are many paths for the transmission of SarsCov2 virus. The main routes are nasal and oral and the droplets carrying the virus can also be transmitted thru ocular and skin tissues. The gastrointestinal (small intestine), nasal, ocular and skin tissues all present an acidic pH milieu and therefore any treatment with antibodies thru these routes has to have the antibodies remain active at acid pH as well as be resistant to typical protease digestion.\n\nTo this end we profiled our anti-SarasCov2 receptor binding domain IgY antibodies for retention of activity at acidic and basic pHs and trypsin digestion. We find that the IgY are strongly resistant to denaturation at acid pH as well as not digested by trypsin. Our data strongly support the use of these IgY in treatment of viral transmission thru the GI, nasal, ocular and skin all tissues where the pH is acidic. We also provide an enabling platform to rapidly asses the suitability of any antibody or protein therapeutic for use at acidic pH.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Sanjana Battula", + "author_inst": "Reagene Innovations Pvt Ltd" + }, + { + "author_name": "Saranya K", + "author_inst": "Reagene Innovations Pvt Ltd" + }, + { + "author_name": "Kranti Meher", + "author_inst": "Reagene Innovations Pvt Ltd" + }, + { + "author_name": "Arpitha Reddy R.N", + "author_inst": "Reagene Innovations Pvt Ltd" + }, + { + "author_name": "Gopi Kadiyala", + "author_inst": "Kyntox Bio Pvt Ltd" + }, + { + "author_name": "Subramanian Iyer", + "author_inst": "Prodigy Bio Inc" + }, + { + "author_name": "Subrahmanyam Vangala", + "author_inst": "Reagene Innovations Pvt Ltd" + }, + { + "author_name": "Satish Chandran", + "author_inst": "Prodigy Bio Inc" + }, + { + "author_name": "Uday Saxena", + "author_inst": "Reagene Innovations Pvt Ltd" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2023.08.29.555368", "rel_title": "SARS-CoV-2 RNA Persists in the Central Nervous System of Non-Human Primates Despite Clinical Recovery", @@ -46904,61 +47603,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2023.08.21.553968", - "rel_title": "Antibody Neutralization of Emerging SARS-CoV-2: EG.5.1 and XBC.1.6", - "rel_date": "2023-08-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.21.553968", - "rel_abs": "SARS-CoV-2 variants EG.5.1 and XBC.1.6 have recently emerged, attracting increased attention due to their rapid expansion globally and in Australia, respectively. EG.5.1 evolved from Omicron subvariant XBB.1.9, harboring additional Q52H and F456L spike substitutions. The F456L mutation is located within the epitopes of many class-1 monoclonal antibodies (mAbs) directed to the receptor-binding domain (RBD), raising concerns about further antibody evasion. XBC.1.6, a descendant of a Delta-BA.2 recombinant, carries 15 additional spike mutations. The extent to which antibody evasion contributes to the growth advantage of XBC.1.6 in Australia remains to be determined. To assess the antibody evasion properties of the emergent variants, we conducted pseudovirus neutralization assays using sera from individuals who received three doses of COVID-19 mRNA monovalent vaccines plus one dose of a BA.5 bivalent vaccine, as well as from patients with BQ or XBB breakthrough infection. The assays were also performed using a panel of 14 mAbs that retained neutralizing activity against prior XBB subvariants. Our data suggested that EG.5.1 was slightly but significantly more resistant (< 2-fold) to neutralization by BQ and XBB breakthrough sera than XBB.1.16, which is known to be antigenically similar to XBB.1.5. Moreover, the F456L mutation in EG.5.1 conferred heightened resistance to certain RBD class-1 mAbs. In contrast, XBC.1.6 was more sensitive to neutralization by sera and mAbs than the XBB subvariants. Notably, XBB breakthrough sera retained only weak neutralization activity against XBB subvariants. In summary, EG.5.1 and XBC.1.6 exhibited distinct antibody evasion properties. The recent global expansion of EG.5.1 might be attributable, in part, to its enhanced neutralization resistance. That XBB breakthrough infections did not elicit a robust antibody neutralization response against XBB subvariants is indicative of immunological imprinting. The high prevalence of XBC.1.6 in Australia is not due to enhanced antibody evasion.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Qian Wang", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Yicheng Guo", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Richard Ma Zhang", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Jerren Ho", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Hiroshi Mohri", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Riccardo Valdez", - "author_inst": "University of Michigan" - }, - { - "author_name": "David M Manthei", - "author_inst": "University of Michigan" - }, - { - "author_name": "Aubree Gordon", - "author_inst": "University of Michigan School of Public Health" - }, - { - "author_name": "Lihong Liu", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "David D Ho", - "author_inst": "Columbia University Irving Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.08.24.554732", "rel_title": "Mucosal antibody responses to SARS-CoV-2 booster vaccination and breakthrough infection", @@ -47119,6 +47763,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2023.08.24.23294503", + "rel_title": "Protection conferred by COVID-19 vaccination, prior SARS-CoV-2 infection, or hybrid immunity against Omicron-associated severe outcomes among community-dwelling adults", + "rel_date": "2023-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.24.23294503", + "rel_abs": "IntroductionWe assessed protection conferred by COVID-19 vaccines and/or prior SARS-CoV-2 infection against Omicron-associated severe outcomes during successive sublineage-predominant periods.\n\nMethodsWe used a test-negative design to estimate protection by vaccines and/or prior infection against hospitalization/death among community-dwelling, PCR-tested adults aged [≥]50 years in Ontario, Canada between January 2, 2022 and June 30, 2023. Multivariable logistic regression was used to estimate the relative change in the odds of hospitalization/death with each vaccine dose (2-5) and/or prior PCR-confirmed SARS-CoV-2 infection (compared with unvaccinated, uninfected subjects) up to 15 months since the last vaccination or infection.\n\nResultsWe included 18,526 cases with Omicron-associated severe outcomes and 90,778 test-negative controls. Vaccine protection was high during BA.1/BA.2 predominance, but was generally <50% during periods of BA.4/BA.5 and BQ/XBB predominance without boosters. A third/fourth dose transiently increased protection during BA.4/BA.5 predominance (third-dose, 6-month: 68%, 95%CI 63%-72%; fourth-dose, 6-month: 80%, 95%CI 77%-83%), but was lower and waned quickly during BQ/XBB predominance (third-dose, 6-month: 59%, 95%CI 48%-67%; 12-month: 49%, 95%CI 41%-56%; fourth-dose, 6-month: 62%, 95%CI 56%-68%, 12-months: 51%, 95%CI 41%-56%). Hybrid immunity conferred nearly 90% protection throughout BA.1/BA.2 and BA.4/BA.5 predominance, but was reduced during BQ/XBB predominance (third-dose, 6-month: 60%, 95%CI 36%-75%; fourth-dose, 6-month: 63%, 95%CI 42%-76%). Protection was restored with a fifth dose (bivalent; 6-month: 91%, 95%CI 79%-96%). Prior infection alone did not confer lasting protection.\n\nConclusionProtection from COVID-19 vaccines and/or prior SARS-CoV-2 infections against severe outcomes is reduced when immune-evasive variants/subvariants emerge and may also wane over time. Our findings support a variant-adapted booster vaccination strategy with periodic review.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Nelson Lee", + "author_inst": "Dalla Lana School of Public Health, University of Toronto" + }, + { + "author_name": "Lena Nguyen", + "author_inst": "ICES, Toronto, Ontario, Canada" + }, + { + "author_name": "Peter C. Austin", + "author_inst": "ICES, Toronto, Ontario" + }, + { + "author_name": "Kevin A. Brown", + "author_inst": "Public Health Ontario, Toronto, Ontario" + }, + { + "author_name": "Ramandip Grewal", + "author_inst": "Public Health Ontario, Toronto" + }, + { + "author_name": "Sarah A Buchan", + "author_inst": "Public Health Ontario, Toronto" + }, + { + "author_name": "Sharifa Nasreen", + "author_inst": "University of Toronto" + }, + { + "author_name": "Jonathan Gubbay", + "author_inst": "British Columbia Children's Hospital, Vancouver" + }, + { + "author_name": "Kevin L Schwartz", + "author_inst": "Public Health Ontario, Toronto" + }, + { + "author_name": "Mina Tadrous", + "author_inst": "Leslie Dan Faculty of Pharmacy, University of Toronto" + }, + { + "author_name": "Kumanan Wilson", + "author_inst": "Department of Medicine, University of Ottawa, Ottawa" + }, + { + "author_name": "Sarah E Wilson", + "author_inst": "Public Health Ontario, Toronto" + }, + { + "author_name": "Jeffrey C Kwong", + "author_inst": "ICES, Toronto, Ontario, Canada" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.08.24.23294557", "rel_title": "An After-Action Review of COVID-19 Cases and Mitigation Measures at US Mission India, March 2020-July 2021", @@ -48458,65 +49169,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.08.23.554434", - "rel_title": "SARS-CoV-2 Nsp13 is a viral RHIM protein promoting cell death linked to Z-RNA sensing and ZBP1-RIPK3 signaling", - "rel_date": "2023-08-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.23.554434", - "rel_abs": "Interferons and regulated cell death pathways counteract virus spread and mount immune responses, but their deregulation often results in inflammatory pathologies. The RIP-homotypic interaction motif (RHIM) is a conserved protein domain critical for assembling higher-order amyloid-like signaling complexes inducing cell death. A few DNA viruses employ viral RHIMs mimicking host RHIMs to alleviate cell death-mediated antiviral defenses. Whether RNA viruses operate such viral RHIMs remains unknown. Host RHIM-protein signaling promotes lung damage and cytokine storm in respiratory RNA virus infections, arguing the presence of viral RHIMs in RNA viruses. Here, we report the identification of novel viral RHIMs in Nsp13 and Nsp14 of SARS-CoV-2 and other bat RNA viruses and provide a basis for bats as the hosts for the evolution of RHIMs in RNA viruses. Nsp13 expression promoted CoV-RHIM-1-dependent cell death after SARS-CoV-2 infection, and its RNA-binding channel conformation was critical for cell death function. Nsp13 interacted and promoted the formation of large insoluble complexes of ZBP1 and RIPK3. Unlike DNA virus RHIMs, SARS-CoV-2 Nsp13 did not restrict host RHIM-dependent cell death. Instead, it promoted ZBP1-RIPK3 signaling-mediated cell death dependent on intracellular RNA ligands. Intriguingly, SARS-CoV-2 genome fragments showed high Z-RNA forming propensity which bound to Z-RNA sensing Z domains and promoted Nsp13-dependent cell death. Our findings reveal the functional viral RHIMs in RNA viruses and the role of SARS-CoV-2 Nsp13 in cell death associated with Z-RNAs and ZBP1-RIPK3 signaling, allowing the understanding of mechanisms of cellular damage and cytokine storm in respiratory virus infections and COVID-19.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC=\"FIGDIR/small/554434v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (66K):\norg.highwire.dtl.DTLVardef@12bf222org.highwire.dtl.DTLVardef@25cc1forg.highwire.dtl.DTLVardef@17c2a2dorg.highwire.dtl.DTLVardef@b4f745_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Sanchita Mishra", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Disha Jain", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Ayushi Amin Dey", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Sahana Nagaraja", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Mansi Srivastava", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Oyahida Khatun", - "author_inst": "Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bengaluru 560012, India. Centre for Infectious Diseas" - }, - { - "author_name": "Keerthana Balamurugan", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Micky Anand", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Shashank Tripathi", - "author_inst": "Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bengaluru 560012, India. Centre for Infectious Diseas" - }, - { - "author_name": "Mahipal Ganji", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Sannula Kesavardhana", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.08.24.554561", "rel_title": "Rationally designed multimeric nanovaccines using icosahedral DNA origami for molecularly controlled display of SARS-CoV-2 receptor binding domain", @@ -48757,6 +49409,45 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2023.08.22.554362", + "rel_title": "Recurrent SARS-CoV-2 mutations at Spike D796 evade antibodies from pre-Omicron convalescent and vaccinated subjects", + "rel_date": "2023-08-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.22.554362", + "rel_abs": "SARS-CoV-2 lineages of the Omicron variant rapidly became dominant in early 2022 and frequently cause human infections despite vaccination or prior infection with other variants. In addition to antibody-evading mutations in the Receptor Binding Domain, Omicron features amino acid mutations elsewhere in the Spike protein, however their effects generally remain ill-defined. The Spike D796Y substitution is present in all Omicron sub-variants and occurs at the same site as a mutation (D796H) selected during viral evolution in a chronically-infected patient. Here we map antibody reactivity to a linear epitope in the Spike protein overlapping position 796. We show that antibodies binding this region arise in pre-Omicron SARS-CoV-2 convalescent and vaccinated subjects, but that both D796Y and D796H abrogate their binding. These results suggest that D796Y contributes to the fitness of Omicron in hosts with pre-existing immunity to other variants of SARS-CoV-2 by evading antibodies targeting this site.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Evan A Elko", + "author_inst": "Northern Arizona University" + }, + { + "author_name": "Heather Mead", + "author_inst": "Translational Genomics Research Institute" + }, + { + "author_name": "Georgia A Nelson", + "author_inst": "Translational Genomics Research Institute Flagstaff" + }, + { + "author_name": "John Zaia", + "author_inst": "Beckman Research Institute of the City of Hope" + }, + { + "author_name": "Jason T Ladner", + "author_inst": "Northern Arizona University" + }, + { + "author_name": "John A Altin", + "author_inst": "Translational Genomics Research Institute Flagstaff" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.08.22.553458", "rel_title": "Administration of vaccine-boosted COVID-19 convalescent plasma to SARS-CoV-2 infected hamsters decreases virus replication in lungs and hastens resolution of the infection despite transiently enhancing disease and lung pathology.", @@ -50248,29 +50939,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.08.16.23294160", - "rel_title": "Unraveling COVID-19: Descriptive Analytics in a Middle-Income Country, Paving the Path Forward", - "rel_date": "2023-08-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.16.23294160", - "rel_abs": "The outbreak of COVID-19 unleashed an unprecedented global pandemic, leaving a profound impact on lives and economies worldwide. Recognizing its severity, the World Health Organization swiftly declared it a public health emergency of international concern. Tragically, the Philippines reported the first death case outside China, leading to a surge in cases following the first instance of local transmission. In response to this crisis, collaborative efforts have been underway to control the disease and minimize its health and socio-economic impacts. The COVID-19 epidemic curve holds vital insights into the history of exposure, transmission, testing, tracing, social distancing measures, community lockdowns, quarantine, isolation, and treatment, offering a comprehensive perspective on the nations response. One approach to gaining crucial insights is through meticulous analysis of available datasets, empowering us to inform future strategies and responses effectively. This paper aims to provide descriptive data analytics of the COVID-19 pandemic in the Philippines, summarizing the countrys fight by visualizing epidemiological and mobility datasets, revisiting scientific papers and news articles, and creating a timeline of the key issues faced during the pandemic. By leveraging these multifaceted analyses, policymakers and health authorities can make informed decisions to enhance preparedness, expand inter-agency cooperation, and combat future public health crises effectively. This study seeks to serve as a valuable resource, guiding nations worldwide in comprehending and responding to the challenges posed by COVID-19 and beyond.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Norvin Patadon Bansilan", - "author_inst": "University of the Philippines Los Banos" - }, - { - "author_name": "Jomar Fajardo Rabajante", - "author_inst": "University of the Philippines Los Banos" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.08.17.553661", "rel_title": "Purification, crystallization, and preliminary structural analysis of multivalent immunogenic effector protein-anchored SARS-CoV-2 RBD", @@ -50387,6 +51055,53 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.08.16.553581", + "rel_title": "Assembly of SARS-CoV-2 ribonucleosomes by truncated N* variant of the nucleocapsid protein", + "rel_date": "2023-08-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.16.553581", + "rel_abs": "The Nucleocapsid (N) protein of SARS-CoV-2 compacts the RNA genome into viral ribonucleoprotein (vRNP) complexes within virions. Assembly of vRNPs is inhibited by phosphorylation of the N protein SR region. Several SARS-CoV-2 variants of concern carry N protein mutations that reduce phosphorylation and enhance the efficiency of viral packaging. Variants of the dominant B.1.1 viral lineage also encode a truncated N protein, termed N* or {Delta}(1-209), that mediates genome packaging despite lacking the N-terminal RNA-binding domain and SR region. Here, we show that {Delta}(1-209) and viral RNA assemble into vRNPs that are remarkably similar in size and shape to those formed with full-length N protein. We show that assembly of {Delta}(1-209) vRNPs requires the leucine-rich helix (LH) of the central disordered region, and that the LH promotes N protein oligomerization. We also find that fusion of a phosphomimetic SR region to {Delta}(1-209) inhibits RNA binding and vRNP assembly. Our results provide new insights into the mechanisms by which RNA binding promotes N protein self-association and vRNP assembly, and how this process is modulated by SR phosphorylation.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Armin Adly", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Maxine Bi", + "author_inst": "UCSF" + }, + { + "author_name": "Christopher Carlson", + "author_inst": "UCSF" + }, + { + "author_name": "Abdullah Muhammad Syed", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Alison Ciling", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Jennifer Doudna", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Yifan Cheng", + "author_inst": "UCSF" + }, + { + "author_name": "David O. Morgan", + "author_inst": "University of California San Francisco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.08.16.553332", "rel_title": "Virological characteristics of the SARS-CoV-2 XBB.1.5 variant", @@ -51750,49 +52465,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.08.13.553144", - "rel_title": "Mutational basis of serum cross-neutralization profiles elicited by infection or vaccination with SARS-CoV-2 variants", - "rel_date": "2023-08-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.13.553144", - "rel_abs": "A series of SARS-CoV-2 variants emerged during the pandemic under selection for neutralization resistance. Convalescent and vaccinated sera show consistently different cross-neutralization profiles depending on infecting or vaccine variants. To understand the basis of this heterogeneity, we modeled serum cross-neutralization titers for 165 sera after infection or vaccination with historically prominent lineages tested against 18 variant pseudoviruses. Cross-neutralization profiles were well captured by models incorporating autologous neutralizing titers and combinations of specific shared and differing mutations between the infecting/vaccine variants and pseudoviruses. Infecting/vaccine variant-specific models identified mutations that significantly impacted cross-neutralization and quantified their relative contributions. Unified models that explained cross-neutralization profiles across all infecting and vaccine variants provided accurate predictions of holdout neutralization data comprising untested variants as infecting or vaccine variants, and as test pseudoviruses. Finally, comparative modeling of 2-dose versus 3-dose mRNA-1273 vaccine data revealed that the third dose overcame key resistance mutations to improve neutralization breadth.\n\nHIGHLIGHTSO_LIModeled SARS-CoV-2 cross-neutralization using mutations at key sites\nC_LIO_LIIdentified resistance mutations and quantified relative impact\nC_LIO_LIAccurately predicted holdout variant and convalescent/vaccine sera neutralization\nC_LIO_LIShowed that the third dose of mRNA-1273 vaccination overcomes resistance mutations\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Kshitij Wagh", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Xiaoying Shen", - "author_inst": "Duke University" - }, - { - "author_name": "James Theiler", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Bethany Girard", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Jean-Claude Marshall", - "author_inst": "Moderna, Inc., Cambridge, MA 02319, USA" - }, - { - "author_name": "David Montefiori", - "author_inst": "Duke University" - }, - { - "author_name": "Bette Korber", - "author_inst": "Los Alamos National Laboratory" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.08.14.553219", "rel_title": "Transmission bottleneck size estimation from de novo viral genetic variation", @@ -51941,6 +52613,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.08.13.553148", + "rel_title": "SARS-CoV-2 Neutralizing Antibodies Following a Second BA.5 Bivalent Booster", + "rel_date": "2023-08-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.13.553148", + "rel_abs": "Bivalent COVID-19 mRNA vaccines expressing both the ancestral D614G and Omicron BA.5 spike proteins were introduced in August 2022 with the goal of broadening immunity to emerging SARS-CoV-2 Omicron subvariants. Subsequent studies on bivalent boosters found neutralizing antibody responses similar to boosters with the original monovalent vaccine, likely the result of immunological imprinting. Guidelines allow for administration of a second bivalent booster in high-risk groups, but it remains unknown whether this would broaden antibody responses. To address this question, we assessed longitudinal serum SARS-CoV-2-neutralizing titers in 18 elderly immunocompetent individuals (mean age 69) following a fourth monovalent booster and two BA.5 bivalent booster vaccines using pseudovirus neutralization assays against D614G, Omicron BA.5, and Omicron XBB.1.5. There was a small but significant increase in peak neutralizing antibody responses against Omicron BA.5 and XBB.1.5 following the first bivalent booster, but no significant increase in peak titers following the second bivalent booster. Omicron-specific neutralizing titers remained low after both doses of the BA.5 bivalent booster. Our results suggest that a second dose of the BA.5 bivalent booster is not sufficient to broaden antibody responses and to overcome immunological imprinting. A monovalent vaccine targeting only the spike of the recently dominant SARS-CoV-2 may mitigate the \"back boosting\" associated with the \"original antigenic sin.\"", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Qian Wang", + "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" + }, + { + "author_name": "Anthony Bowen", + "author_inst": "Columbia University" + }, + { + "author_name": "Jerren Ho", + "author_inst": "Columbia University" + }, + { + "author_name": "Richard Zhang", + "author_inst": "Columbia University" + }, + { + "author_name": "Riccardo Valdez", + "author_inst": "University of Michigan" + }, + { + "author_name": "Emily Stoneman", + "author_inst": "University of Michigan" + }, + { + "author_name": "Aubree Gordon", + "author_inst": "University of Michigan School of Public Health" + }, + { + "author_name": "Liu Lihong", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "David D Ho", + "author_inst": "Columbia University Irving Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.08.09.23293776", "rel_title": "Post-COVID conditions during Delta and early-Omicron SARS-CoV-2 variant periods among adults in the United States", @@ -53120,69 +53843,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.08.07.23293304", - "rel_title": "High-throughput detection of neutralizing antibodies to SARS-CoV-2 variants using flow cytometry", - "rel_date": "2023-08-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.07.23293304", - "rel_abs": "Detecting neutralizing antibodies (NAbs) to SARS-CoV-2 variants is crucial for controlling the spread of COVID-19. In this work, we developed a high-throughput assay for the broad systematic examination of NAbs to eleven SARS-CoV variants of concern (VOCs), which include D614G, Alpha, Beta, Gamma, Delta, Kappa, and Omicron sub-lineages BA.1, BA.2, BA.3, BA.4, and BA.5. The assay is cost-effective, reliable, 35-fold more sensitive than Luminex technology, and can include the new variants during SARS-CoV-2 evolution. Importantly, our results highly correlated with a commercial IgG serological assay (R = 0.89) and cPass, a U.S. FDA-approved surrogate virus neutralization test (sVNT) assay (R = 0.93). With our high-throughput NAb platform, we constructed a comprehensive overview of the interactions between SARS-CoV-2 VOCs Spike trimer proteins and ACE2 receptors, leading to the identification of a monoclonal Ab with broad neutralizing activity. Furthermore, when compared to the D614G variant, we found that the serum NAbs elicited by the third dose vaccine (administered after 28 days) demonstrated decreased inhibition to multiple SARS-CoV-2 variants, including Gamma (0.94x), Alpha (0.91x), Delta (0.91x), Beta (0.81x), Kappa (0.81x), BA.2 (0.44x), BA.1 (0.43x), BA.3 (0.41x), BA.5 (0.35x) and BA.4 (0.33x), in cohort of 56 vaccinated individuals. Altogether, our proteomics platform proves to be an effective tool to detect broad NAbs in the population and aid in the development of future COVID-19 vaccines and vaccination strategies.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Xiaohan Zhang", - "author_inst": "College of Medicine and Integrated Medicine, Nanjing University of Chinese Medicine; State Key Laboratory of Proteomics, Beijing Proteome Research Center, Natio" - }, - { - "author_name": "Yajie Wang", - "author_inst": "Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University" - }, - { - "author_name": "Mansheng Li", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - }, - { - "author_name": "Haolong Li", - "author_inst": "Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College" - }, - { - "author_name": "Xiaomei Zhang", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - }, - { - "author_name": "Xingming Xu", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - }, - { - "author_name": "Di Hu", - "author_inst": "ProteomicsEra Medical Co., Ltd." - }, - { - "author_name": "Te Liang", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - }, - { - "author_name": "Yunping Zhu", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - }, - { - "author_name": "Yongzhe Li", - "author_inst": "Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College" - }, - { - "author_name": "Bingwei Wang", - "author_inst": "College of Medicine and Integrated Medicine, Nanjing University of Chinese Medicine" - }, - { - "author_name": "Xiaobo Yu", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.08.08.552415", "rel_title": "Antiviral efficacy of the SARS-CoV-2 XBB breakthrough infection sera against Omicron subvariants including EG.5", @@ -53355,6 +54015,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.08.04.23293551", + "rel_title": "Genetic Variant rs1205 is Associated with COVID-19 Outcomes: The Strong Heart Study and Strong Heart Family Study.", + "rel_date": "2023-08-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.04.23293551", + "rel_abs": "BackgroundAlthough COVID-19 infection has been associated with a number of clinical and environmental risk factors, host genetic variation has also been associated with the incidence and morbidity of infection. The CRP gene codes for a critical component of the innate immune system and CRP variants have been reported associated with infectious disease and vaccination outcomes. We investigated possible associations between COVID-19 outcome and a limited number of candidate gene variants including rs1205.\n\nMethodology/Principal FindingsThe Strong Heart and Strong Heart Family studies have accumulated detailed genetic, cardiovascular risk and event data in geographically dispersed American Indian communities since 1988. Chi-square tests, logistic regression and generalized linear mixed models (implemented in SOLAR) were used in analysis. Genotypic data and 91 COVID-19 adjudicated deaths or hospitalizations from 2/1/20 through 3/1/23 were identified among 3,780 participants in two subsets. Among 21 candidate variants including genes in the interferon response pathway, APOE, TMPRSS2, TLR3, the HLA complex and the ABO blood group, only rs1205, a 3 untranslated region variant in the CRP gene, showed nominally significant association in T-dominant model analyses (odds ratio 1.859, 95%CI 1.001-3.453, p=0.049) after adjustment for age, sex, center, body mass index, and a history of cardiovascular disease. Within the younger subset, association with the rs1205 T-Dom genotype was stronger, both in the same adjusted logistic model and in the SOLAR analysis also adjusting for other genetic relatedness.\n\nConclusionA T-dominant genotype of rs1205 in the CRP gene is associated with COVID-19 death or hospitalization, even after adjustment for relevant clinical factors and potential participant relatedness. Additional study of other populations and genetic variants of this gene are warranted.\n\nAuthor summaryConsiderable inter-individual variability in COVID-19 clinical outcome has been noted from the onset of this pandemic. Some risk factors, such as age, diabetes, obesity, prior cardiovascular disease (CVD) are well established. The possibility of inherited, host genetic risk factors has also been examined and a number validated in very large, population based datasets. The present study leveraged on-going clinical surveillance of CVD and available genetic information in an American Indian population to investigate potential host genetic contributors to COVID-19 morbidity and mortality. Although the number of cases ascertained was relatively small, a novel variant in the C-reactive protein gene was found to be associated with COVID-19 outcome. This protein constitutes a critical component of the innate immune system and CRP variants have been reported associated with infectious disease and vaccination outcomes. Improved understanding of the pathophysiology of this infection may allow more targeted therapy.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Lyle G Best", + "author_inst": "Missouri Breaks Industries Research Inc" + }, + { + "author_name": "Esther Erdei", + "author_inst": "University of New Mexico - Albuquerque: The University of New Mexico" + }, + { + "author_name": "Karin Haack", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Jack W Kent", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Kimberly Malloy", + "author_inst": "University of Oklahama Norman Campus: The University of Oklahoma" + }, + { + "author_name": "Deborah E Newman", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Marcia O'Leary", + "author_inst": "Missouri Breaks Industries Research Inc" + }, + { + "author_name": "Rae O'Leary", + "author_inst": "Missouri Breaks Industries Research Inc" + }, + { + "author_name": "Quan Sun", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Ana Navas-Acien", + "author_inst": "Columbia University Mailman School of Public Health" + }, + { + "author_name": "Nora Franceschini", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Shelley A Cole", + "author_inst": "Texas Biomedical Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.08.04.23293662", "rel_title": "Socio-demographic determinants of COVID-19 vaccine uptake in Ontario: Exploring differences across the Health Region model", @@ -54622,77 +55345,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.07.28.23293335", - "rel_title": "Healthcare resource utilization and costs associated with COVID-19 among pediatrics managed in the community or hospital setting in England: a population-based cohort study", - "rel_date": "2023-08-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.28.23293335", - "rel_abs": "BackgroundAlthough COVID-19 morbidity is significantly lower in pediatrics than in adults, the risk of severe COVID-19 may still pose substantial healthcare resource burden. This study aimed to describe healthcare resource utilization (HCRU) and costs associated with COVID-19 in pediatrics aged 1-17 years in England.\n\nMethodsA population-based retrospective cohort study of pediatrics with COVID-19 using Clinical Practice Research Datalink (CPRD Aurum) primary care data and, where available, linked Hospital Episode Statistics Admitted Patient Care (HES APC) secondary care data. HCRU and associated costs to the National Health Service (NHS) were stratified by age, risk of severe COVID-19, and immunocompromized status, separately for those with and without hospitalization records (hospitalized cohort: COVID-19 diagnosis August 2020-March 2021; primary care cohort: COVID-19 diagnosis August 2020-January 2022).\n\nResultsThis study included 564,644 patients in the primary care cohort and 60 in the hospitalized cohort. Primary care consultations were more common in those aged 1-4 years (face-to-face: 4.3%; telephone: 6.0%) compared to those aged 5-11 (2.0%; 2.1%) and 12-17 years (2.2%; 2.5%). In the hospitalized cohort, mean [SD] length of stay was longer (5.0 [5.8] days) among those aged 12-17 years (n=24) than those aged 1-4 (n=15; 1.8 [0.9] days) and 5-11 years (n=21; 2.8 [2.1] days).\n\nConclusionsMost pediatrics diagnosed with COVID-19 were managed in the community. However, hospitalizations were an important driver of HCRU and costs, particularly for those aged 12-17 years. Our results may help optimize the management and resource allocation of COVID-19 in this population.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Jingyan Yang", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Kathleen M Andersen", - "author_inst": "Pfizer Inc" - }, - { - "author_name": "Kiran K Rai", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Theo Tritton", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Tendai Mugwagwa", - "author_inst": "Pfizer Ltd" - }, - { - "author_name": "Carmen Tsang", - "author_inst": "Pfizer Ltd" - }, - { - "author_name": "Maya Reimbaeva", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Leah McGrath", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Poppy Payne", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Bethany Emma Backhouse", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Diana Mendes", - "author_inst": "Pfizer Ltd" - }, - { - "author_name": "Rebecca Butfield", - "author_inst": "Pfizer Ltd" - }, - { - "author_name": "Robert Wood", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Jennifer L Nguyen", - "author_inst": "Pfizer Inc" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.07.28.23293338", "rel_title": "Systematic Review and Meta-Analysis Protocol of the Efficacy and Safety of COVID-19 Drug Candidates Targeting Host Enzymes Involved in Immune Response", @@ -54929,6 +55581,33 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.08.03.551784", + "rel_title": "Comparing full variation profile analysis with the conventional consensus method in SARS-CoV-2 phylogeny", + "rel_date": "2023-08-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.03.551784", + "rel_abs": "This study proposes a novel approach to studying SARS-CoV-2 virus mutations through sequencing data comparison. Traditional consensus-based methods, which focus on the most common nucleotide at each position, might overlook or obscure the presence of low-frequency variants. Our method, in contrast, retains all sequenced nucleotides at each position, forming a genomic matrix. Utilizing simulated short reads from genomes with specified mutations, we contrasted our genomic matrix approach with the consensus sequence method. Our matrix methodology accurately reflected the known mutations and true compositions, demonstrating its efficacy in understanding the sample variability and their interconnections. Further tests using real data from GISAID and NCBI-SRA confirmed its reliability and robustness. As we see, the genomic matrix approach offers a more accurate representation of the viral genomic diversity, thereby providing superior insights into virus evolution and epidemiology. Future application recommendations are provided based on our observed results.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Regina Nora Fiam", + "author_inst": "Eotvos Lorand University" + }, + { + "author_name": "Istvan Csabai", + "author_inst": "Eotvos Lorand University" + }, + { + "author_name": "Norbert Solymosi", + "author_inst": "University of Veterinary Medicine Budapest" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.08.02.23293558", "rel_title": "The Lancet peer reviewers and the COVID-19 pandemic", @@ -56348,129 +57027,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.07.28.550957", - "rel_title": "Epigenetic liquid biopsies reveal elevated vascular endothelial cell turnover and erythropoiesis in asymptomatic COVID-19 patients", - "rel_date": "2023-08-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.28.550957", - "rel_abs": "The full spectrum of tissues affected by SARS-CoV-2 infection is crucial for deciphering the heterogenous clinical course of COVID-19. Here, we analyzed DNA methylation and histone modification patterns in circulating chromatin to assess cell type-specific turnover in severe and asymptomatic COVID-19 patients, in relation to clinical outcome. Patients with severe COVID-19 had a massive elevation of circulating cell-free DNA (cfDNA) levels, which originated in lung epithelial cells, cardiomyocytes, vascular endothelial cells and erythroblasts, suggesting increased cell death or turnover in these tissues. The immune response to infection was reflected by elevated B cell and monocyte/macrophage cfDNA levels, and by evidence of an interferon response in cells prior to cfDNA release. Strikingly, monocyte/macrophage cfDNA levels (but not monocyte counts), as well as lung epithelium cfDNA and vascular endothelial cfDNA, predicted clinical deterioration and duration of hospitalization. Asymptomatic patients had elevated levels of immune-derived cfDNA but did not show evidence of pulmonary or cardiac damage. Surprisingly, these patients showed elevated levels of vascular endothelial cell and erythroblast cfDNA, suggesting that sub-clinical vascular and erythrocyte turnover are universal features of COVID-19, independent of disease severity. Epigenetic liquid biopsies provide non-invasive means of monitoring COVID-19 patients, and reveal sub-clinical vascular damage and red blood cell turnover.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Roni Ben Ami", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Netanel Loyfer", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Eden Cohn", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Gavriel Fialkoff", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Israa Sharkia", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Naama Bogot", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Danit Kochan", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "George Kalak", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Amir Jarjoui", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Chen Chen-Shuali", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Hava Azulai", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Hezi Barhoum", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Nissim Arish", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Moshe M Greenberger", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "David Velleman", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Ramzi Kurd", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Eli Ben Chetrit", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Davina Bohm", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Talya Wolak", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Ahmad Quteineh", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Gordon Cann", - "author_inst": "GRAIL LLC" - }, - { - "author_name": "Benjamin Glaser", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Nir Friedman", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Tommy Kaplan", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Ruth Shemer", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Ariel Rokach", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Yuval Dor", - "author_inst": "Hebrew University of Jerusalem" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.08.01.551417", "rel_title": "Phenotyping the virulence of SARS-CoV-2 variants in hamsters by digital pathology and machine learning", @@ -56739,6 +57295,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.07.30.23293233", + "rel_title": "QJHong Model for Novel Coronavirus Disease 2019 (COVID-19) in the United States", + "rel_date": "2023-07-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.30.23293233", + "rel_abs": "We present the methodology of the QJHong model, a machine learning predictive model we built to forecast the COVID-19 daily cases, number of daily deaths, fatality rate, reproductive number, and overall trends in the United States (both national and individual states). We measure the accuracy and compare it to other predictive models. Several forecast analyses consistently demonstrate that the QJHong model outperforms other models submitted to the COVID-19 Forecast Hub with regards to forecasting national data. The Forecast Hub is utilized by the Centers for Disease Control and Prevention (CDC) as a means of disseminating official public communications pertaining to the ongoing pandemic. As such, our model has been identified as a premier performer within this context.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Aanand Mehta", + "author_inst": "BASIS Phoenix" + }, + { + "author_name": "Qi-Jun Hong", + "author_inst": "Arizona State University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.07.28.23293282", "rel_title": "An updated research focus on the employment of computer-aided drug discovery and repurposing techniques for the identification and evaluation of SARS-CoV-2 Main protease inhibitors: A protocol for a systematic review and meta-analysis", @@ -56874,7 +57453,7 @@ "rel_date": "2023-07-31", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.31.23293419", - "rel_abs": "BackgroundThe COVID-19 pandemic caused significant disruption to routine activity in primary care. Medication reviews are an important primary care activity to ensure safety and appropriateness of ongoing prescribing and a disruption could have significant negative implications for patient care.\n\nAimUsing routinely collected data, our aim was to i) describe the SNOMED CT codes used to report medication review activity ii) report the impact of COVID-19 on the volume and variation of medication reviews.\n\nDesign and settingWith the approval of NHS England, we conducted a cohort study of 20 million adult patient records in general practice, in-situ using the OpenSAFELY platform.\n\nMethodFor each month between April 2019 - March 2022, we report the percentage of patients with a medication review coded monthly and in the previous 12 months. These measures were broken down by regional, clinical and demographic subgroups and amongst those prescribed high risk medications.\n\nResultsIn April 2019, 32.3% of patients had a medication review coded in the previous 12 months. During the first COVID-19 lockdown, monthly activity substantially decreased (-21.1% April 2020), but the rate of patients with a medication review coded in the previous 12 months was not substantially impacted according to our classification (-10.5% March 2021). There was regional and ethnic variation (March 2022 - London 21.9% vs North West 33.6%; Chinese 16.8% vs British 33.0%). Following the introduction of \"structured medication reviews\", the rate of structured medication review in the last 12 months reached 2.9% by March 2022, with higher percentages in high risk groups (March 2022 - care home residents 34.1%, 90+ years 13.1%, high risk medications 10.2%). The most used SNOMED CT medication review code across the study period was Medication review done - 314530002 (59.5%).\n\nConclusionWe have reported a substantial reduction in the monthly rate of medication reviews during the pandemic but rates recovered by the end of the study period.", + "rel_abs": "BackgroundThe COVID-19 pandemic caused significant disruption to routine activity in primary care. Medication reviews are an important primary care activity to ensure safety and appropriateness of ongoing prescribing and a disruption could have significant negative implications for patient care.\n\nAimUsing routinely collected data, our aim was to i) describe the SNOMED CT codes used to report medication review activity ii) report the impact of COVID-19 on the volume and variation of medication reviews.\n\nDesign and settingWith the approval of NHS England, we conducted a cohort study of 20 million adult patient records in general practice, in-situ using the OpenSAFELY platform.\n\nMethodFor each month between April 2019 - March 2022, we report the percentage of patients with a medication review coded monthly and in the previous 12 months. These measures were broken down by regional, clinical and demographic subgroups and amongst those prescribed high risk medications.\n\nResultsIn April 2019, 32.3% of patients had a medication review coded in the previous 12 months. During the first COVID-19 lockdown, monthly activity substantially decreased (-21.1% April 2020), but the rate of patients with a medication review coded in the previous 12 months was not substantially impacted according to our classification (-10.5% March 2021). There was regional and ethnic variation (March 2022 - London 21.9% vs North West 33.6%; Chinese 16.8% vs British 33.0%). Following the introduction of \"structured medication reviews\", the rate of structured medication review in the last 12 months reached 2.9% by March 2022, with higher percentages in high risk groups (March 2022 - care home residents 34.1%, 90+ years 13.1%, high risk medications 10.2%). The most used SNOMED CT medication review code across the study period was Medication review done - 314530002 (59.5%).\n\nConclusionWe have reported a substantial reduction in the monthly rate of medication reviews during the pandemic but rates recovered by the end of the study period.\n\nWhat is already known about this subjectO_LIThe COVID-19 pandemic brought substantial disruption to the delivery of routine tasks in primary care.\nC_LIO_LIFor the first time on this scale, our study reports the impact of COVID-19 on medication review activity, including the launch of the structured medication review service in England broken down by key demographic, social, and clinical factors.\nC_LI\n\nWhat this study addsO_LIThere was a substantial reduction in the monthly rate of medication reviews during the pandemic but rates recovered quickly.\nC_LIO_LIThe percentage of patients with a medication review varies according to region and ethnicity.\nC_LIO_LIStructured medication reviews were adopted rapidly and prioritised for patients at greatest risk of harm from their medicines.\nC_LI", "rel_num_authors": 32, "rel_authors": [ { @@ -58422,41 +59001,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.07.25.550568", - "rel_title": "Experimental infection of elk (Cervus canadensis) and mule deer (Odocoileus hemionus) with SARS-CoV-2", - "rel_date": "2023-07-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.25.550568", - "rel_abs": "Elk (Cervus canadensis) and mule deer (Odocoileus hemionus) were experimentally evaluated for susceptibility to SARS-CoV-2. Elk did not shed infectious virus but produced low-level serological responses. Mule deer shed and transmitted virus in addition to mounting pronounced serological responses; they could therefore play a role in the epidemiology of SARS-CoV-2.\n\nArticle Summary LineExperimental infection of elk (Cervus canadensis) and mule deer (Odocoileus hemionus) with SARS-CoV-2 revealed that while elk are minimally susceptible to infection, mule deer become infected, shed infectious virus, and can infect naive contacts.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Stephanie M Porter", - "author_inst": "United States Department of Agriculture" - }, - { - "author_name": "Airn E Hartwig", - "author_inst": "Colorado State University" - }, - { - "author_name": "Helle Bielefeldt-Ohmann", - "author_inst": "University of Queensland" - }, - { - "author_name": "Jeff Root", - "author_inst": "USDA" - }, - { - "author_name": "Angela Bosco-Lauth", - "author_inst": "Colorado State University" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.07.25.550460", "rel_title": "Non-neutralizing SARS-CoV-2 N-terminal domain antibodies protect mice against severe disease using Fc-mediated effector functions", @@ -58661,6 +59205,161 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, + { + "rel_doi": "10.1101/2023.07.20.23292883", + "rel_title": "Impact of COVID-19 on recorded blood pressure screening and hypertension management in England: An analysis of monthly changes in Quality and Outcomes Framework indicators in OpenSAFELY", + "rel_date": "2023-07-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.20.23292883", + "rel_abs": "BackgroundCardiovascular disease management in primary care in England was disrupted during the COVID-19 pandemic.\n\nObjectiveTo describe the impact of the COVID-19 pandemic on blood pressure screening and hypertension management, based upon a national quality of care scheme (Quality and Outcomes Framework, QOF) across key demographic, regional, and clinical subgroups. To this end, we translated complex clinical quality of care schemes from text descriptions into reusable analytic code.\n\nMethodsWith the approval of NHS England, a population based cohort study was conducted on 25.2 million patient records in situ using OpenSAFELY-TPP. We included all NHS patients registered at general practices using TPP software between March 2019 and March 2023. Individuals that were eligible for blood pressure screening and with a diagnosis of hypertension were identified according to the QOF 2021/22 business rules. We examined monthly changes in recorded blood pressure screening in the preceding 5 years in patients aged [≥] 45, recorded hypertension prevalence, and the recorded percentage of patients treated to target (i.e., [≤] 140/90 mmHg for patients [≤] 79 years and [≤] 150/90 mmHg for patients [≥] 80 years) in the preceding 12 months, within demographic, regional, and clinical subgroups as well as the variation across practices.\n\nResultsThe overall percentage of patients aged [≥] 45 who had blood pressure screening recorded in the preceding 5 years decreased from 90% in March 2019 to 85% in March 2023. Recorded hypertension prevalence was relatively stable at 15% throughout the study period. The percentage of patients with a record of hypertension treated to target in the preceding 12 months reduced from a maximum of 71% in March 2020 to a minimum of 47% in February 2021 in patients aged [≤] 79 years, and from 85% in March 2020 to a minimum of 58% in February 2021 in patients aged [≥] 80 years before recovering. Blood pressure screening rates in the preceding 5 years remained stable in older age groups, patients with a record of learning disability, or care home status.\n\nConclusionsThere was substantial disruption to hypertension management QOF indicators during the pandemic, which can likely be attributed to a general reduction of blood pressure measurement including screening. OpenSAFELY can be used to continuously monitor monthly changes in national quality of care schemes to identify changes in key clinical subgroups early and support prioritisation of recovery from disrupted care caused by COVID-19.", + "rel_num_authors": 35, + "rel_authors": [ + { + "author_name": "Milan Wiedemann", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Victoria Speed", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Christine Cunningham", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Rose Higgins", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Helen J Curtis", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Colm Andrews", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Louis Fisher", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Lisa E M Hopcroft", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Christopher T Rentsch", + "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E7HT, United Kingdom" + }, + { + "author_name": "Viyaasan Mahalingasivam", + "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E7HT, United Kingdom" + }, + { + "author_name": "Laurie Tomlinson", + "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E7HT, United Kingdom" + }, + { + "author_name": "Caroline E Morton", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Miriam Samuel", + "author_inst": "Wolfson Institute of Population Health, Queen Mary University of London, E14NS, United Kingdom" + }, + { + "author_name": "Amelia C A Green", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Christopher Wood", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Andrew Brown", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Jon Massey", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Caroline Walters", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Rebecca Smith", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Peter Inglesby", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Dave Evans", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Steve Maude", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Iain Dillingham", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Alex J Walker", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Jessica Morley", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Amir Mehrkar", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Sebastian C J Bacon", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Christopher Bates", + "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, United Kingdom" + }, + { + "author_name": "Jonathan Cockburn", + "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, United Kingdom" + }, + { + "author_name": "John Parry", + "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, United Kingdom" + }, + { + "author_name": "Frank Hester", + "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, United Kingdom" + }, + { + "author_name": "Sam Harper", + "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, United Kingdom" + }, + { + "author_name": "Richard J McManus", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Ben Goldacre", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + }, + { + "author_name": "Brian MacKenna", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG, United Kingdom" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, { "rel_doi": "10.1101/2023.07.24.550423", "rel_title": "Predictive Systems Biology Modeling: Unraveling Host Metabolic Disruptions and Potential Drug Targets in SARS-CoV-2 and Its Variants", @@ -59900,33 +60599,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2023.07.19.23292810", - "rel_title": "Several Mathematical Aspects on Daily Number of COVID-19 Infection Cases in Eight Southeast Asian Places", - "rel_date": "2023-07-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.19.23292810", - "rel_abs": "The number of daily confirmed infected cases is a key parameter to determine emergency management actions to take. The mathematical characteristics of the daily infection number should be explored for working out appropriate control scheme. Several mathematical aspects on the daily number of infected cases will be discussed in 8 Southeastern Asian places using the confirmed daily infection numbers available in public websites. Phase space diagrams of plotting the daily infection rate estimated numerically against daily infection number on those tests are presented first. Modeling parameters including the Farrs Law are also discussed. A parameter is proposed to describe the extent of infection by estimating the transient daily infection number divided by the time.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "C.L. Chow", - "author_inst": "City University of Hong Kong" - }, - { - "author_name": "C.H. Cheng", - "author_inst": "City University of Hong Kong" - }, - { - "author_name": "W.K. Chow", - "author_inst": "The Hong Kong Polytechnic University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2023.07.21.23293001", "rel_title": "Unraveling COVID-19 Relationship with Anxiety Disorders and Symptoms", @@ -60091,6 +60763,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2023.07.17.23292791", + "rel_title": "Exploring COVID-19 vaccine uptake among healthcare workers in Zimbabwe: A mixed methods study", + "rel_date": "2023-07-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.17.23292791", + "rel_abs": "With COVID-19 no longer categorized as a public health emergency of international concern, vaccination strategies and priority groups for vaccination have evolved. Africa Centers for Diseases Prevention and Control proposed the 100-100-70% strategy which aims to vaccinate all healthcare workers, all vulnerable groups, and 70% of the general population. Understanding whether healthcare workers were reached during previous vaccination campaigns and what can be done to address concerns, anxieties, and other influences on vaccine uptake, will be important to optimally plan how to achieve these ambitious targets. In this mixed-methods study, between June 2021 and July 2022 a quantitative survey was conducted with healthcare workers accessing a comprehensive health check in Zimbabwe to determine whether and, if so, when they had received a COVID-19 vaccine. Healthcare workers were categorized as those who had received the vaccine early (before 30.06.2021) and those who had received it late (after 30.06.2021). In addition, 17 in-depth interviews were conducted to understand perceptions and beliefs about COVID-19 vaccines. Of the 2905 healthcare workers employed at 37 facilities who participated in the study, 2818 (97%, 95% CI [92%-102%]) reported that they had received at least one vaccine dose. Geographical location, older age, higher educational attainment and having a chronic condition was associated with receiving the vaccine early. Qualitatively, (mis)information, infection risk perception, quasi-mandatory vaccination requirements, and legitimate concerns such as safety and efficacy influenced vaccine uptake. Meeting the proposed 100-100-70 target entails continued emphasis on strong communication while engaging meaningfully with healthcare workers concerns. Mandatory vaccination may undermine trust and should not be a substitute for sustained engagement.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Tinotenda Taruvinga", + "author_inst": "The Health Research Unit Zimbabwe, Biomedical Research and Training Instritute" + }, + { + "author_name": "Rudo Samantha Chingono", + "author_inst": "Biomedical Research and Training Institute" + }, + { + "author_name": "Edson Marambire", + "author_inst": "Biomedical Research and Training Institute" + }, + { + "author_name": "Leyla Larsson", + "author_inst": "LMU University Hospital, LMU Munich, Germany" + }, + { + "author_name": "Ioana Diana Olaru", + "author_inst": "BRTI: Biomedical Research and Training Institute" + }, + { + "author_name": "Subusisiwe Sibanda", + "author_inst": "Biomedical Research and Training Institute" + }, + { + "author_name": "Farirayi Nzvere", + "author_inst": "Biomedical Research and Training Institute" + }, + { + "author_name": "Nicol Redzo", + "author_inst": "Biomedical Research and Training Institute" + }, + { + "author_name": "Chiratidzo E Ndhlovu", + "author_inst": "University of Zimbabwe" + }, + { + "author_name": "Simbarashe Rusakaniko", + "author_inst": "University of Zimbabwe College of Health Sciences Library: University of Zimbabwe Faculty of Medicine and Health Sciences" + }, + { + "author_name": "Hilda Mujuru", + "author_inst": "University of Zimbabwe" + }, + { + "author_name": "Edwin Sibanda", + "author_inst": "Bulawayo City Council" + }, + { + "author_name": "Prosper Chonzi", + "author_inst": "City of Harare" + }, + { + "author_name": "Maphios Siamuchembu", + "author_inst": "Ministry of Health and Child Welfare: Zimbabwe Ministry of Health and Child Care" + }, + { + "author_name": "Rudo Chikodzore", + "author_inst": "Ministry of Health and Child Welfare: Zimbabwe Ministry of Health and Child Care" + }, + { + "author_name": "Agnes Mahomva", + "author_inst": "Government of Zimbabwe" + }, + { + "author_name": "Rashida A Ferrand", + "author_inst": "Biomedical Research and Training Institute" + }, + { + "author_name": "Justin Dixon", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Katharina Kranzer", + "author_inst": "Biomedical Research and Training Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2023.07.18.23292858", "rel_title": "Risk of SARS-CoV-2 infection and hospitalization in individuals with natural, vaccine-induced and hybrid immunity: a retrospective population-based cohort study from Estonia", @@ -61426,25 +62189,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.07.17.23292426", - "rel_title": "Intranasal lavage with hypochlorous acid safely reduces the symptoms in the ambulatory patient with COVID-19.", - "rel_date": "2023-07-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.17.23292426", - "rel_abs": "OBJECTIVEThis study was designed to investigate intranasal lavage with a hypochlorous acid solution in the reduction of symptoms in the ambulatory COVID-19 patient.\n\nSTUDY DESIGNStudy approval granted by the Institutional Review Board of Reading Hospital (IRB 036-20), with informed consent obtained from all adult participants(age>18 years).\n\nSETTINGAll enrollees, taken from the same ambulatory testing facility, received nasopharyngeal swabs for COVID-19 testing by reverse transcription polymerase chain (RT-PCR) or the COVID-19 antigen specific test (Binax NOW, Abbott Lab)\n\nMETHODSConvenience sampling methodology was utilized. Each enrollee was provided with the study devices which included a Nasaflo Neti Pot (NeilMed Pharmaceutical, Inc.), and the hypochlorous acid solution (Vashe Wound Solution, Urgo Medical North America, LLC). Participants were instructed to irrigate each nostril with 120 cc (four ounces) of the solution for ten consecutive days, and record the presence or absence of symptoms in a scripted diary log.\n\nRESULTSThe study included 88 patients of which 74 (84.1%) completed the ten days of nasal lavage. All data analysis was conducted using SPSS version 25.0.\n\nChi square test of association found no significant difference related to gender, age group race, ethnicity, residence, or living arrangements (all p-values > 0.05). There were no statistical differences in any of the co-morbid conditions. Mild adverse reactions included burning, epistaxis, and oral metallic taste. No enrollees required mechanical ventilation. There were no deaths.\n\nCONCLUSIONThis study suggests the feasibility and safety of using intranasal lavage with a hypochlorous acid solution in relieving symptoms in the ambulatory Covid-19 patient.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Monique Lisa Abner", - "author_inst": "Tower Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.07.14.548971", "rel_title": "Deep spatial proteomic exploration of severe COVID-19-related pulmonary injury in post-mortem specimens", @@ -61641,6 +62385,97 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2023.07.15.549135", + "rel_title": "Pre-existing interferon gamma conditions the lung to mediate early control of SARS-CoV-2", + "rel_date": "2023-07-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.15.549135", + "rel_abs": "Interferons (IFNs) are critical for anti-viral host defence. Type-1 and type-3 IFNs are typically associated with early control of viral replication and promotion of inflammatory immune responses; however, less is known about the role of IFN{gamma} in anti-viral immunity, particularly in the context of SARS-CoV-2. We have previously observed that lung infection with attenuated bacteria Mycobacterium bovis BCG achieved though intravenous (iv) administration provides strong protection against SARS-CoV-2 (SCV2) infection and disease in two mouse models. Assessment of the pulmonary cytokine milieu revealed that iv BCG induces a robust IFN{gamma} response and low levels of IFN{beta}. Here we examined the role of ongoing IFN{gamma} responses due to pre-established bacterial infection on SCV2 disease outcomes in two murine models. We report that IFN{gamma} is required for iv BCG induced reduction in pulmonary viral loads and that this outcome is dependent on IFN{gamma} receptor expression by non-hematopoietic cells. Further analysis revealed that BCG infection promotes the upregulation of interferon-stimulated genes (ISGs) with reported anti-viral activity by pneumocytes and bronchial epithelial cells in an IFN{gamma}-dependent manner, suggesting a possible mechanism for the observed protection. Finally, we confirmed the importance of IFN{gamma} in these anti-viral effects by demonstrating that the recombinant cytokine itself provides strong protection against SCV2 challenge when administered intranasally. Together, our data show that a pre-established IFN{gamma} response within the lung is protective against SCV2 infection, suggesting that concurrent or recent infections that drive IFN{gamma} may limit the pathogenesis of SCV2 and supporting possible prophylactic uses of IFN{gamma} in COVID-19 management.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Kerry L Hilligan", + "author_inst": "Malaghan Institute of Medical Research" + }, + { + "author_name": "Sivaranjani Namasivayam", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Chad S Clancy", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Paul J Baker", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Samuel I Old", + "author_inst": "Malaghan Institute of Medical Research" + }, + { + "author_name": "Victoria Peluf", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Eduardo P Amaral", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Sandra D Oland", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Danielle O'Mard", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Julie Laux", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Melanie Cohen", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Nicole L Garza", + "author_inst": "NIAID: National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Bernard Lafont", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Reed F Johnson", + "author_inst": "NIH, NIAID, DIR, LIR" + }, + { + "author_name": "Carl G Feng", + "author_inst": "The University of Sydney School of Medicine" + }, + { + "author_name": "Dragana Jankovic", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Olivier Lamiable", + "author_inst": "Malaghan Institute of Medical Research" + }, + { + "author_name": "Katrin D Mayer-Barber", + "author_inst": "NIH" + }, + { + "author_name": "Alan Sher", + "author_inst": "National Institute of Allergy and Infectious Diseases" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.07.14.23292660", "rel_title": "Dynamics of T-cell responses following COVID-19 mRNA vaccination and breakthrough infection in older adults", @@ -63020,33 +63855,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2023.07.12.548725", - "rel_title": "Endocytosis Inhibitors Block SARS-CoV-2 Pseudoparticle Infection of Mink Lung Epithelium", - "rel_date": "2023-07-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.12.548725", - "rel_abs": "Both spill over and spill back of SARS-CoV-2 virus have been reported on mink farms in Europe and the United States. Zoonosis is a public health concern as dangerous mutated forms of the virus could be introduced into the human population through spillback. The purpose of our study was to determine the SARS-CoV-2 entry mechanism using mink lung epithelial cell line (Mv1Lu) and to block entry with drug inhibitors. Mv1Lu cells were susceptible to SARS-CoV-2 viral pseudoparticle infection, validating them as a suitable disease model for COVID-19. Inhibitors of TMPRSS2 and of endocytosis, two pathways of viral entry, were tested to identify those that blocked infection. Dyngo4a, a small molecule endocytosis inhibitor, significantly reduced infection, while TMPRSS2 inhibitors had minimal impact, supporting the conclusion that the entry of the SARS-CoV-2 virus into Mv1Lu cells occurs primarily through endocytosis. The small molecule inhibitors that were effective in this study could potentially be used therapeutically to prevent SARS-CoV-2 infection in mink populations. This study will facilitate the development of therapeutics to prevent zoonotic transmission of SARS-CoV-2 variants to other animals, including humans.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ann Song", - "author_inst": "University of California, Riverside" - }, - { - "author_name": "Rattapol Phandthong", - "author_inst": "University of California Riverside" - }, - { - "author_name": "Prue Talbot", - "author_inst": "University of California, Riverside" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2023.07.12.23292570", "rel_title": "COVID-19 Case and Mortality Surveillance using Daily SARS-CoV-2 in Wastewater Samples adjusting for Meteorological Conditions and Sample pH", @@ -63199,6 +64007,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.07.10.23292473", + "rel_title": "Risk-based prediction for optimal timing of booster vaccination for COVID-19 to prevent severe disease", + "rel_date": "2023-07-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.10.23292473", + "rel_abs": "While waning protection from vaccination and natural infection against SARS-CoV-2 infection is well-documented, recent analyses have also found waning of protection against severe COVID-19. This highlights a broader need to understand how different frequency of COVID-19 booster vaccines may mitigate the risk of severe COVID-19, while accounting for waning of protection and differential risk by age and immune status. Here we show that more frequent COVID-19 booster vaccination (every 6-12 months) in older age groups and the immunocompromised population would effectively reduce the burden of severe COVID-19, while frequent boosters in the younger population may only provide modest benefit against severe disease. Analyzing United States COVID-19 surveillance and seroprevalence data in a microsimulation model, we estimated that in persons 75+ years, annual and semiannual boosters would reduce annual absolute risk of severe COVID-19 by 199 (uncertainty interval: 188-229) and 368 (344-413) cases per 100,000 persons, respectively, compared to a one-time booster dose. In contrast, for persons 18-49 years, the model estimated that annual and semiannual boosters would reduce annual absolute risk of severe COVID-19 by 14 (11-19) and 26 (21-35) cases per 100,000 persons, respectively, compared to a one-time booster dose. Persons with prior infection had lower benefit of more frequent boosting, and immunocompromised persons had larger benefit. Scenarios with emerging variants with immune evasion increased the benefit of more frequent variant-targeted boosters. This study underscores the benefit of considering key risk factors to inform frequency of COVID-19 booster vaccines in public health guidance, and ensuring at least annual boosters in high-risk populations.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Hailey J. Park", + "author_inst": "Stanford University" + }, + { + "author_name": "Gregg S. Gonsalves", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Sophia T. Tan", + "author_inst": "Stanford University" + }, + { + "author_name": "J. Daniel Kelly", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "George W. Rutherford", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Robert M. Wachter", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Robert Schechter", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "A David Paltiel", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Nathan C. Lo", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.07.06.23292300", "rel_title": "The ratio between SARS-CoV-2 RNA viral load and culturable viral titer differs depending on stage of infection", @@ -64746,45 +65605,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.07.06.23292296", - "rel_title": "Long-term symptom profiles after COVID-19 vs other acute respiratory infections: a population-based observational study (COVIDENCE UK)", - "rel_date": "2023-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.06.23292296", - "rel_abs": "BackgroundLong COVID is a well recognised, if heterogeneous, entity. Acute respiratory infections (ARIs) due to other pathogens may cause long-term symptoms, but few studies compare post-acute sequelae between SARS-CoV-2 and other ARIs. We aimed to compare symptom profiles between people with previous SARS-CoV-2 infection, people with previous non-COVID-19 ARIs, and contemporaneous controls, and to identify clusters of long-term symptoms.\n\nMethodsCOVIDENCE UK is a prospective, population-based UK study of ARIs in adults. We analysed data on 16 potential long COVID symptoms and health-related quality of life (HRQoL), reported in January, 2021, by participants unvaccinated against SARS-CoV-2. We classified participants as having previous SARS-CoV-2 infection or previous non-COVID-19 ARI ([≥]4 weeks prior) or no reported ARI. We compared symptoms by infection status using logistic and fractional regression, and identified symptom clusters using latent class analysis (LCA).\n\nFindingsWe included 10,203 participants (1343 [13.2%] with SARS-CoV-2 infection, 472 [4.6%] with non-COVID-19 ARI). Both types of infection were associated with increased prevalence/severity of most symptoms and decreased HRQoL compared with no infection. Participants with SARS-CoV-2 infection had increased odds of taste/smell problems and hair loss compared with participants with non-COVID-19 ARIs. Separate LCA models identified three symptom severity groups for each infection type. In the most severe groups (including 23% of participants with SARS-CoV-2, and 21% with non-COVID-19 ARI), SARS-CoV-2 infection presented with a higher probability of memory problems, difficulty concentrating, hair loss, and taste/smell problems than non-COVID-19 ARI.\n\nInterpretationBoth SARS-CoV-2 and non-COVID-19 ARIs are associated with a wide range of long-term symptoms. Research on post-acute sequelae of ARIs should extend from SARS-CoV-2 to include other pathogens.\n\nFundingBarts Charity.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed and Google Scholar for studies on post-acute sequelae of COVID-19 and other acute respiratory infections (ARIs), published up to May 24, 2023. We used search terms relating to COVID-19 and other ARIs (\"COVID-19\", \"SARS\", \"severe acute respiratory syndrome\", \"Middle East respiratory\", \"MERS\", \"respiratory infection\", \"influenza\", \"flu\") and post-acute symptoms (\"long COVID\", \"post-acute\", \"PACS\", \"sequelae\", \"long-term\"). Previous studies have shown a wide range of post-acute sequelae for COVID-19, affecting people with all severities of the acute disease. The few studies that have compared long-term symptoms between people with COVID-19 and non-COVID-19 ARIs have generally found a higher symptom burden among people with COVID-19; however, these studies have been restricted to hospitalised patients or electronic health record data, and thus do not capture the full picture in the community. Research into long COVID phenotypes has been inconclusive, with some analyses classifying people with long COVID according to the types of symptoms experienced, and others classifying them according to the overall severity of their symptoms.\n\nAdded value of this studyIn this population-based study of ARIs in the community, we observed high symptom burden among people with previous SARS-CoV-2 infection when compared with controls, highlighting the extensive reach of long COVID. Our finding of a similar symptom burden among people with non-COVID-19 ARIs suggests that post-acute sequelae of other ARIs may be going unrecognised, particularly given that the vast majority did not experience a severe acute infection. Latent class analyses of symptoms identified groupings based on overall symptom severity, rather than symptom types, for both SARS-CoV-2 infections and non-COVID-19 ARIs, suggesting that overall symptom burden may best characterise the experience of people with post-acute sequelae. Notably, among participants with the most severe symptoms, only half of those with previous SARS-CoV-2 infection attributed their symptoms to long COVID, suggesting they either did not believe the infection was the cause, or they did not consider their symptoms severe enough to qualify as long COVID.\n\nImplications of all the available evidenceThe long-term symptoms experienced by some people with previous ARIs, including SARS-CoV-2, highlights the need for improved understanding, diagnosis, and treatment of post-acute infection syndromes. As much-needed research into long COVID continues, we must take the opportunity to investigate and consider the post-acute burden of ARIs due to other pathogens.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Giulia Vivaldi", - "author_inst": "Blizard Institute and Wolfson Institute of Population Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Paul E Pfeffer", - "author_inst": "Barts Health NHS Trust, London, UK; Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Mohammad Talaei", - "author_inst": "Wolfson Institute of Population Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Jayson Basera", - "author_inst": "Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Seif O Shaheen", - "author_inst": "Wolfson Institute of Population Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Adrian R Martineau", - "author_inst": "Blizard Institute, Barts and The London School of Medicine and Dentistry; and Asthma UK Centre for Applied Research; Queen Mary University of London, London, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2023.07.05.23292278", "rel_title": "Intracardiac Thrombus in COVID-19 Inpatients: A Nationwide Study of Incidence, Predictors and Outcomes", @@ -65045,6 +65865,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.07.03.23291596", + "rel_title": "Risk of COVID-19 death in adults who received booster COVID-19 vaccinations: national retrospective cohort study on 14.6 million people in England", + "rel_date": "2023-07-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.03.23291596", + "rel_abs": "ImportanceThe emergence of the COVID-19 vaccination has been critical in changing the course of the COVID-19 pandemic, with estimates suggesting vaccinations have prevented millions of deaths worldwide. To ensure protection remains high in vulnerable groups booster vaccinations in the UK have been targeted based on age and clinical vulnerabilities.\n\nObjectiveWe sought to identify adults who had received a booster vaccination as part of the autumn 2022 campaign in England yet remained at increased risk of postbooster COVID-19 death and compared to non-COVID-19 risk.\n\nDesign, Setting, and ParticipantsWe undertook a national retrospective cohort study using data from the 2021 Census linked to electronic health records. We fitted cause-specific Cox models to examine the association between health conditions and the risk of COVID-19 death and all-other-cause death for adults aged 50-100-years in England vaccinated with a booster in autumn 2022. Our total population was 14,644,570 people; there were 6,800 COVID-19 deaths and 150,075 non-COVID-19 deaths.\n\nExposureSociodemographic characteristics (sex, age, ethnic group, region), disability, body mass index, and diagnosis of a health condition defined from QCovid2.\n\nMain Outcomes and MeasuresThe primary outcome of this study was COVID-19 death. The secondary outcome was all-cause non-COVID-19 deaths.\n\nResultsHaving learning disabilities or Down Syndrome (hazard ratio=5.07;95% confidence interval=3.69-6.98), pulmonary hypertension or fibrosis (2.88;2.43-3.40), motor neuron disease, multiple sclerosis, myasthenia or Huntingtons disease (2.94, 1.82-4.74), cancer of blood and bone marrow (3.11;2.72-3.56), Parkinsons disease (2.74;2.34-3.20), lung or oral cancer (2.57;2.04 to 3.24), dementia (2.64;2.46 to 2.83) or liver cirrhosis (2.65;1.95 to 3.59) was associated with an increased risk of COVID-19 death. Individuals with cancer of the blood or bone marrow, chronic kidney disease, cystic fibrosis, pulmonary hypotension or fibrosis, or rheumatoid arthritis or systemic lupus erythematosus had a significantly higher risk of COVID-19 death relative to other causes of death compared with individuals who did not have diagnoses.\n\nConclusions, and RelevanceWe identify groups who are at increased risk of postbooster COVID-19 death relative to non-COVID-19 deaths. Policy makers should continue to priorities vulnerable groups for subsequent COVID-19 booster doses to minimise the risk of COVID-19 death.\n\nFundingNational Core Studies-Immunity, National Core Studies-Data and Connectivity, Health Data Research UK, and the Medical Research Council.\n\nKey PointsQuestion: What health conditions are associated with increased risk of postbooster COVID-19 death in adults who received a COVID-19 vaccination in autumn 2022?\n\nFindings: Certain groups were found to be at overall higher risk of postbooster COVID-19 death (e.g., learning disability or Down Syndrome) and certain groups were found to have significantly higher relative risk of COVID-19 death compared to other non-COVID-19 causes (e.g., cancer of the blood or bone marrow).\n\nMeaning: This work has implications for prioritisation of vaccination booster doses worldwide. We highlight which groups with health conditions are at elevated risk of postbooster COVID-19 death.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Isobel L Ward", + "author_inst": "Office for National Statistics, Newport, UK" + }, + { + "author_name": "Chris Robertson", + "author_inst": "Department of Mathematics and Statistics, Strathclyde University, Glasgow, Scotland and Public Health Scotland, Glasgow, Scotland" + }, + { + "author_name": "Utkarsh Agrawal", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, UK" + }, + { + "author_name": "Lynsey Patterson", + "author_inst": "Centre for Public Health, Queen's University Belfast, Belfast, UK and Public Health Agency, Belfast, UK" + }, + { + "author_name": "Declan T Bradley", + "author_inst": "Centre for Public Health, Queen's University Belfast, Belfast, UK and Public Health Agency, Belfast, UK" + }, + { + "author_name": "Ting Shi", + "author_inst": "Usher Institute, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Simon de Lusignan", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, UK" + }, + { + "author_name": "Richard Hobbs", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, UK" + }, + { + "author_name": "Aziz Sheikh", + "author_inst": "Usher Institute, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Vahe Nafilyan", + "author_inst": "Office for National Statistics, Newport, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.07.05.547781", "rel_title": "The receptor binding domain of SARS-CoV-2 spike protein fused with the type IIb E. coli heat-labile enterotoxin A subunit as an intranasal booster after mRNA vaccination", @@ -66880,193 +67755,6 @@ "type": "new results", "category": "developmental biology" }, - { - "rel_doi": "10.1101/2023.06.29.546792", - "rel_title": "Human Immune Cell Epigenomic Signatures in Response to Infectious Diseases and Chemical Exposures", - "rel_date": "2023-06-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.29.546792", - "rel_abs": "Variations in DNA methylation patterns in human tissues have been linked to various environmental exposures and infections. Here, we identified the DNA methylation signatures associated with multiple exposures in nine major immune cell types derived from peripheral blood mononuclear cells (PBMCs) at single-cell resolution. We performed methylome sequencing on 111,180 immune cells obtained from 112 individuals who were exposed to different viruses, bacteria, or chemicals. Our analysis revealed 790,662 differentially methylated regions (DMRs) associated with these exposures, which are mostly individual CpG sites. Additionally, we integrated methylation and ATAC-seq data from same samples and found strong correlations between the two modalities. However, the epigenomic remodeling in these two modalities are complementary. Finally, we identified the minimum set of DMRs that can predict exposures. Overall, our study provides the first comprehensive dataset of single immune cell methylation profiles, along with unique methylation biomarkers for various biological and chemical exposures.", - "rel_num_authors": 43, - "rel_authors": [ - { - "author_name": "Wenliang Wang", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Manoj Hariharan", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Anna Bartlett", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Cesar Barragan", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Rosa Castanon", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Vince Rothenberg", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Haili Song", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Joseph Nery", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Andrew Aldridge", - "author_inst": "Duke University School of Medicine, Bryan Research Building, 311 Research Drive, Durham, NC 27710, USA" - }, - { - "author_name": "Jordan Altshul", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Mia Kenworthy", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Wubin Ding", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Hanqing Liu", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Wei Tian", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Jingtian Zhou", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Huaming Chen", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Bei Wei", - "author_inst": "Department of Genetics, Stanford University, Stanford, CA 94305, USA" - }, - { - "author_name": "Irem B Gunduz", - "author_inst": "Integrative Cellular Biology & Bioinformatics Lab, Saarland University, 66123 Saarbrucken, Germany" - }, - { - "author_name": "Todd Norell", - "author_inst": "Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, 40 S Alcaniz St, Pensacola, FL 32502, USA" - }, - { - "author_name": "Timothy J Broderick", - "author_inst": "Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, 40 S Alcaniz St, Pensacola, FL 32502, USA" - }, - { - "author_name": "Micah McClain", - "author_inst": "Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA., Durham Veteran" - }, - { - "author_name": "Lisa Satterwhite", - "author_inst": "Department of Civil and Environmental Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA" - }, - { - "author_name": "Thomas Burke", - "author_inst": "Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA" - }, - { - "author_name": "Elizabeth Petzold", - "author_inst": "Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA" - }, - { - "author_name": "Xiling Shen", - "author_inst": "Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90024, USA" - }, - { - "author_name": "Chris Woods", - "author_inst": "Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA., Durham Veteran" - }, - { - "author_name": "Vance G Fowler", - "author_inst": "Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA., Duke Clinical " - }, - { - "author_name": "Felicia Ruffin", - "author_inst": "Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA" - }, - { - "author_name": "Parinya Panuwet", - "author_inst": "Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA" - }, - { - "author_name": "Dana B Barr", - "author_inst": "Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA" - }, - { - "author_name": "Jennifer L Beare", - "author_inst": "Battelle Memorial Institute, 505 King Ave Columbus OH 43201, USA" - }, - { - "author_name": "Anthony K Smith", - "author_inst": "Battelle Memorial Institute, 505 King Ave Columbus OH 43201, USA" - }, - { - "author_name": "Rachel R Spurbeck", - "author_inst": "Battelle Memorial Institute, 505 King Ave Columbus OH 43201, USA" - }, - { - "author_name": "Sindhu Vangeti", - "author_inst": "Department of Neurology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA" - }, - { - "author_name": "Irene Ramos", - "author_inst": "Department of Neurology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA" - }, - { - "author_name": "German Nudelman", - "author_inst": "Department of Neurology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA" - }, - { - "author_name": "Stuart C Sealfon", - "author_inst": "Department of Neurology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA" - }, - { - "author_name": "Flora Castellino", - "author_inst": "U.S. Department of Health and Human Services, Administration for Strategic Preparedness and Response, Biomedical Advanced Research and Development Authority, Wa" - }, - { - "author_name": "Anna Maria Walley", - "author_inst": "Vaccitech plc, Unit 6-10, Zeus Building, Rutherford Avenue, Harwell OX11 0DF, United Kingdom" - }, - { - "author_name": "Tom Evans", - "author_inst": "Vaccitech plc, Unit 6-10, Zeus Building, Rutherford Avenue, Harwell OX11 0DF, United Kingdom" - }, - { - "author_name": "Fabian Muller", - "author_inst": "Integrative Cellular Biology & Bioinformatics Lab, Saarland University, 66123 Saarbrucken, Germany" - }, - { - "author_name": "William J Greenleaf", - "author_inst": "Department of Genetics, Stanford University, Stanford, CA 94305, USA" - }, - { - "author_name": "Joseph R Ecker", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA., Howard Hughes Medical Institute, The " - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2023.06.29.546885", "rel_title": "Interaction between host G3BP and viral nucleocapsid protein regulates SARS-CoV-2 replication", @@ -67375,6 +68063,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2023.06.27.546805", + "rel_title": "Identification of cross-reacting IgG hotspots to prevent immune evasion of SARS-CoV-2 variants", + "rel_date": "2023-06-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.27.546805", + "rel_abs": "The major factor that shapes the global perspective for increase or diminution of successive pandemic waves of COVID-19 is the immunological protection. The SARS-CoV-2 virus constantly develops new variants, and capability of immune evasion is among the major factors that promote variant spreading in the human population. After two years of the pandemic and virus evolution, it is almost impossible to explain effects of all possible combinations different viral strains, a few types of vaccinations or new variants infecting an individual patient. Instead of variant-to-variant comparisons, identification of key protein regions linked to immune evasion could be efficient.\n\nHere we report an approach for experimental identification of SARS-CoV-2 protein regions that (i) have characteristics of cross-reacting IgG hot-spots, and (ii) are highly immunogenic. Cross-reacting IgG hot spots are regions of protein frequently recognized in many variants by cross-reacting antibodies. Immunogenic regions efficiently induce specific IgG production in SARS-CoV-2 infected patients. We determined four regions that demonstrate both significant immunogenicity and the activity of a cross-reacting IgG hot-spot in protein S, and two such regions in protein N. Their distribution within the proteins suggests that they may be useful in vaccine design and in serological diagnostics of COVID-19.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Marek Harhala", + "author_inst": "nstitute of Immunology and Experimental Therapy, Polish Academy of Sciences" + }, + { + "author_name": "Katarzyna Gembara", + "author_inst": "Regional Specialist Hospital in Wroc\u0142aw, Research and Development Center" + }, + { + "author_name": "Krzysztof Baniecki", + "author_inst": "Healthcare Centre in Boles\u0142awiec, Jeleniog\u00f3rska 4, Boles\u0142awiec, Poland" + }, + { + "author_name": "Aleksandra Pikies", + "author_inst": "Healthcare Centre in Boles\u0142awiec, Jeleniog\u00f3rska 4, Boles\u0142awiec, Poland" + }, + { + "author_name": "Artur Nahorecki", + "author_inst": "Healthcare Centre in Boles\u0142awiec, Jeleniog\u00f3rska 4, Boles\u0142awiec, Poland" + }, + { + "author_name": "Natalia J\u0119druchniewicz", + "author_inst": "Regional Specialist Hospital in Wroc\u0142aw, Research and Development Center, Kamie?skiego 73a, Wroc\u0142aw, Poland" + }, + { + "author_name": "Zuzanna Ka\u017amierczak", + "author_inst": "Institute of Immunology and Experimental Therapy, Polish Academy of Sciences" + }, + { + "author_name": "Izabela Rybicka", + "author_inst": "Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences" + }, + { + "author_name": "Tomasz Klimek", + "author_inst": "Regional Specialist Hospital in Wroc\u0142aw, Research and Development Center, Kamie\u0142skiego 73a, Wroc\u0142aw, Poland" + }, + { + "author_name": "Wojciech Witkiewicz", + "author_inst": "Regional Specialist Hospital in Wroc\u0142aw, Research and Development Center" + }, + { + "author_name": "Kamil Barczyk", + "author_inst": "Healthcare Centre in Boles\u0142awiec, Jeleniog\u00f3rska 4, Boles\u0142awiec, Poland" + }, + { + "author_name": "Marlena K\u0142ak", + "author_inst": "Regional Specialist Hospital in Wroclaw" + }, + { + "author_name": "Krystyna D\u0105browska", + "author_inst": "Institute of Immunology and Experimental Therapy, Polish Academy of Sciences" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.06.22.23291740", "rel_title": "Demography, hygiene and previous disease prevalence as plausible risk factors associated with Covid-19 deaths across Indian states", @@ -68970,85 +69725,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.06.28.23291986", - "rel_title": "The Role of VSL#3 in the Treatment of Fatigue and Other Symptoms in Long Covid-19 Syndrome: a Randomized, Double-blind, Placebo-controlled Pilot Study (DELong#3)", - "rel_date": "2023-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.28.23291986", - "rel_abs": "Long COVID, also known as Post-acute COVID-19 Syndrome (PACS), is a chronic condition affecting individuals who have recovered from acute COVID-19. It is currently estimated that around 65 million people worldwide suffer from Long COVID. It is characterized by a range of symptoms, including fatigue, exertion intolerance, neurocognitive and sensory impairment, sleep disturbance, myalgia/arthralgia, and dysautonomia. Among them fatigue has emerged as a burdensome and pervasive issue, significantly impacting the quality of life and daily functioning of Long COVID patients. Alterations in the composition of the intestinal microbiota has been reported in COVID-19 patients. Dysbiosis persists even after several months of recovery from acute SARS-CoV-2 infection.\n\nBased on this evidence, we carried out a phase 3, randomized, double-blind, placebo-controlled trial aimed at evaluating the efficacy of VSL#3(R), a consortium of probiotic bacterial strains, in reducing fatigue and improving various aspects of patients well-being in patients with Long COVID syndrome.\n\nHighlightsO_LIPatients suffering from Long-COVID manifest a variety of persistent symptoms impacting daily functioning;\nC_LIO_LIFatigue emerged as a burdensome and pervasive issue, significantly impacting the quality of life;\nC_LIO_LIVSL#3(R) treatment significantly reduced the Chalder Fatigue Scale scores as compared to placebo\nC_LIO_LIChalder Fatigue Scale scores remained significantly reduced in the treatment group 4 weeks post intervention.\nC_LI", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Flavio Caprioli", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy; Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca Gra" - }, - { - "author_name": "Beatrice Marinoni", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy" - }, - { - "author_name": "Alessandro Rimondi", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy" - }, - { - "author_name": "Federico Bottaro", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy" - }, - { - "author_name": "Clorinda Ciafardini", - "author_inst": "Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Chiara Amoroso", - "author_inst": "Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Martina Muia", - "author_inst": "Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Bruna Caridi", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy" - }, - { - "author_name": "Daniele Noviello", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy" - }, - { - "author_name": "Alessandra Bandera", - "author_inst": "Universita degli Studi di Milano, Milan, Italy; Infectious Disease Unit, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Andrea Gori", - "author_inst": "Universita degli Studi di Milano, Milan, Italy; Infectious Disease Unit, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Marco Mantero", - "author_inst": "Universita degli Studi di Milano, Milan, Italy; Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca Granda Ospe" - }, - { - "author_name": "Francesco Blasi", - "author_inst": "Universita degli Studi di Milano, Milan, Italy; Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca Granda Ospe" - }, - { - "author_name": "Roberta Ferrucci", - "author_inst": "ASST Santi Paolo e Carlo, San Paolo University Hospital, 20142 Milan, Italy;6Aldo Ravelli Center for Neurotechnology and Experimental Brain Therapeutics, Depart" - }, - { - "author_name": "Federica Facciotti", - "author_inst": "Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy" - }, - { - "author_name": "Maurizio Vecchi", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy; Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca Gran" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2023.06.27.23291947", "rel_title": "Examining the inter-relationships between social isolation and loneliness and their correlates among older British adults before and during the COVID-19 lockdown: evidence from four British longitudinal studies", @@ -69265,6 +69941,41 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2023.06.27.546719", + "rel_title": "DENetwork: Unveiling Regulatory and Signaling Networks Behind Differentially-Expressed Genes", + "rel_date": "2023-06-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.27.546719", + "rel_abs": "Differential gene expression analysis from RNA-sequencing (RNA-seq) data offers crucial insights into biological differences between sample groups. However, the conventional focus on differentially-expressed (DE) genes often omits non-DE regulators, which are an integral part of such differences. Moreover, DE genes frequently serve as passive indicators of transcriptomic variations rather than active influencers, limiting their utility as intervention targets. To address these shortcomings, we have developed DENetwork. This innovative approach deciphers the intricate regulatory and signaling networks driving transcriptomic variations between conditions with distinct phenotypes. Unique in its integration of both DE and critical non-DE genes in a graphical model, DENetwork enhances the capabilities of traditional differential gene analysis tools, such as DESeq2. Our application of DENetwork to an array of simulated and real datasets showcases its potential to encapsulate biological differences, as demonstrated by the relevance and statistical significance of enriched gene functional terms. DENetwork offers a robust platform for systematically characterizing the biological mechanisms that underpin phenotypic differences, thereby augmenting our understanding of biological variations and facilitating the formulation of effective intervention strategies.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ting-Yi Su", + "author_inst": "McGill University" + }, + { + "author_name": "Quazi S. Islam", + "author_inst": "McGill University" + }, + { + "author_name": "Steven K. Huang", + "author_inst": "University of Michigan" + }, + { + "author_name": "Carolyn J. Baglole", + "author_inst": "McGill University" + }, + { + "author_name": "Jun Ding", + "author_inst": "McGill University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.06.22.23291669", "rel_title": "Quantitative analysis of chest computed tomography of COVID-19 pneumonia using a software widely used in Japan", @@ -70380,121 +71091,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.06.16.23291450", - "rel_title": "High rates of SARS-CoV-2 infection in pregnant Ugandan women and association with stunting in infancy", - "rel_date": "2023-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.16.23291450", - "rel_abs": "BackgroundSARS-CoV-2 has been well studied in resource-rich areas but many questions remain about effects of infection in African populations, particularly in vulnerable groups such as pregnant women.\n\nMethodsWe describe SARS-CoV-2 immunoglobulin (Ig) G and IgM antibody responses and clinical outcomes in mother-infant dyads enrolled in malaria chemoprevention trials in Uganda.\n\nResultsFrom December 2020 to February 2022, among 400 unvaccinated pregnant women, serologic assessments revealed that 128 (32%) were seronegative for anti-SARS-CoV-2 IgG and IgM at enrollment and delivery, 80 (20%) were infected either prior to or early in pregnancy, and 192 (48%) were infected or re-infected with SARS-CoV-2 during pregnancy. We observed preferential binding of plasma IgG to Wuhan-Hu-1-like antigens in individuals seroconverting up to early 2021, and to Delta variant antigens in a subset of individuals in mid-2021. Breadth of IgG binding to all variants improved over time. No participants experienced severe respiratory illness during the study. SARS-CoV-2 infection in early pregnancy was associated with lower median length-for-age Z-score at age 3 months compared with no infection or late pregnancy infection (- 1.54 versus -0.37 and -0.51, p=0.009).\n\nConclusionPregnant Ugandan women experienced high levels of SARS-CoV-2 infection without severe respiratory illness. Variant-specific serology testing demonstrated evidence of antibody affinity maturation at the population level. Early gestational SARS-CoV-2 infection was associated with shorter stature in early infancy.\n\nFundingThis work was supported by: Stanford MCHRI/Stephen Bechtel Endowed Fellowship in Pediatric Translational Medicine (KJ), Swiss National Science Foundation PRIMA grant PR00P3_208580 (KR), the Bill and Melinda Gates Foundation, and NIAID (T32-AI052073, U01- AI141308, U01-AI155325).", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Karen Blake Jacobson", - "author_inst": "Department of Medicine, Stanford School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Katharina R\u00f6ltgen", - "author_inst": "Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland" - }, - { - "author_name": "Brandon Lam", - "author_inst": "Department of Pathology, Stanford School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Patience Nayebare", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Abel Kakuru", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Jimmy Kizza", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Miriam Aguti", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Felistas Nankya", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Jessica Briggs", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Saki Takahashi", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Bryan Greenhouse", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Isabel Rodriguez-Barraquer", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Kattria van der Ploeg", - "author_inst": "Department of Medicine, Stanford School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Jacob N. Wohlstadter", - "author_inst": "Meso Scale Diagnostics LLC, Rockville, MD, USA" - }, - { - "author_name": "George B. Sigal", - "author_inst": "Meso Scale Diagnostics LLC, Rockville, MD, USA" - }, - { - "author_name": "Michelle E. Roh", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Joaniter I. Nankabirwa", - "author_inst": "Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda" - }, - { - "author_name": "Gloria Cuu", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Stephanie L. Gaw", - "author_inst": "Department of Obstetrics, Gynecology & Reproductive Sciences, Division of Maternal-Fetal Medicine, UCSF, San Francisco, CA, USA" - }, - { - "author_name": "Philip J. Rosenthal", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Moses R. Kamya", - "author_inst": "Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda" - }, - { - "author_name": "Isaac Ssewanyana", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Grant Dorsey", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Scott D. Boyd", - "author_inst": "Department of Pathology, Stanford School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Prasanna Jagannathan", - "author_inst": "Department of Medicine, Stanford School of Medicine, Stanford, CA, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.06.16.23291442", "rel_title": "Vaccines at Velocity: Evaluating Potential Lives Saved by Earlier Vaccination in the COVID-19 Pandemic", @@ -70787,6 +71383,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2023.06.16.23291455", + "rel_title": "Anti-SARS-CoV-2 IgG profile of protein subunit, adenovector and mRNA vaccines", + "rel_date": "2023-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.16.23291455", + "rel_abs": "Different vaccine platforms were developed in 2019 and 2020 to provide immunization for protection against the SARS-CoV-2-caused disease COVID-19. The majority of vaccinated individuals will develop antibodies against SARS-CoV-2. The isotype (subclass) and Fc-glycosylation of IgG antibodies determine their affinity for secondary effector functions. For protein subunit vaccines in COVID-19, the IgG profile of the subclass and glycosylation are unknown. Therefore, we measured the IgG subclass and N-297 Fc glycosylation by ELISA and LC-MS/MS of anti-spike IgG from individuals vaccinated with the Taiwanese protein subunit vaccine Medigen, the mRNA vaccines (BNT, Moderna), and the adenovector Astrazeneca. Samples were taken after the first and second doses. For all vaccine types, the main IgG response was dominated by IgG1 and IgG3 as subclasses. For glycosylation, mRNA vaccines presented with an afucosylation after the first dose and a constant significant higher galactosylation and sialylation than non-mRNA vaccines.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sebastian Reinig", + "author_inst": "Chang Gung University" + }, + { + "author_name": "Chin Kuo", + "author_inst": "Chang Gung University" + }, + { + "author_name": "Chia-Chun Wu", + "author_inst": "Chang Gung University" + }, + { + "author_name": "Sheng-yu Huang", + "author_inst": "Chang Gung University" + }, + { + "author_name": "Jau-Song Yu", + "author_inst": "Chang Gung University" + }, + { + "author_name": "Shin-Ru Shih", + "author_inst": "Chang Gung University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2023.06.15.23291472", "rel_title": "Covid19Vaxplorer: a free, online, user-friendly COVID-19 Vaccine Allocation Comparison Tool", @@ -72370,57 +73005,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.06.14.544985", - "rel_title": "Inclusion of glycopeptides in hydrogen/deuterium exchange mass spectrometry analysis of SARS-CoV-2 spike ectodomain provides increased sequence coverage", - "rel_date": "2023-06-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.14.544985", - "rel_abs": "Hydrogen/deuterium exchange mass spectrometry (HDX-MS) can provide precise analysis of a proteins conformational dynamics across varied states, such as heat-denatured vs. native protein structures, localizing regions that are specifically affected by such conditional changes. Maximizing protein sequence coverage provides high confidence that regions of interest were located by HDX-MS, but one challenge for complete sequence coverage is N-glycosylation sites. The deuteration of glycopeptides has not always been identified in previous reports of HDX-MS analyses, causing significant sequence coverage gaps in heavily glycosylated proteins and uncertainty in structural dynamics in many regions throughout a glycoprotein. We report HDX-MS analysis of the SARS-CoV-2 spike protein ectodomain in its trimeric pre-fusion form, which has 22 predicted N-glycosylation sites per monomer, with and without heat treatment. We identified glycopeptides and calculated their isotopic mass shifts from deuteration. Inclusion of the deu-terated glycopeptides increased sequence coverage of spike ectodomain from 76% to 84%, demonstrated that glycopeptides had been deuterated, and improved confidence in results localizing structural re-arrangements. Inclusion of deuterated glycopeptides improves the analysis of the conformational dynamics of glycoproteins such as viral surface antigens and cellular receptors.\n\nAbstract Figure\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC=\"FIGDIR/small/544985v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (34K):\norg.highwire.dtl.DTLVardef@1d8e1f6org.highwire.dtl.DTLVardef@1db0774org.highwire.dtl.DTLVardef@c68d1eorg.highwire.dtl.DTLVardef@15aed98_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Christopher A Haynes", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Theodore R Keppel", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Betlehem Mekonnen", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Sarah H Osman", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Yu Zhou", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Adrian R Woolfitt", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Jakub Baudys", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "John R Barr", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Dongxia Wang", - "author_inst": "Centers for Disease Control and Prevention (CDC)" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.06.14.544834", "rel_title": "Immunogenicity of COVID-19 vaccines and their effect on the HIV reservoir in older people with HIV", @@ -72829,6 +73413,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.06.14.544560", + "rel_title": "AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor", + "rel_date": "2023-06-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.14.544560", + "rel_abs": "Protein-protein interactions (PPIs) offer great opportunities to expand the druggable proteome and therapeutically tackle various diseases, but remain challenging targets for drug discovery. Here, we provide a comprehensive pipeline that combines experimental and computational tools to identify and validate PPI targets and perform early-stage drug discovery. We have developed a machine learning approach that prioritizes interactions by analyzing quantitative data from binary PPI assays and AlphaFold-Multimer predictions. Using the quantitative assay LuTHy together with our machine learning algorithm, we identified high-confidence interactions among SARS-CoV-2 proteins for which we predicted three-dimensional structures using AlphaFold Multimer. We employed VirtualFlow to target the contact interface of the NSP10-NSP16 SARS-CoV-2 methyltransferase complex by ultra-large virtual drug screening. Thereby, we identified a compound that binds to NSP10 and inhibits its interaction with NSP16, while also disrupting the methyltransferase activity of the complex, and SARS-CoV-2 replication. Overall, this pipeline will help to prioritize PPI targets to accelerate the discovery of early-stage drug candidates targeting protein complexes and pathways.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Philipp Trepte", + "author_inst": "Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Str. 10, 13125, Berlin, Germany" + }, + { + "author_name": "Christopher Secker", + "author_inst": "Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Str. 10, 13125, Berlin, Germany" + }, + { + "author_name": "Simona Kostova", + "author_inst": "Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Str. 10, 13125, Berlin, Germany" + }, + { + "author_name": "Sibusiso B Maseko", + "author_inst": "Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Li" + }, + { + "author_name": "Soon Gang Choi", + "author_inst": "Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA" + }, + { + "author_name": "Jeremy Blavier", + "author_inst": "Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Li" + }, + { + "author_name": "Igor Minia", + "author_inst": "RNA Biology and Posttranscriptional Regulation, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems B" + }, + { + "author_name": "Eduardo Silva Ramos", + "author_inst": "Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Str. 10, 13125, Berlin, Germany" + }, + { + "author_name": "Patricia Cassonnet", + "author_inst": "Departement de Virologie, Unite de Genetique Moleculaire des Virus a ARN (GMVR), Institut Pasteur, UMR3569, Centre National de la Recherche Scientifique (CNRS)," + }, + { + "author_name": "Sabrina Golusik", + "author_inst": "Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Str. 10, 13125, Berlin, Germany" + }, + { + "author_name": "Martina Zenkner", + "author_inst": "Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Str. 10, 13125, Berlin, Germany" + }, + { + "author_name": "Stephanie Beetz", + "author_inst": "Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Str. 10, 13125, Berlin, Germany" + }, + { + "author_name": "Mara J Liebich", + "author_inst": "Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Str. 10, 13125, Berlin, Germany" + }, + { + "author_name": "Nadine Scharek", + "author_inst": "Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Str. 10, 13125, Berlin, Germany" + }, + { + "author_name": "Anja Schuetz", + "author_inst": "Protein Production & Characterization, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany" + }, + { + "author_name": "Marcel Sperling", + "author_inst": "Multifunctional Colloids and Coating, Fraunhofer Institute for Applied Polymer Research (IAP), Geiselbergstr. 69, 14476 Potsdam-Golm, Germany" + }, + { + "author_name": "Michael Lisurek", + "author_inst": "Structural Chemistry and Computational Biophysics, Leibniz-Institut fuer Molekulare Pharmakologie (FMP), 13125, Berlin, Germany" + }, + { + "author_name": "Yang Wang", + "author_inst": "Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA" + }, + { + "author_name": "Kerstin Spirohn", + "author_inst": "Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA." + }, + { + "author_name": "Tong Hao", + "author_inst": "Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA" + }, + { + "author_name": "Michael A Calderwood", + "author_inst": "Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA" + }, + { + "author_name": "David E Hill", + "author_inst": "Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA" + }, + { + "author_name": "Markus Landthaler", + "author_inst": "RNA Biology and Posttranscriptional Regulation, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems B" + }, + { + "author_name": "Julien Olivet", + "author_inst": "Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA" + }, + { + "author_name": "Jean-Claude Twizere", + "author_inst": "Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Li" + }, + { + "author_name": "Marc Vidal", + "author_inst": "Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA" + }, + { + "author_name": "Erich E Wanker", + "author_inst": "Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Str. 10, 13125, Berlin, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2023.06.13.544630", "rel_title": "Biophysical evolution of the receptor binding domains of SARS-CoVs", @@ -74132,41 +74839,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2023.06.09.23291202", - "rel_title": "Trends in medication use after the onset of the COVID-19 pandemic in the Republic of Ireland: an interrupted time series study", - "rel_date": "2023-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.09.23291202", - "rel_abs": "The COVID-19 pandemic had a substantial impact on healthcare delivery, particularly in general practice. This study aimed to evaluate how dispensing of medications in primary care in Ireland changed following the COVID-19 pandemics onset compared to expected trends. This interrupted time series study used data on medications prescribed in general practice 2016-2022 to patient eligible for state health cover, approximately one third of the population. Dispensing volumes for all therapeutic subgroups (ATC2 codes) and commonly dispensed medications were summarised. Pre-pandemic data was used to forecast expected trends (with 99% prediction intervals) using the Holt-Winters method, and these were compared to observed dispensing from March 2020 onwards. Most (31/77) therapeutic subgroups had dispensing significantly different from forecast in March 2020. Drugs for obstructive airway disease had the largest difference, with dispensing 26.2% (99%CI 19.5%-33.6%) higher than forecasted. Only two subgroups were significantly lower than forecasted, other gynaecologicals (17.7% lower, 99%CI 6.3%-26.6%) and dressings (11.6%, 99%CI 9.4%-41.6%). Dispensing of amoxicillin products and oral prednisolone were lower than forecasted in the months following the pandemics onset, particularly during winter 2020/2021. There was a spike in dispensing for many long-term medications in March 2020, while pandemic restrictions likely contributed to reductions for other medications.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Molly Mattsson", - "author_inst": "RCSI University of Medicine and Health Sciences" - }, - { - "author_name": "Jung Ah Hong", - "author_inst": "RCSI University of Medicine and Health Sciences" - }, - { - "author_name": "John Scott Frazer", - "author_inst": "University of Oxford" - }, - { - "author_name": "Glenn Ross Frazer", - "author_inst": "Unaffiliated" - }, - { - "author_name": "Frank Moriarty", - "author_inst": "RCSI University of Medicine and Health Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2023.06.07.23290927", "rel_title": "SARS-CoV-2 infections among 12 000 pregnant women, 2020, Finland - cross-testing of neutralization assays", @@ -74371,6 +75043,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.06.09.544432", + "rel_title": "RBD-based high affinity ACE2 antagonist limits SARS-CoV-2 replication in upper and lower airways", + "rel_date": "2023-06-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.09.544432", + "rel_abs": "SARS-CoV-2 has the capacity to evolve mutations to escape vaccine-and infection-acquired immunity and antiviral drugs. A variant-agnostic therapeutic agent that protects against severe disease without putting selective pressure on the virus would thus be a valuable biomedical tool. Here, we challenged rhesus macaques with SARS-CoV-2 Delta and simultaneously treated them with aerosolized RBD-62, a protein developed through multiple rounds of in vitro evolution of SARS-CoV-2 RBD to acquire 1000-fold enhanced ACE2 binding affinity. RBD-62 treatment gave equivalent protection in upper and lower airways, a phenomenon not previously observed with clinically approved vaccines. Importantly, RBD-62 did not block the development of memory responses to Delta and did not elicit anti-drug immunity. These data provide proof-of-concept that RBD-62 can prevent severe disease from a highly virulent variant.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Matthew Gagne", + "author_inst": "Vaccine Research Center, NIH" + }, + { + "author_name": "Barbara J. Flynn", + "author_inst": "Vaccine Research Center, NIH" + }, + { + "author_name": "Christopher Cole Honeycutt", + "author_inst": "Vaccine Research Center, NIH" + }, + { + "author_name": "Dillon R. Flebbe", + "author_inst": "Vaccine Research Center, NIH" + }, + { + "author_name": "Shayne F. Andrew", + "author_inst": "Vaccine Research Center, NIH" + }, + { + "author_name": "Samantha J. Provost", + "author_inst": "Vaccine Research Center, NIH" + }, + { + "author_name": "Lauren McCormick", + "author_inst": "Vaccine Research Center, NIH" + }, + { + "author_name": "Alex Van Ry", + "author_inst": "Bioqual, Inc." + }, + { + "author_name": "Elizabeth McCarthy", + "author_inst": "Vaccine Research Center, NIH" + }, + { + "author_name": "John-Paul M. Todd", + "author_inst": "Vaccine Research Center, NIH" + }, + { + "author_name": "Saran Bao", + "author_inst": "Vaccine Research Center, NIH" + }, + { + "author_name": "I-Ting Teng", + "author_inst": "Vaccine Research Center, NIH" + }, + { + "author_name": "Shir Marciano", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Yinon Rudich", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Chunlin Li", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Laurent Pessaint", + "author_inst": "Bioqual, Inc." + }, + { + "author_name": "Alan Dodson", + "author_inst": "Bioqual, Inc." + }, + { + "author_name": "Anthony Cook", + "author_inst": "Bioqual, Inc." + }, + { + "author_name": "Mark G. Lewis", + "author_inst": "Bioqual, Inc." + }, + { + "author_name": "Hanne Andersen", + "author_inst": "Bioqual, Inc." + }, + { + "author_name": "Ji\u0159\u00ed Zahradn\u00edk", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Martha C. Nason", + "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" + }, + { + "author_name": "Kathryn E. Foulds", + "author_inst": "Vaccine Research Center, NIH" + }, + { + "author_name": "Peter D. Kwong", + "author_inst": "Vaccine Research Center, NIH" + }, + { + "author_name": "Mario Roederer", + "author_inst": "Vaccine Research Center, NIH" + }, + { + "author_name": "Gideon Schreiber", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Robert A. Seder", + "author_inst": "Vaccine Research Center, NIH" + }, + { + "author_name": "Daniel C. Douek", + "author_inst": "Vaccine Research Center, NIH" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.06.12.544667", "rel_title": "Improving modelling for epidemic responses: reflections from members of the UK infectious disease modelling community on their experiences during the COVID-19 pandemic", @@ -75710,41 +76509,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.06.03.543542", - "rel_title": "Species and habitat specific changes in bird activity in an urban environment during Covid 19 lockdown", - "rel_date": "2023-06-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.03.543542", - "rel_abs": "Covid-19 lockdowns provided ecologists with a rare opportunity to examine how animals behave when humans are absent. Indeed many, sometimes contradicting, studies reported various effects of lockdowns on animal activity, especially in urban areas and other human-dominated habitats. We explored how Covid-19 lockdowns in Israel have influenced bird activity in an urban environment by using continuous acoustic recordings to monitor three common bird species that differ in their level of adaptation to the urban ecosystem: (1) the hooded crow, an urban exploiter, which depends heavily on anthropogenic resources; (2) the rose-ringed parakeet, an invasive alien species that has adapted to exploit human resources; and (3) the graceful prinia, an urban adapter, which is relatively shy of humans and can be found urban habitats with shrubs and prairies. Acoustic recordings provided continuous monitoring of bird activity without an effect of the observer on the animal. We performed dense sampling of a 1.3 square km area in northern Tel-Aviv by placing 17 recorders for more than a month in different micro-habitats within this region including roads, residential areas and urban parks. We monitored both lockdown and no-lockdown periods. We portray a complex dynamic system where the activity of specific bird species depended on many environmental parameters and decreases or increases in a habitat-dependent manner during lockdown. Specifically, urban exploiter species decreased their activity in most urban habitats during lockdown, while human adapter species increased their activity during lockdown especially in parks where humans were absent. Our results also demonstrate the value of different habitats within urban environments for animal activity, specifically highlighting the importance of urban parks. These species- and habitat-specific changes in activity might explain the contradicting results reported by others who have not performed a habitat specific analysis.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Congnan Sun", - "author_inst": "Hebei Normal university" - }, - { - "author_name": "Yoel Hassin", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Arjan Boonman", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Assaf Shwartz", - "author_inst": "Israel Institute of Technology" - }, - { - "author_name": "Yossi Yovel", - "author_inst": "Tel Aviv University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "animal behavior and cognition" - }, { "rel_doi": "10.1101/2023.06.03.543589", "rel_title": "A deep learning-based drug repurposing screening and validation for anti-SARS-CoV-2 compounds by targeting the cell entry mechanism", @@ -75945,6 +76709,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.05.31.23290618", + "rel_title": "Social genomics, cognition, and well-being during the COVID-19 pandemic", + "rel_date": "2023-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.31.23290618", + "rel_abs": "INTRODUCTIONAdverse psychosocial exposure is associated with increased proinflammatory gene expression and reduced type-1 interferon gene expression, a profile known as the conserved transcriptional response to adversity (CTRA). Little is known about CTRA activity in the context of cognitive impairment, although chronic inflammatory activation has been posited as one mechanism contributing to late-life cognitive decline.\n\nMETHODSWe studied 171 community-dwelling older adults from the Wake Forest Alzheimers Disease Research Center who answered questions via a telephone questionnaire battery about their perceived stress, loneliness, well-being, and impact of COVID-19 on their life, and who provided a self-collected dried blood spot sample. Of those, 148 had adequate samples for mRNA analysis, and 143 were included in the final analysis, which including participants adjudicated as having normal cognition (NC, n = 91) or mild cognitive impairment (MCI, n = 52) were included in the analysis. Mixed effect linear models were used to quantify associations between psychosocial variables and CTRA gene expression.\n\nRESULTSIn both NC and MCI groups, eudaimonic well-being (typically associated with a sense of purpose) was inversely associated with CTRA gene expression whereas hedonic well-being (typically associated with pleasure seeking) was positively associated. In participants with NC, coping through social support was associated with lower CTRA gene expression, whereas coping by distraction and reframing was associated with higher CTRA gene expression. CTRA gene expression was not related to coping strategies for participants with MCI, or to either loneliness or perceived stress in either group.\n\nDISCUSSIONEudaimonic and hedonic well-being remain important correlates of molecular markers of stress, even in people with MCI. However, prodromal cognitive decline appears to moderate the significance of coping strategies as a correlate of CTRA gene expression. These results suggest that MCI can selectively alter biobehavioral interactions in ways that could potentially affect the rate of future cognitive decline and may serve as targets for future intervention efforts.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "James R. Bateman", + "author_inst": "Department of Neurology, Psychiatry and Behavioral Medicine, and Internal Medicine, Section of Gerontology and Geriatric Medicine, Wake Forest University School" + }, + { + "author_name": "Sudarshan Krishnamurthy", + "author_inst": "Department of Internal Medicine, Section of Gerontology and Geriatric Medicine, Wake Forest University School of Medicine" + }, + { + "author_name": "Ellen E. Quillen", + "author_inst": "Department of Internal Medicine, Section of Molecular Medicine, Wake Forest University School of Medicine" + }, + { + "author_name": "Christian E. Waugh", + "author_inst": "Department of Psychology, Wake Forest University" + }, + { + "author_name": "Kiarri N. Kershaw", + "author_inst": "Department of Preventive Medicine (Epidemiology), Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Samuel N. Lockhart", + "author_inst": "Department of Internal Medicine, Section of Gerontology and Geriatric Medicine, Wake Forest University School of Medicine" + }, + { + "author_name": "Timothy M. Hughes", + "author_inst": "Department of Internal Medicine, Section of Gerontology and Geriatric Medicine, Wake Forest University School of Medicine" + }, + { + "author_name": "Teresa E. Seeman", + "author_inst": "Department of Epidemiology, UCLA Fielding School of Public Health" + }, + { + "author_name": "Steve W. Cole", + "author_inst": "Department of Medicine and Psychiatry and Behavioral Sciences, UCLA School of Medicine" + }, + { + "author_name": "Suzanne Craft", + "author_inst": "Department of Internal Medicine, Section of Gerontology and Geriatric Medicine, Wake Forest University School of Medicine" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2023.05.31.23290774", "rel_title": "POST-COVID ORTHOPAEDIC ELECTIVE RESOURCE PLANNING USING SIMULATION MODELLING", @@ -77960,73 +78779,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2023.05.31.543022", - "rel_title": "Universal features of Nsp1-mediated translational shutdown by coronaviruses", - "rel_date": "2023-06-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.31.543022", - "rel_abs": "Nonstructural protein 1 (Nsp1) produced by coronaviruses shuts down host protein synthesis in infected cells. The C-terminal domain of SARS-CoV-2 Nsp1 was shown to bind to the small ribosomal subunit to inhibit translation, but it is not clear whether this mechanism is broadly used by coronaviruses, whether the N-terminal domain of Nsp1 binds the ribosome, or how Nsp1 specifically permits translation of viral mRNAs. Here, we investigated Nsp1 from three representative Betacoronaviruses - SARS-CoV-2, MERS-CoV, and Bat-Hp-CoV - using structural, biophysical, and biochemical assays. We revealed a conserved mechanism of host translational shutdown across the three coronaviruses. We further demonstrated that the N-terminal domain of Bat-Hp-CoV Nsp1 binds to the decoding center of the 40S subunit, where it would prevent mRNA and eIF1A binding. Structure-based biochemical experiments identified a conserved role of these inhibitory interactions in all three coronaviruses and showed that the same regions of Nsp1 are responsible for the preferential translation of viral mRNAs. Our results provide a mechanistic framework to understand how Betacoronaviruses overcome translational inhibition to produce viral proteins.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Katharina Schubert", - "author_inst": "Eidgenossische Technische Hochschule Zurich" - }, - { - "author_name": "Evangelos D. Karousis", - "author_inst": "University of Bern" - }, - { - "author_name": "Ivo Ban", - "author_inst": "Eidgenossische Technische Hochschule Zurich" - }, - { - "author_name": "Christopher Lapointe", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Marc Leibundgut", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Emilie Baeumlin", - "author_inst": "University of Bern" - }, - { - "author_name": "Eric Kummerant", - "author_inst": "ETH, Zurich" - }, - { - "author_name": "Alain Scaiola", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Tanja Schoenhut", - "author_inst": "ETH, Zurich" - }, - { - "author_name": "Jana Ziegelmueller", - "author_inst": "University of Bern" - }, - { - "author_name": "Joseph Puglisi", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Oliver Muehlemann", - "author_inst": "University of Bern" - }, - { - "author_name": "Nenad Ban", - "author_inst": "ETH Zurich" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.05.31.543129", "rel_title": "CD4+ T-cell immunity of SARS-CoV-2 patients determine pneumonia development", @@ -78295,6 +79047,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.06.01.543234", + "rel_title": "Prenatal SARS-CoV-2 infection alters postpartum human milk-derived extracellular vesicles", + "rel_date": "2023-06-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.01.543234", + "rel_abs": "Human milk-derived extracellular vesicles (HMEVs) are crucial functional components in breast milk, contributing to infant health and development. Maternal conditions could affect HMEV cargos; however, the impact of SARS-CoV-2 infection on HMEVs remains unknown. This study evaluated the influence of SARS-CoV-2 infection during pregnancy on postpartum HMEV molecules. Milk samples (9 prenatal SARS-CoV-2 vs. 9 controls) were retrieved from the IMPRINT birth cohort. After defatting and casein micelle disaggregation, 1 mL milk was subjected to a sequential process of centrifugation, ultrafiltration, and qEV-size exclusion chromatography. Particle and protein characterizations were performed following the MISEV2018 guidelines. EV lysates were analyzed through proteomics and miRNA sequencing, while the intact EVs were biotinylated for surfaceomic analysis. Multi-Omics was employed to predict HMEV functions associated with prenatal SARS-CoV-2 infection. Demographic data between the prenatal SARS-CoV-2 and control groups were similar. The median duration from maternal SARS-CoV-2 test positivity to milk collection was 3 months (range: 1-6 months). Transmission electron microscopy showed the cup-shaped nanoparticles. Nanoparticle tracking analysis demonstrated particle diameters of <200 nm and yields of >1e11 particles from 1 mL milk. Western immunoblots detected ALIX, CD9 and HSP70, supporting the presence of HMEVs in the isolates. Thousands of HMEV cargos and hundreds of surface proteins were identified and compared. Multi-Omics predicted that mothers with prenatal SARS-CoV-2 infection produced HMEVs with enhanced functionalities involving metabolic reprogramming and mucosal tissue development, while mitigating inflammation and lower EV transmigration potential. Our findings suggest that SARS-CoV-2 infection during pregnancy boosts mucosal site-specific functions of HMEVs, potentially protecting infants against viral infections. Further prospective studies should be pursued to reevaluate the short- and long-term benefits of breastfeeding in the post-COVID era.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Somchai Chutipongtanate", + "author_inst": "Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267 USA" + }, + { + "author_name": "Hatice Cetinkaya", + "author_inst": "Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267 USA" + }, + { + "author_name": "Xiang Zhang", + "author_inst": "Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267 USA" + }, + { + "author_name": "Damaris Kuhnell", + "author_inst": "Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267 USA" + }, + { + "author_name": "Desiree Benefield", + "author_inst": "Department of Molecular Cellular Biosciences, Center for Advanced Structural Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267 USA" + }, + { + "author_name": "Wendy Haffey", + "author_inst": "Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267 USA" + }, + { + "author_name": "Michael Wyder", + "author_inst": "Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267 USA" + }, + { + "author_name": "Richa Patel", + "author_inst": "Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267 USA" + }, + { + "author_name": "Shannon C. Conrey", + "author_inst": "Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267 USA" + }, + { + "author_name": "Allison R. Burrell", + "author_inst": "Department of Infectious Disease, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45267 USA" + }, + { + "author_name": "Scott Langevin", + "author_inst": "Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267 USA" + }, + { + "author_name": "Laurie Nommsen-Rivers", + "author_inst": "Department of Rehabilitation, Exercise, and Nutrition, University of Cincinnati College of Allied Health Sciences, Cincinnati, OH 45267 USA" + }, + { + "author_name": "David S. Newburg", + "author_inst": "Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267 USA" + }, + { + "author_name": "Kenneth D. Greis", + "author_inst": "Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267 USA" + }, + { + "author_name": "Mary A. Staat", + "author_inst": "Department of Infectious Disease, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45267 USA" + }, + { + "author_name": "Ardythe L. Morrow", + "author_inst": "Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267 USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2023.05.26.23290622", "rel_title": "ECHOCARDIOGRAPHIC MANIFESTATIONS OF COVID 19 ILLNESS AND DEVELOPMENT OF PERSISTENT RV DYSFUNCTION AND PULMANARY HYPERTENSION AS A LONG TERM SEQUELAE OF COVID 19 ILLNESS: A STUDY AMONG PATIENTS OF SOUTH EAST ASIAN REGION", @@ -80406,93 +81237,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.05.23.542024", - "rel_title": "A Multi-Epitope/CXCL11 Prime/Pull Coronavirus Mucosal Vaccine Boosts the Frequency and the Function of Lung-Resident CD4+ and CD8+ Memory T Cells and Protects Against COVID-19-like Symptoms and Death Caused by SARS-CoV-2 infection", - "rel_date": "2023-05-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.23.542024", - "rel_abs": "The pandemic of the coronavirus disease 2019 (COVID-19) has created the largest global health crisis in almost a century. Following exposure to SARS-CoV-2, the virus particles replicate in the lungs, induce a \"cytokine storm\" and potentially cause life-threatening inflammatory disease. Low frequencies of function SARS-CoV-2-specific CD4+ and CD8+ T cells in the lungs of COVID-19 patients were associated with severe cases of COVID-19. The apparent low level of T cell-attracting CXCL9, CXCL10, and CXCL11 chemokines in infected lungs may not be sufficient enough to assure the sequestration and/or homing of CD4+ and CD8+ T cells from the circulation into infected lungs. We hypothesize that a Coronavirus vaccine strategy that boosts the frequencies of functional SARS-CoV-2-specific CD4+ and CD8+ T cells in the lungs would lead to better protection against SARS-CoV-2 infection, COVID19-like symptoms, and death. In the present study, we designed and pre-clinically tested the safety, immunogenicity, and protective efficacy of a novel multi-epitope//CXCL11 prime/pull mucosal Coronavirus vaccine. This prime/pull vaccine strategy consists of intranasal delivery of a lung-tropic adeno-associated virus type 9 (AAV-9) vector that incorporates highly conserved human B, CD4+ CD8+ cell epitopes of SARS-CoV-2 (prime) and pulling the primed B and T cells into the lungs using the T cell attracting chemokine, CXCL-11 (pull). We demonstrated that immunization of HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic mice with this multi-epitope//CXCL11 prime/pull Coronavirus mucosal vaccine: (i) Increased the frequencies of CD4+ and CD8+ TEM, TCM, and TRM cells in the lungs; and (ii) reduced COVID19-like symptoms, lowered virus replication, and prevented deaths following challenge with SARS-CoV-2. These findings discuss the importance of bolstering the number and function of lung-resident memory CD4+ and CD8+ T cells for better protection against SARS-CoV-2 infection, COVID-19-like symptoms, and death.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Latifa Zayou", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Swayam Prakash", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Nisha R Dhanushkodi", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Afshana Quadiri", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Izabela Coimbra Ibraim", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Mahmoud Singer", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Amirah Salem", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Amin Mohammed Shaik", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Berfin Suzer", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Amruth Chilukuri", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Jennifer Tran", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Pauline Chau Nguyen", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Miyo Sun", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Kathy K Hormi-Carver", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Ahmed Belmouden", - "author_inst": "Laboratory of Cell Biology and Molecular Genetics, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco" - }, - { - "author_name": "Hawa Vahed", - "author_inst": "Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA 92660; USA" - }, - { - "author_name": "Jeffrey B Ulmer", - "author_inst": "Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA 92660; USA" - }, - { - "author_name": "LBACHIR BENMOHAMED", - "author_inst": "GHEI/UCI School of Medecine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.05.25.542297", "rel_title": "Multi-omic Profiling Reveals Early Immunological Indicators for Identifying COVID-19 Progressors", @@ -80701,6 +81445,41 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2023.05.19.23290192", + "rel_title": "The secretory IgA (sIgA) response in human milk against the SARS-CoV-2 Spike is highly durable and neutralizing for at least 1 year of lactation post-infection", + "rel_date": "2023-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.19.23290192", + "rel_abs": "Although in the early pandemic period, COVID-19 pathology among young children and infants was typically less severe compared to that observed among adults, this has not remained entirely consistent as SARS-CoV-2 variants have emerged. There is an enormous body of evidence demonstrating the benefits of human milk antibodies (Abs) in protecting infants against a wide range of enteric and respiratory infections. It is highly plausible that the same holds true for protection against SARS-CoV-2, as this virus infects cells of the gastrointestinal and respiratory mucosae. Understanding the durability of a human milk Ab response over time after infection is critical. Previously, we examined the Abs present in milk of those recently infected with SARS-CoV-2, and concluded that the response was secretory IgA (sIgA)-dominant and that these titers were highly correlated with neutralization potency. The present study aimed to monitor the durability of the SARS-CoV-2 IgA and secretory Ab (sAb) response in milk from COVID-19-recovered lactating individuals over 12 months, in the absence of vaccination or re-infection. This analysis revealed a robust and durable Spike-specific milk sIgA response, that at 9-12 months after infection, 88% of the samples exhibited titers above the positive cutoff for IgA and 94% were above cutoff for sAb. Fifty percent of participants exhibited less than a 2-fold reduction of Spike-specific IgA through 12 months. A strong significant positive correlation between IgA and sAb against Spike persisted throughout the study period. Nucleocapsid-specific Abs were also assessed, which revealed significant background or cross reactivity of milk IgA against this immunogen, as well as limited/inconsistent durability compared to Spike titers. These data suggests that lactating individuals are likely to continue producing Spike-specific Abs in their milk for 1 year or more, which may provide critical passive immunity to infants against SARS-CoV-2 throughout the lactation period.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Xiaoqi Yang", + "author_inst": "Icahn School of Medicine" + }, + { + "author_name": "Alisa Fox", + "author_inst": "Icahn School of Medicine" + }, + { + "author_name": "Claire DeCarlo", + "author_inst": "Icahn School of Medicine" + }, + { + "author_name": "Nicole Pineda", + "author_inst": "Icahn School of Medicine" + }, + { + "author_name": "Rebecca L Powell", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2023.05.26.23290243", "rel_title": "A Long COVID Risk Predictor Focused on Clinical Workflow Integration", @@ -82400,45 +83179,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.05.16.23290033", - "rel_title": "Viral rebound among patients receiving COVID-19 convalescent plasma for treatment of Covid-19 in Uganda.", - "rel_date": "2023-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.16.23290033", - "rel_abs": "BackgroundViral rebound has been reported in people infected with COVID-19 treated with nirmatrelvir/ritonavir, and some cases been reported in patients who did not receive any antiviral treatment. Since the course of COVID-19 has not yet been well defined, we evaluated the incidence of viral rebound among COVID-19 patients treated with COVID-19 Convalescent Plasma (CCP) in Uganda.\n\nMethodsIn the CCP trail, 136 patients were enrolled between 21st September 2020 and 2nd December 2020 who presented to the Mulago National Referral COVID-19 treatment unit. Patients with a positive SARS-CoV-2 reverse transcriptase (RT)-PCR test irrespective of disease severity were hospitalised and randomised to receive either COVID-19 CCP plus standard of care (SOC) or SOC alone. SARS-CoV-2 RT-PCR was done at baseline and on days 3, 5, 7, 14 and 28 post randomisation or until two consecutive negative RT-PCR results were obtained, whichever occurred first. We analysed for occurrence of viral rebound. Viral rebound was defined as a positive SARS-CoV-2 RT-PCR test following a prior negative test.\n\nFindings20% of the participants had viral rebound. Viral rebounders were predominantly male. The median age was 45-64 years and they had at least one co-morbidity. There was no difference in the rebound rates in the study arms, and participants with hypertension had more rebound rates compared to those with other co-morbidities.\n\nInterpretationViral RNA rebound was common among patients receiving CCP. Viral rebound may be a result of the biphasic nature of COVID-19 infection, and not a consequence of the therapeutic interventions.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Patricia Alupo", - "author_inst": "Makerere University Lung Institute" - }, - { - "author_name": "Winters Muttamba", - "author_inst": "Makerere University Lung Institute ; 2.\tDivision of Infection and Global Health, School of Medicine, University of St Andrews; St. Andrews, United Kingdom" - }, - { - "author_name": "Levicatus Mugenyi", - "author_inst": "Makerere University Lung Institute" - }, - { - "author_name": "Ivan Kimuli", - "author_inst": "Makerere University Lung Institute" - }, - { - "author_name": "Winceslaus Katagira", - "author_inst": "Makerere University Lung Institute" - }, - { - "author_name": "Bruce Kirenga", - "author_inst": "Makerere University College of Health Sciences, Department of Medicine. 2. Makerere University Lung Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.05.19.23290234", "rel_title": "Defining the Subtypes of Long COVID and Risk Factors for Prolonged Disease", @@ -82583,6 +83323,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.05.15.23289993", + "rel_title": "Impact of the COVID-19 pandemic on low back pain management in commercially insured and Medicare Advantage cohorts. A retrospective cohort study", + "rel_date": "2023-05-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.15.23289993", + "rel_abs": "BackgroundThe COVID-19 (COVID) pandemic has been associated with care seeking and delivery system changes. Before COVID the management of low back pain (LBP) was variable and a common source of low-value care. The purpose of this retrospective cohort study was to examine how the management of LBP changed during the COVID pandemic in commercially insured (CI) and Medicare Advantage (MA) cohorts.\n\nMethodsA US national sample of LBP episodes with a duration of less than 91 days experienced during 2019-2021 was analyzed. Independent variables included whether an individual had CI or MA coverage, and the timing of LBP onset. Secondary independent variables included individuals home address State. Dependent measures included the percent of individuals initially contacting eighteen types of health care provider (HCP) and receiving twenty-two types of health care services, and total episode cost. Early and late COVID measures were compared with a pre-COVID baseline to examine COVID related change. The impact of the stringency of State level COVID public policy response was evaluated.\n\nResultsThe study included 222,043 CI and 466,125 MA complete episodes of LBP. During the pre-COVID period the MA cohort was older (MA median 72 vs. CI 45), with higher percent female (61% vs. 52%), and from zip codes with a higher Area Deprivation Index (median 52 vs. CI 38). MA and CI cohort attributes remained nearly identical in the early and late COVID periods.\n\nInitial contact with licensed acupuncturists (LAc risk ratio (RR) 0.66) and physical therapists (PT RR 0.82) in the CI cohort, and with PTs (RR 0.78), urgent care (RR 0.86), and emergency medicine (RR 0.87) in the MA cohort experienced the largest decreases during the early COVID period. The largest increase in the CI cohort was to PCPs (RR 1.08), and in the MA cohort to PCPs (RR 1.11) and nurse practitioners (RR 1.09). During the late COVID period the largest decreases in the CI cohort were to neurologists (RR 0.84), PTs (RR 0.86), and physical medicine and rehabilitation physicians (RR PMR 0.87) and in the MA cohort to rheumatologists (RR 0.81), PMR (RR 0.89) and pain management physicians (RR 0.89). The largest increases during the late COVID period in the CI cohort were to radiologists (RR 1.22), hospitals (RR 1.07) and orthopedic surgeons (OS RR 1.04) and in the MA cohort to LAcs (RR 1.32), radiologists (RR 1.11) and hospitals (RR 1.10).\n\nCompared to the pre-COVID period during the early COVID period the percent of episodes including most health care services was unchanged or reduced. In the late COVID period in both the CI and MA cohorts the percent of episodes with imaging studies increased, MRI (RR CI 1.15, MA 1.21), CT (RR 1.16, 1.16), and plain film radiology (RR 1.06, 1.06).\n\nThe stringency of State COVID public policy responses was not associated with significant variability in either the type of HCP initially contacted, or services received for LBP.\n\nConclusionsIn both CI and MA LBP cohorts COVID was associated with changes in the types of HCP initially contacted and subsequent services provided. Guideline concordant first-line service use declined during COVID, and the rate of diagnostic imaging was higher in the late COVID period than the pre-COVID period.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Dave Elton", + "author_inst": "UnitedHealth Group" + }, + { + "author_name": "Meng Zhang", + "author_inst": "Optum" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "rehabilitation medicine and physical therapy" + }, { "rel_doi": "10.1101/2023.05.18.541286", "rel_title": "Contrasting the open access dissemination of COVID-19 and SDG research", @@ -84246,37 +85009,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.05.14.540726", - "rel_title": "Metformin an anti-diabetic drug, possess ACE-2 receptor-SARS- Cov-2 RBD binding antagonist activity, anti-inflammatory and cytokine inhibitory properties suitable for treatment of COVID-19", - "rel_date": "2023-05-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.14.540726", - "rel_abs": "Metformin is a widely used and is a safe anti-diabetic drug. It has also been shown to have anti-inflammatory and anti-viral activities in humans and animal models. Specifically we explored its activity in SARS-CoV-2 initiated COVID19 disease. Here we show that metformin 1. blocks the binding of SARS-CoV-2 spike protein receptor binding domain RBD to human ACE2 receptor 2. We also show that it has anti-inflammatory effects and reduces cytokine secretion as well as blocks the recruitment of monocytes to endothelial cells 3. Finally we show its activity in a hamster in vivo model of SARS-CoV-2 infection as a nasal formulation. Based on the safety and the therapeutic properties relevant to COVID-19 it is feasible to propose a nasal spray of metformin that can be used in treatment of this disease. A nasal spray would deliver the drug to the target organ lung and spare other organs which get exposed upon oral dosing.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Uday Saxena", - "author_inst": "Reagene Innovations Pvt Ltd" - }, - { - "author_name": "Kranti Meher", - "author_inst": "Reagene Innovations Pvt Ltd" - }, - { - "author_name": "Saranya K", - "author_inst": "Reagene Innovations Pvt Ltd" - }, - { - "author_name": "Subrahmanyam Vangala", - "author_inst": "Reagene Innovations Pvt Ltd" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2023.05.10.23289325", "rel_title": "Composite interventions on outcomes of severely and critically ill patients with COVID-19 in Shanghai, China", @@ -84417,6 +85149,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.05.12.23288889", + "rel_title": "Immune response to SARS CoV2 infection by TLR3, TLR4 and TLR7 expression", + "rel_date": "2023-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.12.23288889", + "rel_abs": "Toll-like receptors (TLRs) may be involved both in the initial failure of viral clearance and in the subsequent development of severe clinical manifestations of COVID-19, essentially ARDS (acute respiratory distress syndrome) with fatal respiratory failure. We present the gene expression of TLR 3, 4, and 7 in nasopharyngeal total RNA samples from 150 individuals positive for SARS Cov2 (DET) by molecular techniques of isothermal amplification (Neokit SA) and 152 SARS Cov2 non detectable (ND) ambulatory and hospitalized patients with a non-defined respiratory disease, and we compared with the symptomatology developed by all those patients. We analyzed 4 cohorts: 1-SARS Cov2 genome detected patients with severe to high symptomatology (n=107); 2-SARS Cov2 genome detected patients low to mild symptomatology (n=43); 3-SARS Cov2 genome non detected patients with severe to high symptomatology (n=109); and 4-SARS Cov2 genome non detected patients low to mild symptomatology (n=41).\n\nOur results not only contradict few previous study, it also corrects for sample size bias, showing no significant differences of expression for TLR3, TLR4 and TLR7 between SARS Cov2 DET and ND total cohort of patients (Non Paired T -Test p Value>0.1). When compared severity of symptoms -presence of symptoms from the COVID-19 12 WHO diagnosis symptoms- and gene expression, here we found significant positive correlation between severe symptomatology, and the number of symptoms and death for TLR4 and TLR7 for both DET and ND COVID-19 patients. When the cohort was construct with low/middle and severe symptoms, the Correlation Coefficient showed that expression of TLR4 and TLR7 was significantly amplified in those ND patients with severe symptomatology (p Value= 0.00311) as well as for TLR3 in ND low to mild symptoms cohort of patients. We also showed and discussed the results obtained of these genes expression and the sex and age of patients. In summary, our data suggest that although our innate immune system with TLRs contributes to the elimination of viruses, it can also be associated with harm to the host due to persistent inflammation and tissue destruction. We confirmed that principally TLR4 and TLR7 could be involved not only in the pathogenesis of COVID{square}19 but also in other respiratory diseases with same symptomatology. We agree with previous studies that treatments focus on TLR4 and TLR7 expression in inflammatory respiratory diseases could be a start point against severe symptoms development.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Veronica L Martinez Marignac", + "author_inst": "CICYTTP -CONICET, PROV ER & UADER" + }, + { + "author_name": "Gloria S Oertlin", + "author_inst": "CICYTTP -CONICET, PROV ER y UADER" + }, + { + "author_name": "Jose L Favant", + "author_inst": "CICYTTP -CONICET, PROV ER y UADER" + }, + { + "author_name": "Erika Fleishmann", + "author_inst": "Dr. Nestor Bianchi Laboratory, San Jose Hospital, Diamante, Entre Rios, Argentina." + }, + { + "author_name": "Mercedes Salinas", + "author_inst": "Provincial Epidemiology Laboratory, Health Ministry, Provincia de Entre Rios, Argentina." + }, + { + "author_name": "Gaston Marchetti", + "author_inst": "Office Director - San Jose Hospital Diamante, Entre Rios, Argentina." + }, + { + "author_name": "Zaida Gazali", + "author_inst": "Office Director - San Jose Hospital Diamante, Entre Rios, Argentina." + }, + { + "author_name": "Silvina M Richard", + "author_inst": "Instituto Multidisciplinario de Biologia Celular (IMBICE), La Plata, Buenos Aires, Argentina." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.05.13.540634", "rel_title": "From Collection to Analysis: A Comparison of GISAID and the Covid-19 Data Portal", @@ -85864,57 +86643,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.05.08.539897", - "rel_title": "Evolving spike-protein N-glycosylation in SARS-CoV-2 variants", - "rel_date": "2023-05-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.08.539897", - "rel_abs": "Since >3 years, SARS-CoV-2 has plunged humans into a colossal pandemic. Henceforth, multiple waves of infection have swept through the human population, led by variants that were able to partially evade acquired immunity. The co-evolution of SARS-CoV-2 variants with human immunity provides an excellent opportunity to study the interaction between viral pathogens and their human hosts. The heavily N-glycosylated spike-protein of SARS-CoV-2 plays a pivotal role in initiating infection and is the target for host immune-response, both of which are impacted by host-installed N-glycans. Using highly-sensitive DeGlyPHER approach, we compared the N-glycan landscape on spikes of the SARS-CoV-2 Wuhan-Hu-1 strain to seven WHO-defined variants of concern/interest, using recombinantly expressed, soluble spike-protein trimers, sharing same stabilizing-mutations. We found that N-glycan processing is conserved at most sites. However, in multiple variants, processing of N-glycans from high mannose- to complex-type is reduced at sites N165, N343 and N616, implicated in spike-protein function.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Sabyasachi Baboo", - "author_inst": "Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "Jolene K Diedrich", - "author_inst": "Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "Jonathan L Torres", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "Jeffrey Copps", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "Bhavya Singh", - "author_inst": "Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "Patrick T Garrett", - "author_inst": "Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "Andrew B Ward", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "James C Paulson", - "author_inst": "Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "John R Yates III", - "author_inst": "Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.05.08.539929", "rel_title": "Toll-like receptor 7 (TLR7)-mediated antiviral response protects mice from lethal SARS-CoV-2 infection", @@ -86175,6 +86903,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.05.06.539715", + "rel_title": "SARS-COV-2 Spike Protein Fragment eases Amyloidogenesis of \u03b1-Synuclein", + "rel_date": "2023-05-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.06.539715", + "rel_abs": "Parkinsons Disease is accompanied by presence of amyloids in the brain formed of -synuclein chains. Correlation between COVID-19 and the onset of Parkinsons disease let to the idea that amyloidogenic segments in SARS-COV-2 proteins can induce aggregation of -synuclein. Using molecular dynamic simulations, we show that the fragment FKNIDGYFKI of the spike protein, which is unique for SARS-COV-2, shifts preferentially the ensemble of -synuclein monomer towards rod-like fibril seeding conformations, and at the same time stabilizes differentially this polymorph over the competing twister-like structure. Our results are compared with earlier work relying on a different protein fragment that is not specific for SARS-COV-2.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ulrich H.E. Hansmann", + "author_inst": "University of Oklahoma" + }, + { + "author_name": "Buddhadev Maiti", + "author_inst": "University of Oklahoma" + }, + { + "author_name": "Andrew D Chesney", + "author_inst": "University of Oklahoma" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2023.05.05.539395", "rel_title": "A multiadjuvant polysaccharide-amino acid-lipid (PAL) subunit nanovaccine generates robust systemic and lung-specific mucosal immune responses against SARS-CoV-2 in mice", @@ -87422,89 +88177,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2023.05.03.23289435", - "rel_title": "Improved access to diabetic retinopathy screening through primary care-based teleophthalmology during the COVID-19 pandemic", - "rel_date": "2023-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.03.23289435", - "rel_abs": "BackgroundPrimary care practices play a critical role in ensuring that patients with diabetes undergo an annual eye examination, the importance of which is underscored by the Healthcare Effectiveness Data and Information Set (HEDIS) quality measures. Store-and-forward teleophthalmology, where ocular images are read remotely by an ophthalmologist, has the potential to facilitate this role.\n\nMethodsIn this report, we aim to measure if using a primary care-based teleophthalmology program improves access to eye examinations for diabetic patients as reflected in HEDIS measures. Over a 20-month period, non-mydriatic fundus photographs were obtained at five primary care sites in the San Francisco Bay Area from patients with a new or existing diagnosis of diabetes mellitus type 1 or 2 who needed an annual eye examination. Collected photographs were evaluated remotely by vitreoretinal specialists for diabetic retinopathy. Our primary measures were the proportion and number of annual eye exams of diabetic patients in primary care clinics that participated in the teleophthalmology program compared to clinics that did not participate. Additional measures included the number of patients with DR who were identified through the program, gradeability of fundus photographs, and characteristics of the study population.\n\nResultsThe program screened 760 unique patients, 84 of whom were found to have DR (11.1%). The rate of ungradable photos was 9.7%, which was greater for patients who self-reported as racially non-White. For the duration of the study, including during the COVID-19 pandemic, both the proportion and number of diabetic patients receiving annual eye examination increased (17.1% increase in proportion, 14.8% increase in number). In comparison, primary care sites that did not offer the teleophthalmology service declined in these measures (2.3% decrease in proportion, 17.0% decrease in number).\n\nConclusionsPrimary care-based teleophthalmology improves access to eye exam for diabetic patients and identifies patients with diabetic retinopathy across diverse communities.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Karen Chen", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Eliot Dow", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Marina Basina", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Jimmy Dang", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Nergis Khan", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Michael Kim", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Marcie Lynn Levine", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Kapil Mishra", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Chandrashan Perera", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Anuradha Phadke", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Marilyn Tan", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Kirsti Weng", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Diana Do", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Vinit B Mahajan", - "author_inst": "Stanford University" - }, - { - "author_name": "Prithvi Mruthyunjaya", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Ted Leng", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "David Myung", - "author_inst": "Stanford University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "ophthalmology" - }, { "rel_doi": "10.1101/2023.05.02.23289345", "rel_title": "Persistent immune abnormalities discriminate post-COVID syndrome from convalescence", @@ -87833,6 +88505,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2023.05.01.538506", + "rel_title": "Role of SARS-CoV-2 mutations in the evolution of the COVID-19 pandemic", + "rel_date": "2023-05-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.01.538506", + "rel_abs": "RNA viruses, including SARS-CoV-2, evolve by mutation acquisition, or by hybridization between viral genomes. The SARS-CoV-2 pandemic provided an exceptional opportunity to analyze the mutations that appeared over a three-year period.\n\nIn this study, we analysed the type of mutations and their epidemic consequences on the thousands of genomes produced in our laboratory. These were obtained by next-generation sequencing from respiratory samples performed for genomic surveillance. The frequencies of mutations were calculated using Nextclade, Microsoft Excel, and an in-house Python script. In total, 61,397 genomes matching 483 Pangolin lineages were analyzed; 22,225 nucleotide mutations were identified, and of them 220 (1.0%) were each at the root of at least 836 genomes, a frequency threshold classifying mutations as \"hyperfertile\". Two of these seeded the pandemic in Europe, namely a mutation in the RNA-dependent RNA polymerase associated with an increased mutation rate (P323L) and one in the spike protein (D614G), which plays a particular role in virus fitness. Most of these 220 \"hyperfertile\" mutations occurred in areas not predicted to be associated with increased virulence. Their number was 8{+/-}6 (0-22) per 1,000 nucleotides on average per gene. They were 3.7 times more frequent in accessory than informational genes (14 versus 4; p= 0.0037). Particularly, they were 4.1 times more frequent in ORF8 than in the gene encoding RNA polymerase. Interestingly, stop codons were present in 97 positions, almost only in six accessory genes including ORF7a (25 per 100 codons) and ORF8 (21). Furthermore, 1,661 mutations (16.3%) were associated with a lower number of \"offspring\" (50-835) and classified as \"fertile\".\n\nIn conclusion, except for two initial mutations that could predict a change in the dynamics of the epidemic (mutation rate and change in the virus attachment site), most of the \"hyperfertile\" mutations did not predict the emergence of a new epidemic form. Significantly, some mutations were in non-coding areas and some consisted of stop codons, indicating that some genes (particularly ORF7a and ORF8) were rather \"non-virulence genes\" at a given stage of the epidemic, which is an unusual concept for viruses.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Philippe Colson", + "author_inst": "Aix-Marseille university" + }, + { + "author_name": "Herve Chaudet", + "author_inst": "Assistance Publique-Hopitaux de Marseille" + }, + { + "author_name": "Jeremy Delerce", + "author_inst": "Aix-Marseille University" + }, + { + "author_name": "Pierre Pontarotti", + "author_inst": "CNRS" + }, + { + "author_name": "Anthony Levasseur", + "author_inst": "Aix-Marseille University" + }, + { + "author_name": "Jacques Fantini", + "author_inst": "Aix-Marseille University" + }, + { + "author_name": "Bernard La Scola", + "author_inst": "Aix Marseille University" + }, + { + "author_name": "Christian A. Devaux", + "author_inst": "IHU Mediterranee Infection" + }, + { + "author_name": "Didier Raoult", + "author_inst": "Aix Marseille University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.05.04.539267", "rel_title": "Broad-Spectrum Heavily Mutated Monoclonal Antibody Isolated from COVID-19 Convalescent Vaccinee with Capacity to Neutralize SARS-CoV2 Variants Ranging from B.1 to BQ.1.1", @@ -90040,29 +90763,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2023.04.27.23289205", - "rel_title": "Characterization and Resistance to Mutation of a Single-Channel Multiplex PCR Assay for SARS-CoV-2", - "rel_date": "2023-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.27.23289205", - "rel_abs": "Throughout the COVID-19 pandemic, wastewater surveillance has been used worldwide to provide valuable public health data. RT-qPCR is frequently used as a quantitative methodology for wastewater surveillance but is susceptible to mutations in target regions. These mutations may lead to misinterpretation of surveillance data; a drop in signal could be concluded to be a result of lower viral load, when in fact it is caused by reduced detection efficiency. We describe a novel approach to mitigating the impacts of such mutations: monitoring the cumulative signal from two targets (N1 and N2) via independent amplification reactions using identically labeled probes; a \"single-channel multiplex\" approach. Using the IDEXX Water SARS-CoV-2 RT-qPCR test, we demonstrate equivalent intra-assay repeatability and quantitative results from the combined N1N2 test when compared to individual N1 and N2 assays. Furthermore, we show that while mutations in B.1.1.529, BA.5.2, and BA.5.2.1 significantly impact the performance of the N1 assay, the impact on the N1N2 assay was negligible, and nearly within acceptable margin of error for technical replicates. These findings demonstrate that a single-channel multiplex approach can be used to improve the robustness of wastewater surveillance and minimize the risk of future mutations leading to unreliable public health data.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Amy L. Pednault", - "author_inst": "IDEXX Laboratories, Inc." - }, - { - "author_name": "Brian M Swalla", - "author_inst": "IDEXX Laboratories, Inc." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.04.28.23289257", "rel_title": "The COV50 classifier predicts frailty and future death, independent from SARS-CoV-2 infection", @@ -90267,6 +90967,137 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.04.27.23289157", + "rel_title": "Cohort Profile: A longitudinal Victorian COVID-19 cohort (COVID PROFILE)", + "rel_date": "2023-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.27.23289157", + "rel_abs": "PurposeThe COVID PROFILE cohort is a longitudinal clinical study based in Victoria Australia, which was established to understand immunity to SARS-CoV-2 in a low transmission population setting and to identify immunological markers of long-term immunity and immune-dysregulation after both infection and vaccination. Additionally, this cohort was established as a biobank resource for researchers to address other health-related immunological questions.\n\nParticipantsWe enrolled 178 adult community members, including household contacts, who had either recovered from a SARS-CoV-2 infection or were SARS-CoV-2 naive. Only participants [≥]18 years of age and, in the case of female participants, non-pregnant women at the time of enrollment were included in the study. Detailed COVID-19 clinical data, vaccination status, medical history and demographics was collected.\n\nFindings to dateAt enrollment, we found that 87.8% of COVID-19 recovered individuals were seropositive with detectable levels of anti-SARS-CoV-2 IgG antibodies. Seronegative COVID-19 recovered individuals included asymptomatic individuals or participants that were enrolled more than 12 months after their COVID-19 diagnosis. Except for one individual who was seropositive at baseline despite a previous SARS-CoV-2 PCR negative diagnosis, all household contacts and other community members enrolled as SARS-CoV-2 PCR negative, were seronegative for all SARS-CoV-2-specific antibodies tested. The infection rate (re-infection or new infection) during 24 months of the study was 42.7%, as determined by either rapid antigen tests, PCRs or serology screens. Of the SARS-CoV-2 recovered participants, 32.6% reported ongoing symptoms at enrollment of which 47% had already experienced ongoing symptoms for more than 12 weeks.\n\nFuture PlansCOVID PROFILE will be used to comprehensively understand temporal immunity to SARS-CoV-2 and COVID-19 vaccines and to understand the impact of host immunological composition on such immunity and symptom severity. Additionally, studies focusing on understanding immunity following breakthrough infections and immunological risk factors that contribute towards development of long COVID are planned.\n\nLimitations/Strengths of the studyO_LIExtensive clinical information is available and longitudinal samples (blood, saliva and oropharyngeal swabs) collected at regular intervals up to 2.5 years after initial enrolment.\nC_LIO_LIThis low SARS-CoV-2 transmission population cohort, enables exploration of difference in both the acquisition and maintenance of naturally acquired and vaccine-induced immunity not confounded by prior, frequent and/or undetected exposures.\nC_LIO_LIExtensive biobank of numerous blood fractions and biospecimen enables further exploration of mucosal immunity, nasal microbiome and humoral and cellular immunity over time.\nC_LIO_LIThe cohort may be limited in addressing research questions regarding outcomes and risk factors and their associations where low incidence is expected.\nC_LI", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Emily M Eriksson", + "author_inst": "The Walter and Eliza Hall Institute" + }, + { + "author_name": "Anne Hart", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Maureen Forde", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Siavash Foroughi", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Nicholas Kiernan-Walker", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Ramin Mazhari", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Erin C. Lucas", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Mai Margetts", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Anthony Farchione", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Dylan Sheerin", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "George Ashdown", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Rachel Evans", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Catherine Chen", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Shazia Ruybal-Pesantez", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Eamon Conway", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Marilou H. Barrios", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Jasper Cornish", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Maria Edmonds", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Lee M. Henneken", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Lisa J. Ioannidis", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Sam W. Z. Olechnowicz", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Ryan B. Munnings", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Joanna R. Groom", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Diana S. Hansen", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Rory Bowden", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Anna K. Coussens", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Jason A. Tye-Din", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Vanessa L. Bryant", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia" + }, + { + "author_name": "Ivo Mueller", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.04.27.23289149", "rel_title": "The epidemiological impact of digital and manual contact tracing on the SARS-CoV-2 epidemic in the Netherlands: empirical evidence.", @@ -91954,57 +92785,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2023.04.20.23288904", - "rel_title": "Aerosol Jet Printing Enabled Dual-Function Electrochemical and Colorimetric Biosensor for SARS-CoV-2 Detection", - "rel_date": "2023-04-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.20.23288904", - "rel_abs": "An aerosol jet printing enabled dual-function biosensor for the sensitive detection of pathogens using SARS-CoV-2 RNA as an example has been developed. A CRISPR-Cas13: guide-RNA complex is activated in the presence of a target RNA, leading to the collateral trans-cleavage of ssRNA probes that contain a horseradish peroxidase (HRP) tag. This, in turn, catalyzes the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) by HRP, resulting in a color change and electrochemical signal change. The colorimetric and electrochemical sensing protocol does not require complicated target amplification and probe immobilization and exhibits a detection sensitivity in the femtomolar range. Additionally, our biosensor demonstrates a wide dynamic range of 5 orders of magnitude. This low-cost aerosol inkjet printing technique allows for an amplification-free and integrated dual-function biosensor platform, which operates at physiological temperature and is designed for simple, rapid, and accurate point-of-care (POC) diagnostics in either low-resource settings or hospitals.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Li Liu", - "author_inst": "University of California,Riverside" - }, - { - "author_name": "Zhiheng Xu", - "author_inst": "Rochester Institute of Technology" - }, - { - "author_name": "Adrian Moises Molina Vargas", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Steve Dollery", - "author_inst": "Biological Mimetics, Inc." - }, - { - "author_name": "Michael Schrlau", - "author_inst": "Rochester Institute of Technology" - }, - { - "author_name": "Denis Cormier", - "author_inst": "Rochester Institute of Technology" - }, - { - "author_name": "Mitchell O'Connell", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Gregory Tobin", - "author_inst": "Biological Mimetics, Inc." - }, - { - "author_name": "Ke Du", - "author_inst": "University of California, Riverside" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.04.24.23288921", "rel_title": "Immune signature of patients with cardiovascular disease - in-depth immunophenotyping predicts increased risk for a severe course of COVID-19", @@ -92221,6 +93001,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2023.04.19.23288799", + "rel_title": "Using extracted data from Kaplan-Meier curves to compare COVID-19 vaccine efficacy", + "rel_date": "2023-04-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.19.23288799", + "rel_abs": "Although various COVID-19 vaccines have shown efficacy against placebo in randomized clinical trials, no head-to-head comparisons are yet available. This study aims to compare the efficacy of available COVID-19 vaccines. Vaccine trials searched in May 2021 were included. Data were extracted from Kaplan-Meier (KM) curves using the WebPlotDigitizer program for the individual participant (IP) data simulation. A mixed-effect acceleration failure model with log-logistic and Weibull distributions was used to estimate relative effects for individual vaccines as well as grouped by class: inactivated virus, mRNA, and viral vector. Primary studies were considered as the random effect in the model. Hazard ratios (HR) were estimated and compared across vaccine groups. All vaccines were efficacious in lowering symptomatic infection compared to placebo. CoronaVac, Ad26.COV2.S, ChAdOx1 nCoV-19, rAd26/rAd5, WIV04, HB02, and BNT162b2 showed 7.61 (4.50, 12.87), 6.77 (4.08, 11.24), 5.01 (2.93, 8.57), 4.50 (2.52, 8.01), 3.90 (2.04, 7.45), 3.18 (1.62, 6.21), and 2.15 (1.22, 3.78) times significantly higher risk of infection than mRNA-1273. mRNA vaccines were the most efficacious vaccine group compared to inactivated virus and viral vectors with HRs (95% CI) of 0.27 (0.20, 0.37) and 0.28 (0.21, 0.37), respectively. Although all vaccines showed significant protection compared to no vaccination. mRNA vaccines, including mRNA-1273 and BNT162b2, showed the highest efficacy in preventing symptomatic COVID-19 infection. Simulated IP data from the KM curve might allow treatment comparison when there is no primary study comparing active treatments.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Amarit Tansawet", + "author_inst": "Navamindradhiraj University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2023.04.25.23289080", "rel_title": "Risks of digestive diseases in long COVID: Evidence from a large-scale cohort study", @@ -94084,61 +94883,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.04.17.23288710", - "rel_title": "COVID-19 testing avoidance among patients with cardiovascular disease", - "rel_date": "2023-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.17.23288710", - "rel_abs": "BackgroundRapid coronavirus 2019 (COVID-19) testing in symptomatic cases is extremely important for preventing the spread of COVID-19 infection and early therapeutic intervention. In contrast, whether symptomatic patients are tested depends largely on their health literacy, interpretation, and knowledge of COVID-19. We aimed to investigate the rate of COVID-19 testing avoidance despite having common cold symptoms in patients with cardiovascular disease and examine factors related to testing avoidance.\n\nMethodsA large-scale epidemiological questionnaire survey, the Japan COVID-19 and Society Internet Survey 2022 (JACSIS), was conducted online from April to May 2022. The rate of COVID-19 testing avoidance was investigated in patients aged 20 to 80 years with cardiovascular risk factors (hypertension, dyslipidemia, or diabetes) or a history of cardiovascular disease (angina, myocardial infarction, or stroke), only those exhibiting common cold symptoms during the 2 months in the survey.\n\nResultsOf the 1,565 eligible patients, 58% (909 patients) did not undergo COVID-19 testing. Multivariate analysis revealed that older age, obesity, non-walking regularly, long sedentary time, eating alone, frequent snacking, and having received 4 COVID-19 vaccinations were independently associated with testing avoidance.\n\nConclusionsIn the chronic phase of the COVID-19 pandemic, prompt COVID-19 testing at the time of symptomatic disease is important, and strategies to reduce testing hesitancy should be considered.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Koichiro Matsumura", - "author_inst": "Kindai University Faculty of Medicine" - }, - { - "author_name": "Takahiro Tabuchi", - "author_inst": "Osaka International Cancer Institute" - }, - { - "author_name": "Eijiro Yagi", - "author_inst": "Kindai University Faculty of Medicine" - }, - { - "author_name": "Takeshi Ijichi", - "author_inst": "Tokai University School of Medicine" - }, - { - "author_name": "Misaki Hasegawa", - "author_inst": "Tokai University School of Medicine" - }, - { - "author_name": "Nobuhiro Yamada", - "author_inst": "Kindai University Faculty of Medicine" - }, - { - "author_name": "Yohei Funauchi", - "author_inst": "Kindai University Faculty of Medicine" - }, - { - "author_name": "Kazuyoshi Kakehi", - "author_inst": "Kindai University Faculty of Medicine" - }, - { - "author_name": "Takayuki Kawamura", - "author_inst": "Kinki University Faculty of Medicine" - }, - { - "author_name": "Gaku Nakazawa", - "author_inst": "Kindai University Faculty of Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.04.18.23288715", "rel_title": "Preliminary clinical characteristics of Pediatric Covid-19 cases during the ongoing Omicron XBB.1.16 driven surge in a north Indian city", @@ -94283,6 +95027,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2023.04.19.23288791", + "rel_title": "Outcomes of non-hospitalized isolation service during COVID-19 pandemic", + "rel_date": "2023-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.19.23288791", + "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or COVID-19 affected more than 500 million patients worldwide and overwhelmed hospital resources. Rapid increase of new cases forced patient isolation to be conduct outside the hospital where many strategies have been implemented. This study aimed to compare outcomes among non-hospitalized isolation service.\n\nMethodsA retrospective cohort study was conducted in asymptomatic and mildly symptomatic adult patients who were allocated to home isolation, community isolation, and hospitel (i.e., hotel isolation) under service of Ramathibodi Hospital and Chakri Naruebodindra Medical Institute. Variables including patients characteristics, comorbidities, symptoms, and medication were retrieved for use in inverse-probability-weighted regression adjustment model. Risks and risk differences (RDs) of death, oxygen requirement, and hospitalization were estimated from the model afterward.\n\nResultsA total of 3869 patients were included in the analysis. Mean age was 41.8 {+/-} 16.5 years. Cough was presented in 62.2% of patients, followed by hyposmia (43.7%), runny nose (43.5%), sore throat (42.2%), and fever (38.6%). Among the isolation strategies, hospitel yielded the lowest risks of death (0.3%), oxygen requirement (4.5%), and hospitalization (3.3%). Hospitel had significantly lower oxygen requirements and hospitalization rates compared with home isolation with the RDs (95% CI) of -0.016 (-0.029, -0.002) and -0.025 (-0.038, -0.012), respectively. Death rates did not differ among isolation strategies.\n\nConclusionNon-hospitalized isolation is feasible and could ameliorate hospital demands. Given the lowest risks of death, hospitalization, and oxygen requirement, hospitel might be the best isolation strategy.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Amarit Tansawet", + "author_inst": "Navamindradhiraj University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, { "rel_doi": "10.1101/2023.04.17.23288664", "rel_title": "Post COVID-19 Condition, Work Ability and Occupational Changes: Results from a Population-based Cohort", @@ -96150,37 +96913,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.04.11.23288130", - "rel_title": "Clinical Performance of BD Veritor\u2122 Assay Across SARS-CoV-2 Variants", - "rel_date": "2023-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.11.23288130", - "rel_abs": "BackgroundDifferent rates of morbidity, mortality, transmission, and immune escape are associated with various strains of the SARS-CoV-2 virus. With the emergence of new strains during seasonal outbreaks, ensuring that antigen-based immunoassays can detect SARS-CoV-2 infections across identified circulating viral variants is a crucial component of infection control efforts.\n\nObjectiveTo validate the performance of the BD Veritor System for Rapid Detection of SARS-CoV-2 Assay (BD Veritor assay) to detect SARS-CoV-2 across variants of concern (VOC) and variants of interest (VOI).\n\nMethodsUsing the Illumina NextSeq 2000 Sequencer, viral sequencing was performed on prospectively collected, then frozen, SARS-CoV-2 RT-PCR positive nasal swabs stored in universal transport media (UTM). Specimens from symptomatic and asymptomatic individuals were included in the study. Using the information obtained from the sequencing analysis, the performance of the BD Veritor System assay was evaluated against the highly sensitive molecular RT-PCR Quidel Lyra SARS-CoV-2 assay for each variant.\n\nResultsThe resulting PPA was 97.4% (95% CI: 86.8, 99.5) for detection of SARS-CoV-2 across all variants identified by Next Generation Sequencing (i.e., WHO-labeled variants Alpha, Delta, Gamma, Iota, Lambda, as well as two other non-labeled variants), with a 100% PPA for five of the six variant labels identified.\n\nConclusionThe results demonstrate the robust performance of the BD Veritor assay in detecting SARS-CoV-2 in clinical nasal specimens in selected variants. As new variants emerge, additional studies will be beneficial to ensure the sustained performance of SARS-CoV-2 assays.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Karen Eckert", - "author_inst": "Becton, Dickinson and Company, BD Life Sciences, Integrated Diagnostic Solutions, 7 Loveton Circle, Sparks, MD, USA" - }, - { - "author_name": "Sebastian Gutierrez", - "author_inst": "Becton, Dickinson and Company, BD Life Sciences, Integrated Diagnostic Solutions, 7 Loveton Circle, Sparks, MD, USA" - }, - { - "author_name": "Brittany Knight", - "author_inst": "MRIGlobal, 425 Dr. Martin Luther King Jr. Blvd., Kansas City, MI" - }, - { - "author_name": "Lauren Cooper", - "author_inst": "Becton, Dickinson and Company, BD Life Sciences, Integrated Diagnostic Solutions, 7 Loveton Circle, Sparks, MD, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.04.12.23288362", "rel_title": "Bivalent COVID-19 booster vaccines induce cross-reactive but not BA.5-specific antibodies in polyclonal serum", @@ -96373,6 +97105,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2023.04.12.23288412", + "rel_title": "Severity of Prior COVID-19 Infection is Associated with Postoperative Outcomes Following Major Inpatient Surgery", + "rel_date": "2023-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.12.23288412", + "rel_abs": "ObjectiveTo determine the association between severity of prior history of SARS-CoV-2 infection and postoperative outcomes following major elective inpatient surgery.\n\nSummary Background DataSurgical guidelines instituted early in the COVID-19 pandemic recommended delay in surgery up to 8 weeks following an acute SARS-CoV-2 infection. Given that surgical delay can lead to worse medical outcomes, it is unclear if continuation of such stringent policies is necessary and beneficial for all patients, especially those recovering from asymptomatic or mildly symptomatic COVID-19.\n\nMethodsUtilizing the National Covid Cohort Collaborative (N3C), we assessed postoperative outcomes for adults with and without a history of COVID-19 who underwent major elective inpatient surgery between January 2020 and February 2023. COVID-19 severity and time from SARS-CoV-2 infection to surgery were each used as independent variables in multivariable logistic regression models.\n\nResultsThis study included 387,030 patients, of which 37,354 (9.7%) had a diagnosis of preoperative COVID-19. History of COVID-19 was found to be an independent risk factor for adverse postoperative outcomes even after a 12-week delay for patients with moderate and severe SARS-CoV-2 infection. Patients with mild COVID-19 did not have an increased risk of adverse postoperative outcomes at any time point. Vaccination decreased the odds of mortality and other complications.\n\nConclusionsImpact of COVID-19 on postoperative outcomes is dependent on severity of illness, with only moderate and severe disease leading to higher risk of adverse outcomes. Existing wait time policies should be updated to include consideration of COVID-19 disease severity and vaccination status.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Nathaniel B Verhagen", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "Gopika SenthilKumar", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "Taylor Jaraczewski", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "Nicolas K Koerber", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "Jennifer R Merrill", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "Madelyn A Flitcroft", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "Aniko Szabo", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "Anjishnu Banerjee", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "Xin Yang", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "Bradley W Taylor", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "Carlos E Figueroa Castro", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "Tina W.F. Yen", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "Callisia N Clarke", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "Kathryn Lauer", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "Kurt J Pfeifer", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "Jon C Gould", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "Anai N Kothari", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "- N3C Consortium", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "surgery" + }, { "rel_doi": "10.1101/2023.04.11.23288200", "rel_title": "Effect of face-covering use on adherence to other COVID-19 protective behaviours: a systematic review", @@ -98091,29 +98910,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.04.07.23288262", - "rel_title": "COVID-19 Vaccine Uptake And Its Associated Factors among general population In Basmaia City in Baghdad 2022", - "rel_date": "2023-04-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.07.23288262", - "rel_abs": "ObjectiveVaccination is a vital cornerstone of public health, which has saved countless lives throughout history. Therefore, achieving high vaccination uptake rates is essential for successful vaccination programs. Unfortunately, vaccine uptake has been hindered by deferent factors and challenges. The objective of this study is to assess COVID-19 vaccine uptake and associated factors among the general population.\n\nMethodsThis study is a descriptive cross-sectional study conducted in Basmaia city, Baghdad from June to October 2022. Data were collected through a semi-structured questionnaire using multi-stage random sampling. Statistical analysis was performed using descriptive statistics, chi-square analysis, Mann-Whitney test, and binary and multivariable logistic regression.\n\nResultsThe prevalence of COVID-19 vaccine uptake was 70.4%. The most common reason for getting vaccinated was protection from the disease, while fear of side effects and not needing the vaccine were the main reasons for refusal.\n\nThe study found that gender, age, education level, job title, risk perception, knowledge, and attitude towards the vaccine were significantly associated with COVID-19 vaccine uptake. Males were 2.273 times more likely to get vaccinated than females, and older age groups had higher odds of vaccination than younger age groups. Those with higher education levels were also more likely to receive the vaccine. Participants with higher risk perception, knowledge, and positive attitude towards the vaccine were more likely to get vaccinated.\n\nAnd found that mandatory vaccination policies may negatively impact uptake of subsequent vaccine doses.\n\nConclusionThe study found a high prevalence of COVID-19 vaccine uptake, with gender, age, education level, and job title being significant factors associated with vaccine uptake. Additionally, mandatory vaccination policies may have a negative impact on the uptake of subsequent vaccine doses. Public health efforts should prioritize addressing these factors to increase vaccine uptake.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Hussein Abdalrahim Alhlew", - "author_inst": "ministry of health" - }, - { - "author_name": "Mohammad Asaad Albayaty", - "author_inst": "al-Kindy college of medicine, Baghdad university" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.04.07.23288300", "rel_title": "Association between PM2.5 air pollution, temperature, and sunlight during different infectious stages with the case fatality of COVID-19 in the United Kingdom: a modeling study", @@ -98358,6 +99154,41 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2023.04.07.535766", + "rel_title": "Silymarin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells", + "rel_date": "2023-04-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.07.535766", + "rel_abs": "The study evaluated the invitro ability of Silymarin to inhibit SARS-COV-2 infection on Vero Cells. We set out to evaluate the hypothesis that Silymarin has both preventive and curative against SARS-COV-2. To study this, we first evaluated the safety profile of Silymarin using the Drosophila melanogaster(Harwich strain) model. Silymarin tablet film coated 140mg(Silybon-140) was used for the study. We evaluated the fly for acute toxicity, Locomotor performance, estimation of total thiol level, determination of Acetylcholinesterases (AchE) activity, Catalase activity, Glutathion-S-transferase(GST) activity and fecundity assay. To evaluate the invitro activity of Silymarin against SARS-COV-2, SARS-COV-2 isolates from oropharyngeal swabs and confirmed using qRT-PCR were cultured in Vero E6 monolayer cells. Different concentrations of silymarin concentration were used to determine pre- or post-exposure activity.\n\nThe result showed that daily exposure to silymarin dose between 50% to 2000% adult dose showed no adverse effect after 28 days. Treatment of Vero cells with silymarin at the concentration 250-500ug/ml all revealed a pre-treatment effect to SARS-COV-2 in vitro and no inhibition effect was observed when the virus was first added before the addition of Silymarin. Silymarin had no adverse effect on D. melanogaster and can be used a preventive drug against SARS-COV-2", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Nnaemeka Emmanuel Nnadi", + "author_inst": "Plateau State University" + }, + { + "author_name": "Pam Dachung Luka", + "author_inst": "National Veterinary Research Institute" + }, + { + "author_name": "Simeon Omale", + "author_inst": "University of Jos Faculty of Pharmaceutical Sciences" + }, + { + "author_name": "Nathan Yakubu Shehu", + "author_inst": "Jos University Teaching Hospital" + }, + { + "author_name": "John Chinyere Aguiyi", + "author_inst": "University of Jos Faculty of Pharmaceutical Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.04.05.23288207", "rel_title": "Integration of serial self-testing for COVID-19 as part of contact tracing in the Brazilian public health system: A pragmatic trial protocol", @@ -100033,93 +100864,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2023.04.01.23287538", - "rel_title": "Trends in weight gain recorded in English primary care before and during the Coronavirus-19 pandemic: an observational cohort study using the OpenSAFELY platform", - "rel_date": "2023-04-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.01.23287538", - "rel_abs": "BackgroundWe investigated which clinical and sociodemographic characteristics were associated with unhealthy patterns of weight gain amongst adults living in England during the pandemic.\n\nMethodsWith the approval of NHS England we conducted an observational cohort study of Body Mass Index (BMI) changes between March 2015 and March 2022 using the OpenSAFELY-TPP platform. We estimated individual rates of weight gain before and during the pandemic, and identified individuals with rapid weight gain (>0{middle dot}5kg/m2/year) in each period. We also estimated the change in rate of weight gain between the prepandemic and pandemic period and defined extreme-accelerators as the ten percent of individuals with the greatest increase (>1{middle dot}84kg/m2/year). We estimated associations with these outcomes using multivariate logistic regression.\n\nFindingsWe extracted data on 17,742,365 adults (50{middle dot}1% female, 76{middle dot}1% White British). Median BMI increased from 27{middle dot}8kg/m2 [IQR:24{middle dot}3-32{middle dot}1] in 2019 (March 2019 to February 2020) to 28{middle dot}0kg/m2 [24{middle dot}4-32{middle dot}6] in 2021. Rapid pandemic weight gain (n=3,214,155) was associated with female sex (male vs female: aOR 0{middle dot}76 [95%CI:0{middle dot}76-0{middle dot}76]); younger age (50-59-years vs 18-29-years: aOR 0{middle dot}60 [0{middle dot}60-0{middle dot}61]); White British ethnicity (Black Caribbean vs White British: aOR 0{middle dot}91 [0{middle dot}89-0{middle dot}94]); deprivation (least-deprived-IMD-quintile vs most-deprived: aOR 0{middle dot}77 [0{middle dot}77-0{middle dot}78]); and long-term conditions, of which mental health conditions had the greatest effect (e.g. depression (aOR 1{middle dot}18[1{middle dot}17-1{middle dot}18])). Similar characteristics increased risk of extreme acceleration (n=2,768,695).\n\nInterpretationWe found female sex, younger age, deprivation and mental health conditions increased risk of unhealthy patterns of pandemic weight gain. This highlights the need to incorporate sociodemographic, physical, and mental health characteristics when formulating post-pandemic research, policies, and interventions targeting BMI.\n\nFundingNIHR", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Miriam Samuel", - "author_inst": "Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom" - }, - { - "author_name": "Robin Y Park", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Sophie V Eastwood", - "author_inst": "University College London, London, United Kingdom" - }, - { - "author_name": "Fabiola Eto", - "author_inst": "Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom" - }, - { - "author_name": "Caroline E Morton", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Daniel Stow", - "author_inst": "Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom" - }, - { - "author_name": "Sebastian Bacon", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Jessica Morley", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Iain Dillingham", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "William J Hulme", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Kamlesh Khunti", - "author_inst": "Diabetes Research Centre, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, UK" - }, - { - "author_name": "Rohini Mathur", - "author_inst": "Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom" - }, - { - "author_name": "Jonathan Valabhji", - "author_inst": "Department of Diabetes and Endocrinology, Imperial College Healthcare NHS Trust, London, UK" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Sarah Finer", - "author_inst": "Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom" - }, - { - "author_name": "- The OpenSAFELY Collaborative", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2023.03.30.23287969", "rel_title": "A Graph Embedding Approach for Deciphering the Longitudinal Associations of Global Mobility and COVID-19 Cases", @@ -100284,6 +101028,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.04.02.535277", + "rel_title": "Community structure and temporal dynamics of SARS-CoV-2 epistatic network allows for early detection of emerging variants with altered phenotypes", + "rel_date": "2023-04-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.02.535277", + "rel_abs": "The rise of viral variants with altered phenotypes presents a significant public health challenge. In particular, the successive waves of COVID-19 have been driven by emerging variants of interest (VOIs) and variants of concern (VOCs), which are linked to modifications in phenotypic traits such as transmissibility, antibody resistance, and immune escape. Consequently, devising effective strategies to forecast emerging viral variants is critical for managing present and future epidemics. Although current evolutionary prediction tools mainly concentrate on single amino acid variants (SAVs) or isolated genomic changes, the observed history of VOCs and the extensive epistatic interactions within the SARS-CoV-2 genome suggest that predicting viral haplotypes, rather than individual mutations, is vital for efficient genomic surveillance. However, haplotype prediction is significantly more challenging problem, which precludes the use of traditional AI and Machine Learning approaches utilized in most mutation-based studies.\n\nThis study demonstrates that by examining the community structure of SARS-CoV-2 spike protein epistatic networks, it is feasible to efficiently detect or predict emerging haplotypes with altered transmissibility. These haplotypes can be linked to dense network communities, which become discernible significantly earlier than their associated viral variants reach noticeable prevalence levels. From these insights, we developed HELEN (Heralding Emerging Lineages in Epistatic Networks), a computational framework that identifies densely epistatically connected communities of SAV alleles and merges them into haplotypes using a combination of statistical inference, population genetics, and discrete optimization techniques. HELEN was validated by accurately identifying known SARS-CoV-2 VOCs and VOIs up to 10-12 months before they reached perceptible prevalence and were designated by the WHO. For example, our approach suggests that the spread of the Omicron haplotype or a closely related genomic variant could have been foreseen as early as the start of 2021, almost a year before its WHO designation. Moreover, HELEN offers greater scalability than phylogenetic lineage tracing methods, allowing for the analysis of millions of available SARS-CoV-2 genomes. Besides SARS-CoV-2, our methodology can be employed to detect emerging and circulating strains of any highly mutable pathogen with adequate genomic surveillance data.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Fatemeh Mohebbi", + "author_inst": "Georgia State University" + }, + { + "author_name": "Alex Zelikovsky", + "author_inst": "Georgia State University" + }, + { + "author_name": "Serghei Mangul", + "author_inst": "University of Southern California" + }, + { + "author_name": "Gerardo Chowell", + "author_inst": "Georgia State University" + }, + { + "author_name": "Pavel Skums", + "author_inst": "Georgia State University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.04.03.535401", "rel_title": "nanoCLAMP potently neutralizes SARS-CoV-2 and protects K18-hACE2 mice from infection", @@ -101826,25 +102605,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "transplantation" }, - { - "rel_doi": "10.1101/2023.03.28.23287762", - "rel_title": "Early real world evidence on the relative SARS-COV-2 vaccine effectiveness of bivalent COVID-19 booster doses: a rapid review.", - "rel_date": "2023-03-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.28.23287762", - "rel_abs": "The objective of this review is to give an overall view of COVID-19 bivalent vaccines knowledge and to explore their early available real world effectiveness evidence in the Omicron era.\n\nPresently, bivalent vaccines are generally offered to all groups eligible for their next booster, as defined by the national vaccination campaign, with varying policies between countries.\n\nThe use of bivalent vaccines is supported by immunogenity studies, which, nevetheless, have led to contradictory conclusions, and are not generally designed to measure clinical impact.\n\nIn order to critically appraise the available research on real world effectiveness, a systematic literature search was performed: out of 876 references examined, 14 studies were finally included and extracted. The findings of this review demonstrate modest to moderate additional protection of vaccination with bivalent BA.4-5 or BA.1 mRNA-booster vaccines against COVID-19 associated illness and hospitalization, -if compared with having received a monovalent dose as booster-, during a period when BA.5 and other Omicron sublineage viruses predominated globally,\n\nConsidering the complexity of the current immunity situation at global level, and the high level of heterogeneity both at study and at review level, these findings must be taken with caution. Further research on SARS-CoV-2 vaccine effectiveness against emerging SARS-CoV-2 variants is encouraged.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Monica Sane Schepisi", - "author_inst": "UniCamillus, International Medical University, Rome, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.24.23287658", "rel_title": "Safety and Immunogenicity of the NVX-CoV2373 Vaccine as a Booster in Adults Previously Vaccinated with the BBIBP-CorV Vaccine: An Interim Analysis", @@ -102009,6 +102769,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.03.28.534602", + "rel_title": "Deep repertoire mining uncovers ultra-broad coronavirus neutralizing antibodies targeting multiple epitopes", + "rel_date": "2023-03-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.28.534602", + "rel_abs": "Development of vaccines and therapeutics that are broadly effective against known and emergent coronaviruses is an urgent priority. Current strategies for developing pan-coronavirus countermeasures have largely focused on the receptor binding domain (RBD) and S2 regions of the coronavirus Spike protein; it has been unclear whether the N-terminal domain (NTD) is a viable target for universal vaccines and broadly neutralizing antibodies (Abs). Additionally, many RBD-targeting Abs have proven susceptible to viral escape. We screened the circulating B cell repertoires of COVID-19 survivors and vaccinees using multiplexed panels of uniquely barcoded antigens in a high-throughput single cell workflow to isolate over 9,000 SARS-CoV-2-specific monoclonal Abs (mAbs), providing an expansive view of the SARS-CoV-2-specific Ab repertoire. We observed many instances of clonal coalescence between individuals, suggesting that Ab responses frequently converge independently on similar genetic solutions. Among the recovered antibodies was TXG-0078, a public neutralizing mAb that binds the NTD supersite region of the coronavirus Spike protein and recognizes a diverse collection of alpha- and beta-coronaviruses. TXG-0078 achieves its exceptional binding breadth while utilizing the same VH1-24 variable gene signature and heavy chain-dominant binding pattern seen in other NTD supersite-specific neutralizing Abs with much narrower specificity. We also report the discovery of CC24.2, a pan-sarbecovirus neutralizing mAb that targets a novel RBD epitope and shows similar neutralization potency against all tested SARS-CoV-2 variants, including BQ.1.1 and XBB.1.5. A cocktail of TXG-0078 and CC24.2 provides protection against in vivo challenge with SARS-CoV-2, suggesting potential future use in variant-resistant therapeutic Ab cocktails and as templates for pan-coronavirus vaccine design.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Jonathan Hurtado", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Thomas F Rogers", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "David B Jaffe", + "author_inst": "10X Genomics" + }, + { + "author_name": "Bruce Adams", + "author_inst": "10x Genomics" + }, + { + "author_name": "Sandhya Bangaru", + "author_inst": "Scripps" + }, + { + "author_name": "Elijah Garcia", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Tazio Capozzola", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Terrence Messmer", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Pragati Sharma", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Ge Song", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Nathan Beutler", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Wanting He", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Katharina Dueker", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Rami Musharrafieh", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Michael J T Stubbington", + "author_inst": "10 Genomics" + }, + { + "author_name": "Dennis Burton", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Raiees Andrabi", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Andrew Ward", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Wyatt J McDonnell", + "author_inst": "10x Genomics" + }, + { + "author_name": "Bryan Briney", + "author_inst": "The Scripps Research Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.03.28.23287799", "rel_title": "The effects of weather and mobility on respiratory viruses dynamics before and after the COVID-19 pandemic", @@ -103272,65 +104127,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.03.24.23287700", - "rel_title": "The potential contribution of vaccination uptake to occupational differences in risk of SARS-CoV-2: Analysis of the ONS COVID-19 Infection Survey", - "rel_date": "2023-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.24.23287700", - "rel_abs": "ObjectivesTo assess variation in vaccination uptake across occupational groups as a potential explanation for variation in risk of SARS-CoV-2 infection.\n\nDesignWe analysed data from the UK Office of National Statistics COVID-19 Infection Survey linked to vaccination data from the National Immunisation Management System in England from December 1st 2020 to 11th May 2022. We analysed vaccination uptake and SARS-CoV-2 infection risk by occupational group and assessed whether adjustment for vaccination reduced the variation in risk between occupational groups.\n\nSetting\n\nResultsEstimated rates of triple-vaccination were high across all occupational groups (80% or above), but were lowest for food processing (80%), personal care (82%), hospitality (83%), manual occupations (84%), and retail (85%). High rates were observed for individuals working in health (95% for office-based, 92% for those in patient-facing roles) and education (91%) and office-based workers not included in other categories (90%). The impact of adjusting for vaccination when estimating relative risks of infection was generally modest (ratio of hazard ratios reduced from 1.38 to 1.32), but was consistent with the hypothesis that low vaccination rates contribute to elevated risk in some groups. Conversely, estimated relative risk for some occupational groups, such as people working in education, remained high despite high vaccine coverage.\n\nConclusionsVariation in vaccination coverage might account for a modest proportion of occupational differences in infection risk. Vaccination rates were uniformly very high in this cohort, which may suggest that the participants are not representative of the general population. Accordingly, these results should be considered tentative pending the accumulation of additional evidence.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Jack D Wilkinson", - "author_inst": "University of Manchester" - }, - { - "author_name": "Evangelia Demou", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Mark Cherrie", - "author_inst": "Institute of Occupational Medicine" - }, - { - "author_name": "Rhiannon Edge", - "author_inst": "University of Lancaster" - }, - { - "author_name": "Matthew Gittins", - "author_inst": "University of Manchester" - }, - { - "author_name": "Srinivasa Vittal Katikireddi", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Theocharis Kromydas", - "author_inst": "University of Glasgow" - }, - { - "author_name": "WIll Mueller", - "author_inst": "Institute for Occupational Medicine" - }, - { - "author_name": "Neil Pearce", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Martie van Tongeren", - "author_inst": "University of Manchester" - }, - { - "author_name": "Sarah Rhodes", - "author_inst": "University of Manchester" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2023.03.24.534062", "rel_title": "Intra-Host Mutation Rate of Acute SARS-CoV-2 Infection During the Initial Pandemic Wave", @@ -103715,6 +104511,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.03.23.23287633", + "rel_title": "Analysis of the risk and pre-emptive control of viral outbreaks accounting for within-host dynamics: SARS-CoV-2 antigen testing as a case study", + "rel_date": "2023-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.23.23287633", + "rel_abs": "In the era of living with COVID-19, the risk of localised SARS-CoV-2 outbreaks remains. Here, we develop a multi-scale modelling framework for estimating the local outbreak risk for a viral disease (the probability that a major outbreak results from a single case introduced into the population), accounting for within-host viral dynamics. Compared to population-level models previously used to estimate outbreak risks, our approach enables more detailed analysis of how the risk can be mitigated through pre-emptive interventions such as antigen testing. Considering SARS-CoV-2 as a case study, we quantify the within-host dynamics using data from individuals with omicron variant infections. We demonstrate that regular antigen testing reduces, but may not eliminate, the outbreak risk, depending on characteristics of local transmission. In our baseline analysis, daily antigen testing reduces the outbreak risk by 45% compared to a scenario without antigen testing. Additionally, we show that accounting for heterogeneity in within-host dynamics between individuals affects outbreak risk estimates and assessments of the impact of antigen testing. Our results therefore highlight important factors to consider when using multi-scale models to design pre-emptive interventions against SARS-CoV-2 and other viruses.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "William S Hart", + "author_inst": "University of Oxford" + }, + { + "author_name": "Hyeongki Park", + "author_inst": "Nagoya University" + }, + { + "author_name": "Yong Dam Jeong", + "author_inst": "Nagoya University" + }, + { + "author_name": "Kwang Su Kim", + "author_inst": "Nagoya University" + }, + { + "author_name": "Raiki Yoshimura", + "author_inst": "Nagoya University" + }, + { + "author_name": "Robin N Thompson", + "author_inst": "University of Warwick" + }, + { + "author_name": "Shingo Iwami", + "author_inst": "Nagoya University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.03.24.23287674", "rel_title": "Morbidity and mortality burden of COVID-19 in rural Madagascar: results from a longitudinal cohort and nested seroprevalence study", @@ -104922,57 +105761,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.03.20.23287264", - "rel_title": "Nasopharyngeal Angiotensin Converting Enzyme 2 (ACE2) Expression as a Risk-Factor for SARS-CoV-2 Transmission in Concurrent Hospital Associated Outbreaks", - "rel_date": "2023-03-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.20.23287264", - "rel_abs": "BackgroundWidespread human-to-human transmission of the severe acute respiratory syndrome coronavirus two (SARS-CoV-2) stems from a strong affinity for the cellular receptor angiotensin converting enzyme two (ACE2). We investigate the relationship between a patients nasopharyngeal ACE2 transcription and secondary transmission within a series of concurrent hospital associated SARS-CoV-2 outbreaks in British Columbia, Canada.\n\nMethodsEpidemiological case data from the outbreak investigations was merged with public health laboratory records and viral lineage calls, from whole genome sequencing, to reconstruct the concurrent outbreaks using infection tracing transmission network analysis. ACE2 transcription and RNA viral load were measured by quantitative real-time polymerase chain reaction. The transmission network was resolved to calculate the number of potential secondary cases. Bivariate and multivariable analyses using Poisson and Negative Binomial regression models was performed to estimate the association between ACE2 transcription the number of SARS-CoV-2 secondary cases.\n\nResultsThe infection tracing transmission network provided n = 76 potential transmission events across n = 103 cases. Bivariate comparisons found that on average ACE2 transcription did not differ between patients and healthcare workers (P = 0.86). High ACE2 transcription was observed in 98.6% of transmission events, either the primary or secondary case had above average ACE2. Multivariable analysis found that the association between ACE2 transcription and the number of secondary transmission events differs between patients and healthcare workers. In health care workers Negative Binomial regression estimated that a one unit change in ACE2 transcription decreases the number of secondary cases (B = -0.132 (95%CI: -0.255 to -0.0181) adjusting for RNA viral load. Conversely, in patients a one unit change in ACE2 transcription increases the number of secondary cases (B = 0.187 (95% CI: 0.0101 to 0.370) adjusting for RNA viral load. Sensitivity analysis found no significant relationship between ACE2 and secondary transmission in health care workers and confirmed the positive association among patients.\n\nConclusionOur study suggests that ACE2 transcription has a positive association with SARS-CoV-2 secondary transmission in admitted inpatients, but not health care workers in concurrent hospital associated outbreaks, and it should be further investigated as a risk-factor for viral transmission.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Aidan M Nikiforuk", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Kevin S Kuchinski", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Katy Short", - "author_inst": "Fraser Health Authority" - }, - { - "author_name": "Susan Roman", - "author_inst": "Fraser Health Authority" - }, - { - "author_name": "Michael A Irvine", - "author_inst": "British Columbia Centre for Disease Control" - }, - { - "author_name": "Natalie Prystajecky", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Agatha N Jassem", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "David M Patrick", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Inna Sekirov", - "author_inst": "The University of British Columbia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.03.20.23287490", "rel_title": "The Change of Screen Time and Screen Addiction, and their Association with Psychological Well-being During the COVID-19 Pandemic: An Analysis of US Country-Wide School-Age Children and Adolescents Between 2018 and 2020", @@ -105225,6 +106013,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.03.17.23287140", + "rel_title": "Reconstructing the first COVID-19 pandemic wave with minimal data", + "rel_date": "2023-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.17.23287140", + "rel_abs": "Accurate measurement of exposure to SARS-CoV-2 in the population is crucial for understanding the dynamics of disease transmission and evaluating the impacts of interventions. However, it is particularly challenging to achieve this in the early phase of a pandemic because of the sparsity of epidemiological data. In our previous publication[1], we developed an early pandemic diagnostic tool that can link minimum datasets: seroprevalence, mortality and infection testing data to estimate the true exposure in different regions of England and found levels of SARS-CoV-2 population exposure are considerably higher than suggested by seroprevalence surveys. Here, we re-examined and evaluated the model in the context of reconstructing the first COVID-19 epidemic wave in England from three perspectives: validation from ONS Coronavirus Infection Survey, relationship between model performance and data abundance and time-varying case detection rate. We found that our model can recover the first but unobserved epidemic wave of COVID-19 in England from March 2020 to June 2020 as long as two or three serological measurements are given as model inputs additionally, with the second wave during winter of 2020 validated by the estimates from ONS Coronavirus Infection Survey. Moreover, the model estimated that by the end of October in 2020 the UK governments official COVID-9 online dashboard reported COVID-19 cases only accounted for 9.1% (95%CrI (8.7%,9.8%)) of cumulative exposure, dramatically varying across two epidemic waves in England in 2020 (4.3% (95%CrI (4.1%, 4.6%)) vs 43.7% (95%CrI (40.7%, 47.3%))).", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Siyu Chen", + "author_inst": "Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, United Kingdom" + }, + { + "author_name": "Jennifer A Flegg", + "author_inst": "School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia" + }, + { + "author_name": "Katrina A Lythgoe", + "author_inst": "Big Data Institute, Li Ka Shing Centre for Health Information and Discovery; Department of Biology, University of Oxford, United Kingdom" + }, + { + "author_name": "Lisa J White", + "author_inst": "Department of Biology, University of Oxford, United Kingdom" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.03.13.23287183", "rel_title": "Socio-demographic characteristics associated with COVID-19 vaccination uptake in Switzerland: longitudinal analysis of the CoMix study", @@ -106943,73 +107762,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.03.16.23287322", - "rel_title": "Serial SARS-CoV-2 antibody titers in vaccinated dialysis patients: prevalence of unrecognized infection and duration of seroresponse", - "rel_date": "2023-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.16.23287322", - "rel_abs": "Rationale & ObjectiveSARS-CoV-2 infections are likely underdiagnosed, but the degree of underdiagnosis among maintenance dialysis patients is unknown. Durability of the immune response after third vaccine doses in this population also remains uncertain. This study tracked antibody levels to 1) assess the rate of undiagnosed infections and 2) characterize seroresponse durability after third doses.\n\nStudy DesignRetrospective observational study\n\nSetting & ParticipantsSARS-CoV-2 vaccinated patients receiving maintenance dialysis through a national dialysis provider. Immunoglobulin G spike antibodies (anti-spike IgG) titers were assessed monthly following vaccination.\n\nExposure(s)Two and three doses of SARS-CoV-2 vaccine\n\nOutcome(s)Undiagnosed and diagnosed SARS-CoV-2 infections; anti-spike IgG titers over time\n\nAnalytical Approach\"Undiagnosed\" SARS-CoV-2 infections were identified as an increase in anti-spike IgG titer of [≥] 100 BAU/mL, not associated with receipt of vaccine or \"diagnosed\" SARS-CoV-2 infection (by PCR or antigen test). In descriptive analyses, anti-spike IgG titers were followed over time.\n\nResultsAmong 2660 patients without prior COVID-19 who received an initial two-dose vaccine series, 371 (76%) SARS-CoV-2 infections were diagnosed and 115 (24%) were undiagnosed. Among 1717 patients without prior COVID-19 who received a third vaccine dose, 155 (80%) SARS-CoV-2 infections were diagnosed and 39 (20%) were undiagnosed. In both cohorts, anti-spike IgG levels declined over time. Of the initial two-dose cohort, 66% had a titer [≥] 500 BAU/mL in the first month, with 23% maintaining a titer [≥] 500 BAU/mL at six months. Of the third dose cohort, 95% had a titer [≥] 500 BAU/mL in the first month after the third dose, with 76% maintaining a titer [≥] 500 BAU/mL at six months.\n\nLimitationsAssays used had upper limits.\n\nConclusionsAmong maintenance dialysis patients, 20-24% of SARS-CoV-2 infections were undiagnosed. Given this populations vulnerability to COVID-19, ongoing infection control measures are needed. A three-dose primary mRNA vaccine series optimizes seroresponse rate and durability.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Caroline M Hsu", - "author_inst": "Tufts Medical Center" - }, - { - "author_name": "Daniel E Weiner", - "author_inst": "Tufts Medical Center" - }, - { - "author_name": "Harold J Manley", - "author_inst": "Dialysis Clinic Inc" - }, - { - "author_name": "Dana Miskulin", - "author_inst": "Tufts Medical Center" - }, - { - "author_name": "Vladimir Ladik", - "author_inst": "Dialysis Clinic Inc" - }, - { - "author_name": "Jill Frament", - "author_inst": "Dialysis Clinic Inc" - }, - { - "author_name": "Christos Argyropoulos", - "author_inst": "University of New Mexico" - }, - { - "author_name": "Kenneth Abreo", - "author_inst": "Louisiana State University, Health Sciences Center" - }, - { - "author_name": "Andrew Chin", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Reginald Gladish", - "author_inst": "Nephrology of North Alabama" - }, - { - "author_name": "Loay Salman", - "author_inst": "Albany Medical College" - }, - { - "author_name": "Doug Johnson", - "author_inst": "Dialysis Clinic Inc" - }, - { - "author_name": "Eduardo K Lacson Jr.", - "author_inst": "Dialysis Clinic Inc" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2023.03.16.23287360", "rel_title": "Relative vaccine effectiveness (rVE) of mRNA COVID-19 boosters in the UK vaccination programme, during the Spring-Summer (monovalent vaccine) and Autumn-Winter 2022 (bivalent vaccine) booster campaigns: a prospective test negative case-control study", @@ -107330,6 +108082,129 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.03.17.23287405", + "rel_title": "Molecular Neuropathology and Cerebrospinal Fluid Diagnostic Biomarkers of SARS-Cov2 Infection in Central Nervous System: A Scoping Review Protocol", + "rel_date": "2023-03-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.17.23287405", + "rel_abs": "IntroductionDespite the broad spectrum of neurological symptomatic manifestation in COVID19 patients, the brain tissue susceptibility and permissiveness to SARS-Cov2 infection is yet uncertain. This critical appraisal aims at bridging the gap by consolidating the body of evidence for meticulous evaluation of molecular neuropathological pathways and CSF diagnostic signatures of SARS-Cov2 infection in the central nervous system (CNS) that will underpin further strategic approach for neuroprotection and treatment of neurological COVID19\n\nMethods and AnalysisWe have developed the protocol of this review according to the provisions of Joanna Briggs Institute Reviewers Manual for Evidence Synthesis, 2015 and Arksey and O Malleys Methodological Framewotk, 2005. The articles for this review will be sourced from several electronic databases including EMBASE, PubMed, Scopus, Web of Science (WOS), Cochrane, Crossref Metadata and Semantic scholar. Herein we generated the search strategy using the medical subject headings [ MeSH Terms], term in all field bibliography at all permutations in conjunctions with boolean operators\n\nEthical Clearance and Dissemination planHerein the review will not involve the human participants henceforth the ethical clearance approval is not applicable. We will disseminate the final findings of this review to scientific conferences at local and international level. The manuscript for final findings will be published on reputable journal of neuroscience.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Victor Meza Kyaruzi", + "author_inst": "Muhimbili University of Health and Allied Sciences ,Dar es salaam , Tanzania , Research Department , WINNERS Foundation , Yaounde , Cameroon" + }, + { + "author_name": "Emmanuel Mduma", + "author_inst": "Rabininsia Memorial Hospital , Dar es salaam Tanzania" + }, + { + "author_name": "Soham Bandyopadhyay", + "author_inst": "Oxford University Global Surgery Group, University of Oxford, UK" + }, + { + "author_name": "Arsene Daniel Nyalundja", + "author_inst": "Faculty of Medicine, Universite Catholique de Bukavu, South Kivu, Democratic Republic of Congo ,Center for Tropical Diseases and Global Health, Universite Catho" + }, + { + "author_name": "Kasereka Kamabu", + "author_inst": "Department of Surgery, Neurosurgery, College of Medicine, Makerere University, Uganda" + }, + { + "author_name": "Bydaa Atron", + "author_inst": "Faculty of Medicine, Sivas Cumhuriyet University, Sivas, Turkiye" + }, + { + "author_name": "Mugenyi Nathan", + "author_inst": "Faculty of Medicine, Mbarara University of Science and Technology,Mbarara, Uganda" + }, + { + "author_name": "Jeremiah Oluwatomi Itodo Daniel", + "author_inst": "College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Osun, Nigeria" + }, + { + "author_name": "Yousif Zobidah Elamin", + "author_inst": "Department of histopathology and cytology , Omdurman Islamic University" + }, + { + "author_name": "Boniphace Barnabas Marwa", + "author_inst": "Department of Orthopedics , Traumatology and Neurosurgery, Muhimbili University of Health and Allied Science , Dar es salaam , Tanzania" + }, + { + "author_name": "Rajab Msemo", + "author_inst": "Department of Orthopedics, Traumatology and Neurosurgery, Muhimbili University of Health and Allied sciences , Dar es salaam , Tanzania" + }, + { + "author_name": "Ahmed Naeem", + "author_inst": "Al-Azhar University , Faculty of Medicine for Men in Assyut, Egypt" + }, + { + "author_name": "Tumusifu Manegabe jean de Dieu", + "author_inst": "Surgery Department, School of Medicine , Catholic Univarsity of Bukavu, Bukavu , DR Congo" + }, + { + "author_name": "Tarun Suvari Kumar", + "author_inst": "Rungaraya Medical College, Kakinada, India" + }, + { + "author_name": "Ngepgou Beckline Tazoah", + "author_inst": "Faculty of Health sciences, university of Buea , Cameroon" + }, + { + "author_name": "Ugwoke Franklin Chiazo", + "author_inst": "Faculty of Medicine, University of Calabar, Calabar Nigeria" + }, + { + "author_name": "Samuel Oreoluwa David", + "author_inst": "College of Health Science , Obafemi Awolowo University , Ile-Ife, Nigeria" + }, + { + "author_name": "Yves Jacket Nsavyimana", + "author_inst": "Faculty of Medicine, University of Burundi, Bujumbura, Burundi" + }, + { + "author_name": "Constansia Anselim Bureta", + "author_inst": "Department of Neurosurgery , Muhimbili Orthopedic Institute" + }, + { + "author_name": "Nicephorus Rutabasibwa", + "author_inst": "Department of Neurosurgery , Muhimbili University of Orthopedic Institute" + }, + { + "author_name": "Laurent Lemeri Mchome", + "author_inst": "Department of Neurosurgery , Muhimbili University of Orthopedic Institute" + }, + { + "author_name": "Emnet Tesfaye Shimber", + "author_inst": "Department of Critical Care and Emergency Medicine, Hawassa University, Ethiopia" + }, + { + "author_name": "Abenezer Tirsit", + "author_inst": "Department of Neurosurgery , Addis Ababa University , Addis Ababa , Ethiopia" + }, + { + "author_name": "Sayoki Mfinanga", + "author_inst": "Chief Research Scientist, National Institute of Medical Research, Dar es salaam, Tanzania" + }, + { + "author_name": "Getaw Worku Hassen", + "author_inst": "Department of Emergency Medicine, New York Medical College, New York, USA" + }, + { + "author_name": "Osama Abdellaziz", + "author_inst": "Department of Neurosurgery, Faculty of Medicine, Alexandria University, Alexandria, Egypt" + }, + { + "author_name": "Amos Mwakigonja", + "author_inst": "Department of Pathology, School of Medicine, Muhimbili University of Health and Allied Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2023.03.17.533105", "rel_title": "Magnipore: Prediction of differential single nucleotide changes in the Oxford Nanopore Technologies sequencing signal of SARS-CoV-2 samples", @@ -108829,73 +109704,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2023.03.12.23287049", - "rel_title": "The cost of primary care consultations associated with long COVID in non-hospitalised patients: a retrospective cohort study using UK primary care data", - "rel_date": "2023-03-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.12.23287049", - "rel_abs": "ObjectivesTo assess incremental costs of primary care consultations associated with post-Covid-19 condition or long COVID, to estimate associated national costs for the United Kingdom population, and to assess risk factors associated with increased costs.\n\nDesignA retrospective cohort study using a propensity score matching approach with an incremental cost method to estimate primary care consultation costs associated with long COVID.\n\nSettingUK based primary care general practitioner (GP), nurse and physiotherapist consultation data from the Clinical Practice Research Datalink Aurum primary care database from 31st January 2020 to 15th April 2021.\n\nParticipants472,173 non-hospitalised adults with confirmed SARS-CoV-2 infection were 1:1 propensity score matched to a pool of eligible patients with the same index date, the same number of prior consultations, and similar background characteristics, but without a record of COVID-19. Patients diagnosed with Long COVID (3,871) and those with World Health Organisation (WHO) defined symptoms of long COVID (30,174) formed two subgroups within the cohort with confirmed SARS-CoV-2 infection.\n\nMain outcome measuresCosts were calculated using a bottom-up costing approach with consultation cost per working hour in pound sterling ({pound}) obtained from the Personal Social Services Research Units Unit Costs of Health and Social Care 2021. The average incremental cost in comparison to patients with no record of COVID-19 was produced for each patient group, considering only consultation costs at least 12 weeks from the SARS-CoV-2 infection date or matched date for the comparator group (from 15th April 2020 to 15th April 2021). A sensitivity analysis was undertaken which restricted the study population to only those who had at least 24 weeks of follow-up. National costs were estimated by extrapolating incremental costs to the cumulative incidence of COVID-19 in the UK Office for National Statistics COVID-19 Infection Survey. The impacts of risk factors on the cost of consultations beyond 12 weeks from SARS-CoV-2 infection were assessed using an econometric ordinary least squares (OLS) regression model, where coefficients were interpreted as the percentage change in cost due to a unit increase in the specific factor.\n\nResultsThe incremental cost of primary care consultations potentially associated with long COVID was {pound}2.44 per patient with COVID-19 per year. This increased to {pound}5.72 in the sensitivity analysis. Extrapolating this to the UK population produced a cost estimate of {pound}23,382,452 (90% credible interval: {pound}21,378,567 to {pound}25,526,052) or {pound}54,814,601 (90% credible interval: {pound}50,116,967 to {pound}59,839,762) in the sensitivity analysis. Among patients with COVID-19 infection, a long COVID diagnosis and longer-term reporting of symptoms were associated with a 43% and 44% increase in primary care consultation costs respectively, compared to patients without long COVID symptoms. Older age (49% relative increase in costs in those aged 80 years or older compared to those aged 18 to 29 years), female sex (4% relative increase in costs compared to males), obesity (4% relative increase in costs compared to those of normal weight), comorbidities and the number of prior consultations were all associated with an increase in the cost of primary care consultations. By contrast, those from black ethnic groups had a 6% reduced relative cost compared to those from white ethnic groups.\n\nConclusionsThe costs of primary care consultations associated with long COVID in non-hospitalised adults are substantial. Costs are significantly higher among those diagnosed with long COVID, those with long COVID symptoms, older adults, females, and those with obesity and comorbidities.\n\nWhat is already known on this topic?O_LILong COVID is a global public health challenge, with millions of people affected worldwide.\nC_LIO_LIPeople with a history of long COVID use health services, including primary care, at a higher rate than uninfected individuals even beyond the period of acute infection.\nC_LIO_LIThe cost of this increased healthcare use is unknown, impeding planning and forecasting of resource requirements needed to adequately support people with long COVID.\nC_LI\n\nWhat this study adds?O_LIBeyond 12 weeks from acute infection, non-hospitalised adults with a history of SARS-CoV-2 infection cost primary care services an additional {pound}2.44 per patient per year greater on average than patients with no prior evidence of infection.\nC_LIO_LIDue to the high incidence of COVID-19, this represents a substantial cost to primary care services, in the UK exceeding {pound}20 million for consultations associated with long COVID.\nC_LIO_LIThese incremental costs are greater in those with a formal diagnosis of long COVID, those reporting related symptoms, older adults, females, and those with obesity.\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Jake Tufts", - "author_inst": "University Hospitals of Morecambe Bay NHS Foundation Trust, Lancashire, UK" - }, - { - "author_name": "Dawit T Zemedikun", - "author_inst": "School of Population and Global Health (M431), The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia" - }, - { - "author_name": "Anuradhaa Subramanian", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - }, - { - "author_name": "Naijie Guan", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - }, - { - "author_name": "Krishna Gokhale", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - }, - { - "author_name": "Puja Myles", - "author_inst": "Clinical Practice Research Datalink, Medicines and Healthcare products Regulatory Agency, London" - }, - { - "author_name": "Tim Williams", - "author_inst": "Clinical Practice Research Datalink, Medicines and Healthcare products Regulatory Agency, London" - }, - { - "author_name": "Tom Marshall", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - }, - { - "author_name": "Melanie Calvert", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK; Birmingham Health Partners Centre for Regulatory Science and Innovati" - }, - { - "author_name": "Karen Matthews", - "author_inst": "Long Covid SOS, Charity registered in England & Wales, 11A Westland Road, Faringdon, Oxfordshire, UK" - }, - { - "author_name": "Krishnarajah Nirantharakumar", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - }, - { - "author_name": "Louise Jackson", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - }, - { - "author_name": "Shamil Haroon", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2023.03.11.23287138", "rel_title": "How long is the long COVID? a retrospective analysis of football players in two major European Championships.", @@ -109080,6 +109888,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.03.14.532528", + "rel_title": "Nanobodies against SARS-CoV-2 reduced virus load in the brain of challenged mice and neutralized Wuhan, Delta and Omicron Variants", + "rel_date": "2023-03-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.14.532528", + "rel_abs": "In this work, we developed llama-derived nanobodies (Nbs) directed to the receptor binding domain (RBD) and other domains of the Spike (S) protein of SARS-CoV-2. Nanobodies were selected after the biopanning of two VHH-libraries, one of which was generated after the immunization of a llama (lama glama) with the bovine coronavirus (BCoV) Mebus, and another with the full-length pre-fused locked S protein (S-2P) and the RBD from the SARS-CoV-2 Wuhan strain (WT). Most of the neutralizing Nbs selected with either RBD or S-2P from SARS-CoV-2 were directed to RBD and were able to block S- 2P/ACE2 interaction. Three Nbs recognized the N-terminal domain (NTD) of the S-2P protein as measured by competition with biliverdin, while some non-neutralizing Nbs recognize epitopes in the S2 domain. One Nb from the BCoV immune library was directed to RBD but was non-neutralizing. Intranasal administration of Nbs induced protection ranging from 40% to 80% against COVID-19 death in k18-hACE2 mice challenged with the WT strain. Interestingly, protection was not only associated with a significant reduction of virus replication in nasal turbinates and lungs, but also with a reduction of virus load in the brain. Employing pseudovirus neutralization assays, we were able to identify Nbs with neutralizing capacity against the Alpha, Beta, Delta and Omicron variants. Furthermore, cocktails of different Nbs performed better than individual Nbs to neutralize two Omicron variants (B.1.529 and BA.2). Altogether, the data suggest these Nbs can potentially be used as a cocktail for intranasal treatment to prevent or treat COVID-19 encephalitis, or modified for prophylactic administration to fight this disease.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Mar\u00eda Florencia Pavan", + "author_inst": "INQUIMAE: Instituto de Quimica Fisica de los Materiales Medio Ambiente y Energia" + }, + { + "author_name": "Marina Bok", + "author_inst": "INTA: Instituto Nacional de Tecnologia Agropecuaria" + }, + { + "author_name": "Rafael Betanzos San Juan", + "author_inst": "CONICET: Consejo Nacional de Investigaciones Cientificas y Tecnicas" + }, + { + "author_name": "Juan Pablo Malito", + "author_inst": "INTA: Instituto Nacional de Tecnologia Agropecuaria" + }, + { + "author_name": "Gisela Ariana Marcoppido", + "author_inst": "INTA: Instituto Nacional de Tecnologia Agropecuaria" + }, + { + "author_name": "Diego Rafael Franco", + "author_inst": "INTA: Instituto Nacional de Tecnologia Agropecuaria" + }, + { + "author_name": "Daniela Ayelen Militello", + "author_inst": "INQUIMAE: Instituto de Quimica Fisica de los Materiales Medio Ambiente y Energia" + }, + { + "author_name": "Juan Manuel Schammas", + "author_inst": "INTA: Instituto Nacional de Tecnologia Agropecuaria" + }, + { + "author_name": "Sara Bari", + "author_inst": "INQUIMAE: Instituto de Quimica Fisica de los Materiales Medio Ambiente y Energia" + }, + { + "author_name": "William B. Stone", + "author_inst": "Virginia Tech: Virginia Polytechnic Institute and State University" + }, + { + "author_name": "Krisangel L\u00f3pez", + "author_inst": "Virginia Tech: Virginia Polytechnic Institute and State University" + }, + { + "author_name": "Danielle Porier", + "author_inst": "Virginia Tech: Virginia Polytechnic Institute and State University" + }, + { + "author_name": "John Muller", + "author_inst": "Virginia Tech: Virginia Polytechnic Institute and State University" + }, + { + "author_name": "Albert Jonathan Auguste", + "author_inst": "Virginia Tech: Virginia Polytechnic Institute and State University" + }, + { + "author_name": "Lijuan Yuan", + "author_inst": "Virginia Tech: Virginia Polytechnic Institute and State University" + }, + { + "author_name": "Andr\u00e9s Wigdorovitz", + "author_inst": "INTA: Instituto Nacional de Tecnologia Agropecuaria" + }, + { + "author_name": "Viviana Parreno", + "author_inst": "INTA: Instituto Nacional de Tecnologia Agropecuaria" + }, + { + "author_name": "Lorena Itat\u00ed Iba\u00f1ez", + "author_inst": "Instituto de Qu\u00edmica F\u00edsica de los Materiales Medio Ambiente y Energ\u00eda" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.03.14.532352", "rel_title": "Genomic surveillance reveals circulation of multiple variants and lineages of SARS-CoV-2 during COVID-19 pandemic in Indian city of Bengaluru", @@ -110347,33 +111242,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.03.09.23287043", - "rel_title": "Integrated analyses of single-cell RNA-seq public data reveal the gene regulatory network landscape of respiratory epithelial and peripheral immune cells in COVID-19 patients", - "rel_date": "2023-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.09.23287043", - "rel_abs": "IntroductionInfection with SARS-CoV-2 leads to coronavirus disease 2019 (COVID-19), which can result in acute respiratory distress syndrome and multiple organ failure. However, its comprehensive influence on pathological immune responses in the respiratory epithelium and peripheral immune cells is not yet fully understood.\n\nMethodsIn this study, we integrated multiple public scRNA-seq datasets of nasopharyngeal swab and peripheral blood results to investigate the gene regulatory networks (GRNs) of healthy individuals and COVID-19 patients with mild/moderate and severe disease, respectively. Similar and dissimilar regulons were identified within or between epithelial and immune cells during COVID-19 severity progression. The relative transcription factors (TFs) and their targets were used to construct GRNs among different infection sites and conditions.\n\nResultsBetween respiratory epithelial and peripheral immune cells, different TFs tended to be used to regulate the activity of a cell between healthy individuals and COVID-19 patients, although they had some TFs in common. For example, XBP1, FOS, STAT1, and STAT2 were activated in both the epithelial and immune cells of virus-infected individuals. In contrast, severe COVID-19 cases exhibited activation of CEBPD in peripheral immune cells, while CEBPB was exclusively activated in respiratory epithelial cells. Moreover, in patients with severe COVID-19, CEBPD upregulated S100A8 and S100A9 in CD14 and CD16 monocytes, while S100A9 genes were co-upregulated by different regulators (SPEDEF and ELF3) in goblet and squamous cells. The cell-cell communication analysis suggested that epidermal growth factor receptor signaling among epithelial cells contributes to mild/moderate disease, and chemokine signaling among immune cells contributes to severe disease.\n\nConclusionsThis study identified cell type- and condition-specific regulons in a wide range of cell types from the initial infection site to the peripheral blood, and clarified the diverse mechanisms of maladaptive responses to SARS-CoV-2 infection.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Lin Zhang", - "author_inst": "Tohoku University" - }, - { - "author_name": "Hafumi Nishi", - "author_inst": "Tohoku University; Ochanomizu University" - }, - { - "author_name": "Kengo Kinoshita", - "author_inst": "Tohoku University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.09.23287034", "rel_title": "Real-world effectiveness of sotrovimab for the treatment of SARS-CoV-2 infection during Omicron BA.2 subvariant predominance: a systematic literature review", @@ -110578,6 +111446,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.03.10.23287107", + "rel_title": "Sociodemographic inequity in COVID-19 vaccine uptake among youth in Zimbabwe", + "rel_date": "2023-03-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.10.23287107", + "rel_abs": "IntroductionCOVID-19 vaccine acceptance research has mostly originated from high-income countries and reasons why youth may not get vaccinated may differ in low-income settings. Understanding vaccination coverage across different population groups and the sociocultural influences in healthcare delivery is important to inform targeted vaccination campaigns.\n\nMethodsA population-based survey was conducted in 24 communities across three provinces (Harare, Bulawayo and Mashonaland East) in Zimbabwe between October 2021 and June 2022. Youth aged 18 - 24 years were recruited using random sampling. Data on sociodemographic information and COVID-19 vaccination uptake and reasons for non-uptake were collected.\n\nResultsA total of 17,682 youth were recruited (n=10,743, 60.8% female). The median age of survey participants was 20 (IQR: 19 - 22) years. Almost two thirds (n=10,651, 60.2%) of participants reported receiving at least one dose of COVID-19 vaccine. A higher proportion of men than women had been vaccinated (68.9% vs 54.7%), and vaccination prevalence increased with age (<19 years: 57.5%, 20-22: 61.5%, >23: 62.2%). Lack of time to get vaccinated, belief that the vaccine was unsafe and anxiety about side effects (particularly infertility) were the main reasons for not getting vaccinated. Factors associated with vaccination were male sex (OR=1.69, 95%CI:1.58-1.80), increasing age (>22 years: OR=1.12, 95%CI:1.04-1.21), education level (post-secondary: OR=4.34, 95%CI:3.27-5.76), and socioeconomic status (least poor: OR=1.32, 95%CI:1.20-1.47).\n\nConclusionThis study found vaccine inequity across age, sex, educational attainment and socioeconomic status among youth. Strategies should address these inequities by understanding concerns and tailoring vaccine campaigns to specific groups.\n\nWhat is already known on this topicMany countries have faced challenges when rolling out COVID-19 vaccines. Infrastructure, logistics, misinformation and vaccine hesitancy have been barriers to vaccine access and uptake globally. Vaccine nationalism by high-income countries has particularly affected countries in Africa and Asia, resulting in inequity between countries and regions.\n\nWhat this study addsVaccine uptake among youth in Zimbabwe was more than 50% across all age-groups. Men, those with more education and those living under less socially deprived socioeconomic conditions were more like to be vaccinated. Fear of side effects and myths circulating on social media were barriers. Religion was less of a barrier than other studies reported, likely due to religious institutions collaborations in COVID-19 vaccination efforts.\n\nHow this study might affect research, practice or policyVaccination campaigns should actively address specific concerns of communities, especially concerns around fertility and early death, and provide vaccines in easy-access and convenient locations. Involving community leaders in both education and vaccination efforts is pivotal given the trust and influence they have.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Leyla Sophie Larsson", + "author_inst": "Ludwig Maximilians University Munich" + }, + { + "author_name": "Chido Dziva Chikwari", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Victoria Simms", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Mandikudza Tembo", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Agnes Mahomva", + "author_inst": "Zimbabwe Government Office of the President and Cabinet" + }, + { + "author_name": "Owen Mugurungi", + "author_inst": "Ministry of Health and Child Care, Zimbabwe" + }, + { + "author_name": "Richard Hayes", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Constance Mackworth-Young", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Sarah Bernays", + "author_inst": "University of Sydney - Sydney Medical School Nepean" + }, + { + "author_name": "Constancia Mavodza", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Tinotenda Taruvinga", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Tsitsi Bandason", + "author_inst": "Biomedical Research and Training Institute" + }, + { + "author_name": "Ethel Dauya", + "author_inst": "Biomedical Research and Training Institute" + }, + { + "author_name": "Rashida Ferrand", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Katharina Kranzer", + "author_inst": "London School of Hygiene & Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.03.09.23287038", "rel_title": "Clinical Characteristics, Racial Inequities, and Outcomes in Patients with Breast Cancer and COVID-19: A COVID-19 and Cancer Consortium (CCC19) Cohort Study", @@ -111993,165 +112936,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.03.06.23286834", - "rel_title": "SARS-CoV-2 viral replication persists in the human lung for several weeks after onset of symptomatic severe COVID-19 and is associated with attenuated pulmonary immunity and variant-specific clinical sequalae", - "rel_date": "2023-03-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.06.23286834", - "rel_abs": "RationaleIn the upper respiratory tract replicating (culturable) SARS-CoV-2 is recoverable for [~] 4 to 8 days after symptom onset, however, there is paucity of data about the frequency or duration of replicating virus in the lower respiratory tract (i.e. the human lung).\n\nObjectivesWe undertook lung tissue sampling (needle biopsy), shortly after death, in 42 mechanically ventilated decedents during the Beta and Delta waves. An independent group of 18 ambulatory patents served as a control group.\n\nMethodsLung biopsy cores from decedents underwent viral culture, histopathological analysis, electron microscopy, transcriptomic profiling and immunohistochemistry.\n\nResults38% (16/42) of mechanically ventilated decedents had culturable virus in the lung for a median of 15 days (persisting for up to 4 weeks) after symptom onset. Lung viral culture positivity was not associated with comorbidities or steroid use. Delta but not Beta variant lung culture positivity was associated with accelerated death and secondary bacterial infection (p<0.05). Nasopharyngeal culture was negative in 23.1% (6/26) of decedents despite lung culture positivity. This, hitherto, undescribed bio-phenotype of lung-specific persisting viral replication was associated with an enhanced transcriptomic pulmonary pro-inflammatory response but with concurrent viral culture positivity.\n\nConclusionsConcurrent, rather than sequential active viral replication continues to drive a heightened pro-inflammatory response in the human lung beyond the second week of illness and was associated with variant-specific increased mortality and morbidity. These findings have potential implications for the design of interventional strategies and clinical management of patients with severe COVID-19 disease.\n\nAt a Glance CommentaryO_ST_ABSScientific Knowledge on the SubjectC_ST_ABSInvestigations to understand SARS-CoV-2 viral shedding (determined by PCR or antigen testing) have extensively focused on samples from the upper respiratory tract. The widely accepted view is that acute severe SARS-CoV-2 infection is characterised by a viral replicative phase in the first week of symptomatic illness followed by a pro-inflammatory immunopathologic phase peaking in the second and third weeks of illness. However, it remains unclear whether detection of SARS-CoV-2 beyond 2 weeks after symptom onset in published studies represent active replication competent virus because it may represent residual genomic or antigenic material in the tissue.\n\nWhat This Study Adds to the FieldWe have identified a, hitherto, undescribed bio-phenotype of acute severe COVID-19 characterised by persisting viral replication in the lung for up to 4 weeks after symptom onset. [~]40% of acute severe COVID-19 intensive care unit (ICU) decedents (n=42) had nasopharyngeal swab culture positivity at [~]2 weeks post-symptom onset versus only [~]5% in a group of ambulatory control patients (n=18). There was compartment-specific (nasopharynx versus lung) discordance. The phenotype of lung-specific persisting viral replication was associated with variant-specific accelerated death, an exaggerated inflammatory response, and attenuated T-cell immunity in the lung (based on histopathological and transcriptomic studies). This challenges the traditional view that viral replication occurs during the first 5 to 10 days of illness, which is followed by an effector or hyperinflammatory phase. This is the first study, to our knowledge, to systematically culture virus from the human lung and map out its related clinical determinants, and which describes the human lung transcriptomic profile of culture-positive versus culture-negative patients with severe COVID-19 disease.", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Michele Tomasicchio", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Shameem Jaumdally", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Anil Pooran", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Aliasgar Esmail", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Lindsay Wilson", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Andrea Kotze", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Lynn Semple", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Stuart Meier", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Komala Pillay", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Riyaadh Roberts", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Raymond Kriel", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Richard Meldau", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Suzette Oelofse", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Carley Mandviwala", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Jessica Burns", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Rolanda Londt", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Malika Davids", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Charnay van der Merwe", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Aqeedah Roomaney", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Louie Kuhn", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Tahlia Perumal", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Alex Scott", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Martin Hale", - "author_inst": "University of Witwatersrand" - }, - { - "author_name": "Vicky Baillie", - "author_inst": "University of Witwatersrand" - }, - { - "author_name": "Sana Mahtab", - "author_inst": "University of Witwatersrand" - }, - { - "author_name": "Carolyn Williamson", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Rageema Joseph", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Alex Sigal", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Ivan Joubert", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Jenna Piercy", - "author_inst": "University of Cape Town" - }, - { - "author_name": "David Thomson", - "author_inst": "University of Cape Town" - }, - { - "author_name": "David Fredericks", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Malcolm Miller", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Marta Nunes", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Shabir Madhi", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Keertan Dheda", - "author_inst": "University of Cape Town" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.06.531252", "rel_title": "Unraveling the Interactions between Human DPP4 Receptor, SARS-CoV-2 Variants, and MERS-CoV, converged for Pulmonary Disorders Integrating through Immunoinformatics and Molecular Dynamics", @@ -112352,6 +113136,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.03.07.23286894", + "rel_title": "Evaluating the theoretical performance of aircraft wastewater monitoring as a tool for SARS-CoV-2 surveillance", + "rel_date": "2023-03-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.07.23286894", + "rel_abs": "BackgroundAir travel plays an import role in the cross-border spread of infectious diseases. During the SARS-CoV-2 pandemic many countries introduced strict border testing protocols to monitor the incursion of the virus. However, the high implementation cost and significant inconvenience to passengers has led public health authorities to consider alternative methods of disease surveillance at borders. Aircraft wastewater monitoring has been proposed as one such alternative. In this paper we assess the theoretical limits of aircraft wastewater monitoring and compare its performance to post-arrival border screening approaches.\n\nMethodsWe use an infectious disease model to simulate an unmitigated SARS-CoV-2 epidemic in a seed country. Seeding of the epidemic into the United Kingdom (UK) is simulated through daily flights between the two countries. We use a probabilistic approach to estimate the time of first detection of the disease in the UK in both aircraft wastewater and respiratory swab screening at the border.\n\nResultsFor simulations across a broad range of model parameters, our analysis indicates that the median time between the first incursion of a pathogen and its detection in wastewater would be approximately 17 days (IQR: 7 - 28 days), resulting in a median of 25 cumulative cases (IQR: 6 - 84 cases) in the UK at the point of detection. Comparisons to respiratory swab screening suggest that aircraft wastewater monitoring is as effective as screening of 20% of passengers at the border, using a test with 95% sensitivity. For testing regimes with sensitivity of 85% or less, the required coverage to outperform wastewater monitoring increases to 30%. These results demonstrate the potential use cases of aircraft wastewater monitoring and its utility in a wider system of public health surveillance.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Joseph W Shingleton", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Chris Lilley", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Matthew J Wade", + "author_inst": "UK Health Security Agency" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.03.07.23286910", "rel_title": "Giving a voice to adults with COVID-19: An analysis of open-ended comments from smell longhaulers and non-longhaulers", @@ -113943,41 +114754,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.03.02.23286561", - "rel_title": "Bivalent booster effectiveness against severe COVID-19 outcomes in Finland, September 2022 - January 2023", - "rel_date": "2023-03-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.02.23286561", - "rel_abs": "Bivalent COVID-19 vaccines were introduced in 2022 but knowledge of their effectiveness against severe COVID-19 outcomes is currently limited. In Finnish register-based cohort analyses, we compared the risk of severe COVID-19 outcomes among those who received bivalent vaccination (exposed) between September 2022 and March 2023 to those who did not (unexposed). Among elderly aged 65-110 years, bivalent vaccination reduced the risk of hospitalisation and death due to COVID-19 in September-December 2022; the hazard ratios comparing exposed and unexposed ranged from 0.37 to 0.45 during the first 31-60 days since bivalent vaccination. However, in January-March 2023 the effect disappeared possibly indicating immune evasion of new SARS-CoV-2 variants, waning of vaccine effectiveness and increased presence of hybrid immunity. Among the chronically ill aged 18-64 years bivalent vaccination did not reduce the risk of severe COVID-19 outcomes. These results are important for developing COVID-19 vaccines and programmes worldwide.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Eero Poukka", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Hanna Nohynek", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Sirkka Goebeler", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Tuija Leino", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Ulrike Baum", - "author_inst": "Finnish Institute for Health and Welfare" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.02.23286686", "rel_title": "Impact of COVID-19 pandemic on the etiology and characteristics of community-acquired pneumonia among children requiring bronchoalveolar lavage in northern China", @@ -114218,6 +114994,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.03.01.23286624", + "rel_title": "Risk of cardiovascular events following COVID-19 in people with and without pre-existing chronic respiratory disease", + "rel_date": "2023-03-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.01.23286624", + "rel_abs": "BackgroundCOVID-19 is associated with a higher risk of cardiovascular outcomes in the general population, but it is unknown whether people with pre-existing chronic respiratory disease (CRD) have a higher risk of cardiovascular events post-COVID-19 compared with the general population and, if so, what respiratory-related risk factors may modify this risk in these people.\n\nMethodsPrimary and secondary care data from the National Health Service and COVID-19-specific linked data were used to define a population of adults in England with COVID-19 (index date) between 01/01/2020-30/11/2021. Adjusted Cox Proportional Hazard regression was used to quantify the association between CRD, asthma-related factors, COPD-related factors, and risk of cardiovascular events. CRD included asthma, COPD, bronchiectasis, cystic fibrosis, or pulmonary fibrosis prior to COVID-19 diagnosis. Asthma-specific factors included baseline asthma control, exacerbations, and inhaled corticosteroid (ICS) dose. COPD-specific risk factors included baseline ICS prescriptions and exacerbations. Secondary objectives quantified the impact of COVID-19 hospitalisation and vaccine dose on cardiovascular outcomes.\n\nResultsOf 3,670,455 people, those with CRD had a modest higher risk of cardiovascular events (HRadj 1.11, 95%CI 1.07-1.14), heart failure (HRadj 1.15, 1.09-1.21), and pulmonary emboli (HRadj 1.20, 1.11-1.30) compared with people without CRD. In people with asthma, baseline exacerbations and high-dose ICS were associated with a higher risk of cardiovascular outcomes (HRadj 1.24, 1.15-1.34 and 1.12, 1.01-1.24, respectively). In people with COPD, exacerbations were associated with a higher risk of cardiovascular outcomes (HRadj 1.40, 1.28-1.52). Regardless of CRD, the risk of cardiovascular events was lower with increasing COVID-19 vaccine dose.\n\nConclusionsHigher risk of cardiovascular events following COVID-19 might be explained at least in part by the underlying CRD and severity of that condition. In addition, COVID-19 vaccines were beneficial to both people with and without CRD with regards to CV events.\n\nKey MessagesPre-existing chronic respiratory disease, asthma and COPD severity were associated with a higher risk of various types of cardiovascular outcomes following COVID-19. Regardless of having pre-existing chronic respiratory disease, COVID-19 vaccination reduced the risk of cardiovascular events following COVID-19.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Hannah Whittaker", + "author_inst": "Imperial College London" + }, + { + "author_name": "Costantinos Kallis", + "author_inst": "Imperial College London" + }, + { + "author_name": "Angela Wood", + "author_inst": "Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, United Kingdom" + }, + { + "author_name": "Thomas Bolton", + "author_inst": "Health Data Research UK" + }, + { + "author_name": "Samantha Walker", + "author_inst": "Asthm + Lung" + }, + { + "author_name": "Aziz Sheikh", + "author_inst": "The University of Edinburgh College of Medicine and Veterinary Medicine" + }, + { + "author_name": "Alex Brownrigg", + "author_inst": "Health Data Research UK BREATHE" + }, + { + "author_name": "Ashley Akbari", + "author_inst": "Swansea University" + }, + { + "author_name": "Kamil Sterniczuk", + "author_inst": "Health Data Research UK BREATHE" + }, + { + "author_name": "Jennifer K Quint", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.03.01.23286616", "rel_title": "Virological evidence of the impact of non-pharmaceutical interventions against COVID-19 in a resource-limited setting", @@ -115697,33 +116528,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2023.02.28.530489", - "rel_title": "Coarse-Grained Molecular Simulations and Ensemble-Based Mutational Profiling of Protein Stability in the Different Functional Forms of the SARS-CoV-2 Spike Trimers : Balancing Stability and Adaptability in BA.1, BA.2 and BA.2.75 Variants", - "rel_date": "2023-03-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.28.530489", - "rel_abs": "The evolutionary and functional studies suggested that the emergence of the Omicron variants can be determined by multiple fitness trade-offs including the immune escape, binding affinity, conformational plasticity, protein stability and allosteric modulation. In this study, we embarked on a systematic comparative analysis of the conformational dynamics, electrostatics, protein stability and allostery in the different functional states of spike trimers for BA.1, BA.2, and BA.2.75 variants. Using efficient and accurate coarse-grained simulations and atomistic reconstruction of the ensembles, we examined conformational dynamics of the spike trimers that agrees with the recent functional studies, suggesting that BA.2.75 trimers are the most stable among these variants. A systematic mutational scanning of the inter-protomer interfaces in the spike trimers revealed a group of conserved structural stability hotspots that play a key role in modulation of functional dynamics and are also involved in the inter-protomer couplings through local contacts and interaction networks with the Omicron mutational sites. The results of mutational scanning provided evidence that BA.2.75 trimers are more stable than BA.2 and comparable in stability to BA.1 variant. Using dynamic network modeling of the S Omicron BA.1, BA.2 and BA.2.75 trimers we showed that the key network positions driving long-range signaling are associated with the major stability hotspots that are inter-connected along potential communication pathways, while sites of Omicron mutations may often correspond to weak spots of stability and allostery but are coupled to the major stability hotspots through interaction networks. The presented analysis of the BA.1, BA.2 and BA.2.75 trimers suggested that thermodynamic stability of BA.1 and BA.2.75 variants may be intimately linked with the residue interaction network organization that allows for a broad ensemble of allosteric communications in which signaling between structural stability hotspots may be modulated by the Omicron mutational sites. The findings provided plausible rationale for mechanisms in which Omicron mutations can evolve to balance thermodynamic stability and conformational adaptability in order to ensure proper tradeoff between stability, binding and immune escape.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Gennady Verkhivker", - "author_inst": "Chapman University School of Pharmacy" - }, - { - "author_name": "Mohammed Alshahrani", - "author_inst": "Chapman University" - }, - { - "author_name": "Grace Gupta", - "author_inst": "Chapman Unversity" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2023.02.26.23286261", "rel_title": "SARS-CoV-2 post-vaccine surveillance studies in Australian children and adults with cancer: SerOzNET Statistical Analysis Plan", @@ -116068,6 +116872,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.02.27.530294", + "rel_title": "Rolosense: Mechanical detection of SARS-CoV-2 using a DNA-based motor", + "rel_date": "2023-02-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.27.530294", + "rel_abs": "Assays detecting viral infections play a significant role in limiting the spread of diseases such as SARS-CoV-2. Here we present Rolosense, a virus sensing platform that transduces the motion of synthetic DNA-based motors transporting 5-micron particles on RNA fuel chips. Motors and chips are modified with virus-binding aptamers that lead to stalling of motion. Therefore, motors perform a \"mechanical test\" of viral target and stall in the presence of whole virions which represents a unique mechanism of transduction distinct from conventional assays. Rolosense can detect SARS-CoV-2 spiked in artificial saliva and exhaled breath condensate with a sensitivity of 103 copies/mL and discriminates among other respiratory viruses. The assay is modular and amenable to multiplexing, as we demonstrated one-pot detection of influenza A and SARS-CoV-2. As a proof-of-concept, we show readout can be achieved using a smartphone camera in as little as 15 mins without any sample preparation steps. Taken together, mechanical detection using Rolosense can be broadly applied to any viral target and has the potential to enable rapid, low-cost, point-of-care screening of circulating viruses.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Selma Piranej", + "author_inst": "Emory University" + }, + { + "author_name": "Luona Zhang", + "author_inst": "Emory University" + }, + { + "author_name": "Alisina Bazrafshan", + "author_inst": "Emory University" + }, + { + "author_name": "Mariana Marin", + "author_inst": "Emory University" + }, + { + "author_name": "Gregory B Melikyan", + "author_inst": "Emory University" + }, + { + "author_name": "Khalid Salaita", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2023.02.28.530444", "rel_title": "SARS-CoV-2 surveillance between 2020 and 2021 of all mammalian species in two Flemish zoos (Antwerp Zoo and Planckendael Zoo)", @@ -117487,25 +118330,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.02.15.23285880", - "rel_title": "Has the COVID-19 pandemic ended or not? opinions from the public in the U.S.", - "rel_date": "2023-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.15.23285880", - "rel_abs": "Recently President Joe Biden announced the end to the COVID-19 pandemic in the US but some scientists expressed different opinions. This study aimed to examine the view of the end of the COVID-19 pandemic among the public. Data were collected in September 2022 from an online crowdsourcing platform, and respondents answered if they believed that the pandemic has ended in the United States or not. Logistic regressions were used to estimate the likelihood of agreeing on the end of the pandemic, adjusted by demographics and several related variables. Among 2983 respondents, 78.1% believed that the COVID-19 pandemic had ended, and the percentage decreased to 66.5% after adding weights. Males, younger adults, Hispanics, those with higher levels of educational attainment, those with middle levels of household income, those living in suburban or rural areas, and those living in states that voted for the Republican party in the 2020 Presidential Election were more likely to believe that the pandemic had ended, compared with their counterparts. With about one-third of Americans did not agree that the pandemic had ended and marked demographical and geographical differences, the timing and the way of the pandemic end announcement should be deliberately cautious.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Yong Yang", - "author_inst": "University of Memphis" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.02.16.23286009", "rel_title": "Vaccine-induced correlate of protection against fatal COVID-19 in the old and frail during waves of neutralization resistant variants of concern.", @@ -117862,6 +118686,157 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.02.22.23286293", + "rel_title": "SARS-CoV2 mRNA-vaccination-induced Immunological Memory in Human Non-Lymphoid and Lymphoid Tissues", + "rel_date": "2023-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.22.23286293", + "rel_abs": "Tissue-resident lymphocytes provide organ-adapted protection against invading pathogens. Whereas their biology has been examined in great detail in various infection models, their generation and functionality in response to vaccination has not been comprehensively analyzed in humans. We therefore studied SARS-CoV2 mRNA-vaccine-specific T cells in surgery specimens of kidney, liver, lung, bone marrow and spleen in comparison to paired blood samples from largely virus-naive individuals. As opposed to lymphoid tissues, non-lymphoid organs harbored significantly elevated frequencies of Spike-specific CD4+ T cells compared to paired peripheral blood showing hallmarks of tissue residency and an expanded memory pool. Organ-derived, vaccine-specific T helper (Th) cells were characterized by increased portions of multifunctional cells over those detected in blood. Single-cell RNA sequencing revealed functional rather than organ-specific clusters of Spike-reactive Th cells, indicating similar diversification programs across tissues. T cell receptor (TCR) repertoire analysis indicated that the TCR sequence is a major determinant of transcriptomic state in tissue-resident, vaccine-specific CD4+ T cells. In summary, our data demonstrate that SARS-CoV2 vaccination entails acquisition of tissue memory and residency features in organs distant from the inoculation site, thereby contributing to our understanding of how local tissue protection might be accomplished.\n\nOne sentence summarySARS-CoV2 mRNA vaccination-induced CD4+ Th cells reside in both human lymphoid and non-lymphoid organs showing distinct adaptations in tissues with respect to memory differentiation, retention and function.", + "rel_num_authors": 34, + "rel_authors": [ + { + "author_name": "Vanessa Pross", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Arne Sattler", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Soeren Lukassen", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Laura Toth", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Linda Marie Laura Thole", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Janine Siegle", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Carolin Stahl", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "An He", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Georg Damm", + "author_inst": "University Hospital Leipzig" + }, + { + "author_name": "Daniel Seehofer", + "author_inst": "University Hospital Leipzig" + }, + { + "author_name": "Christina Goetz", + "author_inst": "University Hospital Leipzig" + }, + { + "author_name": "Christian Bayerl", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Pia Jaeger", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Alexander Macke", + "author_inst": "Vivantes Klinikum Neukoelln, Berlin" + }, + { + "author_name": "Stephan Eggeling", + "author_inst": "Vivantes Klinikum Neukoelln, Berlin" + }, + { + "author_name": "Bernadette Kirzinger", + "author_inst": "Vivantes klinikum Neukoelln, Berlin" + }, + { + "author_name": "Thomas Mayr", + "author_inst": "Vivantes Klinikum Neukoelln, Berlin" + }, + { + "author_name": "Hermann Herbst", + "author_inst": "Vivantes Klinikum Neukoelln, Berlin" + }, + { + "author_name": "Katharina Bayer", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Dominik Laue", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Jan Kroenke", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Jan Braune", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Friederike Rosseck", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Frank Friedersdorff", + "author_inst": "Evangelisches Krankenhaus Koenigin Elisabeth Herzberge, Berlin" + }, + { + "author_name": "Mandy Hubatsch", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Sarah Weinberger", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Nils Lachmann", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Veit Hofmann", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Eva Schrezenmeier", + "author_inst": "Charite - Universitaetsmedizin, Berlin" + }, + { + "author_name": "Carolin Ludwig", + "author_inst": "German Red Cross Blood Transfusion Service Baden-Wuerttemberg-Hessen and University Hospital Ulm" + }, + { + "author_name": "Hubert Schrezenmeier", + "author_inst": "University Hospital Ulm" + }, + { + "author_name": "Katharina Jechow", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Christian Conrad", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Katja Kotsch", + "author_inst": "Charite - Universitaetsmedizin Berlin" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2023.02.16.23285979", "rel_title": "Characteristics and Outcomes of Multisystem Inflammatory Syndrome in Children: A Multicenter, Retrospective, Observational Cohort Study in Mexico", @@ -119209,65 +120184,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.02.21.23286181", - "rel_title": "Associations between SARS-CoV-2 infection and incidence of new chronic condition diagnoses: a systematic review", - "rel_date": "2023-02-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.21.23286181", - "rel_abs": "Because of the large number of infected individuals, an estimate of the future burdens of the long-term consequences of SARS-CoV-2 infection is needed. This systematic review examined associations between SARS-CoV-2 infection and incidence of categories of and selected chronic conditions, by age and severity of infection (inpatient vs. outpatient/mixed care). MEDLINE and EMBASE were searched (Jan 1, 2020 to Oct 4, 2022) and reference lists scanned. We included observational studies from high-income OECD countries with a control group adjusting for sex and comorbidities. Identified records underwent a two-stage screening process. Two reviewers screened 50% of titles/abstracts, after which DistillerAI acted as second reviewer. Two reviewers then screened the full texts of stage one selections. One reviewer extracted data and assessed risk of bias; results were verified by another. Random-effects meta-analysis estimated pooled hazard ratios (HR). GRADE assessed certainty of the evidence. Twenty-five studies were included. Among the outpatient/mixed SARS-CoV-2 care group, there is high certainty of a small-to-moderate increase (i.e., HR 1.26 to 1.99) among adults [≥]65 years of any cardiovascular condition, and of little-to-no difference (i.e., HR 0.75 to 1.25) in anxiety disorders for individuals <18, 18-64, and [≥]65 years old. Among 18-64 and [≥]65 year-olds receiving outpatient/mixed care there are probably (moderate certainty) large increases (i.e., HR [≥]2.0) in encephalopathy, interstitial lung disease, and respiratory failure. After SARS-CoV-2 infection, there is probably an increased risk of diagnoses for some chronic conditions; whether the magnitude of risk will remain stable into the future is uncertain.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Lindsay A. Gaudet", - "author_inst": "University of Alberta" - }, - { - "author_name": "Jennifer Pillay", - "author_inst": "University of Alberta" - }, - { - "author_name": "Sabrina Saba", - "author_inst": "University of Alberta" - }, - { - "author_name": "Dianne Zakaria", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Nicholas Cheta", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "H\u00e9l\u00e8ne Gardiner", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Larry Shaver", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Jacqueline Middleton", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Maria Tan", - "author_inst": "University of Alberta" - }, - { - "author_name": "Ben Vandermeer", - "author_inst": "University of Alberta" - }, - { - "author_name": "Lisa Hartling", - "author_inst": "University of Alberta" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.02.14.23285860", "rel_title": "REAL-WORLD EFFECTIVENESS OF NIRMATRELVIR/RITONAVIR ON COVID-19-ASSOCIATED HOSPITALIZATION PREVENTION: A POPULATION-BASED COHORT STUDY IN THE PROVINCE OF QUEBEC, CANADA", @@ -119412,6 +120328,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.02.13.23285851", + "rel_title": "Athlete deaths during the COVID-19 vaccination campaign: contextualisation of online information", + "rel_date": "2023-02-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.13.23285851", + "rel_abs": "Background and aimLay people and medical professionals have suggested a link between (mRNA) COVID-19 vaccination and a purported increase in sudden cardiac arrest (SCA) and death (SCD) among athletes. We aimed to compare the athlete death rate in 2021-2022 with pre-pandemic estimates and investigate the role of vaccination.\n\nMethodsA comprehensive, much referenced, publicly available list of health issues, emergencies, and SCA/SCD in athletes from January 2021 to December 2022 was analysed. Demographic data, country, type of sport, vaccination status, and possible association between reported medical events and vaccination were evaluated for the complete set of athletes. The following data were specifically assessed for cases of SCD in young US athletes and compared to matched data from pre-pandemic studies: average annual SCD number, mean age, male/female ratio, sports with highest death toll, cause and scene of death, and relation to exercise. Descriptive statistics were used.\n\nResultsThe list contained 1653 entries. (Former) athletes, aged 5-86 years, from 99 countries, participated in 61 different sports. In multiple cases, causes of and circumstances surrounding medical events were irretrievable. Many cases involved non-cardiovascular, exercise-unrelated aetiologies. Vaccination details were scarce. In 63 (3.8%) cases, including 9 fatal events, there was a plausible association with COVID-19 vaccination. In US athletes aged 9-40 (mean 22.7) years, 166 SCD cases were identified (average 83/year), mainly in males (83%) and in football (39.8%) and basketball (16.9%). Main causes of death were non-cardiovascular exercise-unrelated (22.9%) or unknown (50.6%). Deaths primarily occurred at rest (32.5%) or under unknown circumstances (38.6%). SCD characteristics were similar to those of two pre-pandemic studies with comparable datasets.\n\nConclusionSCD rate among young US athletes in 2021-2022 was comparable to pre-pandemic estimates. There is currently no evidence to substantiate a link between (mRNA) COVID-19 vaccination and SCD in (young) athletes.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Mathijs Binkhorst", + "author_inst": "Radboudumc" + }, + { + "author_name": "Daniel J Goldstein", + "author_inst": "Montefiore Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "sports medicine" + }, { "rel_doi": "10.1101/2023.02.13.23285848", "rel_title": "Intrinsic and effective severity of COVID-19 cases infected with the ancestral strain and Omicron BA.2 variant in Hong Kong", @@ -120799,69 +121738,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.02.17.23286083", - "rel_title": "Prevalence of anti-SARS-CoV-2 antibodies in people attending the two main Goma markets in the eastern Democratic Republic of Congo", - "rel_date": "2023-02-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.17.23286083", - "rel_abs": "According to official data, the Democratic Republic of the Congo (DRC) has a low prevalence of the coronavirus disease 19 (COVID-19) pandemic. The goal of this cross-sectional study was to determine the COVID-19 seroprevalence in people attending Gomas two largest markets, Kituku and Virunga. This study was conducted between September and November 2021, overlapping by one month with another similar study carried out in a slum of Bukavu, and using the same methodology.\n\nCOVID-19 unvaccinated participants (n = 796 including 454 vendors and 342 customers, 60% of whom were women) were surveyed. The median age of vendors and customers was 34.2 and 30.1 years, respectively.\n\nThe crude and adjusted anti-SARS-CoV-2 antibody seroprevalence rates were 70.2% (95 % CI 66.9-73.4%) and 98.8% (95% CI 94.1-100%), respectively, with no difference between vendors and customers. COVID-19 symptoms were mild or absent in 58.9% and 41.1% of participants with anti-SARS-CoV-2 antibodies respectively. COVID-19 did not require hospitalisation for any of the seropositive participants.\n\nThese findings are consistent with those reported in Bukavu. They confirm that SARS-CoV-2 spread without causing severe symptoms in densely populated settlements and markets, and suggest that many COVID-19 cases went unreported. Based on these results, relevance of an untargeted hypothetical vaccination programme in these communities should be questioned.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Prudence Ndeba Mitangala", - "author_inst": "Universite Catholique de Bukavu, Bukavu, Sud Kivu, Democratic Republic of Congo and Universite Officielle de Ruwenzori, Butembo, Nord Kivu, Democratic Republic" - }, - { - "author_name": "Leonid Mwana Wa Bene Irenge", - "author_inst": "Center for Applied Molecular Technologies (CTMA) Universite catholique de Louvain (UCLouvain) Avenue Hippocrate 54-B1.54.01, 1200 Woluwe-Saint-Lambert, Belgium " - }, - { - "author_name": "Edgar Tsongo Musubao", - "author_inst": "Institut de Techniques Medicales, Goma, Nord Kivu, Democratic Republic of Congo" - }, - { - "author_name": "Jean Bosco Mbeva Kahindo", - "author_inst": "Universite Officielle de Ruwenzori, Butembo, Nord Kivu, Democratic Republic of Congo" - }, - { - "author_name": "Patrick Ndeba Ayonga", - "author_inst": "Departement des maladies infectieuses et tropicales, Universite de Bordeaux, France" - }, - { - "author_name": "Israel Kyembwa Safari", - "author_inst": "Inspection provinciale de la sante du Nord Kivu, Democratic Republic of Congo" - }, - { - "author_name": "Janvier Bonane Kubuya", - "author_inst": "Division provinciale de la sante du Nord Kivu, Democratic Republic of Congo" - }, - { - "author_name": "Edmon Namegabe Ntabe", - "author_inst": "Universite libre des pays des grands lacs, Goma Nord Kivu, Democratic Republic of Congo" - }, - { - "author_name": "Raphael Kakongo Senga Kabangwa", - "author_inst": "Laboratoire Provincial Ami Labo Nord Kivu , Democratic Republic of Congo" - }, - { - "author_name": "Guy Ndongala Mutombo", - "author_inst": "Division provinciale de la sante du Nord Kivu, Democratic Republic of Congo" - }, - { - "author_name": "Jerome Ambroise", - "author_inst": "Center for Applied Molecular Technologies, Universite catholique de Louvain (UCLouvain) Avenue Hippocrate 54/B1.54.01, 1200 Woluwe-Saint-Lambert, Belgium" - }, - { - "author_name": "JEAN-LUC GALA", - "author_inst": "Center for Applied Molecular Technologies, Universite catholique de Louvain (UCLouvain) Avenue Hippocrate 54/B1.54.01, 1200 Woluwe-Saint-Lambert, Belgium" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.02.16.23286061", "rel_title": "How well do we do social distancing?", @@ -120994,6 +121870,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.02.17.528914", + "rel_title": "A burns and COVID-19 shared stress responding gene network deciphers CD1C-CD141- DCs as the key cellular components in septic prognosis", + "rel_date": "2023-02-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.17.528914", + "rel_abs": "Differential body responses to various stresses, infectious or noninfectious, govern clinical outcomes ranging from asymptoma to death. However, the common molecular and cellular nature of the stress responsome across different stimuli is not described. In this study, we compared the expression behaviors between burns and COVID-19 infection by choosing the transcriptome of peripheral blood from related patients as the analytic target since the blood cells reflect the systemic landscape of immune homeostasis. We identified an immune co-stimulator (CD86)-centered network, named stress-response core (SRC), which coordinated multiple immune processes and was robust in membership and highly related to the clinical traits in both burns and COVID-19. An independent whole blood single-cell RNA sequencing of COVID-19 patients demonstrated that the monocyte-dendritic cell (Mono-DC) wing was the major cellular source of the SRC, among which the higher expression of the SRC in the monocyte was associated with the asymptomatic COVID-19 patients, while the quantity-restricted and function-defected CD1C-CD141-DCs were recognized as the key signature which linked to bad consequences in COVID-19. Specifically, the proportion of the CD1C-CD141-DCs and their SRC expression levels were step-wise reduced along with worse clinic conditions while the sub-cluster of CD1C-CD141-DCs of the critical COVID-19 patients was characterized of IFN signaling quiescence, high mitochondrial metabolism and immune-communication inactivation. Thus, our study identified an expression-synchronized and function-focused gene network which was decreased under burns and COVID-19 stress and argued the CD1C-CD141-DC as the prognosis-related cell population which might serve as a new target of diagnosis and therapy.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Qiao Liang", + "author_inst": "Nanjing University" + }, + { + "author_name": "Lei Wang", + "author_inst": "Jiangsu Province Academy of Traditional Chinese Medicine" + }, + { + "author_name": "Jing Xu", + "author_inst": "Nanjing University" + }, + { + "author_name": "Anqi Lin", + "author_inst": "Nanjing University" + }, + { + "author_name": "Yongzheng Wu", + "author_inst": "Nanjing University" + }, + { + "author_name": "Qing Tao", + "author_inst": "Nanjing University" + }, + { + "author_name": "Bin Zhang", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Haiyan Min", + "author_inst": "The Second Affiliated Hospital of Nanjing University of Chinese Medicine" + }, + { + "author_name": "Shiyu Song", + "author_inst": "Nanjing University" + }, + { + "author_name": "Qian Gao", + "author_inst": "Nanjing University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.02.16.528881", "rel_title": "Evaluation of SARS-CoV-2 isolation in cell culture from nasal/nasopharyngeal swabs or saliva specimens of patients with COVID-19", @@ -122841,65 +123772,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.02.13.528349", - "rel_title": "Propylene glycol inactivates respiratory viruses and prevents airborne transmission", - "rel_date": "2023-02-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.13.528349", - "rel_abs": "Viruses are vulnerable as they transmit between hosts and we aimed to exploit this critical window. We found that the ubiquitous, safe, inexpensive and biodegradable small molecule propylene glycol (PG) has robust virucidal activity. Propylene glycol rapidly inactivates influenza, SARS-CoV-2 and a broad range of other enveloped viruses, and reduces disease burden in mice when administered intranasally at concentrations commonly found in nasal sprays. Most critically, aerosolized PG efficiently abolishes influenza and SARS-CoV-2 infectivity within airborne droplets, potently preventing infection at levels significantly below those well-tolerated by mammals. We present PG vapor as a first-in-class non-toxic airborne virucide, to prevent transmission of existing and emergent viral pathogens, with clear and immediate implications for public health.\n\nOne-sentence summaryPropylene glycol is a potent and safe virucidal compound that could be used to limit and control infections.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Christine T Styles", - "author_inst": "Imperial College London" - }, - { - "author_name": "Jie Zhou", - "author_inst": "Imperial College London" - }, - { - "author_name": "Katie E Flight", - "author_inst": "University College London" - }, - { - "author_name": "Jonathan C Brown", - "author_inst": "Imperial College London" - }, - { - "author_name": "Michael Vanden Oever", - "author_inst": "Imperial College London" - }, - { - "author_name": "Thomas P Peacock", - "author_inst": "Imperial College London" - }, - { - "author_name": "Ziyin Wang", - "author_inst": "Imperial College London" - }, - { - "author_name": "Rosie Millns", - "author_inst": "Imperial College London" - }, - { - "author_name": "Wendy S Barclay", - "author_inst": "Imperial College London" - }, - { - "author_name": "John S Tregoning", - "author_inst": "Imperial College London" - }, - { - "author_name": "Rachel S Edgar", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.02.13.528235", "rel_title": "P-Selectin promotes SARS-CoV-2 interactions with platelets and the endothelium", @@ -123128,6 +124000,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.02.10.23285717", + "rel_title": "The long COVID evidence gap: comparing self-reporting and clinical coding of long COVID using longitudinal study data linked to healthcare records.", + "rel_date": "2023-02-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.10.23285717", + "rel_abs": "The term \"long COVID\" (LC) was coined in spring 2020 by individuals with ongoing symptoms following COVID-19, but it took until December 2020 for clinical codes to be created in order to record persistent post-COVID-19 illness and referrals within electronic health records (EHRs). Analysis of whole-population EHR databases have helped understand the epidemiology of LC; yet concerns exist about the completeness of accessible EHRs for LC. UK longitudinal population studies (LPS) collected self-reported data on COVID-19 and LC from early 2020 and deposited these data in the UK Longitudinal Linkage Collaboration (UK LLC) research database where they are systematically linked to the participants EHRs. Comparisons of LPS reported LC with recorded LC in the EHRs of the same individuals may be helpful in understanding the epidemiology of emerging conditions such as LC. We used data from 10 UK LPS in the UK LLC to investigate whether participants self-reporting LC had a LC diagnosis or referral code in their English EHR after 10 to 22 months of follow up. Of 6412 participants with COVID-19 symptom duration data and linkage to health records, 898 (14.0%) self-reported LC of any severity in LPS surveys. Among these, just 42 (4.7%; 95% CI: 3.5, 6.3) were identified with LC-related codes in EHRs. In individuals reporting debilitating LC, this proportion was only marginally higher (5.6%; 95% CI: 3.7, 8.3). Our data show a striking discrepancy between LC as perceived and reported by participants in LPS and evidence of LC recorded in their EHRs; and that this discrepancy was patterned by ethnicity and possibly by indicators of deprivation. Self-reported symptoms may not be reflected in coded EHRs due to factors including variations in individuals help seeking behaviours, clinician coding practices and the availability of appropriate codes. However, these considerations appear unlikely to provide a complete explanation for the substantial observed reporting discrepancy. These results may indicate substantial unmet clinical need, in keeping with patient reports of difficulties accessing healthcare and sub-optimal recognition of, and response to, their illness when they do. They may also indicate potential shortcomings of epidemiological research on LC based on EHR- or LPS-based ascertainment alone and illustrate the value of triangulation between LPS and EHR data where linked and made available through resources such as the UK LLC.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Anika Knuppel", + "author_inst": "MRC Unit of Lifelong Health and Ageing at UCL, University College London, London W1E 7HB, London, United Kingdom" + }, + { + "author_name": "Andy Boyd", + "author_inst": "Institute of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, United Kingdom" + }, + { + "author_name": "John Macleod", + "author_inst": "Institute of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, United Kingdom" + }, + { + "author_name": "Nishi Chaturvedi", + "author_inst": "MRC Unit of Lifelong Health and Ageing at UCL, University College London, London W1E 7HB, London, United Kingdom" + }, + { + "author_name": "Dylan M Williams", + "author_inst": "MRC Unit of Lifelong Health and Ageing at UCL, University College London, London W1E 7HB, London, United Kingdom" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.02.10.23285776", "rel_title": "Quantifying the rate and magnitude of the Omicron outbreak in China after sudden exit from 'zero-COVID' restrictions", @@ -124415,61 +125322,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2023.02.08.23285645", - "rel_title": "Mental health, gender, and care-seeking behavior during the COVID-19 pandemic in Sweden: An exploratory study", - "rel_date": "2023-02-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.08.23285645", - "rel_abs": "ObjectiveTo explore the prevalence of care-seeking avoidance behavior in relation to gender and to describe the effect of (and potential interaction between) gender and care-seeking on mental health during the COVID-19 pandemic in Sweden.\n\nMethodsWe performed a cross-sectional study among 27,562 participants of the Omtanke2020 Study, using data collected at three time points concerning sociodemographic factors, mental health symptoms, and care-seeking behavior. Network analysis and prevalence ratios calculated from modified Poisson regressions were used to explore the relationship between gender, care-seeking behavior, and mental health symptoms (depression, anxiety, and COVID-19-related distress).\n\nResultsIn our study, women reported a higher prevalence of mental health symptoms and avoidance of care-seeking due to COVID-19, compared to men. At baseline and six months thereafter, female gender was positively associated with COVID-19-related distress and previous mental health diagnosis. At 12 months after baseline, female gender was positively associated with anxiety and avoidance of care-seeking for mental health. However, previous mental health diagnosis and care avoidance were more strongly associated with a higher prevalence of mental health symptoms among men, compared to women.\n\nConclusionThis study highlights gender differences in mental health outcomes and care-seeking behavior during the COVID-19 pandemic in Sweden.\n\nFundingThis work was supported with grants from Nordforsk (COVIDMENT, 105668 and 138929).", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Katalin Vincze", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" - }, - { - "author_name": "Gillian Murphy", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" - }, - { - "author_name": "Mary Barker", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" - }, - { - "author_name": "Juan Gonz\u00e1lez-Hij\u00f3n", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" - }, - { - "author_name": "Anna K K\u00e4hler", - "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden" - }, - { - "author_name": "Emma M Frans", - "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden" - }, - { - "author_name": "Patrick F Sullivan", - "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden; Department of Psychiatry, University of North Carolina, Chapel Hill," - }, - { - "author_name": "Unnur A Valdimarsd\u00f3ttir", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Center of Public Health Sciences, University of" - }, - { - "author_name": "Fang Fang", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" - }, - { - "author_name": "Anik\u00f3 Lovik", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Unit of Methodology and Statistics, Department " - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.02.08.23285589", "rel_title": "Clinical severity prediction of COVID-19 admitted patients in Spain: SEMI and REDISSEC cohorts", @@ -124710,6 +125562,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.02.09.23285583", + "rel_title": "Sensitivity of Rapid Antigen Tests Against SARS-CoV-2 Omicron and Delta Variants", + "rel_date": "2023-02-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.09.23285583", + "rel_abs": "Rapid Antigen Tests (RAT) have become an invaluable tool for combating the COVID-19 pandemic. However, concerns have been raised regarding the ability of existing RATs to effectively detect emerging SARS-CoV-2 variants. We compared the performance of eight commercially available, emergency use authorized RATs against the Delta and Omicron SARS-CoV-2 variants using individual patient and serially diluted pooled clinical samples. The RATs exhibited lower sensitivity for Omicron samples when using PCR Cycle threshold (CT) value (a proxy for RNA concentration) as the comparator. Interestingly, however, they exhibited similar sensitivity for Omicron and Delta samples when using quantitative antigen concentration as the comparator. We further found that the Omicron samples had lower ratios of antigen to RNA, which offers a potential explanation for the apparent lower sensitivity of RATs for that variant when using CT value as a reference. Our findings underscore the complexity in assessing RAT performance against emerging variants and highlight the need for ongoing evaluation in the face of changing population immunity and virus evolution.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Anuradha Rao", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Adrianna Westbrook", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Leda Bassit", + "author_inst": "Emory University" + }, + { + "author_name": "Richard Parsons", + "author_inst": "Emory University" + }, + { + "author_name": "Eric Fitts", + "author_inst": "Emory University" + }, + { + "author_name": "Morgan Greenleaf", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Kaleb Benjamin McLendon", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Julie Sullivan", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "William Henry O'Sick", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Tyler Baugh", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Heather Bowers", + "author_inst": "Emory University" + }, + { + "author_name": "Filipp Frank", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Ethan Wang", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Mimi Le", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Jennifer Frediani", + "author_inst": "Emory University School of Nursing" + }, + { + "author_name": "Pavitra Roychoudhury", + "author_inst": "University of Washington" + }, + { + "author_name": "Alexander L. Greninger", + "author_inst": "University of Washington" + }, + { + "author_name": "Robert Jerris", + "author_inst": "Children's Healthcare of Atlanta" + }, + { + "author_name": "Nira R Pollock", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Eric Ortlund", + "author_inst": "Emory University" + }, + { + "author_name": "John D Roback", + "author_inst": "Emory University" + }, + { + "author_name": "Wilbur A. Lam", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Anne Piantadosi", + "author_inst": "Emory University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.02.08.23285658", "rel_title": "Benefits of near-universal vaccination and treatment access to manage COVID-19 burden in the United States", @@ -126125,33 +127084,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.02.08.23285651", - "rel_title": "Individual costs and societal benefits of interventions during the COVID-19 pandemic", - "rel_date": "2023-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.08.23285651", - "rel_abs": "Individual and societal reactions to an ongoing pandemic can lead to social dilemmas: In some cases, each individual is tempted to not follow an intervention, but for the whole society it would be best if they did. Now that in most countries the extent of regulations to reduce SARS-CoV-2 transmission is very small, interventions are driven by individual decision-making. Assuming that individuals act in their best own interest, we propose a framework in which this situation can be quantified, depending on the protection the intervention provides to a user and to others, the risk of getting infected, and the costs of the intervention. We discuss when a tension between individual and societal benefits arises and which parameter comparisons are important to distinguish between different regimes of intervention use.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Arne Traulsen", - "author_inst": "MPI Evolutionary Biology" - }, - { - "author_name": "Simon A Levin", - "author_inst": "Department of Ecology and Evolutionary Biology, Princeton University" - }, - { - "author_name": "Chadi M Saad-Roy", - "author_inst": "University of California Berkeley, Berkeley" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.02.02.23285352", "rel_title": "Safety, Virology, Pharmacokinetics, and Clinical Experience of High-dose Intravenous Sotrovimab for the Treatment of Mild to Moderate COVID-19: An Open-label Clinical Trial", @@ -126504,6 +127436,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2023.02.06.527376", + "rel_title": "A SARS-CoV-2 vaccine designed for manufacturability results in unexpected potency and non-waning humoral response", + "rel_date": "2023-02-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.06.527376", + "rel_abs": "The rapid development of several highly efficacious SARS-CoV-2 vaccines was an unprecedented scientific achievement that saved millions of lives. However, now that SARS-CoV-2 is transitioning to the endemic stage, there exists an unmet need for new vaccines that provide durable immunity, protection against variants, and can be more easily manufactured and distributed. Here we describe a novel protein component vaccine candidate, MT-001, based on a fragment of the SARS-CoV-2 spike protein that encompasses the receptor binding domain (RBD). Mice and hamsters immunized with a prime-boost regimen of MT-001 demonstrated extremely high anti-spike IgG titers, and remarkably this humoral response did not appreciably wane for up to 12 months following vaccination. Further, virus neutralization titers, including titers against variants such as Delta and Omicron BA.1, remained high without the requirement for subsequent boosting. MT-001 was designed for manufacturability and ease of distribution, and we demonstrate that these attributes are not inconsistent with a highly immunogenic vaccine that confers durable and broad immunity to SARS-CoV-2 and its emerging variants. These properties suggest MT-001 could be a valuable new addition to the toolbox of SARS-CoV-2 vaccines and other interventions to prevent infection and curtail additional morbidity and mortality from the ongoing worldwide pandemic.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Elliot Campbell", + "author_inst": "Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854 and Macrotope, Inc., Princeton, NJ 08540" + }, + { + "author_name": "Julie Dobkin", + "author_inst": "Child Health Institute of New Jersey, Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901 and Graduate School of Biome" + }, + { + "author_name": "Louis Osorio", + "author_inst": "Child Health Institute of New Jersey, Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901" + }, + { + "author_name": "Santhamani Ramasamy", + "author_inst": "Public Health Research Institute (PHRI), New Jersey Medical School, Rutgers University, Newark, NJ 07103" + }, + { + "author_name": "Ranjeet Kumar", + "author_inst": "Public Health Research Institute (PHRI), New Jersey Medical School, Rutgers University, Newark, NJ 07103" + }, + { + "author_name": "Derek B. SantAngelo", + "author_inst": "Child Health Institute of New Jersey, Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901" + }, + { + "author_name": "Selvakumar Subbian", + "author_inst": "Public Health Research Institute (PHRI), New Jersey Medical School, Rutgers University, Newark, NJ 07103" + }, + { + "author_name": "Lisa K. Denzin", + "author_inst": "Child Health Institute of New Jersey, Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901" + }, + { + "author_name": "Stephen Anderson", + "author_inst": "Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854 and Macrotope, Inc., Princeton, NJ 08540" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.02.06.527330", "rel_title": "Elevated binding and functional antibody responses to SARS-CoV-2 in infants versus mothers", @@ -127851,29 +128834,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.02.03.526970", - "rel_title": "Epidemic patterns of emerging variants with dynamical social distancing", - "rel_date": "2023-02-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.03.526970", - "rel_abs": "Motivated by the emergence of new variants during the COVID-19 pandemic, we consider an epidemiological model of disease transmission dynamics, where novel strains appear by mutations of the virus. In the considered scenarios, disease prevalence in the population is modulated by social distancing. We study the various patterns that are generated under different assumptions of cross-immunity. If recovery from a given strain provides immunity against all previous strains, but not against more novel strains, then we observe a very regular sequential pattern of strain replacement where newer strains predominate over older strains. However, if protection upon recovery holds only against that particular strain and none of the others, we find much more complicated dynamics with potential recurrence of earlier strains, and co-circulation of various strains. We compare the observed patterns with genomic analysis we have seen during the COVID-19 pandemic.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Golsa Sayyar", - "author_inst": "University of Szeged" - }, - { - "author_name": "Gergely Rost", - "author_inst": "University of Szeged" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2023.02.02.526749", "rel_title": "Investigations on SARS-CoV-2 and other coronaviruses in mink farms in France at the end of the first year of COVID-19 pandemic", @@ -128106,6 +129066,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.01.31.23285300", + "rel_title": "Global generalisability of AI-driven COVID-19 vaccination policies: a cross-sectional observational study", + "rel_date": "2023-02-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.31.23285300", + "rel_abs": "The effectiveness of a vaccine depends on vaccine uptake, which is influenced by various factors, including vaccine hesitancy. Vaccine hesitancy is a complex socio-behavioral issue, influenced by misinformation, distrust in healthcare providers and government organizations, fear of side effects, and cultural or religious beliefs. To address this problem, AI models have been developed, but their global generalizability remains unclear. Therefore, this study aimed to identify global determinants of vaccine uptake and develop a generalizable machine learning model to predict individual-level vaccine uptake. The study used publicly available survey data from 23 countries and employed Bayesian networks and generalized mixed effects models to identify key determinants of vaccine uptake. The results showed that trust in the central government and vaccination restrictions for national and international travel were key determinants of vaccine uptake. A generalized mixed effects model achieved an AUC of 89% (SD=1%), precision of 90% (SD = 4%), and recall of 82% (SD=2%) on unseen testing data from new countries, demonstrating the models generalizability. The findings of this study can inform targeted interventions to improve vaccine uptake globally.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Raghav Awasthi", + "author_inst": "PathCheck Foundation, Cambridge, MA" + }, + { + "author_name": "Aditya Nagori", + "author_inst": "PathCheck Foundation, Cambridge, MA" + }, + { + "author_name": "Bouchra Nasri", + "author_inst": "university of montreal, Canada" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2023.01.30.23285220", "rel_title": "Development of a mobile laboratory system in hydrogen fuel cell buses and evaluation of the performance for COVID-19", @@ -129885,61 +130872,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.29.23285159", - "rel_title": "Probable transmission of SARS-CoV-2 from an African lion to zoo employees", - "rel_date": "2023-01-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.29.23285159", - "rel_abs": "Animal to human transmission of SARS-CoV-2 has not previously been reported in a zoo setting. A vaccinated African lion with physical limitations requiring hand feeding tested positive for SARS-CoV-2 after development of respiratory signs. Zoo employees were screened, monitored prospectively for development of symptoms, then re-screened as indicated, with confirmation by RT-PCR and whole-genome virus sequencing when possible. Trace-back investigation narrowed the source of infection to one of five people. Three exposed employees subsequently developed symptoms, two with viral genomes identical to the lions. Forward contact tracing investigation confirmed probable lion-to-human transmission.\n\nClose contact with large cats is a risk factor for bidirectional zoonotic SARS-CoV-2 transmission that should be considered when occupational health and biosecurity practices at zoos are designed and implemented. SARS-CoV-2 rapid testing and detection methods in big cats and other susceptible animals should be developed and validated to facilitate timely implementation of One Health investigations.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Audrey A Siegrist", - "author_inst": "Potawatomi Zoo" - }, - { - "author_name": "Kira L Richardson", - "author_inst": "Indiana Department of Health" - }, - { - "author_name": "Ria R Ghai", - "author_inst": "Centers for Disease Control" - }, - { - "author_name": "Brian Pope", - "author_inst": "Indiana Department of Health" - }, - { - "author_name": "Jamie Yeadon", - "author_inst": "Indiana Department of Health" - }, - { - "author_name": "Betsy Culp", - "author_inst": "Potawatomi Zoo" - }, - { - "author_name": "Casey Barton Behravesh", - "author_inst": "Centers for Disease Control" - }, - { - "author_name": "Lixia Liu", - "author_inst": "Indiana Department of Health" - }, - { - "author_name": "Jennifer A Brown", - "author_inst": "Indiana Department of Health" - }, - { - "author_name": "Leslie Boyer", - "author_inst": "University of Arizona" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.01.30.526314", "rel_title": "Fitness effects of mutations to SARS-CoV-2 proteins", @@ -130124,6 +131056,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.01.30.23285173", + "rel_title": "Current Status and Emerging Trends of COVID-19-related Studies in Seven ''Tropical Medicine''-entitled Journals", + "rel_date": "2023-01-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.30.23285173", + "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has created enormous medical and economic burdens on human society. However, the co-existence of COVID-19 and diseases in tropical regions is not taken seriously. To improve the understanding of the current status and trends on crosstalk of COVID-19 and tropical diseases, this paper provided an analysis, from a bibliometric perspective, of the COVID-19-related publications in Tropical Medicine-entitled journals.\n\nMethodsWe used Clarivate Analytics and VOSviewer to analyze 783 publications in seven Tropical Medicine-entitled journals. Document overview, basic bibliometric characteristics, citation performance, co-authorship, co-citation, bibliographic coupling, and co-occurrence of keywords and terms were summarized in this article.\n\nResultsDocument overview revealed that 76.12% of the related publications were published in open access mode, and basic bibliometric characteristics indicated that the year 2021 was the peak of the number of publications, the documents in the seven journals were unevenly distributed, and article was the main publication type. The citation performance analysis elucidated that the documents of interest were frequently cited. The co-authorship analysis showed cooperation networks on the level of region, organization and author. General knowledge of COVID-19 was the overlap of co-citation and bibliographic coupling behavior. Finally, the co-occurrence of keywords and terms revealed the current and emerging hotspots.\n\nConclusionsThe main current research focuses in Tropical Medicine-entitled journals are the clinical features of COVID-19 patients, and the emerging trends are the hesitancy in making vaccines against SARS-CoV-2 and the circumstance where COVID-19 coexisted with tropical diseases. In summary, this bibliometric analysis of COVID-19-related studies in seven Tropical Medicine-entitled journals highlights the current research focuses of this field to inspire future studies.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Xuejuan Zhang", + "author_inst": "College of Pharmacy, Jinan University" + }, + { + "author_name": "Ziqiao Zhong", + "author_inst": "College of Pharmacy, Jinan University" + }, + { + "author_name": "Peili Luo", + "author_inst": "College of Pharmacy, Jinan University" + }, + { + "author_name": "Chune Zhu", + "author_inst": "School of Chinese Materia Medica, Guangdong Pharmaceutical University" + }, + { + "author_name": "Ying Huang", + "author_inst": "College of Pharmacy, Jinan University" + }, + { + "author_name": "Chaunbin Wu", + "author_inst": "College of Pharmacy, Jinan University" + }, + { + "author_name": "Xin Pan", + "author_inst": "School of Pharmaceutical Sciences, Sun Yat-sen University" + }, + { + "author_name": "Zhengwei Huang", + "author_inst": "College of Pharmacy, Jinan University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.01.31.526458", "rel_title": "Scalable neighbour search and alignment with uvaia", @@ -131699,81 +132678,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nursing" }, - { - "rel_doi": "10.1101/2023.01.25.23284428", - "rel_title": "Primary care coding activity related to the use of online consultation systems or remote consulting: an analysis of 53 million peoples' health records using OpenSAFELY", - "rel_date": "2023-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.25.23284428", - "rel_abs": "BackgroundThe pandemic accelerated work by the NHS in England to enable and stimulate use of online consultation systems across all practices, for improved access to primary care.\n\nObjectiveWe aimed to explore general practice coding activity associated with the use of online consultation systems in terms of trends, COVID-19 effect, variation and quality.\n\nMethodsWith the approval of NHS England, OpenSAFELY-TPP and OpenSAFELY-EMIS were used to query and analyse in situ records of electronic health record systems of over 53 million patients in over 6,400 practices, mainly in 2019-2020. SNOMED CT codes relevant to online consultation systems and written online consultations were identified. Coded events were described by volumes, practice coverage, trends pre- and post-COVID-19 and inter-practice and sociodemographic variation.\n\nResults3,550,762 relevant coding events were found in TPP practices, with code eConsultation detected in 84% of practices. Coding activity related to digital forms of interaction increased rapidly from March 2020 at the onset of the COVID-19 pandemic, though we found large variation in coding instance rates among practices in England. Code instances were more commonly found among females, those aged 18-40, those least deprived or white. eConsultation coded activity was more commonly found recorded among patients with a history of asthma or depression.\n\nConclusionsWe successfully queried general practice coding activity relevant to the use of online consultation systems, showing increased adoption as well as key areas of variation during the COVID-19 pandemic. The work can be expanded to support monitoring of coding quality and underlying activity. In future, large-scale impact evaluation studies can be implemented within the platform, namely looking at resource utilisation and patient outcomes.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Martina Fonseca", - "author_inst": "NHS England" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "University of Oxford" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "University of Oxford" - }, - { - "author_name": "- The OpenSAFELY Collaborative", - "author_inst": "-" - }, - { - "author_name": "Caroline E Walters", - "author_inst": "University of Oxford" - }, - { - "author_name": "George Hickman", - "author_inst": "University of Oxford" - }, - { - "author_name": "Louis Fisher", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jonathan Pearson", - "author_inst": "NHS England" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "University of Oxford" - }, - { - "author_name": "Seb Bacon", - "author_inst": "University of Oxford" - }, - { - "author_name": "Simon Davy", - "author_inst": "University of Oxford" - }, - { - "author_name": "William Hulme", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ofra Koffman", - "author_inst": "NHS England" - }, - { - "author_name": "Minal Bakhai", - "author_inst": "NHS England" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2023.01.24.23284885", "rel_title": "Impact of vaccination and risk factors on COVID-19 mortality amid delta surge in Libya: a single centre cohort study", @@ -131966,6 +132870,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2023.01.27.23285105", + "rel_title": "Waves in time, but not in space - An analysis of pandemic severity of COVID-19 in Germany based on spatio-temporal clustering", + "rel_date": "2023-01-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.27.23285105", + "rel_abs": "While pandemic waves are often studied on the national scale, they typically are not distributed evenly within countries. This paper employs a novel approach to analyze the tempo-spatial dynamics of the COVID-19 pandemic in Germany. First, we base the analysis on a composite indicator of pandemic severity to gain a more robust understanding of the temporal dynamics of the pandemic. Second, we subdivide the pandemic during the years 2020 and 2021 into fifteen phases, each with a coherent trend of pandemic severity. Third, we analyze the patterns of spatial association during each phase. Fourth, similar types of trajectories of pandemic severity among all German counties were identified through hierarchical clustering. The results imply that the hotspots and cold spots of the first four waves of the pandemic were relatively stationary in space so that the pandemic moved in time but less in space.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Andreas Kuebart", + "author_inst": "Leibniz Institute for Research on Society and Space" + }, + { + "author_name": "Martin Stabler", + "author_inst": "Leibniz Institute for Research on Society and Space" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.01.24.23284890", "rel_title": "SARS-CoV-2 Spike Protein Receptor Binding-ACE2 Interaction Increases Carbohydrate Sulfotransferases and Reduces N-Acetylgalactosamine-4-Sulfatase through Phospho-p38-MAPK and RB-E2F1", @@ -133681,33 +134608,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.23.525275", - "rel_title": "Genome-wide CRISPR screens identify noncanonical translation factor eIF2A as an enhancer of SARS-CoV-2 programmed -1 ribosomal frameshifting", - "rel_date": "2023-01-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.23.525275", - "rel_abs": "Many positive-strand RNA viruses, including all known coronaviruses, employ programmed -1 ribosomal frameshifting (-1 PRF) to regulate the translation of polycistronic viral RNAs. However, only a few host factors have been shown to regulate -1 PRF. Through a reporter-based genome-wide CRISPR/Cas9 knockout screen, we identified several host factors that either suppressed or enhanced -1 PRF of SARS-CoV-2. One of these factors is eukaryotic translation initiation factor 2A (eIF2A), which specifically and directly enhanced -1 PRF in vitro and in cells. Consistent with the crucial role of efficient -1 PRF in transcriptase/replicase expression, loss of eIF2A reduced SARS-CoV-2 replication in cells. Transcriptome-wide analysis of eIF2A-interacting RNAs showed that eIF2A primarily interacted with 18S ribosomal RNA near the contacts between the SARS-CoV-2 frameshift-stimulatory element (FSE) and the ribosome. Thus, our results revealed an unexpected role for eIF2A in modulating the translation of specific RNAs independent of its previously described role during initiation.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Lian-Huan Wei", - "author_inst": "Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA" - }, - { - "author_name": "Yu Sun", - "author_inst": "Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA" - }, - { - "author_name": "Junjie U. Guo", - "author_inst": "Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2023.01.24.525203", "rel_title": "Multimodal characterization of antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection.", @@ -134060,6 +134960,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.01.21.524927", + "rel_title": "CompCorona: A Web Portal for Comparative Analysis of the Host Transcriptome of PBMC and Lung SARS-CoV-2, SARS-CoV, and MERS-CoV", + "rel_date": "2023-01-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.21.524927", + "rel_abs": "MotivationUnderstanding the host response to SARS-CoV-2 infection is crucial for deciding on the correct treatment of this epidemic disease. Although several recent studies reported the comparative transcriptome analyses of the three coronaviridae (CoV) members; namely SARS-CoV, MERS-CoV, and SARS-CoV-2, there is yet to exist a web-tool to compare increasing number of host transcriptome response datasets against the pre-processed CoV member datasets. Therefore, we developed a web application called CompCorona, which allows users to compare their own transcriptome data of infected host cells with our pre-built datasets of the three epidemic CoVs, as well as perform functional enrichment and principal component analyses (PCA).\n\nResultsComparative analyses of the transcriptome profiles of the three CoVs revealed that numerous differentially regulated genes directly or indirectly related to several diseases (e.g., hypertension, male fertility, ALS, and epithelial dysfunction) are altered in response to CoV infections. Transcriptome similarities and differences between the host PBMC and lung tissue infected by SARS-CoV-2 are presented. Most of our findings are congruent with the clinical cases recorded in the literature. Hence, we anticipate that our results will significantly contribute to ongoing studies investigating the pre-and/or post-implications of SARS-CoV-2 infection. In addition, we implemented a user-friendly public website, CompCorona for biomedical researchers to compare users own CoV-infected host transcriptome data against the built-in CoV datasets and visualize their results via interactive PCA, UpSet and Pathway plots.\n\nAvailabilityCompCorona is freely available on the web at http://compcorona.mu.edu.tr\n\nContacttugbasuzek@mu.edu.tr", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Rana Salihoglu", + "author_inst": "University of Wurzburg" + }, + { + "author_name": "Fatih Saracoglu", + "author_inst": "Mugla Sitki Kocman University" + }, + { + "author_name": "Mustafa Sibai", + "author_inst": "Josep Carreras Leukaemia Research Institute" + }, + { + "author_name": "Talip Zengin", + "author_inst": "Mugla Sitki Kocman University" + }, + { + "author_name": "Basak Abak Masud", + "author_inst": "Mugla Sitki Kocman University" + }, + { + "author_name": "Onur Karasoy", + "author_inst": "Mugla Sitki Kocman University" + }, + { + "author_name": "Tugba Onal-Suzek", + "author_inst": "Mugla Sitki Kocman University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.01.23.524390", "rel_title": "Lack of Fzd6 in Ciliated Cells Suppresses Ferroptotic Pulmonary Alveolar Cell Death Induced by LPS and Coronavirus", @@ -135427,77 +136370,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2023.01.16.23284626", - "rel_title": "High proportion of Ugandans with pre-pandemic SARS-CoV-2 cross-reactive CD4+ and CD8+ T-cell responses", - "rel_date": "2023-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.16.23284626", - "rel_abs": "The estimated mortality rate of the SARS-CoV-2 pandemic varied greatly around the world with multiple countries in East, Central, and West Africa having significantly lower rates of COVID-19 related fatalities than many resource-rich nations with significantly earlier wide-spread access to life-saving vaccines. One possible reason for this lower mortality could be the presence of pre-existing cross-reactive immunological responses in these areas of the world. To explore this hypothesis, stored peripheral blood mononuclear cells (PBMC) from Ugandans collected from 2015-2017 prior to the COVID-19 pandemic (n=29) and from hospitalized Ugandan COVID-19 patients (n=3) were examined using flow-cytometry for the presence of pre-existing SARS-CoV-2 cross-reactive CD4+ and CD8+ T-cell populations using four T-cell epitope mega pools. Of pre-pandemic participants, 89.7% (26/29) had either CD4+ or CD8+, or both, SARS-CoV-2 specific T-cell responses. Specifically, CD4+ T-cell reactivity (72.4%) and CD8+ T-cell reactivity (65.5%) were relatively similar, and 13 participants (44.8%) had both types of cross-reactive types of T-cells present. There were no significant differences in response by sex in the population. The rates of cross-reactive T-cell populations in these Ugandans is higher than previous estimates from resource-rich countries like the United States (20-50% reactivity). It is unclear what role, if any, this cross-reactivity played in decreasing COVID-19 related mortality in Uganda and other African countries, but does suggest that a better understanding of global pre-existing immunological cross-reactivity could be an informative data of epidemiological intelligence moving forward.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Annemarie Namuniina", - "author_inst": "IAVI: International Aids Vaccine Initiative" - }, - { - "author_name": "Enoch S Muyanja", - "author_inst": "Emory University" - }, - { - "author_name": "Victoria M Biribawa", - "author_inst": "IAVI: International Aids Vaccine Initiative" - }, - { - "author_name": "Brenda A Okech", - "author_inst": "IAVI: International Aids Vaccine Initiative" - }, - { - "author_name": "Aloysious Ssemaganda", - "author_inst": "University of Manitoba Max Rady College of Medicine" - }, - { - "author_name": "Matt A Price", - "author_inst": "IAVI: International Aids Vaccine Initiative" - }, - { - "author_name": "Nancy Hills", - "author_inst": "UCSF: University of California San Francisco" - }, - { - "author_name": "Ann Nanteza", - "author_inst": "Makerere University" - }, - { - "author_name": "Bernard Ssentalo Bagaya", - "author_inst": "Makerere University" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Catherine Riou", - "author_inst": "UCT Faculty of Health Sciences: University of Cape Town Faculty of Health Sciences" - }, - { - "author_name": "Steven J Reynolds", - "author_inst": "NIAID: National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Ronald M Galwango", - "author_inst": "RHSP: Rakai Health Sciences Program" - }, - { - "author_name": "Andrew Davidson Redd", - "author_inst": "NIAID: National Institute of Allergy and Infectious Diseases" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.01.20.23284812", "rel_title": "Immunogenicity, Safety and Effectiveness of COVID-19 Pfizer-BioNTech (BNT162b2) mRNA Vaccination in Immunocompromised Adolescents and Young Adults: A systematic Review and Meta-Analyses", @@ -135714,6 +136586,65 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.01.18.524571", + "rel_title": "Ensemble of deep learning language models to support the creation of living systematic reviews for the COVID-19 literature: a retrospective study", + "rel_date": "2023-01-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.18.524571", + "rel_abs": "BackgroundThe COVID-19 pandemic has led to an unprecedented amount of scientific publications, growing at a pace never seen before. Multiple living systematic reviews have been developed to assist professionals with up-to-date and trustworthy health information, but it is increasingly challenging for systematic reviewers to keep up with the evidence in electronic databases. We aimed to investigate deep learning-based machine learning algorithms to classify COVID-19 related publications to help scale-up the epidemiological curation process.\n\nMethodsIn this retrospective study, five different pre-trained deep learning-based language models were fine-tuned on a dataset of 6,365 publications manually classified into two classes, three subclasses and 22 sub-subclasses relevant for epidemiological triage purposes. In a k-fold cross-validation setting, each standalone model was assessed on a classification task and compared against an ensemble, which takes the standalone model predictions as input and uses different strategies to infer the optimal article class. A ranking task was also considered, in which the model outputs a ranked list of sub-subclasses associated with the article.\n\nResultsThe ensemble model significantly outperformed the standalone classifiers, achieving a F1-score of 89.2 at the class level of the classification task. The difference between the standalone and ensemble models increases at the sub-subclass level, where the ensemble reaches a micro F1-score of 70% against 67% for the best performing standalone model. For the ranking task, the ensemble obtained the highest recall@3, with a performance of 89%. Using an unanimity voting rule, the ensemble can provide predictions with higher confidence on a subset of the data, achieving detection of original papers with a F1-score up to 97% on a subset of 80% of the collection instead of 93% on the whole dataset.\n\nConclusionThis study shows the potential of using deep learning language models to perform triage of COVID-19 references efficiently and support epidemiological curation and review. The ensemble consistently and significantly outperforms any standalone model. Fine-tuning the voting strategy thresholds is an interesting alternative to annotate a subset with higher predictive confidence.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Julien Knafou", + "author_inst": "HES-SO, University of Applied Sciences and Arts of Western Switzerland" + }, + { + "author_name": "Quentin Haas", + "author_inst": "Risklick AG, Spitalackerstrasse, 3013 Bern" + }, + { + "author_name": "Nikolay Borissov", + "author_inst": "Risklick AG, Spitalackerstrasse, 3013 Bern" + }, + { + "author_name": "Michel Jacques Counotte", + "author_inst": "Wageningen University and Research" + }, + { + "author_name": "Nicola Low", + "author_inst": "University of Bern" + }, + { + "author_name": "Hira Imeri", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" + }, + { + "author_name": "Aziz Mert Ipekci", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" + }, + { + "author_name": "Diana Buitrago-Garcia", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" + }, + { + "author_name": "Leonie Heron", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" + }, + { + "author_name": "Poorya Amini", + "author_inst": "Risklick AG, Spitalackerstrasse, 3013 Bern" + }, + { + "author_name": "Douglas Teodoro", + "author_inst": "Department of Radiology and Medical Informatics, University of Geneva, Geneva, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.01.19.23284738", "rel_title": "A computable phenotype for patients with SARS-CoV2 testing that occurred outside the hospital", @@ -137257,61 +138188,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2023.01.18.524384", - "rel_title": "Cell division tracing combined with single-cell transcriptomics reveals new cell types and differentiation paths in the regenerating mouse lung", - "rel_date": "2023-01-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.18.524384", - "rel_abs": "Understanding the molecular and cellular processes involved in lung epithelial regeneration may fuel the development of new therapeutic approaches for lung diseases. We combined new mouse models that allow diphtheria toxin (DTA)-mediated depletion of specific epithelial cell types and GFP-labeling of dividing cells with single-cell transcriptomics to characterize the regeneration of the distal lung. We uncovered new cell types, some of which likely represent epithelial precursors, propose goblet cells as progenitor cells, and provide evidence that adventitial fibroblasts act as supporting cells in epithelial regeneration. We also found that DTA-expressing cells can persist in the lung, express specific inflammatory factors, and resemble a previously undescribed population in the lungs of COVID-19 patients. Our study provides a comprehensive single-cell atlas of the distal lung that characterizes early transcriptional and cellular responses to defined epithelial injury, encompassing proliferation, differentiation, and cell-to-cell interactions.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Leila R Martins", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Lina Sieverling", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Michelle Michelhans", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Chiara Schiller", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Cihan Erkut", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Sergio Triana", - "author_inst": "European Molecular Biology Laboratory (EMBL), Heidelberg, Germany" - }, - { - "author_name": "Stefan Froehling", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Lars Velten", - "author_inst": "Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain." - }, - { - "author_name": "Hanno Glimm", - "author_inst": "National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germ" - }, - { - "author_name": "Claudia Scholl", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2023.01.17.524469", "rel_title": "A Systematic Survey of Reversibly Covalent Dipeptidyl Inhibitors of the SARS-CoV-2 Main Protease", @@ -137540,6 +138416,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2023.01.18.23284602", + "rel_title": "Assessment of Retrospective Collection of EQ-5D-5L in US Patients with COVID-19", + "rel_date": "2023-01-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.18.23284602", + "rel_abs": "BackgroundThe impact of COVID-19 goes beyond the acute phase of infection. It is imperative to evaluate health related quality of life (HRQoL) pre-COVID-19, but there is currently no evidence of the retrospective application of the EQ-5D-5L for COVID-19 studies.\n\nMethodsSubjects with [≥]1 self-reported symptom and positive RT-PCR for SARS-CoV-2 at CVS Health US test sites were recruited between 01/31/2022-04/30/2022. On the day of enrollment which was around day 3 after testing positive, consented participants completed the EuroQol 5D-5L (EQ-5D-5L) questionnaire twice : a modified version where all the questions were past tense to retrospectively assess pre-COVID-19 baseline QoL, and the standard version in present tense to assess current HRQoL. Duncans new multiple range test was adopted for post analysis of variance pairwise comparisons of EQ-VAS means between problem levels for each of 5 domains. A linear mixed model was applied to check whether the relationship between EQ visual analog scale (VAS) and utility index (UI) was consistent pre-COVID-19 and during COVID-19. Matching-adjusted indirect comparison was used to compare pre-COVID-19 UI and VAS scores with those of the US population. Cohens d was used to quantify the magnitude of difference in means between two groups.\n\nResultsOf 676 participants, 10.2% were age 65 or more years old, 73.2% female and 71.9% white. Diabetes was reported by 4.7% participants and hypertension by 11.2%. The pre-COVID-19 baseline mean UI was 0.924 and the mean VAS was 87.4. The estimated coefficient for the interaction of UI-by-retrospective collection indicator (0=standard prospective collection for Day 3 after COVID-19 testing, 1=retrospective for pre-COVID-19), -4.2 (SE: 3.2), P=0.197, indicates that retrospective collection does not significantly alter the relationship between EQ-VAS and UI. After adjusting for age, gender, diabetes, hypertension, and percent of mobility problems, predicted means of pre-COVID-19 baseline VAS and UI were 84.6 and 0.866, respectively. Both of these means were close to published US population norms (80.4 and 0.851) than those observed (87.4 and 0.924). After adjusting for age, gender, diabetes, and hypertension, 19.0% patients with COVID-19 had mobility problems, which was significantly lower than US population norm 25.2%, P<0.001. The calculated ES for UI and VAS were 0.15 and 0.39, respectively.\n\nConclusionAt a group level the retrospectively collected pre-COVID-19 EQ-5D-5L is adequate and makes it possible to directly evaluate the impact of COVID-19 on HRQoL. Future studies are encouraged that are tailored to directly compare standard prospective assessment with retrospective assessment on the EQ-5D-5L during pre-COVID-19.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Xiaowu Sun", + "author_inst": "CVS Health" + }, + { + "author_name": "Manuela Di Fusco", + "author_inst": "Pfizer Inc." + }, + { + "author_name": "Laura Puzniak", + "author_inst": "Pfizer Inc." + }, + { + "author_name": "Henriette Coetzer", + "author_inst": "CVS Health" + }, + { + "author_name": "Joann M. Zamparo", + "author_inst": "Pfizer Inc." + }, + { + "author_name": "Ying P. Tabak", + "author_inst": "CVS Health" + }, + { + "author_name": "Joseph C. Cappelleri", + "author_inst": "Pfizer Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.01.18.23284681", "rel_title": "Suicide deaths during the COVID-19 pandemic in the United States, by region, March 1, 2020-June 30, 2022", @@ -139167,65 +140086,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.10.523518", - "rel_title": "Anthracyclines inhibit SARS-CoV-2 infection", - "rel_date": "2023-01-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.10.523518", - "rel_abs": "Vaccines and drugs are two effective medical interventions to mitigate SARS-CoV-2 infection. Three SARS-CoV-2 inhibitors, remdesivir, paxlovid, and molnupiravir, have been approved for treating COVID-19 patients, but more are needed, because each drug has its limitation of usage and SARS-CoV-2 constantly develops drug resistance mutations. In addition, SARS-CoV-2 drugs have the potential to be repurposed to inhibit new human coronaviruses, thus help to prepare for future coronavirus outbreaks. We have screened a library of microbial metabolites to discover new SARS-CoV-2 inhibitors. To facilitate this screening effort, we generated a recombinant SARS-CoV-2 Delta variant carrying the nano luciferase as a reporter for measuring viral infection. Six compounds were found to inhibit SARS-CoV-2 at the half maximal inhibitory concentration (IC50) below 1 M, including the anthracycline drug aclarubicin that markedly reduced viral RNA-dependent RNA polymerase (RdRp)-mediated gene expression, whereas other anthracyclines inhibited SARS-CoV-2 by activating the expression of interferon and antiviral genes. As the most commonly prescribed anti-cancer drugs, anthracyclines hold the promise of becoming new SARS-CoV-2 inhibitors.\n\nIMPORTANCEMicrobial metabolites are a rich source of bioactive molecules. The best examples are antibiotics and immunosuppressants that have transformed the practice of modern medicine and saved millions of lives. Recently, some microbial metabolites were reported to have antiviral activity, including the inhibition of Zika virus and Ebola virus. In this study, we discovered several microbial metabolites that effectively inhibit SARS-CoV-2 infection, including anthracyclines that have also been shown to inhibit other viruses including Ebola virus through enhancing interferon responses, which indicates potentially broad antiviral properties of these microbial metabolites and can lead to the discovery of pan-antiviral molecules.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Zhen Wang", - "author_inst": "Lady Davis Institute" - }, - { - "author_name": "Qinghua Pan", - "author_inst": "Lady Davis Institute" - }, - { - "author_name": "Ling Ma", - "author_inst": "Chinese Academy of Medical Sciences" - }, - { - "author_name": "Jianyuan Zhao", - "author_inst": "Chinese Academy of Medical Sciences" - }, - { - "author_name": "Fiona McIntosh", - "author_inst": "Research Institute of the McGill University Health Centre" - }, - { - "author_name": "Zhenlong Liu", - "author_inst": "McGill University" - }, - { - "author_name": "Shilei Ding", - "author_inst": "CRCHUM / Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Rongtuan Lin", - "author_inst": "Lady Davis Institute for Medical Research, McGill University" - }, - { - "author_name": "Cen Shan", - "author_inst": "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College" - }, - { - "author_name": "Andr\u00e9s Finzi", - "author_inst": "CRCHUM, Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Chen Liang", - "author_inst": "Lady Davis Institute for Medical Research" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.01.12.23284481", "rel_title": "Data-driven Targeting of COVID-19 Vaccination Programs: An Analysis of the Evidence on Impact, Implementation, Ethics and Equity", @@ -139354,6 +140214,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.01.13.23284506", + "rel_title": "Effectiveness of Paxlovid - a review", + "rel_date": "2023-01-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.13.23284506", + "rel_abs": "Paxlovid is an oral treatment for mild to moderate COVID-19 cases with a high risk for severe course of the disease. For this review, we have performed a comprehensive literature review. We present a summary of currently available data on Paxlovids ability to reduce the risk of progressing to a severe disease state. Our findings can be concluded as follows: data from the time when the Delta-variant was dominant shows that Paxlovid reduced the risk of hospitalization or death by 87.8% for unvaccinated, non-hospitalized high-risk individuals. Data from the time when the Omicron variant was dominant found decreased risk reductions, varying between 41% and 46%, combining various vaccination statuses. However, one study, which differentiated by age, found that the administration of Paxlovid reduced the risk of hospitalization by 67% for individuals aged 65 and older, but only by 27% for individuals aged 40-64. From the available data, one can conclude that Paxlovid cannot substitute vaccination, but its low manufacturing cost as well as its easy administration make it a valuable tool in fighting COVID-19, especially for countries with a low vaccination rate.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Sydney Paltra", + "author_inst": "Technical University Berlin" + }, + { + "author_name": "Tim Conrad", + "author_inst": "Zuse Institute Berlin" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.01.11.23284098", "rel_title": "Safety and Efficacy of Oral administrated Cepharathine in Non-hospitalized, asymptomatic or mild COVID-19 patients: A Double-blind, Randomized, Placebo-controlled Trial", @@ -140897,65 +141780,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.09.23284380", - "rel_title": "Effectiveness of an eHealth Intervention for Reducing Psychological Distress and Increasing COVID-19 Knowledge and Protective Behaviors among Ethnoracially Diverse Sexual and Gender Minority Adults: A Quasi-experimental Study (#SafeHandsSafeHearts)", - "rel_date": "2023-01-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.09.23284380", - "rel_abs": "PurposeLesbian, gay, bisexual, transgender, queer, and other persons outside of heteronormative and cisgender identities (LGBTQ+) and ethnic/racial minority populations are at heightened vulnerability amid the Covid-19 pandemic. Systemic marginalization and resulting adverse social determinants of health contribute to health disparities among these populations that result in more severe consequences due to Covid-19 and the public health measures to control it. We developed and tested a tailored online intervention (#SafeHandsSafeHearts) to support ethnoracially diverse LGBTQ+ individuals in Toronto, Canada amid the pandemic.\n\nMethodsWe used a quasi-experimental pre-test post-test design to evaluate the effectiveness of a 3-session, peer-delivered eHealth intervention in reducing psychological distress and increasing Covid-19 knowledge and protective behaviors. Individuals [≥]18-years-old, resident in Toronto, and self-identified as sexual or gender minority were recruited online. Depressive and anxiety symptoms, Covid-19 knowledge and protective behaviors were assessed at baseline, 2-weeks postintervention, and 2-months follow-up. We used generalized estimating equations and zero-truncated Poisson models to evaluate the effectiveness of the intervention on the four primary outcomes.\n\nResultsFrom March to November 2021, 202 participants (median age, 27 years [Interquartile rage: 23-32]) were enrolled in #SafeHandsSafeHearts. Over half (54%, n=110) identified as cisgender lesbian or bisexual women or women who have sex with women, 26.2% (n=53) cisgender gay or bisexual men or men who have sex with men, and 19.3% (n=39) transgender or nonbinary individuals. The majority (75.7%, n=143) were Black and other people of color. The intervention led to statistically significant reductions in the prevalence of clinically significant depressive and anxiety symptoms, and increases in Covid-19 protective behaviors from baseline to postintervention.\n\nConclusionWe demonstrated the effectiveness of a brief, peer-delivered eHealth intervention for ethnoracially diverse LGBTQ+ communities in reducing psychological distress and increasing protective behaviors amid the Covid-19 pandemic. Implementation through community-based health services with trained peer educators supports feasibility, acceptability, and the importance of engaging ethnoracially diverse LGBTQ+ communities in pandemic response preparedness. This trial is registered with ClinicalTrials.gov, number NCT04870723.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Peter A. Newman", - "author_inst": "University of Toronto" - }, - { - "author_name": "Venkatesan Chakrapani", - "author_inst": "Centre for Sexuality and Health Research and Policy" - }, - { - "author_name": "Notisha Massaquoi", - "author_inst": "University of Toronto Scarborough" - }, - { - "author_name": "Charmaine C. Williams", - "author_inst": "University of Toronto" - }, - { - "author_name": "Wangari Tharao", - "author_inst": "Women's Health in Women's Hands Community Health Centre" - }, - { - "author_name": "Suchon Tepjan", - "author_inst": "VOICES-Thailand Foundation" - }, - { - "author_name": "Surachet Roungprakhon", - "author_inst": "Rajamangala University of Technology Phra Nakhon" - }, - { - "author_name": "Joelleann Forbes", - "author_inst": "Women's Health in Women's Hands Community Health Centre" - }, - { - "author_name": "Sarah Sebastian", - "author_inst": "Women's Health in Women's Hands Community Health Centre" - }, - { - "author_name": "Pakorn Akkakanjanasupar", - "author_inst": "VOICES-Thailand Foundation" - }, - { - "author_name": "Muna Aden", - "author_inst": "Women's Health in Women's Hands Community Health Centre" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.01.11.23284427", "rel_title": "Genetic determinants of severe COVID-19 in young Asian and Middle Eastern patients", @@ -141204,6 +142028,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.01.10.23284300", + "rel_title": "The Smoldering Pandemic: Self-Reported Prevalence Assessment of Prolonged Grief Disorder. A cross sectional study of bereaving adults during the Covid Pandemic in Pakistan.", + "rel_date": "2023-01-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.10.23284300", + "rel_abs": "IntroductionThe Covid-19 pandemic brought forward unprecedented psycho-social challenges for the world. The devastating loss of human lives created a burden of grief throughout the world. The bereaved were put at a greater risk of grief complications with high death tolls, strict social isolation guidelines and a halt to communal funeral practices. Prolonged Grief Disorder is a young psychiatric condition which refers to an abnormal grief reaction that exceeds the normal cultural, social and religious norms. In this study, we assessed the prevalence of Prolonged Grief Disorder (PGD), as mentioned in ICD-11 in Pakistan, along with its correlation to anxiety, depression and psychological distress. Severity of grief reactions were compared with the place of death and relationship with the deceased.\n\nMethodsA cross sectional online survey was conducted during the month of October 2021. Sample size was calculated using OpenEpi and data was collected through non probability sampling. The questionnaire was validated and shared through multiple social forums. A total of 737 participants residing in Lahore Pakistan, who had lost a close one due to Covid-19 participated in the study. Demographics, loss related information, and self-reported symptoms measured by 13-item Prolonged Grief Disorder Scale, Patient Health Questionnaire-4 and Kessler-6 scales were obtained.\n\nResultsThe prevalence of Prolonged Grief Disorder was found to be 15.4%. There was a significant correlation of grief intensity with depression and anxiety.Prolonged Grief Disorder puts individuals at greater risk of suffering from serious mental illnesses. People who were closely related to the deceased were more likely to experience severe Prolonged Grief Disorder symptoms.\n\nConclusionEarly detection and treatment of high risk individuals is necessary to mitigate the burden of grief and associated risk of anxiety and depression. Overall we conclude that discussions pertaining to grief and measures to curb the psychological effects are crucial in the post-pandemic world.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ayesha Siddiqua", + "author_inst": "Quaid-e-Azam Medical College" + }, + { + "author_name": "Shaaf Ahmad", + "author_inst": "University College of Medicine and Dentistry" + }, + { + "author_name": "Dr.Muhammad Zeeshan", + "author_inst": "Rutgers University" + }, + { + "author_name": "Iqra Nawaz", + "author_inst": "QAMC" + }, + { + "author_name": "Amina Rao", + "author_inst": "QAMC" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2023.01.09.23284360", "rel_title": "Analysis of recurrent research pathways for assessing and improving effectiveness in life sciences laboratories", @@ -142587,153 +143446,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.01.05.23284214", - "rel_title": "The impact of the COVID-19 pandemic on Antipsychotic Prescribing in individuals with autism, dementia, learning disability, serious mental illness or living in a care home: A federated analysis of 59 million patients primary care records in situ using OpenSAFELY", - "rel_date": "2023-01-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.05.23284214", - "rel_abs": "BackgroundThe COVID-19 pandemic significantly affected health and social care services. We aimed to explore whether this impacted the prescribing rates of antipsychotics within at-risk populations.\n\nMethodsWith the approval of NHS England, we completed a retrospective cohort study, using the OpenSAFELY platform to explore primary care data of 59 million patients. We identified patients in five at-risk groups: autism, dementia, learning disability, serious mental illness and care home residents. We then calculated the monthly prevalence of antipsychotic prescribing in the population, as well as the incidence of new prescriptions in each month over the study period (Jan 2019-Dec 2021).\n\nResultsThe average monthly rate of antipsychotic prescribing increased in dementia from 82.75 patients prescribed an antipsychotic per 1000 patients (95% CI 82.30-83.19) in Q1 2019 to 90.1 (95% CI 89.68-90.60) in Q4 2021 and from 154.61 (95% CI 153.79-155.43) in Q1 2019 to 166.95 (95% CI 166.23-167.67) in Q4 2021 in care homes. There were notable spikes in the rate of new prescriptions issued to patients with dementia and in care homes. In learning disability and autism groups, the average monthly rate of prescribing per 1000 decreased from 122.97 (95% CI 122.29-123.66) in Q1 2019 to 119.29 (95% CI 118.68-119.91) in Q4 2021, and from 54.91 (95% CI 54.52-55.29) in Q1 2019 to 51.04 (95% CI 50.74-51.35) in Q4 2021 respectively.\n\nConclusionsDuring each of the lockdowns in 2020, we observed a significant spike in antipsychotic prescribing in the dementia and care home groups. We have shown that these peaks are likely due to prescribing of antipsychotics for palliative care purposes and may have been linked to pre-emptive prescribing, when on-site medical visits would have been restricted. Over the study period, we observed gradual increases in antipsychotic use in patients with dementia and in care homes and a decrease in their use in patients with learning disability or autism.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Orla Macdonald", - "author_inst": "Oxford Health NHS FT" - }, - { - "author_name": "Amelia Green", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Alex J Walker", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Richard Croker", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Helen J Curtis", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Andrew Brown", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Ben Butler-Cole", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Colm Andrews", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Caroline E Morton", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "David Evans", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Iain Dillingham", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Jon Massey", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Louis Fisher", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Seb Bacon", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Simon Davy", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Tom Ward", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "William Hulme", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Jessica Morley", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Chris Bates", - "author_inst": "TPP" - }, - { - "author_name": "Jonathan Cockburn", - "author_inst": "TPP" - }, - { - "author_name": "John Parry", - "author_inst": "TPP" - }, - { - "author_name": "Frank Hester", - "author_inst": "TPP" - }, - { - "author_name": "Sam Harper", - "author_inst": "TPP" - }, - { - "author_name": "Shaun O'Hanlon", - "author_inst": "EMIS" - }, - { - "author_name": "Alex Eavis", - "author_inst": "EMIS" - }, - { - "author_name": "Richard Jarvis", - "author_inst": "EMIS" - }, - { - "author_name": "Dima Avramov", - "author_inst": "EMIS" - }, - { - "author_name": "Ian Wood", - "author_inst": "EMIS" - }, - { - "author_name": "Nasreen Parkes", - "author_inst": "EMIS" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2023.01.05.23284247", "rel_title": "Identification of differences in the magnitude and specificity of SARS-CoV-2 nucleocapsid antibody responses in naturally infected and vaccinated individuals", @@ -142914,6 +143626,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.01.06.23284199", + "rel_title": "Who Gets Long COVID and Suffers its Mental Health and Socioeconomic Consequences in the United States? Preliminary Findings from a Large Nationwide Study", + "rel_date": "2023-01-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.06.23284199", + "rel_abs": "As the number of confirmed COVID-19 cases now exceeds 100 million cases in the United States and continues to climb, concerns have been increasingly raised over the future public health and economic burden of long COVID including disability and concomitant declines in labor force participation. Only a handful of US population-based studies have explored sociodemographic and socioeconomic characteristics that put people at risk of long COVID or have investigated its mental health and socioeconomic sequelae. Herein, I report findings from the largest multivariable analysis to date using US nationally-representative data on 153,543 adults including 19,985 adults with long COVID to explore key predictors and sequelae of long COVID. An estimated 14.0% of adults aged 18-84 y (35.11 million adults) and 15.5% of working-aged adults aged 18-64 y (30.65 million adults) had developed long COVID by November 2022. Several sociodemographic and socioeconomic factors predicted long COVID including lower household income, being aged 30-49 y, Hispanic, female, gay/lesbian or bisexual, and divorced/separated. Even after accounting for such factors, having long COVID was linked to higher risks of recent unemployment, financial hardship, and anxiety and depressive symptomatology, with evidence of dose-response relationships. Overall, an estimated 27.7 million US adults aged 18-84 y and 24.2 million working-aged adults with long COVID who had been or may still be at risk of adverse socioeconomic and mental health outcomes. Lost work was further calculated to be the equivalent of 3 million workers annually, and the estimated annual lost earnings due to long COVID among working-aged adults totaled $175 billion. These preliminary findings highlight the substantial public health and economic implications of long COVID among Americans and should prompt further inquiry and intervention.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Daniel Kim", + "author_inst": "Northeastern University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.01.06.23284282", "rel_title": "OmiCrisp: A CRISPR SARS-CoV-2 test with Omicron detection", @@ -144969,45 +145700,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.02.23284119", - "rel_title": "Participant Demographics and Testing Trends: A Community Pandemic Response Program", - "rel_date": "2023-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.02.23284119", - "rel_abs": "ObjectiveThis study aimed to identify demographic characteristics of test participants and changes in testing participation over time in a community pandemic-response program launched in a college town in California, USA.\n\nMethodsWe described overall testing participation, identified demographic characteristics of frequent testers, and evaluated changes in testing participation over four different periods of the COVID-19 pandemic.\n\nResultsA total of 770,165 tests were performed between November 18, 2020, and June 30, 2022, among 89,924 residents of Yolo County (41.1% of population), with significant participation from racially/ethnically diverse participants and across age groups. Most positive cases (49.9%) were captured during Omicron, which also corresponds to the period with the highest daily participation (895 per 100K population). The proportion of participants which we considered \"frequent testers\" (28.9% vs. 39.7%, p < 0.0001) and individuals that tested once (39.5% vs. 47.9%, p < 0.0001) increased significantly from Delta to Omicron. Women (58.8%), participants of age 19-34 years (38.8%), and White (53.2%) tested more frequently throughout the program. The proportion of tests conducted among Latinos remained steady around 18% over time, with the exception of the post-Omicron period (13%).\n\nConclusionThe unique features of a pandemic response program that supported communitywide access to free asymptomatic testing provides a unique opportunity to evaluate adherence to testing recommendations, and testing trends over time. Identification of individual and group-level factors associated with testing behaviors is essential to improve access and protect communities at-large.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Yury E Garcia", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Leslie Solis", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Maria L Daza-Torres", - "author_inst": "University of California, Davis" - }, - { - "author_name": "J Cricelio Montesinos-Lopez", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Brad H Pollock", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Miriam Nuno", - "author_inst": "University of California, Davis" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.01.02.23284120", "rel_title": "The time between vaccination and infection impacts immunity against SARS-CoV-2 variants", @@ -145256,6 +145948,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.01.03.23284131", + "rel_title": "Estimating long-term vaccine effectiveness against SARS-CoV-2 variants: a model-based approach", + "rel_date": "2023-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.03.23284131", + "rel_abs": "With the ongoing evolution of the SARS-CoV-2 virus, variant-adapted vaccines are likely to be required. Given the challenges of conducting clinical trials against a background of widespread infection-induced immunity, updated vaccines are likely to be adopted based on immunogenicity data. We extended a modelling framework linking immunity levels and protection and fitted the model to vaccine effectiveness data from England for three vaccines (Oxford/AstraZeneca AZD1222, Pfizer-BioNTech BNT162b2, Moderna mRNA-1273) and two variants (Delta and Omicron) to predict longer-term effectiveness against mild disease, hospitalisation and death. We use these model fits to predict the effectiveness of the Moderna bivalent vaccine (mRNA1273.214) against the Omicron variant using immunogenicity data. Our results suggest sustained protection against hospitalisation and death from the Omicron variant over the first six months following boosting with the monovalent vaccines but a gradual waning to moderate protection after 1 year (median predicted vaccine effectiveness at 1 year in 65+ age group: AZD1222 38.9%, 95% CrI 31.8%-46.8%; BNT162b2 53.3%, 95% CrI 49.1%-56.9%; mRNA-1273 60.0%, 95% CrI 56.0%-63.6%). Furthermore, we predict almost complete loss of protection against mild disease over this period (mean predicted effectiveness at 1 year 7.8% for AZD1222, 13.2% for BNT162b2 and 16.7% for mRNA-1273). Switching to a second booster with the bivalent mRNA1273.214 vaccine against Omicron BA.1/2 is predicted to prevent nearly twice as many hospitalisations and deaths over a 1-year period compared to administering a second booster with the monovalent mRNA1273 vaccine. Ongoing production and administration of variant-specific vaccines are therefore likely to play an important role in protecting against severe outcomes from the ongoing circulation of SARS-CoV-2.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Alexandra B Hogan", + "author_inst": "1.\tSchool of Population Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia" + }, + { + "author_name": "Patrick Doohan", + "author_inst": "2.\tMRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK" + }, + { + "author_name": "Sean L Wu", + "author_inst": "3.\tInstitute for Health Metrics and Evaluation, University of Washington, Seattle, USA" + }, + { + "author_name": "Daniela Olivera Mesa", + "author_inst": "2.\tMRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK" + }, + { + "author_name": "Jaspreet Toor", + "author_inst": "2.\tMRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK" + }, + { + "author_name": "Oliver J Watson", + "author_inst": "4.\tLondon School of Hygiene and Tropical Medicine, London, UK" + }, + { + "author_name": "Peter Winskill", + "author_inst": "2.\tMRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK" + }, + { + "author_name": "Giovanni Charles", + "author_inst": "2.\tMRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK" + }, + { + "author_name": "Gregory Barnsley", + "author_inst": "4.\tLondon School of Hygiene and Tropical Medicine, London, UK" + }, + { + "author_name": "Eleanor M Riley", + "author_inst": "5.\tInstitute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, UK" + }, + { + "author_name": "David S Khoury", + "author_inst": "6.\tKirby Institute, University of New South Wales, Sydney, NSW, Australia" + }, + { + "author_name": "Neil M Ferguson", + "author_inst": "2.\tMRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK" + }, + { + "author_name": "Azra Ghani", + "author_inst": "2.\tMRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.01.02.23284123", "rel_title": "Early risk-assessment of pathogen genomic variants emergence", @@ -146835,53 +147594,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.12.24.22283920", - "rel_title": "COVID-19 in Cambodia: Epidemiology, Response, and Lessons Learned, 27 January 2020 to 30 June 2022", - "rel_date": "2022-12-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.24.22283920", - "rel_abs": "As a member state of the International Health Regulation 2005, Cambodia has been continuously strengthening its capacity to respond to health emergencies and prevent the international spread of diseases. Despite this, Cambodias capacity to prevent, detect, and rapidly respond to public health threats remained limited at the onset of the pandemic. This paper describes epidemiological phases, response phases, strategy, and lessons learned in Cambodia between 27 January 2020 and 30 June 2022. We classified epidemiological phases in Cambodia into three phases, in which Cambodia responded using eight measures: (1) detect, isolate/quarantine; (2) face coverings, hand hygiene, and physical distancing measures; (3) risk communication and community engagement; (4) school closures; (5) border closures; (6) public event and gathering cancellation; (7) vaccination; and (8) lockdown. The measures corresponded to six strategies: (1) setting up and managing a new response system, (2) containing the spread with early response, (3) strengthening the identification of cases and contacts, (4) strengthening care for COVID-19 patients, (5) boosting vaccination coverage, and (6) supporting disadvantaged groups. Finally, ten lessons were learned for future health emergency responses. Findings suggest that Cambodia successfully contained the spread of SARS-CoV-2 in the first year and quickly attained high vaccine coverage by the second year of the response. The core of this success was the strong political will and high level of cooperation from the public. However, Cambodia needs to further improve its infrastructure for quarantining and isolating cases and close contacts and laboratory capacity for future health emergencies.\n\nSUMMARY BOXO_LICOVID-19 spread globally, but how the pandemic played out in each country depended on various factors, including government responses and the general publics adherence to COVID-19 measures.\nC_LIO_LIEarly response--Early detection, Early isolation, Early tracing, Early treatment, and Early education--is the core of successful SARS-CoV-2 containment.\nC_LIO_LIAchieving high vaccination coverage quickly leads to a decline in the number of deaths and to eventual full re-opening of the country.\nC_LIO_LIResponding to the pandemic requires decisive leadership and good governance, that refers to decisions being made quickly, in a timely manner, and without delay.\nC_LIO_LIHigh level of cooperation from the public is a fundamental factor for success in containing the spread in the early phase, and the massively successful vaccination campaign in the later stage.\nC_LI", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Srean Chhim", - "author_inst": "National Institute of Public Health" - }, - { - "author_name": "Grace Marie Ku", - "author_inst": "Institute of Tropical Medicine, Antwerp" - }, - { - "author_name": "Sothiro Mao", - "author_inst": "National Institute of Public Health" - }, - { - "author_name": "Willem van de Put", - "author_inst": "Institute of Tropical Medicine, Antwerp" - }, - { - "author_name": "Wim Van Damme", - "author_inst": "Institute of Tropical Medicine, Antwerp" - }, - { - "author_name": "Por Ir", - "author_inst": "National Institute of Public Health" - }, - { - "author_name": "Chhorvann Chhea", - "author_inst": "National Institute of Public Health" - }, - { - "author_name": "Vandine Or", - "author_inst": "Ministry of Health, Phnom Penh, Cambodia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.12.27.22283698", "rel_title": "Safety and Effectiveness of SA58 Nasal Spray against COVID-19 Infection in Medical Personnel\uff1aAn Open-label, Blank-controlled Study", @@ -147110,6 +147822,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2022.12.28.22284008", + "rel_title": "The kinetics of humoral and cellular responses after the booster dose of COVID-19 vaccine in inflammatory arthritis patients", + "rel_date": "2022-12-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.28.22284008", + "rel_abs": "IntroductionImpaired immunogenicity of COVID-19 vaccinations in inflammatory arthritis (IA) patients results in diminished immunity. However, optimal booster vaccination regimens are still unknown, due to not unstudied kinetics of the immune response after booster vaccinations. Therefore, this study aimed to assess the kinetics of humoral and cellular responses in IA patients after the COVID-19 booster.\n\nPatients and MethodsIn 29 IA patients and 16 healthy controls (HC) humoral responses (level of IgG antibodies) and cellular responses (IFN-{gamma} production) were assessed before (T0), after 4 weeks (T1), and after more than 6 months (T2) from the booster vaccination with BNT162b2.\n\nResultsIA patients, but not HC, showed lower anti-S-IgG concentration and IGRA fold change at T2 compared to T1 (p=0.026 and p=0.031). Furthermore, in IA patients the level of cellular response at T2 returned to the pre-booster level (T0). All immunomodulatory drugs, except IL-6 and IL-17 inhibitors for the humoral and IL-17 inhibitors for the cellular response, impaired the immunogenicity of the booster dose at T2. However, none of the immunomodulatory drugs affected the kinetics of both humoral and cellular responses (measured as the difference between response rates at T1 and T2).\n\nConclusionOur study showed impaired kinetics of both humoral and cellular responses after the booster dose of the COVID-19 vaccine in IA patients, which, in the case of cellular response, did not allow the vaccination effect to be maintained for more than 6 months. Repetitive vaccination with subsequent booster doses seems to be necessary for IA patients.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Jakub Wro\u0144ski", + "author_inst": "National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland" + }, + { + "author_name": "Bozena Jaszczyk", + "author_inst": "National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland" + }, + { + "author_name": "Leszek Roszkowski", + "author_inst": "National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland" + }, + { + "author_name": "Anna Felis-Giemza", + "author_inst": "National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland" + }, + { + "author_name": "Krzysztof Bonek", + "author_inst": "National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland" + }, + { + "author_name": "Anna Kornatka", + "author_inst": "National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland" + }, + { + "author_name": "Magdalena Plebanczyk", + "author_inst": "National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland" + }, + { + "author_name": "Tomasz Burakowski", + "author_inst": "National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland" + }, + { + "author_name": "Barbara Lisowska", + "author_inst": "National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland" + }, + { + "author_name": "Brygida Kwiatkowska", + "author_inst": "National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland" + }, + { + "author_name": "Wlodziemierz Maslinski", + "author_inst": "National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland" + }, + { + "author_name": "Malgorzata Wislowska", + "author_inst": "National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland" + }, + { + "author_name": "Magdalena Massalska", + "author_inst": "National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland" + }, + { + "author_name": "Ewa Kuca-Warnawin", + "author_inst": "National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland" + }, + { + "author_name": "Marzena Ciechomska", + "author_inst": "National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "rheumatology" + }, { "rel_doi": "10.1101/2022.12.29.22284048", "rel_title": "Estimated of expected COVID-19 deaths in Mainland China after abandoning zero COVID policy", @@ -148541,57 +149328,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2022.12.25.22283942", - "rel_title": "Study COVID-19 Severity of Patients Admitted to Emergency Room (ER) with Chest X-ray Images", - "rel_date": "2022-12-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.25.22283942", - "rel_abs": "We have conducted a study of the COVID-19 severity with the chest x-ray images, a private dataset collected from our collaborator St Bernards Medical Center. The dataset is comprised of chest x-ray images from 1,550 patients who were admitted to emergency room (ER) and were all tested positive for COVID-19. Our study is focused on the following two questions: (1) To predict patients hospital staying duration, based on the chest x-ray image which was taken when the patient was admitted to the ER. The length of stay ranged from zero hours to 95 days in the hospital and followed a power law distribution. Based on our testing results, it is hard for the prediction models to detect strong signal from the chest x-ray images. No model was able to perform better than a trivial most-frequent classifier. However, each model was able to outperform the most-frequent classifier when the data was split evenly into four categories. This would suggest that there is signal in the images, and the performance may be further improved by the addition of clinical features as well as increasing the training set. (2) To predict if a patient is COVID-19 positive or not with the chest x-ray image. We also tested the generalizability of training a prediction model on chest x-ray images from one hospital and then testing the model on images captures from other sites. With our private dataset and the COVIDx dataset, the prediction model can achieve a high accuracy of 95.9%. However, for our hold-one-out study of the generalizability of the models trained on chest x-rays, we found that the model performance suffers due to a significant reduction in training samples of any class.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jonathan Stubblefield", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Christopher Saldivar", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Anna De Feria", - "author_inst": "St. Bernards Medical Center" - }, - { - "author_name": "James Riddle", - "author_inst": "St. Bernards Medical Center" - }, - { - "author_name": "Abhijit Shivkumar", - "author_inst": "St. Bernards Medical Center" - }, - { - "author_name": "Jason Causey", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Jake Qualls", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Jennifer Fowler", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Xiuzhen Huang", - "author_inst": "Arkansas State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2022.12.24.22283835", "rel_title": "Literature analysis of the efficacy of COVID-19 vaccinations", @@ -148828,6 +149564,121 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.12.23.22283896", + "rel_title": "No patient is the same; lessons learned from antibody repertoire profiling in hospitalized severe COVID-19 patients", + "rel_date": "2022-12-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.23.22283896", + "rel_abs": "Here, by using mass spectrometry-based methods IgG1 and IgA1 clonal repertoires were monitored quantitatively and longitudinally in more than 50 individual serum samples obtained from 17 COVID-19 patients admitted to intensive care units because of acute respiratory distress syndrome. These serological clonal profiles were used to examine how each patient reacted to a severe SARS-CoV-2 infection. All 17 donors revealed unique polyclonal repertoires and changes after infection. Substantial changes over time in the IgG1 and/or IgA1 clonal repertoires were observed in individual patients, with several new clones appearing following the infection, in a few cases leading to a few very high abundant IgG1 and/or IgA1 clones dominating the repertoire. Several of these clones were de novo sequenced through combinations of top-down, middle-down and bottom-up proteomics approaches. This revealed several sequence features in line with sequences deposited in the SARS-CoV-specific database of antibodies. In other patients, the serological Ig profiles revealed the treatment with tocilizumab, as after treatment, this IgG1-mAb dominated the serological IgG1 repertoire. Tocilizumab clearance could be monitored and a half-life of approximately 6 days was established in these patients. Overall, our longitudinal monitoring of IgG1 and IgA1 repertoires of individual donors reveals that antibody responses are highly personalized traits of each patient, affected by the disease and the chosen clinical treatment. The impact of these observations argues for a more personalized and longitudinal approach in patients diagnostics, both in serum proteomics as well as in monitoring immune responses.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Albert Bondt", + "author_inst": "Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht" + }, + { + "author_name": "Max Hoek", + "author_inst": "Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht" + }, + { + "author_name": "Kelly Dingess", + "author_inst": "Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht" + }, + { + "author_name": "Sem Tamara", + "author_inst": "Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht" + }, + { + "author_name": "Bastiaan de Graaf", + "author_inst": "Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht" + }, + { + "author_name": "Weiwei Peng", + "author_inst": "Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht" + }, + { + "author_name": "Maurits A den Boer", + "author_inst": "Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht" + }, + { + "author_name": "Mirjam Damen", + "author_inst": "Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht" + }, + { + "author_name": "Ceri Zwart", + "author_inst": "Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht" + }, + { + "author_name": "Arjan Barendregt", + "author_inst": "Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht" + }, + { + "author_name": "Danique M.H. van Rijswijck", + "author_inst": "Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht" + }, + { + "author_name": "Marloes Grobben", + "author_inst": "Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Meibergdree" + }, + { + "author_name": "Khadija Tejjani", + "author_inst": "Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Meibergdree" + }, + { + "author_name": "Jacqueline van Rijswijk", + "author_inst": "Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Meibergdree" + }, + { + "author_name": "Franziska I Voellmy", + "author_inst": "Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht" + }, + { + "author_name": "Joost Snijder", + "author_inst": "Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht" + }, + { + "author_name": "Francesca Fortini", + "author_inst": "Maria Cecilia Hospital, GVM Care & Research, Cotignola, Italy" + }, + { + "author_name": "Alberto Papi", + "author_inst": "Respiratory Section, Department of Translational Medicine, University of Ferrara, Ferrara, Italy and Respiratory Disease Unit, Azienda Ospedaliero-Universitaria" + }, + { + "author_name": "Carlo Alberto Volta", + "author_inst": "Department of Translational Medicine University of Ferrara, Ferrara, Italy and Intensive Care Unit, Azienda Ospedaliero-Universitaria di Ferrara, Italy" + }, + { + "author_name": "Gianluca Campo", + "author_inst": "Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, University of Ferrara, Ferrara, Italy" + }, + { + "author_name": "Marco Contoli", + "author_inst": "Respiratory Section, Department of Translational Medicine, University of Ferrara, Ferrara, Italy and Respiratory Disease Unit, Azienda Ospedaliero-Universitaria" + }, + { + "author_name": "Marit J van Gils", + "author_inst": "Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Meibergdree" + }, + { + "author_name": "Savino Spadaro", + "author_inst": "Department of Translational Medicine University of Ferrara, Ferrara, Italy and Intensive Care Unit, Azienda Ospedaliero-Universitaria di Ferrara, Italy" + }, + { + "author_name": "Paola Rizzo", + "author_inst": "Maria Cecilia Hospital, GVM Care & Research, Cotignola, Italy" + }, + { + "author_name": "Albert J R Heck", + "author_inst": "Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.22.22283851", "rel_title": "TaME-seq2: Tagmentation-assisted multiplex PCR enrichment sequencing for viral genomic profiling", @@ -150651,65 +151502,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2022.12.22.521201", - "rel_title": "Enhanced neutralization escape to therapeutic monoclonal antibodies by SARS-CoV-2 Omicron sub-lineages", - "rel_date": "2022-12-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.22.521201", - "rel_abs": "The landscape of SARS-CoV-2 variants dramatically diversified with the simultaneous appearance of multiple sub-variants originating from BA.2, BA.4 and BA.5 Omicron sub-lineages. They harbor a specific set of mutations in the spike that can make them more evasive to therapeutic monoclonal antibodies. In this study, we compared the neutralizing potential of monoclonal antibodies against the Omicron BA.2.75.2, BQ.1, BQ.1.1 and XBB variants, with a pre-Omicron Delta variant as a reference. Sotrovimab retains some activity against BA.2.75.2, BQ.1 and XBB as it did against BA.2/BA.5, but is less active against BQ.1.1. Within the Evusheld/AZD7442 cocktail, Cilgavimab lost all activity against all subvariants studied, resulting in loss of Evusheld activity. Finally, Bebtelovimab, while still active against BA.2.75, also lost all neutralizing activity against BQ.1, BQ.1.1 and XBB variants.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Franck Touret", - "author_inst": "Unite des Virus Emergents (UVE: Aix-Marseille University - IRD 190 - Inserm 1207), Marseille, France." - }, - { - "author_name": "Emilie Giraud", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France" - }, - { - "author_name": "Jerome Bourret", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR3569, Molecular Genetics of RNA Viruses, National Reference Center for Respiratory Viruses, Paris, France" - }, - { - "author_name": "Flora Donati", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR3569, Molecular Genetics of RNA Viruses, National Reference Center for Respiratory Viruses, Paris, France" - }, - { - "author_name": "Jaouen Tran-Rajau", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France" - }, - { - "author_name": "Jeanne Chiaravalli", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France" - }, - { - "author_name": "Frederic Lemoine", - "author_inst": "Institut Pasteur, Universite Paris Cite, G5 Evolutionary Genomics of RNA Viruses, Paris, France" - }, - { - "author_name": "Fabrice Agou", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France" - }, - { - "author_name": "Etienne Simon-Loriere", - "author_inst": "Institut Pasteur, Universite Paris Cite, G5 Evolutionary Genomics of RNA Viruses, Paris, France" - }, - { - "author_name": "Sylvie Van Der Werf", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR3569, Molecular Genetics of RNA Viruses, National Reference Center for Respiratory Viruses, Paris, France" - }, - { - "author_name": "Xavier de Lamballerie", - "author_inst": "Unite des Virus Emergents (UVE: Aix-Marseille University - IRD 190 - Inserm 1207), Marseille, France." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.12.22.22283830", "rel_title": "To test or not to test? A new behavioral epidemiology framework for COVID-19", @@ -150806,6 +151598,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.12.21.22283811", + "rel_title": "Antiviral treatments lead to the rapid accrual of hundreds of SARS-CoV-2 mutations in immunocompromised patients", + "rel_date": "2022-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.21.22283811", + "rel_abs": "The antiviral Molnupiravir (Lageviro) is widely used across the world to treat SARS-CoV-2 infection. Molnupiravir reduces viral replication by inducing mutations throughout the genome, yet in patients that do not clear the infection, the longer-term impact of the drug on virus evolution is unclear. Here, we used a case-control approach to monitor SARS-CoV-2 genomes through time in nine immunocompromised -patients with five treated with Molnupiravir. Within days of treatment, we detected a large number of low-frequency mutations in patients and that these new mutations could persist and, in some cases, were fixed in the virus population. All patients treated with the drug accrued new mutations in the spike protein of the virus, including non-synonymous mutations that altered the amino acid sequence. Our study demonstrates that this commonly used antiviral can supercharge viral evolution in immunocompromised patients, potentially generating new variants and prolonging the pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Nicholas M Fountain-Jones", + "author_inst": "University of Tasmania" + }, + { + "author_name": "Robert Vanhaeften", + "author_inst": "Royal Hobart Hospital" + }, + { + "author_name": "Jan Williamson", + "author_inst": "Royal Hobart Hospital" + }, + { + "author_name": "Janelle Maskell", + "author_inst": "Royal Hobart Hospital" + }, + { + "author_name": "I-Ly Chua", + "author_inst": "Royal Hobart Hospital" + }, + { + "author_name": "Michael Charleston", + "author_inst": "University of Tasmania" + }, + { + "author_name": "Louise Cooley", + "author_inst": "Royal Hobart Hospital" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.22.22283842", "rel_title": "Adiposity and Mortality among Patients Severely Ill with COVID-19 and non-COVID-19 Respiratory Conditions: A Cross-Context Comparison Study in the UK", @@ -152125,25 +152960,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.12.19.22283681", - "rel_title": "Tracking the COVID-19 vaccine equity, distribution, and cases in the global south", - "rel_date": "2022-12-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.19.22283681", - "rel_abs": "The rapid development of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has proved to make an important contribution in reducing both viral transmission and disease burden. In this study, we tracked the COVID-19 vaccine equity, distribution, and cases in global south countries using country-level data from Our World in Data using an event study analysis. We used data from 149 global south and 59 non-global south countries from January 2020 to May 2022. All non-global south and 90.32% of global south countries had universal availability of vaccines. The median time since the introduction of the first COVID-19 vaccine in the global south was almost eight weeks later than in non-global south countries. The median number of people fully vaccinated per hundred (68.8 vs 50.31), and the total number of boosters administered per hundred (45.7 vs. 13.02) were higher in non-global south countries compared to global south countries. Using the event study analysis, we found a significant reduction of COVID-19 new cases and deaths after the first COVID-19 vaccination rollout compared to the baseline in global south countries, average coefficient p-value <0.001. Programs aiming at improving vaccine access and distribution to global south countries are essential to effectively control COVID-19.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Tigist Mekonnen Melesse", - "author_inst": "World Bank Group" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2022.12.20.22282909", "rel_title": "The onset of late severe lung impairment in COVID-19 is associated with high inflammation markers at admission and metabolic syndrome markers", @@ -152504,6 +153320,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2022.12.20.22283717", + "rel_title": "Impact of guidance on trends of steroid prescriptions for COVID-19 inpatients: an analysis of the nation-wide administrative database in Japan", + "rel_date": "2022-12-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.20.22283717", + "rel_abs": "BackgroundSince the outbreak of the coronavirus disease 2019 (COVID-19) pandemic, guidance (\"Japanese Guide\") has been published by a working group of several academic societies and announced by the Ministry of Health, Labour, and Welfare. Steroids as a candidate treatment for COVID-19 were noted in the Japanese Guide. However, the prescription details for steroids, and whether the Japanese Guide changed its clinical practice, were unclear. This study aimed to examine the impact of the Japanese Guide on the trends in the prescription of steroids for COVID-19 inpatients in Japan.\n\nMethodsWe selected our study population using Diagnostic Procedure Combination (DPC) data from hospitals participating in the Quality Indicator/Improvement Project (QIP). The inclusion criteria were patients discharged from hospital between January 2020 and December 2020, who had been diagnosed with COVID-19, and were aged 18 years or older. The epidemiological characteristics of cases and the proportion of steroid prescriptions were described on a weekly basis. The same analysis was performed for subgroups classified by disease severity.\n\nResultsThe study population comprised 8603 cases (410 severe cases, 2231 moderate II cases, and 5962 moderate I/mild cases). The maximum proportion of cases prescribed with dexamethasone increased remarkably from 2.5% to 35.2% in the study population before and after week 29 (July 2020), when dexamethasone was included in the guidance. These increases were 7.7% to 58.7% in severe cases, 5.0% to 57.2% in moderate II cases, and 1.1% to 19.2% in moderate I/mild cases. Although the proportion of cases prescribed prednisolone and methylprednisolone decreased in moderate II and moderate I/mild cases, it remained high in severe cases.\n\nConclusionsWe showed the trends of steroid prescriptions in COVID-19 inpatients. The results showed that guidance can influence drug treatment provided during an emerging infectious disease pandemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Takuya Higuchi", + "author_inst": "Department of Healthcare Economics and Quality Management, Graduate School of Medicine, Kyoto University, Kyoto City, Kyoto, Japan" + }, + { + "author_name": "Jung-ho Shin", + "author_inst": "Department of Healthcare Economics and Quality Management, Graduate School of Medicine, Kyoto University, Kyoto City, Kyoto, Japan" + }, + { + "author_name": "Daisuke Takada", + "author_inst": "Department of Healthcare Economics and Quality Management, Graduate School of Medicine, Kyoto University, Kyoto City, Kyoto, Japan" + }, + { + "author_name": "Tetsuji Morishita", + "author_inst": "Department of Healthcare Economics and Quality Management, Graduate School of Medicine, Kyoto University, Kyoto City, Kyoto, Japan" + }, + { + "author_name": "Susumu Kunisawa", + "author_inst": "Department of Healthcare Economics and Quality Management, Graduate School of Medicine, Kyoto University, Kyoto City, Kyoto, Japan" + }, + { + "author_name": "Yuichi Imanaka", + "author_inst": "Department of Healthcare Economics and Quality Management, Graduate School of Medicine, Kyoto University, Kyoto City, Kyoto, Japan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.12.20.22283719", "rel_title": "Impact of Age, Race, and Family History on COVID-19 Related Changes in Breast Cancer Screening among the Boston Mammography Cohort Study", @@ -154271,97 +155126,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.12.18.22283646", - "rel_title": "Association between SARS-CoV-2 Infection and Select Symptoms and Conditions 31 to 150 Days After Testing among Children and Adults", - "rel_date": "2022-12-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.18.22283646", - "rel_abs": "BackgroundAn increasing number of studies have described new and persistent symptoms and conditions as potential post-acute sequelae of SARS-CoV-2 infection (PASC). However, it remains unclear whether certain symptoms or conditions occur more frequently among persons with SARS-CoV-2 infection compared with those never infected with SARS-CoV-2. We compared the occurrence of specific COVID-associated symptoms and conditions as potential PASC 31 to 150 days following a SARS-CoV-2 test among adults ([≥]20 years) and children (<20 years) with positive and negative test results documented in the electronic health records (EHRs) of institutions participating in PCORnet, the National Patient-Centered Clinical Research Network.\n\nMethods and FindingsThis study included 3,091,580 adults (316,249 SARS-CoV-2 positive; 2,775,331 negative) and 675,643 children (62,131 positive; 613,512 negative) who had a SARS-CoV-2 laboratory test (nucleic acid amplification or rapid antigen) during March 1, 2020-May 31, 2021 documented in their EHR. We identified hospitalization status in the day prior through the 16 days following the SARS-CoV-2 test as a proxy for the severity of COVID-19. We used logistic regression to calculate the odds of receiving a diagnostic code for each symptom outcome and Cox proportional hazard models to calculate the risk of being newly diagnosed with each condition outcome, comparing those with a SARS-CoV-2 positive test to those with a negative test. After adjustment for baseline covariates, hospitalized adults and children with a positive test had increased odds of being diagnosed with [≥]1 symptom (adults: adjusted odds ratio[aOR], 1.17[95% CI, 1.11-1.23]; children: aOR, 1.18[95% CI, 1.08-1.28]) and shortness of breath (adults: aOR, 1.50[95% CI, 1.38-1.63]; children: aOR, 1.40[95% CI, 1.15-1.70]) 31-150 days following a SARS-CoV-2 test compared with hospitalized individuals with a negative test. Hospitalized adults with a positive test also had increased odds of being diagnosed with [≥]3 symptoms (aOR, 1.16[95% CI, 1.08 - 1.26]) and fatigue (aOR, 1.12[95% CI, 1.05 - 1.18]) compared with those testing negative. The risks of being newly diagnosed with type 1 or type 2 diabetes (aHR, 1.25[95% CI, 1.17-1.33]), hematologic disorders (aHR, 1.19[95% CI, 1.11-1.28]), and respiratory disease (aHR, 1.44[95% CI, 1.30-1.60]) were higher among hospitalized adults with a positive test compared with those with a negative test. Non-hospitalized adults with a positive SARS-CoV-2 test had higher odds of being diagnosed with fatigue (aOR, 1.11[95% CI, 1.05-1.16]) and shortness of breath (aOR, 1.22[95% CI, 1.15-1.29]), and had an increased risk (aHR, 1.12[95% CI, 1.02-1.23]) of being newly diagnosed with hematologic disorders (i.e., venous thromboembolism and pulmonary embolism) 31-150 days following SARS-CoV-2 test compared with those testing negative. The risk of being newly diagnosed with certain conditions, such as mental health conditions and neurological disorders, was lower among patients with a positive viral test relative to those with a negative viral test.\n\nConclusionsPatients with SARS-CoV-2 infection were at higher risk of being diagnosed with certain symptoms and conditions, particularly fatigue, respiratory symptoms, and hematological abnormalities, after acute infection. The risk was highest among adults hospitalized after SARS-CoV-2 infection.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Yongkang Zhang", - "author_inst": "Cornell University Joan and Sanford I Weill Medical College" - }, - { - "author_name": "Alfonso Romieu-Hernandez", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Tegan K Boehmer", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Eduardo Azziz-Baumgartner", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Thomas Carton", - "author_inst": "Louisiana Public Health Institute" - }, - { - "author_name": "Adi V. Gundlapalli", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Julia Fearrington", - "author_inst": "Harvard Pilgrim Health Care Inc" - }, - { - "author_name": "Kshema Nagavedu", - "author_inst": "Harvard Pilgrim Health Care Inc" - }, - { - "author_name": "Katherine Dea", - "author_inst": "Statlog" - }, - { - "author_name": "Erick Moyneur", - "author_inst": "Statlog" - }, - { - "author_name": "Lindsey G. Cowell", - "author_inst": "UT Southwestern: The University of Texas Southwestern Medical Center" - }, - { - "author_name": "Rainu Kaushal", - "author_inst": "Weill Cornell Medical College: Weill Cornell Medicine" - }, - { - "author_name": "Kenneth H Mayer", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Jon Puro", - "author_inst": "OCHIN: Oregon Community Health Information Network" - }, - { - "author_name": "Sonja A Rasmussen", - "author_inst": "University of Florida" - }, - { - "author_name": "Deepika Thacker", - "author_inst": "Nemours Children's Clinic" - }, - { - "author_name": "Mark G Weiner", - "author_inst": "Weill Cornell Medical College: Weill Cornell Medicine" - }, - { - "author_name": "Sharon Saydeh", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Jason P Block", - "author_inst": "Harvard Pilgrim Health Care Inc" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.12.19.22283668", "rel_title": "A retrospective analysis of COVID-19 non-pharmaceutical interventions for Mexico and Peru: a modeling study", @@ -154614,6 +155378,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.12.15.22283495", + "rel_title": "Impact of COVID-19 on access to healthcare by persons with disabilities", + "rel_date": "2022-12-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.15.22283495", + "rel_abs": "BackgroundThe Sars-Cov-2 pandemic has ravaged societies at their very core and deepened pre-existing inequalities. Meanwhile, persons with disabilities (PwDs), the most oppressed group in Ghana that live in poor and deplorable conditions are most like to be negatively impacted by the Sars-Cov-2 crisis. Therefore, the aim of this study is to explore how the Sars-Cov-2 pandemic is influencing access to healthcare by PwDs in the Sekondi-Takoradi Metropolis (STM).\n\nMethodsWe collected data from 17 participants, nine from the Ghana Blind Union (GBU), five from Ghana Society for the Physically Challenged (GSPC), and three from the Ghana National Association of the Deaf (GNAD). An interview guide containing 25 items was used to gather data from the participants and we employed Phenomenological Analysis (PA) approach in making sense of the data.\n\nResultPWDs encounter many different barriers like; i) stigma and discrimination, ii) cost and availability of transport, iii) poor attitude of healthcare staff, iv) poor communication, v) hospital environment and equipment, vi) handwashing and sanitizing facilities, vii) unsuitable washrooms, viii) cost of healthcare, ix) registration and renewal of NHIS cards, and x) loss of income as they attempt to seek healthcare during this Covid-19 era in the STM.\n\nConclusionCovid-19 pandemic has widened the disproportionate and inequality gaps against PWDs in the STM when they attempt to seek healthcare. in the face of this, STM may lead Ghana to lag in achieving the Sustainable Development Goal (SDG) 3.8, which entreats nations to provide quality healthcare for all persons including PWDs. PWDs need education and empowerment to enable them demand for their rights when accessing healthcare. The findings highlight existing gaps in the implementation of the disability law by healthcare facilities in STM and, re-focus the attention of hospital managers in STM to the healthcare needs of PWDs in STM.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Nkosi Nkosi BOTHA", + "author_inst": "University of Cape Coast" + }, + { + "author_name": "Fortune Selasi ATSU", + "author_inst": "University of Cape Coast" + }, + { + "author_name": "Edward Wilson ANSAH", + "author_inst": "University of Cape Coast" + }, + { + "author_name": "Cynthia Esinam SEGBEDZI", + "author_inst": "University of Cape Coast" + }, + { + "author_name": "Sarah ANNIM", + "author_inst": "University of Cape Coast" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.12.16.22283603", "rel_title": "Booster Vaccination with SARS-CoV-2 mRNA Vaccines and Myocarditis Risk in Adolescents and Young Adults: A Nordic Cohort Study of 8.9 Million Residents", @@ -155981,45 +156780,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.12.16.520599", - "rel_title": "Cholesterol and ceramide facilitate SARS-CoV-2 Spike protein-mediated membrane fusion", - "rel_date": "2022-12-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.16.520599", - "rel_abs": "SARS-CoV-2 entry into host cells is mediated by the Spike (S) protein of the viral envelope. The S protein is composed of two subunits: S1 that induces binding to the host cell via its interaction with the ACE2 receptor of the cell surface and S2 that triggers fusion between viral and cellular membranes. Fusion by S2 depends on its heptad repeat domains that bring membranes close together, and its fusion peptide (FP) that interacts with and perturb the membrane structure to trigger fusion. Recent studies suggest that cholesterol and ceramide lipids from the cell surface may facilitate SARS-CoV-2 entry into host cells, but their exact mode of action remains unknown. We have used a combination of in vitro liposome-liposome and in situ cell-cell fusion assays to study the lipid determinants of S-mediated membrane fusion. We found that cholesterol and ceramide both facilitated fusion, suggesting that targeting lipids could be effective against SARS-CoV-2. As proof of concept, we examined the effect of chlorpromazine (CPZ), an antipsychotic drug known to perturb membrane structure. We found that CPZ inhibited S-mediated membrane fusion and thus potentially SARS-CoV-2 entry.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Kristina Niort", - "author_inst": "Inserm" - }, - { - "author_name": "Julia Dancourt", - "author_inst": "Inserm" - }, - { - "author_name": "Erwan Boedec", - "author_inst": "Inserm" - }, - { - "author_name": "Zahra Al Amir Dache", - "author_inst": "Inserm" - }, - { - "author_name": "Gregory Lavieu", - "author_inst": "Inserm" - }, - { - "author_name": "David Tareste", - "author_inst": "Inserm" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2022.12.14.520265", "rel_title": "COVID-19 Associated Pulmonary Aspergillosis isolates are genomically diverse but similar to each other in their responses to infection-relevant stresses", @@ -156264,6 +157024,93 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.12.15.520569", + "rel_title": "Progressive loss of conserved spike protein neutralizing antibody sites in Omicron sublineages is balanced by preserved T-cell recognition epitopes", + "rel_date": "2022-12-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.15.520569", + "rel_abs": "The continued evolution of the SARS-CoV-2 Omicron variant has led to the emergence of numerous sublineages with different patterns of evasion from neutralizing antibodies. We investigated neutralizing activity in immune sera from individuals vaccinated with SARS-CoV-2 wild-type spike (S) glycoprotein-based COVID-19 mRNA vaccines after subsequent breakthrough infection with Omicron BA.1, BA.2, or BA.4/BA.5 to study antibody responses against sublineages of high relevance. We report that exposure of vaccinated individuals to infections with Omicron sublineages, and especially with BA.4/BA.5, results in a boost of Omicron BA.4.6, BF.7, BQ.1.1, and BA.2.75 neutralization, but does not efficiently boost neutralization of sublineages BA.2.75.2 and XBB. Accordingly, we found in in silico analyses that with occurrence of the Omicron lineage a large portion of neutralizing B-cell epitopes were lost, and that in Omicron BA.2.75.2 and XBB less than 12% of the wild-type strain epitopes are conserved. In contrast, HLA class I and class II presented T-cell epitopes in the S glycoprotein were highly conserved across the entire evolution of SARS-CoV-2 including Alpha, Beta, and Delta and Omicron sublineages, suggesting that CD8+ and CD4+ T-cell recognition of Omicron BQ.1.1, BA.2.75.2, and XBB may be largely intact. Our study suggests that while some Omicron sublineages effectively evade B-cell immunity by altering neutralizing antibody epitopes, S protein-specific T-cell immunity, due to the very nature of the polymorphic cell-mediated immune, response is likely to remain unimpacted and may continue to contribute to prevention or limitation of severe COVID-19 manifestation.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Alexander Muik", + "author_inst": "BioNTech SE" + }, + { + "author_name": "Bonny Gaby Lui", + "author_inst": "BioNTech SE" + }, + { + "author_name": "Huitian Diao", + "author_inst": "BioNTech US" + }, + { + "author_name": "Yunguan Fu", + "author_inst": "InstaDeep" + }, + { + "author_name": "Maren Bacher", + "author_inst": "BioNTech SE" + }, + { + "author_name": "Aras Toker", + "author_inst": "BioNTech SE" + }, + { + "author_name": "Jessica Grosser", + "author_inst": "BioNTech SE" + }, + { + "author_name": "Orkun Ozhelvaci", + "author_inst": "BioNTech SE" + }, + { + "author_name": "Katharina Grikscheit", + "author_inst": "Institute for Medical Virology, University Hospital, Goethe University Frankfurt" + }, + { + "author_name": "Sebastian Hoehl", + "author_inst": "Institute for Medical Virology, University Hospital, Goethe University Frankfurt" + }, + { + "author_name": "Niko Kohmer", + "author_inst": "Institute for Medical Virology, University Hospital, Goethe University Frankfurt" + }, + { + "author_name": "Yaniv Lustig", + "author_inst": "Sackler School of Medicine, Tel-Aviv University" + }, + { + "author_name": "Gili Regev-Yochay", + "author_inst": "Sheba Medical Center Tel Hashomer" + }, + { + "author_name": "Sandra Ciesek", + "author_inst": "Institute for Medical Virology, University Hospital, Goethe University Frankfurt" + }, + { + "author_name": "Karim Beguir", + "author_inst": "InstaDeep Ltd" + }, + { + "author_name": "Asaf Poran", + "author_inst": "BioNTech US" + }, + { + "author_name": "Oezlem Tuereci", + "author_inst": "BioNTech SE" + }, + { + "author_name": "Ugur Sahin", + "author_inst": "BioNTech SE" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.12.15.520561", "rel_title": "SARS-CoV-2 causes periodontal fibrosis by deregulating mitochondrial beta-oxidation", @@ -157950,73 +158797,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.12.10.22283287", - "rel_title": "Reduced mortality among COVID-19 ICU patients after treatment with HemoClear convalescent plasma in Suriname", - "rel_date": "2022-12-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.10.22283287", - "rel_abs": "Convalescent plasma is a promising therapy for coronavirus disease 2019 (COVID-19), but its efficacy in intensive care unit (ICU) patients in a low and middle income country setting such as Suriname is unknown. Bedside plasma separation using the HemoClear device made convalescent plasma therapy accessible as treatment option in Suriname. Two hundred patients with severe SARS-CoV-2 infection requiring intensive care were recruited. Fifty eight patients (29%) received COVID-19 convalescent plasma (CCP) treatment in addition to standard of care (SOC). The CCP treatment and SOC groups were matched by age, sex, and disease severity scores. Mortality in the CCP treatment group was significantly lower than in the SOC group (21% versus 39%; Fishers exact P = 0.0133). Multivariate analysis using ICU days showed that CCP treatment reduced mortality (hazard ratio [HR], 0.35; 95% CI, 0.18-0.66; P = 0.001), while complication of acute renal failure (creatinine levels >110 mol/L; HR, 4.45; 95%CI, 2.54-7.80; P < 0.0001) was independently associated with death. Decrease in chest X-ray score in the CCP treatment group (median -3 points, IQR -4 to -1) was significantly greater than in the SOC group (median -1 point, IQR -3 to 1, Mann Whitney P = 0.0004). Improvement in PaO2/FiOs ratio was also significantly greater in the CCP treatment group (median 83, IQR 8 to 140) than in the SOC group (median 35, IQR -3 to 92, Mann Whitney P = 0.0234). Further research is needed for HemoClear-produced CCP as therapy in SARS-CoV-2 infections together with adequately powered, randomized controlled trials.\n\nImportanceThis study compares mortality and other endpoints between intensive care unit (ICU) COVID-19 patients treated with convalescent plasma plus standard of care (CCP), and a control group of patients hospitalized in the same medical ICU facility treated with standard of care alone (SOC) in a low and middle income country (LMIC) setting using bedside donor whole blood separation by gravity (HemoClear) to produce the CCP. It demonstrates a significant 65% survival improvement in HemoClear-produced CCP recipients (HR 0.35; 95% CI, 0.19-0.66; P = 0.001). Although this is an exploratory study, it clearly shows the benefit of using the HemoClear-produced CCP in ICU patients in the Suriname LMIC setting. Additional studies can further substantiate our findings and their applicability to both LMICs and high income countries and the use of CCP as a prepared readiness method to combat new viral pandemics.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Rosita Bihariesingh-Sanchit", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Rakesh Bansie", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Navin Ramdhani", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Rishi Mangroo", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Debra Bustamente", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Ernesto Diaz", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Cesar Fung A Foek", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Iswardath Thakoer", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Stephen C. Vreden", - "author_inst": "Foundation for Scientific Research Suriname (SWOS)" - }, - { - "author_name": "Zaheeb Choudry", - "author_inst": "Horacio Oduber Hospital" - }, - { - "author_name": "Angelique Bastienne van 't Wout", - "author_inst": "Van 't Wout Pharma Consulting" - }, - { - "author_name": "Dimitri A. Diavatopoulos", - "author_inst": "Radboud University Medical Center, Radboud Institute for Molecular Life Sciences" - }, - { - "author_name": "Arno P. Nierich", - "author_inst": "HemoClear BV" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.12.10.22283298", "rel_title": "The Use and Safety Risk of Repurposed Drugs for COVID-19 patients: Lessons Learned Utilizing the Food and Drug Administrations Adverse Event Reporting System", @@ -158225,6 +159005,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.12.13.22283409", + "rel_title": "Stress, Genetics and Mood: Impact of COVID-19 on a College Freshman Sample", + "rel_date": "2022-12-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.13.22283409", + "rel_abs": "Using a longitudinal approach, we sought to define the interplay between genetic and non-genetic factors in shaping vulnerability or resilience to COVID-19 pandemic stress, as indexed by the emergence of symptoms of depression and/or anxiety. University of Michigan freshmen were characterized at baseline using multiple psychological instruments. Subjects were genotyped and a polygenic risk score for depression (MDD-PRS) was calculated. Daily physical activity and sleep were captured. Subjects were sampled at multiple time points throughout the freshman year on clinical rating scales, including GAD-7 and PHQ-9 for anxiety and depression, respectively. Two cohorts (2019-2021) were compared to a pre-COVID-19 cohort to assess the impact of the pandemic. Across cohorts, 26%-40% of freshmen developed symptoms of anxiety or depression (N=331). Depression symptoms significantly increased in the pandemic years, especially in females. Physical activity was reduced and sleep was increased by the pandemic, and this correlated with the emergence of mood symptoms. While Low MDD-PRS predicted lower risk for depression during a typical freshman year, this apparent genetic advantage was no longer evident during the pandemic. Indeed, females with lower genetic risk accounted for the majority of the pandemic-induced rise in depression. We developed a model that explained approximately half of the variance in follow-up depression scores based on psychological trait and state characteristics at baseline and contributed to resilience in genetically vulnerable subjects. We discuss the concept of multiple types of resilience, and the interplay between genetic, sex and psychological factors in shaping the affective response to different types of stressors.\n\nSignificance StatementBiological and psychological factors that propelled the great rise in mood disorders during the COVID-19 pandemic remain unknown. We used a longitudinal design in three cohorts of college freshmen to parse the variables that contributed to susceptibility vs. resilience to pandemic stress. Low genetic risk (based on a depression polygenic risk score) was protective prior to the pandemic but this \"genetic resilience\" lost its effectiveness during the pandemic. Paradoxically, female students with low genetic risk showed enhanced vulnerability to depression during the pandemic across two cohorts. By contrast, we defined a baseline Affect Score (AS) comprising psychological variables that were predictive of future stress susceptibility or \"psychological resilience\" to stress even in the genetically vulnerable subjects.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Cortney A Turner", + "author_inst": "University of Michigan" + }, + { + "author_name": "Huzefa Khalil", + "author_inst": "University of Michigan" + }, + { + "author_name": "Virginia Murphy-Weinberg", + "author_inst": "University of Michigan" + }, + { + "author_name": "Megan H Hagenauer", + "author_inst": "University of Michigan" + }, + { + "author_name": "Linda Gates", + "author_inst": "University of Michigan" + }, + { + "author_name": "Yu Tang", + "author_inst": "University of Michigan" + }, + { + "author_name": "Lauren Weinberg", + "author_inst": "University of Michigan" + }, + { + "author_name": "Robert Grysko", + "author_inst": "University of Michigan" + }, + { + "author_name": "Leonor Floran-Garduno", + "author_inst": "University of Michigan" + }, + { + "author_name": "Thomas Dokas", + "author_inst": "University of Michigan" + }, + { + "author_name": "Catherine Samaniego", + "author_inst": "University of Michigan" + }, + { + "author_name": "Zhuo Zhao", + "author_inst": "University of Michigan" + }, + { + "author_name": "Yu Fang", + "author_inst": "University of Michigan" + }, + { + "author_name": "Srijan Sen", + "author_inst": "University of Michigan" + }, + { + "author_name": "Juan F Lopez", + "author_inst": "University of Michigan" + }, + { + "author_name": "Stanley J Watson", + "author_inst": "University of Michigan" + }, + { + "author_name": "Huda Akil", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2022.12.12.520172", "rel_title": "Fortuitous Somatic Mutations during Antibody Evolution Endow Broad Neutralization against SARS-CoV-2 Omicron Variants", @@ -159640,33 +160503,6 @@ "type": "new results", "category": "ecology" }, - { - "rel_doi": "10.1101/2022.12.08.22283265", - "rel_title": "Mental health self-care during the COVID-19 pandemic: a prospective cohort study in Australia", - "rel_date": "2022-12-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.08.22283265", - "rel_abs": "Pandemic public health measures have affected mental health for many people, resulting in varied approaches to mental health self-care. During 27 April - 26 July 2020, we surveyed a cohort of 1646 Australians, who were in paid employment prior to the pandemic, on changes in work, health, and managing their mental health concerns. Lifestyle changes were most the most frequently reported action to manage mental health concerns (78%), and were more common for women (OR=2.33, 95%CI=[1.82, 3.03]), and people experiencing recent work loss (OR=1.54, 95%CI=[1.04, 2.28]). Mental health self-care was more common for people experiencing psychological distress, or with pre-exisiting mental health conditions. Talking to friends about mental health, exercise and dietary changes, were more common for women and younger adults. Findings highlight potential benefits of reducing barriers to formal mental health services and supports during crises, particularly for people who less commonly seek help, and those experiencing psychological distress.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Daniel Griffiths", - "author_inst": "Monash University" - }, - { - "author_name": "Vinsensia Maharani Kanya Dhira Pradipta", - "author_inst": "Monash University" - }, - { - "author_name": "Alex Collie", - "author_inst": "Monash University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.12.08.22283272", "rel_title": "Duration of viral shedding of the Omicron variant in asymptomatic and mild COVID-19 cases from Shanghai, China", @@ -159895,6 +160731,81 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.12.08.519593", + "rel_title": "Global loss of cellular m6A RNA methylation following infection with different SARS-CoV-2 variants", + "rel_date": "2022-12-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.08.519593", + "rel_abs": "Host-viral interactions during SARS-CoV-2 infection are needed to understand COVID-19 pathogenesis and may help to guide the design of novel antiviral therapeutics. N6-methyladenosine modification (m6A), one of the most abundant cellular RNA modifications, regulates key processes in RNA metabolism during a stress response. Gene expression profiles observed post-infection with different SARS-CoV-2 variants show changes in the expression of genes related to RNA catabolism, including m6A readers and erasers. We found that infection with SARS-CoV-2 variants caused a loss of m6A in cellular RNAs, whereas m6A was detected abundantly in viral RNA. METTL3, the m6A methyltransferase, showed an unusual cytoplasmic localization post-infection. The B.1.351 variant had a less pronounced effect on METTL3 localization and loss of m6A than the B.1 and B.1.1.7 variants. We also observed a loss of m6A upon SARS-CoV-2 infection in air/liquid interface cultures of human airway epithelia, confirming that m6A loss is characteristic of SARS-CoV-2 infected cells. Further, transcripts with m6A modification were preferentially down-regulated post-infection. Inhibition of the export protein XPO1 resulted in the restoration of METTL3 localization, recovery of m6A on cellular RNA, and increased mRNA expression. Stress granule formation, which was compromised by SARS-CoV-2 infection, was restored by XPO1 inhibition and accompanied by a reduced viral infection in vitro. Together, our study elucidates how SARS-CoV-2 inhibits the stress response and perturbs cellular gene expression in an m6A-dependent manner.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Roshan Vaid", + "author_inst": "Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden" + }, + { + "author_name": "Akram Mendez", + "author_inst": "Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden" + }, + { + "author_name": "Ketan Thombare", + "author_inst": "Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden" + }, + { + "author_name": "Rebeca Burgos-Panadero", + "author_inst": "Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden" + }, + { + "author_name": "Remy Robinot", + "author_inst": "Virus and Immunity Unit, Institut Pasteur, Universite Paris Cite, CNRS UMR 3569, Paris, France" + }, + { + "author_name": "Barbara F Fonseca", + "author_inst": "Virus and Immunity Unit, Institut Pasteur, Universite Paris Cite, CNRS UMR 3569, Paris, France" + }, + { + "author_name": "Nikhil R Gandasi", + "author_inst": "GA08/NRG-lab, Department of Molecular Reproduction, Development and Genetics (MRDG), Indian Institute of Sciences (IISc), Bengaluru-560012, India" + }, + { + "author_name": "Johan Ringlander", + "author_inst": "Department of Infectious Diseases, Sahlgrenska Academy, Gothenburg University, Gothenburg, 41345, Sweden" + }, + { + "author_name": "Mohammad Hassan Baig", + "author_inst": "Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Korea" + }, + { + "author_name": "Jae-June Dong", + "author_inst": "Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Korea" + }, + { + "author_name": "Jae Yong Cho", + "author_inst": "Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Korea" + }, + { + "author_name": "Bjorn Reinius", + "author_inst": "Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden" + }, + { + "author_name": "Lisa A Chakrabarti", + "author_inst": "Virus and Immunity Unit, Institut Pasteur, Universite Paris Cite, CNRS UMR 3569, Paris, France" + }, + { + "author_name": "Kristina Nystrom", + "author_inst": "Department of Infectious Diseases, Sahlgrenska Academy, Gothenburg University, Gothenburg, 41345, Sweden" + }, + { + "author_name": "Tanmoy Mondal", + "author_inst": "Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2022.12.08.519651", "rel_title": "Biochemistry-informed design selects potent siRNAs against SARS-CoV-2", @@ -161418,53 +162329,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.12.02.22281853", - "rel_title": "Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies", - "rel_date": "2022-12-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.02.22281853", - "rel_abs": "The spread of SARS-CoV-2, like that of many other pathogens, is governed by heterogeneity. \"Superspreading,\" or \"over-dispersion,\" is an important factor in transmission, yet it is hard to quantify. Estimates from contact tracing data are prone to potential biases due to the increased likelihood of detecting large clusters of cases, and may reflect variation in contact behavior more than biological heterogeneity. In contrast, the average number of secondary infections per contact is routinely estimated from household surveys, and these studies can minimize biases by testing all members of a household. However, the models used to analyze household transmission data typically assume that infectiousness and susceptibility are the same for all individuals or vary only with predetermined traits such as age. Here we develop and apply a combined forward simulation and inference method to quantify the degree of inter-individual variation in both infectiousness and susceptibility from observations of the distribution of infections in household surveys. First, analyzing simulated data, we show our method can reliably ascertain the presence, type, and amount of these heterogeneities with data from a sufficiently large sample of households. We then analyze a collection of household studies of COVID-19 from diverse settings around the world, and find strong evidence for large heterogeneity in both the infectiousness and susceptibility of individuals. Our results also provide a framework to improve the design of studies to evaluate household interventions in the presence of realistic heterogeneity between individuals.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Thayer L Anderson", - "author_inst": "Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218" - }, - { - "author_name": "Anjalika Nande", - "author_inst": "Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218" - }, - { - "author_name": "Carter Merenstein", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Brinkley Raynor", - "author_inst": "Department of Biostatistics, Epidemiology, & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Anisha Oommen", - "author_inst": "Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218. Department of Biomedical Engineering, Johns Hopkins University, Baltimore, " - }, - { - "author_name": "Brendan J Kelly", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Michael Z Levy", - "author_inst": "Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104" - }, - { - "author_name": "Alison L Hill", - "author_inst": "Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218. Department of Biomedical Engineering, Johns Hopkins University, Baltimore, " - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.12.04.22282996", "rel_title": "COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting", @@ -161725,6 +162589,45 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2022.12.04.519037", + "rel_title": "Genome charaterization based on the Spike-614 and NS8-84 loci of SARS-CoV-2 reveals two major onsets of the COVID-19 pandemic", + "rel_date": "2022-12-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.04.519037", + "rel_abs": "The global COVID-19 pandemic has lasted for three years since its outbreak, however its origin is still unknown. Here, we analyzed the genotypes of 3.14 million SARS-CoV-2 genomes based on the amino acid 614 of the Spke (S) and the amino acid 48 of NS8 (nonstructural protein 8), and identified 16 linkage haplotypes. The GL haplotype (S_614G and NS8_48L) was the major haplotype driving the global pandemic and accounted for 99.2% of the sequenced genomes, while the DL haplotype (S_614D and NS8_48L) caused the pandemic in China in the spring of 2020 and accounted for approximately 60% of the genomes in China and 0.45% of the global genomes. The GS (S_614G and NS8_48S), DS (S_614D and NS8_48S) and NS (S_614N and NS8_48S) haplotypes accounted for 0.26%, 0.06%, and 0.0067% of the genomes, respectively. The main evolutionary trajectory of SARS-CoV-2 is DS[->]DL[->]GL, whereas the other haplotypes are minor byproducts in the evolution. Surprisingly, the newest haplotype GL had the oldest time of most recent common ancestor (tMRCA), which was May 1 2019 by mean, while the oldest haplotype had the newest tMRCA with a mean of October 17, indicating that the ancestral strains that gave birth to GL had been extinct and replaced by the more adapted newcomer at the place of its origin, just like the sequential rise and fall of the delta and omicron variants. However, they arrived and evolved into toxic strains and ignited a pandemic in China where the GL strains did not exist at the end of 2019. The GL strains had spread all over the world before they were discovered, and ignited the global pandemic, which had not been noticed until the pandemic was declared in China. However, the GL haplotype had little influence in China during the early phase of the pandemic due to its late arrival as well as the strict transmission controls in China. Therefore, we propose two major onsets of the COVID-19 pandemic, one was mainly driven by the haplotype DL in China, the other was driven by the haplotype GL globally.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jiaming Zhang", + "author_inst": "Chinese Academy of Tropical Agricultural Sciences" + }, + { + "author_name": "Xiaowen Hu", + "author_inst": "Institute of Tropical Bioscience and Biotechnology" + }, + { + "author_name": "Yaojia Mu", + "author_inst": "Chinese Academy of Tropical Agricultural Sciences" + }, + { + "author_name": "Ruru Deng", + "author_inst": "Public Health Institute" + }, + { + "author_name": "Guohui Yi", + "author_inst": "Hainan Medical University" + }, + { + "author_name": "Lei Yao", + "author_inst": "The Affiliated Hospital of Southwest Medical University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.12.06.22283103", "rel_title": "Heterologous boosting of neutralizing activity against Delta and Omicron SARS-CoV-2 variants in CoronaVac-primed adults; a randomized study with SCB-2019 vaccine", @@ -163296,77 +164199,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2022.12.02.22283026", - "rel_title": "Healthcare in England was affected by the COVID-19 pandemic across the pancreatic cancer pathway: a cohort study using OpenSAFELY-TPP", - "rel_date": "2022-12-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.02.22283026", - "rel_abs": "BackgroundHealthcare across all sectors, in the UK and globally, was negatively affected by the COVID-19 pandemic. We analysed healthcare services delivered to people with pancreatic cancer from January 2015 to March 2023 to investigate the effect of the COVID-19 pandemic.\n\nMethodsWith the approval of NHS England, and drawing from a nationally representative OpenSAFELY-TPP dataset of 24 million patients (over 40% of the English population), we undertook a cohort study of people diagnosed with pancreatic cancer. We queried electronic healthcare records for information on the provision of healthcare services across the pancreatic cancer pathway. To estimate the effect of the COVID-19 pandemic, we predicted the rates of healthcare services if the pandemic had not happened. We used generalised linear models (GLM) and the pre-pandemic data from January 2015 to February 2020 to predict rates in March 2020 to March 2023. The 95% confidence intervals of the predicted values were used to estimate the significance of the difference between the predicted and observed rates.\n\nResultsThe rate of pancreatic cancer and diabetes diagnoses in the cohort was not affected by the pandemic. There were 26,840 people diagnosed with pancreatic cancer from January 2015 to March 2023. The mean age at diagnosis was 72 ({+/-}11 SD), 48% of people were female, 95% were of White ethnicity and 40% were diagnosed with diabetes. We found a reduction in surgical resections by 25% to 28% during the pandemic. In addition, 20%, 10% and 4% fewer people received BMI, HbA1c and liver function tests respectively before they were diagnosed with pancreatic cancer. There was no impact of the pandemic on the number of people making contact with primary care, but the number of contacts increased on average by 1 to 2 per person amongst those who made contact. Reporting of jaundice decreased by 28%, but recovered within twelve months into the pandemic. Emergency department visits, hospital admissions and deaths were not affected.\n\nConclusionsThe pandemic affected healthcare in England across the pancreatic cancer pathway. Positive lessons could be learnt from the services that were resilient and those that recovered quickly. The reductions in healthcare experienced by people with cancer have the potential to lead to worse outcomes. Current efforts should focus on addressing the unmet needs of people with cancer.\n\nFundingThis work was jointly funded by the Wellcome Trust (222097/Z/20/Z); MRC (MR/V015757/1, MC_PC-20059, MR/W016729/1); NIHR (NIHR135559, COV-LT2-0073), and Health Data Research UK (HDRUK2021.000, 2021.0157). This work was funded by Medical Research Council (MRC) grant reference MR/W021390/1 as part of the postdoctoral fellowship awarded to AL and undertaken at the Bennett Institute, University of Oxford. The views expressed are those of the authors and not necessarily those of the NIHR, NHS England, UK Health Security Agency (UKHSA) or the Department of Health and Social Care. Funders had no role in the study design, collection, analysis, and interpretation of data; in the writing of the report; and in the decision to submit the article for publication.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Agnieszka Lemanska", - "author_inst": "University of Surrey" - }, - { - "author_name": "Colm D Andrews", - "author_inst": "University of Oxford" - }, - { - "author_name": "Louis Fisher", - "author_inst": "University of Oxford" - }, - { - "author_name": "Seb Bacon", - "author_inst": "University of Oxford" - }, - { - "author_name": "Adam Frampton", - "author_inst": "Oncology Section, Surrey Cancer Research Institute, Department of Clinical and Experimental Medicine, University of Surrey, Guildford, UK and HPB Surgical Unit," - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "University of Oxford" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "University of Oxford" - }, - { - "author_name": "Simon Davy", - "author_inst": "University of Oxford" - }, - { - "author_name": "Keith J Roberts", - "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK" - }, - { - "author_name": "Praveetha Patalay", - "author_inst": "University College London" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "University of Oxford" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "University of Oxford" - }, - { - "author_name": "- The OpenSAFELY Collaborative", - "author_inst": "" - }, - { - "author_name": "Alex J Walker", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.11.30.22282946", "rel_title": "Discovering Social Determinants of Health from Case Reports using Natural Language Processing: Algorithmic Development and Validation", @@ -163499,6 +164331,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.12.02.22283046", + "rel_title": "The Societal Value of Vaccines: Expert-Based Conceptual Framework and Methods Using COVID-19 Vaccines as A Case Study", + "rel_date": "2022-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.02.22283046", + "rel_abs": "Health technology assessments (HTAs) of vaccines typically focus on the direct health benefits to individuals and healthcare systems. COVID-19 highlighted the widespread societal impact of infectious diseases and the value of vaccines in averting adverse clinical consequences and in maintaining or resuming social and economic activities. Using COVID-19 as a case study, this research work aimed to set forth a conceptual framework capturing the broader value elements of vaccines and to identify appropriate methods to quantify value elements not routinely considered in HTAs. A two-step approach was adopted combining a targeted literature review and three rounds of expert elicitation based on a modified Delphi method, leading to a conceptual framework of 30 value elements related to broader health effects, societal and economic impact, public finances, and uncertainty value. When applying the framework to COVID-19 vaccines in post-pandemic settings, 13 value elements were consensually rated highly important by the experts for consideration in HTAs. The experts reviewed over 10 methods that could be leveraged to quantify broader value elements and provided technical forward-looking recommendations. Limitations of the framework and the identified methods were discussed. This study supplements on-going efforts aimed towards a broader recognition of the full societal value of vaccines.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Manuela Di Fusco", + "author_inst": "Pfizer Inc" + }, + { + "author_name": "Diana Mendes", + "author_inst": "Pfizer Inc" + }, + { + "author_name": "Lotte Steuten", + "author_inst": "Office of Health Economics, London" + }, + { + "author_name": "David E Bloom", + "author_inst": "Department of global Health and Population, Harvard T. H. Chan School of Public Health, Boston, USA" + }, + { + "author_name": "Michael Drummond", + "author_inst": "Centre for Health Economics, Alcuin A Block, University of York" + }, + { + "author_name": "Katharina Hauck", + "author_inst": "Department of Infectious Disease Epidemiology, Faculty of Medicine, School of Public Health, Imperial College London, London, UK" + }, + { + "author_name": "Jonathan Pearson-Stuttard", + "author_inst": "School of Public Health, Imperial College London, London; Health Analytics, Lane Clark & Peacock, London, UK" + }, + { + "author_name": "Rachel Power", + "author_inst": "The Patients Association" + }, + { + "author_name": "David Salisbury", + "author_inst": "Programme for Global Health, Royal Institute of International Affairs, Chatham House" + }, + { + "author_name": "Adrian Towse", + "author_inst": "Office of Health Economics, London" + }, + { + "author_name": "Julie Roiz", + "author_inst": "Evidence, Value and Access by PPD, Evidera, London" + }, + { + "author_name": "Gabor Szabo", + "author_inst": "Evidence, Value and Access by PPD, Evidera, Budapest" + }, + { + "author_name": "Jingyan Yang", + "author_inst": "Pfizer Inc; Institute for Social and Economic Research and Policy, Graduate School of Arts and Science, Columbia University, New York" + }, + { + "author_name": "Kinga Marczell", + "author_inst": "Evidence, Value and Access by PPD, Evidera, Budapest" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2022.12.02.22283040", "rel_title": "Evaluating primary and booster vaccination prioritization strategies for COVID-19 by age and high-contact employment status using data from contact surveys", @@ -165222,61 +166125,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.11.29.22282857", - "rel_title": "Vaccine hesitancy, reactogenicity and immunogenicity of BNT162b2 and CoronaVac in pediatric patients with neuromuscular diseases", - "rel_date": "2022-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.29.22282857", - "rel_abs": "IntroductionCOVID-19 causes global health and psychosocial devastation, particularly to high-risk patients such as those with neuromuscular diseases (NMDs). The mRNA-based BNT162b2 and inactivated whole-virus CoronaVac are two novel COVID-19 vaccines widely used across the world that confer immune protection to healthy individuals. However, hesitancy towards COVID-19 vaccination was common for patients with NMDs early in the pandemic due to the paucity of data on the safety and efficacy in this specific patient population. Therefore, we examined the underlying factors associated with vaccine hesitancy across time for these patients and included the assessment of the reactogenicity and immunogenicity of these two vaccines.\n\nMethodsPediatric patients were screened from our NMD registry. For the vaccine hesitancy arm, those aged 8-18 years with no cognitive delay were invited to complete surveys in January and April 2022. For the reactogenicity and immunogenicity arm, patients aged 2-21 years were enrolled for COVID-19 vaccination between June 2021 to April 2022. Participants recorded adverse reactions (ARs) for 7 days after vaccination. Peripheral blood was obtained before BNT162b2 or CoronaVac and within 49 days after vaccination to measure their serological antibody responses as compared to healthy children and adolescents.\n\nResultsForty-one patients completed vaccine hesitancy surveys for both timepoints, and 22 joined our reactogenicity and immunogenicity arm of the study. Two or more family members vaccinated against COVID-19 was positively associated with intention of vaccination (odds ratio 11.7, 95% CI 1.81-75.1, p=0.010). Pain at the injection site, fatigue and myalgia were the commonest ARs. Most ARs were mild (75.5%, n=71/94). All 19 patients seroconverted against the wildtype SARS-CoV-2 after two doses of BNT162b2 or CoronaVac, although there was lower neutralization against the Omicron BA.1 variant.\n\nDiscussionThis study demonstrated vaccine hesitancy amongst patients with NMDs was influenced by family members and changed across time. BNT162b2 and CoronaVac were safe and immunogenic even for patients on low-dose corticosteroids. Future research is required to assess the durability of the COVID-19 vaccines, the effectiveness of booster doses and other routes of administration against emerging SARS-CoV-2 variants for these patients.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Michael Kwan Leung Yu", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Hoi Shan Sophelia Chan", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Samuel Cheng", - "author_inst": "School of Public Health, The University of Hong Kong" - }, - { - "author_name": "Daniel Leung", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Sau Man Chan", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Amy Ka Yan Suen", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Wilfred Hing Sang Wong", - "author_inst": "1Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Malik Peiris", - "author_inst": "School of Public Health, The University of Hong Kong" - }, - { - "author_name": "Yu Lung Lau", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Jaime S Rosa Duque", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2022.11.30.22282922", "rel_title": "Epidemiological impact of a large number of incorrect negative SARS-CoV-2 test results in South West England during September and October 2021", @@ -165501,6 +166349,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.11.29.22282903", + "rel_title": "Effect of COVID-19 during pregnancy: Studying the maternal and neonatal outcomes and assessing the placental changes related to SARS-CoV-2", + "rel_date": "2022-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.29.22282903", + "rel_abs": "BackgroundPregnant females affected with COVID-19 are reported to have poorer disease outcomes as compared to non-pregnant females of a similar age group. COVID-19 may lead to adverse changes in the placenta, which needs to be studied.\n\nMethodsThis is a case series of 63 pregnant women hospitalized with COVID-19 from May 2020 to February 2021.The primary outcomes were maternal death or complications.\n\nResults63 women were studied. 83.3% of women were in the age group of 26 to 35 years. 33% women had associated comorbidities. 68.3% of women tested positive in their third trimester, 15.9% and 11% tested positive in their second and first trimesters respectively. 73% women had mild disease and 27% women required oxygen support. 3/63 women died. One woman in the second and two women in the third trimester died respectively. Histopathological examination in 13 placentae (of 19 placentae examined) were suggestive of maternal and fetal malperfusion.\n\nConclusionPregnant COVID-19 women may develop disease-related as well as obstetric complications.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Surabhi Madan", + "author_inst": "Care Institute of Medical Sciences" + }, + { + "author_name": "Dharshni Ramar", + "author_inst": "Care Institute of Medical Sciences" + }, + { + "author_name": "Devang Patel", + "author_inst": "Care Institute of Medical Sciences" + }, + { + "author_name": "Amit Chitaliya", + "author_inst": "Care Institute of Medical Sciences" + }, + { + "author_name": "Nitesh Shah", + "author_inst": "Care Institute of Medical Sciences" + }, + { + "author_name": "Bhagyesh Shah", + "author_inst": "Care Institute of Medical Sciences" + }, + { + "author_name": "Vipul Thakkar", + "author_inst": "Care Institute of Medical Sciences" + }, + { + "author_name": "Hardik Shah", + "author_inst": "Care Institute of Medical Sciences" + }, + { + "author_name": "Rashmi Chovatia", + "author_inst": "Care Institute of Medical Sciences" + }, + { + "author_name": "Pradip Dabhi", + "author_inst": "Care Institute of Medical Sciences" + }, + { + "author_name": "Minesh Patel", + "author_inst": "Care Institute of Medical Sciences" + }, + { + "author_name": "Amit Patel", + "author_inst": "Care Institute of Medical Sciences" + }, + { + "author_name": "Nirav Bapat", + "author_inst": "GMERS Medical College, Sola" + }, + { + "author_name": "Parloop Bhatt", + "author_inst": "Care Institute of Medical Sciences" + }, + { + "author_name": "Aarya Naik", + "author_inst": "Care Institute of Medical Sciences" + }, + { + "author_name": "Manish Rana", + "author_inst": "GMERS Medical College, Sola" + }, + { + "author_name": "Himanshu Nayak", + "author_inst": "AMC MET Medical College" + }, + { + "author_name": "Karun Dev Sharma", + "author_inst": "Medical University of the Americas, West Indies" + }, + { + "author_name": "Prashant Parikh", + "author_inst": "Neuberg Supratech Reference Laboratories, Ahmedabad" + }, + { + "author_name": "Bhavna Mehta", + "author_inst": "Neuberg Supratech Reference Laboratories, Ahmedabad" + }, + { + "author_name": "Bhavini Shah", + "author_inst": "Care Institute of Medical Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.11.29.518438", "rel_title": "Targeted photodynamic neutralization of SARS-CoV-2 mediated by singlet oxygen", @@ -166776,45 +167723,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.11.29.22282887", - "rel_title": "Disruption in seasonality, patient characteristics and disparities of respiratory syncytial virus infection among young children in the US during and before the COVID-19 pandemic: 2010-2022", - "rel_date": "2022-11-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.29.22282887", - "rel_abs": "Respiratory syncytial virus (RSV) infections and hospitalization have surged sharply among young children. Here we test how the seasonal patterns of RSV infections in 2022 compared with those from other COVID-19 pandemic and pre-pandemic years. For this purpose, we analyzed a nation-wide and real-time database of electronic health records of 56 million patients across 50 states in the US. The monthly incidence rate of first-time RSV infection in young children (<5 years of age) and very young children (<1 year of age) followed a seasonal pattern from 2010 to 2019 with increases during the autumn, peaking in winter, subsiding in spring and summer. This seasonal pattern was significantly disrupted during the COVID-19 pandemic. In 2020, the incidence rate of RSV infections was remarkably low throughout the year. In 2021, the RSV season expanded to 9 months starting in the early summer and peaking in October. In 2022, RSV infections started to rise in May and were significantly higher than in previous years reaching a historically highest incidence rate in November 2022. There were significant racial and ethnic disparities in the peak RSV infection rate during 2010-2021 and the disparities further exacerbated in 2022 with peak incidence rate in black and Hispanic children 2-3 times that in white children. Among RSV-infected children in 2022, 19.2% had prior documented COVID-19 infection, significantly higher than the 9.7% among uninfected children, suggesting that prior COVID-19 could be a risk factor for RSV infection or that there are common risk factors for both viral infections. Our study calls for continuous monitoring of RSV infection in young children alongside its clinical outcomes and for future work to assess potential COVID-19 related risk factors.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Lindsey Wang", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "pamela B Davis", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Nathan A Berger", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "David C Kaelber", - "author_inst": "Metrohealth" - }, - { - "author_name": "Nora Volkow", - "author_inst": "National Institute on Drug Abuse" - }, - { - "author_name": "Rong Xu", - "author_inst": "Case Western Reserve University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.11.29.518406", "rel_title": "Atomic-level characterization of the conformational transition pathways in SARS-CoV-1 and SARS-CoV-2 spike proteins", @@ -167051,6 +167959,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.11.23.22282280", + "rel_title": "The impacts of social restrictions during the COVID-19 pandemic on the physical activity levels of over 50-year olds: the CHARIOT COVID-19 Rapid Response (CCRR) cohort study", + "rel_date": "2022-11-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.23.22282280", + "rel_abs": "ObjectivesTo quantify the associations between shielding status and loneliness at the start of the COVID-19 pandemic, and physical activity (PA) levels throughout the pandemic.\n\nMethodsDemographic, health and lifestyle characteristics of 7748 cognitively healthy adults aged >50, and living in London, were surveyed from April 2020 to March 2021. The International Physical Activity Questionnaire (IPAQ) short-form assessed PA before COVID-19 restrictions, and up to 6 times over 11 months. Linear mixed models investigated associations between baseline shielding status, loneliness, and time-varying PA.\n\nResultsParticipants who felt often lonely at the outset of the pandemic completed an average of 522 and 547 fewer Metabolic Equivalent of Task (MET) minutes/week (95% CI: -809, -236, p<0.001) (95% CI: -818, -275, p<0.001) than those who felt never lonely in univariable and multivariable models adjusted for demographic factors respectively. Those who felt sometimes lonely completed 112 fewer MET minutes/week (95% CI: -219, -5, p=0.041) than those who felt never lonely following adjustment for demographic factors.\n\nParticipants who were shielding at the outset of the pandemic completed an average of 352 fewer MET minutes/week than those who were not (95% CI: -432, -273; p<0.001) in univariable models and 228 fewer MET minutes/week (95% CI: -307, -150, p<0.001) following adjustment for demographic factors. No significant associations were found after further adjustment for health and lifestyle factors.\n\nConclusionsThose shielding or lonely at pandemic onset were likely to have completed low levels of PA during the pandemic. These associations are influenced by co-morbidities and health status.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Conall Green", + "author_inst": "School of Public Health, Imperial College London" + }, + { + "author_name": "Thomas Beaney", + "author_inst": "Primary Care and Public Health, School of Public Health, Imperial College London" + }, + { + "author_name": "David Salman", + "author_inst": "Primary Care and Public Health, School of Public Health, Imperial College London; MSk lab, Faculty of Medicine, Imperial College London" + }, + { + "author_name": "Catherine Robb", + "author_inst": "Ageing Epidemiology Research Unit (AGE), School of Public Health, Faculty of Medicine, Imperial College Londonl; Epidemiology and Preventive Medicine Alfred Ho" + }, + { + "author_name": "Celeste de Jager Loots", + "author_inst": "Ageing Epidemiology Research Unit (AGE), School of Public Health, Faculty of Medicine, Imperial College London" + }, + { + "author_name": "Parthenia Giannakopoulou", + "author_inst": "Ageing Epidemiology Research Unit (AGE), School of Public Health, Faculty of Medicine, Imperial College London" + }, + { + "author_name": "Chi Theresa Udeh-Momoh", + "author_inst": "Ageing Epidemiology Research Unit (AGE), School of Public Health, Faculty of Medicine, Imperial College London" + }, + { + "author_name": "Sarah Ahmadi Abhari", + "author_inst": "Ageing Epidemiology Research Unit (AGE), School of Public Health, Faculty of Medicine, Imperial College London" + }, + { + "author_name": "Azeem Majeed", + "author_inst": "Primary Care and Public Health, School of Public Health, Imperial College London; Public Health Directorate, Imperial College NHS Healthcare Trust," + }, + { + "author_name": "Leftkos Middleton", + "author_inst": "Ageing Epidemiology Research Unit (AGE), School of Public Health, Faculty of Medicine, Imperial College London, Public Health Directorate, Imperial College NHS " + }, + { + "author_name": "Alison McGregor", + "author_inst": "MSk Lab Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.11.22.22282627", "rel_title": "Strengthening response coordination through public health emergency operations centers in Africa: Lessons learned from 56-week webinar sessions, 2020-2021", @@ -168830,49 +169797,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.11.23.22282686", - "rel_title": "Assessment of Attitude and Hesitancy Towards Covid-19 Vaccine among Hepatitis B and C Patients in Pakistan", - "rel_date": "2022-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.23.22282686", - "rel_abs": "OBJECTIVEThe research aimed to evaluate the attitude and perceptions towards the covid-19 vaccine among Hepatitis B and C patients in Peshawar, Khyber Pakhtunkhwa, Muzaffarabad, Azad Kashmir, Pakistan.\n\nMETHODSA survey-based study was adopted to evaluate the attitude of Hepatitis B and C patients towards immunization against covid-19 in Peshawar (KPK) and Muzaffarabad (AJK) cities of Pakistan. The study continued from January 2020 to February 2021. Participants were also assessed for their perception towards covid-19 vaccination.\n\nRESULTSA total of 839 (33.6%) individuals participated in the study. About 52 % of Hepatitis B patients were immunized against Covid-19, whereas the number of Hepatitis C patients was recorded at around 48%. About 53.7 % of participants refused to get the vaccine without any reason. About 63.2% of patients showed concern about the insufficient data available on the vaccine safety and efficacy published by the Public Health Department. Individuals with higher education were observed to be more open towards vaccination then those without a formal education. More than half of the participants (61.5 %) were concerned about the interference of the vaccine with their hepatitis treatment whereas 54.7 % patients refused vaccine because of a poor liver condition.\n\nCONCLUSIONSThe data indicated that limited data availability regarding the vaccine efficacy in viral hepatitis patients and negative attitudes of people toward covid-19 vaccination is the main cause of Covid-19 vaccination refusal among hepatitis B and C patients.\n\nDESCRIPTORSHepatitis B, Hepatitis C, covid-19, immunization, vaccine refusal, Pakistan.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Farheen Shafique", - "author_inst": "University of Azad Jammu and Kashmir Muzaffarabad, Pakistan" - }, - { - "author_name": "Mahreen Ul Hassan", - "author_inst": "Shaheed Benazir Bhutto Women University Peshawar, Pakistan" - }, - { - "author_name": "Sadia Butt", - "author_inst": "Shaheed Benazir Bhutto Women University Peshawar, Pakistan" - }, - { - "author_name": "Sadia Siddique", - "author_inst": "Shaheed Benazir Bhutto Women University Peshawar, Pakistan" - }, - { - "author_name": "Nazia Akbar", - "author_inst": "Hazara University" - }, - { - "author_name": "Azra Abrar", - "author_inst": "Abasyn University Peshawar, Pakistan" - }, - { - "author_name": "Irshad Rehman", - "author_inst": "University of Peshawar, Pakistan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.11.23.22282648", "rel_title": "An Early SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint-Petersburg, Russia", @@ -169149,6 +170073,105 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2022.11.23.517609", + "rel_title": "Individual bat viromes reveal the co-infection, spillover and emergence risk of potential zoonotic viruses", + "rel_date": "2022-11-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.23.517609", + "rel_abs": "Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the diversity and abundance of viruses within bats at the level of individual animals, and hence the frequency of virus co-infection and inter-species transmission. Using an unbiased meta-transcriptomics approach we characterised the mammalian associated viruses present in 149 individual bats sampled from Yunnan province, China. This revealed a high frequency of virus co-infection and species spillover among the animals studied, with 12 viruses shared among different bat species, which in turn facilitates virus recombination and reassortment. Of note, we identified five viral species that are likely to be pathogenic to humans or livestock, including a novel recombinant SARS-like coronavirus that is closely related to both SARS-CoV-2 and SARS-CoV, with only five amino acid differences between its receptor-binding domain sequence and that of the earliest sequences of SARS-CoV-2. Functional analysis predicts that this recombinant coronavirus can utilize the human ACE2 receptor such that it is likely to be of high zoonotic risk. Our study highlights the common occurrence of inter-species transmission and co-infection of bat viruses, as well as their implications for virus emergence.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Jing Wang", + "author_inst": "Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University" + }, + { + "author_name": "Yuanfei Pan", + "author_inst": "Fudan University" + }, + { + "author_name": "Li-fen Yang", + "author_inst": "Yunnan Institute of Endemic Disease Control and Prevention" + }, + { + "author_name": "Wei-hong Yang", + "author_inst": "Yunnan Institute of Endemic Disease Control and Prevention" + }, + { + "author_name": "Chu-ming Luo", + "author_inst": "Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University" + }, + { + "author_name": "Juan Wang", + "author_inst": "Yunnan Institute of Endemic Disease Control and Prevention" + }, + { + "author_name": "Guo-peng Kuang", + "author_inst": "Yunnan Institute of Endemic Disease Control and Prevention" + }, + { + "author_name": "Wei-chen Wu", + "author_inst": "Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University" + }, + { + "author_name": "Qin-yu Gou", + "author_inst": "Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University" + }, + { + "author_name": "Gen-yang Xin", + "author_inst": "Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University" + }, + { + "author_name": "Bo Li", + "author_inst": "Yunnan University" + }, + { + "author_name": "Huan-le Luo", + "author_inst": "Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University" + }, + { + "author_name": "Yao-qing Chen", + "author_inst": "Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University" + }, + { + "author_name": "Yue-long Shu", + "author_inst": "Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University" + }, + { + "author_name": "Deyin Guo", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Zi-hou Gao", + "author_inst": "Yunnan Institute of Endemic Diseases Control and Prevention" + }, + { + "author_name": "Guodong Liang", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Jun Li", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Edward C Holmes", + "author_inst": "University of Sydney" + }, + { + "author_name": "Yun Feng", + "author_inst": "Yunnan Institute of Endemic Disease Control and Prevention" + }, + { + "author_name": "Mang Shi", + "author_inst": "Sun Yat-sen University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.11.20.22282552", "rel_title": "Use of whole genome sequencing to identify low-frequency mutations in COVID-19 patients treated with remdesivir", @@ -170584,49 +171607,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.11.20.517193", - "rel_title": "Differential haplotype expression in class I MHC genes during SARS-CoV-2 infection of human lung cell lines", - "rel_date": "2022-11-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.20.517193", - "rel_abs": "Cell entry of SARS-CoV-2 causes genome-wide disruption of the transcriptional profiles of genes and biological pathways involved in the pathogenesis of COVID-19. Expression allelic imbalance is characterized by a deviation from the Mendelian expected 1:1 expression ratio and is an important source of allele-specific heterogeneity. Expression allelic imbalance can be measured by allele-specific expression analysis (ASE) across heterozygous informative expressed single nucleotide variants (eSNVs). ASE reflects many regulatory biological phenomena that can be assessed by combining genome and transcriptome information. ASE contributes to the interindividual variability associated with disease. We aim to estimate the transcriptome-wide impact of SARS-CoV-2 infection by analyzing eSNVs. We compared ASE profiles in the human lung cell lines Calu-3, A459, and H522 before and after infection with SARS-CoV-2 using RNA-Seq experiments. We identified 34 differential ASE (DASE) sites in 13 genes (HLA-A, HLA-B, HLA-C, BRD2, EHD2, GFM2, GSPT1, HAVCR1, MAT2A, NQO2, SUPT6H, TNFRSF11A, UMPS), all of which are enriched in protein binding functions and play a role in COVID-19. Most DASE sites were assigned to the MHC class I locus and were predominantly upregulated upon infection. DASE sites in the MHC class I locus also occur in iPSC-derived airway epithelium basal cells infected with SARS-CoV-2. Using an RNA-Seq haplotype reconstruction approach, we found DASE sites and adjacent eSNVs in phase (i.e., predicted on the same DNA strand), demonstrating differential haplotype expression upon infection. We found a bias towards the expression of the HLA alleles with a higher binding affinity to SARS-CoV-2 epitopes. Independent of gene expression compensation, SARS-CoV-2 infection of human lung cell lines induces transcriptional allelic switching at the MHC loci. This suggests a response mechanism to SARS-CoV-2 infection that swaps HLA alleles with poor epitope binding affinity, an expectation supported by publicly available proteome data.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ronaldo da Silva Francisco Junior", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Jairo R Temerozo", - "author_inst": "Oswaldo Cruz Institute" - }, - { - "author_name": "Cristina dos Santos Ferreira", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Yasmmin Martins", - "author_inst": "Instituto de Calculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA), Buenos Aires, Argentina" - }, - { - "author_name": "Thiago Moreno L Souza", - "author_inst": "Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro" - }, - { - "author_name": "Enrique Medina-Acosta", - "author_inst": "Molecular Identification and Diagnostics Unit (NUDIM), Laboratory of Biotechnology, Center for Biosciences and Biotechnology, Universidade Estadual do Norte Flu" - }, - { - "author_name": "Ana Tereza Ribeiro de Vasconcelos", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2022.11.21.517338", "rel_title": "Ultrasound treatment inhibits SARS-CoV-2 in vitro infectivity", @@ -170827,6 +171807,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.11.18.22282414", + "rel_title": "Immunogenicity and safety of a 4th homologous booster dose of a SARS-CoV-2 recombinant spike protein vaccine (NVX-CoV2373): a phase 2, randomized, placebo-controlled trial", + "rel_date": "2022-11-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.18.22282414", + "rel_abs": "BackgroundThe emergence of SARS-CoV-2 variants has significantly reduced the efficacy of some approved vaccines. A fourth dose of NVX-CoV2373 (5{micro}g SARS-CoV-2 rS + 50{micro}g Matrix-M adjuvant) was evaluated to determine induction of cross-reactive antibodies to variants of concern.\n\nMethodsA phase 2 randomized study assessed a fourth dose of NVX-CoV2373 in adults 18-84 years of age (2-dose primary series followed by third and fourth doses at 6-month intervals). Local/systemic reactogenicity was assessed the day of vaccination and for 6 days thereafter. Unsolicited adverse events (AEs) were reported. Immunogenicity was measured before, and 14 days after, fourth dose administration using anti-spike neutralization assays against the ancestral SARS-CoV-2 strain and Omicron sublineages. Antigenic cartography assessed antigenic distances between ancestral and variant strains.\n\nResultsAmong 1283 enrolled participants, 258 were randomized to receive the 2-dose primary series, of whom 104 received a third dose, and 45 received a fourth dose of NVX-CoV2373. The incidence of local/systemic reactogenicity events increased after the first three doses of NVX-CoV2373, and leveled off after dose four. Unsolicited AEs were reported in 9% of participants after dose 4 (none severe or serious). Neutralization antibody titers increased following booster doses. Antigenic cartography demonstrated reductions in antigenic distance between ancestral and variant SARS-CoV-2 strains with increased number of NVX-CoV2373 doses.\n\nConclusionsA fourth dose of NVX-CoV2373 enhanced immunogenicity without increasing reactogenicity. Antigenic cartography demonstrated a more universal-like response against SARS-CoV-2 variants after a fourth dose of NVX-CoV2373, indicating that updates to the vaccine composition may not be warranted.\n\nTrial registration numberNCT04368988", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Katia Alves", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Joyce S. Plested", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Shirley Galbiati", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Gordon Chau", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Shane Cloney-Clark", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Mingzhu Zhu", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Raj Kalkeri", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Nita Patel", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Kathy Smith", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Alex Marcheschi", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Susan Pfeiffer", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Heather McFall", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Gale Smith", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Gregory M. Glenn", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Filip Dubovsky", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Raburn M. Mallory", + "author_inst": "Novavax, Inc." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.11.19.22282546", "rel_title": "Oligosymptomatic long-term carriers of SARS-CoV-2 display impaired innate resistance and high Spike-specific neutralizing antibodies", @@ -172350,45 +173409,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.11.18.22282510", - "rel_title": "Mindfulness supports emotional resilience in children during the COVID-19 Pandemic", - "rel_date": "2022-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.18.22282510", - "rel_abs": "An important aspect of mental health in children is emotional resilience, the capacity to adapt to, and recover from, stressors and emotional challenges. Variation in trait mindfulness, ones disposition to attend to experiences with an open and nonjudgmental attitude, may be an important individual difference in children that supports emotional resilience. In this study, we investigated whether trait mindfulness was related to emotional resilience in response to stressful changes in education and home-life during the COVID-19 pandemic in the United States. We conducted a correlational study examining self-report data from July 2020 to February 2021, from 163 eight-to-ten-year-old children living in the US. Higher trait mindfulness scores correlated with less stress, anxiety, depression, and negative affect in children, and lower ratings of COVID-19 impact on their lives. Mindfulness moderated the relationship between COVID-19 child impact and negative affect. Children scoring high on mindfulness showed no correlation between rated COVID-19 impact and negative affect, whereas those who scored low on mindfulness showed a positive correlation between child COVID-19 impact and negative affect. Higher levels of trait mindfulness may have helped children to better cope with a wide range of COVID-19 stressors. Future studies should investigate the mechanisms by which trait mindfulness supports emotional resilience in children.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Isaac N Treves", - "author_inst": "MIT: Massachusetts Institute of Technology" - }, - { - "author_name": "Cindy Li", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Kimberly Wang", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Ola Ozernov-Palchik", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Halie Olson", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "John Gabrieli", - "author_inst": "Massachusetts Institute of Technology" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.11.16.22282406", "rel_title": "Special Olympics global report on COVID-19 vaccination and reasons not to vaccinate among adults with intellectual disabilities", @@ -172585,6 +173605,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.11.16.22282121", + "rel_title": "A single-centre, observational study to evaluate immune response to Covid-19 vaccines in immunocompromised patients with haematological disorders (COVAC-IC)", + "rel_date": "2022-11-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.16.22282121", + "rel_abs": "ObjectiveTo evaluate immunological response to Covid-19 vaccines in immunocompromised haematology patients and compare with immunocompetent healthy controls\n\nDesignWe compared total Anti-SARS-CoV-2 spike antibody and T cell response in 45 immunocompromised haematology patients with 30 healthy adults following 2 doses of Covid-19 vaccine for 3 -5 months at 30 day intervals\n\nSettingSingle Centre, University Hospital, United Kingdom, March 2021-December 2021\n\nMain Outcome measuresPeak quantitative total spike-specific antibody and cellular responses\n\nResultsWe found\n\nO_LINon - significant difference in T cell and total Anti-SARS-CoV-2 S antibody response between study and control group patients\nC_LIO_LISix (13%) study group participants did not have detectable Total Anti-SARS -Cov-2 S antibodies at any time point throughout the study monitoring period.\nC_LIO_LIThree (7%) of the study group participants had no response, even after additional booster doses of Covid-19 vaccine.\nC_LIO_LIAll (100%) of the control group had detectable Anti-SARS-Cov-2 S antibodies after 2 doses of Covid-19 vaccine.\nC_LIO_LINo participant died or was hospitalised due to severe Covid-19 infection during the study period. This included study group participants who had no antibody response at any time point.\nC_LI\n\nConclusionsThough there was a non - significant difference in T cell and total Anti-SARS-CoV-2 S antibody response between immunocompromised patients and healthy controls this did not result in any severe infection or Covid-19 related mortality in our study cohort. We did not identify any patient-specific factor (age, gender), specific haematological condition or treatment as determinant of response. Covid-19 vaccination was well tolerated without major side effects in both groups.\n\nWhat was already known about this topicprior to starting this study there were no studies to confirm immunological response following Covid-19 vaccination in immunocompromised haematology patients. During the conduct of our study there have been publications from researchers confirming blunted serological response in 62-66% of immunocompromised haematology patients compared to 74-95% in healthy controls.\n\nWhat this study addsOur study did not identify a significant difference in serological or T cell response between immunocompromised and healthy groups. Though 13% of immunocompromised patients had no response to Covid-19 vaccination none of them suffered from severe Covid-19 infection. We believe T cell response to Covid-19 vaccination has an important role in providing protective efficacy against Covid-19.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "DEEPAK CHANDRA", + "author_inst": "UNIVERSITY HOSPITALS OF NORTH MIDLANDS" + }, + { + "author_name": "- COAVC-IC INVESTIGATORS", + "author_inst": "" + }, + { + "author_name": "Lucy O'Mara", + "author_inst": "Directorate of Research and Innovation, University Hospitals of North Midlands, Stoke-on-Trent ST4 6Q" + }, + { + "author_name": "Lucy Bailey", + "author_inst": "Directorate of Research and Innovation, University Hospitals of North Midlands" + }, + { + "author_name": "Mathew Aspey", + "author_inst": "Directorate of Research and Innovation, University Hospitals of North Midlands" + }, + { + "author_name": "Md Asaduzzaman", + "author_inst": "Department of Engineering, School of Digital, Technologies and Arts, Staffordshire University Stoke-on-Trent ST4 2DE" + }, + { + "author_name": "Krishna Banavathi", + "author_inst": "Department of Microbiology, University Hospitals of North Midlands, Stoke-on-Trent ST4 6QG" + }, + { + "author_name": "Simon Lea", + "author_inst": "Directorate of Research and Innovation, University Hospitals of North Midlands, Stoke-on-Trent ST4 6QG" + }, + { + "author_name": "Rob Bowler", + "author_inst": "Directorate of Research and Innovation, University Hospitals of North Midlands, Stoke-on-Trent ST4 6QG" + }, + { + "author_name": "Jayasekara Prasangika", + "author_inst": "Department of Haematology, University Hospitals of North Midlands, Stoke-on-Trent ST4 6QG" + }, + { + "author_name": "Neil Phillips", + "author_inst": "Department of Haematology, University Hospitals of North Midlands, Stoke-on-Trent ST4 6QG" + }, + { + "author_name": "Fauzia Wasim", + "author_inst": "Department of Haematology, University Hospitals of North Midlands, Stoke-on-Trent ST4 6QG" + }, + { + "author_name": "Buddhika Badugama", + "author_inst": "Department of Haematology, University Hospitals of North Midlands, Stoke-on-Trent ST4 6QG" + }, + { + "author_name": "Nausheen Kamran", + "author_inst": "Department of Haematology, University Hospitals of North Midlands, Stoke-on-Trent ST4 6QG" + }, + { + "author_name": "Kumari Perera", + "author_inst": "Department of Haematology, University Hospitals of North Midlands, Stoke-on-Trent ST4 6QG" + }, + { + "author_name": "Fehmida Bano", + "author_inst": "Department of Haematology, University Hospitals of North Midlands, Stoke-on-Trent ST4 6QG" + }, + { + "author_name": "Srinivas Pillai", + "author_inst": "Department of Haematology, University Hospitals of North Midlands, Stoke-on-Trent ST4 6QG" + }, + { + "author_name": "Peter Dyer", + "author_inst": "Department of Haematology, University Hospitals of North Midlands, Stoke-on-Trent ST4 6QG" + }, + { + "author_name": "Muzna Aquil", + "author_inst": "Department of Haematology, University Hospitals of North Midlands, Stoke-on-Trent ST4 6QG" + }, + { + "author_name": "Sarah Goddard", + "author_inst": "Department of Clinical Immunology, University Hospitals of North Midlands, Stoke-on-Trent ST4 6QG" + }, + { + "author_name": "Aviva Ogbolosingha", + "author_inst": "Directorate of Research and Innovation, University Hospitals of North Midlands, Stoke-on-Trent ST4 6QG" + }, + { + "author_name": "Alda Remegoso", + "author_inst": "Directorate of Research and Innovation, University Hospitals of North Midlands, Stoke-on-Trent ST4 6QG" + }, + { + "author_name": "Judith Lee", + "author_inst": "Directorate of Research and Innovation, University Hospitals of North Midlands, Stoke-on-Trent ST4 6QG" + }, + { + "author_name": "Keira Watts", + "author_inst": "Directorate of Research and Innovation, University Hospitals of North Midlands, Stoke-on-Trent ST4 6QG" + }, + { + "author_name": "Kamaraj Karunanithi", + "author_inst": "Directorate of Research and Innovation, University Hospitals of North Midlands, Stoke-on-Trent ST4 6QG" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2022.11.16.22282100", "rel_title": "Particulate matter air pollution and COVID-19 infection, severity, and mortality: A systematic review", @@ -174028,109 +175163,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.11.12.22282116", - "rel_title": "Conceptualising the Episodic Nature of Disability among Adults Living with Long COVID: A Qualitative Study", - "rel_date": "2022-11-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.12.22282116", - "rel_abs": "ObjectivesTo describe episodic nature of disability among adults living with Long COVID.\n\nMethodsWe conducted a community-engaged qualitative descriptive study involving online semi-structured interviews and participant visual illustrations. We recruited participants via collaborator community organizations in Canada, Ireland, United Kingdom, and United States.\n\nParticipantsAdults who self-identified as living with Long COVID. We purposively recruited for diversity in age, gender, race/ethnicity, sexual orientation, and duration since initial COVID-19 infection.\n\nMain Outcome Measure(s)We used a semi-structured interview guide to explore experiences of disability living with Long COVID, specifically health-related challenges and how they were experienced over time. We asked participants to draw their health trajectory and conducted a group-based content analysis.\n\nResultsAmong the 40 participants, the median age was 39 years (interquartile range: 32, 49); majority were women (63%), white (73%), heterosexual (75%), and living with Long COVID for [≥]1 year (83%). Participants described their disability experiences as episodic in nature, characterized by fluctuations in presence and severity of health-related challenges (disability) that may occur both within a day and over the long-term living with Long COVID. They described living with ups and downs, flare-ups, and peaks followed by crashes, troughs, and valleys, likened to a yo-yo rolling hills, and rollercoaster ride with relapsing/remitting, waxing/waning, fluctuations in health. Drawn illustrations demonstrated variety of trajectories across health dimensions, some more episodic than others. Uncertainty intersected with the episodic nature of disability, characterized as unpredictability of episodes, their length, severity and triggers, and process of long-term trajectory, which had implications on broader health.\n\nConclusionsAmong this sample of adults living with Long COVID, experiences of disability were described as episodic, characterized by fluctuating health challenges, which may be unpredictable in nature. Results help to better understand experiences of disability among adults living with Long COVID to inform healthcare and rehabilitation.\n\nKEY MESSAGESO_LIWhat is already known on this topic: Globally, a growing number of individuals are living with persistent and prolonged signs and symptoms following infection consistent with COVID-19, referred to as Long COVID, Post COVID-19 Condition (PCC) or Post-acute sequelae of SARS-CoV2 (PASC). Individuals living with Long COVID are experiencing a range of symptoms and impairments that impact their ability to carry out day to day activities or engage in social and community life roles.\nC_LIO_LIWhat this study adds: Disability living with Long COVID was described as episodic, characterized by fluctuations in presence and severity of health related challenges, which may be unpredictable in nature, occurring both within the day, and over the long-term of months and years living with Long COVID.\nC_LIO_LIHow this study might affect research, practice or policy: Results will help researchers, healthcare providers, policymakers, employers, and community members to better understand experiences of disability among adults living with Long COVID, to inform future disability measurement, health and rehabilitation care and service delivery, programs and policies for insurance, return to work, and workplace accommodations.\nC_LI", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Kelly O'Brien", - "author_inst": "Univesrity of Toronto" - }, - { - "author_name": "Darren A Brown", - "author_inst": "Chelsea and Westminster Hospital NHS Foundation Trust" - }, - { - "author_name": "Kiera McDuff", - "author_inst": "University of Toronto" - }, - { - "author_name": "Natalie St. Clair-Sullivan", - "author_inst": "Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom" - }, - { - "author_name": "Patricia Solomon", - "author_inst": "McMaster University" - }, - { - "author_name": "Soo Chan Carusone", - "author_inst": "McMaster University" - }, - { - "author_name": "Lisa McCorkell", - "author_inst": "Patient-Led Research Collaborative" - }, - { - "author_name": "Hannah Wei", - "author_inst": "Patient-Led Research Collaborative" - }, - { - "author_name": "Susie Goulding", - "author_inst": "COVID Long-Haulers Support Group Canada, Canada" - }, - { - "author_name": "Margaret O'Hara", - "author_inst": "Long Covid Support, United Kingdom" - }, - { - "author_name": "Catherine Thomson", - "author_inst": "Long COVID Physio, United Kingdom" - }, - { - "author_name": "Niamh Roche", - "author_inst": "Long COVID Ireland" - }, - { - "author_name": "Ruth Stokes", - "author_inst": "Long COVID Ireland" - }, - { - "author_name": "Jaime H. Vera", - "author_inst": "Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom" - }, - { - "author_name": "Kristine Erlandson", - "author_inst": "University of Colorado Denver-Anschutz Medical Campus, Aurora, Colorado, United States" - }, - { - "author_name": "Colm Bergin", - "author_inst": "St James's Hospital, Dublin, Ireland" - }, - { - "author_name": "Larry Robinson", - "author_inst": "Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada" - }, - { - "author_name": "Angela M. Cheung", - "author_inst": "University Health Network, Toronto, Ontario, Canada; University of Toronto, Ontario, Canada" - }, - { - "author_name": "Brittany Torres", - "author_inst": "University of Toronto, Ontario, Canada" - }, - { - "author_name": "Lisa Avery", - "author_inst": "University Health Network, Toronto, Ontario, Canada; University of Toronto, Ontario, Canada" - }, - { - "author_name": "Ciaran Bannan", - "author_inst": "St James's Hospital" - }, - { - "author_name": "Richard Harding", - "author_inst": "King's College London, United Kingdom" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "rehabilitation medicine and physical therapy" - }, { "rel_doi": "10.1101/2022.11.11.22282032", "rel_title": "COVID Seq as Laboratory Developed Test (LDT) for diagnosis of SARS-CoV-2 Variants of Concern (VOC)", @@ -174395,6 +175427,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.11.11.516206", + "rel_title": "SARS-CoV-2 vaccination of laboratory rhesus monkeys (Macaca mulatta): Monitoring and efficacy", + "rel_date": "2022-11-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.11.516206", + "rel_abs": "The availability of effective vaccines and a high vaccination rate allowed the recent mitigation, or even withdrawal, of many protective measures for containing the SARS CoV-2 pandemic. At the same time, new and highly mutated variants of the virus are found to have significantly higher transmissibility and reduced vaccine efficacy, thus causing high infection rates during the third year of the pandemic. The combination of reduced measures and increased infectivity poses a particular risk for unvaccinated individuals, including animals susceptible to the virus. Among the latter, non-human primates (NHPs) are particularly vulnerable. They serve as important models in various fields of biomedical research and because of their cognitive capabilities, they receive particular attention in animal welfare regulations around the world. Yet, although they played an extraordinarily important role for developing and testing vaccines against SARS-CoV-2, the protection of captive rhesus monkeys against Covid-19 has rarely been discussed. We here report upon twofold mRNA vaccination of a cohort of 19 rhesus monkeys (Macaca mulatta) against infection by SARS-CoV-2. All animals were closely monitored on possible side effects of vaccination, and were tested for neutralising antibodies against the virus. The data show that vaccination of rhesus monkeys is a safe and reliable measure to protect these animals against SARS-CoV-2.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Dan Qi Priscilla Oh", + "author_inst": "Brain Research Institute, University of Bremen, Bremen, Germany" + }, + { + "author_name": "Iris Grothe", + "author_inst": "Brain Research Institute, University of Bremen, Bremen, Germany" + }, + { + "author_name": "Herbert Luka\u00df", + "author_inst": "Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany" + }, + { + "author_name": "Andreas K. Kreiter", + "author_inst": "Brain Research Institute, University of Bremen, Bremen, Germany" + }, + { + "author_name": "Markus Hoffmann", + "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" + }, + { + "author_name": "Detlef Wegener", + "author_inst": "Brain Research Institute, University of Bremen, Bremen, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.11.11.516052", "rel_title": "Genetic and structural data on the SARS-CoV-2 Omicron BQ.1 variant reveal its low potential for epidemiological expansion", @@ -175966,89 +177037,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2022.11.07.22282028", - "rel_title": "Comparison of the reactogenicity and immunogenicity between two-dose mRNA COVID-19 vaccine and inactivated followed by an mRNA vaccine in children aged 5 - 11 years", - "rel_date": "2022-11-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.07.22282028", - "rel_abs": "ObjectiveTo compare the reactogenicity and immunogenicity between the two-dose mRNA COVID-19 vaccine regimen and one or two doses of inactivated vaccine followed by an mRNA vaccine regimen in healthy children between 5-11 years of age.\n\nMethodsA prospective cohort study was performed at King Chulalongkorn Memorial Hospital in Thailand between March to June 2022. Healthy children between 5-11 years of age were enrolled and received the two-dose mRNA COVID-19 vaccine (BNT162b2) regimen or the inactivated (CoronaVac) vaccine followed by the BNT162b2 vaccine regimen. In addition, healthy children who received two doses of BBIBP-CorV between 1-3 months prior were enrolled to receive a heterologous BNT162b2 as a third dose (booster).\n\nReactogenicity was assessed by a self-reported online questionnaire. Immunogenicity analysis was performed to determine binding and surrogate neutralizing antibodies to SARS-CoV-2 wild-type and Omicron variants.\n\nResultsOverall, 166 eligible children were enrolled. Local and systemic AE which occurred within 7 days after vaccination were mild to moderate and well-tolerated. At one-month, post-two or post-three doses, children vaccinated with two-dose BNT162b2, CoronaVac/BNT162b2, and two-dose BBIBP-CorV followed by BNT162b2 elicited similar levels of anti-receptor-binding domain (RBD) IgG. However, the two-dose BNT162b2 and two-dose BBIBP-CorV followed by BNT162b2 groups elicited higher neutralizing activities against Omicron BA.2 variant than the CoronaVac/BNT162b2 group.\n\nConclusionThe heterologous, CoronaVac vaccine followed by the BNT162b2 vaccine, regimen elicited lower neutralizing activities against the emerging Omicron BA.2 variant than the two-dose mRNA regimen. A third dose (booster) mRNA vaccine should be prioritized for this group.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Nasamon Wanlapakorn", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Sitthichai Kanokudom", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Harit Phowatthanasathian", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Jira Chansaenroj", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Nungruthai Suntronwong", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Suvichada Assawakosri", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Ritthideach Yorsaeng", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Pornjarim Nilyanimit", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Preeyaporn Vichaiwattana", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Sirapa Klinfueng", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Thanunrat Thongmee", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Ratchadawan Aeemjinda", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Nongkanok Khanarat", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Donchida Srimuan", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Thaksaporn Thatsanatorn", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Natthinee Sudhinaraset", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Yong Poovorawan", - "author_inst": "Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2022.11.07.22282030", "rel_title": "Neurologic sequalae of COVID-19 are determined by immunologic imprinting from previous Coronaviruses.", @@ -176289,6 +177277,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.11.08.22282086", + "rel_title": "Assessing the accuracy of California county level COVID-19 hospitalization forecasts to inform public policy decision making", + "rel_date": "2022-11-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.08.22282086", + "rel_abs": "BackgroundThe COVID-19 pandemic has highlighted the role of infectious disease forecasting in informing public policy. However, significant barriers remain for effectively linking infectious disease forecasts to public health decision making, including a lack of model validation. Forecasting model performance and accuracy should be evaluated retrospectively to understand under which conditions models were reliable and could be improved in the future.\n\nMethodsUsing archived forecasts from the California Department of Public Healths California COVID Assessment Tool (https://calcat.covid19.ca.gov/cacovidmodels/), we compared how well different forecasting models predicted COVID-19 hospitalization census across California counties and regions during periods of Alpha, Delta, and Omicron variant predominance.\n\nResultsBased on mean absolute error estimates, forecasting models had variable performance across counties and through time. When accounting for model availability across counties and dates, some individual models performed consistently better than the ensemble model, but model rankings still differed across counties. Local transmission trends, variant prevalence, and county population size were informative predictors for determining which model performed best for a given county based on a random forest classification analysis. Overall, the ensemble model performed worse in less populous counties, in part because of fewer model contributors in these locations.\n\nConclusionsEnsemble model predictions could be improved by incorporating geographic heterogeneity in model coverage and performance. Consistency in model reporting and improved model validation can strengthen the role of infectious disease forecasting in real-time public health decision making.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Lauren A White", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Ryan McCorvie", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "David Crow", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Seema Jain", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Tomas M Leon", + "author_inst": "California Department of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.11.05.22281903", "rel_title": "Virtual Home Visits Reduce Asthma Burden in Underserved Communities amidst the COVID-19 Pandemic", @@ -177668,69 +178691,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2022.11.04.22281855", - "rel_title": "Disproportionate impacts of COVID-19 in a large US city", - "rel_date": "2022-11-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.04.22281855", - "rel_abs": "COVID-19 has disproportionately impacted individuals depending on where they live and work, and based on their race, ethnicity, and socioeconomic status. Studies have documented catastrophic disparities at critical points throughout the pandemic, but have not yet systematically tracked their severity through time. Using anonymized hospitalization data from March 11, 2020 to June 1, 2021, we estimate the time-varying burden of COVID-19 by age group and ZIP code in Austin, Texas. During this 15-month period, we estimate an overall 16.9% (95% CrI: 16.1-17.8%) infection rate and 34.1% (95% CrI: 32.4-35.8%) case reporting rate. Individuals over 65 were less likely to be infected than younger age groups (8.0% [95% CrI: 7.5-8.6%] vs 18.1% [95% CrI: 17.2-19.2%]), but more likely to be hospitalized (1,381 per 100,000 vs 319 per 100,000) and have their infections reported (51% [95% CrI: 48-55%] vs 33% [95% CrI: 31-35%]). Children under 18, who make up 20.3% of the local population, accounted for only 5.5% (95% CrI: 3.8-7.7%) of all infections between March 1 and May 1, 2020 compared with 20.4% (95% CrI: 17.3-23.9%) between December 1, 2020 and February 1, 2021. We compared ZIP codes ranking in the 75th percentile of vulnerability to those in the 25th percentile, and found that the more vulnerable communities had 2.5 (95% CrI: 2.0-3.0) times the infection rate and only 70% (95% CrI: 61%-82%) the reporting rate compared to the less vulnerable communities. Inequality persisted but declined significantly over the 15-month study period. For example, the ratio in infection rates between the more and less vulnerable communities declined from 12.3 (95% CrI: 8.8-17.1) to 4.0 (95% CrI: 3.0-5.3) to 2.7 (95% CrI: 2.0-3.6), from April to August to December of 2020, respectively. Our results suggest that public health efforts to mitigate COVID-19 disparities were only partially effective and that the CDCs social vulnerability index may serve as a reliable predictor of risk on a local scale when surveillance data are limited.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Spencer J Fox", - "author_inst": "The University of Georgia" - }, - { - "author_name": "Emily Javan", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Remy Pasco", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Graham C Gibson", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Briana Betke", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Jos\u00e9 L Herrera Diestra", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Spencer Woody", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Kelly Pierce", - "author_inst": "The Texas Advanced Computing Center" - }, - { - "author_name": "Kaitlyn E Johnson", - "author_inst": "The Rockefeller Foundation" - }, - { - "author_name": "Maureen Johnson-Le\u00f3n", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Michael Lachmann", - "author_inst": "The Santa Fe Institute" - }, - { - "author_name": "Lauren Ancel Meyers", - "author_inst": "The University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.11.04.22281943", "rel_title": "Fine scale human mobility changes in 26 US cities in 2020 in response to the COVID-19 pandemic were associated with distance and income", @@ -177931,6 +178891,49 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2022.11.05.515305", + "rel_title": "Novel inhibitors against COVID-19 main protease suppressed viral infection", + "rel_date": "2022-11-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.05.515305", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of COVID-19, can cause severe disease with high mortality rates, especially among older and vulnerable populations. Despite the recent success of vaccines and approval of first-generation anti-viral inhibitor against SARS-CoV-2, an expanded arsenal of anti-viral compounds that limit viral replication and ameliorate disease severity is still urgently needed in light of the continued emergence of viral variants of concern (VOC). The main protease (Mpro) of SARS-CoV-2 is the major non-structural protein required for the processing of viral polypeptides encoded by the open reading frame 1 (ORF1) and ultimately replication. Structural conservation of Mpro among SARS-CoV-2 variants make this protein an attractive target for the anti-viral inhibition by small molecules. Here, we developed a structure-based in-silico screening of approximately 11 million compounds in ZINC15 database inhibiting Mpro, which prioritized 9 lead compounds for the subsequent in vitro validation in SARS-CoV-2 replication assays using both Vero and Calu-3 cells. We validated three of these compounds significantly inhibited SARS-CoV-2 replication in the micromolar range. In summary, our study identified novel small-molecules significantly suppressed infection and replication of SARS-CoV-2 in human cells.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Vijayan Ramachandran", + "author_inst": "University of Arizona" + }, + { + "author_name": "Yanyun Liu", + "author_inst": "University of Arizona" + }, + { + "author_name": "Qianying He", + "author_inst": "University of Arizona" + }, + { + "author_name": "Andrew Tang", + "author_inst": "University of Arizona" + }, + { + "author_name": "Patrick Ronaldson", + "author_inst": "University of Arizona" + }, + { + "author_name": "Dominik Schenten", + "author_inst": "University of Arizona" + }, + { + "author_name": "Rui Chang", + "author_inst": "University of Arizona" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2022.11.06.515327", "rel_title": "Temporal Vascular Endothelial Growth Factor Sub-type gene Switching in SARS-CoV Pathogenesis. Interpretation through in vivo Murine C57BL Models", @@ -179290,57 +180293,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2022.11.03.22281925", - "rel_title": "Prior infections and effectiveness of SARS-CoV-2 vaccine in test-negative study: A systematic review and meta-analysis", - "rel_date": "2022-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.03.22281925", - "rel_abs": "BackgroundPrior infection with SARS-CoV-2 can provide protection against infection and severe COVID-19. In settings with high pre-existing immunity, vaccine effectiveness (VE) should decrease with higher levels of immunity among unvaccinated individuals. Here, we conducted a systematic review and meta-analysis to understand the influence of prior infection on VE.\n\nMethodsWe included test-negative design (TND) studies that examined VE against infection or severe disease (hospitalization, ICU admission, or death) for primary vaccination series. To determine the impact of prior infections on VE estimates, we compared studies that excluded or included people with prior COVID-19 infection. We also compared VE estimates by the cumulative incidence of cases before the start of and incidence rates during each study in the study locations, as further measures of prior infections in the community.\n\nFindingsWe identified 67 studies that met inclusion criteria. Pooled VE among studies that included people with prior COVID-19 infection was lower against infection (pooled VE: 77%; 95% confidence interval (CI): 72%, 81%) and severe disease (pooled VE: 86%; 95% CI: 83%, 89%), compared with studies that excluded people with prior COVID-19 infection (pooled VE against infection: 87%; 95% CI: 85%, 89%; pooled VE against severe disease: 93%; 95% CI: 91%, 95%). There was a negative correlation between the cumulative incidence of cases before the start of the study and VE estimates against infection (spearman correlation ({rho}) = -0.32; 95% CI: -0.45, -0.18) and severe disease ({rho} = -0.49; 95% CI: -0.64, -0.30). There was also a negative correlation between the incidence rates of cases during the study period and VE estimates against infection ({rho} = - 0.48; 95% CI: -0.59, -0.34) and severe disease ({rho} = -0.42; 95% CI: -0.58, -0.23).\n\nInterpretationBased on a review of published VE estimates we found clear empirical evidence that higher levels of pre-existing immunity in a population were associated with lower VE estimates. Excluding previously infected individuals from VE studies may result in higher VE estimates with limited generalisability to the wider population. Prior infections should be treated as confounder and effect modificatory when the policies were targeted to whole population or stratified by infection history, respectively.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Tim Tsang", - "author_inst": "The university of Hong Kong" - }, - { - "author_name": "SheenaG Sullivan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Xiaotong Huang", - "author_inst": "The university of Hong Kong" - }, - { - "author_name": "Can Wang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Yifan Wang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Joshua Nealon", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Bingyi Yang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Kylie E.C Ainslie", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Ben J Cowling", - "author_inst": "The University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.11.02.22281821", "rel_title": "Screening COVID-19 by Swaasa AI Platform using cough sounds: A cross-sectional study", @@ -179577,6 +180529,41 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.11.01.22281794", + "rel_title": "COVID-19 and non-Hodgkins lymphoma: a common susceptibility pattern?", + "rel_date": "2022-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.01.22281794", + "rel_abs": "ObjectivTo explore the link between COVID-19 incidence, socio-economic covariates, and NHL incidence.\n\nDesignEcological study design.\n\nSettingSardinia, Italy.\n\nParticipantsWe used official reports on the total cases of COVID-19 in 2020, published data on NHL incidence, and socio-economic indicators by administrative unit, covering the whole regional population.\n\nMain outcomes and measuresWe used multivariable regression analysis to explore the association between the natural logarithm (ln) of the 2020 cumulative incidence of COVID-19 and the ln-transformed NHL incidence in 1974-2003, weighing by population size and adjusting by socioeconomic deprivation and other covariates.\n\nResultsThe cumulative incidence of COVID-19 increased in relation to past incidence of NHL (p < 0.001), socioeconomic deprivation (p = 0.006), and proportion of elderly residents (p < 0.001) and decreased with urban residency (p = 0.001). Several sensitivity analyses confirmed the finding of an association between COVID-19 and NHL.\n\nConclusionThis ecological study found an ecological association between NHL and COVID-19. If further investigation would confirm our findings, shared susceptibility factors should be investigated among the plausible underlying mechanisms.\n\nStrengths and limitations of this studyO_LIThis study exploited the availability of incidence data for non-Hodgkins lymphoma over a 30-year time frame and the 2020 cumulative incidence data for COVID-19 available for all administrative units in the Sardinia region, Italy.\nC_LIO_LIUsing an ecological study design, we observed that COVID-19 occurrence increased with past incidence of non-Hodgkins lymphoma.\nC_LIO_LILimitations of the ecological study design require further investigation for confirmation and for identification of susceptibility factors possibly shared between the two diseases.\nC_LI", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "De Matteis Sara", + "author_inst": "University of Cagliari: Universita degli Studi Di Cagliari" + }, + { + "author_name": "Cosetta Minelli", + "author_inst": "Imperial College London" + }, + { + "author_name": "Giorgio Broccia", + "author_inst": "Oncologico A. Businco Hospital: Azienda Ospedaliera Brotzu" + }, + { + "author_name": "Paolo Vineis", + "author_inst": "Imperial College London" + }, + { + "author_name": "Pierluigi Cocco", + "author_inst": "University of Cagliari" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.11.01.22281787", "rel_title": "Use of Interviewer-Administered Telephone Surveys during Infectious Disease Outbreaks, Epidemics, and Pandemics: A Scoping Review", @@ -180612,20 +181599,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.10.31.22281764", - "rel_title": "SARS-CoV-2 antibody prevalence among industrial livestock operation workers and nearby community residents, North Carolina, USA, 2021-2022", - "rel_date": "2022-11-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.31.22281764", - "rel_abs": "Industrial livestock operations (ILOs), particularly processing facilities, emerged as centers of coronavirus disease 2019 (COVID-19) outbreaks in spring 2020. Confirmed cases of COVID-19 underestimate true prevalence. To investigate prevalence of antibodies against SARS-CoV-2, we enrolled 279 participants in North Carolina from February 2021 to July 2022: 90 from households with at least one ILO worker (ILO), 97 from high-ILO intensity areas (ILO neighbors - ILON), and 92 from metropolitan areas (Metro). Participants provided a saliva swab we analyzed for SARS-CoV-2 IgG using a multiplex immunoassay. Prevalence of infection-induced IgG (positive for nucleocapsid and receptor binding domain) was higher among ILO (63%) compared to ILON (42.9%) and Metro (48.7%) participants (prevalence ratio [PR] =1.38; 95% confidence interval [CI]: 1.06, 1.80; ref. ILON and Metro combined). Prevalence of infection-induced IgG was also higher among ILO participants compared to an Atlanta healthcare worker cohort (PR=2.45, 95% CI: 1.8, 3.3) and a general population cohort in North Carolina (PRs 6.37-10.67). Infection-induced IgG prevalence increased over the study period. Participants reporting not masking in public in the past two weeks had higher infection-induced IgG prevalence (78.6%) compared to participants reporting masking (49.3%) (PR=1.59; 95% CI: 1.19, 2.13). Lower education, more people per bedroom, Hispanic/Latino ethnicity, and more contact with people outside the home were also associated with higher infection-induced IgG prevalence. Similar proportions of ILO (51.6%), ILON (48.4%), and Metro (55.4%) participants completed the COVID-19 primary vaccination series; median completion was more than four months later for ILO compared to ILON and Metro participants.\n\nImportanceFew studies have measured COVID-19 seroprevalence in North Carolina, especially among rural, Black, and Hispanic/Latino communities that have been heavily affected. Antibody results show high rates of COVID-19 among industrial livestock operation workers and their household members. Antibody results add to evidence of health disparities in COVID-19 by socioeconomic status and ethnicity. Associations between masking and physical distancing with antibody results also add to evidence of the effectiveness of these prevention strategies. Delays in the timing of receipt of COVID-19 vaccination reinforce the importance of dismantling vaccination barriers, especially for industrial livestock operation workers and their household members.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.10.28.22281588", "rel_title": "A novel hospital-at-home model for patients with COVID-19 built by a team of local primary care clinics and clinical outcomes: A multi-center retrospective cohort study", @@ -180802,6 +181775,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.10.28.22281636", + "rel_title": "Long-term humoral response following simultaneous Delta and Omicron BA.1 co-infection", + "rel_date": "2022-10-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.28.22281636", + "rel_abs": "To provide insight into the long-term immune response following bivalent vaccines, we sampled vaccinated patients simultaneously co-infected with Delta and BA.1. We reported that simultaneous exposure to the Delta and BA.1 S protein does not confer an additional immune advantage compared to exposure to the Omicron BA.1 S protein alone.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Carla Saade", + "author_inst": "Centre international de recherche en infectiologie" + }, + { + "author_name": "Bruno Pozzetto", + "author_inst": "University of Saint-Etienne" + }, + { + "author_name": "Melyssa Yaugel Novoa", + "author_inst": "Centre International de Recherche en Infectiologie" + }, + { + "author_name": "Bruno Lina", + "author_inst": "Centre International de Recherche en Infectiologie" + }, + { + "author_name": "Stephane Paul", + "author_inst": "Centre Internationale de Recherche en Infectiologie" + }, + { + "author_name": "Antonin Bal", + "author_inst": "Hospices Civils de Lyon" + }, + { + "author_name": "Sophie Trouillet-Assant", + "author_inst": "Hospices Civils de Lyon" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.30.22281627", "rel_title": "Evaluation of real and perceived risk to health care workers caring for patients with the Omicron variant of the SARS-CoV-2 virus in surgery and obstetrics", @@ -182649,53 +183665,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.10.26.22281575", - "rel_title": "Impact of COVID-19 related maternal stress on fetal brain development: A Multimodal MRI study", - "rel_date": "2022-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.26.22281575", - "rel_abs": "BackgroundDisruptions in perinatal care and support due to the COVID-19 pandemic was an unprecedented but significant stressor among pregnant women. Various neurostructural differences have been re-ported among fetuses and infants born during the pandemic compared to pre-pandemic counterparts. The relationship between maternal stress due to pandemic related disruptions and fetal brain is yet unexamined.\n\nMethodsPregnant participants with healthy pregnancies were prospectively recruited in 2020-2022 in the greater Los Angeles Area. Participants completed multiple self-report assessments for experiences of pandemic related disruptions, perceived stress, and coping behaviors and underwent fetal MRI. Maternal perceived stress exposures were correlated with quantitative multimodal MRI measures of fetal brain development using ltivariate models.\n\nResultsFetal brain stem volume increased with increased maternal perception of pandemic related stress positively correlated with normalized fetal brainstem volume (suggesting accelerated brainstem maturation). In contrast, increased maternal perception of pandemic related stress correlated with reduced global fetal brain temporal functional variance (suggesting reduced functional connectivity).\n\nConclusionsWe report alterations in fetal brainstem structure and global functional fetal brain activity associated with increased maternal stress due to pandemic related disruptions, suggesting altered fetal programming. Long term follow-up studies are required to better understand the sequalae of these early multi-modal brain disruptions among infants born during the COVID-19 pandemic.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Vidya Rajagopalan", - "author_inst": "Childrens Hospital Los Angeles" - }, - { - "author_name": "William T. Reynolds", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Jeremy Zepeda", - "author_inst": "Childrens Hospital Los Angeles" - }, - { - "author_name": "Jeraldine Lopez", - "author_inst": "The Saban Research Institute" - }, - { - "author_name": "Skorn Ponrartana", - "author_inst": "Keck School of Medicine University of Southern California" - }, - { - "author_name": "John Wood", - "author_inst": "Childrens Hospital Los Angeles" - }, - { - "author_name": "Rafael Ceschin", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Ashok Panigrahy", - "author_inst": "University of Pittsburgh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2022.10.26.22278866", "rel_title": "Experiences in the use of multiple doses of convalescent plasma in critically ill patients with COVID-19", @@ -182964,6 +183933,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.27.514054", + "rel_title": "Intranasal virus-particle mimicking vaccine enhances SARS-CoV-2 clearance in the Syrian hamster model", + "rel_date": "2022-10-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.27.514054", + "rel_abs": "Multiple vaccines have been developed and licensed for SARS-CoV-2. While these vaccines reduce disease severity, they do not prevent infection, and SARS-CoV-2 continues to spread and evolve. To prevent infection and limit transmission, vaccines must be developed that induce immunity in the respiratory tract. Therefore, we performed proof-of-principle vaccination studies with an intranasal nanoparticle vaccine against SARS-CoV-2. The vaccine candidate consisted of the self-assembling 60-subunit I3-01 protein scaffold covalently decorated with the SARS-CoV-2 receptor binding domain (RBD) using the SpyCatcher-SpyTag system. We verified the intended antigen display features by reconstructing the I3-01 scaffold to 3.4A using cryo-EM, and then demonstrated that the scaffold was highly saturated when grafted with RBD. Using this RBD-grafted SpyCage scaffold (RBD+SpyCage), we performed two unadjuvanted intranasal vaccination studies in the \"gold-standard\" preclinical Syrian hamster model. Hamsters received two vaccinations 28 days apart, and were then challenged 28 days post-boost with SARS-CoV-2. The initial study focused on assessing the immunogenicity of RBD+SpyCage, which indicated that vaccination of hamsters induced a non-neutralizing antibody response that enhanced viral clearance but did not prevent infection. In an expanded study, we demonstrated that covalent bonding of RBD to the scaffold was required to induce an antibody response. Consistent with the initial study, animals vaccinated with RBD+SpyCage more rapidly cleared SARS-CoV-2 from both the upper and lower respiratory tract. These findings demonstrate the intranasal SpyCage vaccine platform can induce protection against SARS-CoV-2 and, with additional modifications to improve immunogenicity, is a versatile platform for the development of intranasal vaccines targeting respiratory pathogens.\n\nIMPORTANCEDespite the availability of efficacious COVID vaccines that reduce disease severity, SARS-CoV-2 continues to spread. To limit SARS-CoV-2 transmission, the next generation of vaccines must induce immunity in the mucosa of the upper respiratory tract. Therefore, we performed proof-of-principle, unadjuvanted intranasal vaccination studies with a recombinant protein nanoparticle scaffold, SpyCage, decorated with the receptor-binding domain (RBD) of the S protein (SpyCage+RBD). We show that SpyCage+RBD was immunogenic and enhanced SARS-CoV-2 clearance from the nose and lungs of Syrian hamsters. Moreover, covalent grafting of the RBD to the scaffold was required to induce an immune response when given via the intranasal route. These proof-of-concept findings indicate that with further enhancements to immunogenicity (e.g., adjuvant incorporation, antigen optimization), the SpyCage scaffold has potential as a versatile, intranasal vaccine platform for respiratory pathogens.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Devanshi R Patel", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Allen M Minns", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Derek G Sims", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Cassandra J Field", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Abigail E Kerr", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Talia Heinly", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Erin H Luley", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Randall M Rossi", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Carol Bator", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Ibrahim M Mostafa", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Susan L Hafenstein", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Scott E Lindner", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Troy C Sutton", + "author_inst": "Pennsylvania State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.10.24.513632", "rel_title": "Characterization of Three Variants of SARS-CoV-2 in vivo Shows Host-Dependent Pathogenicity in Hamsters", @@ -185023,125 +186059,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2022.10.23.22281414", - "rel_title": "Impact of vaccination on the presence and severity of symptoms of hospitalised patients with an infection by the Omicron variant (B.1.1.529) of the SARS-CoV-2 (subvariant BA.1).", - "rel_date": "2022-10-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.23.22281414", - "rel_abs": "ObjectivesThe emergence of SARS-CoV-2 variants raised questions over the extent to which vaccines designed in 2020 have remained effective. We aimed to assess whether vaccine status was associated with the severity of Omicron SARS-CoV-2 infection in hospitalised patients.\n\nMethodsWe conducted an international, multicentric, retrospective study in 14 centres (Bulgaria, Croatia, France, Turkey). We collected data on patients hospitalised [≥]24 hours between 01/12/2021 and 03/03/2022, with PCR-confirmed infection at a time of exclusive Omicron circulation, with hospitalisation related or not to the infection. Patients who had received prophylaxis by monoclonal antibodies were excluded. Patients were considered fully vaccinated if they had received at least 2 injections of either mRNA and/or ChAdOx1-S, or 1 injection of Ad26.CoV2-S vaccines.\n\nResultsAmong the 1215 patients (median [IQR] age 73.0 [57.0; 84.0]; 51.3% males), 746 (61.4%) were fully vaccinated. In multivariate analysis, being vaccinated was associated with lower 28-day mortality (RR=0.50 [0.32-0.77]), ICU admission (R=0.40 [0.26-0.62], and oxygen requirement (RR=0.34 [0.25-0.46]), independently of age and comorbidities. When co-analysing these Omicron patients with 948 Delta patients from a study we recently conducted, Omicron infection was associated with lower 28-day mortality (RR=0.53 [0.37-0.76]), ICU admission (R=0.19 [0.12-0.28], and oxygen requirements (RR=0.50 [0.38-0.67]), independently of age, comorbidities and vaccination status.\n\nConclusionsmRNA- and adenovirus-based vaccines have remained effective on severity of Omicron SARS-CoV-2 infection. Omicron is associated with a lower risk of severe forms, independently of vaccination and patient characteristics.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Guillaume Beraud", - "author_inst": "University Hospital of Poitiers" - }, - { - "author_name": "Laura Bouetard", - "author_inst": "APHP, Hopital Antoine Beclere, Service de Medecine Interne, Clamart, France and Universite Paris-Saclay, UVSQ, INSERM U1018, CESP, Le Kremlin-Bicetre, France." - }, - { - "author_name": "Rok Civljak", - "author_inst": "University Hospital for Infectious Diseases \"Dr. Fran Mihaljevic\", Zagreb, Croatia and University of Zagreb School of Medicine, Zagreb, Croatia." - }, - { - "author_name": "Jocelyn Michon", - "author_inst": "Department of Infectious diseases, University Hospital of Caen, Caen, France" - }, - { - "author_name": "Necla Tulek", - "author_inst": "Atilim University, Department of Infectious Diseases and Clinical Microbiology Ankara Training and Research Hospital, Turkey" - }, - { - "author_name": "Sophie Lejeune", - "author_inst": "Infectious diseases, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France" - }, - { - "author_name": "Romain Millot", - "author_inst": "Infectious disease department, University Hospital of Poitiers, Poitiers, France" - }, - { - "author_name": "Aurelie Garchet-Beaudron", - "author_inst": "Infectious Disease Department, CH, Le Mans, France" - }, - { - "author_name": "Maeva Lefebvre", - "author_inst": "Infectious Disease Department, Centre for Prevention of Infectious and Transmissible Diseases, CHU Nantes, Nantes, France and INSERM UIC 1413 Nantes University," - }, - { - "author_name": "Petar Velikov", - "author_inst": "Infectious Disease Hospital \"Prof. Ivan Kirov\", Medical University of Sofia, Bulgaria" - }, - { - "author_name": "Benjamin Festou", - "author_inst": "CHU Limoges, Department of Infectious Diseases and Tropical Medicine, Limoges France" - }, - { - "author_name": "Sophie Abgrall", - "author_inst": "APHP, Hopital Antoine Beclere, Service de Medecine Interne, Clamart, France and Universite Paris-Saclay, UVSQ, INSERM U1018, CESP, Le Kremlin-Bicetre, France." - }, - { - "author_name": "Ivan Kresimir Lizatovic", - "author_inst": "University Hospital for Infectious Diseases \"Dr. Fran Mihaljevic\", Zagreb, Croatia" - }, - { - "author_name": "Aurelie Baldolli", - "author_inst": "Department of Infectious diseases, University Hospital of Caen, Caen, France" - }, - { - "author_name": "Huseyin Esmer", - "author_inst": "Atilim University, Department of Infectious Diseases and Clinical Microbiology Ankara Training and Research Hospital, Turkey" - }, - { - "author_name": "Sophie Blanchi", - "author_inst": "Infectious Disease Department, CH, Le Mans, France" - }, - { - "author_name": "Gabrielle Froidevaux", - "author_inst": "Infectious Disease Department, Centre for Prevention of Infectious and Transmissible Diseases, CHU Nantes, Nantes, France" - }, - { - "author_name": "Nikol Kapincheva", - "author_inst": "Infectious Disease Hospital \"Prof. Ivan Kirov\", Medical University of Sofia, Bulgaria" - }, - { - "author_name": "Jean-Francois Faucher", - "author_inst": "CHU Limoges, Department of Infectious Diseases and Tropical Medicine, Limoges France and INSERM U1094, Limoges, France." - }, - { - "author_name": "Mario Duvnjak", - "author_inst": "Clinic for Infectious Diseases, University Hospital Centre Osijek, Osijek, Croatia and Faculty of Medicine Osijek, J. J. Strossmayer University of Osijek, Osije" - }, - { - "author_name": "Elcin Afsar", - "author_inst": "Atilim University, Vocational School of Health Services, Ankara, Turkey" - }, - { - "author_name": "Luka Svitek", - "author_inst": "Clinic for Infectious Diseases, University Hospital Centre Osijek, Osijek, Croatia and Faculty of Medicine Osijek, J. J. Strossmayer University of Osijek, Osije" - }, - { - "author_name": "Saliha Yarimoglu", - "author_inst": "Karaman Training and Research Hospital, Turkey" - }, - { - "author_name": "Rafet Yarimoglu", - "author_inst": "Karaman Training and Research Hospital, Turkey" - }, - { - "author_name": "Cecile Janssen", - "author_inst": "Infectious Disease Unit, Centre Hospitalier Annecy Genevois, Annecy, France" - }, - { - "author_name": "olivier EPAULARD", - "author_inst": "centre hospitalier universitaire Grenoble Alpes" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.24.513610", "rel_title": "Fever temperatures modulate intraprotein dynamics and enhance the binding affinity between monoclonal antibodies and the Spike protein from SARS-CoV-2", @@ -185498,6 +186415,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.10.22.513349", + "rel_title": "Antibody responses to Omicron BA.4/BA.5 bivalent mRNA vaccine booster shot", + "rel_date": "2022-10-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.22.513349", + "rel_abs": "The SARS-CoV-2 Omicron variant and its numerous sub-lineages have exhibited a striking ability to evade humoral immune responses induced by prior vaccination or infection. The Food and Drug Administration (FDA) has recently granted Emergency Use Authorizations (EUAs) to new bivalent formulations of the original Moderna and Pfizer mRNA SARS-CoV-2 vaccines that target both the ancestral strain as well as the Omicron BA.4/BA.5 variant. Despite their widespread use as a vaccine boost, little is known about the antibody responses induced in humans. Here, we collected sera from several clinical cohorts: individuals after three or four doses of the original monovalent mRNA vaccines, individuals receiving the new bivalent vaccines as a fourth dose, and individuals with BA.4/BA.5 breakthrough infection following mRNA vaccination. Using pseudovirus neutralization assays, these sera were tested for neutralization against an ancestral SARS-CoV-2 strain, several Omicron sub-lineages, and several related sarbecoviruses. At ~3-5 weeks post booster shot, individuals who received a fourth vaccine dose with a bivalent mRNA vaccine targeting BA.4/BA.5 had similar neutralizing antibody titers as those receiving a fourth monovalent mRNA vaccine against all SARS-CoV-2 variants tested, including BA.4/BA.5. Those who received a fourth monovalent vaccine dose had a slightly higher neutralizing antibody titers than those who received the bivalent vaccine against three related sarbecoviruses: SARS-CoV, GD-Pangolin, and WIV1. When given as a fourth dose, a bivalent mRNA vaccine targeting Omicron BA.4/BA.5 and an ancestral SARS-CoV-2 strain did not induce superior neutralizing antibody responses in humans, at the time period tested, compared to the original monovalent vaccine formulation.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Qian Wang", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Anthony Bowen", + "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" + }, + { + "author_name": "Riccardo Valdez", + "author_inst": "University of Michigan" + }, + { + "author_name": "Carmen Gherasim", + "author_inst": "University of Michigan" + }, + { + "author_name": "Aubree Gordon", + "author_inst": "University of Michigan" + }, + { + "author_name": "Liu Lihong", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "David D Ho", + "author_inst": "Columbia University Irving Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.10.24.513415", "rel_title": "Vaccine- and BTI-elicited pre-Omicron immunity more effectively neutralizes Omicron sublineages BA.1, BA.2, BA.4 and BA.5 than pre-Omicron infection alone", @@ -187033,29 +187993,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2022.10.18.22281063", - "rel_title": "Deep reinforcement learning framework for controlling infectious disease outbreaks in the context of multi-jurisdictions", - "rel_date": "2022-10-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.18.22281063", - "rel_abs": "In the absence of pharmaceutical interventions, social distancing and lockdown have been key options for controlling new or reemerging respiratory infectious disease outbreaks. The timely implementation of these interventions is vital for effectively controlling and safeguarding the economy.\n\nMotivated by the COVID-19 pandemic, we evaluated whether, when, and to what level lockdowns are necessary to minimize epidemic and economic burdens of new disease outbreaks. We formulated the question as a sequential decision-making Markov Decision Process and solved it using deep Q-network algorithm. We evaluated the question under two objective functions: a 2-objective function to minimize economic burden and hospital capacity violations, suitable for diseases with severe health risks but with minimal death, and a 3-objective function that additionally minimizes the number of deaths, suitable for diseases that have high risk of mortality. A key feature of the model is that we evaluated the above questions in the context of two-geographical jurisdictions that interact through travel but make autonomous and independent decisions, evaluating under cross-jurisdictional cooperation and non-cooperation.\n\nIn the 2-objective function under cross-jurisdictional cooperation, the optimal policy was to aim for shutdowns at 50% and 25% per day. Though this policy avoided hospital capacity violations, the shutdowns extended until a large proportion of the population reached herd immunity. Delays in initiating this optimal policy or non-cooperation from an outside jurisdiction required shutdowns at a higher level of 75% per day, thus adding to economic burdens. In the 3-objective function, the optimal policy under cross-jurisdictional cooperation was to aim for shutdowns of up to 75% per day to prevent deaths by reducing infected cases. This optimal policy continued for the entire duration of the simulation, suggesting that, until pharmaceutical interventions such as treatment or vaccines become available, contact reductions through physical distancing would be necessary to minimize deaths. Deviating from this policy increased the number of shutdowns and led to several deaths.\n\nIn summary, we present a decision-analytic methodology for identifying optimal lockdown strategy under the context of interactions between jurisdictions that make autonomous and independent decisions. The numerical analysis outcomes are intuitive and, as expected, serve as proof of the feasibility of such a model.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Seyedeh Nazanin khatami", - "author_inst": "MGH Institute for Technology Assessment, Harvard Medical School, Boston, MA 02114, , USA" - }, - { - "author_name": "Chaitra Gopalappa", - "author_inst": "University of Massachusetts Amherst" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.10.20.22281317", "rel_title": "The COVID-19 burnout scale: Development and initial validation", @@ -187224,6 +188161,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.20.22281300", + "rel_title": "Uptake of COVID-19 vaccines among healthcare workers within primary healthcare facilities, Entebbe municipality Uganda", + "rel_date": "2022-10-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.20.22281300", + "rel_abs": "BackgroundRoutine vaccination is an essential highly successfully public health intervention in the prevention of infectious diseases that greatly depends on high coverage, and health care workers (HCWs) who play a pivotal role in ensuring the high uptake of vaccines in the population. COVID-19 vaccines have been proven efficacious, and vaccination campaigns have been ongoing, however, there is a perceived high vaccine hesitancy among health care workers in Uganda. This study describes the level and determinants of uptake of COVID-19 vaccines among HCWs in Entebbe municipality, Uganda.\n\nMaterials and methodsWe conducted a health facility based cross-sectional study among HCWs from private and government health facilities in Entebbe municipality between July 2021 and August 2021. Structured questionnaires were used, and data were analysed using Stata version 12. We defined uptake as having received at least the first doze of COVID-19 vaccine or completed the two dozes.\n\nResultsThe level of vaccine uptake was 65.6%with higher uptake among males than females. HCWs aged 30-39 years were 2.7 times more likely to have been vaccinated than those less than 30 years (OR 2.72, 95% CI: 1.26-5.88, P-value <0.01), and the odds of having been vaccinated were 4 times higher among health workers above 40 years (OR 4.29, 95% CI 1.50-12.24, P-value < 0.01). Additionally, the odds of having been vaccinated were 4 times higher among health care workers that participated in COVID-19 vaccine related activities (OR 4.18, 95% CI 2.16-8.10, p-value <0.001). Healthcare workers (98%) had confidence in the vaccines although 45% of those that were not vaccinated felt that the vaccines were ineffective.\n\nConclusionVaccine uptake among HCWs was relatively high compared to the WHO recommended uptake of 70% by mid-2022, although some HCWs were still hesitant. The convenience of vaccination services was an important factor in vaccine uptake. Hence, governments should endeavour to improve access to vaccination both for HCWs and the public.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Nassim Kyakuwa", + "author_inst": "Uganda Virus Research Institute" + }, + { + "author_name": "Christine Atuhairwe", + "author_inst": "Uganda Martyrs University" + }, + { + "author_name": "Hamza Kalutte", + "author_inst": "Uganda Virus Research Institute" + }, + { + "author_name": "Simon Mpooya", + "author_inst": "Uganda Virus Research Institute" + }, + { + "author_name": "Flavia Nakanjako", + "author_inst": "Uganda Virus Research Institute" + }, + { + "author_name": "Laurent Perez", + "author_inst": "University of Lausanne: Universite de Lausanne" + }, + { + "author_name": "Bernard Kikaire", + "author_inst": "Makerere University Medical School: Makerere University College of Health Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.19.22281286", "rel_title": "Safety and effectiveness of COVID-19 mRNA vaccination and risk factors for hospitalisation caused by the omicron variant in 0.8 million adolescents: A nationwide cohort study in Sweden", @@ -189079,81 +190059,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.18.22281172", - "rel_title": "Antibody-mediated protection against symptomatic COVID-19 can be achieved at low serum neutralizing titers", - "rel_date": "2022-10-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.18.22281172", - "rel_abs": "Multiple studies of vaccinated and convalescent cohorts have demonstrated that serum neutralizing antibody (nAb) titers correlate with protection against COVID-19. However, the induction of multiple layers of immunity following SARS-CoV-2 exposure has complicated the establishment of nAbs as a mechanistic correlate of protection (CoP) and hindered the definition of a protective nAb threshold. Here, we show that a half-life extended monoclonal antibody (adintrevimab) provides approximately 50% protection against symptomatic COVID-19 in SARS-CoV-2-naive adults at low serum nAb titers on the order of 1:30. Vaccine modeling supports a similar 50% protective nAb threshold, suggesting low levels of serum nAb can protect in both monoclonal and polyclonal settings. Extrapolation of adintrevimab pharmacokinetic data suggests that protection against susceptible variants could be maintained for approximately 3 years. The results provide a benchmark for the selection of next-generation vaccine candidates and support the use of broad, long-acting monoclonal antibodies as an alternative or supplement to vaccination in high-risk populations.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Pete Schmidt", - "author_inst": "Invivyd, Inc" - }, - { - "author_name": "Kristin Narayan", - "author_inst": "Invivyd, Inc." - }, - { - "author_name": "Yong Li", - "author_inst": "Invivyd, Inc" - }, - { - "author_name": "Chengzi Kaku", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Michael Brown", - "author_inst": "Adimab, LLC" - }, - { - "author_name": "Elizabeth Champney", - "author_inst": "Adimab, LLC" - }, - { - "author_name": "James Geoghegan", - "author_inst": "Adimab, LLC" - }, - { - "author_name": "Maximiliano Vasquez", - "author_inst": "Adimab, LLC" - }, - { - "author_name": "Eric Krauland", - "author_inst": "Adimab, LLC" - }, - { - "author_name": "Thomas Yockachonis", - "author_inst": "Washington State University" - }, - { - "author_name": "Shuangyi Bai", - "author_inst": "Washington State University" - }, - { - "author_name": "Bronwyn Gunn", - "author_inst": "Washington State University" - }, - { - "author_name": "Anthony Cammarata", - "author_inst": "Institute for Clinical Pharmacodynamics" - }, - { - "author_name": "Chris Rubino", - "author_inst": "Institute for Clinical Pharmacodynamics" - }, - { - "author_name": "Laura M Walker", - "author_inst": "Invivyd, Inc." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.17.22281161", "rel_title": "Clinical antiviral efficacy of remdesivir and casirivimab/imdevimab against the SARS-CoV-2 Delta and Omicron variants", @@ -189498,6 +190403,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.19.512816", + "rel_title": "A collaborative approach to improving representation in viral genomic surveillance", + "rel_date": "2022-10-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.19.512816", + "rel_abs": "The lack of routine viral genomic surveillance delayed the initial detection of SARS-CoV-2, allowing the virus to spread unfettered at the outset of the U.S. epidemic. Over subsequent months, poor surveillance enabled variants to emerge unnoticed. Against this backdrop, long-standing social and racial inequities have contributed to a greater burden of cases and deaths among minority groups. To begin to address these problems, we developed a new variant surveillance model geared toward building microbial genome sequencing capacity at universities in or near rural areas and engaging the participation of their local communities. The resulting genomic surveillance network has generated more than 1,000 SARS-CoV-2 genomes to date, including the first confirmed case in northeast Louisiana of Omicron, and the first and sixth confirmed cases in Georgia of the emergent BA.2.75 and BQ.1.1 variants, respectively. In agreement with other studies, significantly higher viral gene copy numbers were observed in Delta variant samples compared to those from Omicron BA.1 variant infections, and lower copy numbers were seen in asymptomatic infections relative to symptomatic ones. Collectively, the results and outcomes from our collaborative work demonstrate that establishing genomic surveillance capacity at smaller academic institutions in rural areas and fostering relationships between academic teams and local health clinics represent a robust pathway to improve pandemic readiness.\n\nAuthor summaryGenomic surveillance involves decoding a pathogens genetic code to track its spread and evolution. During the pandemic, genomic surveillance programs around the world provided valuable data to scientists, doctors, and public health officials. Knowing the complete SARS-CoV-2 genome has helped detect the emergence of new variants, including ones that are more transmissible or cause more severe disease, and has supported the development of diagnostics, vaccines, and therapeutics. The impact of genomic surveillance on public health depends on representative sampling that accurately reflects the diversity and distribution of populations, as well as rapid turnaround time from sampling to data sharing. After a slow start, SARS-CoV-2 genomic surveillance in the United States grew exponentially. Despite this, many rural regions and ethnic minorities remain poorly represented, leaving significant gaps in the data that informs public health responses. To address this problem, we formed a network of universities and clinics in Louisiana, Georgia, and Mississippi with the goal of increasing SARS-CoV-2 sequencing volume, representation, and equity. Our results demonstrate the advantages of rapidly sequencing pathogens in the same communities where the cases occur and present a model that leverages existing academic and clinical infrastructure for a powerful decentralized genomic surveillance system.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Paul Kim", + "author_inst": "Grambling State University" + }, + { + "author_name": "Audrey Y. Kim", + "author_inst": "Grambling State University" + }, + { + "author_name": "Jamie J. Newman", + "author_inst": "Louisiana Tech University" + }, + { + "author_name": "Eleonora Cella", + "author_inst": "University of Central Florida" + }, + { + "author_name": "Thomas C. Bishop", + "author_inst": "Louisiana Tech University" + }, + { + "author_name": "Peter J. Huwe", + "author_inst": "Mercer University School of Medicine" + }, + { + "author_name": "Olga N. Uchakina", + "author_inst": "Mercer University School of Medicine" + }, + { + "author_name": "Robert J. McKallip", + "author_inst": "Mercer University School of Medicine" + }, + { + "author_name": "Vance L. Mack", + "author_inst": "Mercer University School of Medicine" + }, + { + "author_name": "Marnie P. Hill", + "author_inst": "Mercer University School of Medicine" + }, + { + "author_name": "Ifedayo Victor Ogungbe", + "author_inst": "Jackson State University" + }, + { + "author_name": "Olawale Adeyinka", + "author_inst": "Jackson State University" + }, + { + "author_name": "Samuel Jones", + "author_inst": "Jackson State University" + }, + { + "author_name": "Gregory Ware", + "author_inst": "Louisiana State University Health Sciences Center Shreveport: LSU Health Shreveport" + }, + { + "author_name": "Jennifer L. Carroll", + "author_inst": "Louisiana State University Health Sciences Center Shreveport: LSU Health Shreveport" + }, + { + "author_name": "Jarrod F. Sawyer", + "author_inst": "Louisiana State University Health Sciences Center Shreveport: LSU Health Shreveport" + }, + { + "author_name": "Kenneth H. Densmore", + "author_inst": "Louisiana State University Health Sciences Center Shreveport: LSU Health Shreveport" + }, + { + "author_name": "Michael Foster", + "author_inst": "Louisiana Tech University" + }, + { + "author_name": "Lescia Valmond", + "author_inst": "Grambling State University" + }, + { + "author_name": "John Thomas", + "author_inst": "Grambling State University" + }, + { + "author_name": "Taj Azarian", + "author_inst": "University of Central Florida" + }, + { + "author_name": "Krista Queen", + "author_inst": "Louisiana State University Health Sciences Center Shreveport: LSU Health Shreveport" + }, + { + "author_name": "Jeremy P. Kamil", + "author_inst": "Louisiana State University Health Sciences Center" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.10.18.512746", "rel_title": "Regional epidemic dynamics and Delta variant diversity resulted in varying rates of spread of Omicron-BA.1 in Mexico", @@ -191209,61 +192221,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.16.22281142", - "rel_title": "Making use of an App (Tawakkalna) to track and reduce COVID transmission in KSA", - "rel_date": "2022-10-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.16.22281142", - "rel_abs": "Since March 2020, the Kingdom of Saudi Arabia (KSA) has launched several digital applications to support the intervention response to reduce the spread of SARS-CoV-2. At the beginning of 2021, the KSA Government introduced a mandatory immunity passport to regulate access to public venues. The passport was part of the strategy of resuming public activities before reaching high vaccination coverage. The passport was implemented as a new service in the Tawakkalna mobile phone application (App). The immunity passport allowed access to public locations only for the users who recovered from COVID-19 or those who were double vaccinated. Our study aimed to evaluate the effectiveness of the immunity passport, implemented through the Tawakkalna App, on SARS-CoV-2 spread. We built a spatial-explicit individual-based model to represent the whole KSA population (IBM-KSA) and its dynamic on a national scale. The IBM-KSA was parameterized using country demographic, remote sensing, and epidemiological data. The model included non-pharmaceutical interventions and vaccination coverage. A social network was created to represent contact heterogeneity and interaction among age groups of the population. The IBM-KSA also simulated the movement of people across the country based on a gravity model. We used the IBM-KSA to evaluate the effect of the immunity passport on the COVID-19 epidemics outcomes. The IBM-KSA results showed that implementing the immunity passport through the Tawakkalna App mitigated the SARS-CoV2 spread. In a scenario without the immunity passport, the KSA could have reported 1,515,468 (95% confidence interval [CI]: 965,725-1,986,966) cases, and 30,309 (95% CI: 19,314-39,739) deaths from March 2021 to November 2021. The comparison of IBM-KSA results with COVID-19 official reporting estimated that the passport effectively reduced the number of cases, hospitalizations, and deaths by 8.7 times, 13.5 times, and 11.9 times, respectively. These results showed that the introduction of the immunity passport through the Tawakkalna App was able to control the spread of the SARS-COV-2 until vaccination reached high coverage. By introducing the immunity passport, The KSA was able to allow to resume most of public activities safely.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Donal Bisanzio", - "author_inst": "RTI International, Washington, D.C., USA." - }, - { - "author_name": "Richard Reithinger", - "author_inst": "RTI International, Washington, D.C., USA." - }, - { - "author_name": "Sami Almudarra", - "author_inst": "Saudi Ministry of Health, Riyadh, Saudi Arabia" - }, - { - "author_name": "Reem F Alsukait", - "author_inst": "Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Di Dong", - "author_inst": "World Bank, Washington, D.C., USA." - }, - { - "author_name": "Yi Zhang", - "author_inst": "World Bank, Washington, D.C., USA." - }, - { - "author_name": "Sameh El-Saharty", - "author_inst": "World Bank, Washington, D.C., USA." - }, - { - "author_name": "Hala Almossawi", - "author_inst": "RTI International, Washington, D.C., USA." - }, - { - "author_name": "Christopher H Herbst", - "author_inst": "World Bank, Washington, D.C., USA" - }, - { - "author_name": "Ada Alqunaibet", - "author_inst": "Saudi Public Health Authority, Riyadh, Saudi Arabia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.10.14.512325", "rel_title": "The impact of the ABO/Rh blood group on susceptibility and severity among COVID-19 patients in Luanda, Angola", @@ -191424,6 +192381,25 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.10.15.512346", + "rel_title": "Comparative Mutagenesis of SARS-CoV-2 Nonstructural Proteins (NSPs) Across Variants: The Case for RdRp as a Therapeutic Target", + "rel_date": "2022-10-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.15.512346", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogenicity has been studied extensively from the perspective of structural (S, E, M, N) proteins for purposes in vaccine development. The virus nonstructural protein (nsp) components are less characterized, and demonstrate significant potential in efforts to develop novel therapeutic agents. NSP 7, 8, and 12, formed from the cleavage of pp1a and pp1ab polyproteins, comprise the viral replicase (RdRp) complex1, the site for the mechanism of action of Remdesivir2. Presented herein is a phylogenetic analysis for the evolution of SARS-CoV-2 replicase components between variant and related coronaviruses with the aim to delineate its current and long-term efficacy as a drug target.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Nathan Lanclos", + "author_inst": "University of South Florida" + } + ], + "version": "1", + "license": "cc_no", + "type": "confirmatory results", + "category": "genomics" + }, { "rel_doi": "10.1101/2022.10.16.512436", "rel_title": "The Impact of Protein Dynamics on Residue-Residue Coevolution and Contact Prediction", @@ -193227,41 +194203,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.10.13.512053", - "rel_title": "SARS-CoV-2 infection in domestic rats after transmission from their infected owner", - "rel_date": "2022-10-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.13.512053", - "rel_abs": "We report the transmission of SARS-CoV-2 Omicron variant from a COVID-19 symptomatic individual to two domestic rats, one of which developed severe symptoms. Omicron carries several mutations which permit rodent infection. This report demonstrates that pet, and likely wild, rodents could therefore contribute to SARS-CoV-2 spread and evolution.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Xavier Montagutelli", - "author_inst": "Institut Pasteur, Universite Paris Cite, Mouse Genetics Laboratory, Paris, France" - }, - { - "author_name": "Berenice Decaudin", - "author_inst": "Service NAC, Centre Hospitalier Veterinaire Advetia, Velizy-Villacoublay, France" - }, - { - "author_name": "Maxime Beretta", - "author_inst": "Institut Pasteur, Universite Paris Cite, Laboratory of Humoral Immunology, Paris, France" - }, - { - "author_name": "Hugo Mouquet", - "author_inst": "Institut Pasteur, Universite Paris Cite, Laboratory of Humoral Immunology, Paris, France" - }, - { - "author_name": "Etienne Simon-Loriere", - "author_inst": "Institut Pasteur, Universite Paris Cite, G5 Evolutionary Genomics of RNA Viruses, Paris, France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.10.12.512011", "rel_title": "Laboratory evaluation of a quaternary ammonium compound (QAC)-based antimicrobial coating used in public transport during the COVID-19 pandemic", @@ -193490,6 +194431,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.11.22280860", + "rel_title": "Risk of Myocarditis and Pericarditis Following Coronavirus Disease 2019 Messenger RNA Vaccination - A Nationwide Study", + "rel_date": "2022-10-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.11.22280860", + "rel_abs": "BackgroundAn extended interval between the two primary doses may reduce the risk of myocarditis/pericarditis after COVID-19 mRNA vaccination. Taiwan has implemented a two-dose regimen with a 12-week interval for adolescents. Here we present nationwide data of mRNA COVID-19 vaccination-associated myocarditis and pericarditis in Taiwan.\n\nMethodsData on adverse events of myocarditis/pericarditis were from the Taiwan Vaccine Adverse Events Reporting System between March 22, 2021, and February 9, 2022. The rates according to sex, age, and vaccine type were calculated. We investigated the reporting rates among young individuals under different two-dose intervals and among those who received two doses of different vaccines.\n\nResultsAmong 204 cases who met the case definition of myocarditis/pericarditis, 75 cases occurred after the first dose and 129 after the second. The reporting rate of myocarditis/pericarditis after COVID-19 vaccination varied across sex and age groups and was highest after the second dose in males aged 12-17 years (126.79 cases per million vaccinees) for the BNT162b2 vaccine and in males aged 18-24 years (93.84 cases per million vaccinees) for the mRNA-1273 vaccine. The data did not suggest an association between longer between-dose interval and lower rate of myocarditis/pericarditis among males and females aged 18-24 or 25-29 years who received two doses of the BNT162b2 or mRNA-1273 vaccine. Rates of myocarditis/pericarditis in males and females aged 18-49 years after receiving ChAdOx1-S - mRNA-1273 vaccination was significantly higher than after ChAdOx1-S - ChAdOx1-S vaccination.\n\nConclusionsMyocarditis and pericarditis are rare following mRNA vaccination, with higher risk occurring in young males after the second dose.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Wei-Ju Su", + "author_inst": "Centers for Disease Control, Ministry of Health and Welfare" + }, + { + "author_name": "Yu-Lun Liu", + "author_inst": "Centers for Disease Control, Ministry of Health and Welfare" + }, + { + "author_name": "Chia-Hsuin Chang", + "author_inst": "Department of Internal Medicine, National Taiwan University Hospital" + }, + { + "author_name": "Yen-Ching Lin", + "author_inst": "College of Medicine, National Taiwan University" + }, + { + "author_name": "Wei-I Huang", + "author_inst": "Taiwan Drug Relief Foundation" + }, + { + "author_name": "Li-Chiu Wu", + "author_inst": "National Taiwan University Hospital" + }, + { + "author_name": "Shu-Fong Chen", + "author_inst": "Centers for Disease Control, Ministry of Health and Welfare" + }, + { + "author_name": "Yu-Sheng Lin", + "author_inst": "Centers for Disease Control, Ministry of Health and Welfare" + }, + { + "author_name": "Yee-Lin Hsieh", + "author_inst": "Centers for Disease Control, Ministry of Health and Welfare" + }, + { + "author_name": "Chiao-An Yang", + "author_inst": "Centers for Disease Control, Ministry of Health and Welfare" + }, + { + "author_name": "Chiu-Hsiang Lin", + "author_inst": "Centers for Disease Control, Ministry of Health and Welfare" + }, + { + "author_name": "Kim-Wei Arnold Chan", + "author_inst": "Department of Medical Research, National Taiwan University Hospital" + }, + { + "author_name": "Ping-Ing Lee", + "author_inst": "Department of Pediatrics, National Taiwan University Hospital" + }, + { + "author_name": "Jen-Hsiang Chuang", + "author_inst": "Centers for Disease Control, Ministry of Health and Welfare" + }, + { + "author_name": "Chin-Hui Yang", + "author_inst": "Centers for Disease Control, Ministry of Health and Welfare" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2022.10.10.22280933", "rel_title": "Understanding mental health trends during COVID-19 pandemic in the United States using network analysis", @@ -195189,29 +196205,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.10.22280683", - "rel_title": "Sensitivity of endemic behaviour of Covid-19 under a multi-dose vaccination regime, to various biological parameters and control variables", - "rel_date": "2022-10-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.10.22280683", - "rel_abs": "For an infectious disease such as Covid-19, we present a new four-stage vaccination model (un-vaccinated, dose 1+2, booster, repeated boosters), which examines the impact of vaccination coverage, vaccination rate, generation interval, control reproduction number, vaccine efficacies, and rates of waning immunity, upon the dynamics of infection. We derive a single equation that allows computation of equilibrium prevalence and incidence of infection, given knowledge about these parameter and variable values. Based upon a 20 compartment model, we develop a numerical simulation of the associated differential equations. The model is not a forecasting or even predictive one, given the uncertainty about several biological parameter values. Rather, it is intended to aid qualitative understanding of how equilibrium levels of infection may be impacted upon, by the parameters of the system. We examine one at a time sensitivity analysis around a base case scenario. The key finding which should be of interest to policy makers, is that while factors such as improved vaccine efficacy, increased vaccination rates, lower waning rates, and more stringent non-pharmaceutical interventions might be thought to improve equilibrium levels of infection, this might only be done to good effect, if vaccination coverage on a recurrent basis, is sufficiently high.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "John S Dagpunar", - "author_inst": "School of Mathematical Sciences, University of Southampton" - }, - { - "author_name": "Chenchen Wu", - "author_inst": "Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.09.22280878", "rel_title": "Associations Between Reported Post-COVID-19 Symptoms and Subjective Well-Being, Israel, July 2021 -April 2022", @@ -195492,6 +196485,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.10.22280762", + "rel_title": "Immune response after SARS-CoV-2 infection with residual post COVID symptoms", + "rel_date": "2022-10-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.10.22280762", + "rel_abs": "BACKGROUNDIn a number of patients, post-acute COVID syndrome develops after acute infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Long COVID [LC]). Here, we examined the immune responses and clinical characteristics of individuals with LC compared to age- and gender-matched healthy recovered COVID individuals (HC) during the Omicron pandemic. Immune responses following BNT162b2 (Pfizer) booster are also determined.\n\nMETHODSThis retrospective cohort study included 292 patients (LC, 158; HC, 134) confirmed to have SARS-CoV-2 infection from January to August 2022. We determined anti-SARS-CoV-2 receptor-binding domain immunoglobulin G (anti-RBD IgG), surrogate virus neutralization test (sVNT), T-cell subsets, and neutralization of wild-type, BA.1 and BA.5. A subset of patients was voluntarily recruited for booster vaccination with BNT162b2 vaccine and immunogenicity was assessed 4weeks after vaccination.\n\nRESULTSCycle thresholds were higher in the HC group than in the LC group (20.7 vs. 19.7; P<0.039). Anti-RBD IgG was higher at [≤]56 days after COVID-19 onset (PC) in 3-dose vaccines compared with 2-dose vaccines in the LC group (P=0.02) and after 57-84 days PC in 3-dose vaccines in the HC group (P<0.001). The sVNT in LC was significantly high against Wuhan and sVNT was 30% lower against the Omicron than the Wuhan. sVNT was relatively sustained in 3-dose vaccines than [≤] 2-dose vaccines. sVNT in the HC group reached its peak at 57-84 days PC as compared with the LC group.\n\nCONCLUSIONSThese findings imply that LC produced increased neutralizing antibody responses than those with HC. During the Omicron pandemic, immunity after LC has still waned; therefore, a booster vaccine may be needed after 2-3 months from last infection. (ClinicalTrials.gov number, NCT05484700)", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Tanyaporn Pongkunakorn", + "author_inst": "Siriraj Population Health and Nutrition Research Group, Department of Research and Development, Siriraj Medical Research Center, Mahidol University" + }, + { + "author_name": "Thamonwan Manosan", + "author_inst": "Siriraj Population Health and Nutrition Research Group, Department of Research and Development, Siriraj Medical Research Center, Mahidol University" + }, + { + "author_name": "Apinya Surawit", + "author_inst": "Siriraj Population Health and Nutrition Research Group, Department of Research and Development, Siriraj Medical Research Center, Mahidol University" + }, + { + "author_name": "Suphawan Ophakas", + "author_inst": "Siriraj Population Health and Nutrition Research Group, Department of Research and Development, Siriraj Medical Research Center, Mahidol University" + }, + { + "author_name": "Pichanun Mongkolsucharitkul", + "author_inst": "Siriraj Population Health and Nutrition Research Group, Department of Research and Development, Siriraj Medical Research Center, Mahidol University" + }, + { + "author_name": "Sureeporn Pumiem", + "author_inst": "Siriraj Population Health and Nutrition Research Group, Department of Research and Development, Siriraj Medical Research Center, Mahidol University" + }, + { + "author_name": "Sophida Suta", + "author_inst": "Siriraj Population Health and Nutrition Research Group, Department of Research and Development, Siriraj Medical Research Center, Mahidol University" + }, + { + "author_name": "Bonggochpass Pinsawas", + "author_inst": "Siriraj Population Health and Nutrition Research Group, Department of Research and Development, Siriraj Medical Research Center, Mahidol University" + }, + { + "author_name": "Nitat Sookrung", + "author_inst": "Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol Univer" + }, + { + "author_name": "Nawannaporn Saelim", + "author_inst": "Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol Univer" + }, + { + "author_name": "Kodchakorn Mahasongkram", + "author_inst": "Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol Univer" + }, + { + "author_name": "Pannathee Prangtaworn", + "author_inst": "Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol Univer" + }, + { + "author_name": "Anchalee Tungtrongchitr", + "author_inst": "Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol Univer" + }, + { + "author_name": "Watip Tangjittipokin", + "author_inst": "Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University" + }, + { + "author_name": "Kobporn Boonnak", + "author_inst": "Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University" + }, + { + "author_name": "Tassanee Narkdontri", + "author_inst": "Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University" + }, + { + "author_name": "Nipaporn Teerawattanapong", + "author_inst": "Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University" + }, + { + "author_name": "Anan Jongkaewwattana", + "author_inst": "National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency" + }, + { + "author_name": "Korapat Mayurasakorn", + "author_inst": "Siriraj Population Health and Nutrition Research Group, Department of Research and Development, Siriraj Medical Research Center, Mahidol University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.08.22280836", "rel_title": "GRAd-COV2 vaccine provides potent and durable immunity in a randomised placebo-controlled phase 2 trial (COVITAR)", @@ -197063,41 +198147,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.10.04.510837", - "rel_title": "Community engagement through student-led science for dengue prevention during the COVID-19 pandemic in Cordoba, Argentina.", - "rel_date": "2022-10-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.04.510837", - "rel_abs": "BackgroundDuring 2019-2020 while COVID-19 pandemic, the Americas were facing the biggest dengue fever epidemic in recent history. Traditional vector control programs, based on insecticide application have been insufficient to control the spread of dengue fever. Several studies suggest refocusing on education with the aim of an integrated vector management strategy within the local ecological-community context. We aim to assess community perceptions, knowledge, attitude, preventive practice, and action through student-led science assignments regarding dengue fever, prevention, and socio-ecological factors in temperate Cordoba, Argentina.\n\nMethodsThe study was conducted during the COVID-19 quarantine when schools switched to online education for the first time. Several activities through Google Classroom platform included a survey to one students family member, and an outdoor activity to assess their attitudes and to clean the backyard and gardens.\n\nResultsSignificant number of respondents developed good preventive practices and increased their knowledge about the vector and disease highlighting that 75% of responders knew that dengue fever was transmitted by a mosquito, 81.96% declared having obtained knowledge regarding dengue and vector through television, 56% affirm that dengue is a severe illness, 67% of respondents admitted that individuals play an important role in the prevention of dengue. Regarding mosquito control activities, 90% of respondents reported turning containers.\n\nConclusionsThis highlights the need for school programs with curricula to address vector biology and the prevention of vector-borne diseases not only during activity periods when mosquitoes batter people but all year long to do real prevention.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Elizabet Lilia Estallo", - "author_inst": "Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET)" - }, - { - "author_name": "Magali Madelon", - "author_inst": "Instituto Jesus Maria" - }, - { - "author_name": "Elisabet Benitez", - "author_inst": "Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET)" - }, - { - "author_name": "Anna Maria Stewart-Ibarra", - "author_inst": "InterAmerican Institute for Global Change Research" - }, - { - "author_name": "Francisco Felipe Luduena-Almeida", - "author_inst": "Facultad de Ciencias Exactas, Fisicas y Naturales, Universidad Nacional de Cordoba." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "scientific communication and education" - }, { "rel_doi": "10.1101/2022.10.03.22280660", "rel_title": "Effectiveness and duration of a second COVID-19 vaccine booster", @@ -197354,6 +198403,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.04.22280696", + "rel_title": "Vaccines alone cannot slow the evolution of SARS-CoV-2", + "rel_date": "2022-10-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.04.22280696", + "rel_abs": "The rapid emergence of immune-evading viral variants of SARS-CoV-2 calls into question the practicality of a vaccine-only public health strategy for managing the ongoing COVID-19 pandemic. It has been suggested that widespread vaccination is necessary to prevent the emergence of future immune-evading mutants. Here we examine that proposition using stochastic computational models of viral transmission and mutation. Specifically, we look at the likelihood of emergence of immune escape variants requiring multiple mutations, and the impact of vaccination on this process. Our results suggest that the transmission rate of intermediate SARS-CoV-2 mutants will impact the rate at which novel immune-evading variants will appear. While vaccination can lower the rate at which new variants appear, other interventions that reduce transmission can also have the same effect. Crucially, relying solely on widespread and repeated vaccination (vaccinating the entire population multiple times a year) is not sufficient to prevent the emergence of novel immune-evading strains if transmission rates remain high within the population. Thus, vaccines alone are incapable of slowing the pace of evolution of immune evasion, and vaccinal protection against severe and fatal outcomes for COVID-19 patients is therefore not assured.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Debra Van Egeren", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Madison Stoddard", + "author_inst": "Fractal Therapeutics" + }, + { + "author_name": "Laura White", + "author_inst": "Boston University" + }, + { + "author_name": "Natasha S. Hochberg", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Michael S. Rogers", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Bruce Zetter", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Diane Joseph-McCarthy", + "author_inst": "Boston University" + }, + { + "author_name": "Arijit Chakravarty", + "author_inst": "Fractal Therapeutics" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.10.04.22280700", "rel_title": "Evaluation of the Abbott PanbioTM COVID-19 antigen detection rapid diagnostic test among healthcare workers in elderly care", @@ -199109,41 +200205,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.10.03.22280646", - "rel_title": "Impact of Omicron Wave and Associated Infection Prevention and Control Measures in Shanghai on Health Management and Psychosocial Well-Being of Patients with Chronic Conditions", - "rel_date": "2022-10-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.03.22280646", - "rel_abs": "BackgroundCOVID-19 and associated controls may be particularly problematic in the context of chronic conditions. This study investigated health management, well-being, and pandemic-related perspectives in these patients in the context of stringent measures, and associated correlates.\n\nMethodsA self-report survey was administered via Wenjuanxing in Simplified Chinese between March-June 2022 during the Omicron wave lockdown in Shanghai, China. Items from the Somatic Symptom Scale (SSS) and Symptom Checklist-90 (SCL-90) were administered, as well as pandemic-related items created by a working group of the Chinese Preventive Medical Association. Chronic disease patients in this cross-sectional study were recruited through an associated community family physician group.\n\nResultsOverall, 1775 patients, mostly married females with hypertension, participated. Mean SSS scores were 36.1{+/-}10.5/80, with 41.5% scoring in the elevated range (i.e., above 36). In an adjusted model, female, diagnosis of coronary artery disease and arrhythmia, perceived impact of pandemic on life, duration can tolerate control measures, perception of future & control measures, impact of pandemic on health condition and change to exercise routine due to pandemic were significantly associated with greater distress. Approximately one-quarter (24.5%) perceived the pandemic had a permanent impact on their life, and 44.1% perceived at least a minor impact on their health. One-third (33.5%) discontinued exercise due to the pandemic. While 47.6% stocked up on their medications before the lockdown, their remaining supply was mostly only enough for a couple of weeks and 17.5% of participants discontinued use. Chief among their fears were inability to access healthcare (83.2%), and what they stated they most needed to manage their condition was medication access (65.6%).\n\nConclusionsSince 2020 when we assessed a similar cohort, distress and perceived impact of the pandemic has worsened. Greater access to cardiac rehabilitation in China could address these issues.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Zhimin Xu", - "author_inst": "Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China" - }, - { - "author_name": "Gabriela Lima de Melo Ghisi", - "author_inst": "Cardiovascular Prevention and Rehabilitation Program, Toronto Rehabilitation Institute, University Health Network, University of Toronto, Toronto" - }, - { - "author_name": "Xia Liu", - "author_inst": "Chengdu Wanda UPMC Hospital, Chengdu, China" - }, - { - "author_name": "Lixian Cui", - "author_inst": "Division of Arts and Sciences, NYU Shanghai, Shanghai, China" - }, - { - "author_name": "Sherry Grace", - "author_inst": "Faculty of Health, York University, Toronto M3J 1P3, Canada; and KITE-Toronto Rehabilitation Institute & Peter Munk Cardiac Centre, University Health Network, U" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.10.02.22280627", "rel_title": "Dynamics of Vaccine-Hesitant Parents' Considerations Regarding Covid-19 Vaccination", @@ -199416,6 +200477,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.04.22280689", + "rel_title": "Population-level relative effectiveness of the COVID-19 vaccines and the contribution of naturally acquired immunity", + "rel_date": "2022-10-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.04.22280689", + "rel_abs": "BackgroundImmune protection against SARS-CoV-2 can be induced by natural infection or vaccination or both. The interaction between vaccine-induced immunity and naturally acquired immunity at the population level has been understudied.\n\nMethodsWe used regression models to evaluate whether the impact of COVID-19 vaccines differed across states with different levels of naturally acquired immunity from March 2021 to April 2022 in the United States. Analysis was conducted for three evaluation periods separately (Alpha, Delta, and Omicron waves). As a proxy of the proportion of the population with naturally acquired immunity, we used either the reported seroprevalence or the estimated proportion of the population ever infected in each state.\n\nResultsCOVID-19 mortality decreased as the coverage of [≥]1 dose increased among people [≥]65 years of age, and this effect did not vary by seroprevalence or the proportion of the total population ever infected. Seroprevalence and the proportion ever infected were not associated with COVID-19 mortality, after controlling for vaccine coverage. These findings were consistent in all evaluation periods.\n\nConclusionsCOVID-19 vaccination was associated with a sustained reduction in mortality at the state level during the Alpha, Delta, and Omicron periods. The effect did not vary by naturally acquired immunity.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Kayoko Shioda", + "author_inst": "Emory University" + }, + { + "author_name": "Yangping Chen", + "author_inst": "Emory University" + }, + { + "author_name": "Matthew H Collins", + "author_inst": "Emory University" + }, + { + "author_name": "Benjamin Lopman", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.02.22280610", "rel_title": "Protective effectiveness of prior SARS-CoV-2 infection and hybrid immunity against Omicron infection and severe disease: a systematic review and meta-regression", @@ -201171,77 +202263,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.09.30.510287", - "rel_title": "Correlating the differences in the receptor binding domain of SARS-CoV-2 spike variants on their interactions with human ACE2 receptor", - "rel_date": "2022-09-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.30.510287", - "rel_abs": "Spike protein of SARS-CoV-2 variants play critical role in the infection and transmission through its interaction with hACE2 receptor. Prior findings using molecular docking and biomolecular studies reported varied findings on the difference in the interactions among the spike variants with hACE2 receptor. Hence, it is a prerequisite to understand these interactions in a more precise manner. To this end, firstly, we performed ELISA with trimeric spike proteins of Wild (Wuhan Hu-1), Delta, C.1.2 and Omicron variants. Further, to study the interactions in a more specific manner by mimicking the natural infection, we developed hACE2 receptor expressing HEK-293T cell line and evaluated binding efficiencies of the variants and competitive binding of spike variants with D614G spike pseudotyped virus. In lines with the existing findings, we observed that Omicron had higher binding efficiency compared to Delta in both ELISA and Cellular models. Intriguingly, we found that cellular models could differentiate the subtle differences between the closely related C.1.2 and Delta in their binding to hACE2. From the analysis in receptor binding domain (RBD) revealed that a single common modification, N501Y, present in both Omicron and C.1.2 is driving the enhanced spike binding to the receptor and showed two-fold superior competitive binding than Delta. Our study using cellular model provides a precise method to evaluate the binding interactions between spike sub-lineages to hACE2 receptors and signifies the role of single common modification N501Y in RBD towards imparting superior binding efficiencies. Our approach would be instrumental in understanding the disease progression and developing therapeutics.\n\nAuthor SummarySpike proteins of evolving SARS-CoV2 variants demonstrated their signature binding to hACE2 receptor, in turn contributed to driving the infection and transmission. Prior studies to scale the binding efficiencies between the spike variant and the receptor had consensus in distinct variants, but discrepancies in the closely related ones. To this end, we compared spike variants-receptor interactions with ELISA, from cells expressing hACE2 receptor. Intriguingly, we found that cellular models could differentiate the subtle differences between the closely related C.1.2 and Delta in their binding to hACE2. More importantly, competitive binding studies in presence of pseudovirus, demonstrated that a single common modification, N501Y, present in both Omicron and C.1.2 showed two fold superior competitive binding than Delta. Collectively, our study suggests a precise approach to evaluate the binding interactions between spike sub-lineages to hACE2 receptor. This would be instrumental in understanding the disease progression and developing therapeutics.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Gokulnath Mahalingam", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Porkizhi Arjunan", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Yogapriya Periasami", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Ajay Kumar Dhyani", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Nivedhitha Devaraju", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Vignesh Rajendiran", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Abhisha Crystal Christopher", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Ramya Devi KT", - "author_inst": "SRM University: SRM Institute of Science and Technology" - }, - { - "author_name": "Immanuel Darasingh", - "author_inst": "Vellore Institute of Technology: VIT University" - }, - { - "author_name": "Saravanabhavan Thangavel", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Mohankumar Murugesan", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Mahesh Moorthy", - "author_inst": "CMCH: Christian Medical College Vellore" - }, - { - "author_name": "Alok Srivastava", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Srujan Marepally", - "author_inst": "CSCR: Center for Stem Cell Research" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2022.09.28.22280472", "rel_title": "Covid-19: Qualitative Change in the Behavior of the \"Virus vs Human\" System - From Limit Cycle to Sustained Focus", @@ -201450,6 +202471,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.09.28.22280465", + "rel_title": "Differences in COVID-19 cyclicity and predictability among U.S. counties and states reflect the effectiveness of protective measures", + "rel_date": "2022-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.28.22280465", + "rel_abs": "Data available for COVID-19 in the USA make it possible to assess the dynamics of disease spread with 20:20 hindsight. Here, we analyze archived data to explain variation among counties and states in the cyclicity and predictability (that is, the extent to which predictions are possible) of disease dynamics, using a combination of statistical and simulation models. For the period after the initial outbreak but before widespread vaccination (May 2020 - February 2021), we show that for half the counties and states the spread rate of COVID-19, r(t), was predictable at most 9 weeks and 8 weeks ahead, respectively, corresponding to at most 40% and 35% of an average cycle length of 23 weeks and 26 weeks. However, there were large differences among counties and states, and high predictability was associated with high cyclicity of r(t). Furthermore, predictability was negatively associated with R0 values from the pandemics onset. This suggests that a severe initial outbreak induced strong and sustained protective measures to lower disease transmission, and these protective measures in turn reduced both cyclicity and predictability. Thus, decreased predictability of disease spread should be viewed as a by-product of positive and sustained steps that people take to protect themselves and others.\n\nSignificance statementDuring the COVID-19 pandemic, many quantitative approaches were employed to predict the course of disease spread. However, forecasting faces the challenge of inherently unpredictable spread dynamics, setting a limit to the accuracy of all models. For counties and states in the USA, we document very high variation in predictability after the initial outbreak and before widespread vaccination. Jurisdictions with high predictability were those that showed pronounced cyclic re-emergences ( waves). The variation in predictability can be explained by differences in the human responses to disease: jurisdictions in which individuals and authorities took strong and sustained protective measures against COVID-19 successfully curbed subsequent waves of disease spread, but at the same time unintentionally decreased its predictability.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Claudio Bozzuto", + "author_inst": "Wildlife Analysis GmbH" + }, + { + "author_name": "Anthony R Ives", + "author_inst": "University of Wisconsin-Madison" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.09.28.22280462", "rel_title": "Trend and co-occurrence network study of symptoms through social media: an example of COVID-19", @@ -203109,97 +204153,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.26.22280364", - "rel_title": "Clinical Subphenotypes of Multisystem Inflammatory Syndrome in Children: An EHR-based cohort study from the RECOVER program", - "rel_date": "2022-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.26.22280364", - "rel_abs": "BackgroundMulti-system inflammatory syndrome in children (MIS-C) represents one of the most severe post-acute sequelae of SARS-CoV-2 infection in children, and there is a critical need to characterize its disease patterns for improved recognition and management. Our objective was to characterize subphenotypes of MIS-C based on presentation, demographics and laboratory parameters.\n\nMethodsWe conducted a retrospective cohort study of children with MIS-C from March 1, 2020 - April 30, 2022 and cared for in 8 pediatric medical centers that participate in PEDSnet. We included demographics, symptoms, conditions, laboratory values, medications and outcomes (ICU admission, death), and grouped variables into eight categories according to organ system involvement. We used a heterogeneity-adaptive latent class analysis model to identify three clinically-relevant subphenotypes. We further characterized the sociodemographic and clinical characteristics of each subphenotype, and evaluated their temporal patterns.\n\nFindingsWe identified 1186 children hospitalized with MIS-C. The highest proportion of children (44{middle dot}4%) were aged between 5-11 years, with a male predominance (61.0%), and non- Hispanic white ethnicity (40{middle dot}2%). Most (67{middle dot}8%) children did not have a chronic condition. Class 1 represented children with a severe clinical phenotype, with 72{middle dot}5% admitted to the ICU, higher inflammatory markers, hypotension/shock/dehydration, cardiac involvement, acute kidney injury and respiratory involvement. Class 2 represented a moderate presentation, with 4-6 organ systems involved, and some overlapping features with acute COVID-19. Class 3 represented a mild presentation, with fewer organ systems involved, lower CRP, troponin values and less cardiac involvement. Class 1 initially represented 51{middle dot}1% of children early in the pandemic, which decreased to 33{middle dot}9% from the pre-delta period to the omicron period.\n\nInterpretationMIS-C has a spectrum of clinical severity, with degree of laboratory abnormalities rather than the number of organ systems involved providing more useful indicators of severity. The proportion of severe/critical MIS-C decreased over time.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed and preprint articles from December 2019, to July 2022, for studies published in English that investigated the clinical subphenotypes of MIS-C using the terms \"multi-system inflammatory syndrome in children\" or \"pediatric inflammatory multisystem syndrome\" and \"phenotypes\". Most previous research described the symptoms, clinical characteristics and risk factors associated with MIS-C and how these differ from acute COVID-19, Kawasaki Disease and Toxic Shock Syndrome. One single-center study of 63 patients conducted in 2020 divided patients into Kawasaki and non-Kawasaki disease subphenotypes. Another CDC study evaluated 3 subclasses of MIS-C in 570 children, with one class representing the highest number of organ systems, a second class with predominant respiratory system involvement, and a third class with features overlapping with Kawasaki Disease. However, this study evaluated cases from March to July 2020, during the early phase of the pandemic when misclassification of cases as Kawasaki disease or acute COVID-19 may have occurred. Therefore, it is not known from the existing literature whether the presentation of MIS-C has changed with newer variants such as delta and omicron.\n\nAdded value of this studyPEDSnet provides one of the largest MIS-C cohorts described so far, providing sufficient power for detailed analyses on MIS-C subphenotypes. Our analyses span the entire length of the pandemic, including the more recent omicron wave, and provide an update on the presentations of MIS-C and its temporal dynamics. We found that children have a spectrum of illness that can be characterized as mild (lower inflammatory markers, fewer organ systems involved), moderate (4-6 organ involvement with clinical overlap with acute COVID-19) and severe (higher inflammatory markers, critically ill, more likely to have cardiac involvement, with hypotension/shock and need for vasopressors).\n\nImplications of all the available evidenceThese results provide an update to the subphenotypes of MIS-C including the more recent delta and omicron periods and aid in the understanding of the various presentations of MIS-C. These and other findings provide a useful framework for clinicians in the recognition of MIS-C, identify factors associated with children at risk for increased severity, including the importance of laboratory parameters, for risk stratification, and to facilitate early evaluation, diagnosis and treatment.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Suchitra Rao", - "author_inst": "University of Colorado School of Medicine and Children's Hospital Colorado" - }, - { - "author_name": "Naimin Jing", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Xiaokang Liu", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Vitaly Lorman", - "author_inst": "Children's Hospital of Philadelphia" - }, - { - "author_name": "Mitchell Maltenfort", - "author_inst": "Children's Hospital of Philadelphia" - }, - { - "author_name": "Julia Schuchard", - "author_inst": "Children's Hospital of Philadelphia" - }, - { - "author_name": "Qiong Wu", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Jiayi Tong", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Hanieh Razzaghi", - "author_inst": "Children's Hospital of Philadelphia" - }, - { - "author_name": "Asuncion Mejias", - "author_inst": "Nationwide Children's Hospital and The Ohio State University" - }, - { - "author_name": "Grace M. Lee", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Nathan M Pajor", - "author_inst": "Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine" - }, - { - "author_name": "Grant S. Schulert", - "author_inst": "Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine" - }, - { - "author_name": "Deepika Thacker", - "author_inst": "Nemours Children's Health" - }, - { - "author_name": "Ravi Jhaveri", - "author_inst": "Ann & Robert H. Lurie Children's Hospital of Chicago" - }, - { - "author_name": "Dimitri A. Christakis", - "author_inst": "Seattle Children's Hospital" - }, - { - "author_name": "L. Charles Bailey", - "author_inst": "Children's Hospital of Philadelphia and University of Pennsylvania" - }, - { - "author_name": "Christopher B. Forrest", - "author_inst": "Children's Hospital of Philadelphia and University of Pennsylvania" - }, - { - "author_name": "Yong Chen", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2022.09.22.22280262", "rel_title": "Development and validation of a methodology to measure exhaled carbon dioxide (CO2) and control indoor air renewal", @@ -203340,6 +204293,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2022.09.27.22280403", + "rel_title": "Comparative adverse effects, perceptions and attitudes related to BNT162b2, mRNA1273, or JNJ-78436735 SARS-CoV-2 vaccines: A population-based longitudinal cohort", + "rel_date": "2022-09-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.27.22280403", + "rel_abs": "ImportanceLong-term control of SARS-CoV-2 requires effective vaccination strategies. This has been challenged by public mistrust and spread of misinformation regarding vaccine safety. Hence, better understanding and communication on the longer-term and comparative experiences of general population individuals following SARS-CoV-2 vaccination are required.\n\nObjectiveTo evaluate and compare self-reported adverse effects following SARS-CoV-2 vaccination, participants perceptions regarding vaccinations and their compliance with recommended public health measures.\n\nDesign, Setting and ParticipantsPopulation-based longitudinal cohort of 575 adults, randomly selected from all individuals presenting to the reference vaccination center of the Canton of Zurich, Switzerland, for receipt of BNT162b2, mRNA1273, or JNJ-78436735.\n\nExposuresBNT162b2, mRNA1273, or JNJ-78436735 vaccines.\n\nMain Outcomes and MeasuresPrimary outcomes included period prevalence, onset, duration, and severity of self-reported adverse effects over 12 weeks following vaccination with a specific focus on the proportion of participants reporting allergic reactions, menstrual irregularities, or cardiac adverse effects, or requiring hospitalization. Secondary outcomes included risk factors associated with reporting adverse effects, perception of vaccine importance, trust in public health authorities and pharmaceutical companies, and compliance with recommended public health measures.\n\nResults454 (79.0%) participants reported at least one adverse effect during 12 weeks after vaccination. Prevalence was highest among mRNA-1273 recipients (88.7% vs. 77.3% after BNT162b2, 69.1% after JNJ-78436735). Most adverse effects were systemic (72%), occurred within 24 hours (67.9%), and resolved in less than three days (76.3%). 85.2% were reported as mild or moderate. Allergic reactions were reported by 0.4% of participants, hospitalizations by 0.7%, cardiac adverse effects by 1.4%. Menstrual irregularities were reported by 9% of female participants younger than 50 years. Female sex, younger age, higher education, and receipt of mRNA-1273 were associated with reporting adverse effects. Compared to JNJ-78436735 recipients, a higher proportion of mRNA vaccine recipients agreed that vaccination is important (87.5% vs. 28.5%), and trusted public health authorities (80.2% vs. 30.3%) and pharmaceutical companies (71.7% vs. 23.6%).\n\nConclusions and RelevanceOur population-based cohort provided real-world data on self-reported adverse effects following SARS-CoV-2 vaccination and highlights the importance of transparent communication regarding adverse effects and building trust in public health authorities to ensure successful future vaccination campaigns.\n\nMain PointsOur representative population-based cohort study demonstrated the safety of three SARS-CoV-2 vaccines and provides real-world estimates on adverse effect incidence.Transparent communication of expected adverse effects to vaccine-seeking individuals is pivotal to build trust in current or future vaccination campaigns.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Oliver Vaclav Buerzle", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich (UZH)" + }, + { + "author_name": "Dominik Menges", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich (UZH)" + }, + { + "author_name": "Julian D Maier", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich (UZH)" + }, + { + "author_name": "Daniel Schams", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich (UZH)" + }, + { + "author_name": "Milo Alan Puhan", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich (UZH)" + }, + { + "author_name": "Jan Fehr", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich (UZH)" + }, + { + "author_name": "Tala Ballouz", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich (UZH)" + }, + { + "author_name": "Anja Frei", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich (UZH)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.26.22280381", "rel_title": "Nation-wide mammography screening participation in Denmark during the COVID-19 pandemic: An observational study", @@ -205195,57 +206195,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.09.23.22280278", - "rel_title": "Impact of COVID-19 on lifestyle and mental wellbeing in a drought-affected rural Australian population: A mixed method approach", - "rel_date": "2022-09-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.23.22280278", - "rel_abs": "BackgroundThe Coronavirus disease 2019 (COVID-19) pandemic has caused unprecedented social and economic disruption, accompanied by the enactment of a multitude of public health measures to restrain disease transmission. These public health and social measures have had a considerable impact on lifestyle and mental wellbeing, which has been well-studied in metropolitan populations, but very little in rural populations. Additionally, the development and use of a standardised scoring system for an overall assessment of patient lifestyle management, and monitoring of changes in these, may be warranted in clinical practice.\n\nMethodsThe associations between psychological distress and changes in SNAPS health behaviours (smoking, nutrition, alcohol, physical activity, sleep) since the onset of COVID-19 in rural Australia were examined. A cross-sectional anonymous online survey was distributed among adults in the Western New South Wales Primary Health Network in August 2020. The survey included measures of psychological distress, income, disposition, lifestyle factors and behaviours during the pandemic, as well as changes in lifestyle due to COVID-19. A novel Global Lifestyle Score (GLS) was generated as a holistic assessment of lifestyle across multiple domains.\n\nResultsThe survey was completed by 308 individuals (modal age group: 45-54 years old, 86.4% female). High distress on the K5 scale was present in over one-third of respondents (n=98, 34.3%). Negative change was reported for sleep (24.4%), nutrition (14.3%), alcohol (17.8%), physical exercise (33.8%) and smoking (26.6%) since the onset of the pandemic. Additionally, changes in sleep, nutrition, physical activity and smoking were associated with distress. Respondents with a poor lifestyle (GLS) during the pandemic were significantly more distressed. Perceived COVID-19 impact was associated with high distress, level of drought impact and loss of income.\n\nConclusionHigh rates of distress amongst rural Australians during the COVID-19 pandemic was linked, worsening lifestyles as measured by the GLS and loss of income. Lifestyle promotion strategies should be considered by health professionals for the management of crisis-related distress. Further research may explore the impact of COVID-19 on a larger population, including a greater proportion of male respondents, and the impact of modifying lifestyle factors on the reduction of distress in the context of a stressor such as this pandemic.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jack Carlson", - "author_inst": "Western Sydney University - Campbelltown Campus" - }, - { - "author_name": "Kevin Chan", - "author_inst": "University of Western Sydney: Western Sydney University" - }, - { - "author_name": "Jonah Gray", - "author_inst": "Western Sydney University - Campbelltown Campus" - }, - { - "author_name": "Houston Xue", - "author_inst": "Western Sydney University School of Medicine" - }, - { - "author_name": "Krista Reed", - "author_inst": "Western Sydney University School of Medicine" - }, - { - "author_name": "Jannine K Bailey", - "author_inst": "Western Sydney University School of Medicine" - }, - { - "author_name": "Tegan Dutton", - "author_inst": "Western Sydney University School of Medicine" - }, - { - "author_name": "Uchechukwu L. Osuagwu", - "author_inst": "Western Sydney University - Campbelltown Campus" - }, - { - "author_name": "Robyn Vines", - "author_inst": "Western Sydney University School of Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2022.09.23.22279458", "rel_title": "Pan-Canadian survey on the impact of the COVID-19 pandemic on cervical cancer screening and management", @@ -205966,6 +206915,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.09.23.22280281", + "rel_title": "The impact of COVID-19 vaccination in the US: averted burden of SARS-COV-2-related cases, hospitalizations and deaths", + "rel_date": "2022-09-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.23.22280281", + "rel_abs": "By August 1, 2022, the SARS-CoV-2 virus had caused over 90 million cases of COVID-19 and one million deaths in the United States. Since December 2020, SARS-CoV-2 vaccines have been a key component of US pandemic response; however, the impacts of vaccination are not easily quantified. Here, we use a dynamic county-scale metapopulation model to estimate the number of cases, hospitalizations, and deaths averted due to vaccination during the first six months of vaccine availability. We estimate that COVID-19 vaccination was associated with over 8 million fewer confirmed cases, over 120 thousand fewer deaths, and 700 thousand fewer hospitalizations during the first six months of the campaign.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Teresa K Yamana", + "author_inst": "Columbia University" + }, + { + "author_name": "Marta Galanti", + "author_inst": "Columbia University Mailman School of Public Health" + }, + { + "author_name": "Sen Pei", + "author_inst": "Columbia University Mailman School of Public Health" + }, + { + "author_name": "Manuela Di Fusco", + "author_inst": "Pfizer Inc" + }, + { + "author_name": "Frederick J Angulo", + "author_inst": "Pfizer Vaccines Research Unit" + }, + { + "author_name": "Mary Moran", + "author_inst": "Pfizer Vaccines Research Unit" + }, + { + "author_name": "Farid Khan", + "author_inst": "Pfizer Vaccines Research Unit" + }, + { + "author_name": "David Swerdlow", + "author_inst": "Pfizer Vaccines Research Unit" + }, + { + "author_name": "Jeffrey Shaman", + "author_inst": "Columbia University Mailman School of Public Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.09.24.22280310", "rel_title": "Post-Concussion Assessment as a diagnostic and mechanistic framework for treating patients with Long COVID", @@ -207569,145 +208569,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.09.22.509040", - "rel_title": "SARS-CoV-2 Omicron boosting induces de novo B cell response in humans", - "rel_date": "2022-09-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.22.509040", - "rel_abs": "The primary two-dose SARS-CoV-2 mRNA vaccine series are strongly immunogenic in humans, but the emergence of highly infectious variants necessitated additional doses of these vaccines and the development of new variant-derived ones1-4. SARS-CoV-2 booster immunizations in humans primarily recruit pre-existing memory B cells (MBCs)5-9. It remains unclear, however, whether the additional doses induce germinal centre (GC) reactions where reengaged B cells can further mature and whether variant-derived vaccines can elicit responses to novel epitopes specific to such variants. Here, we show that boosting with the original SARS- CoV-2 spike vaccine (mRNA-1273) or a B.1.351/B.1.617.2 (Beta/Delta) bivalent vaccine (mRNA-1273.213) induces robust spike-specific GC B cell responses in humans. The GC response persisted for at least eight weeks, leading to significantly more mutated antigen-specific MBC and bone marrow plasma cell compartments. Interrogation of MBC-derived spike-binding monoclonal antibodies (mAbs) isolated from individuals boosted with either mRNA-1273, mRNA-1273.213, or a monovalent Omicron BA.1-based vaccine (mRNA-1273.529) revealed a striking imprinting effect by the primary vaccination series, with all mAbs (n=769) recognizing the original SARS-CoV-2 spike protein. Nonetheless, using a more targeted approach, we isolated mAbs that recognized the spike protein of the SARS-CoV-2 Omicron (BA.1) but not the original SARS-CoV-2 spike from the mRNA-1273.529 boosted individuals. The latter mAbs were less mutated and recognized novel epitopes within the spike protein, suggesting a naive B cell origin. Thus, SARS-CoV-2 boosting in humans induce robust GC B cell responses, and immunization with an antigenically distant spike can overcome the antigenic imprinting by the primary vaccination series.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Wafaa B. Alsoussi", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Sameer K. Malladi", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Julian Q. Zhou", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Zhuoming Liu", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Baoling Ying", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Wooseob Kim", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Aaron J. Schmitz", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Tingting Lei", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Stephen C. Horvath", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Alexandria J. Sturtz", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Katherine M. McIntire", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Birk Evavold", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Fangjie Han", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Suzanne M. Scheaffer", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Isabella F. Fox", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Luis Parra-Rodriguez", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Raffael Nachbagauer", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Biliana Nestorova", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Spyros Chalkias", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Christopher W. Farnsworth", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Michael K. Klebert", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Iskra Pusic", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Benjamin S. Strnad", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "William D. Middleton", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Sharlene A. Teefey", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Sean P.J. Whelan", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Michael S. Diamond", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Robert Paris", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Rachel M. Presti", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Jackson S. Turner", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Ali H. Ellebedy", - "author_inst": "Washington University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.09.22.508999", "rel_title": "Triple COVID-19 vaccination induces humoral and cellular immunity to SARS-CoV-2 with cross-recognition of the Omicron variant and IgA secretion", @@ -207932,6 +208793,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2022.09.21.22280193", + "rel_title": "Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in Amazonas, a Brazilian setting with high levels of hybrid immunity", + "rel_date": "2022-09-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.21.22280193", + "rel_abs": "The SARS-CoV-2 variants of concern (VOCs) Delta and Omicron spread globally during mid and late 2021, respectively, with variable impact according to the immune population landscape. In this study, we compare the dissemination dynamics of these VOCs in the Amazonas state, one of Brazils most heavily affected regions. We sequenced the virus genome from 4,128 patients collected in Amazonas between July 1st, 2021 and January 31st, 2022 and investigated the lineage replacement dynamics using a phylodynamic approach. The VOCs Delta and Omicron displayed similar patterns of phylogeographic spread but significantly different epidemic dynamics. The Delta and Omicron epidemics were fueled by multiple introduction events, followed by the successful establishment of a few local transmission lineages of considerable size that mainly arose in the Capital, Manaus. The VOC Omicron spread and became dominant much faster than the VOC Delta. We estimate that under the same epidemiological conditions, the average Re of Omicron was [~]3.3 times higher than that of Delta and the average Re of the Delta was [~]1.3 times higher than that of Gamma. Furthermore, the gradual replacement of Gamma by Delta occurred without an upsurge of COVID-19 cases, while the rise of Omicron fueled a sharp increase in SARS-CoV-2 infection. The Omicron wave displayed a shorter duration and a clear decoupling between the number of SARS-CoV-2 cases and deaths compared with previous (B.1.* and Gamma) waves in the Amazonas state. These findings suggest that the high level of hybrid immunity (infection plus vaccination) acquired by the Amazonian population by mid-2021 was able to limit the spread of the VOC Delta and was also probably crucial to curb the number of severe cases, although not the number of VOC Omicron new infections.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Ighor Arantes", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "Gonzalo Bello", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "Valdinete Nascimento", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "Victor Souza", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "Arlesson da Silva", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "Dejanane Silva", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "Fernanda Nascimento", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "Matilde MejIa", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "Maria Julia Brandao", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "Luciana Goncalves", + "author_inst": "Oswaldo Cruz Foundation and Amazonas Health Surveillance Foundation Dr Rosemary Costa Pinto" + }, + { + "author_name": "George Silva", + "author_inst": "Oswaldo Cruz Foundation and Foundation Center for Oncology Control of the State of Amazonas" + }, + { + "author_name": "Cristiano Fernandes da Costa", + "author_inst": "Amazonas Health Surveillance Foundation" + }, + { + "author_name": "Ligia Abdalla", + "author_inst": "State University of Amazonas" + }, + { + "author_name": "Joao Hugo Santos", + "author_inst": "Manaus Adventist Hospital" + }, + { + "author_name": "Tatyana Amorin Ramos", + "author_inst": "Amazonas Health Surveillance Foundation Dr Rosemary Costa Pinto" + }, + { + "author_name": "Chayada Piantham", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Kimihito Ito", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Marilda Mendonca Siqueira", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "Paola Cristina Resende", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "Gabriel Luz Wallau", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "Edson Delatorre", + "author_inst": "Federal University of Espirito Santo" + }, + { + "author_name": "Tiago Graf", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "Felipe Naveca", + "author_inst": "Oswaldo Cruz Foundation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.20.22280170", "rel_title": "Reconstructing the SARS-CoV-2 epidemic in eastern Uganda through longitudinal serosurveillance in a malaria cohort", @@ -209547,77 +210515,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.18.22280022", - "rel_title": "Liquid biomarkers of macrophage dysregulation and circulating spike protein illustrate the biological heterogeneity in patients with post-acute sequelae of COVID-19", - "rel_date": "2022-09-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.18.22280022", - "rel_abs": "Post-acute sequelae of COVID-19 (PASC) are long-term consequences of SARS-CoV-2 infection that can substantially impair quality of life. Underlying mechanisms ranging from persistent virus to innate and adaptive immune dysregulation have been discussed. Here, we profiled plasma of 181 individuals from the cohort study for digital health research in Germany (DigiHero) including individuals after mild to moderate COVID-19 with or without PASC and uninfected controls. We focused on soluble factors related to monocyte/macrophage biology and on circulating SARS-CoV-2 spike (S1) protein as potential biomarker for persistent viral reservoirs. At a median time of eight months after infection, we found pronounced dysregulation in almost all tested soluble factors including both pro-inflammatory and pro-fibrotic cytokines. These perturbations were remarkably independent of ongoing symptoms, but further correlation and regression analyses suggested PASC specific patterns involving CCL2/MCP-1 and IL-8 as well as long-term persistence of high IL-5 and IL-17F levels. None of the analyzed factors correlated with the detectability or levels of circulating S1 indicating that this represents an independent subset of patients with PASC. This data confirms prior evidence of immune dysregulation and persistence of viral protein in PASC and illustrates its biological heterogeneity that still awaits correlation with clinically defined PASC subtypes.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Christoph Schultheiss", - "author_inst": "Martin-Luther-University Halle-Wittenberg, Internal Medicine IV" - }, - { - "author_name": "Edith Willscher", - "author_inst": "Martin-Luther-University Halle-Wittenberg, Internal Medicine IV" - }, - { - "author_name": "Lisa Paschold", - "author_inst": "Martin-Luther-University Halle-Wittenberg, Internal Medicine IV" - }, - { - "author_name": "Cornelia Gottschick", - "author_inst": "Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther Univer" - }, - { - "author_name": "Bianca Klee", - "author_inst": "Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther Univer" - }, - { - "author_name": "Lidia Bosurgi", - "author_inst": "I. Department of Medicine, University Medical Center Hamburg-Eppendorf; Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine" - }, - { - "author_name": "Jochen Dutzmann", - "author_inst": "Mid-German Heart Center, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Daniel Sedding", - "author_inst": "Mid-German Heart Center, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Thomas Frese", - "author_inst": "Institute of General Practice and Family Medicine, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Matthias Girndt", - "author_inst": "Department of Internal Medicine II, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Jessica I. Hoell", - "author_inst": "Pediatric Hematology and Oncology, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Michael Gekle", - "author_inst": "Julius Bernstein-Institute of Physiology, Faculty of Medicine, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Rafael Mikolajczyk", - "author_inst": "Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther Univer" - }, - { - "author_name": "Mascha Binder", - "author_inst": "Martin-Luther-University Halle-Wittenberg, Internal Medicine IV" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.09.19.22280079", "rel_title": "The impact of prior COVID-19 on vaccine response and the resultant hybrid immunity are age-dependent", @@ -209874,6 +210771,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.09.13.22279702", + "rel_title": "Accounting for assay performance when estimating the temporal dynamics in SARS-CoV-2 seroprevalence in the U.S.", + "rel_date": "2022-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.13.22279702", + "rel_abs": "Estimating the incidence of SARS-CoV-2 infection is central to understanding the state of the pandemic. Seroprevalence studies are often used to assess cumulative infections as they can identify asymptomatic infection. Since July 2020, commercial laboratories have conducted nationwide serosurveys for the U.S. CDC. They employed three assays, with different sensitivities and specificities, potentially introducing biases in seroprevalence estimates. Using mechanistic models, we show that accounting for assays explains some of the observed state-to-state variation in seroprevalence, and when integrating case and death surveillance data, we show that when using the Abbott assay, estimates of proportions infected can differ substantially from seroprevalence estimates. We also found that states with higher proportions infected (before or after vaccination) had lower vaccination coverages, a pattern corroborated using a separate dataset. Finally, to understand vaccination rates relative to the increase in cases, we estimated the proportions of the population that received a vaccine prior to infection.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Bernardo Garc\u00eda-Carreras", + "author_inst": "University of Florida" + }, + { + "author_name": "Matt DT Hitchings", + "author_inst": "University of Florida" + }, + { + "author_name": "Michael A Johansson", + "author_inst": "U.S. Centers for Disease Control and Prevention" + }, + { + "author_name": "Matthew Biggerstaff", + "author_inst": "U.S. Centers for Disease Control and Prevention" + }, + { + "author_name": "Rachel B Slayton", + "author_inst": "U.S. Centers for Disease Control and Prevention" + }, + { + "author_name": "Jessica M Healy", + "author_inst": "U.S. Centers for Disease Control and Prevention" + }, + { + "author_name": "Justin Lessler", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Talia Quandelacy", + "author_inst": "University of Colorado" + }, + { + "author_name": "Henrik Salje", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Angkana T Huang", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Derek AT Cummings", + "author_inst": "University of Florida" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.09.16.22280017", "rel_title": "Post-vaccination neutralization responses to Omicron sub-variants", @@ -211509,25 +212465,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.09.10.22279806", - "rel_title": "Cognitive status and rehabilitation outcomes of patients in acute rehabilitation post Covid-19", - "rel_date": "2022-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.10.22279806", - "rel_abs": "ObjectiveThis study aims to 1) characterize cognitive functioning in patients admitted for inpatient rehabilitation due to Covid-19 diagnosis and 2) examine how cognitive status at admission is associated with rehabilitation outcomes.\n\nDesignRetrospective chart review.\n\nSettingAn inpatient rehabilitation center located in Chicago, Illinois.\n\nParticipants80 participants in acute rehabilitation due to Covid-19 disease\n\nInterventionNot applicable.\n\nMain Outcome MeasuresCognitive functioning as measured by the Montreal Cognitive Assessment (MoCA) and rehabilitation outcomes as measured by Functional Index Measure (FIM) and Section GG items for self-care and mobility (GG-SC and GG-M respectively).\n\nResultsOn average, our sample presented with mild cognitive impairment as assessed by the (MoCA). The most significant deficits were demonstrated in executive function, attention, language, and delayed free recall measures. Higher levels of overall cognitive function were associated with higher cognitive measures of rehabilitation outcomes. Weaker associations were observed with outcome measures of self-care and motor functioning.\n\nConclusionCognitive impairments are common in patients in acute rehabilitation due to Covid-19 and cognitive performance may help predict rehabilitation outcomes.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Madli Vahtra", - "author_inst": "Ascension St Alexius" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2022.09.09.22279763", "rel_title": "COVID-19 induced birth sex ratio changes in England and Wales", @@ -211820,6 +212757,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.09.14.22279931", + "rel_title": "Detecting changes in population trends in infection surveillance using community SARS-CoV-2 prevalence as an exemplar", + "rel_date": "2022-09-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.14.22279931", + "rel_abs": "BackgroundMonitoring infection trends is vital to informing public health strategy. Detecting and quantifying changes in growth rates can inform policymakers rationale for implementing or continuing interventions aimed at reducing impact. Substantial changes in SARS-CoV-2 prevalence with emergence of variants provides opportunity to investigate different methods to do this.\n\nMethodsWe included PCR results from all participants in the UKs COVID-19 Infection Survey between 1 August 2020-30 June 2022. Change-points for growth rates were identified using iterative sequential regression (ISR) and second derivatives of generalised additive models (GAMs).\n\nConsistency between methods and timeliness of detection were compared.\n\nFindingsOf 8,799,079 visits, 147,278 (1{middle dot}7%) were PCR-positive. Over the time period, change-points associated with emergence of major variants were estimated to occur a median 4 days earlier (IQR 0-8) in GAMs versus ISR, with only 2/48 change-points identified by only one method. Estimating recent change-points using successive data periods, four change-points (4/96) identified by GAMs were not found when adding later data or by ISR; 77% (74/96) of change-points identified by successive GAMs were identified by ISR. Change-points were detected 3-5 weeks after they occurred in both methods but could be detected earlier within specific subgroups.\n\nInterpretationChange-points in growth rates of SARS-CoV-2 can be detected in near real-time using ISR and second derivatives of GAMs. To increase certainty about changes in epidemic trajectories both methods could be run in parallel. Running either method in near real-time on different infection surveillance data streams could provide timely warnings of changing underlying epidemiology.\n\nFundingUK Health Security Agency, Department of Health and Social Care (UK), Welsh Government, Department of Health (on behalf of the Northern Ireland Government), Scottish Government, National Institute for Health Research.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Emma Elizabeth Pritchard", + "author_inst": "University of Oxford" + }, + { + "author_name": "Karina-Doris Vihta", + "author_inst": "University of Oxford" + }, + { + "author_name": "David W Eyre", + "author_inst": "University of Oxford" + }, + { + "author_name": "Susan Hopkins", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Tim EA Peto", + "author_inst": "University of Oxford" + }, + { + "author_name": "Philippa C Matthews", + "author_inst": "The Francis Crick Institute, London" + }, + { + "author_name": "Nicole Stoesser", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ruth Studley", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Emma Rourke", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Ian Diamond", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Koen B Pouwels", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ann Sarah Walker", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.09.12.507659", "rel_title": "Fast bioluminescent nucleic acid detection using one-pot isothermal amplification and dCas9-based split luciferase complementation", @@ -213291,125 +214291,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.14.507842", - "rel_title": "Molecular engineering of a cryptic epitope in Spike RBD improves manufacturability and neutralizing breadth against SARS-CoV-2 variants", - "rel_date": "2022-09-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.14.507842", - "rel_abs": "There is a continued need for sarbecovirus vaccines that can be manufactured and distributed in low- and middle-income countries (LMICs). Subunit protein vaccines are manufactured at large scales at low costs, have less stringent temperature requirements for distribution in LMICs, and several candidates have shown protection against SARS-CoV-2. We previously reported an engineered variant of the SARS-CoV-2 Spike protein receptor binding domain antigen (RBD-L452K-F490W; RBD-J) with enhanced manufacturability and immunogenicity compared to the ancestral RBD. Here, we report a second-generation engineered RBD antigen (RBD-J6) with two additional mutations to a hydrophobic cryptic epitope in the RBD core, S383D and L518D, that further improved expression titers and biophysical stability. RBD-J6 retained binding affinity to human convalescent sera and to all tested neutralizing antibodies except antibodies that target the class IV epitope on the RBD core. K18-hACE2 transgenic mice immunized with three doses of a Beta variant of RBD-J6 displayed on a virus-like particle (VLP) generated neutralizing antibodies (nAb) to nine SARS-CoV-2 variants of concern at similar levels as two doses of Comirnaty. The vaccinated mice were also protected from challenge with Alpha or Beta SARS-CoV-2. This engineered antigen could be useful for modular RBD-based subunit vaccines to enhance manufacturability and global access, or for further development of variant-specific or broadly acting booster vaccines.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Sergio Andre Rodriguez-Aponte", - "author_inst": "MIT" - }, - { - "author_name": "Neil Chandra Dalvie", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Ting Y. Wong", - "author_inst": "West Virginia University" - }, - { - "author_name": "Ryan S. Johnston", - "author_inst": "MIT" - }, - { - "author_name": "Christopher A. Naranjo", - "author_inst": "MIT" - }, - { - "author_name": "Sakshi Bajoria", - "author_inst": "University of Kansas" - }, - { - "author_name": "Ozan S. Kumru", - "author_inst": "University of Kansas" - }, - { - "author_name": "Kawaljit Kaur", - "author_inst": "University of Kansas" - }, - { - "author_name": "Brynnan P. Russ", - "author_inst": "West Virginia University" - }, - { - "author_name": "Katherine S. Lee", - "author_inst": "West Virginia University" - }, - { - "author_name": "Holly A. Cyphert", - "author_inst": "West Virginia University" - }, - { - "author_name": "Mariette Barbier", - "author_inst": "West Virginia University" - }, - { - "author_name": "Harish D. Rao", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Meghraj P. Rajurkar", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Rakesh R. Lothe", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Umesh Shaligram", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Saurabh Batwal", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Rahul Chandrasekaran", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Gaurav Nagar", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Harry Kleanthous", - "author_inst": "Bill & Melinda Gates Foundation" - }, - { - "author_name": "Sumi Biswas", - "author_inst": "Spybiotech Limited" - }, - { - "author_name": "Justin R. Bevere", - "author_inst": "West Virginia University" - }, - { - "author_name": "Sangeeta B. Joshi", - "author_inst": "University of Kansas" - }, - { - "author_name": "David B. Volkin", - "author_inst": "University of Kansas" - }, - { - "author_name": "Fredrick Heath Damron", - "author_inst": "West Virginia University" - }, - { - "author_name": "J. Christopher Love", - "author_inst": "Koch Institute at MIT" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2022.09.14.507985", "rel_title": "Analysis and comprehensive lineage identification for SARS-CoV-2 genomes through scalable learning methods", @@ -213570,6 +214451,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.09.12.507671", + "rel_title": "Evaluation of endogenous and therapeutic 25-hydroxycholesterols in murine models of pulmonary SARS-CoV-2 infection", + "rel_date": "2022-09-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.12.507671", + "rel_abs": "Oxysterols (i.e., oxidized cholesterol species) have complex roles in biology. 25-hydroxycholesterol (25HC), a product of activity of cholesterol-25-hydroxylase (CH25H) upon cholesterol, has recently been shown to be broadly antiviral, suggesting therapeutic potential against SARS-CoV-2. However, 25HC can also amplify inflammation and tissue injury and be converted by CYP7B1 to 7,25HC, a lipid with chemoattractant activity via the G protein-coupled receptor, EBI2/GPR183. Here, using in vitro studies and two different murine models of SARS-CoV-2 infection, we investigate the effects of these two oxysterols on SARS-CoV-2 pneumonia. We show that while 25HC and enantiomeric-25HC are antiviral in vitro against human endemic coronavirus-229E, they did not inhibit SARS-CoV-2; nor did supplemental 25HC reduce pulmonary SARS-CoV-2 titers in the K18-human ACE2 mouse model in vivo. 25HC treatment also did not alter immune cell influx into the airway, airspace cytokines, lung pathology, weight loss, symptoms, or survival but was associated with increased airspace albumin, an indicator of microvascular injury, and increased plasma pro-inflammatory cytokines. Conversely, mice treated with the EBI2/GPR183 inhibitor NIBR189 displayed a modest increase in lung viral load only at late time points, but no change in weight loss. Consistent with these findings, although Ch25h was upregulated in the lungs of SARS-CoV-2-infected WT mice, lung viral titers and weight loss in Ch25h-/- and Gpr183-/- mice infected with the beta variant were similar to control animals. Taken together, endogenous 25-hydroxycholesterols do not significantly regulate early SARS-CoV-2 replication or pathogenesis and supplemental 25HC may have pro-injury rather than therapeutic effects in SARS-CoV-2 pneumonia.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Michael B Fessler", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Jennifer Madenspacher", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Paul J Baker", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Kerry L Hilligan", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Ehydel Castro", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Julie Meacham", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Shih-Heng Chen", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Reed F Johnson", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Negin P Martin", + "author_inst": "National Institute of Environmental Health Sciences (NIEHS)" + }, + { + "author_name": "C J Tucker", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Debabrata Mahapatra", + "author_inst": "Integrated Laboratory Systems" + }, + { + "author_name": "Mark Cesta", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Katrin D Mayer-Barber", + "author_inst": "National Institute of Allergy and Infectious Diseases," + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.09.12.507647", "rel_title": "Humoral immunogenicity of a Coronavirus Disease 2019 (COVID-19) DNA Vaccine in Rhesus Macaques (Macaca mulatta) Delivered using Needle-free Jet Injection", @@ -215361,65 +216309,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.09.06.22279658", - "rel_title": "Persistence of a SARS-CoV-2 variant with a frameshifting deletion for the duration of a major outbreak", - "rel_date": "2022-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.06.22279658", - "rel_abs": "Australia experienced widespread COVID-19 outbreaks from infection with the SARS-CoV-2 Delta variant between June 2021 and February 2022. Whole-genome sequencing of virus from an early case revealed a sub-consensus level of sequencing reads supporting a 17-nucleotide frameshift-inducing deletion in ORF7a that truncated the peptide sequence. The variant rapidly became represented at the consensus level (Delta-ORF7a{Delta}17del) in most of the outbreak cases in Australia. Retrospective analysis of ORF7a deletions in all GISAID clade GK Delta genomes showed that of 4,018,216 genomes, 134,751 ([~]3.35%) possessed a deletion in ORF7a, with the ORF7a{Delta}17del mutation by far the most common. Approximately 99.05% of Delta-ORF7a{Delta}17del genomes on GISAID originated from the Australian Delta outbreak, and comprised 87% of genomes in the outbreak. In vitro comparison of lineages in cell culture showed a significantly greater proportion of cells were infected with Delta-ORF7a{Delta}17del than with a contemporaneous Delta variant without ORF7a{Delta}17del (Delta-ORF7aintact), and the proportion was also measurably higher than an early SARS-CoV-2 strain (A.2.2). These results showed that Delta-ORF7a{Delta}17del potentially has a slight growth advantage compared to Delta-ORF7aintact. Delta-ORF7a{Delta}17del viruses still produced ORF7a protein, but significantly less than A.2.2, in a different cellular distribution with a more diffuse expression throughout the cytoplasm of infected cells. These data suggest that the proliferation of Delta-ORF7a{Delta}17del genomes during the Australian Delta outbreak was likely not a result of an intrinsic benefit of the ORF7a{Delta}17del mutation, but rather a chance founder effect. Nonetheless, the abundance of different ORF7a deletions in genomes worldwide suggests these have some benefit to virus transmission.\n\nIMPORTANCEDeletions in the ORF7a region of SARS-CoV-2 have been noted since early in the COVID-19 pandemic, but are generally reported as transient mutations that are quickly lost in the population. Consequently, ORF7a deletions are considered disadvantageous to the virus through possible loss-of-function effects. In constrast to these earlier reports, we present the first report of a SARS-CoV-2 variant with an ORF7a deletion that dominated for the entirety of a protracted outbreak, and found no associated fitness disadvantage or advantage in cell culture. The relatively common rise and fall of ORF7a deletion variants over time likely represent chance founder events followed by proliferation until a more fit variant(s) is introduced to the population. Our global clade-level survey of ORF7a deletions will be a useful resource for future studies into this gene region.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Charles S.P. Foster", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Rowena Bull", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Nicodemus Tedla", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Fernando Santiago", - "author_inst": "University of New South Wales" - }, - { - "author_name": "David Agapiou", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Anurag Adhikari", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Gregory J Walker", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Lok Bahadur Shrestha", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Sebastiaan van Hal", - "author_inst": "Royal Prince Alfred Hospital" - }, - { - "author_name": "Ki Wook Kim", - "author_inst": "University of New South Wales" - }, - { - "author_name": "William D Rawlinson", - "author_inst": "Prince of Wales Hospital" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2022.09.08.22279729", "rel_title": "Image-based and machine learning-guided multiplexed serology test for SARS-CoV-2", @@ -215776,6 +216665,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.09.06.22279649", + "rel_title": "Portable Breath-Based Volatile Organic Compound Monitoring for the Detection of COVID-19: Challenges of Emerging Variants", + "rel_date": "2022-09-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.06.22279649", + "rel_abs": "ImportanceBreath analysis has been explored as a non-invasive means to detect COVID-19. However, the impact of the emerging variants such as Omicron on the exhaled breath profile and hence the accuracy of breath analysis is unknown.\n\nObjectiveTo evaluate the diagnostic accuracies of breath analysis on detecting COVID-19 patients in periods where Delta and Omicron were most prevalent.\n\nDesign, Setting, and ParticipantsA convenience cohort of patients testing positive and negative for COVID-19 using reverse transcriptase polymerase chain reaction (RT-PCR) were studied and included 167 COVID and non-COVID patients recruited between April 2021 and May 2022, which covers the period when Delta (and other variants prior to Delta) was the dominant variant (April - December 2021) and when Omicron was the dominant variant (January - May 2022). The breath from those patients were collected and analyzed for volatile organic compounds (VOCs) with a newly developed portable gas chromatography-based breath analyzer. Diagnostic patterns and algorithms were developed.\n\nResultsA total of 205 breath samples were analyzed from 167 COVID and non-COVID patients. The RT-PCR was conducted within 18 hours of the breath analysis to confirm the COVID status of the patients. Among 94 COVID positive samples, 41 samples were collected from the patients in 2021 who were assumed to be infected by the Delta variant (or other variants occurring in 2021) and 53 samples from the patients in 2022 who were assumed to be infected by the Omicron variant (BA.1 and BA.2). Breath analysis using a set of 4 VOC biomarkers was able to distinguish between COVID (Delta and other variants in 2021) and non-COVID with an overall accuracy of 94.7%. However, the accuracy dropped significantly to 82.1% when the same set of biomarkers were applied to the Omicron variant with and 21 out of 53 COVID positive being misidentified. A new set of 4 VOC biomarkers were found to distinguish the Omicron variant and non-COVID, which yielded an overall accuracy of 90.9%. Breath analysis was also found to be able to distinguish between COVID (for all the variants occurring between April 2021 and May 2022) and non-COVID with an overall accuracy of 90.2%, and between the Omicron variant and the earlier variants (Delta and other variants occurring in 2021) with an overall accuracy of 91.5%.\n\nConclusions and RelevanceBreath analysis of VOCs using point of care gas chromatography may be a promising diagnostic modality for detection of COVID and similar diseases that result in VOC production. However, similar to other diagnostic modalities such as rapid antigen testing, challenges are posed by the dynamic emergence of viral variants. The results of this study warrant additional investment and evaluation on how to overcome these challenges and to exploit breath analysis to improve the diagnosis and care of patients.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSCan volatile organic compounds (VOCs) in exhaled breath provide diagnostic information on COVID-19? Will variants such as Omicron B.1.1.529 and others affect the accuracy in breath analysis?\n\nFindingsA set of 4 VOC biomarkers were found to distinguish between Delta (and the variants occurring in 2021) from non-COVID. The Omicron variant (occurring in 2022) significantly affects VOC profiles requiring the search for a new set of VOC biomarkers to distinguish between Omicron and non-COVID.\n\nMeaninThese findings demonstrate the ability of breath analysis to distinguish between COVID and non-COVID, but also reveal the significant difference in the exhaled breath profile between COVID-19 patients during the period when Delta was most prevalent and when Omicron was most prevalent.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Ruchi Sharma", + "author_inst": "University of Michigan Ann Arbor, Department of Biomedical Engineering" + }, + { + "author_name": "Wenzhe Zang", + "author_inst": "University of Michigan Ann Arbor, Department of Biomedical Engineering" + }, + { + "author_name": "Ali Tabartehfarahani", + "author_inst": "University of Michigan Ann Arbor, Department of Biomedical Engineering" + }, + { + "author_name": "Andres Lam", + "author_inst": "University of Michigan Ann Arbor, Department of Biomedical Engineering" + }, + { + "author_name": "Xiaheng Huang", + "author_inst": "University of Michigan Ann Arbor, Department of Biomedical Engineering" + }, + { + "author_name": "Anjali D. Sivakumar", + "author_inst": "University of Michigan Ann Arbor, Department of Biomedical Engineering" + }, + { + "author_name": "Chandrakalavathi Thota", + "author_inst": "University of Michigan Ann Arbor, Department of Biomedical Engineering" + }, + { + "author_name": "Shuo Yang", + "author_inst": "University of Michigan Ann Arbor, Department of Biomedical Engineering" + }, + { + "author_name": "Robert P. Dickson", + "author_inst": "University of Michigan Ann Arbor, Department of Internal Medicine, Division of Pulmonary Critical Care Medicine" + }, + { + "author_name": "Michael W. Sjoding", + "author_inst": "University of Michigan Ann Arbor, Department of Internal Medicine, Division of Pulmonary Critical Care Medicine" + }, + { + "author_name": "Erin Bisco", + "author_inst": "University of Michigan Ann Arbor, Department of Emergency Medicine" + }, + { + "author_name": "Carmen Colmenero Mahmood", + "author_inst": "University of Michigan Ann Arbor, Department of Emergency Medicine" + }, + { + "author_name": "Kristen Machado Diaz", + "author_inst": "University of Michigan Ann Arbor, Department of Emergency Medicine" + }, + { + "author_name": "Nicholas Sautter", + "author_inst": "University of Michigan Ann Arbor" + }, + { + "author_name": "Sardar Ansari", + "author_inst": "University of Michigan Ann Arbor, Department of Emergency Medicine" + }, + { + "author_name": "Kevin R. Ward", + "author_inst": "University of Michigan Ann Arbor, Department of Emergency Medicine" + }, + { + "author_name": "Xudong Fan", + "author_inst": "University of Michigan Ann Arbor, Department of Biomedical Engineering" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.05.22279620", "rel_title": "Time trends between vaccination coverage and voting patterns before and during the COVID-19 pandemic: analysis of COVID-19 and flu surveys in the United States", @@ -217347,57 +218319,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.09.08.507221", - "rel_title": "Use of the particle agglutination/particle agglutination-inhibition test for antigenic analysis of SARS-CoV-2", - "rel_date": "2022-09-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.08.507221", - "rel_abs": "The antigenicity of SARS-CoV-2 is a critical issue for the effectiveness of the vaccine, and thus it should be phenotypically evaluated by serological assays as new field isolates emerge. The hemagglutination/hemagglutination-inhibition (HA/HI) tests are well-known as a representative method for antigenic analysis of influenza viruses, but SARS-CoV-2 is unlikely to agglutinate to human or guinea pig red blood cells. Therefore, the antigenic analysis requires complicated enzyme-linked immunosorbent assay (ELISA) or cell-based assays such as the microneutralization assay. In this study, we developed the particle agglutination/particle agglutination-inhibition (PA/PAI) test to easily and rapidly quantify the virus and antibody using human angiotensin-converting enzyme 2 (hACE2)-bound latex beads. The PA titer was positively correlated with the plaque-forming units. The PAI titer using post-infection Syrian hamster antisera clearly revealed the antigenic difference between the omicron and previous variants. The results show the PAI test is useful for easy and rapid antigenic analysis of SARS-CoV-2.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jun Kobayashi", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Shutoku Matsuyama", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Masayuki Shirakura", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Tomoko Arita", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Yasushi Suzuki", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Hideki Asanuma", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Shinji Watanabe", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Hideki Hasegawa", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Kazuya Nakamura", - "author_inst": "National Institute of Infectious Diseases" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.09.09.507257", "rel_title": "Cellular stress modulates severity of the acute respiratory distress syndrome in COVID-19", @@ -217586,6 +218507,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.09.07.506919", + "rel_title": "A clinical stage LMW-DS drug inhibits cell infection by coronaviruses and modulates reactive cytokine release from microglia", + "rel_date": "2022-09-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.07.506919", + "rel_abs": "Most coronaviruses infect animals including bats, birds and mammals, which act as hosts and reservoirs for the viruses, but the viruses can sometimes move host species and infect humans. Coronoviruses were first identified as human pathogens in the 1960s and now there are seven types known to infect humans. Whilst four of these types cause mild-to-moderate respiratory disease, the other three may cause more severe and possibly even fatal disease in vulnerable individuals particularly, with the most recent SARS-CoV-2 pandemic being associated with severe acute respiratory syndrome (SARS) in many infected people. The aim of the present study was to evaluate the potential of a unique low molecular weight dextran sulphate (LMW-DS) clinical stage drug, ILB(R), to inhibit infection of human cells by the NL63 coronavirus assessed by immunofluorescence of viral particles, and also to see if the drug directly blocked the interaction of the SARS-CoV-2 viral spike protein with the ACE2 receptor. Furthermore, we evaluated if ILB(R) could modulate the downstream consequences of viral infection including the reactive cytokine release from human microglia induced by various SARS-CoV-2 variant spike proteins. We demonstrated that ILB(R) blocked ACE2:spike protein interaction and inhibited coronaviral infection. ILB(R) also attenuated the omicron-induced release of pro-inflammatory cytokines, including TNF, from human microglia, indicating control of post-viral neuroinflammation. In conclusion, given the safety profile of ILB(R) established in a number of Phase I and Phase II clinical trials, these results highlight the potential of ILB(R) to treat patients infected with coronaviruses to both limit infectivity and attenuate the progression to severe disease. There is now an opportunity to translate these findings quickly by the clinical investigation of drug efficacy.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Ann Logan", + "author_inst": "University of Warwick" + }, + { + "author_name": "Michela Mazzon", + "author_inst": "Virology Research Services Ltd" + }, + { + "author_name": "Lars Bruce", + "author_inst": "Tikomed AB" + }, + { + "author_name": "Nicholas M Barnes", + "author_inst": "University of Birmingham" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.09.05.506640", "rel_title": "Future COVID-19 surges prediction based on SARS-CoV-2 mutations surveillance", @@ -219529,45 +220481,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.09.03.506470", - "rel_title": "Optimization and deoptimization of codons in SARS-CoV-2 and the implications for vaccine development", - "rel_date": "2022-09-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.03.506470", - "rel_abs": "The spread of Coronavirus Disease 2019 (COVID-19), caused by the SARS-CoV-2 coronavirus, has progressed into a global pandemic. To date, thousands of genetic variants have been identified across SARS-CoV-2 isolates from patients. Sequence analysis reveals that the codon usage of viral sequences decreased over time but fluctuated from time to time. In this study, through evolution modeling, we found that this phenomenon might result from the virus preference for mutations during transmission. Using dual luciferase assays, we further discovered that the deoptimization of codons on viruses might weaken protein expression during the virus evolution, indicating that the choice of codon usage might play important role in virus fitness. Finally, given the importance of codon usage in protein expression and particularly for mRNA vaccine, we designed several omicron BA.2.12.1 and BA.4/5 spike mRNA vaccine candidates based on codon optimization, and experimentally validated their high levels of expression. Our study highlights the importance of codon usage in virus evolution and mRNA vaccine development.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Xinkai Wu", - "author_inst": "Peking university" - }, - { - "author_name": "Kejia Shan", - "author_inst": "Peking University" - }, - { - "author_name": "Fuwen Zan", - "author_inst": "Chinese Academy of Medical Sciences" - }, - { - "author_name": "Xiaolu Tang", - "author_inst": "Peking University" - }, - { - "author_name": "Zhaohui Qian", - "author_inst": "Chinese Academy of Medical Sciences" - }, - { - "author_name": "Jian Lu", - "author_inst": "Peking University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2022.09.02.22279526", "rel_title": "Spatial determination of COVID-19 mortality", @@ -219828,6 +220741,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2022.09.04.22279366", + "rel_title": "Frequency and Risk Factors of Resident Burnout Before and During the COVID19 Pandemic", + "rel_date": "2022-09-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.04.22279366", + "rel_abs": "ObjectiveTo explore the prevalence and contributing factors of resident burnout in a University Hospital before and during the COVID 19 pandemic.\n\nMethodsThirty Faculty of Medicine departments were included in the survey, where 400 university hospital residents filled out the Maslach Burnout Inventory (MBI) in January 2018 and April 2020. Related scores of emotional exhaustion (EE), decreased accomplishment (DA) and depersonalization (DP) were calculated and compared between the different groups. Correlation between scores and possible contributing factors, including demographics, work-life circumstances, exposure to workplace violence, were investigated. Contributing factors were compared between the time points.\n\nResultsThe EE and DA scores were significantly higher in junior residents than in senior residents. Both scores were higher among residents who had experienced abuse or violence. The emergency medicine residents had significantly higher DP scores, while the EE scores of radiology residents were lower than others. Thirty percent of all residents smoked cigarettes. This percentage was even higher among the residents of the departments of surgery and emergency medicine (45-50%). A significant correlation was demonstrated between the scores of MBI and smoking, while analysis with other demographics did not yield any relation. According to the study results, basic science residents had significantly increased scores in all MBI subgroups during the pandemic.\n\nConclusionResident physician burnout was found to be related to the work environment, smoking cigarettes and exposure to violence at workplace.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Sevcan Turk", + "author_inst": "University of Michigan" + }, + { + "author_name": "Anil Kalyoncu", + "author_inst": "Penn State Health Milton S. Hershey Medical Center" + }, + { + "author_name": "Ozlem Surel Karabilgin Ozturkcu", + "author_inst": "Ege University Faculty of Medicine" + }, + { + "author_name": "Hayriye Elbi", + "author_inst": "Ege University Faculty of Medicine" + }, + { + "author_name": "Mehmet Orman", + "author_inst": "Ege University Faculty of Medicine" + }, + { + "author_name": "Aziz Cem Yaman", + "author_inst": "Ege University Faculty of Medicine" + }, + { + "author_name": "Muratcan Toptas", + "author_inst": "Ege University Faculty of Medicine" + }, + { + "author_name": "Yasar Caglar Bekki", + "author_inst": "Ege University Faculty of Medicine" + }, + { + "author_name": "Muratcan Ozlutas", + "author_inst": "Ege University Faculty of Medicine" + }, + { + "author_name": "Mehmet Burak Esenturk", + "author_inst": "Ege University Faculty of Medicine" + }, + { + "author_name": "Jayapalli Bapuraj", + "author_inst": "University of Michigan" + }, + { + "author_name": "Suha Sureyya Ozbek", + "author_inst": "Ege University Faculty of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "medical education" + }, { "rel_doi": "10.1101/2022.09.02.22279556", "rel_title": "A pattern shift in SARS-CoV-2 Omicron variant transmission after the city lockdown--observational study based upon daily reported addresses of infected cases", @@ -221211,33 +222187,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.31.22279430", - "rel_title": "Periodic epidemic outbursts explained by local saturation of clusters", - "rel_date": "2022-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.31.22279430", - "rel_abs": "Adding the notion of spatial locality to the susceptible-infected-recovered (or SIR) model, allows to capture local saturation of an epidemic. The resulting minimum model of an epidemic, consisting of five ordinary differential equations with constant model coefficients, reproduces slowly decaying periodic outbursts, as observed in the COVID-19 or Spanish flu epidemic. It is shown that if immunity decays, even slowly, the model yields a fully periodic dynamics.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Louis Gostiaux", - "author_inst": "Univ Lyon, Ecole Centrale de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS, Laboratoire de Mecanique des Fluides et d'Acoustique, UMR 5509, 36 Avenue " - }, - { - "author_name": "Wouter Bos", - "author_inst": "Univ Lyon, Ecole Centrale de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS, Laboratoire de Mecanique des Fluides et d'Acoustique, UMR 5509, 36 Avenue " - }, - { - "author_name": "Jean-Pierre Bertoglio", - "author_inst": "Univ Lyon, Ecole Centrale de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS, Laboratoire de Mecanique des Fluides et d'Acoustique, UMR 5509, 36 Avenue " - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.08.31.22279444", "rel_title": "Effectiveness of the COVID-19 vaccines against severe disease with Omicron sub-lineages BA.4 and BA.5 in England", @@ -221546,6 +222495,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.08.31.22279450", + "rel_title": "Risk averse reproduction numbers improve resurgence detection", + "rel_date": "2022-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.31.22279450", + "rel_abs": "The effective reproduction number R is a prominent statistic for inferring the transmissibility of infectious diseases and effectiveness of interventions. R purportedly provides an easy-to-interpret threshold for deducing whether an epidemic will grow (R>1) or decline (R<1). We posit that this interpretation can be misleading and statistically overconfident when applied to infections accumulated from groups featuring heterogeneous dynamics. These groups may be delineated by geography, infectiousness or sociodemographic factors. In these settings, R implicitly weights the dynamics of the groups by their number of circulating infections. We find that this weighting can cause delayed detection of outbreak resurgence and premature signalling of epidemic control because it underrepresents the risks from highly transmissible groups. Applying E-optimal experimental design theory, we develop a weighting algorithm to minimise these issues, yielding the risk averse reproduction number E. Using simulations, analytic approaches and real-world COVID-19 data stratified at the city and district level, we show that E meaningfully summarises transmission dynamics across groups, balancing bias from the averaging underlying R with variance from directly using local group estimates. An E>1 generates timely resurgence signals (upweighting risky groups), while an E<1 ensures local outbreaks are under control. We propose E as an alternative to R for informing policy and assessing transmissibility at large scales (e.g., state-wide or nationally), where R is commonly computed but well-mixed or homogeneity assumptions break down.\n\nAuthor SummaryHow can we meaningfully summarise the transmission dynamics of an infectious disease? This question, although fundamental to epidemiology and crucial for informing the design and implementation of interventions (e.g., quarantines), is still not resolved. Current practice is to estimate the effective reproduction number R, which counts the average number of new infections generated per past infection, at large scales (e.g., nationally). An estimated R>1 signals epidemic growth. While R is easily interpreted and computed in real time, it averages infections across diverse locations or socio-demographic groups that likely possess different transmission dynamics. We prove that this averaging in R reduces sensitivity to resurgence, making R>1 slow to reflect realistic epidemic growth. This delay can substantially misinform policymakers and impede interventions. We apply optimal design theory to derive the risk averse reproduction number E as an alternative summary of diverse transmission dynamics. Using mathematical arguments, simulations and empirical COVID-19 datasets, we show that E>1 is an improved threshold for resurgence, providing timelier signals for informing policy or interventions and better uncertainty quantification. Further, E maintains the computability and interpretability of R. We propose E as meaningful statistic at large scales, where the averaging within R likely misrepresents the diversity of transmission dynamics.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Kris V Parag", + "author_inst": "Imperial College London" + }, + { + "author_name": "Uri Obolski", + "author_inst": "Tel Aviv University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.01.22279485", "rel_title": "COVID-19 individual participant data meta-analyses. Can there be too many? Results from a rapid systematic review", @@ -222989,77 +223961,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.08.29.505777", - "rel_title": "Can SARS-CoV-2 transmit from a dead body?", - "rel_date": "2022-08-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.29.505777", - "rel_abs": "Although it has been 2.5 years since the COVID-19 pandemic began, the transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a dead infected body remains unclear, and often, in Japan bereaved family members are not allowed to view in-person a loved one who has died from COVID-19. In this study, we analyzed the possibility of SARS-CoV-2 transmission from a dead body by using the hamster model. We also analyzed the effect of Angel-care--in which the pharynx, nostril, and rectum are plugged--and embalming on reducing transmissibility from dead bodies. We found that SARS-CoV-2 could be transmitted from the body of animals that died within a few days of infection; however, Angel-care and embalming were effective in preventing transmission from the dead body. These results suggest that protection from infection is essential when in contact with a SARS-CoV-2-infected dead body, and that sealing the cavities of a dead body is an important infection control step if embalming is not done.\n\nImportanceWe found that SARS-CoV-2 could be transmitted from a dead body presumably via postmortem gases. However, we also found that postmortem care, such as plugging the pharynx, nostrils, and rectum, or embalming could prevent transmission from the dead body. These results indicate that protection from infection is essential when handling infected corpses, and that appropriate care of SARS-CoV-2-infected corpses is important.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Kiyoko Iwatsuki-Horimoto", - "author_inst": "Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Hiroshi Ueki", - "author_inst": "The University of Tokyo Institute of Medical Science" - }, - { - "author_name": "Mutsumi Ito", - "author_inst": "Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Sayaka Nagasawa", - "author_inst": "Graduate School of Medicine, Chiba University" - }, - { - "author_name": "Yuichiro Hirata", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Kenichiro Hashizume", - "author_inst": "GSI Co., LTD" - }, - { - "author_name": "Kazuho Ushiwata", - "author_inst": "GSI Co., LTD" - }, - { - "author_name": "Hirotaro Iwase", - "author_inst": "Graduate School of Medicine, Chiba University" - }, - { - "author_name": "Yohsuke Makino", - "author_inst": "Graduate School of Medicine, University of Tokyo" - }, - { - "author_name": "Tetsuo Ushiku", - "author_inst": "Yokohama City University Hospital" - }, - { - "author_name": "Shinji Akitomi", - "author_inst": "Japan Medical Association Research Institute" - }, - { - "author_name": "Masaki Imai", - "author_inst": "The University of Tokyo Institute of Medical Science" - }, - { - "author_name": "Hisako Saitoh", - "author_inst": "Graduate School of Medicine, Chiba University" - }, - { - "author_name": "Yoshihiro Kawaoka", - "author_inst": "University of Wisconsin System" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.08.29.22279161", "rel_title": "Organizational impact of an ID NOW COVID-19 point-of-care testing for SARS-CoV2 detection in a maternity ward", @@ -223252,6 +224153,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.08.30.505897", + "rel_title": "BindingSiteAugmentedDTA: Enabling A Next-Generation Pipeline for Interpretable Prediction Models in Drug-Repurposing", + "rel_date": "2022-08-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.30.505897", + "rel_abs": "While research into Drug-Target Interaction (DTI) prediction is fairly mature, generalizability and interpretability are not always addressed in the existing works in this field. In this paper, we propose a deep learning-based framework, called BindingSite-AugmentedDTA, which improves Drug-Target Affinity (DTA) predictions by reducing the search space of potential binding sites of the protein, thus making the binding affinity prediction more efficient and accurate. Our BindingSite-AugmentedDTA is highly generalizable as it can be integrated with any DL-based regression model, while it significantly improves their prediction performance. Also, unlike many existing models, our model is highly interpretable due to its architecture and self-attention mechanism, which can provide a deeper understanding of its underlying prediction mechanism by mapping attention weights back to protein binding sites. The computational results confirm that our framework can enhance the prediction performance of seven state-of-the-art DTA prediction algorithms in terms of 4 widely used evaluation metrics, including Concordance Index (CI), Mean Squared Error (MSE), modified squared correlation coefficient [Formula], and the Area Under the Precision Curve (AUPC). We also contribute to the two most commonly used DTA benchmark datasets, namely Kiba and Davis, by including additional information on 3D structure of all proteins contained in these two datasets. We manually extracted this information from Protein Data Bank (PDB) files of proteins available at https://www.uniprot.org/. Furthermore, we experimentally validate the practical potential of our proposed framework through in-lab experiments. We measure the binding interaction between several drug candidate compounds for the inhibition of binding between (SARS-CoV-2 S-protein RBD) Spike and ACE-2 (host cell binding target) proteins. We then compare the computationally-predicted results against the ones experimentally-observed in the laboratory. The relatively high agreement between computationally-predicted and experimentally-observed binding interactions supports the potential of our framework as the next-generation pipeline for prediction models in drug repurposing.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Niloofar Yousefi", + "author_inst": "University of Central Florida" + }, + { + "author_name": "Mehdi Yazdani-Jahromi", + "author_inst": "University of Central Florida" + }, + { + "author_name": "Aida Tayebi", + "author_inst": "University of Central Florida" + }, + { + "author_name": "Elayaraja Kolanthai", + "author_inst": "University of Central Florida" + }, + { + "author_name": "Craig J. Neal", + "author_inst": "University of Central Florida" + }, + { + "author_name": "Tanumoy Banerjee", + "author_inst": "Lehigh University" + }, + { + "author_name": "Agnivo Gosai", + "author_inst": "Independent Researcher" + }, + { + "author_name": "Ganesh Balasubramanian", + "author_inst": "Lehigh University" + }, + { + "author_name": "Sudipta Seal", + "author_inst": "University of Central Florida" + }, + { + "author_name": "Ozlem Ozmen Garibay", + "author_inst": "University of Central Florida" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.08.28.22279258", "rel_title": "GHSI COVID-19 puzzle: did highly developed countries indeed fare worse?", @@ -224931,49 +225887,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.08.23.22279123", - "rel_title": "The Role of Modelling and Analytics in South African COVID-19 Planning and Budgeting", - "rel_date": "2022-08-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.23.22279123", - "rel_abs": "BackgroundThe South African COVID-19 Modelling Consortium (SACMC) was established in late March 2020 to support planning and budgeting for COVID-19 related healthcare in South Africa. We developed several tools in response to the needs of decision makers in the different stages of the epidemic, allowing the South African government to plan several months ahead of time.\n\nMethodsOur tools included epidemic projection models, several cost and budget impact models, and online dashboards to help government and the public visualise our projections, track case development and forecast hospital admissions. Information on new variants, including Delta and Omicron, were incorporated in real time to allow the shifting of scarce resources when necessary.\n\nResultsGiven the rapidly changing nature of the outbreak globally and in South Africa, the model projections were updated regularly. The updates reflected 1) the changing policy priorities over the course of the epidemic; 2) the availability of new data from South African data systems; and 3) the evolving response to COVID-19 in South Africa such as changes in lockdown levels and ensuing mobility and contact rates, testing and contact tracing strategies, and hospitalisation criteria. Insights into population behaviour required updates by incorporating notions of behavioural heterogeneity and behavioural responses to observed changes in mortality. We incorporated these aspects into developing scenarios for the third wave and developed additional methodology that allowed us to forecast required inpatient capacity. Finally, real-time analyses of the most important characteristics of the Omicron variant first identified in South Africa in November 2021 allowed us to advise policymakers early in the fourth wave that a relatively lower admission rate was likely.\n\nConclusionThe SACMCs models, developed rapidly in an emergency setting and regularly updated with local data, supported national and provincial government to plan several months ahead of time, expand hospital capacity when needed, allocate budgets, and procure additional resources where possible. Across four waves of COVID-19 cases, the SACMC continued to serve the planning needs of the government, tracking waves and supporting the national vaccine rollout.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Gesine Meyer-Rath", - "author_inst": "Boston University School of Public Health" - }, - { - "author_name": "Rachel Hounsell", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Juliet Pulliam", - "author_inst": "University of Stellenbosch: Stellenbosch University" - }, - { - "author_name": "Lise Jamieson", - "author_inst": "University of the Witwatersrand Johannesburg" - }, - { - "author_name": "Brooke Nichols", - "author_inst": "Boston University School of Public Health" - }, - { - "author_name": "Harry Moultrie", - "author_inst": "NHLS: National Health Laboratory Service" - }, - { - "author_name": "Sheetal Prakash Silal", - "author_inst": "University of Cape Town" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.24.22279159", "rel_title": "Dynamics of anti-S IgG antibodies titers after the second dose of COVID 19 mRNA and non-mRNA vaccines in the manual and craft worker population of Qatar", @@ -225294,6 +226207,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.23.22278585", + "rel_title": "Nirmatrelvir/ritonavir and molnuipiravir in the treatment of mild/moderate COVID-19: results of a real-life study", + "rel_date": "2022-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.23.22278585", + "rel_abs": "Molnupiravir and Nirmatrelvir are the first available oral antivirals (OA) active against SARS-CoV-2. However, the trials evaluating the efficacy of OAs involved patients unvaccinated and infected with variants different from those currently circulating. The purpose of this study is to provide real-life data on the efficacy and safety of OAs during the omicron surge of COVID-19 pandemic in a cohort of mostly vaccinated patients.\n\nWe conducted a retrospective study on patients with confirmed SARS-CoV-2 infection treated with OAs during the omicron surge in Italy.\n\nWe enrolled 257 patients. Of these, 146 (56.8%) were treated with molnupiravir and 111 (43.2%) with nirmatrelvir/ritonavir. Patients in molnupiravir group were older, had a lower body mass index, and a higher rate of chronic heart disease than those treated with nirmatrelvir/ritonavir.\n\nDuring the 14-day follow-up, four hospitalizations were recorded (1.6%), three in molnupiravir (2.1%) and 1 in nirmatrelvir/ritonavir (0.9%) group. Only one patient (who had received molnupiravir) died. Median time-to-negativity of nasal swab was 8 days (8 days in nirmatrelvir/ritonavir vs. 10 days in molnupiravir group, p<0.01).\n\nGlobally, we recorded 37 adverse drug reactions (mainly dysgeusia, diarrhea, and nausea) in 31 of 257 individuals (12.1%). Only two patients (0.8%), both receiving molnupiravir, terminated treatment due to the development of adverse drug reactions.\n\nIn conclusion, during the omicron surge, in a population of mostly vaccinated patients treated with molnupiravir or nirmatrelvir/ritonavir, we observed a low rate of hospitalization, death, and adverse drug reactions. These rates were even lower than those reported in pivotal trials.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Ivan Gentile", + "author_inst": "Department of Clinical medicine and Surgery; University of Naples Federico II; Naples Italy" + }, + { + "author_name": "Riccardo Scotto", + "author_inst": "Department of Clinical medicine and Surgery; University of Naples Federico II; Naples Italy" + }, + { + "author_name": "Nicola Schiano Moriello", + "author_inst": "Department of Clinical medicine and Surgery; University of Naples Federico II; Naples Italy" + }, + { + "author_name": "Biagio Pinchera", + "author_inst": "Department of Clinical medicine and Surgery; University of Naples Federico II; Naples Italy" + }, + { + "author_name": "Riccardo Villari", + "author_inst": "Department of Clinical medicine and Surgery; University of Naples Federico II; Naples Italy" + }, + { + "author_name": "Emilia Trucillo", + "author_inst": "Department of Clinical medicine and Surgery; University of Naples Federico II; Naples Italy" + }, + { + "author_name": "Luigi Ametrano", + "author_inst": "Department of Clinical medicine and Surgery; University of Naples Federico II; Naples Italy" + }, + { + "author_name": "Ludovica Fusco", + "author_inst": "Department of Clinical medicine and Surgery; University of Naples Federico II; Naples Italy" + }, + { + "author_name": "Giuseppe Castaldo", + "author_inst": "Department of Molecular Medicine and Medical Biotechnologies University of Naples Federico II, Naples Italy; CEINGE Advanced Biotechnologies, Naples Italy" + }, + { + "author_name": "Antonio Riccardo Buonomo", + "author_inst": "Department of Clinical medicine and Surgery; University of Naples Federico II; Naples Italy" + }, + { + "author_name": "- Federico II COVID Team", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.25.22279202", "rel_title": "T cell responses to SARS-CoV-2 vaccination in people with multiple sclerosis differ between disease-modifying therapies", @@ -226653,185 +227625,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.22.22279080", - "rel_title": "Humoral and cellular response induced by a second booster of an inactivated SARS-CoV-2 vaccine in adults", - "rel_date": "2022-08-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.22.22279080", - "rel_abs": "The SARS-CoV-2 Omicron variant has challenged the control of the COVID-19 pandemic even in highly vaccinated countries. While a second booster of mRNA vaccines improved the immunity against SARS-CoV-2, the humoral and cellular responses induced by a second booster of an inactivated SARS-CoV-2 vaccine have not been studied. In the context of a phase 3 clinical study, we report that a second booster of CoronaVac(R) increased the neutralizing response against the ancestral virus yet showed poor neutralization against the Omicron variant. Additionally, isolated PBMCs displayed equivalent activation of specific CD4+ T cells and IFN-{gamma} production when stimulated with a mega-pool of peptides derived from the spike protein of the ancestral virus or the Omicron variant. In conclusion, a second booster dose of CoronaVac(R) does not improve the neutralizing response against the Omicron variant compared with the first booster dose, yet it helps maintaining a robust spike-specific CD4+ T cell response.", - "rel_num_authors": 41, - "rel_authors": [ - { - "author_name": "Felipe Melo-Gonzalez", - "author_inst": "Universidad Andres Bello, Santiago, Chile/Pontificia Universidad Catolica de Chile." - }, - { - "author_name": "Constanza Mendez", - "author_inst": "Pontificia Universidad Catolica de Chile." - }, - { - "author_name": "Hernan F Penaloza", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Barbara M Schultz", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Alejandro Pina-Iturbe", - "author_inst": "Pontificia Universidad Catolica Chile" - }, - { - "author_name": "Mariana Rios", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Daniela Moreno-Tapia", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Patricia Pereira-Sanchez", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Diane Leighton", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Claudia Orellana", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Consuelo Covarrubias", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Nicolas MS Galvez", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Jorge A Soto", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "LUISA F DUARTE", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Daniela Rivera-Perez", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Yaneisi Vazquez", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Alex Cabrera", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Sergio Bustos", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Carolina Iturriaga", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Marcela Urzua", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Maria S Navarrete", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Alvaro Rojas", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Rodrigo Fasce", - "author_inst": "Instituto de Salud Publica de Chile" - }, - { - "author_name": "Jorge Fernandez", - "author_inst": "Instituto de Salud Publica de Chile" - }, - { - "author_name": "Judith Mora", - "author_inst": "Instituto de Salud Publica de Chile" - }, - { - "author_name": "Eugenio Ramirez", - "author_inst": "Instituto de Salud Publica de Chile" - }, - { - "author_name": "Aracelly Gaete-Argel", - "author_inst": "Universidad de Chile" - }, - { - "author_name": "Monica Acevedo", - "author_inst": "Universidad de Chile" - }, - { - "author_name": "Fernando Valiente-Echeverria", - "author_inst": "Universidad de Chile" - }, - { - "author_name": "Ricardo Soto-Rifo", - "author_inst": "Universidad de Chile" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute For Allergy & Immunology" - }, - { - "author_name": "Alba Grifoni", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "La Jolla Institute for Allergy & Immunology" - }, - { - "author_name": "Gang Zeng", - "author_inst": "Sinovac Biotech" - }, - { - "author_name": "Weining Meng", - "author_inst": "Sinovac Biotech" - }, - { - "author_name": "- CoronaVac03CL Study Group", - "author_inst": "-" - }, - { - "author_name": "Jose V Gonzalez-Aramundiz", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Pablo A Gonzalez", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Katia Abarca", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Susan M Bueno", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Alexis M Kalergis", - "author_inst": "Pontificia Universidad Catolica de Chile" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.22.22279079", "rel_title": "Assessing Vulnerability to COVID-19 in High-Risk Populations: The Role of SARS-CoV-2 Spike-Targeted Serology", @@ -227108,6 +227901,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.08.22.22278955", + "rel_title": "Rates of COVID-19-Associated Hospitalization in Immunocompromised Individuals in Omicron-era: A Population-Based Observational Study Using Surveillance Data in British Columbia, Canada", + "rel_date": "2022-08-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.22.22278955", + "rel_abs": "BackgroundPeople with immune dysfunction have a higher risk for severe COVID-19 outcomes. Omicron variant is associated with a lower rate of hospitalization but higher vaccine escape. This population-based study quantifies COVID-19 hospitalization rate in the Omicron-dominant era among vaccinated people with immune dysfunction, identified as clinically extremely vulnerable (CEV) population before COVID-19 treatment was widely offered.\n\nMethodsAll COVID-19 cases were reported to the British Columbia Centre for Disease Control (BCCDC) between January 7, 2022 and March 14, 2022. Case and population hospitalization rates were estimated across CEV status, age groups and vaccination status. Cumulative rates of hospitalizations for the study period were also compared between CEV and non-CEV individuals matched by sex, age group, region, and vaccination characteristics.\n\nFindingsA total of 5,591 COVID-19 reported cases and 1,153 hospitalizations among CEV individuals were included. A third vaccine dose with mRNA vaccine offered additional protection against severe illness in CEV individuals. Vaccinated CEV population still had a significantly higher breakthrough hospitalization rate compared with non-CEV individuals.\n\nInterpretationCEV population remains a higher risk group and may benefit from additional booster doses and pharmacotherapy.\n\nFundingBC Centre for Disease Control and Provincial Health Services Authority", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Taraneh Bahremand", + "author_inst": "British Columbia Centre for Disease Control (BCCDC), Vancouver, Canada" + }, + { + "author_name": "Jiayun Angela Yao", + "author_inst": "British Columbia Centre for Disease Control (BCCDC), Vancouver, Canada" + }, + { + "author_name": "Christopher Mill", + "author_inst": "British Columbia Centre for Disease Control (BCCDC), Vancouver, Canada" + }, + { + "author_name": "Jolanta Piszczek", + "author_inst": "Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada" + }, + { + "author_name": "Jennifer M. Grant", + "author_inst": "Division of Infectious Diseases and Medical Microbiology, Vancouver Coastal Health, Vancouver, Canada; Department of Pathology and Laboratory Medicine, Universi" + }, + { + "author_name": "Kate Smolina", + "author_inst": "British Columbia Centre for Disease Control (BCCDC), Vancouver, Canada; School of Population and Public Health, University of British Columbia, Vancouver, Canad" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.08.22.22279097", "rel_title": "\"All of the things to everyone everywhere\": A mixed methods analysis of community perspectives on equitable access to monoclonal antibody treatment for COVID-19", @@ -228527,93 +229359,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2022.08.21.22279029", - "rel_title": "Humoral and cellular immune correlates of protection against COVID-19 in kidney transplant recipients", - "rel_date": "2022-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.21.22279029", - "rel_abs": "As solid organ recipients are at high risk of severe COVID-19 and respond poorly to primary SARS-CoV-2 mRNA vaccination, they have been prioritized for booster vaccination. However, an immunological correlate of protection has not been identified in this vulnerable population. We conducted a prospective monocentric cohort study of 65 kidney transplant recipients who received three doses of SARS-CoV-2 BNT162b2 mRNA vaccination. Associations between symptomatic breakthrough infection (BTI) and vaccine responses, patient demographic and clinical characteristics were explored. Symptomatic COVID-19 was diagnosed in 32% of kidney transplant recipients during a period of six months after the administration of the third vaccine dose. During this period, SARS-CoV-2 delta and omicron were the dominant variants in the general population. Univariate analyzes identified avidity of SARS-CoV-2 receptor binding domain (RBD) binding IgG, neutralizing antibodies and SARS-CoV-2 S2 domain-specific IFN-{gamma} responses as correlates of protection against BTI. Some demographic and clinical parameters correlated with vaccine responses, but none correlated with the risk of BTI. In multivariate analysis, the risk of BTI was best predicted by neutralizing antibody and S2-specific IFN-{gamma} responses, adjusting for age, graft function and mycophenolate mofetil use. In conclusion, both antibody and T cell responses predict the risk of BTI in kidney transplant recipients who received three doses of SARS-CoV-2 mRNA vaccine. T cell responses may help compensate for the suboptimal antibody response to vaccination in this vulnerable population.\n\nOne Sentence SummaryAntibody and T cell responses to booster SARS-CoV-2 vaccination predict the risk of symptomatic breakthrough infection in kidney transplant recipients", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Delphine KEMLIN", - "author_inst": "Hopital Erasme, ULB, Bruxelles" - }, - { - "author_name": "Nicolas Gemander", - "author_inst": "Institute for Medical Immunology and ULB Centre for Research in Immunology (U-CRI), Universite Libre de Bruxelles (ULB), Gosselies, Belgium" - }, - { - "author_name": "Stephanie Depickere", - "author_inst": "Scientific Direction Infectious Diseases in Humans, Sciensano, Brussels, Belgium" - }, - { - "author_name": "Veronique Olislagers", - "author_inst": "Institute for Medical Immunology and ULB Centre for Research in Immunology (U-CRI), Universite Libre de Bruxelles (ULB), Gosselies, Belgium" - }, - { - "author_name": "Daphnee Georges", - "author_inst": "Institute for Medical Immunology and ULB Centre for Research in Immunology (U-CRI), Universite Libre de Bruxelles (ULB), Gosselies, Belgium" - }, - { - "author_name": "Alexandra Waegemans", - "author_inst": "Institute for Medical Immunology and ULB Centre for Research in Immunology (U-CRI), Universite Libre de Bruxelles (ULB), Gosselies, Belgium" - }, - { - "author_name": "Pieter Pannus", - "author_inst": "Scientific Direction Infectious Diseases in Humans, Sciensano, Brussels, Belgium" - }, - { - "author_name": "Anne Lemy", - "author_inst": "Department of Nephrology, Hopital Marie Curie, Charleroi, Belgium" - }, - { - "author_name": "Maria E Goossens", - "author_inst": "Scientific Direction Infectious Diseases in Humans, Sciensano, Brussels, Belgium" - }, - { - "author_name": "Isabelle Desombere", - "author_inst": "Scientific Direction Infectious Diseases in Humans, Sciensano, Brussels, Belgium" - }, - { - "author_name": "Johan Michiels", - "author_inst": "Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium" - }, - { - "author_name": "Marylene Vandevenne", - "author_inst": "Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liege, Liege, Belgium" - }, - { - "author_name": "Leo Heyndrickx", - "author_inst": "Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium" - }, - { - "author_name": "Kevin K Arien", - "author_inst": "Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium" - }, - { - "author_name": "Andre Matagne", - "author_inst": "Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liege, Liege, Belgium" - }, - { - "author_name": "Margaret E Ackerman", - "author_inst": "Thayer School of Engineering, Dartmouth College, Hanover, NH, USA" - }, - { - "author_name": "Alain Le Moine", - "author_inst": "Department of Nephrology, Dialysis and Transplantation, Erasme Hospital, Universite Libre de Bruxelles (ULB), Bruxelles, Belgium" - }, - { - "author_name": "Arnaud Marchant", - "author_inst": "Institute for Medical Immunology and ULB Centre for Research in Immunology (U-CRI), Universite Libre de Bruxelles (ULB), Gosselies, Belgium" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "transplantation" - }, { "rel_doi": "10.1101/2022.08.20.22279023", "rel_title": "Brain microstructural changes and fatigue after COVID-19", @@ -228794,6 +229539,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.19.22278987", + "rel_title": "Protection against symptomatic disease with the delta and omicron BA.1/BA.2 variants of SARS-CoV-2 after infection and vaccination in adolescents: national observational test-negative case control study, August 2021 to March 2022, England", + "rel_date": "2022-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.19.22278987", + "rel_abs": "BackgroundLittle is known about the protection following prior infection with different SARS-CoV-2 variants, COVID-19 vaccination, and a combination of the two (hybrid immunity) in adolescents.\n\nMethodsWe used national SARS-CoV-2 testing and COVID-19 mRNA vaccination data in England to estimate protection following previous infection and vaccination against symptomatic PCR-confirmed delta and omicron BA.1/BA.2 variants in 11-17-year-olds using a test-negative case-control design.\n\nFindingsBy 31 March 2022, 63.6% of 16-17-year-olds and 48.2% of 12-15-year-olds had received [≥]1 COVID-19 mRNA vaccine dose.Between 08 August 2021 and 31 March 2022, 1,161,704 SARS-CoV-2 PCR-tests were successfully linked to COVID-19 vaccination status. In unvaccinated adolescents, prior infection with wildtype, alpha or delta provided greater protection against subsequent delta infection than subsequent omicron; prior omicron infection provided had the highest protection against omicron reinfection (59.3%; 95%CI: 46.7-69.0). In infection-naive adolescents, vaccination provided lower protection against symptomatic omicron infection than delta, peaking at 64.5% (95%CI; 63.6-65.4) 2-14 days after dose two and 62.9% (95%CI; 60.5-65.1) 2-14 weeks after dose three, with rapidly waning protection after each dose. Previously infected and vaccinated adolescents had the highest protection, irrespective of primary infecting SARS-CoV-2 strain. The highest protection against omicron was observed in vaccinated adolescents with prior omicron infection, reaching 96.4% (95%CI, 84.4-99.1) at 15-24 weeks post dose two.\n\nInterpretationAll variants provide some protection against symptomatic reinfection and vaccination adds to protection. Vaccination provides low-to-moderate protection against symptomatic omicron infection, with waning protection after each dose, while hybrid immunity provides the most robust protection.\n\nFundingNone\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe have previously reported COVID-19 vaccine effectiveness in previously uninfected adolescents. There are, however, limited data on the protection offered by natural infection with different SARS-CoV-2 variants, and the added value of vaccination in previously-infected adolescents. Most studies have focused on adults and show significant protection from previous infection against re-infection with pre-omicron variants, but lower protection against omicron variants, with hybrid immunity providing the most robust protection.\n\nAdded value of this studyUsing national SARS-CoV-2 testing and COVID-19 mRNA vaccination data in England, we were able to estimate protection afforded by previous infection, vaccination, and a combination of the two using a test-negative case-control design against PCR-confirmed symptomatic COVID-19. We found that protection against symptomatic infection with the delta variant was greater than protection against symptomatic omicron infection in those previously infected with wild-type, alpha or delta variants. Similar trends were observed in previously uninfected but vaccinated individuals. Prior omicron infection along with vaccination provided the greatest protection against further omicron variant infections.\n\nImplications of all the available evidenceAll variants provide some protection against future SARS-CoV-2 infection, as does COVID-19 mRNA vaccination. Our findings demonstrate, for the first time in adolescents, the additional protection afforded by hybrid immunity. In the context of the UKs recent waves of omicron infections, our findings provide important evidence of only modest short-term protection against mild disease with omicron variants following vaccination. This has important implications for the consideration of future adolescent COVID-19 vaccination and booster programmes.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Annabel A Powell", + "author_inst": "UKHSA" + }, + { + "author_name": "Freja Kirsebom", + "author_inst": "UKHSA" + }, + { + "author_name": "Julia Stowe", + "author_inst": "UKHSA" + }, + { + "author_name": "Jamie Lopez-Bernal", + "author_inst": "UKHSA" + }, + { + "author_name": "Mary Ramsay", + "author_inst": "UKHSA" + }, + { + "author_name": "Nick Andrews", + "author_inst": "UKHSA" + }, + { + "author_name": "Shamez N Ladhani", + "author_inst": "UKHSA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.08.19.22277959", "rel_title": "Pharmacokinetics of nirmatrelvir and ritonavir in COVID-19 patients with end stage renal disease on intermittent haemodialysis", @@ -230233,117 +231021,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.17.22278913", - "rel_title": "Field assessment of BinaxNOW antigen tests as COVID-19 treatment entry point at a community testing site in San Francisco during evolving omicron surges", - "rel_date": "2022-08-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.17.22278913", - "rel_abs": "BackgroundCOVID-19 oral treatments require initiation within 5 days of symptom onset. Although antigen tests are less sensitive than RT-PCR, rapid results could facilitate entry to treatment. As SARS-CoV-2 variants and host immunity evolve, it is important to characterize the use case for rapid antigen tests for treatment entry.\n\nMethodsWe collected anterior nasal swabs for BinaxNOW and RT-PCR testing and clinical data at a walk-up, community site in San Francisco, California between January and June 2022. SARS-CoV-2 genomic sequences were generated from positive samples and classified according to subtype and variant. Monte Carlo simulations were conducted to estimate the expected proportion of SARS-CoV-2 infected persons who would have been diagnosed within 5 days of symptom onset using RT-PCR versus BinaxNOW testing.\n\nResultsAmong 25,309 persons tested with BinaxNOW, 2,952 had concomitant RT-PCR. 1321/2952 (44.7%) were SARS-CoV-2 RT-PCR positive. We identified waves of predominant omicron BA.1, BA.2, BA.2.12, BA.4, and BA.5 among 720 sequenced samples. Among 1,321 RT-PCR positive samples, 938/1321 (71%) were detected by BinaxNOW; 95% (774/817) of those with Ct value <30 were detected by BinaxNOW. BinaxNOW detection was consistent over lineages. In analyses to evaluate entry to treatment, BinaxNOW detected 82.7% (410/496, 95% CI: 79-86%) of persons with COVID-19 within 5 days of symptom onset. In comparison, RT-PCR (24-hour turnaround) detected 83.1% (412/496 95% CI: 79-86%) and RT-PCR (48-hour turnaround) detected 66.3% (329/496 95% CI: 62-70%) of persons with COVID-19 within 5 days of symptom onset.\n\nConclusionsBinaxNOW detected high viral load from anterior nasal swabs consistently across omicron sublineages emerging between January and June of 2022. Simulations support BinaxNOW as an entry point for COVID-19 treatment in a community field setting.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "John Schrom", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Carina Marquez", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Chung-Yu Wang", - "author_inst": "CZ Biohub" - }, - { - "author_name": "Aditi Saxena", - "author_inst": "CZ Biohub" - }, - { - "author_name": "Anthea Mitchell", - "author_inst": "CZ Biohub" - }, - { - "author_name": "Salustiano Ribeiro", - "author_inst": "Unidos en Salud" - }, - { - "author_name": "Genay Pilarowski", - "author_inst": "CZ Biohub" - }, - { - "author_name": "Robert Nakamura", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Susana Rojas", - "author_inst": "Unidos en Salud" - }, - { - "author_name": "Douglas Black", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Maria Contreras Oseguera", - "author_inst": "Unidos en Salud" - }, - { - "author_name": "Edgar Castellanos Diaz", - "author_inst": "Unidos en Salud" - }, - { - "author_name": "Joselin Payan", - "author_inst": "Unidos en Salud" - }, - { - "author_name": "Susy Rojas", - "author_inst": "Unidos en Salud" - }, - { - "author_name": "Diane Jones", - "author_inst": "Unidos en Salud" - }, - { - "author_name": "Valerie Tulier-Laiwa", - "author_inst": "Unidos en Salud and Latino Task Force" - }, - { - "author_name": "Aleks Zavaleta", - "author_inst": "Unidos en Salud and Latino Task Force" - }, - { - "author_name": "Jacqueline Martinez", - "author_inst": "Unidos en Salud" - }, - { - "author_name": "Gabriel Chamie", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Carol Glaser", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Kathy Jacobson", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Maya Petersen", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Joseph DeRisi", - "author_inst": "CZ Biohub" - }, - { - "author_name": "Diane Havlir", - "author_inst": "University of California, San Francisco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.17.22278893", "rel_title": "Uptake of Sotrovimab for prevention of severe COVID-19 and its safety in the community in England", @@ -230548,6 +231225,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.08.12.22278203", + "rel_title": "Trends in risk factors and symptoms associated with SARS-CoV-2 and Rhinovirus test positivity in King County, Washington: A Test-Negative Design Study of the Greater Seattle Coronavirus Assessment Network", + "rel_date": "2022-08-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.12.22278203", + "rel_abs": "ImportanceFew US studies have reexamined risk factors for SARS-CoV-2 positivity in the context of widespread vaccination and new variants or considered risk factors for co-circulating endemic viruses, such as rhinovirus.\n\nObjectiveTo understand how risk factors and symptoms associated with SARS-CoV-2 test positivity changed over the course of the pandemic and to compare these to the factors associated with rhinovirus test positivity.\n\nDesignThis test-negative design study used multivariable logistic regression to assess associations between SARS-CoV-2 and rhinovirus test positivity and self-reported demographic and symptom variables over a 22-month period.\n\nSettingKing County, Washington, June 2020-April 2022\n\nParticipants23,278 symptomatic individuals of all ages enrolled in a cross-sectional community surveillance study.\n\nExposuresSelf-reported data for 15 demographic and health behavior variables and 16 symptoms.\n\nMain Outcome(s) and Measure(s)RT-PCR confirmed SARS-CoV-2 or rhinovirus infection.\n\nResultsClose contact with a SARS-CoV-2 case (adjusted odds ratio, aOR 4.3, 95% CI 3.7-5.0) and loss of smell/taste (aOR 3.7, 95% CI 3.0-4.5) were the variables most associated with SARS-CoV-2 test positivity, but both attenuated during the Omicron period. Contact with a vaccinated case (aOR 2.4, 95% CI 1.7-3.3) was associated with a lower odds of test positivity than contact with an unvaccinated case (aOR 4.4, 95% CI 2.7-7.3). Sore throat was associated with Omicron infection (aOR 2.3, 95% CI 1.6-3.2) but not Delta. Vaccine effectiveness for participants fully vaccinated with a booster dose was 43% (95% CI 11-63%) for Omicron and 92% (95% CI 61-100%) for Delta.\n\nVariables associated with rhinovirus test positivity included age <12 years (aOR 4.0, 95% CI 3.5-4.6) and reporting a runny or stuffy nose (aOR 4.6, 95% CI 4.1-5.2). Race, region, and household crowding were significantly associated with both SARS-CoV-2 and rhinovirus test positivity.\n\nConclusions and RelevanceEstimated risk factors and symptoms associated with SARS-CoV-2 infection have changed over time. There was a shift in reported symptoms between the Delta and Omicron variants as well as reductions in the protection provided by vaccines. Racial and socioeconomic disparities persisted in the third year of SARS-CoV-2 circulation and were also present in rhinovirus infection, although the causal pathways remain unclear. Trends in testing behavior and availability may influence these results.\n\nKey Points\n\nQuestionWhat are the characteristics associated with SARS-CoV-2 and rhinovirus infection?\n\nFindingsIn this test-negative design study of 23,278 participants, reporting close contact with a SARS-CoV-2 case was the strongest risk factor associated with test positivity. Loss of smell and taste was associated with the Delta variant, but not the Omicron variant. Vaccination and prior infection provided greater protection against Delta infection than Omicron Infection. Young age was the strongest predictor of rhinovirus positivity. Sociodemographic disparities were present for both SARS-CoV-2 and rhinovirus.\n\nMeaningMonitoring factors associated with respiratory pathogen test positivity remains important to identify at-risk populations in the post-SARS-CoV-2 pandemic period.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Chelsea L Hansen", + "author_inst": "Fogarty International Center, National Institutes of Health, Bethesda, MD; Brotman Baty Institute, University of Washington, Seattle, WA" + }, + { + "author_name": "Amanda Perofsky", + "author_inst": "Fogarty International Center, National Institutes of Health, Bethesda, MD; Brotman Baty Institute, University of Washington, Seattle, WA" + }, + { + "author_name": "Roy Burstein", + "author_inst": "Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA" + }, + { + "author_name": "Michael Famulare", + "author_inst": "Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA" + }, + { + "author_name": "Shanda Boyle", + "author_inst": "Brotman Baty Institute, University of Washington, Seattle, WA" + }, + { + "author_name": "Robin Prentice", + "author_inst": "Brotman Baty Institute, University of Washington, Seattle, WA" + }, + { + "author_name": "Cooper Marshall", + "author_inst": "Brotman Baty Institute, University of Washington, Seattle, WA" + }, + { + "author_name": "Benjamin JJ McCormick", + "author_inst": "Fogarty International Center, National Institutes of Health, Bethesda, MD" + }, + { + "author_name": "David Reinhart", + "author_inst": "Brotman Baty Institute, University of Washington, Seattle, WA" + }, + { + "author_name": "Ben Capodanno", + "author_inst": "Brotman Baty Institute, University of Washington, Seattle, WA" + }, + { + "author_name": "Melissa Truong", + "author_inst": "Brotman Baty Institute, University of Washington, Seattle, WA" + }, + { + "author_name": "Kristen Schwabe-Fry", + "author_inst": "Brotman Baty Institute, University of Washington, Seattle, WA" + }, + { + "author_name": "Kayla Kuchta", + "author_inst": "Brotman Baty Institute, University of Washington, Seattle, WA" + }, + { + "author_name": "Brian Pfau", + "author_inst": "Brotman Baty Institute, University of Washington, Seattle, WA" + }, + { + "author_name": "Zack Acker", + "author_inst": "Brotman Baty Institute, University of Washington, Seattle, WA" + }, + { + "author_name": "Jover Lee", + "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA" + }, + { + "author_name": "Thomas R Sibley", + "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA" + }, + { + "author_name": "Evan McDermot", + "author_inst": "Brotman Baty Institute, University of Washington, Seattle, WA" + }, + { + "author_name": "Leslie Rodriguez-Salas", + "author_inst": "Brotman Baty Institute, University of Washington, Seattle, WA" + }, + { + "author_name": "Jeremy Stone", + "author_inst": "Brotman Baty Institute, University of Washington, Seattle, WA" + }, + { + "author_name": "Luis Gamboa", + "author_inst": "Brotman Baty Institute, University of Washington, Seattle, WA" + }, + { + "author_name": "Peter D Han", + "author_inst": "Brotman Baty Institute, University of Washington, Seattle, WA; Department of Genome Sciences, University of Washington, Seattle, WA" + }, + { + "author_name": "Jeffery S Duchin", + "author_inst": "Public Health Seattle and King County, Seattle, WA; Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA; " + }, + { + "author_name": "Alpana Waghmare", + "author_inst": "Department of Pediatrics, University of Washington, Seattle, WA; Seattle Children's Research Institute, Seattle, WA; Vaccine and Infectious Disease Division, Fr" + }, + { + "author_name": "Janet A Englund", + "author_inst": "Seattle Children's Research Institute, Seattle, WA; Brotman Baty Institute, University of Washington, Seattle, WA; Department of Pediatrics, University of Washi" + }, + { + "author_name": "Jay Shendure", + "author_inst": "Brotman Baty Institute, University of Washington, Seattle, WA; Department of Genome Sciences, University of Washington, Seattle, WA; Howard Hughes Medical Insti" + }, + { + "author_name": "Trevor Bedford", + "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA; Howard Hughes Medical Institute, Seattle, WA; Brotman Baty Institute, Unive" + }, + { + "author_name": "Helen Y Chu", + "author_inst": "Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA" + }, + { + "author_name": "Lea M Starita", + "author_inst": "Brotman Baty Institute, University of Washington, Seattle, WA; Department of Genome Sciences, Univeristy of Washington, Seattle, WA" + }, + { + "author_name": "C\u00e9cile Viboud", + "author_inst": "Fogarty International Center, National Institutes of Health, Bethesda, MD" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.08.16.22278871", "rel_title": "How Have Global Scientists Responded to Tackling COVID-19?", @@ -231855,49 +232667,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.08.11.503706", - "rel_title": "The P681H mutation in the Spike glycoprotein escapes IFITM restriction and is necessary for type I interferon resistance in the SARS-CoV-2 alpha variant", - "rel_date": "2022-08-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.11.503706", - "rel_abs": "The appearance of new dominant variants of concern (VOCs) of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) threatens the global response to the COVID-19 pandemic. Of these, the alpha variant (also known as B.1.1.7) that appeared initially in the UK became the dominant variant in much of Europe and North America in the first half of 2021. The Spike (S) glycoprotein of alpha acquired seven mutations and two deletions compared to the ancestral virus, including the P681H mutation in the polybasic cleavage site that has been suggested to enhance S cleavage. Here, we show that the alpha S protein confers a level of resistance to the effects of interferon-{beta} (IFN{beta}) in human lung epithelial cells. This correlates with resistance to an entry restriction mediated by interferon-induced transmembrane protein 2 (IFITM2) and a pronounced infection enhancement by IFITM3. Furthermore, the P681H mutation is essential for resistance to IFN{beta} and context-dependent resistance to IFITMs in the alpha S. However, while this appears to confer changes in sensitivity to endosomal protease inhibition consistent with enhanced cell-surface entry, its reversion does not reduce cleaved S incorporation into particles, indicating a role downstream of furin cleavage. Overall, we suggest that, in addition to adaptive immune escape, mutations associated with VOCs may well also confer replication and/or transmission advantage through adaptation to resist innate immune mechanisms.\n\nIMPORTANCEThe emergence of Variants of Concern of SARS-CoV-2 has been a key challenge in the global response to the COVID-19 pandemic. Accumulating evidence suggests VOCs are being selected to evade the human immune response, with much interest focussed on mutations in the Spike protein that escape from neutralizing antibody responses. However, resistance to the innate immune response is essential for efficient viral replication and transmission. Here we show that the alpha (B.1.1.7) VOC of SARS-CoV-2 is substantially more resistant to type-1 interferons than the parental Wuhan-like virus. This correlates with resistance to the antiviral protein IFITM2, and enhancement by its paralogue IFITM3, that block virus entry into target cells. The key determinant of this is a proline to histidine change at position 681 in S adjacent to the furin-cleavage site that we have shown previously modulates IFITM2 sensitivity. Unlike other VOCs, in the context of the alpha spike, P681H modulates cell entry pathways of SARS-CoV-2, further reducing its dependence one endosomal proteases. Reversion of position 681 to a proline in viruses bearing the alpha spike is sufficient to restore interferon and IFITM2 sensitivity without reducing furin-mediated spike cleavage, suggesting post cleavage conformational changes in S are changing the viral entry pathway and therefore sensitivity to interferon. These data highlight the dynamic nature of the SARS CoV-2 S as it adapts to both innate and adaptive immunity in the human population.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Giuditta De Lorenzo", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Vanessa Cowton", - "author_inst": "MRC-University of Glasgow Centre For Virus Research" - }, - { - "author_name": "Wilhelm Furnon", - "author_inst": "MRC-University of Glasgow Centre For Virus Research" - }, - { - "author_name": "Nicol\u00e1s M. Su\u00e1rez", - "author_inst": "MRC-University of Glasgow Centre For Virus Research" - }, - { - "author_name": "Richard Orton", - "author_inst": "Medical Research Council - University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Massimo Palmirini", - "author_inst": "MRC-University of Glasgow Centre For Virus Research" - }, - { - "author_name": "Arvind H. Patel", - "author_inst": "University of Glasgow" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.08.12.503822", "rel_title": "The Spike protein of SARS-coV2 19B (S) clade mirrors critical features of viral adaptation and coevolution", @@ -232106,6 +232875,45 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2022.08.13.503846", + "rel_title": "Monkeypox virus shows potential to infect a diverse range of native animal species across Europe, indicating high risk of becoming endemic in the region", + "rel_date": "2022-08-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.13.503846", + "rel_abs": "BackgroundMonkeypox is a zoonotic virus which persists in animal reservoirs and periodically spills over into humans, causing outbreaks. During the current 2022 outbreak, monkeypox virus has persisted via human-human transmission, across all major continents and for longer than any previous record. This unprecedented spread creates the potential for the virus to spillback into local susceptible animal populations. Persistent transmission amongst such animals raises the prospect of monkeypox virus becoming enzootic in new regions. However, the full and specific range of potential animal hosts and reservoirs of monkeypox remains unknown, especially in newly at-risk non-endemic areas.\n\nMethodsHere, utilising ensembles of classifiers comprising different class balancing techniques and incorporating instance weights, we identify which animal species are potentially susceptible to monkeypox virus. Subsequently, we generate spatial distribution maps to highlight high-risk geographic areas at high resolution.\n\nFindingsWe show that the number of potentially susceptible species is currently underestimated by 2.4 to 4.3-fold, and that a high density of wild susceptible species are native to Europe. We provide lists of these species, and highlight high-risk hosts for spillback and potential long-term reservoirs, which may enable monkeypox virus to become endemic.\n\nInterpretationWe highlight the European red fox and brown rat, as they have established interactions with potentially contaminated urban waste and sewage, which provides a mechanism for potential spillback. We anticipate that our results will enable targeted active surveillance of potential spillback event, to minimise risk of the virus becoming endemic in these regions. Our results also indicate the potential of domesticated cats and dogs (latter now confirmed) being susceptible to monkeypox virus, and hence support many health organisations advice for infected humans to avoid physical interaction with pets.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Marcus S C Blagrove", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Jack Pilgrim", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Aurelia Kotsiri", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Melody Hui", + "author_inst": "University of Liverpoool" + }, + { + "author_name": "Matthew Baylis", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Maya Wardeh", + "author_inst": "University of Liverpool" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "ecology" + }, { "rel_doi": "10.1101/2022.08.15.504010", "rel_title": "Host and viral determinants of airborne transmission of SARS-CoV-2 in the Syrian hamster", @@ -233941,109 +234749,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.05.22278483", - "rel_title": "Antibody feedback regulation of memory B cell development in SARS-CoV-2 mRNA vaccination", - "rel_date": "2022-08-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.05.22278483", - "rel_abs": "Feedback inhibition of humoral immunity by antibodies was initially documented in guinea pigs by Theobald Smith in 1909, who showed that passive administration of excess anti-Diphtheria toxin inhibited immune responses1. Subsequent work documented that antibodies can enhance or inhibit immune responses depending on antibody isotype, affinity, the physical nature of the antigen, and engagement of immunoglobulin (Fc) and complement (C) receptors2, 3. However, little is known about how pre-existing antibodies might influence the subsequent development of memory B cells. Here we examined the memory B cell response in individuals who received two high-affinity IgG1 anti-SARS-CoV-2 receptor binding domain (RBD)-specific monoclonal antibodies, C144-LS and C135-LS, and subsequently two doses of a SARS-CoV-2 mRNA vaccine. The two antibodies target Class 2 and 3 epitopes that dominate the initial immune response to SARS-CoV-2 infection and mRNA vaccination4-8. Antibody responses to the vaccine in C144-LS and C135-LS recipients produced plasma antigen binding and neutralizing titers that were fractionally lower but not statistically different to controls. In contrast, memory B cells enumerated by flow cytometry after the second vaccine dose were present in higher numbers than in controls. However, the memory B cells that developed in antibody recipients differed from controls in that they were not enriched in VH3-53, VH1-46 and VH3-66 genes and predominantly expressed low-affinity IgM antibodies that carried small numbers of somatic mutations. These antibodies showed altered RBD target specificity consistent with epitope masking, and only 1 out of 77 anti-RBD memory antibodies tested neutralized the virus. The results indicate that pre-existing high-affinity antibodies bias memory B cell selection and have a profound effect on the development of immunological memory in humans that may in part explain the shifting target profile of memory antibodies elicited by the 3rd mRNA vaccine dose.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Dennis Schaefer-Babajew", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Zijun Wang", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Frauke Muecksch", - "author_inst": "Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Alice Cho", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Raphael Raspe", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Brianna Johnson", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Marie Canis", - "author_inst": "Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Justin DaSilva", - "author_inst": "Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Victor Ramos", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Martina Turroja", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Katrina Millard", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Fabian Schmidt", - "author_inst": "Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Juan Dizon", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Irina Shimeliovich", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Kai-Hui Yao", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Thiago Oliveira", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Anna Gazumyan", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA & Howard Hughes Medical Institute, New York, NY, USA" - }, - { - "author_name": "Christian Gaebler", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Paul D. Bieniasz", - "author_inst": "Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA & Howard Hughes Medical Institute, New York, NY, USA" - }, - { - "author_name": "Theodora Hatziioannou", - "author_inst": "Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Marina Caskey", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Michel C. Nussenzweig", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA & Howard Hughes Medical Institute, New York, NY, USA" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2022.08.09.22274874", "rel_title": "Procalcitonin and High APACHE Scores are Associated with the Development of Acute Kidney Injury in Patients with SARS-CoV-2", @@ -234392,6 +235097,153 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.09.22278329", + "rel_title": "Efficacy and safety of convalescent plasma to treat hospitalised COVID-19 patients with or without underlying immunodeficiency: a randomized clinical trial", + "rel_date": "2022-08-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.09.22278329", + "rel_abs": "ObjectivesEfficacy of convalescent plasma in COVID-19 pneumonia (CPP) is uncertain, especially in immunocompromised patients. CORIMUNO-CORIPLASM is an open-label, Bayesian randomised clinical trial embedded in the CORIMUNO trials platform that evaluated the efficacy of CCP in patients with moderate COVID-19.\n\nSetting19 university and general hospitals across France.\n\nParticipantsAdult hospitalized with a positive SARS-CoV2 test, duration of symptoms < 9 days and WHO score severity 4 or 5 who signed written inform consent.\n\nInterventionOpen label randomisation to either usual care (UC) or 4 units (200-220 ml/unit, 2 units/day over 2 consecutive days) of convalescent plasma (CCP) with a seroneutralisation titer > 40.\n\nOutcomesPrimary outcome was proportion of patients with a WHO-Clinical Progression Score (CPS) [≥]6 on the 10-point scale on day (d) 4 (higher values indicating a worse outcome) and survival without ventilation or additional immunomodulatory treatment by day 14. Secondary outcomes included evolution of WHO-CPS, overall survival, time to discharge and time to oxygen supply independency. Pre-defined subgroups analyses included immunosuppression status, duration of symptoms before randomization and use of steroids.\n\nResultsA total of 120 patients were recruited and assigned to CCP (n=60) or UC (n=60), including 22 (CCP) and 27 (UC) immunocompromised patients. Thirteen (22%) patients with CCP had a WHO-CPS [≥]6 at day 4 versus 8 (13%) with UC, adjusted odds ratio (aOR) 1.88 [95%CrI 0.71 to 5.24]. By day 14, 19 (31.6%) patients with CCP and 20 (33.3%) patients with UC had ventilation, additional immunomodulatory treatment or had died. Cumulative incidence of death was 3 (5%) with CCP and 8 (13%) with UC at day 14 (aHR 0.40 [95%CrI 0{middle dot}10 -1{middle dot}53]), and 7 (12%) with CCP and 12 (20%) with UC at day 28 (aHR 0.51 [95%CrI 0.20-1.32]). I n a s ubgroup analysis performed in immunocompromised patients, the association of CCP with mortality was HR 0.39 [95%CI 0.14-1.10].\n\nConclusionsCCP did not improve early outcomes in patients with moderate COVID-19. Its efficacy in immunocompromised patients needs to be further explored.\n\nTrial registrationclinicaltrials.gov Identifier: NCT04345991\n\nKEY MESSAGES BOXO_ST_ABSWhat is already known on this topic?C_ST_ABSO_LIConvalescent plasma treatment, i.e., passive polyclonal antibody administration to provide immediate immunity, has been used to improve the survival rate of patients with severe acute respiratory syndromes of viral etiology in emergency settings and times where there was no specific antiviral treatment\nC_LIO_LIAt the early stages of the COVID-19 pandemic, using high titre COVID-19 convalescent plasma (CCP) appeared to be an immediate therapeutic option.\nC_LIO_LIHowever, a large number of randomised clinical trials and observational studies have yielded conflicting results regarding the efficacy of CCP.\nC_LIO_LIFurthermore, the efficacy of CCP in patients with underlying immunosuppression has been evaluated only in a limited manner.\nC_LIO_LIThe emergence of variants resistant to other passive immunotherapy approaches, ie monoclonal antibodies, has limited the therapeutics options for such patients\nC_LI\n\nWhat this study adds ?O_LIThis multicentre randomised clinical trial provided evidence that high titre CCP in a population hospitalised with a mild to moderate form of COVID-19 within 9 days of symptoms onset may not improve early outcome.\nC_LIO_LIIn the subgroup of patients with immunosuppression, there was evidence suggesting a lower odds of death 14 and 28 days after CCP transfusion, albeit without reaching significance.\nC_LI\n\nHow does this study might affect research, practice of policyO_LIThe result of study, along with the recent data obtained from other trials and cohort studies supports further evaluation of CCP transfusion in patients with underlying immunosuppression for whom therapeutic options are currently scarce if non-existent, due to the ever changing genetic variability of SARS-CoV2.\nC_LI", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Karine Lacombe", + "author_inst": "Sorbonne Universite, Paris" + }, + { + "author_name": "Thomas Hueso", + "author_inst": "Institut Gustave Roussy, Villejuif" + }, + { + "author_name": "Raphael Porcher", + "author_inst": "Sorbonne Universite, Paris" + }, + { + "author_name": "Arsene Mekinian", + "author_inst": "Sorbonne Universite, Paris" + }, + { + "author_name": "Thibault Chiarabini", + "author_inst": "Hopital Saint Antoine APHP , Paris" + }, + { + "author_name": "Sophie Georgin-Lavialle", + "author_inst": "Sorbonne Universite, Paris" + }, + { + "author_name": "Florence Ader", + "author_inst": "Universite Claude Bernard, Lyon" + }, + { + "author_name": "Julien Saison", + "author_inst": "CH Valence, Valence" + }, + { + "author_name": "Guillaume Martin-Blondet", + "author_inst": "CHU Toulouse" + }, + { + "author_name": "Nathalie A De Castro", + "author_inst": "Hopital Tenon APHP" + }, + { + "author_name": "Fabrice Bonnet", + "author_inst": "CHU Bordeaux" + }, + { + "author_name": "Charles Cazanave", + "author_inst": "CHU Bordeaux" + }, + { + "author_name": "Anne Francois", + "author_inst": "Etablissement Francais du Sang" + }, + { + "author_name": "Pascal Morel", + "author_inst": "Etablissement Francais du Sang" + }, + { + "author_name": "Olivier Hermine", + "author_inst": "Hopital Necker Enfants Malades" + }, + { + "author_name": "Valerie Pourcher", + "author_inst": "Hopital Pitie Salpertriere" + }, + { + "author_name": "Marc Michel", + "author_inst": "Hopital Est Creteil APHP" + }, + { + "author_name": "Xavier Lescure", + "author_inst": "Hopital Bichat APHP" + }, + { + "author_name": "Nora Soussi", + "author_inst": "Hopital St Antoine APHP" + }, + { + "author_name": "Phillipe Brun", + "author_inst": "CH Valence" + }, + { + "author_name": "Fanny Pommeret", + "author_inst": "Institut Gustave Roussy" + }, + { + "author_name": "Pierre Sellier", + "author_inst": "Hopital Lariboisiere APHP" + }, + { + "author_name": "Stella Rousset", + "author_inst": "CHU Toulouse" + }, + { + "author_name": "Lione Piroth", + "author_inst": "CHU Dijon" + }, + { + "author_name": "Jean-Marie Michot", + "author_inst": "Institut Gustave Roussy" + }, + { + "author_name": "gabriel baron", + "author_inst": "Hopital Hotel Dieu APHP" + }, + { + "author_name": "Xavier de Lamballerie", + "author_inst": "Aix-Marseille univ -Inserm - IRD" + }, + { + "author_name": "Xavier Mariette", + "author_inst": "Hopital Bicetre APHP" + }, + { + "author_name": "Pierre-Louis Tharaux", + "author_inst": "Universite Paris Cite" + }, + { + "author_name": "Matthieu Resche-Rigaux", + "author_inst": "Hopital St Louis, APHP" + }, + { + "author_name": "Philippe Ravaud", + "author_inst": "Sorbonne Universite" + }, + { + "author_name": "Tabassome Simon", + "author_inst": "Sorbonne Universite" + }, + { + "author_name": "Pierre Tiberghien", + "author_inst": "Etablissement Francais du Sang" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.09.22278540", "rel_title": "SARS-CoV-2 viral clearance and viral load kinetics in young children (1-6 years) compared to adults: Results of a longitudinal study in Germany", @@ -236067,53 +236919,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.07.22278506", - "rel_title": "The prognostic value of transthoracic echocardiography findings in hospitalized adult patients with COVID-19: A single-center retrospective analysis", - "rel_date": "2022-08-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.07.22278506", - "rel_abs": "BackgroundCardiac involvement in coronavirus disease 2019 (COVID-19) is associated with poor outcomes. Transthoracic echocardiography (TTE) can be used to assess cardiac structure and function non-invasively, and has been shown to influence management in COVID-19.\n\nObjectivesWe aim to investigate the prognostic value of TTE findings in hospitalized adults with confirmed COVID-19.\n\nMethodsAll consecutive hospitalized adult patients with confirmed COVID-19 who underwent TTE assessment between 3rd April 2020 - 6th April 2021 were included. Comprehensive clinical data including TTE findings were collected from electronic medical records. Patients with mild-moderate and severe-critical COVID-19 were compared. Within the severe-critical group, patients who survived hospitalization and died were compared. Further analyses were conducted after matching for age >60 years, obesity, and diabetes.\n\nResultsA total of 488 COVID-19 patients were included in this study; 202 with mild-moderate and 286 severe-critical disease. All mild-moderate patients and 152 severe-critical patients survived hospitalization. In the matched cohorts, TTE findings associated with severe-critical COVID-19 included left ventricular (LV) hypertrophy (OR: 1.91; CI: 1.21 - 3.02), LV diastolic dysfunction (OR: 1.55; CI: 1.00 - 2.38), right ventricular (RV) dysfunction (OR: 3.86; CI: 1.06 - 14.08), wall motion abnormalities (WMAs) (OR: 2.76; CI: 1.28 - 5.96), and any TTE abnormalities (OR: 2.99; CI: 1.73 - 5.17). TTE findings associated with mortality included RV dysfunction (OR: 3.53; CI: 1.12 - 11.19) and WMAs (OR: 2.63; CI: 1.26 - 5.49).\n\nConclusionTTE is a non-invasive modality that can potentially be used for risk-stratification of hospitalized COVID-19 patients. These findings must be confirmed in larger prospective studies.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Hary Sakti Muliawan", - "author_inst": "Department of Cardiology and Vascular Medicine, Faculty of Medicine, Universitas Indonesia/ Universitas Indonesia Hospital" - }, - { - "author_name": "Raksheeth Agarwal", - "author_inst": "Faculty of Medicine, Universitas Indonesia" - }, - { - "author_name": "Raka Aldy Nugraha", - "author_inst": "Department of Cardiology and Vascular Medicine, Universitas Indonesia Hospital" - }, - { - "author_name": "Gatut Priyonugroho", - "author_inst": "Department of Pulmonology, Universitas Indonesia Hospital" - }, - { - "author_name": "Siti Hertine", - "author_inst": "Department of Cardiology and Vascular Medicine, Universitas Indonesia Hospital" - }, - { - "author_name": "Sony Hilal Wicaksono", - "author_inst": "Department of Cardiology and Vascular Medicine, Universitas Indonesia Hospital" - }, - { - "author_name": "Prima Almazini", - "author_inst": "Department of Cardiology and Vascular Medicine, Universitas Indonesia Hospital" - }, - { - "author_name": "Dian Zamroni", - "author_inst": "Department of Cardiology and Vascular Medicine, Universitas Indonesia Hospital" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2022.08.07.22278510", "rel_title": "Metabolomic and gut microbiome profiles across the spectrum of community-based COVID and non-COVID disease: A COVID-19 Biobank study.", @@ -236402,6 +237207,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.08.08.22278493", + "rel_title": "Inequalities in colorectal cancer screening uptake in Wales: examination of the impact of the temporary suspension of the screening programme during the COVID-19 pandemic", + "rel_date": "2022-08-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.08.22278493", + "rel_abs": "BackgroundResponse to the early stages of the COVID-19 pandemic resulted in the temporary disruption of cancer screening in the UK, and strong public messaging to stay safe and to protect NHS capacity. Following reintroduction in services, we explored the impact on inequalities in uptake of the Bowel Screening Wales (BSW) programme to identify groups who may benefit from tailored interventions.\n\nMethodsRecords within the BSW were linked to electronic health records (EHR) and administrative data within the Secured Anonymised Information Linkage (SAIL) Databank. Ethnic group was obtained from a linked data method available within SAIL. We examined uptake for the first 3 months of invitations (August to October) following the reintroduction of BSW programme in 2020, compared to the same period in the preceding 3 years. Uptake was measured across a 6 month follow-up period. Logistic models were conducted to analyse variations in uptake by sex, age group, income deprivation quintile, urban/rural location, ethnic group, and clinically extremely vulnerable (CEV) status in each period; and to compare uptake within sociodemographic groups between different periods.\n\nResultsUptake during August to October 2020 (period 2020/21; 60.4%) declined compared to the same period in 2019/20 (62.7%) but remained above the 60% Welsh standard. Variation by sex, age, income deprivation, and ethnic groups was observed in all periods studied. Compared to the pre-pandemic period in 2019/20, uptake declined for most demographic groups, except for older individuals (70-74 years) and those in the most income deprived group. Uptake continues to be lower in males, younger individuals, people living in the most income deprived areas and those of Asian and unknown ethnic backgrounds.\n\nConclusionsOur findings are encouraging with overall uptake achieving the 60% Welsh standard during the first three months after the programme restarted in 2020 despite the disruption. Inequalities did not worsen after the programme resumed activities but variations in CRC screening in Wales associated with sex, age, deprivation and ethnicity remain. This needs to be considered in targeting strategies to improve uptake and informed choice in CRC screening to avoid exacerbating disparities in CRC outcomes as screening services recover from the pandemic.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Diana Bright", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Sharon Hillier", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Jiao Song", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Dyfed W Huws", + "author_inst": "Public Health Wales; Population Data Science, Swansea University Medical School, Faculty of Medicine, Health & Life Science, Swansea University, Swansea, Wales" + }, + { + "author_name": "Giles Greene", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Karen Hodgson", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Ashley Akbari", + "author_inst": "Population Data Science, Swansea University Medical School, Faculty of Medicine, Health & Life Science, Swansea University, Swansea, Wales" + }, + { + "author_name": "Rowena Griffiths", + "author_inst": "Population Data Science, Swansea University Medical School, Faculty of Medicine, Health & Life Science, Swansea University, Swansea, Wales" + }, + { + "author_name": "Alisha R Davies", + "author_inst": "Public Health Wales" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.08.09.22278587", "rel_title": "Cyclical Student Shifting Models in a Limited Face-to-Face Learning Modality in the time of COVID-19 Pandemic in the Philippines", @@ -238085,37 +238941,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.08.04.22278431", - "rel_title": "Determining population-level allocation strategies for COVID-19 treatments in the United States using a quantitative framework, a case study using nirmatrelvir/ritonavir", - "rel_date": "2022-08-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.04.22278431", - "rel_abs": "BackgroundNew COVID-19 medications force decision makers to weigh limited evidence of efficacy and cost in determining which patient populations to target for treatment. A case in point is nirmatrelvir/ritonavir, a drug that has been recommended for elderly, high-risk individuals, regardless of vaccination status, even though clinical trials have only evaluated it in unvaccinated patients. A simple optimization framework might inform a more reasoned approach to the tradeoffs implicit in the treatment allocation decision.\n\nMethodsWe used a mathematical model to analyze the cost-effectiveness of four nirmatrelvir/ritonavir allocation strategies, stratified by vaccination status and risk for severe disease. We considered treatment effectiveness at preventing hospitalization ranging from 21% to 89%. Sensitivity analyses were performed on major parameters of interest. A web-based tool was developed to permit decision-makers to tailor the analysis to their settings and priorities.\n\nResultsProviding nirmatrelvir/ritonavir to unvaccinated patients at high-risk for severe disease was cost-saving when effectiveness against hospitalization exceeded 33% and cost-effective under all other data scenarios we considered. The cost-effectiveness of other allocation strategies, including those for vaccinated adults and those at lower-risk for severe disease, depended on willingness-to-pay thresholds, treatment cost and effectiveness, and the likelihood of severe disease.\n\nConclusionsPriority for nirmatrelvir/ritonavir treatment should be given to unvaccinated persons at high-risk of severe disease from COVID-19. Further priority may be assigned by weighing treatment effectiveness, disease severity, drug cost, and willingness to pay for deaths averted.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Alexandra Savinkina", - "author_inst": "Yale University" - }, - { - "author_name": "Gregg S. Gonsalves", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Joseph S. Ross", - "author_inst": "Yale University" - }, - { - "author_name": "A David Paltiel", - "author_inst": "Yale School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2022.08.05.22278466", "rel_title": "Performance of Screening for SARS-CoV-2 using Rapid Antigen Tests to Detect Incidence of Symptomatic and Asymptomatic SARS-CoV-2 Infection: findings from the Test Us at Home prospective cohort study", @@ -238516,6 +239341,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2022.08.04.22278391", + "rel_title": "Forecasting COVID-19 activity in Australia to support pandemic response: May to October 2020", + "rel_date": "2022-08-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.04.22278391", + "rel_abs": "As of January 2021, Australia had effectively controlled local transmission of COVID-19 despite a steady influx of imported cases and several local, but contained, outbreaks in 2020. Throughout 2020, state and territory public health responses were informed by weekly situational reports that included an ensemble forecast for each jurisdiction. We present here an analysis of one forecasting model included in this ensemble across the variety of scenarios experienced by each jurisdiction from May to October 2020. We examine how successfully the forecasts characterised future case incidence, subject to variations in data timeliness and completeness, showcase how we adapted these forecasts to support decisions of public health priority in rapidly-evolving situations, evaluate the impact of key model features on forecast skill, and demonstrate how to assess forecast skill in real-time before the ground truth is known. Conditioning the model on the most recent, but incomplete, data improved the forecast skill, emphasising the importance of developing strong quantitative models of surveillance system characteristics, such as ascertainment delay distributions. Forecast skill was highest when there were at least 10 reported cases per day, the circumstances in which authorities were most in need of forecasts to aid in planning and response.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Robert Moss", + "author_inst": "The University of Melbourne" + }, + { + "author_name": "David J Price", + "author_inst": "The University of Melbourne" + }, + { + "author_name": "Nick Golding", + "author_inst": "Telethon Kids Institute and Curtin University" + }, + { + "author_name": "Peter Dawson", + "author_inst": "Defence Science and Technology Group" + }, + { + "author_name": "Jodie McVernon", + "author_inst": "The Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Rob J Hyndman", + "author_inst": "Monash University" + }, + { + "author_name": "Freya M Shearer", + "author_inst": "The University of Melbourne" + }, + { + "author_name": "James M McCaw", + "author_inst": "The University of Melbourne" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.04.22278415", "rel_title": "Early Side Effects after Administration of the 1st Dose of Oxford-AstraZeneca Vaccine", @@ -240451,29 +241323,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.02.22278349", - "rel_title": "Geospatial disparities in federal COVID-19 test-to-treat program", - "rel_date": "2022-08-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.02.22278349", - "rel_abs": "BackgroundPaxlovid is authorized for the treatment of COVID-19 and must be used within the first 5 days of symptom onset. This limited window for initiating treatment makes rapid access critical. Federal Test-to-Treat programs provide tests, prescriptions, and medication in one visit3.\n\nObjectiveThe objective of this study was to map the location of and identify disparities in access to Test-to-Treat programs in the United States (U.S.).\n\nMethodsWe obtained location data for public providers of Paxlovid and Test-to-Treat programs in the contiguous U.S. and examined their spatial distribution at the zip code tabulation area level. We defined zip codes as underserved if there was no Test-to-Treat program located within the zip code or within 20 miles of its boundaries.\n\nResultsMore than 52,000,000 people--representing 16% of the continental U.S. population--do not have access to a Test-to-Treat program in their zip code or within 20 miles. The majority of zip codes representing metropolitan areas have a Test-to-Treat program within 20 miles (77%). In contrast, only 30% of small towns and 23% of rural areas have nearby access. Zip codes with a high proportion of Hispanic and Black residents were likely to have access to nearby Test-to-Treat programs (72%, 70%). In contrast, zip codes with a high proportion of Native American residents were likely to be underserved (70%). About half of high-poverty zip codes do not have access to a Test-to-Treat program within 20 miles.\n\nDiscussionDisparities in outcomes related to COVID-19 have been apparent since the beginning of the pandemic and continue to grow. While the multi-dimensional measure of social vulnerability was used to expand the federal Test-to-Treat program, some populations remain without access.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Emily R. Smith", - "author_inst": "George Washington University" - }, - { - "author_name": "Erin M Oakley", - "author_inst": "The George Washington University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.08.03.22278359", "rel_title": "COVID-19 convalescent plasma for the treatment of immunocompromised patients: a systematic review.", @@ -240702,6 +241551,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.08.01.22278286", + "rel_title": "Nano assembly of plasmonic probe-virus particles enabled rapid and ultrasensitive point-of-care SARS-CoV-2 detection", + "rel_date": "2022-08-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.01.22278286", + "rel_abs": "The current COVID-19 global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus has become a major public health concern. The ability to identify the viruss presence in infected hosts with sufficient speed and sensitivity is critical to control the epidemic timely. Here, we use self-assembly of arrayed gold nanoparticles (AuNPs) on the coronavirus, which we call the \"plasmo-virus particle,\" to achieve a rapid, sensitive, sample preparation-free assay enabling direct detection of SARS-CoV-2 in a point-of-care (POC) setting. The AuNPs of the plasmo-virus particle serve as plasmonic nanoprobes that specifically bind to the spike protein (S-protein) sites on the surface of SARS-CoV-2. Optical interactions between the self-assembled plasmonic nanoprobes generate multiple modes of highly enhanced plasmonic coupling. Measuring changes of the multimode plasmonic coupling-induced extinction peaks allows for quantifying SARS-CoV-2 at low titers with a limit of detection (LOD) of 1.4 x 101 pfu/mL. Using a miniaturized standalone biochip reading device, we further demonstrate the nano assembly assay for smartphone-operated SARS-CoV-2 detection for viral transport medium (VTM) samples within 10 min without any sample purification steps. We anticipate that the high sensitivity and speed of the POC detection performance of this biosensor technology could be broadly accepted for timely personalized diagnostics of infectious agents under low-resource settings.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Younggeun Park", + "author_inst": "University of Michigan" + }, + { + "author_name": "Byunghoon Ryu", + "author_inst": "University of Michigan" + }, + { + "author_name": "Seungjune Ki", + "author_inst": "University of Michigan" + }, + { + "author_name": "Mingze Chen", + "author_inst": "University of Michigan" + }, + { + "author_name": "Xiaogan Liang", + "author_inst": "University of Michigan" + }, + { + "author_name": "Katsuo Kurabayashi", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.02.22278277", "rel_title": "Real-life evaluation of a rapid antigen test (DPP SARS-CoV-2 Antigen) for COVID-19 diagnosis of primary healthcare patients, in the context of the Omicron-dominant wave in Brazil", @@ -242161,101 +243049,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2022.07.31.500554", - "rel_title": "Memory B cells and memory T cells induced by SARS-CoV-2 booster vaccination or infection show different dynamics and efficacy to the Omicron variant.", - "rel_date": "2022-08-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.31.500554", - "rel_abs": "Although BNT162b2 vaccination was shown to prevent infection and reduce COVID-19 severity, and the persistence of immunological memory generated by the vaccination has not been well elucidated. We evaluated memory B and T cell responses to the SARS-CoV-2 spike protein before and after the third BNT162b2 booster. Although the antibody titer against the spike receptor-binding domain (RBD) decreased significantly 8 months after the second vaccination, the number of memory B cells continued to increase, while the number of memory T cells decreased slowly. Memory B and T cells from unvaccinated infected patients showed similar kinetics. After the third vaccination, the antibody titer increased to the level of the second vaccination, and memory B cells increased at significantly higher levels before the booster, while memory T cells recovered close to the second vaccination levels. In memory T cells, the frequency of CXCR5+CXCR3+CCR6- cTfh1 was positively correlated with RBD-specific antibody-secreting B cells. Furthermore, T cell-dependent antibody production from reactivated memory B cells in vitro was correlated to the Tfh-like cytokine levels. For the response to variant RBDs, although 60%-80% of memory B cells could bind to the Omicron RBD, their binding affinity was low, while memory T cells show an equal response to the Omicron spike. Thus, the persistent presence of memory B and T cells will quickly upregulate antibody production and T cell responses after Omicron strain infection, which prevents severe illness and death due to COVID-19.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Setsuko Mise-Omata", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Mari Ikeda", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Masaru Takeshita", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Yoshifumi Uwamino", - "author_inst": "Keio Univeristy School of Medicine" - }, - { - "author_name": "Masatoshi Wakui", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Tomoko Arai", - "author_inst": "Keio University Hospital" - }, - { - "author_name": "Ayumi Yoshifuji", - "author_inst": "Tokyo Saiseikai Central Hospital" - }, - { - "author_name": "Kensaku Murano", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Haruhiko Siomi", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Kensuke Nakagawara", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Masaki Ohyagi", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Makoto Ando", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Naoki Hasegawa", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Hideyuki Saya", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Mitsuru Murata", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Koichi Fukunaga", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Ho Namkoong", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Xiuyuan Lu", - "author_inst": "Osaka University" - }, - { - "author_name": "Sho Yamasaki", - "author_inst": "Osaka University" - }, - { - "author_name": "Akihiko Yoshimura", - "author_inst": "Keio University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.07.29.502014", "rel_title": "Coronaviruses using different strategies to antagonize antiviral responses and pyroptosis", @@ -242508,6 +243301,53 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.07.31.501809", + "rel_title": "InterClone: Store, Search and Cluster Adaptive Immune Receptor Repertoires", + "rel_date": "2022-08-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.31.501809", + "rel_abs": "B and T cell receptor repertoire data has the potential to fundamentally change the way we diagnose and treat a wide range of diseases. However, there are few resources for storing or analyzing repertoire data. InterClone provides tools for storing, searching, and clustering repertoire datasets. Efficiency is achieved by encoding the complementarity-determining regions of sequences as mmseqs2 databases. Single chain search or cluster results can be merged into paired (alpha-beta or heavy-light) results for analysis of single-cell sequencing data. We illustrate the use of InterClone with two recently reported examples: 1) searching for SARS-CoV-2 infection-enhancing antibodies in bulk COVID-19 and healthy donor repertoires; 2) identification of SARS-CoV-2 specific TCRs by clustering paired and bulk sequences from COVID-19, BNT162b2 vaccinated and healthy unvaccinated donors. The core functions of InterClone have been implemented as a web server and integrated database (https://sysimm.org/interclone). All source code is available upon request.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Zichang Xu", + "author_inst": "Osaka University, Research Institute for Microbial Diseases" + }, + { + "author_name": "Hendra S Ismanto", + "author_inst": "Osaka University, Research Institute for Microbial Diseases" + }, + { + "author_name": "Songling Li", + "author_inst": "Osaka University, Research Institute for Microbial Diseases" + }, + { + "author_name": "Shunsuke Teraguchi", + "author_inst": "Faculty of Data Science, Shiga University" + }, + { + "author_name": "Mara Anais Llamas Covarrubias", + "author_inst": "Osaka University, Research Institute for Microbial Diseases" + }, + { + "author_name": "Xiuyuan Lu", + "author_inst": "Immunology Frontier Research Center, Osaka University" + }, + { + "author_name": "Sho Yamasaki", + "author_inst": "Osaka University, Research Institute for Microbial Diseases" + }, + { + "author_name": "Daron M Standley", + "author_inst": "Osaka University. Research Institute for Microbial Diseases" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.07.28.22270513", "rel_title": "Use of a Self-Care and Educational Mobile App to Improve Outcomes of Patients with Acute Decompensated Heart Failure during the COVID-19 Pandemic", @@ -244003,45 +244843,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2022.07.26.22277958", - "rel_title": "Induction of poxviral immunity by synthetic MVA-based dual-antigen COVID-19 vaccine COH04S1", - "rel_date": "2022-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.26.22277958", - "rel_abs": "The recent outbreak of monkeypox (MPXV) outside its endemic boundaries has attracted global attention and prompted world leaders to reserve millions of doses of the only approved third-generation smallpox/MPXV vaccine, Jynneos, which is based on the highly attenuated modified vaccinia Ankara (MVA) vector. We previously developed COH04S1, a multiantigen SARS-CoV-2 vaccine built on a synthetic MVA (sMVA) platform. COH04S1 was extensively tested for efficacy and immunogenicity in animal models, including non-human primates (NHP), and was found to be safe and to induce SARS-CoV-2-specific immunity in a Phase 1 clinical trial in healthy adults. Here we demonstrate that one or two vaccinations of NHP with either COH04S1 or sMVA elicit robust othopoxvirus-specific binding and neutralizing antibody responses. Furthermore, healthy adults vaccinated with COH04S1 at different dose levels develop robust othopoxvirus-specific humoral and cellular immune responses that are durable for over six months post-vaccination. Importantly, both COH04S1 and sMVA vaccinations induce elevated and sustained antibody responses to MPXV-proteins that are major targets of protective neutralizing antibodies. These results demonstrate that COH04S1 and sMVA are valuable vaccine candidates to stimulate robust orthopox/MPXV-specific humoral and cellular immunity.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Flavia Chiuppesi", - "author_inst": "City of Hope National Medical Center" - }, - { - "author_name": "John A Zaia", - "author_inst": "City of Hope National Medical Center" - }, - { - "author_name": "Sandra Ortega Francisco", - "author_inst": "City of Hope National Medical Center" - }, - { - "author_name": "Michael Ly", - "author_inst": "City of Hope National Medical Center" - }, - { - "author_name": "Felix Wussow", - "author_inst": "City of Hope National Medical Center" - }, - { - "author_name": "Don J Diamond", - "author_inst": "City of Hope National Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.24.22277784", "rel_title": "Efficacy of a patient isolation hood in reducing exposure to airborne infectious virus in a simulated healthcare setting", @@ -244274,6 +245075,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.27.22278129", + "rel_title": "Immune Heterogeneity and Epistasis Explain Punctuated Evolution of SARS-CoV-2", + "rel_date": "2022-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.27.22278129", + "rel_abs": "Identifying drivers of viral diversity is key to understanding the evolutionary as well as epidemiological dynamics of the COVID-19 pandemic. Using rich viral genomic data sets, we show that periods of steadily rising diversity have been punctuated by sudden, enormous increases followed by similarly abrupt collapses of diversity. We introduce a mechanistic model of saltational evolution with epistasis and demonstrate that these features parsimoniously account for the observed temporal dynamics of inter-genomic diversity. Our results provide support for recent proposals that saltational evolution may be a signature feature of SARS-CoV-2, allowing the pathogen to more readily evolve highly transmissible variants. These findings lend theoretical support to a heightened awareness of biological contexts where increased diversification may occur. They also underline the power of pathogen genomics and other surveillance streams in clarifying the phylodynamics of emerging and endemic infections. In public health terms, our results further underline the importance of equitable distribution of up-to-date vaccines.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Bjarke Frost Nielsen", + "author_inst": "PandemiX Center, Roskilde University and Niels Bohr Institute, University of Copenhagen" + }, + { + "author_name": "Yimei Li", + "author_inst": "Department of Ecology and Evolutionary Biology, Princeton University" + }, + { + "author_name": "Kim Sneppen", + "author_inst": "Niels Bohr Institute, University of Copenhagen" + }, + { + "author_name": "Lone Simonsen", + "author_inst": "PandemiX Center, Roskilde University" + }, + { + "author_name": "Cecile Viboud", + "author_inst": "Fogarty International Center, National Institutes of Health" + }, + { + "author_name": "Simon A. Levin", + "author_inst": "Department of Ecology & Evolutionary Biology, Princeton University" + }, + { + "author_name": "Bryan T. Grenfell", + "author_inst": "Department of Ecology & Evolutionary Biology, Princeton University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.26.22278056", "rel_title": "Level of Compliance and Predictors with Personal COVID-19-preventive measures Among Office Government Employees Returning to work in the post-epidemic period in Western Ethiopia: A Multicenter Cross-sectional Study", @@ -245893,49 +246737,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.07.20.22277848", - "rel_title": "Virtual care use among older immigrant adults in Ontario, Canada during the COVID-19 pandemic: a repeated cross-sectional analysis", - "rel_date": "2022-07-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.20.22277848", - "rel_abs": "The critical role of virtual care during the COVID-19 pandemic has raised concerns about the widening disparities to access by vulnerable populations including older immigrants. This paper aims to describe virtual care use in older immigrant populations residing in Ontario, Canada.\n\nIn this population-based, repeated cross-sectional study, we used linked administrative data to describe virtual care and healthcare utilization among immigrants aged 65 years and older before and during the COVID-19 pandemic. Visits were identified weekly from January 2018 to March 2021 among various older adult immigrant populations.\n\nAmong older immigrants, over 75% were high users of virtual care (had two or more virtual visits) during the pandemic. Rates of virtual care use increased for both older adult immigrant and non-immigrant populations. At the start of the pandemic, virtual care use was lower among immigrants compared to non-immigrants (weekly average of 77 vs 86 visits). As the pandemic progressed, the rates between these groups became similar (80 vs 79 visits). Virtual care use was consistently lower among immigrants in the family class (75 visits) compared to the economic (82 visits) or refugee (89 visits) classes, and was lower among those who only spoke French (69 visits) or neither French nor English (73 visits) compared to those who were fluent in English (81 visits).\n\nThis study found that use of virtual care was comparable between older immigrants and non-immigrants overall, though there may have been barriers to access for older immigrants early on in the pandemic. However, within older immigrant populations, immigration category and language ability were consistent differentiators in the rates of virtual care use throughout the pandemic.\n\nAuthor SummaryWhen the COVID-19 pandemic began, healthcare systems pivoted from in-person to virtual care to maintain physical distancing. Studies have shown that virtual care use became much more frequent during the pandemic as a result. What we do not know is whether virtual care is being used equitably, that is, whether everybody has fair access to the resource. This can be a big issue particularly amongst older adults, who are often battling several diseases and use healthcare frequently. Many older adults are immigrants who may face challenges in accessing healthcare due to reasons such as limited language fluency and resource support. Our study found that older adult immigrants aged 65 and above living in Ontario, Canada had lower use of virtual care initially, but their use eventually caught up with non-immigrants as the pandemic progressed. We also found that older adult immigrants from the family class had lower virtual care use compared to those from the economic, refugee, or other immigration classes. Additionally, immigrants who were not fluent in English had lower use compared to those who were fluent. These results show that virtual care access remains an issue for vulnerable minorities and steps should be taken to ensure these groups are receiving adequate care.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Janette Brual", - "author_inst": "Women's College Hospital" - }, - { - "author_name": "Cherry Chu", - "author_inst": "Women's College Hospital" - }, - { - "author_name": "Jiming Fang", - "author_inst": "Institute for Clinical Evaluative Sciences" - }, - { - "author_name": "Cathleen Fleury", - "author_inst": "Women's College Hospital" - }, - { - "author_name": "Vess Stamenova", - "author_inst": "Women's College Hospital" - }, - { - "author_name": "Onil Bhattacharyya", - "author_inst": "Women's College Hospital" - }, - { - "author_name": "Mina Tadrous", - "author_inst": "Women's College Hospital" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "geriatric medicine" - }, { "rel_doi": "10.1101/2022.07.26.22278045", "rel_title": "Effectiveness of the BNT162b2 vaccine against SARS-CoV-2 infection among children and adolescents in Qatar", @@ -246288,6 +247089,69 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.07.26.22278084", + "rel_title": "Visual Transformer and Deep CNN Prediction of High-risk COVID-19 Infected Patients using Fusion of CT Images and Clinical Data", + "rel_date": "2022-07-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.26.22278084", + "rel_abs": "Despite the globally reducing hospitalization rates and the much lower risks of Covid-19 mortality, accurate diagnosis of the infection stage and prediction of outcomes are clinically of interest. Advanced current technology can facilitate automating the process and help identifying those who are at higher risks of developing severe illness. Deep-learning schemes including Visual Transformer and Convolutional Neural Networks (CNNs), in particular, are shown to be powerful tools for predicting clinical outcomes when fed with either CT scan images or clinical data of patients.\n\nThis paper demonstrates how a novel 3D data fusion approach through concatenating CT scan images with patients clinical data can remarkably improve the performance of Visual Transformer and CNN models in predicting Covid-19 infection outcomes. Here, we explore and represent comprehensive research on the efficiency of Video Swin Transformers and a number of CNN models fed with fusion datasets and CT scans only vs a set of conventional classifiers fed with patients clinical data only. A relatively large clinical dataset from 380 Covid-19 diagnosed patients was used to train/test the models. Results show that the 3D Video Swin Transformers fed with the fusion datasets of 64 sectional CT scans+67 (or 30 selected) clinical labels outperformed all other approaches for predicting outcomes in Covid-19-infected patients amongst all techniques (i.e., TPR=0.95, FPR=0.40, F0.5 score=0.82, AUC=0.77, Kappa=0.6). Results indicate possibilities of predicting the severity of outcome using patients CT images and clinical data collected at the time of admission to hospital.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Hamid Abbasi", + "author_inst": "University of Auckland" + }, + { + "author_name": "Sara Saberi Moghadam Tehrani", + "author_inst": "Faculty of Engineering, Alzahra University, Tehran, Iran," + }, + { + "author_name": "Maral Zarvani", + "author_inst": "Faculty of Engineering, Alzahra University, Tehran, Iran," + }, + { + "author_name": "Pariya Amiri", + "author_inst": "Pooyandegan Rah Saadat Company, Tehran, Iran," + }, + { + "author_name": "Reza Azmi", + "author_inst": "Faculty of Engineering, Alzahra University, Tehran, Iran," + }, + { + "author_name": "Zahra Ghods", + "author_inst": "Faculty of Engineering, Alzahra University, Tehran, Iran," + }, + { + "author_name": "Narges Nourozi", + "author_inst": "Faculty of Engineering, Alzahra University, Tehran, Iran," + }, + { + "author_name": "Masoomeh Raoufi", + "author_inst": "Department of Radiology, School of Medicine, Imam Hossein Hospital, Shahid Beheshti, University of Medical Sciences." + }, + { + "author_name": "Seyed Amir Ahmad Safavi-Naini", + "author_inst": "Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran." + }, + { + "author_name": "Amirali Soheili", + "author_inst": "Medical Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran." + }, + { + "author_name": "Sara Abolghasemi", + "author_inst": "Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medial Sciences, Tehran, Iran," + }, + { + "author_name": "Mohammad Javad Gharib", + "author_inst": "Auckland City Hospital, Auckland, 1010, New Zealand," + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2022.07.22.501212", "rel_title": "SARS-CoV-2 Non-Structural Protein 1(NSP1) Mutation Virulence and Natural Selection: Evolutionary Trends in the Six Continents", @@ -247691,53 +248555,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.07.23.22277948", - "rel_title": "Predicting intention to vaccinate against COVID-19 in older Syrian refugees in Lebanon: findings from a multi-wave study", - "rel_date": "2022-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.23.22277948", - "rel_abs": "IntroductionCOVID-19 vaccine acceptance among refugees in the Arab region remains low. This study aimed to examine the prevalence, reasons and predictors of COVID-19 vaccine refusal among older Syrian refugees in Lebanon.\n\nMethodA nested cross-sectional study among older Syrian refugees in Lebanon. The sampling frame was a complete listing of beneficiary households of a humanitarian organization with an adult aged 50 years or older. Telephone surveys were completed between September 2020 and May 2021. Logistic regression models were used to identify predictors of COVID-19 vaccine refusal. Models were internally validated using bootstrap methods and the models calibration and discrimination were presented.\n\nResultsOf 3,173 Syrian refugees, 61% intended to receive the COVID-19 vaccine, 31% refused and 7% were undecided. Reasons for vaccine refusal were: preference to follow preventive measures (27%) and belief that the vaccine is not essential (21%). Despite high vaccine acceptance, only 6% of older Syrian refugees were registered on the national platform to receive the vaccine. Reasons for not registering included: being unsure about how to register (36%), and not wanting to receive the vaccine (33%). Predictors of COVID-19 vaccine refusal included: sex (female), older age, education, living outside informal tented settlements, perceiving COVID-19 as not severe and vaccines as not safe or effective, and using social media for information on COVID-19. After adjusting for optimization, the final model showed moderate discrimination (C-statistic: 0.65 (95% CI:(0.63-0.67)) and good calibration (C-Slope: 0.93 (95% CI:0.82-1.06)).\n\nConclusionThis study developed predictive model for vaccination intention with a moderate discriminative ability and good calibration. Prediction models in humanitarian settings can help to identify refugees at higher risk of not intending to receive the COVID-19 vaccine for public health targeting.\n\nWhat is already known on this topicDespite global efforts towards more inclusive national deployment vaccination plans, vaccine coverage and uptake among migrants and refugees remains low. Refugees and migrants, the majority of whom live in low and middle income countries, bear the double burden of vaccine inequity and face several challenges and barriers to vaccination including low vaccine supply, inability to access health services, fear of arrest and deportation, lack of accessible information as well as other language, and economic barriers. Research on COVID-19 vaccine intentions among refugees in the region has been limited. Understanding intentions and predictors to vaccinate among refugees, and addressing barriers to vaccine acceptance and registration, is crucial to ensure equitable vaccination and coverage, reduce the spread of COVID-19 and achieve herd immunity.\n\nWhat this study addsThis study is one of the first to develop and internally validate a model of intention to refuse vaccination against COVID-19 in older Syrian refugees. Predictors of intention to refuse the vaccine include age, education, living outside informal tented settlements, sex, perceiving COVID-19 as not a serious infection and vaccines as not safe or effective, and using social media as a source of information on COVID-19. The primary reasons for vaccine refusal were: preference to follow preventive measures, concerns that the vaccine is too new, and belief that the vaccine is not essential. Registration on the national platform to receive the vaccine was low and the reasons for not registering included: being unsure about how to register, and not wanting to receive the vaccine.\n\nHow this study might affect research, practice or policyThis study highlights the need for targeted interventions to enhance vaccine acceptance and uptake among older Syrian refugees, and address barriers to vaccine registration. Predictors of COVID-19 vaccine refusal among older Syrian refugees will inform humanitarian programming and public health campaigns, and guide resource allocation and deployment planning. Findings inform future research to better understand the predictors of vaccine refusal.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Noura Joseph El Salibi", - "author_inst": "American University of Beirut Faculty of Health Sciences" - }, - { - "author_name": "Sawsan Abdulrahim", - "author_inst": "American University of Beirut" - }, - { - "author_name": "Maria El Haddad", - "author_inst": "American University of Beirut" - }, - { - "author_name": "Berthe Abi Zeid", - "author_inst": "American University of Beirut Faculty of Health Sciences" - }, - { - "author_name": "Marwan Alawieh", - "author_inst": "Norwegian Refugee Council" - }, - { - "author_name": "Zeinab Ramadan", - "author_inst": "Norwegian Refugee Council" - }, - { - "author_name": "Hala Ghattas", - "author_inst": "American University of Beirut Faculty of Health Sciences" - }, - { - "author_name": "Stephen J McCall", - "author_inst": "American University of Beirut" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.07.22.22277947", "rel_title": "High titre neutralizing antibodies in response to SARS-CoV-2 infection require RBD-specific CD4 T cells that include proliferative memory cells.", @@ -248006,6 +248823,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.21.22277907", + "rel_title": "The Effect of SARS-COV-2 Variant on Respiratory Features and Mortality Among Vaccinated and Non-Fully Vaccinated Patients", + "rel_date": "2022-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.21.22277907", + "rel_abs": "BackgroundSARS-CoV-2 (COVID-19) has caused over 80 million infections and 973,000 deaths in the United States, and mutations are linked to increased transmissibility. This study aimed to determine the effect of SARS-CoV-2 variants on respiratory features and mortality and to determine the effect of vaccination status.\n\nMethodA retrospective review of medical records (n=63,454 unique patients) using The University of California Health COvid Research Data Set (UC CORDS) was performed to identify respiratory features, vaccination status, and mortality. Variants were identified using the CDC data tracker.\n\nResultsIncreased odds of death were observed among those not fully vaccinated (Delta OR: 1.64, p = 0.052; Omicron OR: 1.96, p < 0.01). Later variants (i.e., Delta and Omicron) demonstrated a reduction in the frequency of lower respiratory tract features with a concomitant increase in upper respiratory tract features. Vaccination status was associated with survival and a decrease in the frequency of many upper and lower respiratory tract features.\n\nDiscussionSARS-CoV-2 variants show a reduction in lower respiratory tract features with an increase in upper respiratory tract features. Being fully vaccinated results in fewer respiratory features and higher odds of survival, supporting vaccination in preventing morbidity and mortality from COVID-19.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Thomas D Hughes", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Ajan Subramanian", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Rana Chakraborty", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Shannon A. Cotton", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Maria Del Pilar Giraldo Herrera", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Yong Huang", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Natalie Lambert", + "author_inst": "Indiana University" + }, + { + "author_name": "Melissa D. Pinto", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Amir M. Rahmani", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Carmen Josefa Sierra", + "author_inst": "University of Miami" + }, + { + "author_name": "Charles A Downs", + "author_inst": "University Of Miami" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.21.22277910", "rel_title": "A distinct symptom pattern emerges for COVID-19 Long-Haul: A nationwide study", @@ -249337,81 +250213,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.07.19.22277248", - "rel_title": "COVID-19 could cause long term peripheral nerve demyelination and axonal loss: A One Year Prospective Cohort Study", - "rel_date": "2022-07-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.19.22277248", - "rel_abs": "BackgroundThere is a lack of studies on large-sample, medium-, or long-term follow-up data of peripheral neuropathy (PNP) in the COVID-19 survivors. This study evaluated the characteristics and related risk factors of PNP in the medium- and long-term rehabilitation, which provided real-world study data for the complete recovery of COVID-19 patients.\n\nMethodsThis study was a prospective cohort study of the COVID-19 survivors. We collected data on baseline characteristics, symptoms at onset and after discharge during the 6-month and 12-month follow-up. Peripheral nerves were measured by electromyography and inducible potentiometer. We used multivariable logistic regression to analyze the influencing factors of PNP. Additionally, we compared the difference between the two measurements among the population who completed both measurements.\n\nResults313 patients were included in the study and all of them underwent nerve conduction study. 67 patients completed two measurements at 6-month and 12-month follow-up. Commonly reported symptoms contained memory loss (86%), hair loss (28%), anxiety (24%), and sleep difficulties (24%). 232 patients (74%) were found with PNP, including 51 (16%) with mononeuropathy and 181 (58%) with generalized PNP. Patients with measurement at 12-month follow-up had a higher prevalence of generalized PNP (p=0.006). For pathological types, 64 (20%) patients had only axonal loss, 67 (21%) had only demyelination, and 101 (32%) had a mixed type. There was no significant difference in the prevalence of accompanying symptoms after discharge between the two groups with or without PNP. After adjustment, age was positively associated with PNP (OR=1.22 per 10-year increase of age, 95% CI, 1.05-1.41). Compared with less than the median amount of IgG at discharge, higher amount of IgG was associated with decreased risk of F-wave abnormality (OR=0.32, 95%CI, 0.11-0.82), but no significant difference in other types of PNP.\n\nConclusions and RelevanceSARS-CoV-2 could cause PNP in hospital survivors with COVID-19, which persisted and was associated with age, education, and IgG antibody at discharge, but had no significant correlation with symptoms after discharge.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Yubin Zhao", - "author_inst": "People' Hospital Shijiazhuang,Hebei Province,China" - }, - { - "author_name": "Qian Yang", - "author_inst": "People's Hospital,Shijiazhuang,Hebei Province,China" - }, - { - "author_name": "Feng Sun", - "author_inst": "School of Public Health, Peking University" - }, - { - "author_name": "Meng Zhang", - "author_inst": "Peking university" - }, - { - "author_name": "Yanhui Lai", - "author_inst": "People' Hospital Shijiazhuang,Hebei Province,China" - }, - { - "author_name": "Xuzhao Liu", - "author_inst": "North China University of Science and Technology" - }, - { - "author_name": "Fengshuang Liu", - "author_inst": "Hebei University of Chinese Medicine" - }, - { - "author_name": "Hongmin Zang", - "author_inst": "Hebei University of Chinese Medicine" - }, - { - "author_name": "Jinzhong Song", - "author_inst": "Hebei University of Chinese Medicine" - }, - { - "author_name": "Na Li", - "author_inst": "People' Hospital Shijiazhuang,Hebei Province,China" - }, - { - "author_name": "Shuhua Cui", - "author_inst": "People' Hospital Shijiazhuang,Hebei Province,China" - }, - { - "author_name": "Wei Shao", - "author_inst": "Peking university" - }, - { - "author_name": "Jiang Ma", - "author_inst": "People' Hospital Shijiazhuang,Hebei Province,China" - }, - { - "author_name": "Zhibo Wang", - "author_inst": "People' Hospital Shijiazhuang,Hebei Province,China" - }, - { - "author_name": "Ling Cui", - "author_inst": "People' Hospital Shijiazhuang,Hebei Province,China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.20.22277838", "rel_title": "National and regional prevalence of SARS-CoV-2 antibodies in primary and secondary school children in England: the School Infection Survey, a national open cohort study, November 2021", @@ -249652,6 +250453,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.07.21.500897", + "rel_title": "Buying time: detecting VOCs in SARS-CoV-2 via co-evolutionary signals", + "rel_date": "2022-07-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.21.500897", + "rel_abs": "We present a novel framework facilitating the rapid detection of variants of interest (VOI) and concern (VOC) in a viral multiple sequence alignment (MSA). The framework is purely based on the genomic sequence data, without requiring prior established biological analysis. The frameworks building blocks are sets of co-evolving sites (motifs), identified via co-evolutionary signals within the MSA. Motifs form a weighted simplicial complex, whose vertices are sites that satisfy a certain nucleotide diversity. Higher dimensional simplices are constructed using distances quantifying the co-evolutionary coupling of pairs and in the context of our method maximal motifs manifest as clusters. The framework triggers an alert via a cluster with a significant fraction of newly emerging polymorphic sites. We apply our method to SARS-CoV-2, analyzing all alerts issued from November 2020 through August 2021 with weekly resolution for England, USA, India and South America. Within a week at most a handful of alerts, each of which involving on the order of 10 sites are triggered. Cross referencing alerts with a posteriori knowledge of VOI/VOC-designations and lineages, motif-induced alerts detect VOIs/VOCs rapidly, typically weeks earlier than current methods. We show how motifs provide insight into the organization of the characteristic mutations of a VOI/VOC, organizing them as co-evolving blocks. Finally we study the dependency of the motif reconstruction on metric and clustering method and provide the receiver operating characteristic (ROC) of our alert criterion.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Christopher Barrett", + "author_inst": "University of Virginia/Biocomplexity Institute" + }, + { + "author_name": "Andrei C. Bura", + "author_inst": "University of Virginia/Biocomplexity Institute" + }, + { + "author_name": "Qijun He", + "author_inst": "University of Virginia/Biocomplexity Institute" + }, + { + "author_name": "Fenix W. Huang", + "author_inst": "University of Virginia/Biocomplexity Institute" + }, + { + "author_name": "Thomas J.X. Li", + "author_inst": "University of Virginia/Biocomplexity Institute" + }, + { + "author_name": "Christian M. Reidys", + "author_inst": "University of Virginia/Biocomplexity Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.07.19.500637", "rel_title": "Vaccination shapes evolutionary trajectories of SARS-CoV-2", @@ -251139,49 +251979,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2022.07.18.22276918", - "rel_title": "Drivers and prevalence of COVID-19 vaccine uptake among homeless and precariously housed people in France: a cross-sectional population-based study", - "rel_date": "2022-07-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.18.22276918", - "rel_abs": "BackgroundFew global data exist regarding COVID-19 vaccine coverage in people experiencing homelessness (PEH) or precariously housed (PH) who are at high risk for COVID-19 infection, hospitalization, and death. Given the absence of documented French data, we aimed to determine COVID-19 vaccine coverage in PEH/PH in France, and its drivers.\n\nMethodsWe carried out a cross-sectional study following a two-stage cluster-sampling design in Ile-de-France and Marseille, France, in late 2021. Participants aged over 18 years were recruited where they slept the previous night, and then stratified for analysis into three housing groups (\"Streets\", \"Accommodated\", and \"Housed\"). Interviews were conducted face-to-face in the participants preferred language. Multilevel univariate and multivariable logistic regression models were built.\n\nFindings3,690 individuals were surveyed: 855 in the \"Housed\" stratum, 2,321 in the \"Accommodated\" stratum and 514 in the \"Streets\" stratum. 76{middle dot}2% (95%CI 74{middle dot}3-78{middle dot}1) reported receiving at least one COVID-19 vaccine dose. Vaccine uptake varied by stratum, with uptake highest (85.6%; reference) in \"Housed\", followed by \"Accommodated\" (75{middle dot}4%; AOR=0{middle dot}79 ; 95%CI 0{middle dot}51-1{middle dot}09 vs Housed) and lowest in \"Streets\" (42{middle dot}0%; AOR=0{middle dot}38 ; 95%CI 0{middle dot}25-0{middle dot}57 vs Housed). Use for vaccine certificate, socioeconomic drivers and vaccine hesitancy explained vaccine coverage.\n\nInterpretationIn France, PEH/PH are less likely than the general population likely to receive COVID-19 vaccines; with the most excluded being the least likely. The influence of both structural drivers and vaccine beliefs in PEH/PH reinforces the importance of targeted outreach, on-site vaccination and sensitisation activities to further vaccine uptake.\n\nFundingSante Publique France, Agence Nationale de Recherches sur le Sida/Capnet, Agence Regionale de Sante - Ile de France, Medecins Sans Frontieres, and Societe de Pathologie Infectieuse de Langue Francaise.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Thomas ROEDERER", - "author_inst": "Epicentre, Paris, France" - }, - { - "author_name": "Bastien MOLLO", - "author_inst": "Medecins Sans Frontieres, Paris, France" - }, - { - "author_name": "Charline VINCENT", - "author_inst": "Epicentre, Paris, France" - }, - { - "author_name": "Ghislain LEDUC", - "author_inst": "Epicentre, Paris, France" - }, - { - "author_name": "Jessica SAYYAD", - "author_inst": "Epicentre, Paris, France" - }, - { - "author_name": "Marine MOSNIER", - "author_inst": "Prospective et Cooperation, Marseille, France" - }, - { - "author_name": "Stephanie VANDENTORREN", - "author_inst": "Sante Publique France, Saint Maurice, France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.07.16.22277716", "rel_title": "The association of typical and atypical symptoms on in-hospital mortality of older adults with COVID-19: a multicentre cohort study", @@ -251474,6 +252271,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.17.22277721", + "rel_title": "A simple SEIR-V model to estimate COVID-19 prevalence and predict SARS-CoV-2 transmission using wastewater-based surveillance data", + "rel_date": "2022-07-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.17.22277721", + "rel_abs": "Wastewater-based surveillance (WBS) has been widely used as a public health tool to monitor SARS-CoV-2 transmission. However, epidemiological inference from WBS data remains understudied and limits its application. In this study, we have established a quantitative framework to estimate COVID-19 prevalence and predict SARS-CoV-2 transmission through integrating WBS data into an SEIR-V model. We conceptually divide the individual-level viral shedding course into exposed, infectious, and recovery phases as an analogy to the compartments in population-level SEIR model. We demonstrated that the temperature effect on viral losses in the sewer can be straightforwardly incorporated in our framework. Using WBS data from the second wave of the pandemic (Oct 02, 2020 - Jan 25, 2021) in the Great Boston area, we showed that the SEIR-V model successfully recapitulates the temporal dynamics of viral load in wastewater and predicts the true number of cases peaked earlier and higher than the number of reported cases by 16 days and 8.6 folds (R = 0.93), respectively. This work showcases a simple, yet effective method to bridge WBS and quantitative epidemiological modeling to estimate the prevalence and transmission of SARS-CoV-2 in the sewershed, which could facilitate the application of wastewater surveillance of infectious diseases for epidemiological inference and inform public health actions.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Tin Phan", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Samantha Brozak", + "author_inst": "Arizona State University" + }, + { + "author_name": "Bruce Pell", + "author_inst": "Lawrence Technological University" + }, + { + "author_name": "Anna Gitter", + "author_inst": "The University of Texas Health Science Center at Houston" + }, + { + "author_name": "Kristina D Mena", + "author_inst": "The University of Texas Health Science Center at Houston" + }, + { + "author_name": "Yang Kuang", + "author_inst": "Arizona State University" + }, + { + "author_name": "Fuqing Wu", + "author_inst": "The University of Texas Health Science Center at Houston" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.18.22277749", "rel_title": "COVID-19 vaccine effectiveness against progression to in-hospital mortality -- Zambia, 2021-2022", @@ -253129,41 +253969,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.07.12.22277450", - "rel_title": "Effect of Vitamin D3 supplementation vs. dietary-hygienic measures on SARS-COV-2 infection rates in hospital workers with 25-hydroxyvitamin D3 levels >20 ng/mL", - "rel_date": "2022-07-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.12.22277450", - "rel_abs": "BackgroundThere is scant information on the effect of supplementation with vitamin D3 in SARS-COV-2 infection cases when patient 25-hydroxyvitamin D3 [25(OH)D3] levels are between 20-100ng/mL. Our aim was to evaluate the effect of supplementation with vitamin D3 vs. dietary-hygienic measures on the SARS-COV-2 infection rate in participants with serum 25(OH)D3 levels [≥]20ng/mL.\n\nMethodsWe invited hospital workers with 25(OH)D3 levels between 20-100 ng/mL and no previous SARS-COV-2 infection; they were randomized as follows: treatment options were a) vitamin D3 supplementation (52,000 IU monthly, G1) or b) dietary-hygienic measures (G2). We conducted a 3- to 6-month follow-up of SARS-COV-2 infections. Participants with 25(OH)D3 levels <20 ng/mL were also analyzed. We divided these latter participants depending on whether they were supplemented (G3) or not (G4).\n\nResultsWe analyzed 198 participants, with an average age of 44.4 (SD 9) years, and 130 (65.7%) were women. G1 had less cases of SARS-COV-2 infection than G2 after a follow-up of 3- to 6-months (p<0.05). There were no differences between G3 and G4 at the 3- and 6-month follow-up cutoff points (p>0.05). Using mixed effect Cox regression analysis in 164 participants that completed six months of follow-up, vitamin D3 supplementation appeared to act as a protective factor against SARS-COV-2 infection (HR 0.21, p=0.008) in G1 and G2. None of the participants treated with the supplementation doses had serum 25(OH)D3 levels > 100ng/mL.\n\nConclusionVitamin D3 supplementation in participants with 25(OH)D3 levels between 20-100 ng/mL have a lower rate of SARS-COV-2 infection in comparison with the use of dietary-hygienic measures at six months follow-up.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Maria Elena Romero-Ibarguengoitia", - "author_inst": "Hospital Clinica Nova" - }, - { - "author_name": "Dalia Gutierrez-Gonzalez", - "author_inst": "Hospital Clinica Nova" - }, - { - "author_name": "Carlos Cantu-Lopez", - "author_inst": "Hospital Clinica Nova" - }, - { - "author_name": "Miguel Angel Sanz-Sanchez", - "author_inst": "Hospital Clinica Nova" - }, - { - "author_name": "Arnulfo Gonzalez-Cantu", - "author_inst": "Hospital Clinica Nova" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.12.22277518", "rel_title": "Tracing the international arrivals of SARS-CoV-2 Omicron variants after Aotearoa New Zealand reopened its border", @@ -253592,6 +254397,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.07.14.22277643", + "rel_title": "Bubble-PAPR: Phase I clinical evaluation of an in-house developed prototype powered air-purifying respirator for use by healthcare workers", + "rel_date": "2022-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.14.22277643", + "rel_abs": "Structured abstractO_ST_ABSObjectivesC_ST_ABSWe aimed to design and produce a low-cost, ergonomic, hood-integrated Powered Air-Purifying Respirator (Bubble-PAPR) for pandemic healthcare use, offering optimal and equitable protection to all staff. We hypothesised that participants would rate Bubble-PAPR more highly than current FFP3 face mask respiratory protective equipment (RPE).\n\nDesignRapid design and evaluation cycles occurred based on the identified user needs. We conducted diary card and focus group exercises to identify relevant tasks requiring RPE. Lab-based safety standards established against British Standard BS-EN-12941 and EU2016/425. Questionnaire-based usability data from participating frontline healthcare staff before (usual RPE) and after using Bubble-PAPR.\n\nSettingOverseen by a trial safety committee, evaluation progressed sequentially through laboratory, simulated, low-risk, then high-risk clinical environments of a single tertiary NHS hospital.\n\nParticipants15 staff completed diary cards and focus groups. 91 staff from a range of clinical and non-clinical roles completed the study, wearing Bubble-PAPR for a median of 45 minutes (IQR 30-80 [15-120]). Participants self-reported a range of heights (mean 1.7m [SD 0.1, range 1.5-2.0]), weights (72.4kg [16.0, 47-127]) and body mass indices (25.3 [4.7,16.7-42.9]).\n\nOutcome measuresPrimary: \"How comfortable do you feel in your PPE?\" (Likert scale bounded by 1 [very uncomfortable] to 7 [very comfortable]). Secondary outcomes: perceived safety, communication, anxiety, discomfort, and performance.\n\nResultsBubble-PAPR mean comfort score was 5.64(SD 1.55) versus usual FFP3 2.96(1.44) (mean difference 2.68 (95% CI 2.23-3.14, p<0.001). There was a significant difference in favour of Bubble-PAPR across all secondary outcomes.\n\nConclusionsBubble-PAPR achieved its primary purpose of keeping staff safe from airborne particulate material whilst improving comfort and the user experience. The design and development of Bubble-PAPR were conducted using a careful evaluation strategy addressing key regulatory and safety steps, in contrast to many devices rapidly developed and deployed during the pandemic.\n\nTrial registrationIRAS ID:288493, REC Ref:21/WA/0018. ClinicalTrials.gov (NCT04681365).\n\nStrengths and limitations of this studyO_LIWe employed user-centred design, engineering optimisation and staged feasibility testing to develop a novel Powered Air-Purifying Respirator (Bubble-PAPR) for use specifically in frontline healthcare settings.\nC_LIO_LIDiverse, frontline healthcare staff compared Bubble-PAPR with usual FFP3 face masks.\nC_LIO_LIThe design and development of Bubble-PAPR were conducted using a careful strategy addressing key regulatory and safety steps, in contrast to many devices rapidly developed and deployed during the pandemic.\nC_LIO_LIBubble-PAPR is an excellent example of developing a cosmopolitan network that could become a key feature of future system resilience.\nC_LI", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Brendan A McGrath", + "author_inst": "Manchester University NHS Foundation Trust" + }, + { + "author_name": "Clifford L Shelton", + "author_inst": "Lancaster University" + }, + { + "author_name": "Angela Gardner", + "author_inst": "Manchester University NHS Foundation Trust" + }, + { + "author_name": "Ruth Coleman", + "author_inst": "Manchester University NHS Foundation Trust" + }, + { + "author_name": "James Lynch", + "author_inst": "Manchester University NHS Foundation Trust" + }, + { + "author_name": "Peter G Alexander", + "author_inst": "Manchester University NHS Foundation Trust" + }, + { + "author_name": "Glen Cooper", + "author_inst": "The University of Manchester" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2022.07.12.22277533", "rel_title": "Fully Quantitative Measurements of the Antibody Levels for SARS-CoV-2 Infections and Vaccinations calibrated against the NISTmAb Standard IgG Antibody", @@ -255063,89 +255911,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.07.14.500039", - "rel_title": "SARS-CoV-2 BA.4 infection triggers more cross-reactive neutralizing antibodies than BA.1", - "rel_date": "2022-07-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.14.500039", - "rel_abs": "SARS-CoV-2 variants of concern (VOCs) differentially trigger neutralizing antibodies with variable cross-neutralizing capacity. Here we show that unlike SARS-CoV-2 Omicron BA.1, which triggered neutralizing antibodies with limited cross-reactivity, BA.4/5 infection triggers highly cross-reactive neutralizing antibodies. Cross-reactivity was observed both in the absence of prior vaccination and also in breakthrough infections following vaccination. This suggests that next-generation vaccines incorporating BA.4, which is spreading globally, might result in enhanced neutralization breadth.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Simone Richardson", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Thopisang Motlou", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Mieke van der Mescht", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Bronwen Lambson", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Josie Everatt", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Daniel Amoako", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Anne Van Gottberg", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Nicole Wolter", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Zelda de Beer", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Talita Roma de Villiers", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Annie Bodenstein", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Gretha van den Berg", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Theresa M. Rossouw", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Michael Boswell", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Veronica Ueckermann", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Jinal Bhiman", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Penny Moore", - "author_inst": "University of the Witwatersrand" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.07.14.500068", "rel_title": "Ending transmission of SARS-CoV-2: sterilizing immunity using an intranasal subunit vaccine", @@ -255378,6 +256143,125 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.07.14.500063", + "rel_title": "Genome-first detection of emerging resistance to novel therapeutic agents for SARS-CoV-2", + "rel_date": "2022-07-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.14.500063", + "rel_abs": "Some COVID-19 patients are unable to clear their infection or are at risk of severe disease, requiring treatment with neutralising monoclonal antibodies (nmAb) and/or antivirals. The rapid roll-out of novel therapeutics means there is limited understanding of the likely genetic barrier to drug resistance. Unprecedented genomic surveillance of SARS-CoV-2 in the UK has enabled a genome-first approach to the detection of emerging drug resistance. Here we report the accrual of mutations in Delta and Omicron cases treated with casirivimab+imdevimab and sotrovimab respectively. Mutations occur within the epitopes of the respective nmAbs. For casirivimab+imdevimab these are present on contiguous raw reads, simultaneously affecting both components. Using surface plasmon resonance and pseudoviral neutralisation assays we demonstrate these mutations reduce or completely abrogate antibody affinity and neutralising activity, suggesting they are driven by immune evasion. In addition, we show that some mutations also reduce the neutralising activity of vaccine-induced serum.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Manon Ragonnet-Cronin", + "author_inst": "Imperial College London" + }, + { + "author_name": "Rungtiwa Nutalai", + "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "Jiandong Huo", + "author_inst": "Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK" + }, + { + "author_name": "Aiste Dijokaite-Guraliuc", + "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "Raksha Das", + "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "Aekkachai Tuekprakhon", + "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "Piyada Supasa", + "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "Chang Liu", + "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "Muneeswaran Selvaraj", + "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "Natalie Groves", + "author_inst": "Genomics Public Health Analysis, UK Health Security Agency" + }, + { + "author_name": "Hassan Hartman", + "author_inst": "Genomics Public Health Analysis, UK Health Security Agency" + }, + { + "author_name": "Nicholas Ellaby", + "author_inst": "Genomics Public Health Analysis, UK Health Security Agency" + }, + { + "author_name": "J. Mark Sutton", + "author_inst": "Genomics Public Health Analysis, UK Health Security Agency" + }, + { + "author_name": "Mohammad W. Bahar", + "author_inst": "Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK" + }, + { + "author_name": "Daming Zhou", + "author_inst": "Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK" + }, + { + "author_name": "Elizabeth Fry", + "author_inst": "Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK" + }, + { + "author_name": "Jingshan Ren", + "author_inst": "Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK" + }, + { + "author_name": "Colin Brown", + "author_inst": "Genomics Public Health Analysis, UK Health Security Agency" + }, + { + "author_name": "Paul Klenerman", + "author_inst": "Nuffield Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "Susan J. Dunachie", + "author_inst": "Nuffield Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "Juthathip Mongkolsapaya", + "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "Susan Hopkins", + "author_inst": "Genomics Public Health Analysis, UK Health Security Agency" + }, + { + "author_name": "Meera Chand", + "author_inst": "Genomics Public Health Analysis, UK Health Security Agency" + }, + { + "author_name": "David I. Stuart", + "author_inst": "Genomics Public Health Analysis, UK Health Security Agency" + }, + { + "author_name": "Gavin R. Screaton", + "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "Sakib Rokadiya", + "author_inst": "Genomics Public Health Analysis, UK Health Security Agency" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2022.07.15.500170", "rel_title": "Pangenome analysis of SARS-CoV2 strains to Identify Potential vaccine targets by Reverse Vaccinology", @@ -256677,161 +257561,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.07.11.22277368", - "rel_title": "Structural epitope profiling identifies antibodies associated with critical COVID-19 and long COVID", - "rel_date": "2022-07-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.11.22277368", - "rel_abs": "Antibodies can have beneficial, neutral, or harmful effects so resolving an antibody repertoire to its target epitopes may explain heterogeneity in susceptibility to infectious disease. However, the three-dimensional nature of antibody-epitope interactions limits discovery of important targets. We describe and experimentally validated a novel computational method and synthetic biology pipeline for identifying epitopes that are structurally stable and functionally important and apply it to the SARS-CoV-2 proteome. We show patterns of epitope-binding antibodies associated with immunopathology, including a non-isotype switching IgM response to a Membrane protein epitope which is amongst the strongest immunological features associated with severe COVID-19 to date (adjusted OR 72.14, 95% CI: 9.71 - 1300.15). Consistent with a hypothesis that the mechanism driving the non-switching response was T independent B cell activation, we find that B cells secrete IgM and proliferate on exposure to virus-like particles lacking Spike. We also identified persistence (> 1 year) of this response in individuals with longCOVID particularly affected by fatigue and depression. These findings point to a previously unrecognized coronavirus host-pathogen interaction. We demonstrate that the Membrane epitope is a promising vaccine and monoclonal antibody target, which may complement spike-directed vaccination broadening immunological protection.\n\nOne-Sentence SummaryUsing a protein-structure-based B cell epitope discovery method with a wide range of possible applications, we have identified a novel host-pathogen signature associated with SARS-CoV-2 immunopathology and suggest the viral Membrane protein contains a pathological T independent antigen.", - "rel_num_authors": 35, - "rel_authors": [ - { - "author_name": "Patrick K.A. Kearns", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Charles Dixon", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Western General Hospital. Crewe Road, Edinburgh EH4 2XU" - }, - { - "author_name": "Mihaly Badonyi", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Western General Hospital. Crewe Road, Edinburgh EH4 2XU" - }, - { - "author_name": "Kim Lee", - "author_inst": "Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh; The King's Buildings, Ashworth Laboratories, Charlotte A" - }, - { - "author_name": "Rafal Czapiewski", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Western General Hospital. Crewe Road, Edinburgh EH4 2XU" - }, - { - "author_name": "Olivia Fleming", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Western General Hospital. Crewe Road, Edinburgh EH4 2XU" - }, - { - "author_name": "Lukas Gerasimivicous", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Western General Hospital. Crewe Road, Edinburgh EH4 2XU" - }, - { - "author_name": "Rinal Sahputra", - "author_inst": "Division of Infection, Immunity & Respiratory Medicine, School of Biological Sciences, University of Manchester; Oxford Rd, Manchester, United Kingdom M13 9PL" - }, - { - "author_name": "Bethany Potts", - "author_inst": "Division of Infection, Immunity & Respiratory Medicine, School of Biological Sciences, University of Manchester; Oxford Rd, Manchester, United Kingdom M13 9PL" - }, - { - "author_name": "Sam Benton", - "author_inst": "Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh; The King's Buildings, Ashworth Laboratories, Charlotte A" - }, - { - "author_name": "Jacky Guy", - "author_inst": "Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh; CH Waddington Building, Kings Buildings, Mayfield Road, Edinbu" - }, - { - "author_name": "Scott Neilson", - "author_inst": "Edinburgh Genome Foundry, University of Edinburgh; Michael Swann Building, Max Born Crescent, Edinburgh, United Kingdom EH9 3BF" - }, - { - "author_name": "Helen Wise", - "author_inst": "Department of Clinical Biochemistry, Royal Infirmary of Edinburgh; 51 Little France Cres, Old Dalkeith Rd, Edinburgh, United Kingdom EH16 4SA" - }, - { - "author_name": "Sara Jenks", - "author_inst": "Department of Clinical Biochemistry, Royal Infirmary of Edinburgh; 51 Little France Cres, Old Dalkeith Rd, Edinburgh, United Kingdom EH16 4SA" - }, - { - "author_name": "Kate Templeton", - "author_inst": "Department of Clinical Biochemistry, Royal Infirmary of Edinburgh; 51 Little France Cres, Old Dalkeith Rd, Edinburgh, United Kingdom EH16 4SA" - }, - { - "author_name": "Christina Dold", - "author_inst": "Oxford Vaccine Group, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford; Churchill Hospital Old Road, Headington, Oxford, United Kingd" - }, - { - "author_name": "Teresa Lambe", - "author_inst": "Oxford Vaccine Group, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford; Churchill Hospital Old Road, Headington, Oxford, United Kingd" - }, - { - "author_name": "Alexander J. Mentzer", - "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, United Kingdom OX3 7BN" - }, - { - "author_name": "Julian Knight", - "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, United Kingdom OX3 7BN" - }, - { - "author_name": "- COMBAT", - "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, United Kingdom OX3 7BN" - }, - { - "author_name": "Andrew Pollard", - "author_inst": "Oxford Vaccine Group, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford; Churchill Hospital Old Road, Headington, Oxford, United Kingd" - }, - { - "author_name": "Eleanor Barnes", - "author_inst": "Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, UK" - }, - { - "author_name": "Paul Klenerman", - "author_inst": "Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, UK" - }, - { - "author_name": "Susanna Dunachie", - "author_inst": "Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, UK" - }, - { - "author_name": "Tracy Hussell", - "author_inst": "Division of Infection, Immunity & Respiratory Medicine, School of Biological Sciences, University of Manchester; Oxford Rd, Manchester, United Kingdom M13 9PL" - }, - { - "author_name": "- CIRCO", - "author_inst": "Division of Infection, Immunity & Respiratory Medicine, School of Biological Sciences, University of Manchester; Oxford Rd, Manchester, United Kingdom M13 9PL" - }, - { - "author_name": "Laura McWhirter", - "author_inst": "Centre for Clinical Brain Sciences, University of Edinburgh; 49 Little France Crescent, Edinburgh, United Kingdom EH16 4SB" - }, - { - "author_name": "Alan Carson", - "author_inst": "Centre for Clinical Brain Sciences, University of Edinburgh; 49 Little France Crescent, Edinburgh, United Kingdom EH16 4SB" - }, - { - "author_name": "Rennos Fragkoudis", - "author_inst": "Edinburgh Genome Foundry, University of Edinburgh; Michael Swann Building, Max Born Crescent, Edinburgh, United Kingdom EH9 3BF" - }, - { - "author_name": "Susan Rosser", - "author_inst": "Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh; CH Waddington Building, Kings Buildings, Mayfield Road, Edinbu" - }, - { - "author_name": "David Cavanagh", - "author_inst": "Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh; The King's Buildings, Ashworth Laboratories, Charlotte A" - }, - { - "author_name": "Madhvi Menon", - "author_inst": "Division of Infection, Immunity & Respiratory Medicine, School of Biological Sciences, University of Manchester; Oxford Rd, Manchester, United Kingdom M13 9PL" - }, - { - "author_name": "Joseph A. Marsh", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Western General Hospital. Crewe Road, Edinburgh EH4 2XU" - }, - { - "author_name": "Dirk A. Kleinjan", - "author_inst": "Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh; CH Waddington Building, Kings Buildings, Mayfield Road, Edinbu" - }, - { - "author_name": "Nick Gilbert", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Western General Hospital. Crewe Road, Edinburgh EH4 2XU" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.12.22277538", "rel_title": "Dengue seroprevalence study during COVID-19 pandemic in Bali", @@ -257116,6 +257845,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.07.11.499644", + "rel_title": "Insights from Incorporating Quantum Computing into Drug Design Workflows", + "rel_date": "2022-07-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.11.499644", + "rel_abs": "While many quantum computing (QC) methods promise theoretical advantages over classical counterparts, quantum hardware remains limited. Exploiting near-term QC in computer-aided drug design (CADD) thus requires judicious partitioning between classical and quantum calculations. We present HypaCADD, a hybrid classical-quantum workflow for finding ligands binding to proteins, while accounting for genetic mutations. We explicitly identify modules of our drug design workflow currently amenable to replacement by QC: non-intuitively, we identify the mutation-impact predictor as the best candidate. HypaCADD thus combines classical docking and molecular dynamics with quantum machine learning (QML) to infer the impact of mutations. We present a case study with the SARS-CoV-2 protease and associated mutants. We map a classical machine-learning module onto QC, using a neural network constructed from qubit-rotation gates. We have implemented this in simulation and on two commercial quantum computers. We find that the QML models can perform on par with, if not better than, classical baselines. In summary, HypaCADD offers a successful strategy for leveraging QC for CADD.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Bayo Lau", + "author_inst": "HypaHub, Inc." + }, + { + "author_name": "Prashant Siva Emani", + "author_inst": "Yale University" + }, + { + "author_name": "Jackson Chapman", + "author_inst": "Yale University" + }, + { + "author_name": "Lijing Yao", + "author_inst": "HypaHub, Inc." + }, + { + "author_name": "Tarsus Lam", + "author_inst": "HypaHub, Inc." + }, + { + "author_name": "Paul Merrill", + "author_inst": "HypaHub, Inc." + }, + { + "author_name": "Jonathan Warrell", + "author_inst": "Yale University" + }, + { + "author_name": "Mark B. Gerstein", + "author_inst": "Yale University" + }, + { + "author_name": "Hugo Lam", + "author_inst": "HypaHub, Inc." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.07.12.22277529", "rel_title": "Comparative analysis of retracted pre-print and peer-reviewed articles on COVID-19", @@ -259027,89 +259807,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.07.08.22277388", - "rel_title": "Manifestations Associated with Post Acute Sequelae of SARS-CoV2 Infection (PASC) Predict Diagnosis of New-Onset Psychiatric Disease: Findings from the NIH N3C and RECOVER Studies", - "rel_date": "2022-07-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.08.22277388", - "rel_abs": "Acute COVID-19 infection can be followed by diverse clinical manifestations referred to as Post Acute Sequelae of SARS-CoV2 Infection (PASC). Studies have shown an increased risk of being diagnosed with new-onset psychiatric disease following a diagnosis of acute COVID-19. However, it was unclear whether non-psychiatric PASC-associated manifestations (PASC-AMs) are associated with an increased risk of new-onset psychiatric disease following COVID-19.\n\nA retrospective EHR cohort study of 1,603,767 individuals with acute COVID-19 was performed to evaluate whether non-psychiatric PASC-AMs are associated with new-onset psychiatric disease. Data were obtained from the National COVID Cohort Collaborative (N3C), which has EHR data from 65 clinical organizations. EHR codes were mapped to 151 non-psychiatric PASC-AMs recorded 28-120 days following SARS-CoV-2 diagnosis and before diagnosis of new-onset psychiatric disease. Association of newly diagnosed psychiatric disease with age, sex, race, pre-existing comorbidities, and PASC-AMs in seven categories was assessed by logistic regression.\n\nThere was a significant association between six categories and newly diagnosed anxiety, mood, and psychotic disorders, with odds ratios highest for cardiovascular (1.35, 1.27-1.42) PASC-AMs. Secondary analysis revealed that the proportions of 95 individual clinical features significantly differed between patients diagnosed with different psychiatric disorders.\n\nOur study provides evidence for association between non-psychiatric PASC-AMs and the incidence of newly diagnosed psychiatric disease. Significant associations were found for features related to multiple organ systems. This information could prove useful in understanding risk stratification for new-onset psychiatric disease following COVID-19. Prospective studies are needed to corroborate these findings.\n\nFundingNCATS U24 TR002306", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Ben Coleman", - "author_inst": "The Jackson Laboratory, Genomic Medicine, Farmington 6032, CT, USA" - }, - { - "author_name": "Elena Casiraghi", - "author_inst": "AnacletoLab, Dipartimento di Informatica, Universita degli Studi di Milano, Italy" - }, - { - "author_name": "Tiffany J Callahan", - "author_inst": "University of Colorado Anschutz Medical Campus, Center for Health AI, Aurora 80045, CO, USA" - }, - { - "author_name": "Hannah Blau", - "author_inst": "The Jackson Laboratory, Genomic Medicine, Farmington 6032, CT, USA" - }, - { - "author_name": "Lauren Chan", - "author_inst": "College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA" - }, - { - "author_name": "Bryan Laraway", - "author_inst": "University of Colorado Anschutz Medical Campus, Center for Health AI, Aurora 80045, CO, USA" - }, - { - "author_name": "Kevin B Clark", - "author_inst": "Cures Within Reach, Chicago, IL, USA" - }, - { - "author_name": "Yochai Re'em", - "author_inst": "Weill Cornell Medicine, Department of Psychiatry, New York, NY, USA" - }, - { - "author_name": "Ken R Gersing", - "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland." - }, - { - "author_name": "Ken Wilkins", - "author_inst": "Biostatistics Program, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland" - }, - { - "author_name": "Nomi Harris", - "author_inst": "Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA" - }, - { - "author_name": "Giorgio Valentini", - "author_inst": "AnacletoLab, Dipartimento di Informatica, Universita degli Studi di Milano, Italy" - }, - { - "author_name": "Melissa A Haendel", - "author_inst": "University of Colorado Anschutz Medical Campus, Center for Health AI, Aurora 80045, CO, USA" - }, - { - "author_name": "Justin Reese", - "author_inst": "Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA" - }, - { - "author_name": "Peter N Robinson", - "author_inst": "The Jackson Laboratory, Genomic Medicine, Farmington 6032, CT, USA" - }, - { - "author_name": "- N3C Consortium", - "author_inst": "" - }, - { - "author_name": "- RECOVER Consortium", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.07.08.22276768", "rel_title": "Healthcare utilization following SARS-CoV-2 infection in children and adolescents with chronic conditions: An EHR-based Cohort Study from the RECOVER Program", @@ -259414,6 +260111,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.07.22277394", + "rel_title": "A Case-Crossover Phenome-wide Association Study (PheWAS) for Understanding Post-COVID-19 Diagnosis Patterns", + "rel_date": "2022-07-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.07.22277394", + "rel_abs": "ImportancePost COVID-19 condition (PCC) is known to affect a large proportion of COVID-19 survivors. Robust study design and methods are needed to understand post-COVID-19 diagnosis patterns in all COVID-19 survivors, not just the ones clinically diagnosed with PCC.\n\nObjectiveTo assess which diagnoses appear more frequently after a COVID-19 infection and how they differ by COVID-19 severity and vaccination status.\n\nDesignWe applied a case-crossover phenome-wide association study (PheWAS) in a retrospective cohort of COVID-19 survivors, comparing the occurrences of 1,649 diagnosis-based phenotype codes (PheCodes) pre- and post-COVID-19 infection periods in the same individual using a conditional logistic regression.\n\nSettingPatients tested for or diagnosed with COVID-19 at Michigan Medicine from March 10, 2020 through May 1, 2022.\n\nParticipants36,856 SARS-CoV-2-positive patients and 141,615 age- and sex-matched SARS-CoV-2-negative patients as a comparison group for sensitivity analysis.\n\nExposureSARS-CoV-2 virus infection as determined by RT-PCR testing and/or clinical evaluation.\n\nMain Outcomes and MeasuresWe compared the rate of occurrence of 1,649 disease classification codes in \"pre-\" and \"post-COVID-19 periods\". We studied how this pattern varied by COVID-19 severity and vaccination status at the time of infection.\n\nResultsUsing a case-crossover PheWAS framework, we found mental, circulatory, and respiratory disorders to be strongly associated with the \"post-COVID-19 period\" for the overall COVID-19-positive cohort. A total of 325 PheCodes reached phenome-wide significance (p<3e-05), and top hits included cardiac dysrhythmias (OR=1.7 [95%CI: 1.6-1.9]), respiratory failure, insufficiency, arrest (OR=3.1 [95%CI: 2.7-3.5]) and anxiety disorder (OR=1.7 [95%CI: 1.6-1.8]). In the patients with severe disease, we found stronger associations with many respiratory and circulatory disorders, such as pneumonia (p=2.1e-18) and acute pulmonary heart disease (p=2.4e-8), and the \"post-COVID-19 period,\" compared to those with mild/moderate disease.\n\nTest negative patients exhibited a somewhat similar association pattern to those fully vaccinated, with mental health and chronic circulatory diseases rising to the top of the association list in these groups.\n\nConclusions and RelevanceOur results confirm that patients experience myriad symptoms more than 28 days after SARS-CoV-2 infection, but especially mental, circulatory, and respiratory disorders. Our case-crossover PheWAS approach controls for within-person confounders that are time-invariant. Comparison to test negatives with a similar design helped identify enrichment specific to COVID-19. As we look into the future, we must be aware of COVID-19 survivors healthcare needs in the period after infection.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat patterns of clinical diagnosis tend to occur more frequently after a COVID-19 infection and how do they vary by COVID-19 severity and vaccination status?\n\nFindingsIn a cohort of 36,856 COVID-19-positive patients, using a case-crossover phenome-wide association analysis that controls for within-subject confounders, we found symptoms such as anxiety disorder, cardiac dysrhythmias, and respiratory failure to be significantly associated with the \"post-COVID-19 period.\" Patients with severe COVID-19 were more likely to receive diagnoses related to respiratory conditions in their \"post-COVID-19 period\" compared to those with mild/moderate COVID-19. The landscape of phenome-wide association signals for the vaccinated group featured common chronic conditions when compared to the signals in the unvaccinated group.\n\nMeaningSymptoms across multiple organ systems, especially in the mental, circulatory, and respiratory domains, were associated with the \"post-COVID-19 period.\" Characterization of post-COVID-19 diagnosis patterns is crucial to understand the long term and future healthcare burden of COVID-19.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Spencer R. Haupert", + "author_inst": "University of Michigan School of Public Health" + }, + { + "author_name": "Xu Shi", + "author_inst": "University of Michigan School of Public Health" + }, + { + "author_name": "Chen Chen", + "author_inst": "University of Michigan School of Public Health" + }, + { + "author_name": "Lars G. Fritsche", + "author_inst": "University of Michigan School of Public Health" + }, + { + "author_name": "Bhramar Mukherjee", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.06.22277014", "rel_title": "Genomic Surveillance Identifies SARS-CoV-2 Transmission Patterns in Local University Populations, Wisconsin, USA, 2020-2022", @@ -261089,53 +261821,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.07.04.22277239", - "rel_title": "Drivers of Mortality in COVID ARDS Depend on Patient Sub-Type", - "rel_date": "2022-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.04.22277239", - "rel_abs": "BackgroundThe most common cause of death in people with COVID-19 is acute respiratory distress syndrome (ARDS). ARDS is a heterogeneous syndrome, however, subgroups that have been identified among non-COVID-19 ARDS patients do not clearly apply to COVID-19 ARDS patients. Additionally, studies of COVID-19 ARDS have been limited by sample size.\n\nMethodsWe applied an iterative clustering and machine learning framework to electronic health record data from thousands of hospitalized COVID-19 ARDS patients with the goal of defining and characterizing clinically-relevant COVID-19 ARDS subgroups (phenoclusters). We then applied a supervised model to identify risk factors for hospital mortality for each phenocluster and compared these between phenoclusters and the entire cohort.\n\nFindingsRisk factors that predict mortality in the overall cohort of COVID-19 ARDS patients do not necessarily predict mortality in phenoclusters. In fact, some risk factors increase the risk of hospital mortality in some phenoclusters, but decrease mortality in others.\n\nInterpretationThese phenocluster-specific risk factors would not have been observed with a single predictive model. Heterogeneity in phenoclusters of COVID-19 ARDS as well as drivers of mortality may partially explain challenges in finding effective treatments when applied to all patients with ARDS.\n\nFundingThis work was supported by philanthropic funds to the Feinstein Institutes for Medical Research. The funding source did not control any aspect of the study and did not review the results. All authors had full access to the full data in the study and accept responsibility to submit for publication.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Helen Cheyne", - "author_inst": "BioSymetrics, Inc" - }, - { - "author_name": "Amir Gandomi", - "author_inst": "Feinstein Institutes for Medical Research" - }, - { - "author_name": "Shahrzad Hosseini Vajargah", - "author_inst": "BioSymetrics, Inc" - }, - { - "author_name": "Victoria M Catterson", - "author_inst": "BioSymetrics, Inc" - }, - { - "author_name": "Travis Mackoy", - "author_inst": "BioSymetrics, Inc" - }, - { - "author_name": "Lauren Mccullagh", - "author_inst": "BioSymetrics, Inc" - }, - { - "author_name": "Gabriel Musso", - "author_inst": "BioSymetrics, Inc" - }, - { - "author_name": "Negin Hajizadeh", - "author_inst": "Feinstein Institutes for Medical Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2022.07.04.22277193", "rel_title": "Reductions in stillbirths and preterm birth in COVID-19 vaccinated women: a multi-center cohort study of vaccination uptake and perinatal outcomes", @@ -261468,6 +262153,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.04.22277103", + "rel_title": "Design and Performance Characteristics of the Elecsys Anti-SARS-CoV-2 S assay", + "rel_date": "2022-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.04.22277103", + "rel_abs": "BackgroundAutomated, high throughput assays are required to quantify the immune response after infection with or vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study on the Roche Elecsys(R) Anti-SARS-CoV-2 S (ACOV2S) assay provides insights on the assay design and performance.\n\nMethodsThe ACOV2S assay quantifies antibodies to the receptor-binding domain of the SARS-CoV-2 spike protein. The assigned units and the underlying standardization were compared to the international reference standard in BAU/mL. Assay specificity was assessed in samples (n=5981) collected prior to the COVID-19 pandemic and in samples from patients with non-COVID-19 respiratory infections (n=697) or other infectious diseases (n=771). Sensitivity was measured in 1313 samples from patients with mild COVID-19 and 297 samples from patients hospitalized with COVID-19. Comparison of results was performed to a comparator semi-quantitative anti-S1 assay of indirect detection format as well as a commercially available and an in-house version of a surrogate neutralization assay (ACE2-RBD).\n\nResultsThe originally assigned units for the ACOV2S assay were shown to be congruent to the units of the First International WHO Standard for anti-SARS-CoV-2 immunoglobulins. Overall specificity was 99.98% with no geographical differences noted and no loss of specificity in samples containing potentially cross-reacting antibodies. High sensitivity was observed, with 98.8% of samples reported to be reactive >14 days after infection and sustained detection of antibodies over time. For all samples, ACOV2S titers and neutralization capacities developed with comparable dynamics. Robust standardization and assay setup enable excellent reproducibility of results, independent of lot or analyzer used.\n\nConclusionThe results from this study confirmed that ACOV2S is a highly sensitive and specific assay and correlates well with surrogate neutralization assays. The units established for ACOV2S are also interchangeable with the units of the First International WHO Standard for anti-SARS-CoV-2 immunoglobulins. Worldwide availability of the assay and analyzers render ACOV2S a highly practical tool for population-wide assessment and monitoring of the humoral response to SARS-CoV-2 infection or vaccination.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Karin Taffertshofer", + "author_inst": "Research and Development Immunoassays, Roche Diagnostics GmbH, Penzberg, Germany" + }, + { + "author_name": "Mirko Walter", + "author_inst": "Research and Development Immunoassays, Roche Diagnostics GmbH, Penzberg, Germany" + }, + { + "author_name": "Peter Mackeban", + "author_inst": "Research and Development Immunoassays, Roche Diagnostics GmbH, Penzberg, Germany" + }, + { + "author_name": "Julia Kraemer", + "author_inst": "Research and Development Immunoassays; Roche Diagnostics GmbH, Penzberg, Germany" + }, + { + "author_name": "Sergej Potapov", + "author_inst": "Biostatistics & Data Science, Roche Diagnostics GmbH, Penzberg, Germany" + }, + { + "author_name": "Simon Jochum", + "author_inst": "Roche Diagnostics" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.05.498881", "rel_title": "Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors", @@ -264419,57 +265143,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.06.28.22276786", - "rel_title": "Hybrid immunity expands the functional humoral footprint of both mRNA and vector-based SARS-CoV-2 vaccines", - "rel_date": "2022-07-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.28.22276786", - "rel_abs": "The COVID-19 pandemic catalyzed a revolution in vaccine development, leading to the testing and approval of several global vaccine platforms that have shown tremendous promise in curbing the pandemic. Yet, despite these successes, waning immunity, and the emergence of variants of concern linked to rising breakthrough infections among vaccinees, have begun to highlight opportunities to improve vaccine platforms and deployment. Real-world vaccine efficacy has highlighted the reduced risk of breakthrough infection and disease among individuals infected and vaccinated, otherwise referred to as hybrid immunity. Hybrid immunity points to the potential for more vigorous or distinct immunity primed by the infection and may confer enhanced protection from COVID-19. Beyond augmented hybrid induced neutralizing antibody and T cell immune responses, here we sought to define whether hybrid immunity may shape the functional humoral immune response to SARS-CoV-2 following Pfizer/BNT162b2 and Moderna mRNA1273 mRNA-based, and ChadOx1/AZ1222 and Ad26.COV2.S vector-based SARS-CoV-2 vaccination. Each vaccine exhibited a unique functional humoral immune profile in the setting of naive or hybrid immunity. However, hybrid immunity showed a unique augmentation in S2-domain specific functional humoral immunity that was poorly induced in the setting of naive immune response. These data highlight the immunodominant effect of the S1-domain in the setting of natural immunity, which is highly variable during viral evolution, and the importance of natural infection in breaking this immunodominance in driving immunity to the S2 region of the SARS-CoV-2 S2 domain that is more conserved across variants of concern.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Paulina Kaplonek", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Yixiang Deng", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Jessica Shih-Lu Lee", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Heather Zar", - "author_inst": "Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Dace Zavadska", - "author_inst": "Childrens Clinical University Hospital, Riga, Latvia" - }, - { - "author_name": "Marina Johnson", - "author_inst": "Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London, London, UK" - }, - { - "author_name": "Douglas A Lauffenburger", - "author_inst": "MIT" - }, - { - "author_name": "David Goldblatt", - "author_inst": "University College London Institute of Child Health" - }, - { - "author_name": "Galit Alter", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.02.495455", "rel_title": "SARS-CoV-2 3CLpro mutations confer resistance to Paxlovid (nirmatrelvir/ritonavir) in a VSV-based, non-gain-of-function system", @@ -264690,6 +265363,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.06.30.22277080", + "rel_title": "MENTAL STATUS OVERVIEW IN THE ELDERLY DURING THE COVID-19 PANDEMIC: A PHYLOSOPHICAL PERSPECTIVE", + "rel_date": "2022-07-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.30.22277080", + "rel_abs": "BackgroundDuring the Covid-19 pandemic, there was a change in the mental status of the elderly, namely anxiety disorders and depression. It is important to know the mental status of the elderly and the role of effective communication because elderly people are easily infected with Covid-19. Therefore, it is necessary to carry out early detection in basic health services.\n\nObjectiveTo know the description of the mental status of the elderly during the Covid-19 pandemic.\n\nMethodNon-experimental quantitative design through a descriptive survey approach. The sample size is 202 people using quota sampling technique. Collecting data through home visits and implementing Covid-19 health protocols. The instruments used were the Geriatric Depression Scale 15 (Cronbachs alpha 0.75) and the Geriatric Anxiety Scale (Cronbachs alpha 0.93).\n\nResultsThere were 50.0% did not experience depression and 44.6% had mild depression. Although small, there is a small proportion of respondents experiencing moderate depression as much as 4.5% and 1.0% experiencing severe depression. There are 77.2% experiencing mild anxiety. A total of 21.8% experienced moderate anxiety. Although a small proportion, there are respondents experiencing severe anxiety as much as 1%.\n\nConclusionDuring the Covid-19 pandemic, most of the elderly experienced a change in mental status.\n\nSuggestionHealth workers are expected to carry out early detection of changes in mental status in the elderly.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Andriani Andriani", + "author_inst": "Hasanuddin University" + }, + { + "author_name": "Fransisca Lio", + "author_inst": "Onekore Community Health Center, Ende Regency, Southeast Sulawesi" + }, + { + "author_name": "Ariyanti Saleh", + "author_inst": "Hasanuddin Unversity" + }, + { + "author_name": "Andi Muhammad Fiqri", + "author_inst": "Hasanuddin University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "nursing" + }, { "rel_doi": "10.1101/2022.06.30.22277052", "rel_title": "Impact of SARS-Cov-2 on Clinical Trial Unit workforce in the United Kingdom; An observational study", @@ -266061,81 +266765,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.06.29.498158", - "rel_title": "Vitamin D and the ability to produce 1,25(OH)2D are critical for protection from viral infection of the lungs.", - "rel_date": "2022-06-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.29.498158", - "rel_abs": "Vitamin D supplementation has been linked to improved outcomes from respiratory virus infection, and the COVID19 pandemic has renewed interest in understanding the potential role of vitamin D in protecting the lung from viral infections. Therefore, we evaluated the role of Vitamin D using animal models of pandemic H1N1 influenza and SARS-CoV-2 infection. In mice, dietary induced vitamin D deficiency resulted in lung inflammation that was present prior to infection. Vitamin D sufficient (D+) and deficient (D-) wildtype (WT) and D+ and D-Cyp27B1 (Cyp) knockout (KO, cannot produce 1,25(OH)2D) mice were infected with pandemic H1N1. D- WT, D+ Cyp KO, and D- Cyp KO mice all exhibited significantly reduced survival compared to D+ WT mice. Importantly, survival was not the result of reduced viral replication as influenza M gene expression in the lungs was similar for all animals. Based on these findings, additional experiments were performed using the mouse and hamster models of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. In these studies, high dose vitamin D supplementation reduced lung inflammation in mice but not hamsters. A trend to faster weight recovery was observed in 1,25(OH)2D treated mice that survived SARS-CoV-2 infection. There was no effect of vitamin D on SARS-CoV-2 N gene expression in the lung of either mice or hamsters. Therefore, vitamin D deficiency enhanced disease severity, while vitamin D sufficient/supplementation reduced inflammation following infections with H1N1 influenza and SARS-CoV-2.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Juhi Arora", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Devanshi R Patel", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "McKayla J Nicol", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Cassandra J Field", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Katherine H Restori", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Jinpeng Wang", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Nicole E Froelich", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Bhuvana Katkere", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Josey A Terwilliger", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Veronika Weaver", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Erin Luley", - "author_inst": "Animal Diagnostic Laboratory, Pennsylvania State University" - }, - { - "author_name": "Kathleen Kelly", - "author_inst": "Animal Diagnostic Laboratory, Pennsylvania State University" - }, - { - "author_name": "Girish S Kirimanjeswara", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Troy C Sutton", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Margherita Teresa-Anna Cantorna", - "author_inst": "Pennsylvania State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.06.29.498191", "rel_title": "Inhibitory effects of GT0918 on acute lung injury and the molecular mechanisms of anti-inflammatory response", @@ -266352,6 +266981,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.30.22277084", + "rel_title": "The Citation of Retracted COVID-19 Papers is Common and Rarely Critical", + "rel_date": "2022-06-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.30.22277084", + "rel_abs": "BackgroundRetraction is the final safeguard against research error/misconduct. In principle, retraction exists to prevent serious issues identified in published research through post-publication review. Our study investigated the citing of clinical research papers retracted during the COVID-19 pandemic.\n\nMethodsWe used the Retraction Watch database extracted as of 27/01/2022 to identify retracted COVID-19 papers and the Google Scholar citation function to gather a dataset of citations of retracted clinical research. We reviewed key aspects of the citing research.\n\nResultsIn total, the Retraction Watch database included 212 entries for retracted COVID-19 papers. Of these, 53 papers were clinical. There were a total of 1,141 citations of retracted papers, with 105 errors, leaving 1,036 citations to analyze. The majority (86%) of citations were not critical. The majority (80%) of papers citing retracted research were published after the retraction date.\n\nConclusionsThe citation of retracted and withdrawn COVID-19 clinical studies is common, and rarely critical. Most researchers who cite retracted research do not identify that the paper is retracted, even when submitting long after the paper has been withdrawn. This has serious implications for the reliability of published research and the academic literature, which need to be addressed.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Gideon Meyerowitz-Katz", + "author_inst": "University of Wollongong" + }, + { + "author_name": "Praba Sekhar", + "author_inst": "Monash University SPHPM: Monash University School of Public Health and Preventive Medicine" + }, + { + "author_name": "Lonni Besan\u00e7on", + "author_inst": "Linkopings universitet: Norrkoping, SE" + }, + { + "author_name": "Tari Turner", + "author_inst": "Monash University SPHPM: Monash University School of Public Health and Preventive Medicine" + }, + { + "author_name": "Steve McDonald", + "author_inst": "Monash University SPHPM: Monash University School of Public Health and Preventive Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.06.30.22277089", "rel_title": "Influenza and pneumococcal vaccination and the risk of COVID-19: A systematic review and meta-analysis", @@ -267859,49 +268523,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "urology" }, - { - "rel_doi": "10.1101/2022.06.27.22276790", - "rel_title": "BNT162b2 effectiveness against Delta & Omicron variants in teens by dosing interval and duration", - "rel_date": "2022-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.27.22276790", - "rel_abs": "Background and ObjectivesTwo- and three-dose BNT162b2 (Pfizer-BioNTech) mRNA vaccine effectiveness (VE) against SARS-CoV-2 infection, including Delta and Omicron variants, was assessed among adolescents in two Canadian provinces where first and second doses were spaced longer than the manufacturer-specified 3-week interval.\n\nMethodsTest-negative design estimated VE against laboratory-confirmed SARS-CoV-2 infection among 12-17-year-olds in Quebec and British Columbia, Canada between September 5, 2021 (epi-week 36), and April 30, 2022 (epi-week 17). Delta-dominant and Omicron-dominant periods spanned epi-weeks 36-47 and 51-17, respectively. VE was assessed from 14 days and explored by interval between first and second doses, time since second dose, and with administration of a third dose.\n\nResultsMedian first-second dosing-interval was [~]8 weeks and second-third dosing-interval was [~]29-31 weeks. Median follow-up post-second dose was [~]10-11 weeks for Delta-dominant and [~]21-22 weeks for Omicron-dominant periods, and [~]2-7 weeks post-third dose. VE against Delta was [≥]90% to at least the 5th month post-second dose. VE against Omicron declined from [~]65-75% at 2-3 weeks to [≤]50% by the 3rd month post-vaccination, restored to [~]65% shortly following a third dose. VE exceeded 90% against Delta regardless of dosing-interval but appeared improved against Omicron with [≥]8 weeks between first and second doses.\n\nConclusionIn adolescents, two BNT162b2 doses provided strong and sustained protection against Delta but reduced and rapidly-waning VE against Omicron. Longer interval between first and second doses and a third dose improved Omicron protection. Updated vaccine antigens, increased doses and/or dosing-intervals may be needed to improve adolescent VE against immunological-escape variants.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Iulia G Ionescu", - "author_inst": "Centre Hospitalier Universitaire (CHU) de Qu\u00e9bec-Universit\u00e9 Laval Research Center" - }, - { - "author_name": "Danuta M Skowronski", - "author_inst": "BC Centre for Disease Control, Communicable Diseases and Immunization Services" - }, - { - "author_name": "Chantal Sauvageau", - "author_inst": "Institut national de sant\u00e9 publique du Qu\u00e9bec, Biological and Occupational Risks" - }, - { - "author_name": "Erica Chuang", - "author_inst": "BC Centre for Disease Control, Data and Analytics Services" - }, - { - "author_name": "Manale Ouakki", - "author_inst": "Institut national de sant\u00e9 publique du Qu\u00e9bec, Biological and Occupational Risks" - }, - { - "author_name": "Shinhye Kim", - "author_inst": "BC Centre for Disease Control, Communicable Diseases and Immunization Services" - }, - { - "author_name": "Gaston De Serres", - "author_inst": "Institut national de sant\u00e9 publique du Qu\u00e9bec, Biological and Occupational Risks" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.28.22276851", "rel_title": "The COVID-19 pandemic sparked off a large-scale outbreak of carbapenem-resistant Acinetobacter baumannii from the endemic strains of an Italian hospital", @@ -268318,6 +268939,81 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.06.27.497875", + "rel_title": "Combination therapy with nirmatrelvir and molnupiravir improves the survival of SARS-CoV-2 infected mice", + "rel_date": "2022-06-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.27.497875", + "rel_abs": "As the SARS-CoV-2 pandemic remains uncontrolled owing to the continuous emergence of variants of concern, there is an immediate need to implement the most effective antiviral treatment strategies, especially for risk groups. Here, we evaluated the therapeutic potency of nirmatrelvir, remdesivir, and molnupiravir and their combinations in SARS-CoV-2-infected K18-hACE2 transgenic mice. Systemic treatment of mice with each drug (20 mg/kg) resulted in slightly enhanced antiviral efficacy and yielded an increased life expectancy of only about 20-40% survival. However, combination therapy with nirmatrelvir (20 mg/kg) and molnupiravir (20 mg/kg) in lethally infected mice showed profound inhibition of SARS-CoV-2 replication in both the lung and brain and synergistically improved survival times up to 80% compared to those with nirmatrelvir (P= 0.0001) and molnupiravir (P= 0.0001) administered alone. This combination therapy effectively reduced clinical severity score, virus-induced tissue damage, and viral distribution compared to those in animals treated with these monotherapies. Furthermore, all these assessments associated with this combination were also significantly higher than that of mice receiving remdesivir monotherapy (P= 0.0001) and the nirmatrelvir (20 mg/kg) and remdesivir (20 mg/kg) combination (P= 0.0001), underscored the clinical significance of this combination. By contrast, the nirmatrelvir and remdesivir combination showed less antiviral efficacy, with lower survival compared to nirmatrelvir monotherapy, demonstrating the inefficient therapeutic effect of this combination. The combination therapy with nirmatrelvir and molnupiravir contributes to alleviated morbidity and mortality, which can serve as a basis for the design of clinical studies of this combination in the treatment of COVID-19 patients.\n\nIMPORTANCESince SARS-CoV-2 spread rapidly with the emergence of new variants of concerns, it is necessary to develop effective treatment strategies to treat elderly individuals and those with comorbidities. Antiviral therapy using a combination of drugs is more effective in eradicating viruses and will undoubtedly improve the clinical outcome and survival probability of hospitalized SARS-CoV-2 patients. In the current study, we observed three FDA-approved antivirals nirmatrelvir, remdesivir, and molnupiravir have therapeutic significance with moderate survival for their monotherapies against SARS-CoV-2 infected K18-hACE2 mouse model. The combination of nirmatrelvir and molnupiravir showed significant antiviral activity and a higher survival rate of approximately 80%, providing in vivo evidence of the potential utility of this combination. In contrast, nirmatrelvir and remdesivir combination showed less antiviral potency and emphasized the ineffective significance with less survival. The current study suggests that the nirmatrelvir and molnupiravir combination is an effective drug regimen strategy in treating SARS-CoV-2 patients.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Ju Hwan Jeong", + "author_inst": "College of Medicine and Medical Research Institute, Chungbuk National University" + }, + { + "author_name": "Santosh Chokkakula", + "author_inst": "College of Medicine and Medical Research Institute, Chungbuk National University" + }, + { + "author_name": "Seong Cheol Min", + "author_inst": "College of Medicine and Medical Research Institute" + }, + { + "author_name": "Beomkyu Kim", + "author_inst": "College of Medicine and Medical Research Institute" + }, + { + "author_name": "Won-Suk Choi", + "author_inst": "Chungbuk National University" + }, + { + "author_name": "Sol Oh", + "author_inst": "College of Medicine and Medical Research Institute" + }, + { + "author_name": "Yu Soo Yun", + "author_inst": "College of Medicine and Medical Research Institute" + }, + { + "author_name": "Da Hyeon Kang", + "author_inst": "College of Medicine and Medical Research Institute" + }, + { + "author_name": "Ok-Jun Lee", + "author_inst": "Chungbuk National University" + }, + { + "author_name": "Eung-Gook Kim", + "author_inst": "Chungbuk National University" + }, + { + "author_name": "Jang-Hoon Choi", + "author_inst": "Korea national institute of health" + }, + { + "author_name": "Joo-Yeon Lee", + "author_inst": "Korea National Institute of Health" + }, + { + "author_name": "Young Ki Choi", + "author_inst": "Chungbuk National University" + }, + { + "author_name": "Yun Hee Baek", + "author_inst": "Chungbuk National University" + }, + { + "author_name": "Min-Suk Song", + "author_inst": "Chungbuk National University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.06.27.497883", "rel_title": "The Staphylococcus aureus iron-regulated surface determinant A (IsdA) increases SARS CoV-2 replication by modulating JAK-STAT signaling", @@ -269513,65 +270209,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.06.26.22276861", - "rel_title": "The burden of respiratory conditions in the emergency department of Muhimbili National Hospital in Tanzania in the first two years of the COVID-19 pandemic", - "rel_date": "2022-06-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.26.22276861", - "rel_abs": "BackgroundGlobally, respiratory diseases cause 10 million deaths every year. With the COVID-19 pandemic, the burden of respiratory illness increased and led to significant morbidity and mortality in both high- and low-income countries. This study assessed the burden and trend of respiratory conditions among patients presenting to the emergency department of Muhimbili National Hospital in Tanzania and compared with national COVID-19 data to determine if this knowledge may be useful for the surveillance of disease outbreaks in settings of limited specific diagnostic testing.\n\nMethodsThe study used routinely collected data from the electronic information system in the Emergency Medical Department (EMD) of Muhimbili National Hospital in Tanzania. All patients presenting to the EMD in a 2-year period, 2020 and 2021 with respiratory conditions were included. Descriptive statistics and graphical visualizations were used to describe the burden of respiratory conditions and the trends over time and to compare to national Tanzanian COVID-19 data during the same period.\n\nResultsOne in every four patients who presented to the EMD of the Muhimbili National Hospital had a respiratory condition - 1039 patients per month. Of the 24,942 patients, 52% were males, and the median age (IQR) was 34.7 (21.7, 53.7) years. The most common respiratory diagnoses were pneumonia (52%), upper respiratory tract infections (31%), asthma (4.8%) and suspected COVID-19 (2.5%). There were four peaks of respiratory conditions coinciding with the four waves in the national COVID-19 data.\n\nConclusionsThere is a high burden of respiratory conditions among patients presenting to the EMD of Muhimbili National Hospital. The trend shows four peaks of respiratory conditions in 2020-2021 seen to coincide with the four waves in the national COVID-19 data. Real-time hospital-based surveillance tools may be useful for early detection of respiratory disease outbreaks and other public health emergencies in settings with limited diagnostic testing.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Harrieth Peter Ndumwa", - "author_inst": "Muhimbili University of Health and Allied Sciences" - }, - { - "author_name": "Erick A Mboya", - "author_inst": "Muhimbili University of Health and Allied Sciences" - }, - { - "author_name": "Davis Elias Amani", - "author_inst": "Muhimbili University of Health and Allied Sciences" - }, - { - "author_name": "Ramadhani Mashoka", - "author_inst": "Muhimbili National Hospital" - }, - { - "author_name": "Paulina Nicholaus", - "author_inst": "Muhimbili National Hospital" - }, - { - "author_name": "Rashan Haniffa", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit" - }, - { - "author_name": "Abi Beane", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit" - }, - { - "author_name": "Juma Mfinanga", - "author_inst": "Muhimbili National Hospital" - }, - { - "author_name": "Bruno Sunguya", - "author_inst": "Muhimbili University of Health and Allied Sciences" - }, - { - "author_name": "Hendry R. Sawe", - "author_inst": "Muhimbili University of Health and Allied Sciences" - }, - { - "author_name": "Tim Baker", - "author_inst": "Muhimbili University of Health and Allied Sciences" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2022.06.27.22276736", "rel_title": "An Economic Evaluation of a virtual Covid Ward in Leicester, Leicestershire, and Rutland", @@ -269792,6 +270429,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.06.26.22276913", + "rel_title": "Analysis of 16S rRNA gene sequence of nasopharyngeal exudate from healthy donors reveals changes in key microbial communities associated with aging", + "rel_date": "2022-06-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.26.22276913", + "rel_abs": "BackgroundFunctional or compositional perturbations of the microbiome can occur at different sites of the body and this dysbiosis has been linked to various diseases. Changes in the nasopharyngeal microbiome are associated to patients susceptibility to multiple viral infections, including COVID-19, supporting the idea that the nasopharynx may be playing an important role in health and disease. Most studies on the nasopharyngeal microbiome have focused on a specific component in the lifespan, such as infanthood or the elderly, or have other limitations such as low sample sizes. Therefore, detailed studies analyzing the age- and sex-associated changes in the nasopharyngeal microbiome of healthy people across their whole life are essential to understand the relevance of the nasopharynx in the pathogenesis of multiple diseases, particularly viral infections such as COVID-19.\n\nResults120 nasopharyngeal samples from healthy subjects of all ages and both sexes were analyzed by 16s rRNA sequencing. Nasopharyngeal bacterial alpha diversity did not vary in any case between age or sex groups. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were the predominant phyla in all the age groups, with several sex-associated differences probably due to the different levels of sex hormones between both sexes. Acinetobacter, Brevundimonas, Dolosigranulum, Finegoldia, Haemophilus, Leptotrichia, Moraxella, Peptoniphilus, Pseudomonas, Rothia, and Staphylococcus were the only 11 bacterial genera that presented significant age-associated differences. Other bacterial genera such as Anaerococcus, Burkholderia, Campylobacter, Delftia, Prevotella, Neisseria, Propionibacterium, Streptococcus, Ralstonia, Sphingomonas, and Corynebacterium appeared in the population with a very high frequency, suggesting that their presence might be biologically relevant.\n\nConclusionsIn contrast to other anatomical areas such as the gut, bacterial diversity in the nasopharynx of healthy subjects remains very stable and resistant to perturbations throughout the whole life and in both sexes. Age-associated changes in taxonomic composition were observed at phylum, family, and genus levels, as well as several sex-associated changes probably due to the different levels of sex hormones present in both sexes at certain ages. Our results provide a complete and valuable dataset that will be useful for future research aiming for studying the relationship between changes in the nasopharyngeal microbiome and susceptibility to or severity of multiple diseases, including COVID-19.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Sergio Candel", + "author_inst": "Universidad de Murcia" + }, + { + "author_name": "Fernando Perez-Sanz", + "author_inst": "IMIB" + }, + { + "author_name": "Sylwia D Tyrkalska", + "author_inst": "Universidad de Murcia" + }, + { + "author_name": "Antonio Moreno-Docon", + "author_inst": "HCUVA" + }, + { + "author_name": "Angel Esteban", + "author_inst": "IMIB" + }, + { + "author_name": "Maria L Cayuela", + "author_inst": "IMIB" + }, + { + "author_name": "Victoriano Mulero", + "author_inst": "Universidad de Murcia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2022.06.26.22276919", "rel_title": "Predicting Hand, Foot, and Mouth Disease in Japan Using Google Trends: Infodemiology Study", @@ -271291,29 +271971,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.22.22276298", - "rel_title": "Mathematical modelling of COVID-19 with periodic transmission: The case of South Africa", - "rel_date": "2022-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.22.22276298", - "rel_abs": "The data on SARS-CoV-2 (COVID-19) in South Africa shows seasonal transmission patterns to date, with the peaks having occurred in winter and summer since the out-breaks began. The transmission dynamics have mainly been driven by variations in environmental factors and virus evolution, and the two are at the center of driving the different waves of the disease. It is thus important to understand the role of seasonality in the transmission dynamics of COVID-19. In this paper a compartmental model with a time dependent transmission rate is formulated and the stabilities of the steady states analysed. We note that if R0 < 1, the disease-free equilibrium is globally asymptotically stable, and the disease completely dies out and when R0 > 1, the system admits a positive periodic solution, and the disease is uniformly or periodically persistent. The model is fitted to data on new cases in South Africa for the first four waves. The model results clearly indicate the need to consider seasonality in the transmission dynamics of COVID-19 and its importance in modelling fluctuations in the data for new cases. The potential impact of seasonality in the transmission patterns of COVID-19 and the public health implications are discussed.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Farai Nyabadza", - "author_inst": "University of Johannesburg" - }, - { - "author_name": "Belthasara Assan", - "author_inst": "University of Johannesburg" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.22.22276362", "rel_title": "Immune Correlates Analysis of the PREVENT-19 COVID-19 Vaccine Efficacy Clinical Trial", @@ -271674,6 +272331,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2022.06.22.22276782", + "rel_title": "Receipt of anti-SARS-CoV-2 pharmacotherapies among U.S. Veterans with mild to moderate COVID-19, January-February 2022", + "rel_date": "2022-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.22.22276782", + "rel_abs": "BackgroundOlder adults and persons with medical co-morbidities are at increased risk for severe COVID-19. Several pharmacotherapies demonstrated to reduce the risk of COVID-19-related hospitalization and death have been authorized for use. We describe factors associated with receipt of outpatient COVID-19 pharmacotherapies in the Veterans Health Administration.\n\nMethodsWe conducted a retrospective cohort study among Veterans with risk factors for severe COVID-19 who tested positive for SARS-CoV-2 during January and February 2022. We compared receipt of any COVID-19 pharmacotherapy, including sotrovimab, nirmatrelvir plus ritonavir, molnupiravir, or remdesivir versus no antiviral or monoclonal antibody treatment according to demographic characteristics, place of residence, underlying medical conditions, and COVID-19 vaccination using multivariable logistic regression.\n\nResultsDuring January and February 2022, 16,546 courses of sotrovimab, nirmatrelvir, and molnupiravir were allocated across the Veterans Health Administration. Among 111,717 Veterans testing positive for SARS-CoV-2, 4,233 (3.8%) received any COVID-19 pharmacotherapy, including 2,870 of 92,396 (3.1%) in January and 1,363 of 19,321 (7.1%) in February. Among a subset of 56,206 Veterans with documented COVID-19-related symptoms in the 30 days preceding positive SARS-CoV-2 test, 3,079 of 53,206 (5.5%) received any COVID-19 pharmacotherapy. Untreated Veterans had a median age of 60 years (interquartile range [IQR] 46-71 years) and median 3 underlying medical conditions (IQR 2-5). Veterans receiving any treatment were more likely to be older (adjusted odds ratio [aOR] 1.66, 95% confidence interval [CI] 1.52-1.80, 65-74 versus 50-64 years; aOR 1.67, 95% CI 1.53-1.84 [≥]75 versus 50-64 years) and have a higher number of underlying conditions (aOR 1.63, 95% CI 1.48-1.79, 3-4 versus 1-2 conditions; aOR 2.17, 95% CI 1.98-2.39, [≥]5 versus 1-2 conditions). Persons of Black versus White race (aOR 0.65, 95% CI 0.60-0.72) and well as persons of Hispanic ethnicity (aOR 0.88, 95% CI 0.77-0.99) were less likely to receive treatment.\n\nConclusions and RelevanceAlthough supply of outpatient COVID-19 pharmacotherapies during January and February 2022 was limited, prescription of these pharmacotherapies was underutilized, consistent with early national patterns in dispensing. Racial and ethnic minorities were less likely to receive any pharmacotherapy.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Kristina L Bajema", + "author_inst": "Veterans Affairs Portland Health Care System, Oregon Health and Science University" + }, + { + "author_name": "Xiao Qing Wang", + "author_inst": "Veterans Affairs Ann Arbor Health Care System" + }, + { + "author_name": "Denise M Hynes", + "author_inst": "Veterans Affairs Portland Health Care System, Oregon State University" + }, + { + "author_name": "Mazhgan Rowneki", + "author_inst": "Veterans Affairs Portland Health Care System" + }, + { + "author_name": "Alex Hickok", + "author_inst": "Veterans Affairs Portland Health Care System" + }, + { + "author_name": "Francesca Cunningham", + "author_inst": "Veterans Affairs Center for Medication Safety - Pharmacy Benefit Management (PBM) Services" + }, + { + "author_name": "Amy Bohnert", + "author_inst": "Veterans Affairs Ann Arbor Health Care System, University of Michigan" + }, + { + "author_name": "Edward J Boyko", + "author_inst": "Veterans Affairs Puget Sound Health Care System" + }, + { + "author_name": "Theodore J Iwashyna", + "author_inst": "Veterans Affairs Ann Arbor Health Care System, University of Michigan Medical School" + }, + { + "author_name": "Matthew L Maciejewski", + "author_inst": "Durham Veterans Affairs Medical Center, Duke University School of Medicine, Duke University" + }, + { + "author_name": "Elizabeth M Viglianti", + "author_inst": "Veterans Affairs Ann Arbor Health Care System, University of Michigan Medical School" + }, + { + "author_name": "Elani Streja", + "author_inst": "Veterans Affairs Connecticut Health Care System" + }, + { + "author_name": "Lei Yan", + "author_inst": "Veterans Affairs Connecticut Health Care System, Yale School of Public Health" + }, + { + "author_name": "Mihaela Aslan", + "author_inst": "Veterans Affairs Connecticut Health Care System, Yale School of Medicine" + }, + { + "author_name": "Grant D Huang", + "author_inst": "Office of Research and Development, Veterans Health Administration" + }, + { + "author_name": "George N Ioannou", + "author_inst": "Veterans Affairs Puget Sound Health Care System, University of Washington" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.22.22276072", "rel_title": "A Multi-Institutional Study Benchmarking Cycle Threshold Values for Major Clinical SARS-CoV-2 RT-PCR Assays", @@ -273229,45 +273965,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.06.22.497134", - "rel_title": "Mutational insights among the structural proteins of SARS-CoV-2: frequencies and evolutionary trends in American countries", - "rel_date": "2022-06-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.22.497134", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a role in the mortality of more than 6 million people worldwide. This virus owns the genome, which contains four structural proteins, including spike (S), envelope (E), membrane (M), and nucleocapsid (N). The occurrence of structural mutations can induce the emergence of new variants. Depending on the mutations, the variants may display different patterns of infectivity, mortality, and sensitivity toward drugs and vaccines. In this study, we analyzed samples of amino-acid sequences (AASs) for structural proteins from the coronavirus 2019 (COVID-19) declaration as a pandemic to April 2022 among American countries. The analysis process included considering mutations frequencies, locations, and evolutionary trends utilizing sequence alignment to the reference sequence. In the following, the results were compared with the same analyses among the samples of the entire world. Results displayed that despite samples of North America and international countries that own the region of 508 to 635 with the highest mutation frequency among S AASs, the region with the same characteristic was concluded as 1 to 127 in South America. Besides, the most frequent mutations in S, E, M, and N proteins from North America and worldwide samples were concluded as D614G, T9I, I82T, and R203M. In comparison, R203K was the first frequent mutation in N samples in South America. Widely comparing mutations between North America and South America and between the Americas and the world can help scientists introduce better drug and vaccine development strategies.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Mohammad Abavisani", - "author_inst": "mashhad universiy of medical sciences" - }, - { - "author_name": "Karim Rahimian", - "author_inst": "Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran." - }, - { - "author_name": "Reza Khayami", - "author_inst": "Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran." - }, - { - "author_name": "Mahsa Mollapour Sisakht", - "author_inst": "ErasmusMC" - }, - { - "author_name": "Mohammadamin Mahmanzar", - "author_inst": "Department of Bioinformatics, Kish International Campus University of Tehran, Kish, Iran" - }, - { - "author_name": "Zahra Meshkat", - "author_inst": "Antimicrobial Resistance Research Center & Department of Medical Bacteriology and Virology, Bu-Ali Research Institute & Ghaem University Hospital, Faculty of Me" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.06.21.497047", "rel_title": "Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection", @@ -273652,6 +274349,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.06.22.22276766", + "rel_title": "Acceleration of regional, racial and gender disparities in drug overdoses across the United States driven by COVID-19 and fentanyl use", + "rel_date": "2022-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.22.22276766", + "rel_abs": "ObjectivesTo examine trends in drug overdose deaths by gender, race and geography in the United States during the period 2013-2020.\n\nMethodsWe used the final National Vital Statistics System multiple cause-of-death mortality files to extract crude rates by gender and race and to calculate the male-to-female ratios of crude rates between 2013 and 2020. We established 2013-2019 temporal trends for four major drug types: psychostimulants with addiction potential (T43.6, such as methamphetamines); heroin (T40.1); natural and semi-synthetic opioids (T40.2, such as those contained in prescription pain-killers); synthetic opioids (T40.4, such as fentanyl and its derivatives) through a quadratic regression and determined whether changes in the pandemic year 2020 were statistically significant. We also identified states, race and gender categories most impacted by drug overdoses.\n\nResultsNationwide, the year 2020 saw statistically significant increases in overdoses for all drug categories except heroin, surpassing predictions based on 2013-2019 trends. Crude rates for Blacks of both genders surpassed those for Whites for fentanyl and psychostimulants in 2018 creating a gap that widened through 2020. In some regions mortality among Whites decreased while overdose rates for Blacks kept rising. The largest 2020 mortality statistic is for Black males in the District of Columbia, with a record 134 overdoses per 100,000 due to fentanyl, 9.4 times more than the fatality rate among White males. Male overdose crude rates in 2020 remain larger than those of females for all drug categories except in Idaho, Utah and Arkansas where crude rates of overdoses by natural and semisynthetic opioids for females exceeded those of males.\n\nPublic Health ImplicationsDrug prevention, mitigation and no-harm strategies should include racial, geographical and gender-specific efforts, to better identify and serve at risk groups.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Lucas B\u00f6ttcher", + "author_inst": "Frankfurt School of Finance & Management gGmbH" + }, + { + "author_name": "Maria R. D'Orsogna", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Tom Chou", + "author_inst": "University of California Los Angeles" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.06.22.22276765", "rel_title": "COVID-19 vaccine breakthrough infections among fully vaccinated Health Care Workers in Lagos, Nigeria", @@ -275123,85 +275847,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.06.20.22275994", - "rel_title": "Characterising patterns of COVID-19 and long COVID symptoms: Evidence from nine UK longitudinal studies", - "rel_date": "2022-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.20.22275994", - "rel_abs": "Multiple studies across global populations have established the primary symptoms characterising COVID-19 (Coronavirus Disease 2019) and long COVID. However, as symptoms may also occur in the absence of COVID-19, a lack of appropriate controls has often meant that specificity of symptoms to acute COVID-19 or long COVID could not be examined. We aimed to characterise patterns of COVID-19 and long COVID symptoms across nine UK longitudinal studies, totalling over 42,000 participants. Conducting latent class analyses separately in three groups ( no COVID-19, COVID-19 in last 12 weeks, COVID-19 > 12 weeks ago), the data did not support the presence of more than two distinct symptom patterns, representing high and low symptom burden, in each group. Comparing the high symptom burden classes between the COVID-19 in last 12 weeks and no COVID-19 groups we identified symptoms characteristic of acute COVID-19, including loss of taste and smell, fatigue, cough, shortness of breath and muscle pains or aches. Comparing the high symptom burden classes between the COVID-19 > 12 weeks ago and no COVID-19 groups we identified symptoms characteristic of long COVID, including fatigue, shortness of breath, muscle pain or aches, difficulty concentrating and chest tightness. The identified symptom patterns among individuals with COVID-19 > 12 weeks ago were strongly associated with self-reported length of time unable to function as normal due to COVID-19 symptoms, suggesting that the symptom pattern identified corresponds to long COVID. Building the evidence base regarding typical long COVID symptoms will improve diagnosis of this condition and the ability to elicit underlying biological mechanisms, leading to better patient access to treatment and services.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Ruth C E Bowyer", - "author_inst": "King's College London" - }, - { - "author_name": "Charlotte Huggins", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Renin Toms", - "author_inst": "University of Bristol" - }, - { - "author_name": "Richard John Shaw", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Bo Hou", - "author_inst": "Bradford Institute for Health Research" - }, - { - "author_name": "Ellen J Thompson", - "author_inst": "King's College London" - }, - { - "author_name": "Alex Siu Fung Kwong", - "author_inst": "University of Bristol" - }, - { - "author_name": "Dylan M Williams", - "author_inst": "UCL" - }, - { - "author_name": "Milla Kibble", - "author_inst": "King's College London" - }, - { - "author_name": "George B Ploubidis", - "author_inst": "University College London" - }, - { - "author_name": "Nicholas J Timpson", - "author_inst": "University of Bristol" - }, - { - "author_name": "Jonathan A C Sterne", - "author_inst": "University of Bristol" - }, - { - "author_name": "Nishi Chaturvedi", - "author_inst": "University College London" - }, - { - "author_name": "Claire J Steves", - "author_inst": "King's College London" - }, - { - "author_name": "Kate Tilling", - "author_inst": "University of Bristol" - }, - { - "author_name": "Richard J Silverwood", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.06.17.22276229", "rel_title": "Low level of knowledge about COVID-19 among a sample of Deaf persons in Ghana.", @@ -275386,6 +276031,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.06.18.22276591", + "rel_title": "Estimating RSV seasonality from pandemic disruptions: a modelling study", + "rel_date": "2022-06-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.18.22276591", + "rel_abs": "BackgroundRespiratory syncytial virus (RSV) is a leading cause of respiratory tract infections and bronchiolitis in young children. The seasonal pattern of RSV is shaped by short-lived immunity, seasonally varying contact rates and pathogen viability. The magnitude of each of these parameters is not fully clear. The disruption of the regular seasonality of RSV during the COVID pandemic in 2020 due to control measures, and the ensuing delayed surge in RSV cases provides an opportunity to disentangle these factors and to understand the implication for vaccination strategies. A better understanding of the drivers of RSV seasonality is key for developing future vaccination strategies.\n\nMethodsWe developed a mathematical model of RSV transmission, which simulates the sequential re-infection (SEIRRS4) and uses a flexible Von Mises function to model the seasonal forcing. Using MCMC we fit the model to laboratory confirmed RSV data from 2010-2022 from NSW while accounting for the reduced contact rates during the pandemic with Google mobility data. We estimated the baseline transmission rate, its amplitude and shape during RSV season as well as the duration of immunity. The resulting parameter estimates were compared to a fit to pre-pandemic data only, and to a fit with a cosine forcing function. We then simulated the expected shifts in peak timing and amplitude under two vaccination strategies: continuous and seasonal vaccination.\n\nResultsWe estimate that RSV dynamics in NSW can be best explained by a high effective baseline transmission rate (2.94/d, 95% CrI 2.72-3.19) and a narrow peak with a maximum 13% increase compared to the baseline transmission rate. We also estimate the duration of post infection temporary but sterilizing immunity to be 412 days (95% CrI 391-434). A cosine forcing resulted in a similar fit and posterior estimates. Excluding the data from the pandemic period in the fit increased parameter correlation and yielded less informative posterior distributions. The continuous vaccination strategy led to more extreme seasonal incidence with a delay in the peak timing and a higher amplitude whereas seasonal vaccination flattened the incidence curves.\n\nConclusionQuantifying the parameters that govern RSV seasonality is key in determining potential indirect effects from immunization strategies as those are being rolled out in the next few years.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Fabienne Krauer", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Tor Erlend Fjelde", + "author_inst": "Computational and Biological Learning, Department of Engineering, University of Cambridge, UK" + }, + { + "author_name": "Mihaly Koltai", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK" + }, + { + "author_name": "David Hodgson", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK" + }, + { + "author_name": "Marina Treskova-Schwarzbach", + "author_inst": "Robert Koch Institut, Berlin, Germany" + }, + { + "author_name": "Christine Harvey", + "author_inst": "Health Protection NSW, NSW Ministry of Health" + }, + { + "author_name": "Mark Jit", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK" + }, + { + "author_name": "Ole Wichmann", + "author_inst": "Robert Koch Institut, Berlin, Germany" + }, + { + "author_name": "Thomas Harder", + "author_inst": "Robert Koch Institut, Berlin, Germany" + }, + { + "author_name": "Stefan Flasche", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.06.17.496635", "rel_title": "Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1", @@ -277061,49 +277761,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.15.22276427", - "rel_title": "Efficacy and Safety of Nebulized Ethanol Inhalation in COVID-19 Treatment. A Randomized, Clinical Trial", - "rel_date": "2022-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.15.22276427", - "rel_abs": "BackgroundConsidering anti coronavirus effects of ethanol, the efficacy of its administration was evaluated in this research. Because of respiratory tract entrance of virus in COVID-19, this study was done by inhalation of nebulized ethanol.\n\nMethodsNinety-nine positive SARS-CoV-2-PCR patients who had been admitted at a respiratory clinic were included in this study. Patients were randomly assigned to the control (distilled water spray) and intervention (35% ethanol spray) group. Both groups were instructed to inhale 3 puffs of spray and inhale it, every six hours for a week. Global symptomatic score (GSS), clinical status scale,0020Blood Oxygenation, and C-Reactive Protein (CRP) at the first visit and days 3, 7, 14 were measured and compared between groups.\n\nResultsThe GSS decreased more and faster in the intervention group (ethanol) (1.4+1.4 vs 2.3+1.7, P=0.035) two weeks after starting intervention. On day 14, the odds of intervention group to have better clinical status was 5.715 times (95% CI, 2.47 to 13.19) than of control group a statistically significant effect, Wald {chi}2 (1) =16.67, P =0.001. Blood oxygen saturation also improved earlier in the ethanol group but without statistical significance difference. The readmission rate was lower in the intervention group (zero vs 10.9%, P=0.02).\n\nConclusionInhaled ethanol seems to be effective in improvement, mitigating clinical symptoms and reducing the need to repeat treatment. Considering the low cost, availability and no significant adverse events of ethanol, research and additional efforts are recommended to evaluate its curative effects in the early stages of COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ali Amoushahi", - "author_inst": "Department of Anesthesiology and Intensive Care Unit, Isabn-e- Maryam Hospital, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Elham Moazam", - "author_inst": "Isabn-e-Maryam Hospital, Cancer Prevention Research Center, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Amin Reza Tabatabaei", - "author_inst": "Isabn-e-Maryam Hospital, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Golnaz Ghasimi", - "author_inst": "Isabn-e-Maryam Hospital, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Pietro Salvatori", - "author_inst": "Formerly, ENT Department, Humanitas San Pio X Hospital, Milan, Italy" - }, - { - "author_name": "Ian Grant-Whyte", - "author_inst": "Diplomat of the American Board of family practice, Canada" - }, - { - "author_name": "Ahmed Ragab Ezz", - "author_inst": "Mansoura University, Dakahlia Governorate, Egypt" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.15.22276466", "rel_title": "Effectiveness of mRNA COVID-19 vaccine boosters against infection, hospitalization and death: a target trial emulation in the omicron (B.1.1.529) variant era", @@ -277276,6 +277933,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.06.15.22276467", + "rel_title": "The influence of place on COVID-19 vaccine coverage in Alberta: A multilevel analysis", + "rel_date": "2022-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.15.22276467", + "rel_abs": "BackgroundWhile there is evidence of urban/rural disparities in COVID-19 vaccination coverage, there is limited data on the influence of other place-based variables.\n\nMethodsIn this cross-sectional study, we analyzed population-based linked administrative health data to examine vaccination coverage for 3,945,103 residents in Alberta, Canada. We used multilevel logistic regression to examine the association of vaccination coverage with various place-based variables.\n\nResultsAfter 4 months of widely available COVID-19 vaccine, coverage varied widely between rural and urban areas (58% to 73%) and between geographic health authority zones (55.8% to 72.8%). Residents living in neighborhoods with lower COVID-19 disease incidence had the lowest vaccination coverage (63.2%), while coverage in higher incidence neighborhoods ranged from 68.3% to 71.9%. The multilevel logistic regression model indicated that residence in metro (adjusted odds ratio [aOR] 1.37; 95% CI: 1.31-1.42) and urban areas (aOR 1.11; 95% CI: 1.08-1.14) was associated with higher vaccine coverage than residence in rural areas. Similarly, residence in Edmonton, Calgary, and South health zones was associated with higher vaccine coverage compared to residence in Central zone. Higher income neighborhoods reported higher vaccine coverage than the lowest-income neighborhoods, and the highest COVID-19 risk neighborhoods reported higher vaccine coverage than the lowest risk neighborhoods (aOR 1.52; 95% CI: 1.12-2.05).\n\nConclusionIn the first four months of wider vaccine availability in Alberta, COVID-19 vaccine coverage varied according to various place-based characteristics. Vaccine distribution strategies need to consider place-based variables for program prioritization and delivery.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Yuba Raj Paudel", + "author_inst": "University of Alberta" + }, + { + "author_name": "Crystal Du", + "author_inst": "University of Alberta" + }, + { + "author_name": "Shannon E MacDonald", + "author_inst": "University of Alberta" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.06.16.22276479", "rel_title": "Mental health of healthcare workers in England during the COVID-19 pandemic: a longitudinal cohort study", @@ -279371,81 +280055,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.06.13.22276312", - "rel_title": "Quantifying Inequities in COVID-19 Vaccine Distribution Over Time by social vulnerability, race and ethnicity, and location: A Population-Level Analysis in St. Louis and Kansas City, Missouri", - "rel_date": "2022-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.13.22276312", - "rel_abs": "BACKGROUNDEquity in vaccination coverage is a cornerstone to a successful public health response to COVID-19. To deepen understand of the extent to which vaccination coverage compared to initial strategies for equitable vaccination, we explore primary vaccine series and booster rollout over time and by race/ethnicity, social vulnerability, and geography.\n\nMETHODS AND FINDINGSWe analyzed data from the Missouri State Department of Health and Senior Services on all COVID-19 vaccinations administered across 7 counties in the St. Louis region and 4 counties in the Kansas City Region. We compared rates of receiving the primary COVID-19 vaccine series and boosters relative to time, race/ethnicity, zip code-level social vulnerability index (SVI), vaccine location type, and COVID-19 disease burden. We adapted a well-established tool for measuring inequity--the Lorenz curve--to quantify inequities in COVID-19 vaccination relative to these key metrics. Between 12/15/2020 and 2/15/2022, 1,762,508 individuals completed the primary series and 871,896 had received a booster. During early phases of the primary series rollout, Black and Hispanic individuals from high SVI zip codes were vaccinated at less than half the rate of White individuals, but rates increased over time until they were higher than rates in White individuals after June 2021; Asian individuals maintained high levels of vaccination throughout. Increasing vaccination rates in Black and Hispanic communities corresponded with periods when more vaccinations were offered at small community-based sites such as pharmacies rather than larger health systems and mass vaccination sites. Using Lorenz curves, zip codes in the quartile with the lowest rates of primary series completion accounted for 19.3%, 18.1%, 10.8%, and 8.8% of vaccinations but represented 25% of either the total population, cases, deaths, or population-level SVI, respectively. When tracking Gini coefficients, these disparities were greatest earlier during rollout, but improvements were slow and modest and vaccine disparities remained across all metrics even after one year. Patterns of disparities for boosters were similar but often of much greater magnitude during rollout in Fall 2021. Study limitations include inherent limitations in vaccine registry dataset such as missing and misclassified race/ethnicity and zip code variables and potential changes in zip code population sizes since census enumeration.\n\nCONCLUSIONSRacial inequity in the initial COVID-19 vaccination and booster rollout in two large U.S. metropolitan areas were apparent across racial/ethnic communities, across levels of social vulnerability, over time, and across types of vaccination administration sites. Disparities in receipt of the primary vaccine series attenuated over time during a period in which sites of vaccination administration diversified, but were recapitulated during booster rollout. These findings highlight how public health strategies from the outset must directly target these deeply embedded structural and systemic determinants of disparities and track equity metrics over time to avoid perpetuating inequities in health care access.\n\nAUTHOR SUMMARYO_ST_ABSWhy Was This Study Done?C_ST_ABSO_LIEquitable vaccine strategies are critical for the public health response to COVID-19, but there is limited understanding of how vaccination campaigns compared to different metrics for equity.\nC_LIO_LIMany initial approaches to vaccine allocation sought to acknowledge the known disparities in exposure risk, disease burden, needs, and access by formally considering social vulnerability or race/ethnicity in plans to prioritize vaccinations, but there is limited empirical evaluation of how actual primary vaccine series and subsequent booster efforts aligned with the initial goals set out for equity.\nC_LIO_LIWe quantify COVID-19 vaccine-related inequities in receipt of the primary vaccine series and booster across key equity metrics including race/ethnicity, social vulnerability, location, and time using a novel application of Lorenz curves and Gini coefficients--tools from economics to measure inequalities--in the St. Louis and Kansas City regions of Missouri.\nC_LI\n\nWhat Did the Researchers Do and Find?O_LIWe analyzed data from the Missouri State Department of Health and Senior Services on all COVID-19 vaccinations administered in the St. Louis region and Kansas City Regions. We compared rates of receiving the primary COVID-19 vaccine series and boosters relative to time, race/ethnicity, zip code-level social vulnerability index (SVI), vaccine location type, and COVID-19 disease burden. We adapted Lorenz curves and Gini coefficients to quantify the inequities in COVID-19 vaccination relative to these key metrics and examined how they changed over time.\nC_LIO_LIBlack and Hispanic individuals from high SVI zip codes completed the primary series at less than half the rate of White individuals during early phases of the primary series rollout, but surpassed rates in White individuals after June 2021. These relative increases in primary series completion rates in Black and Hispanic communities corresponded to periods when vaccinations became more available at small community-based sites.\nC_LIO_LILorenz curves demonstrated that zip codes in the quartile with the lowest rates of primary series completion accounted for 19.3%, 18.1%, 10.8%, and 8.8% of vaccinations but represented 25% of either the total population, cases, deaths, or population-level SVI, respectively. Tracking Gini coefficients over time demonstrated that these disparities were greatest earlier during rollout, but only improved slowly and modestly over time.\nC_LIO_LIPatterns of disparities for boosters were similar but often of much greater magnitude that those seen with completion of the primary vaccine series. patterns of disparities were similar but often of greater magnitude during booster rollout in Fall 2021.\nC_LI\n\nWhat Do These Findings Mean?O_LIVaccination coverage for both the primary series and boosters demonstrated substantial disparities across race/ethnicity, levels of social vulnerability, types of vaccine administration sites, and over time.\nC_LIO_LIDespite well-documented inequities for COVID-19 and need for equitable vaccine approaches, the strategies employed did not overcome deeply entrenched systemic inequities in health care and society.\nC_LIO_LIPublic health strategies must proactively target these deeply embedded structural determinants of disparities from the outset and should systematically track equity metrics over time to avoid perpetuating inequities in health care access.\nC_LI", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Aaloke Mody", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Cory Bradley", - "author_inst": "Washington University in St Louis School of Medicine" - }, - { - "author_name": "Salil Redkar", - "author_inst": "Washington University in St Louis School of Medicine" - }, - { - "author_name": "Branson Fox", - "author_inst": "Washington University in St Louis School of Medicine" - }, - { - "author_name": "Ingrid Eshun-Wilson", - "author_inst": "Washington University in St Louis School of Medicine" - }, - { - "author_name": "Matifadza G. Hlatshwayo", - "author_inst": "St. Louis City Department of Health" - }, - { - "author_name": "Anne Trolard", - "author_inst": "Washington University in St Louis School of Medicine" - }, - { - "author_name": "Khai Hoan Tram", - "author_inst": "University of Washington School of Medicine" - }, - { - "author_name": "Lindsey Filiatreau", - "author_inst": "Washington University in St Louis School of Medicine" - }, - { - "author_name": "Franda Thomas", - "author_inst": "St. Louis City Department of Health" - }, - { - "author_name": "Matt Haslam", - "author_inst": "St. Louis City Department of Health" - }, - { - "author_name": "George Turabelidze", - "author_inst": "Missouri Department of Health and Senior Services" - }, - { - "author_name": "Vetta Sanders-Thompson", - "author_inst": "Washington University in St Louis George Warren Brown School of Social Work" - }, - { - "author_name": "William G. Powderly", - "author_inst": "Washington University in St Louis School of Medicine" - }, - { - "author_name": "Elvin H. Geng", - "author_inst": "Washington University in St Louis School of Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.06.14.22276393", "rel_title": "Nirmatrelvir plus ritonavir for early COVID-19 and hospitalization in a large US health system", @@ -279714,6 +280323,89 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.06.14.496214", + "rel_title": "Oxysterols drive inflammation via GPR183 during influenza virus and SARS-CoV-2 infection", + "rel_date": "2022-06-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.14.496214", + "rel_abs": "RationaleSevere viral respiratory infections are often characterized by extensive myeloid cell infiltration and activation and persistent lung tissue injury. However, the immunological mechanisms driving excessive inflammation in the lung remain elusive.\n\nObjectivesTo identify the mechanisms that drive immune cell recruitment in the lung during viral respiratory infections and identify novel drug targets to reduce inflammation and disease severity.\n\nMethodsPreclinical murine models of influenza virus and SARS-CoV-2 infection.\n\nResultsOxidized cholesterols and the oxysterol-sensing receptor GPR183 were identified as drivers of monocyte-macrophage infiltration to the lung during influenza virus (IAV) and SARS-CoV-2 infections. Both IAV and SARS-CoV-2 infections upregulated the enzymes cholesterol 25-hydroxylase (CH25H) and cytochrome P450 family 7 subfamily member B1 (CYP7B1) in the lung, resulting in local production of the oxidized cholesterols 25-hydroxycholesterol and 7,25-dihydroxycholesterol (7,25-OHC). Loss-of-function mutation of GPR183, or treatment with a GPR183 antagonist, reduced macrophage infiltration and inflammatory cytokine production in the lungs of IAV- or SARS-CoV-2-infected mice. The GPR183 antagonist also significantly attenuated the severity of SARS-CoV-2 infection by reducing weight loss and viral loads.\n\nConclusionThis study demonstrates that oxysterols drive inflammation in the lung and provides the first preclinical evidence for therapeutic benefit of targeting GPR183 during severe viral respiratory infections.\n\nAuthor SummaryViral infections trigger oxysterol production in the lung, attracting macrophages via GPR183. Blocking GPR183 reduced inflammation and disease severity in SARS-CoV-2 infection, making GPR183 a putative target for therapeutic intervention.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Cheng Xiang Foo", + "author_inst": "Mater Research Institute - The University of Queensland" + }, + { + "author_name": "Stacey Bartlett", + "author_inst": "Mater Research Institute - The University of Queensland" + }, + { + "author_name": "Keng Yih Chew", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Minh Dao Ngo", + "author_inst": "Mater Research Institute - The University of Queensland" + }, + { + "author_name": "Helle Bielefeldt-Ohmann", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Buddhika Jayakody Arachchige", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Benjamin Matthews", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Sarah Reed", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Ran Wang", + "author_inst": "Mater Research Institute - The University of Queensland" + }, + { + "author_name": "Matthew J. Sweet", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Lucy Burr", + "author_inst": "Mater Research Institute - The University of Queensland" + }, + { + "author_name": "Jane E. Sinclair", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Rhys Parry", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Alexander Khromykh", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Kirsty R. Short", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Mette M. Rosenkilde", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Katharina Ronacher", + "author_inst": "Mater Research Institute - The University of Queensland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.06.12.22276290", "rel_title": "Impact of non-pharmaceutical interventions targeted at the COVID-19 pandemic on influenza cases in the UK Armed Forces", @@ -281221,41 +281913,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.06.09.22276209", - "rel_title": "Blood biomarkers representing maternal-fetal interface tissues used to predict early-and late-onset preeclampsia but not COVID-19 infection", - "rel_date": "2022-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.09.22276209", - "rel_abs": "BackgroundA well-known blood biomarker (soluble fms-like tyrosinase-1 [sFLT-1]) for preeclampsia, i.e., a pregnancy disorder, was found to predict severe COVID-19, including in males. True biomarker may be masked by more-abrupt changes related to endothelial instead of placental dysfunction. This study aimed to identify blood biomarkers that represent maternal-fetal interface tissues for predicting preeclampsia but not COVID-19 infection.\n\nMethodsThe surrogate transcriptome of the tissues was determined by that in maternal blood, utilizing four datasets (n=1,354) which were collected before the COVID-19 pandemic. Applying machine learning, a preeclampsia prediction model was chosen between those using blood transcriptome (differentially expressed genes [DEGs]) and the blood-derived surrogate for the tissues. We selected the most predictive model by the area under receiver operating characteristic (AUROC) using a dataset for developing the model, and well-replicated in datasets either with or without intervention. To identify eligible blood biomarkers that predicted any-onset preeclampsia from the datasets but did not predict positives in the COVID-19 dataset (n=47), we compared several methods of predictor discovery: (1) the best prediction model; (2) gene sets by standard pipelines; and (3) a validated gene set for predicting any-onset preeclampsia during the pandemic (n=404). We chose the most predictive biomarkers from the best method with the significantly largest number of discoveries by a permutation test. The biological relevance was justified by exploring and reanalyzing low- and high-level, multi-omics information.\n\nResultsA prediction model using the surrogates developed for predicting any-onset preeclampsia (AUROC of 0.85, 95% confidence interval [CI] 0.77 to 0.93) was the only that was well-replicated in an independent dataset with no intervention. No model was well-replicated in datasets with a vitamin D intervention. None of the blood biomarkers with high weights in the best model overlapped with blood DEGs. Blood biomarkers were transcripts of integrin-5 (ITGA5), interferon regulatory factor-6 (IRF6), and P2X purinoreceptor-7 (P2RX7) from the prediction model, which was the only method that significantly discovered the eligible blood biomarkers (n=3/100 combinations, 3.0%; P=.036). Most of the predicted events (73.70%) among any-onset preeclampsia were cluster A as defined by ITGA5 (Z-score [≥]1.1), but were only a minority (6.34%) among positives in the COVID-19 dataset. The remaining were the predicted events (26.30%) among any-onset preeclampsia or those among COVID-19 infection (93.66%) if IRF6 Z-score was [≥]-0.73 (clusters B and C), in which none was the predicted events among either late-onset preeclampsia (LOPE) or COVID-19 infection if P2RX7 Z-score was <0.13 (cluster B). Greater proportion of predicted events among LOPE were cluster A (82.85% vs. 70.53%) compared to early-onset preeclampsia (EOPE). The biological relevance by multi-omics information explained the biomarker mechanism, polymicrobial infection in any-onset preeclampsia by ITGA5, viral co-infection in EOPE by ITGA5-IRF6, a shared prediction with COVID-19 infection by ITGA5-IRF6-P2RX7, and non-replicability in datasets with a vitamin D intervention by ITGA5.\n\nConclusionsIn a model that predicts preeclampsia but not COVID-19 infection, the important predictors were maternal-blood genes that were not extremely expressed, including the proposed blood biomarkers. The predictive performance and biological relevance should be validated in future experiments.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Herdiantri Sufriyana", - "author_inst": "Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taiwan; Department of Medical Physiology, Fa" - }, - { - "author_name": "Hotimah Masdan Salim", - "author_inst": "Department of Molecular Biology, Faculty of Medicine, Universitas Nahdlatul Ulama Surabaya, Indonesia." - }, - { - "author_name": "Akbar Reza Muhammad", - "author_inst": "Faculty of Medicine, Universitas Nahdlatul Ulama Surabaya, Indonesia." - }, - { - "author_name": "Yu-Wei Wu", - "author_inst": "Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taiwan; Clinical Big Data Research Center, T" - }, - { - "author_name": "Emily Chia-Yu Su", - "author_inst": "Graduate Institute of Biomedical Informatics, College of Medical Science and Technology and Research Center for Artificial Intelligence in Medicine, Taipei Medi" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2022.06.08.22276134", "rel_title": "Implementation of a digital early warning score (NEWS2) in a cardiac specialist and general hospital settings in the COVID-19 pandemic: A qualitative study.", @@ -281672,6 +282329,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.08.22276125", + "rel_title": "Pediatric ARDS phenotypes in critical COVID-19: implications for therapies and outcomes.", + "rel_date": "2022-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.08.22276125", + "rel_abs": "Purposeto describe lung mechanics in Pediatric Acute Respiratory Disease Syndrome (PARDS) associated with COVID-19. We hypothesize two phenotypes according to respiratory system mechanics and clinical diagnosis.\n\nMethodsa concurrent multicenter observational study was performed, analyzing clinical variables and pulmonary mechanics of PARDS associated with COVID-19 in 4 Pediatric intensive care units (PICUs) of Peru. Subgroup analysis included PARDS associated with multisystem inflammatory syndrome in children (MIS-C), MIS-PARDS, and PARDS with COVID-19 primary respiratory infection, C-PARDS. In addition, receiver operator curve analysis (ROC) for mortality was performed.\n\nResults30 patients were included. Age was 7.5(4-11) years, 60% male, and mortality 23%. 47% corresponded to MIS-PARDS and 53% to C-PARDS phenotypes. C-PARDS had positive RT-PCR in 67% and MIS-PARDS none (p<0.001). C-PARDS group had more profound hypoxemia (P/Fratio<100, 86%vs38%,p<0.01) and higher driving-pressure (DP) [14(10-22)vs10(10-12)cmH2O], and lower compliance of the respiratory system (CRS)[0.5(0.3-0.6)vs 0.7(0.6-0.8)ml/kg/cmH2O] compared to MIS-PARDS (all p<0.05). ROC-analysis for mortality showed that DP had the best performance [AUC 0.91(95%CI0.81-1.00), with the best cut-point of 15 cmH2O (100% sensitivity and 87% of specificity). Mortality in C-PARDS was 38% and 7% in MIS-PARDS(p=0.09). MV free-days were 12(0-23) in C-PARDS and 23(21-25) in MIS-PARDS(p=0.02)\n\nConclusioncritical pediatric COVID-19 is heterogeneous in children. COVID-19 PARDS had two phenotypes with distinctive pulmonary mechanics features. Characteristics of C-PARDS are like a classic primary PARDS, while a decoupling between compliance and hypoxemia was more frequent in MIS-PARDS. In addition, C-PARDS had fewer MV free-days. DP [≥] 15 cmH2O had the best performance of the quasi-static calculations to discriminate for mortality. Standardized pulmonary mechanics measurements in PARDS might reveal essential information to tailor the ventilatory strategy in pediatric critical COVID-19.\n\n Take-home messageO_LIPARDS associated with COVID-19 have two different phenotypes based on clinical diagnosis and pulmonary mechanics.\nC_LIO_LIC-PARDS group was characterized as a classic moderate to severe primary ARDS. A decoupling between compliance and hypoxemia was more frequent in MIS-PARDS. Regarding outcomes, C-PARDS had less VFD and a trend toward higher mortality.\nC_LIO_LIData from the quasi-static calculations were associated with mortality; DP[≥] 15 cmH2O was the best discriminator.\nC_LIO_LIStandardized pulmonary mechanics measurements in PARDS might reveal essential information to tailor the ventilatory strategy, characterizing different phenotypes and parameters associated with outcomes.\nC_LI\n\nTweetLung mechanics help to differentiate two different phenotypes in PARDS associated with COVID-19. C-PARDS associated with respiratory infection, and MIS-PARDS, associated with MIS-C. Also, lung mechanics variables were associated with mortality, being DP [≥] 15 cmH2O the best discriminator.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Jesus Angel Dominguez Rojas", + "author_inst": "HOSPITAL EDGARDO REBAGLIATI MARTINS" + }, + { + "author_name": "Yesica Luna-Delgado", + "author_inst": "Hospital Nacional Regional de Cusco" + }, + { + "author_name": "Patrick Caqui-Vilca", + "author_inst": "Hospital Nacional Hipolito Unanue" + }, + { + "author_name": "Carlos Martel Ramirez", + "author_inst": "Hospital Nacional Hipolito Unanue" + }, + { + "author_name": "Miguel Quispe Chipana", + "author_inst": "Hospital Nacional Hipolito Unanue" + }, + { + "author_name": "Marico Cruz-Arpi", + "author_inst": "Hospital Nacional Hipolito Unanue" + }, + { + "author_name": "Noe Atamari-Anahui", + "author_inst": "Universidad San Ignacio de Loyola, Vicerrectorado de Investigacion" + }, + { + "author_name": "Cleotilde Mireya Munoz Ramirez", + "author_inst": "Instituto Nacional de Pediatria, Ciudad de Mexico" + }, + { + "author_name": "Gaudi Quispe Flores", + "author_inst": "Hospital Nacional Edgardo Rebagliati Martins" + }, + { + "author_name": "Mariela Tello Pezo", + "author_inst": "Instituto Nacional de Salud del Nino San Borja" + }, + { + "author_name": "Pablo Cruces", + "author_inst": "Hospital El Carmen de Maipu, Unidad de Cuidados Intensivos Pediatricos, Chile" + }, + { + "author_name": "Pablo Vasquez-Hoyos", + "author_inst": "LARed Network, Universidad Nacional de Colombia" + }, + { + "author_name": "FRANCO DIAZ", + "author_inst": "Hospital El Carmen de Maipu. Chile" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2022.06.13.22276327", "rel_title": "The prevalence of mental ill-health in women during pregnancy and after childbirth during the Covid-19 pandemic: a Systematic review and Meta-analysis", @@ -282947,69 +283671,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.06.10.495677", - "rel_title": "The Fc-effector function of COVID-19 convalescent plasma contributes to SARS-CoV-2 treatment efficacy in mice", - "rel_date": "2022-06-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.10.495677", - "rel_abs": "COVID-19 convalescent plasmas (CCPs) are chosen for plasma therapy based on neutralizing titers and anti-Spike immunoglobulin levels. However, specific CCP characteristics that promote SARS-CoV-2 control in recipients are complex and incompletely defined. Using an in vivo imaging approach, we demonstrate that CCPs with low neutralizing and high Fc-effector activity, in contrast to those with poor Fc-function, afford effective prophylaxis and therapy in K18-hACE2 mice lethally challenged with SARS-CoV-2-nLuc. Macrophages and neutrophils significantly contributed to CCP effects during therapy but to a reduced extent under prophylaxis. Both IgG and Ig(M+A) were required during therapy, but the IgG fraction alone was sufficient during prophylaxis. Finally, despite neutralizing poorly, SARS-CoV-2 Wuhan-elicited CCPs delayed Delta and Beta variants of concern (VOC)-induced mortality in mice illustrating the contribution of polyclonal Fc-effector functions in immunity against VOCs. Thus, in addition to neutralization, Fc-effector activity is a significant criterion for CCP selection for therapeutic applications.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Irfan Ullah", - "author_inst": "Yale University" - }, - { - "author_name": "Guillaume Beaudoin-Bussieres", - "author_inst": "CRCHUM" - }, - { - "author_name": "Kelly Symmes", - "author_inst": "Yale University" - }, - { - "author_name": "Marc Cloutier", - "author_inst": "Hema-Quebec, Affaires Medicales et Innovation" - }, - { - "author_name": "Eric Ducas", - "author_inst": "Hema-Quebec" - }, - { - "author_name": "Alexandra Tauzin", - "author_inst": "Centre de Recherche du CHUM" - }, - { - "author_name": "Annemarie Laumaea", - "author_inst": "Universite de Montreal" - }, - { - "author_name": "Philippe Begin", - "author_inst": "CHUM-MED" - }, - { - "author_name": "Walther Mothes", - "author_inst": "Yale University" - }, - { - "author_name": "Renee Bazin", - "author_inst": "Hema-Quebec" - }, - { - "author_name": "Andres Finzi", - "author_inst": "Universite de Montreal" - }, - { - "author_name": "Pradeep D Uchil", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.06.10.22276252", "rel_title": "Ivermectin for Treatment of Mild-to-Moderate COVID-19 in the Outpatient Setting: A Decentralized, Placebo-controlled, Randomized, Platform Clinical Trial", @@ -283182,6 +283843,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.06.10.495670", + "rel_title": "SARS-CoV-2 minor variant genomes at the start of the pandemic contained markers of VoCs", + "rel_date": "2022-06-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.10.495670", + "rel_abs": "SARS-CoV-2 emerged through limited zoonotic spillovers and was predicted to have constrained sequence diversity. The dominant consensus and minor variant genomes were determined from the earliest samples associated with the Huanan market and the start of the pandemic. The sequence data confirmed that the dominant consensus genomes shared very close homology. However, there were minor variant genomes present in each sample, which encompassed synonymous and non-synonymous changes. Fusion sequences characteristic of defective RNAs were identified that could be linked between patients. Several substitutions (but not deletions) associated with much later variants of concern (VoCs) were already present as minor variant genomes. This suggests it may be possible to predict futures variants at the start of a pandemic by examining where variability in sequence occurs.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Xiaofeng Dong", + "author_inst": "Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, UK." + }, + { + "author_name": "Julian Alexander Hiscox", + "author_inst": "Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, UK." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.06.08.22276091", "rel_title": "Environmental circulation of adenovirus 40/41 and SARS-CoV-2 in the context of the emergence of acute hepatitis of unknown origin", @@ -284625,25 +285309,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.05.22276023", - "rel_title": "Modeling the Omicron Dynamics and Development in China: with a Deep Learning Enhanced Compartmental Model", - "rel_date": "2022-06-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.05.22276023", - "rel_abs": "BackgroundCompartmental models dominate epidemic modeling. Estimations of transmission parameters between compartments are typically done through stochastic parameterization processes that depend upon detailed statistics on transmission characteristics, which are economically and resource-wide expensive to collect.\n\nObjectivesWe apply deep learning techniques as a lower data dependency alternative to estimate transmission parameters of a customized compartmental model, for the purpose of simulating the dynamics of the Omicron phase of the COVID-19 epidemics and projecting its further development in China and subregions within the country.\n\nMethodsWe construct a compartmental model, and develop a multivariate, multistep deep learning methodology to estimate the models transmission parameters. We then feed the estimated transmission parameters to the compartmental model to predict the development of the COVID-19 epidemics in China and subregions within the country for 28 days.\n\nResultsIn China (excluding Hong Kong and Taiwan), the daily Omicron infection increase is between 60 and 260 in the 28-day forecast period between June 4 and July 1, 2022. On July 1, 2022, there would be 768,622 cumulative confirmed cases and 591 cumulative deceased cases. The CFR would stabilize at 0.077%{+/-}0.00025%. Assuming a 25% infection rate, the total deaths with Omicron would be up to 280,000 without non-pharmaceutical intervention (NPI).\n\nConclusionsCurrent compartmental models require stochastic parameterization to estimate the transmission parameters. These models effectiveness depends upon detailed statistics on transmission characteristics. As an alternative, deep learning techniques are effective in estimating these stochastic parameters with greatly reduced dependency on data particularity.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "QI DENG", - "author_inst": "Zhejiang Normal University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.06.07.22275493", "rel_title": "Precarious employment and associations with health during COVID-19: a nationally representative survey in Wales, UK", @@ -284932,6 +285597,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.06.07.495101", + "rel_title": "Predicting clinical outcomes of SARS-CoV-2 drug treatments with a high throughput human airway on chip platform", + "rel_date": "2022-06-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.07.495101", + "rel_abs": "Despite the relatively common observation of therapeutic efficacy in discovery screens with immortalized cell lines, the vast majority of drug candidates do not reach clinical development. Candidates that do move forward often fail to demonstrate efficacy when progressed from animal models to humans. This dilemma highlights the need for new drug screening technologies that can parse drug candidates early in development with regard to predicted relevance for clinical use. PREDICT96-ALI is a high-throughput organ-on-chip platform incorporating human primary airway epithelial cells in a dynamic tissue microenvironment. Here we demonstrate the utility of PREDICT96-ALI as an antiviral screening tool for SARS-CoV-2, combining the high-throughput functionality of a 96-well plate format in a high containment laboratory with the relevant biology of primary human tissue. PREDICT96-ALI resolved differential efficacy in five antiviral compounds over a range of drug doses. Complementary viral genome quantification and immunofluorescence microscopy readouts achieved high repeatability between devices and replicate plates. Importantly, results from testing the three antiviral drugs currently available to patients (nirmatrelvir, molnupiravir, and remdesivir) tracked with clinical outcomes, demonstrating the value of this technology as a prognostic drug discovery tool.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Christine R Fisher", + "author_inst": "Draper" + }, + { + "author_name": "Felix Mba Medie", + "author_inst": "Draper" + }, + { + "author_name": "Rebeccah J Luu", + "author_inst": "Draper" + }, + { + "author_name": "Landys Lopez Quezada", + "author_inst": "Draper" + }, + { + "author_name": "Robert B Gaibler", + "author_inst": "Draper" + }, + { + "author_name": "Thomas J Mulhern", + "author_inst": "Draper" + }, + { + "author_name": "Logan D Rubio", + "author_inst": "Draper" + }, + { + "author_name": "Elizabeth E Marr", + "author_inst": "Draper" + }, + { + "author_name": "Elizabeth P Gabriel", + "author_inst": "Draper" + }, + { + "author_name": "Jeffrey T Borenstein", + "author_inst": "Draper" + }, + { + "author_name": "Ashley L Gard", + "author_inst": "Draper" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.06.07.494579", "rel_title": "GABA-receptors are a new druggable target for limiting disease severity, lung viral load, and death in SARS-CoV-2 infected mice", @@ -286739,33 +287463,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.06.05.494906", - "rel_title": "Implications of Spike Protein Interactions with Zn-bound form of ACE2: A Computational Structural Study", - "rel_date": "2022-06-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.05.494906", - "rel_abs": "The COVID-19 pandemic has generated a major interest in designing inhibitors to prevent SARS-CoV-2 binding on host cells to protect against infection. One promising approach to such research utilizes molecular dynamics (MD) to identify potential inhibitors that can prevent the interaction between spike (S) protein on the virus and angiotensin converting enzyme 2 (ACE2) receptor on the host cells. In these studies, many groups have chosen to exclude a zinc (Zn) ion bound to the ACE2 molecule which is critical for enzymatic activity. While the relatively distant location of Zn ion from the S protein binding site (S1 domain), combined with the difficulties in modeling this ion have motivated the decision of exclusion, Zn can potentially contribute to the structural stability of the entire protein, and thus, may have implications on spike protein interaction. In this study, we explored the effects of excluding Zn on the structural stability and binding free energy of the ACE2-S1 protein complex. We generated two versions of an experimentally-derived structure of the ACE2-S1 protein complex: one with Zn and one without. Examining the differences between these two complexes during MD simulation, we found that the Zn-bound complex exhibited greater instability at nearly all residues except for the interacting residues, which were more stable in the Zn-bound complex. Additionally, the Zn-bound complex had a stronger binding free energy at all internal dielectric constants greater than one. Since binding free energy is often used to score inhibitors performances, excluding Zn could potentially have implications on inhibitor selection and performance, both in the ACE2-S1 protein system and other protein complexes that include the Zn ion.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Peter R. Fatouros", - "author_inst": "Clarkson University" - }, - { - "author_name": "Urmi Roy", - "author_inst": "Clarkson University" - }, - { - "author_name": "Shantanu Sur", - "author_inst": "Clarkson University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2022.06.06.22276040", "rel_title": "Transcriptomics Meta-Analysis Predicts Two Robust Human Biomarkers for Severe Infection with SARS-CoV-2", @@ -286918,6 +287615,109 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.06.06.494969", + "rel_title": "The unique ORF8 protein from SARS-CoV-2 binds to human dendritic cells and induces a hyper-inflammatory cytokine storm", + "rel_date": "2022-06-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.06.494969", + "rel_abs": "The novel coronavirus pandemic, whose first outbreak was reported in December 2019 in Wuhan, China (COVID-19), is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Tissue damage caused by the virus leads to a strong immune response and activation of antigen-presenting cells, which can elicit acute respiratory distress syndrome (ARDS) characterized by the rapid onset of widespread inflammation, the so-called cytokine storm. In many viral infections the recruitment of monocytes into the lung and their differentiation to dendritic cells (DCs) are seen as a response to the viral infection. DCs are critical players in the development of the acute lung inflammation that causes ARDS. Here we focus on the interaction of the ORF8 protein, a specific SARS-CoV-2 open reading frame protein, with dendritic cells (DCs). We show that ORF8 binds to dendritic cells, causes a pre-maturation of differentiating DCs, and induces the secretion of multiple pro-inflammatory cytokines by these cells. In addition, we identified dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN) as a possible interaction partner of ORF8 on dendritic cells. Blockade of ORF8 signaling leads to reduced production of IL-1{beta}, IL-6, IL-12p70, TNF-, MCP-1 (CCL2), and IL-10 by dendritic cells. Analysis of patient sera with high anti-ORF8 antibody titers showed that there was nearly no neutralization of the ORF8 protein and its function. Therefore, a neutralizing antibody that has the capacity of blocking the cytokine and chemokine response mediated by ORF8 protein might be an essential and novel additional step in the therapy of severe SARS-CoV-2 cases.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Matthias Hamdorf", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + }, + { + "author_name": "Thomas Imhof", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + }, + { + "author_name": "Ben Allan Bailey-Elkin", + "author_inst": "University of Manitoba" + }, + { + "author_name": "Janina Betz", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + }, + { + "author_name": "Sebastian J Theobald", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + }, + { + "author_name": "Alexander Simonis", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + }, + { + "author_name": "Veronica Di Cristanziano", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + }, + { + "author_name": "Lutz Gieselmann", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + }, + { + "author_name": "Felix Dewald", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + }, + { + "author_name": "Clara Lehmann", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + }, + { + "author_name": "Max Augustin", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + }, + { + "author_name": "Florian Klein", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + }, + { + "author_name": "Miguel Alejandre Alcazar", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + }, + { + "author_name": "Robert Rogisch", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + }, + { + "author_name": "Mario Fabri", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + }, + { + "author_name": "Jan Rybniker", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + }, + { + "author_name": "Heike Goebel", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + }, + { + "author_name": "J\u00f6rg Stetefeld", + "author_inst": "University of Manitoba" + }, + { + "author_name": "Bent Brachvogel", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + }, + { + "author_name": "Claus Cursiefen", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + }, + { + "author_name": "Manuel Koch", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + }, + { + "author_name": "Felix Bock", + "author_inst": "University Hospital Cologne: Uniklinik Koln" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.06.06.494494", "rel_title": "SARS-CoV-2 S protein antagonizes type I interferon downstream signal pathway through interacting and attenuating phosphorylation of STAT1/STAT2", @@ -288481,29 +289281,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2022.06.02.22275908", - "rel_title": "Asymptotic Analysis of Optimal Vaccination Policies", - "rel_date": "2022-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.02.22275908", - "rel_abs": "Targeted vaccination policies can have a significant impact on the number of infections and deaths in an epidemic. However, optimising such policies is complicated and the resultant solution may be difficult to explain to policy-makers and to the public. The key novelty of this paper is a derivation of the leading order optimal vaccination policy under multi-group SIR (Susceptible-Infected-Recovered) dynamics in two different cases. Firstly, it considers the case of a small vulnerable subgroup in a population and shows that (in the asymptotic limit) it is optimal to vaccinate this group first, regardless of the properties of the other groups. Then, it considers the case of a small vaccine supply and transforms the optimal vaccination problem into a simple knapsack problem by linearising the final size equations. Both of these cases are then explored further through numerical examples which show that these solutions are also directly useful for realistic parameter values. Moreover, the findings of this paper give some general principles for optimal vaccination policies which will help policy-makers and the public to understand the reasoning behind optimal vaccination programs in more generic cases.\n\nAuthor summaryThe COVID-19 pandemic has illustrated the importance of vaccination programs in preventing infections and deaths from an epidemic. A common feature of vaccination programs across the world has been a prioritisation of different groups within each countrys population, particularly those who are more vulnerable to the disease. Finding the best priority order is crucial, but may be complicated and difficult to justify to policy-makers and the public. In this paper, we consider two extreme cases where the best prioritisation order can be mathematically derived. Firstly, we consider the case of a population with a very small, very vulnerable group and show that this group should always be vaccinated first. Then, we consider the case of a small supply of vaccines and derive an equation which gives the best prioritisation order. Understanding these extreme cases is important, as it highlights general principles of optimal policies which will be useful when understanding the solution in more complicated settings.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Matthew J Penn", - "author_inst": "University of Oxford" - }, - { - "author_name": "Christl A. Donnelly", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.05.31.22275835", "rel_title": "One Million and Counting: Estimates of Deaths in the United States from Ancestral SARS-CoV-2 and Variants", @@ -288820,6 +289597,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.06.01.494385", + "rel_title": "Characterization of entry pathways, species-specific ACE2 residues determining entry, and antibody neutralization evasion of Omicron BA.1, BA.1.1, BA.2, and BA.3 variants", + "rel_date": "2022-06-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.01.494385", + "rel_abs": "The SARS-CoV-2 Omicron variants were first detected in November 2021, and several Omicron lineages (BA.1, BA.2, BA.3, BA.4, and BA.5) have since rapidly emerged. Studies characterizing the mechanisms of Omicron variant infection and sensitivity to neutralizing antibodies induced upon vaccination are ongoing by several groups. In the present study, we used pseudoviruses to show that the transmembrane serine protease 2 (TMPRSS2) enhances infection of BA.1, BA.1.1, BA.2, and BA.3 Omicron variants to lesser extent compared to ancestral D614G. We further show that Omicron variants have higher sensitivity to inhibition by soluble angiotensin converting enzyme 2 (ACE2) and the endosomal inhibitor chloroquine compared to D614G. The Omicron variants also more efficiently used ACE2 receptors from nine out of ten animal species tested, and unlike the D614G variant, used mouse ACE2 due to the Q493R and Q498R spike substitutions. Finally, neutralization of the Omicron variants by antibodies induced by three doses of Pfizer/BNT162b2 mRNA vaccine was 7-8-fold less potent than the D614G, and the Omicron variants still evade neutralization more efficiently.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Sabari Nath Neerukonda", + "author_inst": "Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration" + }, + { + "author_name": "Richard Wang", + "author_inst": "Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration" + }, + { + "author_name": "Russell Vassell", + "author_inst": "Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration" + }, + { + "author_name": "Haseebullah Baha", + "author_inst": "Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration" + }, + { + "author_name": "Sabrina Lusvarghi", + "author_inst": "Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration" + }, + { + "author_name": "Shufeng Liu", + "author_inst": "Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration" + }, + { + "author_name": "Tony Wang", + "author_inst": "Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration" + }, + { + "author_name": "Carol D. Weiss", + "author_inst": "Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration" + }, + { + "author_name": "Wei Wang", + "author_inst": "Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.06.01.22275882", "rel_title": "Longitudinal profiles of plasma gelsolin, cytokines and antibody expression predict COVID-19 severity and hospitalization outcomes", @@ -290199,89 +291027,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2022.05.31.22275802", - "rel_title": "SARS-CoV-2 genomic surveillance in Rwanda: Introductions and local transmission of the B.1.617.2 (Delta) variant of concern", - "rel_date": "2022-05-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.31.22275802", - "rel_abs": "The emergence of the SARS-CoV-2 Delta variant of concern (lineage B.1.617.2) in late 2020 resulted in a new wave of infections in many countries across the world, where it often became the dominant lineage in a relatively short amount of time. We here report on a novel genomic surveillance effort in Rwanda in the time period from June to September 2021, leading to 201 SARS-CoV-2 genomes being generated, the majority of which were identified as the Delta variant of concern. We show that in Rwanda, the Delta variant almost completely replaced the previously dominant A.23.1 and B.1.351 (Beta) lineages in a matter of weeks, and led to a tripling of the total number of COVID-19 infections and COVID-19-related fatalities over the course of only three months. We estimate that Delta in Rwanda had an average growth rate advantage of 0.034 (95% CI 0.025-0.045) per day over A.23.1, and of 0.022 (95% CI 0.012-0.032) over B.1.351. Phylogenetic analysis reveals the presence of at least seven local Delta transmission clusters, with two of these clusters occurring close to the border with the Democratic Republic of the Congo, and another cluster close to the border with Tanzania. A smaller Delta cluster of infections also appeared close to the border with Uganda, illustrating the importance of monitoring cross-border traffic to limit the spread between Rwanda and its neighboring countries. We discuss our findings against a background of increased vaccination efforts in Rwanda, and also discuss a number of breakthrough infections identified during our study. Concluding, our study has added an important collection of data to the available genomes for the Eastern Africa region, with the number of Delta infections close to the border with neighboring countries highlighting the need to further strengthen genomic surveillance in the region to obtain a better understanding of the impact of border crossings on lowering the epidemic curve in Rwanda.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Yvan Butera", - "author_inst": "Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda; Rwanda National Joint Task Force COVID-19, Rwanda Biom" - }, - { - "author_name": "Samuel L. Hong", - "author_inst": "Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium" - }, - { - "author_name": "Muhammed Semakula", - "author_inst": "Center for Excellence in Data Science, University of Rwanda, Kigali, Rwanda; Centre for Statistics, Hasselt Biostatistics and Statistical Bioinformatics Center," - }, - { - "author_name": "Nena Bollen", - "author_inst": "Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium" - }, - { - "author_name": "Verity Hill", - "author_inst": "Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, Scotland" - }, - { - "author_name": "Aine O'Toole", - "author_inst": "Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, Scotland" - }, - { - "author_name": "Barney I. Potter", - "author_inst": "Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium" - }, - { - "author_name": "Dieudonne Mutangana", - "author_inst": "Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda; School of Science, College of Science and Technology, " - }, - { - "author_name": "Reuben Sindayiheba", - "author_inst": "National Reference Laboratory, Rwanda Biomedical Center, Kigali, Rwanda" - }, - { - "author_name": "Robert Rutayisire", - "author_inst": "Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda; National Reference Laboratory, Rwanda Biomedical Center" - }, - { - "author_name": "Maria Artesi", - "author_inst": "Laboratory of Human Genetics, GIGA Research Institute, Liege, Belgium" - }, - { - "author_name": "Vincent Bours", - "author_inst": "Laboratory of Human Genetics, GIGA Research Institute, Liege, Belgium; Department of Human Genetics, University Hospital of Liege, Liege, Belgium" - }, - { - "author_name": "Nadine Rujeni", - "author_inst": "Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda; School of Health Sciences, College of Medicine and Heal" - }, - { - "author_name": "Simon Dellicour", - "author_inst": "Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium; Spatial Epidemiology Laboratory, University Libre de Bru" - }, - { - "author_name": "Keith Durkin", - "author_inst": "Laboratory of Human Genetics, GIGA Research Institute, Liege, Belgium" - }, - { - "author_name": "Leon Mutesa", - "author_inst": "Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda; Rwanda National Joint Task Force COVID-19, Rwanda Biom" - }, - { - "author_name": "Guy Baele", - "author_inst": "Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2022.05.31.22275814", "rel_title": "Heterogeneous evolution of SARS-CoV-2 seroprevalence in school-age children: Results from the Ciao Corona study in November-December 2021 in the canton of Zurich", @@ -290474,6 +291219,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.05.30.22275787", + "rel_title": "SARS-COV-2 Delta and Omicron community transmission networks", + "rel_date": "2022-05-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.30.22275787", + "rel_abs": "To date, calculations of SARS-CoV-2 transmission networks at a population level have not been performed. Networks that estimate infections between individuals and whether this results in a mutation, can evaluate fitness of a mutational clone by how much it expands in number as well as determining the likelihood a transmission results in a new variant.\n\nTransmission networks of SARS-CoV-2 infection between individuals in Australia were estimated for Delta and Omicron variants using a novel method. Many of the sequences were identical, with clone sizes following power law distributions driven by negative binomial probability distributions for both the number of infections per individual and the number of mutations per transmission (mean 1.0 nucleotide change for Delta and 0.79 for Omicron). Using these distributions, an agent based model was able to replicate the observed clonal network structure, providing a basis for more detailed COVID-19 modelling. Recombination events, tracked by insertion/deletion (indel) patterns, occurred for each variant in these outbreaks. The residue at position 142 in the S open reading frame (ORF), frequently changed between G and D for Delta sequences, but this was independent of other mutations. On the other hand, several Omicron mutations were significantly connected across different ORF. This model reveals key transmission characteristics of SARS-CoV-2 and may complement traditional contact tracing and other public health strategies. This methodology can also be applied to other diseases as genetic sequencing of viruses becomes more commonplace.\n\nAuthor summaryAs SARS-COV-2 spreads through a community, it can mutate and generate new variants. How likely this is to occur and how much a particular viral clone expands, can indicate mutational probabilities and whether some mutations are fitter than others. By better understanding these aspects, future predictions can more accurately encapsulate possible changes in the epidemic within a community. We have developed a new method for piecing together the individual SARS-COV-2 cases that have been sequenced, to generate the structure of transmissions and mutational clones for an outbreak. While this method can be applied to other virus epidemics given sufficient sequenced data, we apply it to Delta and Omicron outbreaks in Australia. Interestingly, transmissions between individuals frequently do not result in mutations, with some clones growing very large. We characterise the probability that a mutation will occur, and track how these changes lead to sequential mutations in these outbreaks.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "John Murray", + "author_inst": "UNSW Sydney" + }, + { + "author_name": "Daniel Murray", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Evelyne Schvoerer", + "author_inst": "Centre Hospitalier Regional Universitaire de Nancy/Universite de Lorraine" + }, + { + "author_name": "Elma Akand", + "author_inst": "UNSW Sydney" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.05.31.494162", "rel_title": "The salivary and nasopharyngeal microbiomes are associated with SARS-CoV-2 infection and disease severity", @@ -291845,25 +292621,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2022.05.24.22275504", - "rel_title": "The connection between COVID-19 vaccine abundance, vaccination coverage, and public trust in government across the globe", - "rel_date": "2022-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.24.22275504", - "rel_abs": "This study investigates that how the number of COVID-19 vaccines secured correlates with the vaccination coverage (full and booster) depending on whether there is trust in national government or not across 47 countries. The data are based on global figures as of Nov. 2021 and Feb. 2022 while measures for confidence in government is according to Gallup World Poll, Oct. 2021. The model includes an interaction term of the two key variables, also controls for a range of socio-economic factors and country specific variables. The results indicate a non-linear and mixed relationship between the number secured, the public trust, and the vaccination rate. In Feb. 2022, with confidence in government, securing number of vaccines to cover 200% of the population (or more) increased the full vaccination rate by 12.26% (95% CI: 11.70 - 12.81); where number secured was 300% (or more), the coverage increased by 7.46% (95% CI: 6.95 - 7.97). Under similar scenarios, rate of booster shots increased by 13.16% (95% CI: 12.62 - 13.70; p < 0.01) and 14.36% (95% CI: 13.86 - 14.85; p < 0.01), respectively. Where the number secured fell below 200%, confidence in government had a revers relationship with the rate of full vaccination (-2.65; 95% CI: -3.32 - -1.99), yet positive with the rate of booster shots (1.65; 95% CI: 1.18 - 2.12). These results indicate that better success can be achieved by a combination of factors including securing sufficient number of vaccines and also ensuring the public trust. Vaccine abundance, however, cannot be translated into greater success in vaccination coverage. This study highlights the importance of efficiency in acquiring vaccine resources and need for improvement in public belief in immunization programmes rather than stock piling.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ida G. Monfared", - "author_inst": "Georg-August-Universitat Gottingen" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.05.27.22275708", "rel_title": "Identifying COVID-19 phenotypes using cluster analysis and assessing their clinical outcomes", @@ -292108,6 +292865,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.05.29.22275732", + "rel_title": "Uncertainty Quantification in COVID-19 Detection Using Evidential Deep Learning", + "rel_date": "2022-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.29.22275732", + "rel_abs": "Considering the immense pace of developments in deep learning (DL), its applications in medicine are relatively limited. One main issue that hinders the utilization of DL in the medical practice workflow is its reliability. A radiologist interpreting an image can easily say \"I dont know\", while a DL model is forced to output a result. Evidential deep learning (EDL) is one of the methods for uncertainty quantification (UQ). In this work, we aimed to use EDL to express model uncertainty in detecting COVID-19. We used SIIM-FISABIO-RSNA COVID-19 chest x-ray dataset and trained a model to diagnose typical COVID-19 pneumonia. When applied to a separate test set, it yielded an accuracy of 88% with median uncertainty scores of 0.25 and 0.07 for normal and typical COVID-19 images, respectively. Moreover, the model labeled unseen indeterminate and atypical COVID-19 x-rays with median uncertainties of 0.32 and 0.35, respectively. Our models performance was superior to the exact model trained with conventional approach of DL (i.e., using the cross-entropy loss), which is not able to express the uncertainty level. Overall, this study demonstrates applicability of UQ in disease detection that could facilitate the use of DL in practice by increasing its reliability.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Bardia Khosravi", + "author_inst": "Department of Radiology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran." + }, + { + "author_name": "Shahriar Faghani", + "author_inst": "Interdisciplinary Neuroscience Research Program (INRP), Tehran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Amir Ashraf Ganjouei", + "author_inst": "Interdisciplinary Neuroscience Research Program (INRP), Tehran University of Medical Sciences, Tehran, Iran" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2022.05.27.22275673", "rel_title": "CMV seropositivity in older adults changes T cell functionality, but does not prevent antibody or cellular SARS-CoV-2 vaccine responses", @@ -293831,33 +294615,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2022.05.27.493693", - "rel_title": "Development of a Novel SARS-CoV-2 Immune Complex Vaccine Candidate (CRCx) with Broad Immune Responses: A Preclinical Trial in Animal Model", - "rel_date": "2022-05-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.27.493693", - "rel_abs": "BackgroundThe ongoing pandemic of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses a serious threat to global public health and imposes a severe burden on the entire human population. Faced with a virus that can mutate its structure while immunity is incapacitated, a need to develop a universal vaccine that can boost immunity to coronaviruses is highly needed.\n\nDesignFive formulations of two types (CRCx2 and CRCx3) of immune complexes with an immunogen adjuvant were evaluated in a mouse model as candidate SARS CoV-2 vaccines in a pretrial prior to clinical trials in humans. CRCx3 comprises 3 different formulas and CRCx2 comprises 2. Balb/c mice were vaccinated intraperitoneally on days 0/7 with a high or low dose of CRCx2 or on days 0/7/14 with a high, medium, or low dose of CRCx3 series, and their blood was sampled for serum antibody measurements. Mice were challenged with live virus after immunization with either vaccine to evaluate prophylaxis ability or treated with them after challenge to evaluate therapeutic ability on day 15. Immunological markers and histopathological studies as well as titration of neutralizing antibodies to the vaccines were evaluated and analyzed.\n\nResultsCRCx 3 and CRCx 2 vaccine candidates induced elevated levels of positive neutralizing antibodies as well as a cellular immune response with safety, efficient productivity, and good genetic stability for vaccine manufacturing to provide protection against SARS-CoV-2 with relatively higher levels with the high dose CRCx2 candidate combination.\n\nConclusionsHighly efficient protection and therapeutic effect against SARS-CoV-2 were obtained with a double-dose immunization schedule spaced at 7-day intervals using injections 0.25 of or 0.40 ml of CRCx2 vaccine formulations with a 25-mm needle. These results support further evaluation of CRCx in a clinical trial on humans.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Khalid Mahmoud El Sayed Zayed", - "author_inst": "Ain Shams University" - }, - { - "author_name": "Sherif Salah Abdulaziz", - "author_inst": "Cairo University" - }, - { - "author_name": "Khaled Omar Abdallah", - "author_inst": "Ain Shams University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.05.24.22275478", "rel_title": "Effective antiviral regimens to reduce COVID-19 hospitalizations: a systematic comparison of randomized controlled trials", @@ -294630,6 +295387,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2022.05.25.22275590", + "rel_title": "Impact of school closures and reopening on COVID-19 caseload in 6 cities of Pakistan: An Interrupted Time Series Analysis", + "rel_date": "2022-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.25.22275590", + "rel_abs": "Schools were closed all over Pakistan on November 26, 2020 to reduce community transmission of COVID-19 and reopened between January 18 and February 1, 2021. However, these closures were associated with significant economic and social costs, prompting a review of effectiveness of school closures to reduce the spread of COVID-19 infections in a developing country like Pakistan. A single-group interrupted time series analysis (ITSA) was used to measure the impact of school closures, as well as reopening schools on daily new COVID-19 cases in 6 major cities across Pakistan: Lahore, Karachi, Islamabad, Quetta, Peshawar, and Muzaffarabad. We found that closing schools reduced COVID-19 incidence in the community by approximately a third of all cases nationwide. However, any benefits were contingent on continued closure of schools, as cases bounced back once schools reopened. School closures are associated with a clear and statistically significant reduction in COVID-19 cases by 0.07 to 0.63 cases per 100,000 population, while reopening schools is associated with a statistically significant increase. Lahore is an exception to the effect of school closures, but it too saw an increase in COVID-19 cases after schools reopened in early 2021. We show that closing schools was a viable policy option, especially before vaccines became available. However, its social and economic costs must also be considered.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Abdul Mueed", + "author_inst": "Akhter Hameed Khan Foundation" + }, + { + "author_name": "Taimoor Ahmad", + "author_inst": "Akhter Hameed Khan Foundation" + }, + { + "author_name": "Mujahid Abdullah", + "author_inst": "Akhter Hameed Khan Foundation" + }, + { + "author_name": "Faisal Sultan", + "author_inst": "Shaukat Khanum Memorial Cancer Hospital and Research Centre" + }, + { + "author_name": "Adnan Khan", + "author_inst": "Research and Development Solutions" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.25.22275592", "rel_title": "COVID-19 pandemic impact on preterm birth and stillbirth rates associated with socioeconomic disparities: A quasi-experimental study", @@ -296141,81 +296933,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.05.24.493187", - "rel_title": "Hemin shows antiviral activity in vitro, possibly through suppression of viral entry mediators.", - "rel_date": "2022-05-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.24.493187", - "rel_abs": "Heme oxygenase-1 (HO-1) is a stress-induced enzyme that catalyzes the breakdown of heme into biliverdin, carbon monoxide, and iron. Targeting HO-1 to treat severe COVID-19 has been suggested by several groups, yet the role of HO-1 in SARS-CoV-2 infection remains unclear. Based on this, we aimed to investigate the antiviral activity of Hemin, an activator of HO-1. Infectivity of SARS-CoV-2 was decreased in Vero E6 cells treated with Hemin. Hemin also decreased TMPRSS2 and ACE2 mRNA levels in non-infected cells, possibly explaining the observed decrease in infectivity. TMPRSS2 protein expression and proteolytic activity were decreased in Vero E6 cells treated with Hemin. Besides that, experimental studies supported with in silico calculations. Overall, our study supports further exploration of Hemin as a potential antiviral and inflammatory drug for the treatment of COVID-19.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Mehmet Altay UNAL", - "author_inst": "Ankara University Stem Cell" - }, - { - "author_name": "Ceylan Verda BITIRIM", - "author_inst": "Ankara University Stem Cell Institute" - }, - { - "author_name": "Julia SOMERS", - "author_inst": "Oregon Health & Science Univerity" - }, - { - "author_name": "Gokce Yagmur SUMMAK", - "author_inst": "Ankara University Stem Cell Institute" - }, - { - "author_name": "Omur BUL BESBINAR", - "author_inst": "Ankara University Stem Cell Institute" - }, - { - "author_name": "Ebru KOCAKAYA", - "author_inst": "Ankara University Stem Cell Institute" - }, - { - "author_name": "Cansu GURCAN", - "author_inst": "Ankara University Stem Cell Institute" - }, - { - "author_name": "Hasan NAZIR", - "author_inst": "Ankara University Faculty of Science Department of Chemistry" - }, - { - "author_name": "Zeynep Busra Aksoy Ozer", - "author_inst": "Ankara University Stem Cell Institute" - }, - { - "author_name": "Sibel Aysil OZKAN", - "author_inst": "Ankara University Faculty of Pharmacy" - }, - { - "author_name": "Sidar BEREKETOGLU", - "author_inst": "Ankara University Faculty of Science" - }, - { - "author_name": "Aykut OZKUL", - "author_inst": "Ankara University Faculty of Veterinary Medicine" - }, - { - "author_name": "Emek DEMIR", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Kamil Can AKCALI", - "author_inst": "Ankara Universiy Faculty of Medicine Depatment of Biophysics" - }, - { - "author_name": "Acelya YILMAZER", - "author_inst": "Ankara University Faculty of Engineering Department of Biomedical Engineering" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2022.05.24.22275529", "rel_title": "Depressive and anxiety symptoms during the COVID-19 pandemic: A two-year follow-up", @@ -296552,6 +297269,37 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.05.23.22275454", + "rel_title": "Measuring Community Resilience During the COVID-19 based on Community Wellbeing and Resource Distribution", + "rel_date": "2022-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.23.22275454", + "rel_abs": "The COVID-19 pandemic has severely harmed every aspect of our daily lives, resulting in a slew of social problems. Therefore, it is critical to accurately assess the current state of community functionality and resilience under this pandemic for successful recovery. To this end, various types of social sensing tools, such as tweeting and publicly released news, have been employed to understand individuals and communities thoughts, behaviors, and attitudes during the COVID-19 pandemic. However, some portions of the released news are fake and can easily mislead the community to respond improperly to disasters like COVID-19. This paper aims to assess the correlation between various news and tweets collected during the COVID-19 pandemic on community functionality and resilience. We use fact-checking organizations to classify news as real, mixed, or fake, and machine learning algorithms to classify tweets as real or fake to measure and compare community resilience (CR). Based on the news articles and tweets collected, we quantify CR based on two key factors, community wellbeing and resource distribution, where resource distribution is assessed by the level of economic resilience, and community capital. Based on the estimates of these two factors, we quantify CR from both news articles and tweets and analyze the extent to which CR measured from the news articles can reflect the actual state of CR measured from tweets. To improve the operationalization and sociological significance of this work, we use dimension reduction techniques to integrate the dimensions.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jaber Valinejad", + "author_inst": "Harvard University" + }, + { + "author_name": "Zhen Guo", + "author_inst": "Virginia Tech: Virginia Polytechnic Institute and State University" + }, + { + "author_name": "Jin-Hee Cho", + "author_inst": "Virginia Tech: Virginia Polytechnic Institute and State University" + }, + { + "author_name": "Ing-Ray Chen", + "author_inst": "Virginia Tech: Virginia Polytechnic Institute and State University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2022.05.23.22275458", "rel_title": "Covid-19 is a leading cause of death in children and young people ages 0-19 years in the United States", @@ -298075,57 +298823,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.05.21.22275368", - "rel_title": "Variant-specific symptoms of COVID-19 among 1,542,510 people in England", - "rel_date": "2022-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.21.22275368", - "rel_abs": "Infection with SARS-CoV-2 virus is associated with a wide range of symptoms. The REal-time Assessment of Community Transmission -1 (REACT-1) study has been monitoring the spread and clinical manifestation of SARS-CoV-2 among random samples of the population in England from 1 May 2020 to 31 March 2022. We show changing symptom profiles associated with the different variants over that period, with lower reporting of loss of sense of smell and taste for Omicron compared to previous variants, and higher reporting of cold-like and influenza-like symptoms, controlling for vaccination status. Contrary to the perception that recent variants have become successively milder, Omicron BA.2 was associated with reporting more symptoms, with greater disruption to daily activities, than BA.1. With restrictions lifted and routine testing limited in many countries, monitoring the changing symptom profiles associated with SARS-CoV-2 infection and induced changes in daily activities will become increasingly important.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Matthew Whitaker", - "author_inst": "Imperial College London" - }, - { - "author_name": "Joshua Elliott", - "author_inst": "Imperial College London" - }, - { - "author_name": "Barbara Bodinier", - "author_inst": "Imperial College London" - }, - { - "author_name": "Wendy S Barclay", - "author_inst": "Imperial College London" - }, - { - "author_name": "Helen Ward", - "author_inst": "Imperial College London" - }, - { - "author_name": "Graham Cooke", - "author_inst": "Imperial College London" - }, - { - "author_name": "Christl A Donnelly", - "author_inst": "Imperial College London" - }, - { - "author_name": "Marc Chadeau-Hyam", - "author_inst": "Imperial College London" - }, - { - "author_name": "Paul Elliott", - "author_inst": "Imperial College London School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.21.492928", "rel_title": "Modeling suggests that multiple immunizations or infections will reveal the benefits of updating SARS-CoV-2 vaccines", @@ -298450,6 +299147,205 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.05.23.493121", + "rel_title": "Anti-chemokine antibodies after SARS-CoV-2 infection correlate with favorable disease course", + "rel_date": "2022-05-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.23.493121", + "rel_abs": "Infection by SARS-CoV-2 leads to diverse symptoms, which can persist for months. While antiviral antibodies are protective, those targeting interferons and other immune factors are associated with adverse COVID-19 outcomes. Instead, we discovered that antibodies against specific chemokines are omnipresent after COVID-19, associated with favorable disease, and predictive of lack of long COVID symptoms at one year post infection. Anti-chemokine antibodies are present also in HIV-1 infection and autoimmune disorders, but they target different chemokines than those in COVID-19. Monoclonal antibodies derived from COVID- 19 convalescents that bind to the chemokine N-loop impair cell migration. Given the role of chemokines in orchestrating immune cell trafficking, naturally arising anti-chemokine antibodies associated with favorable COVID-19 may be beneficial by modulating the inflammatory response and thus bear therapeutic potential.\n\nOne-Sentence SummaryNaturally arising anti-chemokine antibodies associate with favorable COVID-19 and predict lack of long COVID.", + "rel_num_authors": 46, + "rel_authors": [ + { + "author_name": "Jonathan Muri", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Valentina Cecchinato", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Andrea Cavalli", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Akanksha A. Shanbhag", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Milos Matkovic", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Maira Biggiogero", + "author_inst": "Clinical Research Unit, Clinica Luganese Moncucco, Lugano, Switzerland" + }, + { + "author_name": "Pier Andrea Maida", + "author_inst": "Clinical Research Unit, Clinica Luganese Moncucco, Lugano, Switzerland" + }, + { + "author_name": "Jacques Moritz", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Chiara Toscano", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Elaheh Ghovehoud", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Raffaello Furlan", + "author_inst": "Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Milan, Italy" + }, + { + "author_name": "Franca Barbic", + "author_inst": "Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Milan, Italy" + }, + { + "author_name": "Antonio Voza", + "author_inst": "Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Milan, Italy" + }, + { + "author_name": "Guendalina De Nadai", + "author_inst": "Emergency Medicine Residency School, Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4 - 20090 Pieve Emanuele, Milan, Italy" + }, + { + "author_name": "Carlo Cervia", + "author_inst": "Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Yves Zurbuchen", + "author_inst": "Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Patrick Taeschler", + "author_inst": "Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Lilly A. Murray", + "author_inst": "Lyme & Tick-Borne Diseases Research Center at Columbia University Irving Medical Center, New York, NY, USA" + }, + { + "author_name": "Gabriela Danelon-Sargenti", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Simone Moro", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Tao Gong", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Pietro Piffaretti", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Filippo Bianchini", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Virginia Crivelli", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Lucie Podesvova", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Mattia Pedotti", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "David Jarrossay", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Jacopo Sgrignani", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Sylvia Thelen", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Mario Uhr", + "author_inst": "Synlab Suisse, Bioggio, Switzerland" + }, + { + "author_name": "Enos Bernasconi", + "author_inst": "Regional Hospital Lugano, and Universita della Svizzera italiana, Lugano, Switzerland" + }, + { + "author_name": "Andri Rauch", + "author_inst": "Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern" + }, + { + "author_name": "Antonio Manzo", + "author_inst": "Rheumatology and Translational Immunology Research Laboratories, Division of Rheumatology, IRCCS Policlinico San Matteo Foundation, University of Pavia, Pavia, " + }, + { + "author_name": "Adrian Ciurea", + "author_inst": "Department of Rheumatology, Zurich University Hospital, University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Marco Bruno Luigi Rocchi", + "author_inst": "Department of Biomolecular Sciences, Biostatistics Unit, University of Urbino, Urbino, Italy" + }, + { + "author_name": "Luca Varani", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Bernhard Moser", + "author_inst": "Division of Infection & Immunity, Henry Wellcome Building, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4YS, UK" + }, + { + "author_name": "Barbara Bottazzi", + "author_inst": "IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy" + }, + { + "author_name": "Marcus Thelen", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Brian A. Fallon", + "author_inst": "Lyme & Tick-Borne Diseases Research Center at Columbia University Irving Medical Center, New York, NY, USA" + }, + { + "author_name": "Onur Boyman", + "author_inst": "Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland." + }, + { + "author_name": "Alberto Mantovani", + "author_inst": "Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Milan, Italy" + }, + { + "author_name": "Christian Garzoni", + "author_inst": "Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, Lugano, Switzerland" + }, + { + "author_name": "Alessandra Franzetti-Pellanda", + "author_inst": "Clinical Research Unit, Clinica Luganese Moncucco, Lugano, Switzerland" + }, + { + "author_name": "Mariagrazia Uguccioni", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + }, + { + "author_name": "Davide F. Robbiani", + "author_inst": "Institute for Research in Biomedicine, Bellinzona, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.05.21.492922", "rel_title": "Using a reverse genetics system to generate recombinant SARS-CoV-2 expressing robust levels of reporter genes", @@ -299981,57 +300877,6 @@ "type": "new results", "category": "ecology" }, - { - "rel_doi": "10.1101/2022.05.19.22275339", - "rel_title": "Covid-19 Vaccine Acceptance Among People Incarcerated in Connecticut State Jails", - "rel_date": "2022-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.19.22275339", - "rel_abs": "ObjectiveTo assess the Connecticut Department of Corrections (DOC) COVID-19 vaccine program within jails.\n\nMethodsWe conducted a retrospective cohort analysis among people who were incarcerated in a DOC-operated jail between February 2 and November 8, 2021, and were eligible for vaccination at the time of incarceration (intake). We compared the vaccination rates before and after incarceration using an age-adjusted survival analysis with a time-varying exposure of incarceration and an outcome of vaccination.\n\nResultsDuring the study period, 3,716 people spent [≥]1 night in jail and were eligible for vaccination at intake. Of these residents, 136 were vaccinated prior to incarceration, 2,265 had a recorded vaccine offer, and 476 were vaccinated while incarcerated. The age-adjusted hazard of vaccination following incarceration was significantly higher than prior to incarceration (12.5; 95% CI: 10.2-15.3).\n\nConclusionsWe found that residents were more likely to become vaccinated in jail than the community. Though these findings highlight the utility of vaccination programs within jails, the low level of vaccination in this population speaks to the need for additional program development within jails and the community.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Margaret Lind", - "author_inst": "Yale University" - }, - { - "author_name": "Byron S Kennedy", - "author_inst": "Connecticut Department of Correction" - }, - { - "author_name": "Murilo Dorion Nieto", - "author_inst": "Yale University" - }, - { - "author_name": "Amy J Houde", - "author_inst": "Connecticut Department of Corrections" - }, - { - "author_name": "Peri Sosensky", - "author_inst": "Yale University" - }, - { - "author_name": "Ryan Borg", - "author_inst": "Yale University" - }, - { - "author_name": "Derek A.T. Cummings", - "author_inst": "University of Florida" - }, - { - "author_name": "Albert Ko", - "author_inst": "Yale University School of Public Health" - }, - { - "author_name": "Robert P Richeson", - "author_inst": "Connecticut Department of Corrections" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.05.20.492819", "rel_title": "Revealing druggable cryptic pockets in the Nsp-1 of SARS-CoV-2 and other \u03b2-coronaviruses by simulations and crystallography", @@ -300268,6 +301113,73 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.05.20.492832", + "rel_title": "The spike-stabilizing D614G mutation interacts with S1/S2 cleavage site mutations to promote the infectious potential of SARS-CoV-2 variants", + "rel_date": "2022-05-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.20.492832", + "rel_abs": "SARS-CoV-2 remained genetically stable during the first three months of the pandemic, before acquiring a D614G spike mutation that rapidly spread worldwide, and then generating successive waves of viral variants with increasingly high transmissibility. We set out to evaluate possible epistatic interactions between the early occurring D614G mutation and the more recently emerged cleavage site mutations present in spike of the Alpha, Delta, and Omicron variants of concern. The P681H/R mutations at the S1/S2 cleavage site increased spike processing and fusogenicity but limited its incorporation into pseudoviruses. In addition, the higher cleavage rate led to higher shedding of the spike S1 subunit, resulting in a lower infectivity of the P681H/R-carrying pseudoviruses compared to those expressing the Wuhan wild-type spike. The D614G mutation increased spike expression at the cell surface and limited S1 shedding from pseudovirions. As a consequence, the D614G mutation preferentially increased the infectivity of P681H/R-carrying pseudoviruses. This enhancement was more marked in cells where the endosomal route predominated, suggesting that more stable spikes could better withstand the endosomal environment. Taken together, these findings suggest that the D614G mutation stabilized S1/S2 association and enabled the selection of mutations that increased S1/S2 cleavage, leading to the emergence of SARS-CoV-2 variants expressing highly fusogenic spikes.\n\nAUTHOR SUMMARYThe successive emergence of SARS-CoV-2 variants is fueling the COVID pandemic, thus causing a major and persistent public health issue. The parameters involved in the emergence of variants with higher pathogenic potential remain incompletely understood. The first SARS-CoV-2 variant that spread worldwide in early 2020 carried a D614G mutation in the viral spike, making this protein more stable in its cleaved form at the surface of virions, and resulting in viral particles with higher infectious capacity. The Alpha and the Delta variants that spread in late 2020 and early 2021, respectively, proved increasingly transmissible and pathogenic when compared to the original SARS-CoV-2 strain. Interestingly, Alpha and Delta both carried mutations in a spike cleavage site that needs to be processed by cellular proteases prior to viral entry. The cleavage site mutations P681H/R made the Alpha and Delta spikes more efficient at viral fusion, by generating a higher fraction of cleaved spikes subunits S1 and S2. We show here that the early D614G mutation and the late P681H/R mutations act synergistically to increase the fusion capacity of SARS-CoV-2 variants. Specifically, viruses with increased spike cleavage due to P681H/R were even more dependent on the stabilizing effect of D614G mutation, which limited the shedding of cleaved S1 subunits from viral particles. These findings suggest that the worldwide spread of the D614G mutation was a prerequisite to the emergence of more pathogenic SARS-CoV-2 variants with highly fusogenic spikes.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Stacy Gellenoncourt", + "author_inst": "Virus and Immunity Unit, Institut Pasteur, Universite Paris Cite, CNRS UMR 3569, Paris, France" + }, + { + "author_name": "Nell Saunders", + "author_inst": "Virus and Immunity Unit, Institut Pasteur, Universite Paris Cite, CNRS UMR 3569, Paris, France" + }, + { + "author_name": "Remy Robinot", + "author_inst": "Virus and Immunity Unit, Institut Pasteur, Universite Paris Cite, CNRS UMR 3569, Paris, France" + }, + { + "author_name": "Lucas Auguste", + "author_inst": "Virus and Immunity Unit, Institut Pasteur, Universite Paris Cite, CNRS UMR 3569, Paris, France" + }, + { + "author_name": "Maaran Michael Rajah", + "author_inst": "Virus and Immunity Unit, Institut Pasteur, Universite Paris Cite, CNRS UMR 3569, Paris, France" + }, + { + "author_name": "Jerome Kervevan", + "author_inst": "Virus and Immunity Unit, Institut Pasteur, Universite Paris Cite, CNRS UMR 3569, Paris, France" + }, + { + "author_name": "Raphael Jeger-Madiot", + "author_inst": "Virus and Immunity Unit, Institut Pasteur, Universite Paris Cite, CNRS UMR 3569, Paris, France" + }, + { + "author_name": "Isabelle Staropoli", + "author_inst": "Virus and Immunity Unit, Institut Pasteur, Universite Paris Cite, CNRS UMR 3569, Paris, France" + }, + { + "author_name": "Cyril Planchais", + "author_inst": "Laboratory of Humoral Immunology, Institut Pasteur, Universite Paris Cite, Paris, France" + }, + { + "author_name": "Hugo Mouquet", + "author_inst": "Laboratory of Humoral Immunology, Institut Pasteur, Universite Paris Cite, Paris, France" + }, + { + "author_name": "Julian Buchrieser", + "author_inst": "Virus and Immunity Unit, Institut Pasteur, Universite Paris Cite, CNRS UMR 3569, Paris, France" + }, + { + "author_name": "Olivier Schwartz", + "author_inst": "Virus and Immunity Unit, Institut Pasteur, Universite Paris Cite, CNRS UMR 3569, Paris, France" + }, + { + "author_name": "Lisa A. Chakrabarti", + "author_inst": "Virus and Immunity Unit, Institut Pasteur, Universite Paris Cite, CNRS UMR 3569, Paris, France" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.05.20.492815", "rel_title": "Structural basis for substrate selection by the SARS-CoV-2 replicase", @@ -301899,73 +302811,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2022.05.19.22275053", - "rel_title": "Evaluating the impact on health outcomes of an event that resulted in a delay in contact tracing of COVID-19 cases", - "rel_date": "2022-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.19.22275053", - "rel_abs": "ObjectiveIn September 2020, records of 15,861 SARS-CoV-2 cases failed to upload from the Second Generation Laboratory Surveillance System (SGSS) to the Contact Tracing Advisory Service (CTAS) tool, resulting in a delay in the contact tracing of these cases. This study used CTAS data to determine the impact of this delay on health outcomes: transmission events, hospitalisations, and mortality. Previously, a modelling study had suggested a substantial impact.\n\nDesignObservational study\n\nSettingEngland.\n\nPopulationIndividuals testing positive for SARS-CoV-2 and their reported contacts.\n\nMain outcome measuresSecondary attack rates (SARs), hospitalisations, and deaths amongst primary and secondary contacts were calculated, compared to all other concurrent, unaffected cases. SGSS records affected by the event were matched to CTAS records and successive contacts and cases were identified.\n\nResultsThe initiation of contact tracing was delayed by 3 days on average in the primary cases in the delay group (6 days) compared to the control group (3 days). This was associated with lower completion of contact tracing of primary cases in the delay group: 80% (95%CI: 79-81%) in the delay group and 83% (95%CI: 83-84%) in the control group. There was some evidence to suggest an increase in transmission to non-household contacts amongst those affected by the delay. The SAR for non-household contacts was higher amongst secondary contacts in the delay group than the control group (delay group: 7.9%, 95%CI:6.4% to 9.2%; control group: 5.9%, 95%CI: 5.3% to 6.6%). There was no evidence of a difference between the delay and control groups in the odds of hospitalisation (crude odds ratio: 1.1 (95%CI: 0.9 to 1.2) or death (crude odds ratio: 0.7 (0.1 to 4.0)) amongst secondary contacts.\n\nConclusionsThe delay in contact tracing had a limited impact on population health outcomes.\n\nStrengths and limitations of the studyO_LIShows empirical data on the health impact of an event leading to a delay in contact tracing so can test hypotheses generated by models of the potential impact of a delay in contact tracing\nC_LIO_LIEstimates the extent of further transmission and odds of increased mortality or hospitalisation in up to the third generation of cases affected by the event\nC_LIO_LIThe event acts as a natural experiment to describe the possible impact of contact tracing, comparing a group affected by chance by delayed contact tracing to a control group who experienced no delay\nC_LIO_LIContact tracing was not completed for all individuals, so the study might not capture all affected contacts or transmissions\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Lucy Findlater", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Livia Pierotti", - "author_inst": "University of Bristol" - }, - { - "author_name": "Charlie Turner", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Adrian Wensley", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Cong Chen", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Shaun Seaman", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Pantelis Samartsidis", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Andre Charlett", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Charlotte Anderson", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Gareth Hughes", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Matthew Hickman", - "author_inst": "University of Bristol" - }, - { - "author_name": "Obaghe Edeghere", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Isabel Oliver", - "author_inst": "UK Health Security Agency" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.05.19.22275055", "rel_title": "How Should COVID-19 Vaccines be Distributed between the Global North and South? A Discrete Choice Experiment in Six European Countries", @@ -302094,6 +302939,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.05.19.492649", + "rel_title": "Programming the lymph node immune response with Amphiphile-CpG induces potent cellular and humoral immunity following COVID-19 subunit vaccination in mice and non-human primates", + "rel_date": "2022-05-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.19.492649", + "rel_abs": "Despite the success of currently authorized vaccines for the reduction of severe COVID-19 disease risk, rapidly emerging viral variants continue to drive pandemic waves of infection, resulting in numerous global public health challenges. Progress will depend on future advances in prophylactic vaccine activity, including advancement of candidates capable of generating more potent induction of cross-reactive T cells and durable cross-reactive antibody responses. Here we evaluated an Amphiphile (AMP) adjuvant, AMP-CpG, admixed with SARS-CoV-2 Spike receptor binding domain (RBD) immunogen, as a lymph node-targeted protein subunit vaccine (ELI-005) in mice and non-human primates (NHPs). AMP-mediated targeting of CpG DNA to draining lymph nodes resulted in comprehensive local immune activation characterized by extensive transcriptional reprogramming, inflammatory proteomic milieu, and activation of innate immune cells as key orchestrators of antigen-directed adaptive immunity. Prime-boost immunization with AMP-CpG in mice induced potent and durable T cell responses in multiple anatomical sites critical for prophylactic efficacy and prevention of severe disease. Long-lived memory responses were rapidly expanded upon re-exposure to antigen. In parallel, RBD-specific antibodies were long-lived, and exhibited cross-reactive recognition of variant RBD. AMP-CpG-adjuvanted prime-boost immunization in NHPs was safe and well tolerated, while promoting multi-cytokine-producing circulating T cell responses cross-reactive across variants of concern (VOC). Expansion of RBD-specific germinal center (GC) B cells in lymph nodes correlated to rapid seroconversion with variant-specific neutralizing antibody responses exceeding those measured in convalescent human plasma. These results demonstrate the promise of lymph-node adjuvant-targeting to coordinate innate immunity and generate robust adaptive responses critical for vaccine efficacy.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Lochana M Seenappa", + "author_inst": "Elicio Therapeutics" + }, + { + "author_name": "Aniela Jakubowski", + "author_inst": "Elicio Therapeutics" + }, + { + "author_name": "Martin P Steinbuck", + "author_inst": "Elicio Therapeutics" + }, + { + "author_name": "Erica Palmer", + "author_inst": "Elicio Therapeutics" + }, + { + "author_name": "Christopher M Haqq", + "author_inst": "Elicio Therapeutics" + }, + { + "author_name": "Crystal Carter", + "author_inst": "New Iberia Research Center University of Louisiana at Lafayette" + }, + { + "author_name": "Jane Fontenot", + "author_inst": "New Iberia Research Center University of Louisiana at Lafayette" + }, + { + "author_name": "Francois Villinger", + "author_inst": "New Iberia Research Center University of Louisiana at Lafayette" + }, + { + "author_name": "Peter C DeMuth", + "author_inst": "Elicio Therapeutics" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.05.15.22275051", "rel_title": "Infectious viral shedding of SARS-CoV-2 Delta following vaccination: a longitudinal cohort study", @@ -303417,57 +304313,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.05.17.492198", - "rel_title": "SARS-CoV-2 accessory proteins ORF7a and ORF3a use distinct mechanisms to downregulate MHC-I surface expression", - "rel_date": "2022-05-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.17.492198", - "rel_abs": "Major histocompatibility complex class I (MHC-I) molecules, which are dimers of a glycosylated polymorphic transmembrane heavy chain and the small protein {beta}2-microglobulin ({beta}2m), bind peptides in the endoplasmic reticulum that are generated by the cytosolic turnover of cellular proteins. In virus-infected cells these peptides may include those derived from viral proteins. Peptide-MHC-I complexes then traffic through the secretory pathway and are displayed at the cell surface where those containing viral peptides can be detected by CD8+ T lymphocytes that kill infected cells. Many viruses enhance their in vivo survival by encoding genes that downregulate MHC-I expression to avoid CD8+ T cell recognition. Here we report that two accessory proteins encoded by SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic, downregulate MHC-I expression using distinct mechanisms. One, ORF3a, a viroporin, reduces global trafficking of proteins, including MHC-I, through the secretory pathway. The second, ORF7a, interacts specifically with the MHC-I heavy chain, acting as a molecular mimic of {beta}2m to inhibit its association. This slows the exit of properly assembled MHC-I molecules from the endoplasmic reticulum. We demonstrate that ORF7a reduces antigen presentation by the human MHC-I allele HLA-A*02:01. Thus, both ORF3a and ORF7a act post-translationally in the secretory pathway to lower surface MHC-I expression, with ORF7a exhibiting a novel and specific mechanism that allows immune evasion by SARS-CoV-2.\n\nSignificance StatementViruses may down-regulate MHC class I expression on infected cells to avoid elimination by cytotoxic T cells. We report that the accessory proteins ORF7a and ORF3a of SARS-CoV-2 mediate this function and delineate the two distinct mechanisms involved. While ORF3a inhibits global protein trafficking to the cell surface, ORF7a acts specifically on MHC-I by competing with {beta}2m for binding to the MHC-I heavy chain. This is the first account of molecular mimicry of {beta}2m as a viral mechanism of MHC-I down-regulation to facilitate immune evasion.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Najla Arshad", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Maudry Laurent-Rolle", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Wesam S Ahmed", - "author_inst": "Hamad Bin Khalifa University" - }, - { - "author_name": "Jack Chun-Chieh Hsu", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Susan M Mitchell", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Joanna Pawlak", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Debrup Sengupta", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Kabir Hassan Biswas", - "author_inst": "Hamad Bin Khalifa University" - }, - { - "author_name": "Peter Cresswell", - "author_inst": "Yale University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.05.15.22275086", "rel_title": "Clinical Performance of Direct RT-PCR Testing of Raw Saliva for Detection of SARS-CoV-2 in Symptomatic and Asymptomatic Individuals", @@ -303696,6 +304541,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.05.11.22274966", + "rel_title": "Infection prevention and control preparedness among public hospitals and COVID-19 temporary treatment and monitoring facilities in the Philippines", + "rel_date": "2022-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.11.22274966", + "rel_abs": "ObjectivesAn effective response to COVID-19 necessitates rigid compliance of health facilities to infection prevention and control (IPC) protocols to protect HCWs, prevent onward transmission, and mitigate the impact of the outbreak on the health care system. The study aims to assess the compliance of public hospitals and temporary treatment and monitoring facilities (TTMFs) to IPC standards for COVID-19.\n\nMethodsA baseline assessment survey was conducted between July 20 to August 18, 2020, from selected facilities in 38 local government units (LGU) across the country utilising a 35-point questionnaire corresponding to a set of standards issued by the Philippine Department of Health.\n\nResultsThe study shows that public hospitals reported sufficient IPC preparedness and compliance compared to TTMFs in the domains of engineering and administrative controls. Both types of facilities reported weak compliance in the use of color-coded bags and in having a central storage for infectious waste. In addition, among TTMFs adherence to proper labelling of waste bins, presence of instructional materials for waste disposal, directional signages for movements of HCWs and patients, availability of an IPC policy, and advocacy materials on proper handwashing, respiratory etiquette, and physical distancing, and PPE use were also low.\n\nConclusionThe COVID-19 pandemic has shown the importance of IPC preparedness among health care facilities to effectively prevent disease transmission and mitigate its impact on the health care system. The findings suggests that periodic monitoring and augmentation of resources are needed to immediately address the compliance gaps. However, systemic improvements and long-term investments are required to sustain IPC practices over time.\n\nWhat is already known?Infection prevention and control measures are effective at protecting patients and health care workers from facility-acquired infections and averting onward transmission of the disease.\n\nWhat are the new findings?Findings from this study highlight the critical gaps in infection prevention and control preparedness among established healthcare settings like hospitals and in repurposed spaces such as temporary facilities for COVID-19 isolation that were primarily set up to manage the surge in cases.\n\nWhat do the new findings imply?It focuses attention on the periodic monitoring of health facilities compliance to standard infection prevention and control practices especially during outbreak situations as a basis for identifying immediate resource and technical requirements, and for planning the needed investments in the long term.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Vergil de Claro", + "author_inst": "RTI International Philippines" + }, + { + "author_name": "Noemi Bautista", + "author_inst": "RTI International Philippines" + }, + { + "author_name": "Ma. Rosario Torralba", + "author_inst": "RTI International Philippines" + }, + { + "author_name": "Vina Vanessa Castro", + "author_inst": "RTI International Philippines" + }, + { + "author_name": "Miguel Angelo Lucero", + "author_inst": "RTI International Philippines" + }, + { + "author_name": "Lady Jedfeliz Molleno", + "author_inst": "RTI International Philippines" + }, + { + "author_name": "Laurentiu Stan", + "author_inst": "RTI International Philippines" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.12.22274990", "rel_title": "Post COVID-19 condition of the Omicron variant of SARS-CoV-2", @@ -305091,33 +305979,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2022.05.16.22275147", - "rel_title": "Quantifying the information in noisy epidemic curves", - "rel_date": "2022-05-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.16.22275147", - "rel_abs": "Reliably estimating the dynamics of transmissible diseases from noisy surveillance data is an enduring problem in modern epidemiology. Key parameters, such as the instantaneous reproduction number, Rt at time t, are often inferred from incident time series, with the aim of informing policymakers on the growth rate of outbreaks or testing hypotheses about the effectiveness of public health interventions. However, the reliability of these inferences depends critically on reporting errors and latencies innate to those time series. While studies have proposed corrections for these issues, methodology for formally assessing how these sources of noise degrade Rt estimate quality is lacking. By adapting Fisher information and experimental design theory, we develop an analytical framework to quantify the uncertainty induced by under-reporting and delays in reporting infections. This yields a novel metric, defined by the geometric means of reporting and cumulative delay probabilities, for ranking surveillance data informativeness. We apply this metric to two primary data sources for inferring Rt: epidemic case and death curves. We find that the assumption of death curves as more reliable, commonly made for acute infectious diseases such as COVID-19 and influenza, is not obvious and possibly untrue in many settings. Our framework clarifies and quantifies how actionable information about pathogen transmissibility is lost due to surveillance limitations.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Kris V Parag", - "author_inst": "Imperial College London" - }, - { - "author_name": "Christl A. Donnelly", - "author_inst": "Imperial College London" - }, - { - "author_name": "Alexander E Zarebski", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.15.22273842", "rel_title": "Summaries, Analysis and Simulations of Recent COVID-19 Epidemic in Shanghai", @@ -305350,6 +306211,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2022.05.10.22274869", + "rel_title": "Tracking changes in SARS-CoV-2 transmission with a novel outpatient sentinel surveillance system in Chicago, USA", + "rel_date": "2022-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.10.22274869", + "rel_abs": "Public health indicators typically used for COVID-19 surveillance can be biased or lag changing community transmission patterns. The United States city of Chicago opportunistically investigated whether sentinel surveillance of recently symptomatic individuals receiving outpatient diagnostic testing for SARS-CoV-2 could accurately assess the instantaneous reproductive number R(t) and provide early warning of changes in transmission. Patients tested at community-based diagnostic testing sites between September 2020 and June 2021, and reporting symptom onset within four days preceding their test, formed the sentinel population. R(t) calculated from sentinel cases agreed well with R(t) from other indicators. Retrospectively, trends in sentinel cases did not precede trends in COVID-19 hospital admissions by any identifiable lead time. In deployment, sentinel surveillance held an operational recency advantage of nine days over hospital admissions. The promising performance of opportunistic sentinel surveillance suggests that deliberately designed outpatient sentinel surveillance would provide robust early warning of increasing transmission.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Reese Anthony Keith Richardson", + "author_inst": "Northwestern University and Chicago Department of Public Health" + }, + { + "author_name": "Emile Jorgensen", + "author_inst": "Chicago Department of Public Health" + }, + { + "author_name": "Philip Arevalo", + "author_inst": "University of Chicago" + }, + { + "author_name": "Tobias M Holden", + "author_inst": "Northwestern University" + }, + { + "author_name": "Katelyn M Gostic", + "author_inst": "University of Chicago" + }, + { + "author_name": "Massimo Pacilli", + "author_inst": "Chicago Department of Public Health" + }, + { + "author_name": "Isaac Ghinai", + "author_inst": "Chicago Department of Public Health" + }, + { + "author_name": "Shannon Lightner", + "author_inst": "Illinois Department of Public Health" + }, + { + "author_name": "Sarah Cobey", + "author_inst": "University of Chicago" + }, + { + "author_name": "Jaline Gerardin", + "author_inst": "Northwestern University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.05.10.22274892", "rel_title": "Acceptability of a behavioural intervention to mitigate the psychological impacts of COVID-19 restrictions in older people with long-term conditions: a qualitative study", @@ -306793,61 +307709,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.05.09.22274769", - "rel_title": "COVID-19 vaccination in pregnancy: views and vaccination uptake rates in pregnancy, a mixed methods analysis from the Born In Wales study", - "rel_date": "2022-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.09.22274769", - "rel_abs": "BackgroundVaccine hesitancy amongst pregnant women has been found to be a concern during past epidemics.\n\nObjectivesThe aims of this study were to 1) estimate COVID-19 vaccination rates among pregnant women in Wales and their association with age, ethnicity, and area of deprivation, using electronic health records (EHR) linkage, and 2) explore pregnant womens views on receiving the COVID-19 vaccine during pregnancy using data from a survey recruiting via social media (Facebook, Twitter), through midwives, and posters in hospitals (Born in Wales Cohort).\n\nDesignA mixed methods study utilising routinely collected linked data from the Secure Anonymised Information Linkage (SAIL) (Objective 1) and the Born In Wales Birth Cohort participants (Objective 2). SAIL combines data from general practice, hospital admissions, the national community child health dataset, maternal indicators dataset, and COVID-19 vaccination databases.\n\nSetting and participantsObjective 1) All women documented as being pregnant on or after 13th April 2021, aged 18 years or older, and eligible for COVID-19 vaccination were identified in routine health care. They were linked to the vaccination data up to and including 31st December 2021. Objective 2) Separately, a cross-section of pregnant women in Wales were invited to complete an online survey via social media advertising. The survey asked what their views were on having the COVID-19 vaccination during pregnancy, and if they had already received, or intended to receive, the COVID-19 vaccination during their pregnancies. They were also asked to give reasons for their decisions.\n\nOutcomes1 (a). Rate of vaccination uptake per month during pregnancy among women eligible for vaccination. 1 (b). Survival analysis was utilised to examine and compare the length of time to vaccination uptake in pregnancy, and variation in uptake by; age, ethnicity, and deprivation area was examined using hazard ratios (HR) from Cox regression. 2.Expectant mothers views of the COVID-19 vaccination during pregnancy.\n\nResults\n\nPopulation-level data linkage (objective 1)Within the population cohort, 32.7% (n = 8,203) were vaccinated (at least one dose of the vaccine) during pregnancy, 34.1% (n = 8,572) remained unvaccinated throughout follow-up period, and 33.2% (n = 8,336) received the vaccine postpartum. Younger women (<30 years) were less likely to have the vaccine and those living in areas of high deprivation were also less likely to have the vaccine (HR=0.88, 95% CI 0.82 to 0.95). Asian and other ethnic groups were 1.12 and 1.18 times more likely to have the vaccine in pregnancy compared to women of White ethnicity (HR=1.12, 95% CI 1.00 to 1.25) and (HR=1.18, 95% CI 1.03 to 1.37) respectively.\n\nSurvey responses (objective 2)69% of participants stated that they would be happy to have the vaccine during pregnancy (n = 207). The remainder, 31%, indicated that they would not have the vaccine during pregnancy (n = 94). Reasons for having the vaccine related to protecting self and baby, perceived risk level, and receipt of sufficient evidence and advice. Reasons for vaccine refusal included lack of research about long-term outcomes for the baby, anxiety about vaccines, inconsistent advice/information, and preference to wait until after the pregnancy.\n\nConclusionPotentially only 1 in 3 pregnant women would have the COVID-19 vaccine during pregnancy, even though 2 in 3 reported they would have the vaccination, thus it is critical to develop tailored strategies to increase its acceptance rate and to decrease vaccine hesitancy. A targeted approach to vaccinations may be required for groups such as younger people and those living in higher deprivation level areas.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Mohamed Mhereeg", - "author_inst": "Swansea University Medical School, Swansea, Wales, UK" - }, - { - "author_name": "Hope Jones", - "author_inst": "Swansea University Medical School, Swansea, Wales, UK." - }, - { - "author_name": "Jonathan Kennedy", - "author_inst": "Swansea University Medical School, Swansea, Wales, UK." - }, - { - "author_name": "Michael Seaborne", - "author_inst": "Swansea University Medical School, Swansea, Wales, UK." - }, - { - "author_name": "Michael Parker", - "author_inst": "Swansea University Medical School, Swansea, Wales, UK." - }, - { - "author_name": "Natasha Kennedy", - "author_inst": "Swansea University Medical School, Swansea, Wales, UK." - }, - { - "author_name": "Sarah Beeson", - "author_inst": "Swansea University Medical School, Swansea, Wales, UK." - }, - { - "author_name": "Luisa Zuccolo", - "author_inst": "Bristol Medical School, University of Bristol, Bristol, England, UK." - }, - { - "author_name": "Alisha Davies", - "author_inst": "Public Health Wales, UK" - }, - { - "author_name": "Sinead Brophy", - "author_inst": "Swansea University Medical School, Swansea, Wales, UK" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.05.09.22274776", "rel_title": "Early detection of fraudulent COVID-19 products from Twitter chatter", @@ -307056,6 +307917,65 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2022.05.09.491179", + "rel_title": "Adenovirus-Vectored SARS-CoV-2 Vaccine Expressing S1-N Fusion Protein", + "rel_date": "2022-05-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.09.491179", + "rel_abs": "Additional COVID-19 vaccines that are safe, easy to manufacture, and immunogenic are needed for global vaccine equity. Here, we developed a recombinant type 5 adenovirus vector encoding for the SARS-CoV-2-S1 subunit antigen and nucleocapsid as a fusion protein (Ad5.SARS-CoV-2-S1N) delivered to BALB/c mice through multiple vaccine administration routes. A single subcutaneous (S.C.) immunization with Ad5.SARS-CoV-2-S1N induced a similar humoral response, along with a significantly higher S1-specific cellular response, as a recombinant type 5 adenovirus vector encoding for S1 alone (Ad5.SARS-CoV-2-S1). Immunogenicity was improved by homologous prime boost strategies, using either S.C. or intranasal (I.N.) delivery of Ad5.SARS-CoV-2-S1N, and further improved through heterologous prime boost, with traditional intramuscular (I.M.) injection, using subunit recombinant S1 protein. Priming with low dose (1x1010 v.p.) of Ad5.SARS-CoV-2-S1N and boosting with either wildtype recombinant rS1 or B.1.351 recombinant rS1 induced a robust neutralizing response, that was sustained against immune evasive Beta and Gamma SARS-CoV-2 variants, along with a long-lived plasma cell response in the bone marrow 29 weeks post vaccination. This novel Ad5-vectored SARS-CoV-2 vaccine candidate showed promising immunogenicity in mice and supports the further development of COVID-19 based vaccines incorporating the nucleoprotein as a target antigen.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Muhammad Sohaib Khan", + "author_inst": "University of Pittsburgh School of Public Health" + }, + { + "author_name": "Eun Kim", + "author_inst": "University of Pittsburgh School of Medicine" + }, + { + "author_name": "Alex McPherson", + "author_inst": "University of Pittsburgh School of Public Health" + }, + { + "author_name": "Florian J Weisel", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Shaohua Huang", + "author_inst": "University of Pittsburgh School of Medicine" + }, + { + "author_name": "Thomas W Kenniston", + "author_inst": "University of Pittsburgh School of Medicine" + }, + { + "author_name": "Elena Percivalle", + "author_inst": "Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Irene Cassaniti", + "author_inst": "Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Fausto Baldanti", + "author_inst": "Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Marlies Meisel", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Andrea Gambotto", + "author_inst": "University of Pittsburgh School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.05.03.22274607", "rel_title": "A New Paper Framework to Increase Reproducibility: Example Relating to Web Pharmacovigilance During COVID-19 in Italy", @@ -308847,49 +309767,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.10.22274918", - "rel_title": "Unrealistic optimism in the eye of the storm: Positive bias towards the consequences of COVID-19 during the second and third waves of the pandemic.", - "rel_date": "2022-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.10.22274918", - "rel_abs": "Research conducted at the outset of the pandemic shows that people are vulnerable to unrealistic optimism (UO). However, the Weinstein model suggests that this tendency may not persist as the pandemic progresses. Our research aimed at verifying whether UO persists during the second (Study 1) and the third wave (Study 2) of the pandemic in Poland, whether it concerns the assessment of the chances of COVID-19 infection (Study 1 and Study 2), the chances of severe course of the disease and adverse vaccine reactions (Study 2). We show that UO towards contracting COVID-19 persists throughout the pandemic. However, in situations where we have little influence on the occurrence of the event, the participants do not show UO. The exceptions are those who have known personally someone who has died from a coronavirus infection. These results are discussed in terms of self-esteem protection and the psychological threat reduction mechanism.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ada Maksim", - "author_inst": "Jagiellonian University: Uniwersytet Jagiellonski w Krakowie" - }, - { - "author_name": "S\u0142awomir \u015apiewak", - "author_inst": "Jagiellonian University: Uniwersytet Jagiellonski w Krakowie" - }, - { - "author_name": "Natalia Lipp", - "author_inst": "Jagiellonian University: Uniwersytet Jagiellonski w Krakowie" - }, - { - "author_name": "Natalia Du\u017cma\u0144ska-Misiarczyk", - "author_inst": "Jagiellonian University: Uniwersytet Jagiellonski w Krakowie" - }, - { - "author_name": "Krzysztof R\u0119bilas", - "author_inst": "Jagiellonian University: Uniwersytet Jagiellonski w Krakowie" - }, - { - "author_name": "Grzegorz Gustaw", - "author_inst": "Jagiellonian University: Uniwersytet Jagiellonski w Krakowie" - }, - { - "author_name": "Pawe\u0142 Strojny", - "author_inst": "Jagiellonian University: Uniwersytet Jagiellonski w Krakowie" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.05.09.491201", "rel_title": "COVID-19 mRNA third dose induces a unique hybrid immunity-like antibody response", @@ -309190,6 +310067,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.05.10.22274889", + "rel_title": "Machine learning uncovers blood test patterns subphenotypes at hospital admission discerning increased 30-day ICU mortality rates in COVID-19 elderly patients", + "rel_date": "2022-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.10.22274889", + "rel_abs": "BackgroundElderly patients with COVID-19 are among the most numerous populations being admitted in the ICU due to its high mortality rate and high comorbidity incidence. An early severity risk stratification at hospital admission could help optimize ICU usage towards those more vulnerable and critically ill patients.\n\nMethodsOf 503 Spanish patients aged>64 years admitted in the ICU between 26 Feb and 02 Nov 2020 in two Spanish hospitals, we included 193 quality-controlled patients. The subphenotyping combined PCA and t-SNE dimensionality reduction methods to maximize non-linear correlation and reduce noise among age and full blood count tests (FBC) at hospital admission, followed by hierarchical clustering.\n\nFindingsWe identified five subphenotypes (Eld-ICU-COV19 clusters) with heterogeneous FBC patterns associated to significantly disparate 30-day ICU mortality rates ranging from 2% in a healthy cluster to 44% in a severe cluster, along three moderate clusters.\n\nInterpretationsTo our knowledge, this is the first study using age and FBC at hospital admission to early stratify the risk of death in ICU at 30 days in elderly patients. Our results provide guidance to comprehend the phenotypic classification and disparate severity patterns among elderly ICU patients with COVID-19, based only on age and FBC, that have the potential to establish target groups for early risk stratification or early triage systems to provide personalized treatments or aid the decision-making during resource allocation process for each target Eld-ICU-COV19 cluster, especially in those circumstances with resource scarcity problem.\n\nFundingFONDO SUPERA COVID-19 by CRUE-Santander Bank grant SUBCOVERWD-19.\n\nO_TEXTBOXResearch in contextEvidence before this study\n\nWe searched on PubMed and Google Scholar using the search terms \"COVID-19\", \"SARS-CoV2\", \"phenotypes\" for research published between 2020 to 2022, with no language restriction, to detect any published study identifying and characterizing phenotypes among ICU COVID-19 patients. A previous COVID-19 phenotyping study found three phenotypes from hospitalized patients associated with significantly disparate 30-day mortality rates (ranging from 2{middle dot}5 to 60{middle dot}7%). However, it seems to become harder to find phenotypes with discriminative mortality rates among ICU COVID-19 patients. For example, we found one study that uncovered two phenotypes from 39 ICU COVID-19 patients based on biomarkers with 39% and 63% mortality rates, but such difference was not statistically significant. We also found another study with more success that uncovered two ICU COVID-19 phenotypes using two different trajectories with somehow disparate 28-day mortality rates of 27% versus 37% (Ventilatory ratio trajectories) and of 25% versus 39% (mechanical power trajectories).\n\nAdded value of this study\n\nTo our knowledge, this is the first study that uses age and laboratory results at hospital admission (i.e., before ICU admission) in elderly patients to early stratify, prior ICU admission, the risk of death in ICU at 30 days. We classified 193 patients with COVID-19, based on age and ten Full Blood Count (FBC) tests, into five subphenotypes (one healthy, three moderate, and one severe) that showed significantly disparate 30-day ICU mortality rates from 2% to 44%.\n\nImplications of all the available evidence\n\nIdentifying, from elderly ICU patients with COVID-19 (Eld-ICU-COV19), subphenotypes could spur further investigation to analyze the potential differences in their underlying disease mechanisms, acquire better phenotypical understanding among Eld-ICU-COV19 toward better decision-making in distributing the limited resources (including both logistic and medical) as well as shedding light on tailoring personalized treatment for each specific target subgroup in future medical research and clinical trial.\n\nC_TEXTBOX", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Lexin Zhou", + "author_inst": "Biomedical Data Science Lab, Instituto Universitario de Tecnolog\u00edas de la Informaci\u00f3n y Comunicaciones (ITACA), Universitat Polit\u00e8cnica de Val\u00e8ncia (UPV), Camin" + }, + { + "author_name": "Nekane Romero-Garc\u00eda", + "author_inst": "Biomedical Data Science Lab, Instituto Universitario de Tecnolog\u00edas de la Informaci\u00f3n y Comunicaciones (ITACA), Universitat Polit\u00e8cnica de Val\u00e8ncia (UPV), Camin" + }, + { + "author_name": "Rafael Badenes", + "author_inst": "Department of Anesthesiology and Surgical-Trauma Intensive Care, Hospital Clinic Universitari de Valencia. Department of Surgery, University of Valencia. Espa\u00f1a" + }, + { + "author_name": "Mar\u00eda Teresa Garc\u00eda Morales", + "author_inst": "Department of Clinical Research, Hospital Universitario 12 de octubre, Madrid, Espa\u00f1a" + }, + { + "author_name": "David Lora", + "author_inst": "Department of Clinical Research, Hospital Universitario 12 de octubre, Madrid, Espa\u00f1a" + }, + { + "author_name": "Agust\u00edn G\u00f3mez de la C\u00e1mara", + "author_inst": "Department of Clinical Research, Hospital Universitario 12 de octubre, Madrid, Espa\u00f1a" + }, + { + "author_name": "Francisco Tom\u00e1s Garc\u00eda Ruiz", + "author_inst": "Biomedical Data Science Lab, Instituto Universitario de Tecnolog\u00edas de la Informaci\u00f3n y Comunicaciones (ITACA), Universitat Polit\u00e8cnica de Val\u00e8ncia (UPV), Camin" + }, + { + "author_name": "Juan M Garc\u00eda-G\u00f3mez", + "author_inst": "Biomedical Data Science Lab, Instituto Universitario de Tecnolog\u00edas de la Informaci\u00f3n y Comunicaciones (ITACA), Universitat Polit\u00e8cnica de Val\u00e8ncia (UPV), Camin" + }, + { + "author_name": "Carlos S\u00e1ez", + "author_inst": "Biomedical Data Science Lab, Instituto Universitario de Tecnolog\u00edas de la Informaci\u00f3n y Comunicaciones (ITACA), Universitat Polit\u00e8cnica de Val\u00e8ncia (UPV), Camin" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2022.05.06.22274584", "rel_title": "Substance abuse and the risk of severe COVID-19: Mendelian randomization confirms the causal role of opioids but hints a negative causal effect for cannabinoids.", @@ -310657,25 +311585,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.04.22274677", - "rel_title": "A statistical definition of epidemic waves", - "rel_date": "2022-05-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.04.22274677", - "rel_abs": "The timely identification of expected surges of cases during infectious disease epidemics is essential for allocating resources and preparing interventions. This study describes a simple way to evaluate whether an epidemic wave is likely to be present based on daily new case count data. The proposed measure compares two models that assume exponential or linear dynamics, respectively. Technically, the output of two regression analyses is used to approximate a Bayes factor, which quantifies the support for the exponential over the linear model and can be used for epidemic wave detection. The trajectory of the coronavirus epidemic in three countries is analyzed and discussed for illustration. The proposed measure detects epidemic waves at an early stage, which are otherwise visible only by inspecting the development of case count data retrospectively. In addition to informing public health decision making, the outlined approach may serve as a starting point for scientific discussions on epidemic waves.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Levente Kriston", - "author_inst": "University Medical Center Hamburg-Eppendorf" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.05.06.22274701", "rel_title": "COVID-19 vaccine effectiveness during a prison outbreak when the Omicron was the dominant circulating variant, Zambia, December 2021", @@ -311024,6 +311933,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2022.05.07.22274792", + "rel_title": "Assessing the feasibility of sustaining a 'Zero-COVID' policy in China in the era of highly transmissible variants", + "rel_date": "2022-05-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.07.22274792", + "rel_abs": "We developed a spatially structured, fully stochastic, individual-based SARS-CoV-2 transmission model to evaluate the feasibility of sustaining SARS-CoV-2 local containment in mainland China considering currently dominant Omicron variants, Chinas current immunization level, and non-pharmaceutical interventions (NPIs). We also built a statistical model to estimate the overall disease burden under various hypothetical mitigation scenarios. We found that due to high transmissibility, neither Omicron BA.1 or BA.2 could be contained by Chinas pre-Omicron NPI strategies which were successful prior to the emergence of the Omicron variants. However, increased intervention intensity, such as enhanced population mobility restrictions and multi-round mass testing, could lead to containment success. We estimated that an acute Omicron epidemic wave in mainland China would result in significant number of deaths if China were to reopen under current vaccine coverage with no antiviral uptake, while increasing vaccination coverage and antiviral uptake could substantially reduce the disease burden. As Chinas current vaccination has yet to reach high coverage in older populations, NPIs remain essential tools to maintain low levels of infection while building up protective population immunity, ensuring a smooth transition out of the pandemic phase while minimizing the overall disease burden.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yan Wang", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China." + }, + { + "author_name": "Kaiyuan Sun", + "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA" + }, + { + "author_name": "Zhaomin Feng", + "author_inst": "Beijing Center for Disease Prevention and Control (CDC), China" + }, + { + "author_name": "Lan Yi", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Yanpeng Wu", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China." + }, + { + "author_name": "Hengcong Liu", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China." + }, + { + "author_name": "Quanyi Wang", + "author_inst": "Beijing Center for Disease Prevention and Control (CDC), China." + }, + { + "author_name": "Marco Ajelli", + "author_inst": "Laboratory of Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomingto" + }, + { + "author_name": "Cecile Viboud", + "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA." + }, + { + "author_name": "Hongjie Yu", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.03.22274517", "rel_title": "Escape of SARS-CoV-2 variant Omicron to mucosal immunity in vaccinated subjects.", @@ -312551,61 +313515,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.05.04.22274647", - "rel_title": "Protection against omicron severe disease 0-7 months after BNT162b2 booster", - "rel_date": "2022-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.04.22274647", - "rel_abs": "Following a rise in cases due to the delta variant and evidence of waning immunity after 2 doses of the BNT162b2 vaccine, Israel began administering a third BNT162b2 dose (booster) in July 2021. Recent studies showed that the 3rd dose provides a much lower protection against infection with the omicron variant compared to the delta variant and that this protection wanes quickly. In this study, we used data from Israel to estimate the protection of the 3rd dose against severe disease up to 7 months from receiving the booster dose. The analysis shows that protection conferred by the 3rd dose against omicron did not wane over a 7-month period and that a 4th dose further increased protection, with a severe disease rate approximately 3-fold lower than in the 3-dose cohorts.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Ofra Amir", - "author_inst": "Technion - Israel Institute of Technology, Israel" - }, - { - "author_name": "Yair Goldberg", - "author_inst": "Technion - Israel Institute of Technology, Israel" - }, - { - "author_name": "Micha Mandel", - "author_inst": "The Hebrew University of Jerusalem, Israel" - }, - { - "author_name": "Yinon M. Bar-On", - "author_inst": "Department of Plant and Environmental Sciences, Weizmann Institute of Science, Israel" - }, - { - "author_name": "Omri Bodenheimer", - "author_inst": "Israel Ministry of Health, Israel" - }, - { - "author_name": "Laurence Freedman", - "author_inst": "The Bio-statistical and Bio-mathematical Unit, The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center, Israel" - }, - { - "author_name": "Sharon Alroy-Preis", - "author_inst": "Israel Ministry of Health, Israel" - }, - { - "author_name": "Nachman Ash", - "author_inst": "Israel Ministry of Health, Israel" - }, - { - "author_name": "Amit Huppert", - "author_inst": "The Bio-statistical and Bio-mathematical Unit, The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center, Israel" - }, - { - "author_name": "Ron Milo", - "author_inst": "Department of Plant and Environmental Sciences, Weizmann Institute of Science, Israel" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.05.04.490614", "rel_title": "SARS-CoV-2 variants do not evolve to promote further escape from MHC-I recognition", @@ -312834,6 +313743,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.05.02.22274575", + "rel_title": "SOFA score performs worse than age for predicting mortality in patients with COVID-19", + "rel_date": "2022-05-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.02.22274575", + "rel_abs": "The use of the Sequential Organ Failure Assessment (SOFA) score, originally developed to describe disease morbidity, is commonly used to predict in-hospital mortality. During the COVID-19 pandemic, many protocols for crisis standards of care used the SOFA score to select patients to be deprioritized due to a low likelihood of survival. A prior study found that age outperformed the SOFA score for mortality prediction in patients with COVID-19, but was limited to a small cohort of intensive care unit (ICU) patients and did not address whether their findings were unique to patients with COVID-19. Moreover, it is not known how well these measures perform across races.\n\nIn this retrospective study, we compare the performance of age and SOFA scores in predicting in-hospital mortality across two cohorts: a cohort of 2,648 consecutive adult patients diagnosed with COVID-19 who were admitted to a large academic health system in the northeastern United States over a 4-month period in 2020 and a cohort of 75,601 patients admitted to one of 335 ICUs in the eICU database between 2014 and 2015.\n\nAmong the COVID-19 cohort, age (area under receiver-operating characteristic curve (AU-ROC) 0.795, 95% CI 0.762, 0.828) had a significantly better discrimination than SOFA score (AU-ROC 0.679, 95% CI 0.638, 0.721) for mortality prediction. Conversely, age (AU-ROC 0.628 95% CI 0.608, 0.628) underperformed compared to SOFA score (AU-ROC 0.735, 95% CI 0.726, 0.745) in non-COVID-19 ICU patients in the eICU database. There was no difference between Black and White COVID-19 patients in performance of either age or SOFA Score. Our findings bring into question the utility of SOFA score-based resource allocation in COVID-19 crisis standards of care.\n\nAuthor SummaryThe COVID-19 pandemic has prompted hospitals to develop protocols for allocating resources if the number of patients exceed their capacity in order to save as many lives as possible. Many of these protocols use the Sequential Organ Failure Assessment (SOFA) score to identify patients who are unlikely to survive and thus should be deprioritized for care. There are concerns that the SOFA score may not accurately predict mortality in patients with COVID-19 or perform better in one racial group over another. We asked whether a simple measure, patient age, could better predict mortality than SOFA score in a group of adult patients admitted to a large academic health system in 2020. To see if any findings are unique to patients with COVID-19, we performed the same analysis in a group of adult patients taken from the eICU database, a large publicly available dataset that was collected prior to the COVID-19 pandemic. We found that age was better than SOFA score at predicting patient mortality in patients with COVID-19, but not in patients without COVID. For COVID-19, neither age or SOFA score performed better in one racial group over another. Caution is needed when applying an established disease severity index model to a new illness.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Raphael Adam Gutmann Sherak", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Hoomaan Sajjadi", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Naveed Khimani", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Benjamin Tolchin", + "author_inst": "Yale School of Medicine: Yale University School of Medicine" + }, + { + "author_name": "Karen Jubanyik", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "R. Andrew Taylor", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Wade Schulz", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Bobak J. Mortazavi", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Adrian D Haimovich", + "author_inst": "Yale University School of Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2022.05.01.22274548", "rel_title": "Immunogenicity and reactogenicity of a third dose of BNT162b2 vaccine for COVID-19 after a primary regimen with BBIBP-CorV or BNT162b2 vaccines in Lima, Peru.", @@ -314785,29 +315745,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.04.29.22274494", - "rel_title": "Forecast Intervals for Infectious Disease Models", - "rel_date": "2022-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.29.22274494", - "rel_abs": "Forecast intervals for infectious disease transmission and mortality have long been overconfident -- i.e., the advertised coverage probabilities of those intervals fell short of their subsequent performances. Further, there was no apparent relation between how good models claimed to be (as measured by their purported forecast uncertainties) and how good the models really were (as measured by their actual forecast errors). The main cause of this problem lies in the misapplication of textbook methods for uncertainty quantification. A solution lies in the creative use of predictive tail probabilities to obtain valid interval coverages. This approach is compatible with all probabilistic predictive models whose forecast error behavior does not change \"too quickly\" over time.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Rick Picard", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Dave Osthus", - "author_inst": "Los Alamos National Laboratory" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.29.22274485", "rel_title": "Human behaviour, NPI and mobility reduction effects on COVID-19 transmission in different countries of the world", @@ -314964,6 +315901,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, + { + "rel_doi": "10.1101/2022.04.28.22274086", + "rel_title": "Quantifying the relationship between sub-population wastewater samples and community-wide SARS-CoV-2 seroprevalence", + "rel_date": "2022-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.28.22274086", + "rel_abs": "BackgroundWastewater-based epidemiology is a promising approach but robust epidemiological models to relate wastewater to community prevalence are lacking. Assessments of SARS-CoV-2 infection rates have relied primarily on convenience sampling, which does not provide reliable estimates of community prevalence because of inherent biases.\n\nMethodsFrom August 2020 to February 2021, we conducted a serial stratified randomized samplings to estimate the prevalence of anti-SARS-CoV-2 antibodies in 3,717 participants, and weekly sampling of community wastewater for SARS-CoV-2 concentrations in Jefferson County, KY. With the use of a Susceptible, Infected, Recovered (SIR)-type model, we obtained longitudinal estimates of prevalence and compared these with wastewater concentration, using regression analysis.\n\nFindingsModel analysis revealed significant temporal differences in epidemic peaks; the average incidence rate based on serological sampling in some areas was up to 50% higher than health department rates based on convenience sampling. The model-estimated average prevalence rates correlated well with wastewater (correlation=0{middle dot}63). In regression analysis, a weekly unit increase in wastewater concentration of SARS-CoV-2 corresponded to an average increase of between 1-1{middle dot}3 cases of SARS-CoV-2 infection per 100K residents.\n\nInterpretationPublicly available health department incidence rates vastly underestimate true community incidence and wastewater has a high potential to provide robust estimates of community spread of infection.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSAdministratively reported clinical case rates of coronavirus disease 2019 (COVID-19) infected individuals are biased due to a wide range of factors from testing access to concerns about missing low and non-symptomatic and self-tested individuals. Wastewater estimates offer an alternative to support community monitoring based on fecal shedding of the virus but are difficult to interpret when compared with the available public health data sets of infection rates. We examined all English literature until February 24, 2022, on Web of Science and PubMed with the terms [\"seroprevalence\" or \"antibody\"] AND [\"COVID-19\" or \"SARS-CoV-2\"] AND [\"wastewater\"]. We identified six studies. None of these studies considered randomized COVID-19 community anti-SARS-CoV-2 antibody testing paired with wastewater data.\n\nAdded value of this studyThe study demonstrates how results from serial stratified randomized serological sampling of the community can be used to build a longitudinal model that can interpolate and extrapolate community levels of infection beyond specific testing dates. Such a model correlates well with wastewater concentrations indicating its utility as a surrogate for infection prevalence. The testing data used in the study were collected before wide availability of COVID-19 vaccines and are therefore unique as they are unlikely to include a significant number of false positive results.\n\nImplications of all the available evidenceThe study demonstrates that convenience sampling obtained data from health department reporting seriously underestimates community-wide prevalence of infection. In contrast, wastewater-based epidemiology may be a faster, cost-effective, and more robust method of estimating the prevalence of viral infections within specific urban areas.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Ted Smith", + "author_inst": "University of Louisville" + }, + { + "author_name": "Rochelle H Holm", + "author_inst": "University of Louisville" + }, + { + "author_name": "Rachel J Keith", + "author_inst": "University of Louisville" + }, + { + "author_name": "Alok R Amraotkar", + "author_inst": "University of Louisville" + }, + { + "author_name": "Chance R Alvarado", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Krzysztof Banecki", + "author_inst": "Warsaw University of Technology" + }, + { + "author_name": "Boseung Choi", + "author_inst": "Korea University" + }, + { + "author_name": "Ian C Santisteban", + "author_inst": "University of Louisville" + }, + { + "author_name": "Adrienne M Bushau-Sprinkle", + "author_inst": "University of Louisville" + }, + { + "author_name": "Kathleen T Kitterman", + "author_inst": "University of Louisville" + }, + { + "author_name": "Joshua Fuqua", + "author_inst": "University of Louisville" + }, + { + "author_name": "Krystal Hamorsky", + "author_inst": "University of Louisville" + }, + { + "author_name": "Kenneth E Palmer", + "author_inst": "University of Louisville" + }, + { + "author_name": "J Michael Brick", + "author_inst": "Westat, Inc." + }, + { + "author_name": "Grzegorz Rempala", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Aruni Bhatnagar", + "author_inst": "University of Louisville" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.04.29.22274486", "rel_title": "How did the COVID-19 pandemic affect access to condoms, chlamydia and HIV testing, and cervical cancer screening at a population level in Britain? (Natsal-COVID)", @@ -316499,33 +317515,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.04.26.22274273", - "rel_title": "COVID-19 third wave experience in India, a survey of 5971 adults", - "rel_date": "2022-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.26.22274273", - "rel_abs": "BackgroundThe third wave of the pandemic in India lasted from January till March 2022, and breakthrough infections were common. Third dose of vaccine was rolled out to priority groups in the beginning of 2022. There is no published information available about the clinical outcomes in this context.\n\nAimsO_LITo assess the community level experience of the pandemic, with focus on the third wave and vaccination in India.\nC_LIO_LITo describe the experience of the boosted and non-boosted population during the 3rd wave.\nC_LIO_LITo study the public perception about the precautionary (3rd) dose in India.\nC_LI\n\nResultsAmong 5971 respondents, 98.6% were vaccinated, 40% of whom had also received the 3rd dose. Age range: 24% were below 40, 50% were 40-59, 26% were >60 years.\n\n45% were women, 53% were healthcare workers.\n\nCOVID-19 was reported by 3361 (56%) respondents. Among those who reported COVID-19, 2311 (70%) were infected during the third wave. Severe symptoms occurred in <1%, while moderate severity was reported by 42%. Repeated bouts of infection were common; 15% of those with a history of COVID-19 had been infected at least twice. 44% of the respondents (2610/5971) did not report a history of COVID-19.\n\nThe third dose was taken by 2383 individuals, of whom 30% reported COVID-19 during the 3rd wave. The boosted group also had higher N95 use, and a greater proportion of healthcare workers. Among those who did not take a 3rd dose, 45% reported COVID-19 in the 3rd wave. COVID-19 incidence was lower at 27% among those in this group who had recently received their second dose. Longer gap after the second dose correlated with higher chance of infection during 3rd wave. Giving a 3rd dose before a 6-month gap since the second dose did not make a difference in infection rate.\n\nCovaxin and Covishield recipients had the same incidence of COVID-19 during the third wave.\n\nWhile 35% of the respondents believed it was helpful, 65% of the respondents were either uncertain or disapproving of the benefit of a 3rd dose.\n\nConclusionsO_LI30% of respondents who received a 3rd dose went on to get COVID-19 during the 3rd wave.\nC_LIO_LIYounger adults were more likely to be affected during 3rd wave.\nC_LIO_LIAlthough severe disease was rare, 42% reported having symptoms of moderate severity that could temporarily incapacitate people, affecting their routine and productivity.\nC_LIO_LIThe proportion of different grades of severity was similar among all vaccinated people, regardless of whether they received a 3rd dose.\nC_LIO_LIReinfections occurred in 15%, and were not always milder.\nC_LIO_LIAmong those who did not receive a 3rd dose, 45% reported COVID-19 in the 3rd wave. However, this group had lower use of N95 masks (50%) than the 3rd dose group (68%) which may have reduced the overall protection.\nC_LIO_LIThe longer the gap after the second dose, the greater was the chance of reporting COVID-19.\nC_LIO_LIPeople who received their second dose recently had the same incidence of third wave COVID-19 as following a 3rd dose.\nC_LIO_LIThe 3rd dose, given too close to the second dose, made no difference in the infection rate.\nC_LIO_LICovaxin and Covishield recipients had the same rate of COVID-19 in the third wave.\nC_LIO_LIAlthough the respondents were 98.6% vaccinated at baseline, there was considerable uncertainty (65%) amongst them about the benefit of a 3rd dose.\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Rajeev Jayadevan", - "author_inst": "Sunrise Hospital" - }, - { - "author_name": "Ramesh Shenoy", - "author_inst": "Lisie Hospital Cochin India" - }, - { - "author_name": "Anithadevi TS", - "author_inst": "Little Flower Hospital Angamaly Kerala India" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.26.22274301", "rel_title": "Trends in non-COVID-19 hospitalizations prior to and during the COVID-19 pandemic period, United States, 2017-2021", @@ -316698,6 +317687,297 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.04.27.22274269", + "rel_title": "CRISIS AFAR: An International Collaborative Study of the Impact of the COVID-19 Pandemic on Youth with Autism and Neurodevelopmental Conditions.", + "rel_date": "2022-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.27.22274269", + "rel_abs": "ImportanceHeterogeneous mental health outcomes during the COVID-19 pandemic are recognized in the general population, but it has not been systematically assessed in youth with neurodevelopmental disorders (NDD), including autism spectrum (ASD).\n\nObjectiveIdentify subgroups of youth with ASD/NDD based on the pandemic impact on symptoms and service changes, as well as predictors of outcomes.\n\nDesign, Setting, and ParticipantsThis is a naturalistic observational study conducted across 14 North American and European clinical and/or research sites. Parent responses on the Coronavirus Health and Impact Survey Initiative (CRISIS) adapted for Autism and Related Neurodevelopmental Conditions (AFAR) were cross-sectionally collected from April to October 2020. The sample included 1275, 5-21 year-old youth with ASD and/or NDD who were clinically well-characterized prior to the pandemic.\n\nMain Outcomes and MeasuresTo identify impact subgroups, hierarchical clustering analyzed eleven AFAR factors measuring pre- to pandemic changes in clinically relevant symptoms and service access. Random forest classification assessed the relative contribution in predicting subgroup membership of 20 features including socio-demographics, pre-pandemic service, and clinical severity along with indices of COVID-19 related experiences and environments empirically-derived from AFAR parent responses and global open sources.\n\nResultsClustering analyses revealed four ASD/NDD impact subgroups. One subgroup - broad symptom worsening only (20% of the aggregate sample) - included youth with worsening symptoms that were above and beyond that of their ASD/NDD peers and with similar service disruptions as those in the aggregate average. The three other subgroups showed symptom changes similar to the aggregate average but differed in service access: primarily modified services (23%), primarily lost services (6%), and average services/symptom changes (53%). Pre-pandemic factors (e.g., number of services), pandemic environments and experiences (e.g., COVID-19 cases, related restrictions, COVID-19 Worries), and age emerged in unique combinations as distinct protective or risk factors for each subgroup. Together they highlighted the role of universal risk factors, such as risk perception, and the protective role of services before and during the pandemic, in middle childhood.\n\nConclusions and RelevanceConcomitant assessment of changes in both symptoms and services access is critical to understand heterogeneous impact of the pandemic on ASD/NDD youth. It enabled the delineation of pathways to risk and resilience that include universal and ASD/NDD specific contributors.", + "rel_num_authors": 69, + "rel_authors": [ + { + "author_name": "Bethany Vibert", + "author_inst": "Autism Center, Child Mind Institute, New York, NY, USA" + }, + { + "author_name": "Patricia Segura", + "author_inst": "Autism Center, Child Mind Institute, New York, NY, USA" + }, + { + "author_name": "Louise Gallagher", + "author_inst": "Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland" + }, + { + "author_name": "Stelios Georgiades", + "author_inst": "Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada" + }, + { + "author_name": "Panagiota Pervanidou", + "author_inst": "University of Athens, National & Kapodistrian University of Athens, School of Medicine, First Department of Pediatrics, Unit of Developmental and Behavioral Ped" + }, + { + "author_name": "Audrey Thurm", + "author_inst": "Neurodevelopmental and Behavioral Phenotyping Service, National Institute of Mental Health, Bethesda, Maryland, USA" + }, + { + "author_name": "Lindsay Alexander", + "author_inst": "Center for the Developing Brain, Child Mind Institute, New York, NY, USA" + }, + { + "author_name": "Evdokia Anagnostou", + "author_inst": "Autism Research Centre, Bloorview Research Institute, Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada; Department of Paediatrics, University" + }, + { + "author_name": "Yuta Aoki", + "author_inst": "Medical Institute of Developmental Disabilities Research, Showa University, Tokyo, Japan" + }, + { + "author_name": "Catherine S.N. Birken", + "author_inst": "Department of Pediatrics, School of Medicine, University of Toronto, Toronto, ON, Canada; Division of Paediatric Medicine, Hospital for Sick Children, Toronto, " + }, + { + "author_name": "Somer L. Bishop", + "author_inst": "Department of Psychiatry and Behavioral Sciences and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, USA" + }, + { + "author_name": "Jessica Boi", + "author_inst": "Department of Biomedical Sciences, Section of Neuroscience & Clinical Pharmacology, University of Cagliari, Cagliari, Italy" + }, + { + "author_name": "Carmela Bravaccio", + "author_inst": "UOSD di Neuropsichiatria Infantile - Dipartimento di Scienze Mediche Traslazionali, Universita Federico II di Napoli - Italy" + }, + { + "author_name": "Helena Brentani", + "author_inst": "Department of Psychiatry, Hospital das Clinicas HCFMUSP, Faculty of Medicine, University of Sao Paulo (USP), Sao Paulo, Brazil" + }, + { + "author_name": "Paola Canevini", + "author_inst": "Department of Health Sciences, Universita degli Studi di Milano,Milan, Italy; Epilepsy Center - Sleep Medicine Center, Childhood and Adolescence Neuropsychiatry" + }, + { + "author_name": "Alessandra Carta", + "author_inst": "Department of Medical Surgical and Experimental Sciences, Unit of Child Neuropsychiatry, University Hospital of Sassari, Sassari, Italy" + }, + { + "author_name": "Alice Charach", + "author_inst": "Department of Psychiatry, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, 6th Floor, Toronto, On, M5G 0A4, Canada; De" + }, + { + "author_name": "Antonella Costantino", + "author_inst": "Child and Adolescent Neuropsychiatric Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy" + }, + { + "author_name": "Katherine T. Cost", + "author_inst": "Department of Psychiatry, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, 6th Floor, Toronto, On, M5G 0A4, Canada" + }, + { + "author_name": "Elaine Andrade Cravo", + "author_inst": "Department of Psychiatry, School of Medicine, Universidade Federal do Parana, Curitiba, PR, Brazil" + }, + { + "author_name": "Jennifer Crosbie", + "author_inst": "Department of Psychiatry, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, 6th Floor, Toronto, On, M5G 0A4, Canada; De" + }, + { + "author_name": "Chiara Davico", + "author_inst": "Department of Public Health and Pediatric Sciences, Section of Child and Adolescent Neuropsychiatry, University of Turin, Turin, Italy" + }, + { + "author_name": "Alessandra Gabellone", + "author_inst": "Department of Biomedical Sciences and Human Oncology, University of Bari \"Aldo Moro\", Bari, Italy" + }, + { + "author_name": "Federica Donno", + "author_inst": "Department of Biomedical Sciences, Section of Neuroscience & Clinical Pharmacology, University of Cagliari, Cagliari, Italy" + }, + { + "author_name": "Junya Fujino", + "author_inst": "Department of Psychiatry and Behavioral Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan" + }, + { + "author_name": "Cristiane Tezzari Geyer", + "author_inst": "Department of Psychiatry, School of Medicine, Universidade Federal do Parana, Curitiba, PR, Brazil" + }, + { + "author_name": "Tomoya Hirota", + "author_inst": "Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, California, USA; Department of Neuropsychiatry, Graduat" + }, + { + "author_name": "Stephen Kanne", + "author_inst": "Center for Autism and the Developing Brain, Department of Psychiatry, Weill Cornell Medicine, New York, NY" + }, + { + "author_name": "Makiko Kawashima", + "author_inst": "Koishikawa Tokyo Hospital, Tokyo, Japan" + }, + { + "author_name": "Elizabeth Kelley", + "author_inst": "Department of Psychology, Queens University, Kingston, ON, Canada" + }, + { + "author_name": "Hosanna Kim", + "author_inst": "The UCSF Center for ASD & NDDs, University of California San Francisco, San Francisco, California" + }, + { + "author_name": "Young Shin Kim", + "author_inst": "The UCSF Center for ASD & NDDs, University of California San Francisco, San Francisco, California" + }, + { + "author_name": "So Hyun (Sophy) Kim", + "author_inst": "Center for Autism and the Developing Brain, Department of Psychiatry, Weill Cornell Medicine, New York, NY" + }, + { + "author_name": "Daphne J. Korczak", + "author_inst": "Department of Psychiatry, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, 6th Floor, Toronto, On, M5G 0A4, Canada; De" + }, + { + "author_name": "Meng-Chuan Lai", + "author_inst": "Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada; Autism Research Centre, Department of Psychiatry, University of C" + }, + { + "author_name": "Lucia Margari", + "author_inst": "Department of Biomedical Sciences and Human Oncology, University of Bari \"Aldo Moro\", Bari, Italy" + }, + { + "author_name": "Gabriele Masi", + "author_inst": "IRCCS Stella Maris Foundation, Pisa (Calambrone), Italy" + }, + { + "author_name": "Lucia Marzulli", + "author_inst": "Department of Biomedical Sciences and Human Oncology, University of Bari \"Aldo Moro\", Bari, Italy" + }, + { + "author_name": "Luigi Mazzone", + "author_inst": "Child Neurology and Psychiatry Unit, Systems Medicine Department,University of Rome Tor Vergata, Rome, Italy" + }, + { + "author_name": "Jane McGrath", + "author_inst": "Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland; ADMiRE, Linn Dara Child and Adolescent Mental Health Services, Cherry Orc" + }, + { + "author_name": "Suneeta Monga", + "author_inst": "Department of Psychiatry, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, 6th Floor, Toronto, On, M5G 0A4, Canada; De" + }, + { + "author_name": "Paola Morosini", + "author_inst": "Unita' Operativa di Neuropsichiatria dell' Infanzia e dell' adolescenza, Lodi, Italy" + }, + { + "author_name": "Shinichiro Nakajima", + "author_inst": "Keio University School of Medicine, Tokyo, Japan" + }, + { + "author_name": "Antonio Narzisi", + "author_inst": "IRCCS Stella Maris Foundation, Pisa (Calambrone), Italy" + }, + { + "author_name": "Rob Nicolson", + "author_inst": "Department of Psychiatry, University of Western Ontario, London, Ontario" + }, + { + "author_name": "Aki Nikolaidis", + "author_inst": "Center for the Developing Brain, Child Mind Institute, New York, NY, USA" + }, + { + "author_name": "Yoshihiro Noda", + "author_inst": "Keio University School of Medicine, Tokyo, Japan" + }, + { + "author_name": "Kerri Nowell", + "author_inst": "Thompson Center of Neurodevelopmental Disorders, University of Missouri, Columbia, MO, USA" + }, + { + "author_name": "Miriam Polizzi", + "author_inst": "UOSD di Neuropsichiatria Infantile - Dipartimento di Scienze Mediche Traslazionali, Universita Federico II di Napoli - Italy" + }, + { + "author_name": "Joana Portolese", + "author_inst": "Department of Psychiatry, Hospital das Clinicas HCFMUSP, Faculty of Medicine, University of Sao Paulo (USP), Sao Paulo, Brazil" + }, + { + "author_name": "Maria Pia Riccio", + "author_inst": "UOSD di Neuropsichiatria Infantile - Dipartimento di Scienze Mediche Traslazionali, Universita Federico II di Napoli - Italy" + }, + { + "author_name": "Manabu Saito", + "author_inst": "Department of Neuropsychiatry, Graduate School of Medicine, Hirosaki University, Hirosaki, Aomori, Japan; Research Center for Child Mental Development, Graduate" + }, + { + "author_name": "Anish K. Simhal", + "author_inst": "Autism Center, Child Mind Institute, New York, NY, USA; Medical Physics, Memorial Sloan Kettering Cancer Center, NY, USA" + }, + { + "author_name": "Martina Siracusano", + "author_inst": "Child Neurology and Psychiatry Unit, Systems Medicine Department,University of Rome Tor Vergata, Rome, Italy" + }, + { + "author_name": "Stefano Sotgiu", + "author_inst": "Department of Medical Surgical and Experimental Sciences, Unit of Child Neuropsychiatry, University Hospital of Sassari, Sassari, Italy" + }, + { + "author_name": "Jacob Stroud", + "author_inst": "Autism Center, Child Mind Institute, New York, NY, USA" + }, + { + "author_name": "Fernando Sumiya", + "author_inst": "Department of Psychiatry, Hospital das Clinicas HCFMUSP, Faculty of Medicine, University of Sao Paulo (USP), Sao Paulo, Brazil" + }, + { + "author_name": "Ida Schwartz", + "author_inst": "Medical Genetics Service/HCPA, Genetics Department/UFRGS, Brazil" + }, + { + "author_name": "Yoshiyuki Tachibana", + "author_inst": "Division of Infant and Toddler Mental Health, Department of Psychosocial Medicine, National Center for Child Health and Development, Tokyo, Japan" + }, + { + "author_name": "Nicole Takahashi", + "author_inst": "Thompson Center of Neurodevelopmental Disorders, University of Missouri, Columbia, MO, USA" + }, + { + "author_name": "Riina Takahashi", + "author_inst": "Koishikawa Tokyo Hospital, Tokyo, Japan" + }, + { + "author_name": "Hiroki Tamon", + "author_inst": "Division of Infant and Toddler Mental Health, Department of Psychosocial Medicine, National Center for Child Health and Development, Tokyo, Japan" + }, + { + "author_name": "Raffaella Tancredi", + "author_inst": "IRCCS Stella Maris Foundation, Pisa (Calambrone), Italy" + }, + { + "author_name": "Benedetto Vitiello", + "author_inst": "Department of Public Health and Pediatric Sciences, Section of Child and Adolescent Neuropsychiatry, University of Turin, Turin, Italy" + }, + { + "author_name": "Alessandro Zuddas", + "author_inst": "Department of Biomedical Sciences, Section of Neuroscience & Clinical Pharmacology, University of Cagliari, Cagliari, Italy; Child & Adolescent Neuropsychiatry" + }, + { + "author_name": "Bennett Leventhal", + "author_inst": "University of Chicago, Chicago, IL, USA" + }, + { + "author_name": "Kathleen Merikangas", + "author_inst": "Genetic Epidemiology Research Branch, Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA" + }, + { + "author_name": "Michael P. Milham", + "author_inst": "Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA" + }, + { + "author_name": "Adriana Di Martino", + "author_inst": "Autism Center, Child Mind Institute, New York, NY, USA" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2022.04.27.22274377", "rel_title": "Which countries need COVID-19 vaccines the most? Development of a prioritisation tool", @@ -318329,37 +319609,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.04.25.22274291", - "rel_title": "Epidemiological behavior of the contamination curve by COVID-19 in Brazil: a time series study", - "rel_date": "2022-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.25.22274291", - "rel_abs": "The Brazil is experiencing the greatest episode of sanitary collapse ever known in the countrys history. Therefore, the relevance of this study is highlighted for the scientific advance on the epidemiological behavior of the virus in Brazil, enabling the development of analyses and discussions on the factors that influenced the high rates of contamination by SARS-CoV-2 in the country. Given the above, the study in question aims to analyze the epidemiological behavior of the contamination curve by COVID-19 by epidemiological week (EW), in the years 2020-2021, in Brazil. This is an ecological study of time series, prepared using information collected through secondary means. The country of origin of the study is Brazil, and its main theme is the number of those infected during the pandemic of COVID-19, this being the dependent variable of the study. The data been analyzed from February 23, 2020, when the first case was confirmed in Brazil, to January 1, 2022. In 2021, the countrys graph shows an exorbitant growth, reaching a peak of approximately 250 new cases per 100,000 inhabitants in the 12th EW. This data became the highest rate of the pandemic in Brazil, and did not vary significantly for the next twelve weeks. Thus, it was identified that Brazil was severely impacted by the new coronavirus, considering the high rates of confirmed cases of the virus in the country, the low adhesion of the population to preventive measures, the late start of mass vaccination in the Brazilian population, and the lack of structure in the health system, which was not properly prepared for the high demand generated by COVID-19.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Thiffany Nayara Bento de Morais", - "author_inst": "Federal University of Rio Grande do Norte: Universidade Federal do Rio Grande do Norte" - }, - { - "author_name": "Ketyllem Tayanne da Silva Costa", - "author_inst": "Federal University of Rio Grande do Norte: Universidade Federal do Rio Grande do Norte" - }, - { - "author_name": "Gustavo Nepomuceno Capistrano", - "author_inst": "Federal University of Rio Grande do Norte: Universidade Federal do Rio Grande do Norte" - }, - { - "author_name": "F\u00e1bia Barbosa de Andrade", - "author_inst": "Federal University of Rio Grande do Norte: Universidade Federal do Rio Grande do Norte" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.04.25.22273197", "rel_title": "Clinical characteristics and outcome of immunocompromised patients with COVID-19 caused by the Omicron variant: a prospective observational study", @@ -318600,6 +319849,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.23.22274186", + "rel_title": "Determinants of motivated behavior are linked to fatigue and its perturbation by SARS-CoV-2 vaccination", + "rel_date": "2022-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.23.22274186", + "rel_abs": "BackgroundFatigue has an adaptive function and serves as a temporary signal to rest and save energy often in response to immune activation. It may, however, also persist in a pathological condition incurring significant burden. While subjective symptoms and scientific consensus indicate that both physical and mental determinants of motivated behavior are affected in fatigue, the underlying processes are rarely examined using objective, task-based indicators.\n\nMethodsIn three consecutive studies, including validation (N = 48) and reliability assessments (N = 27), we use an experimental task to jointly objectify reward learning and effort execution as two determinants of behavioral motivation. In addition, we tested how fatigue and its acute perturbation in response to immune activation after SARS-CoV-2 vaccination are linked to these task-based indicators of motivation in a longitudinal cross-over design (N = 55).\n\nResultsThe validation study showed the utility of the experimental task for simultaneously assessing learning, effort exertion, and its regulation based on subjective confidence. The reliability assessment over a one-week period indicated that symptoms of fatigue and task behavior are highly reliable and that repetition effects have little impact on motivated behavior. Finally, in the vaccination trial, we found significant links between fatigue and task behavior. Baseline levels of fatigue predicted how effort is gauged in dependence of current confidence about reward outcomes, and state perturbations of fatigue in the context of the SARS-CoV-2 vaccination reduced confidence during learning. Importantly, task success was significantly lower in subjects who reported high fatigue at baseline and who additionally experienced stronger increase in fatigue in response to vaccination.\n\nDiscussionOur results demonstrate that the experimental task allows to jointly assess determinants of motivated behavior, and to link its constituent processes to subjective fatigue. This suggests that our understanding of fatigue and its perturbation due to acute immune activation can benefit from objective, task-based indicators of the underlying motivational mechanisms. Future studies could build on these findings to further deepen the understanding of neurobehavioral mechanisms underlying fatigue in the context of immune activation.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "David S Stolz", + "author_inst": "Department of Psychiatry and Psychotherapy, University of L\u00fcbeck" + }, + { + "author_name": "Finn Luebber", + "author_inst": "Department of Psychiatry and Psychotherapy, University of L\u00fcbeck; Department of Rheumatology and Clinical Immunology, University of L\u00fcbeck" + }, + { + "author_name": "Tanja Lange", + "author_inst": "Department of Rheumatology and Clinical Immunology, University of L\u00fcbeck" + }, + { + "author_name": "Stefan Borgwardt", + "author_inst": "Department of Psychiatry and Psychotherapy, University of L\u00fcbeck" + }, + { + "author_name": "Malte Ziemann", + "author_inst": "Institute of Transfusion Medicine, University Hospital of Schleswig-Holstein," + }, + { + "author_name": "Gabriela Riemekasten", + "author_inst": "Department of Rheumatology and Clinical Immunology, University of L\u00fcbeck" + }, + { + "author_name": "Jan Rupp", + "author_inst": "Department of Infectious Diseases and Microbiology, University of L\u00fcbeck" + }, + { + "author_name": "Laura M\u00fcller-Pinzler", + "author_inst": "Department of Psychiatry and Psychotherapy, University of L\u00fcbeck" + }, + { + "author_name": "Frieder M Paulus", + "author_inst": "Department of Psychiatry and Psychotherapy, University of L\u00fcbeck" + }, + { + "author_name": "S\u00f6ren Krach", + "author_inst": "Department of Psychiatry and Psychotherapy, University of L\u00fcbeck" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2022.04.25.22274251", "rel_title": "Long-COVID post-viral chronic fatigue syndrome and affective symptoms are associated with oxidative damage, lowered antioxidant defenses and inflammation: a proof of concept and mechanism study.", @@ -319919,25 +321223,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.04.22.22274198", - "rel_title": "Estimation of the Ascertainment Bias in Covid Case Detection During the Omicron Wave", - "rel_date": "2022-04-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.22.22274198", - "rel_abs": "Covid cases in the general population have been historically underreported due to a variety of reasons including limited access to PCR testing at the start of the pandemic, lack of nation-wide surveillance testing, and discouraged testing unless symptomatic. Concerns about underreporting have increased during the Omicron surge due to the expanded use of at-home rapid tests which are not required to be officially reported. For the state of Illinois, we have found that reported cases constituted only 50%-70% of the actual cases during the pre-Omicron waves (August 2020-December 2021). During the first Omicron (BA1) wave, this fraction dropped to 20-29% (i.e., only 1 in 4 to 1 in 5 cases are reported). During the ongoing second Omicron (BA2) surge, this fraction has further decreased to 12-18% (i.e., only 1 in 6 to 1 in 8 cases are reported). These estimates have important implications on understanding the extent of the Omicron surge at the state and national levels.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ahmed Elbanna", - "author_inst": "University of Illinois Urbana Champaign" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.19.22274030", "rel_title": "Estimating the distribution of COVID-19-susceptible, -recovered, and -vaccinated individuals in Germany up to April 2022", @@ -320162,6 +321447,153 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.04.22.22274032", + "rel_title": "Antibody Responses In Non-Severe SARS-CoV-2 Infections Are Driven By CD4+ T cells and Age.", + "rel_date": "2022-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.22.22274032", + "rel_abs": "SARS-CoV-2 infection causes a spectrum of clinical outcomes and diverse memory responses. Population studies indicate that viral neutralizing antibody responses are protective, but do not always develop post-infection. Other antiviral antibody effector functions, T-cell responses, or immunity to seasonal coronaviruses (OC43, 229E) have been implicated but not defined in all ages. Here, we identify that children and adult subjects generate polyfunctional antibodies to the spike protein after asymptomatic infection or mild disease, with some subjects developing cellular responses without seroconversion. Diversity in immunity was explained by two clusters distinguished by CD4+ T-cell cytokines, age, and antibodies to seasonal coronaviruses. Post-vaccination neutralizing responses were predicted by specific post-infection immune measures, including IL-2, spike-IgA, OC43-IgG1, 229E-IgM. We confirm a key role for CD4+ T cell cytokines in functionality of anti-spike antibodies, and show that antibody diversity is impacted by age, Th/Th2 cytokine biases, and antibody isotypes to SARS-CoV-2 and seasonal coronaviruses.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Amelie E Murrell", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Enwono Eyoh", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Jeffrey G Shaffer", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Monika L Dietrich", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Ivy V Trinh", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Thomas J yockachonis", + "author_inst": "Washington State University School of Molecular Biosciences" + }, + { + "author_name": "Shuangyi Bai", + "author_inst": "Washington State University School of Molecular Biosciences" + }, + { + "author_name": "Crystal Y Zheng", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Celia V Mayne", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Sofia E Cabrera", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Anyssa Aviles-Amaro", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Addison E Stone", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Saraswatie Rambaran", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Sruti Chandra", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Debra H Elliott", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Ashley R Smira", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Sara N Harris", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Katharine E Olson", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Samantha J Bilton", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Medea J Gabriel", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Nicole D Falgout", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Emily J Engel", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Alisha D Prystowsky", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Bo Ning", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Tony Hu", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Jay K Kolls", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Samuel J Landry", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Stacy S Drury", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "John S Schieffelin", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Kevin J Zwezdaryk", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "James E Robinson", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Gunn M Browyn", + "author_inst": "Washington State University School of Molecular Biosciences" + }, + { + "author_name": "Elizabeth B Norton", + "author_inst": "Tulane University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2022.04.20.488933", "rel_title": "A Quantum Dot Biomimetic for SARS-CoV-2 to Interrogate Dysregulation of the Neurovascular Unit Relevant to Brain Inflammation", @@ -321553,153 +322985,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.20.22274046", - "rel_title": "Elevated plasma Complement Factor H Regulating Protein 5 is associated with venous thromboembolism and COVID-19 severity", - "rel_date": "2022-04-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.20.22274046", - "rel_abs": "Venous thromboembolism (VTE), comprising both deep vein thrombosis (DVT) and pulmonary embolism (PE) is a common, multi-causal disease with potentially serious short- and long-term complications. In clinical practice, there is a need for improved plasma biomarker-based tools for VTE diagnosis and risk prediction. We used multiplex proteomics profiling to screen plasma from patients with suspected acute VTE, and a case-control study of patients followed up after ending anticoagulant treatment for a first VTE. With replication in 5 independent studies, together totalling 1137 patients and 1272 controls, we identify Complement Factor H Related Protein (CFHR5), a regulator of the alternative pathway of complement activation, as a novel VTE associated plasma biomarker. Using GWAS analysis of 2967 individuals we identified a genome-wide significant pQTL signal on chr1q31.3 associated with CFHR5 levels. We showed that higher CFHR5 levels are associated with increased thrombin generation in patient plasma and that recombinant CFHR5 enhances platelet activation in vitro. Thrombotic complications are a frequent feature of COVID-19; in hospitalised patients we found CFHR5 levels at baseline were associated with short-time prognosis of disease severity, defined as maximum level of respiratory support needed during hospital stay. Our results indicate a clinically important role for regulation of the alternative pathway of complement activation in the pathogenesis of VTE and pulmonary complications in acute COVID-19. Thus, CFHR5 is a potential diagnostic and/or risk predictive plasma biomarker reflecting underlying pathology in VTE and acute COVID-19.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Laura Sanchez-Rivera", - "author_inst": "Science for Life Laboratory, KTH Royal Institute of Technology" - }, - { - "author_name": "Maria Jesus Iglesias", - "author_inst": "Science for Life Laboratory, KTH Royal Institute of Technology" - }, - { - "author_name": "Manal Ibrahim-Kosta", - "author_inst": "Aix-Marseille Univ, INSERM, INRAE, C2VN, - Hopitaux de Marseille." - }, - { - "author_name": "Julia Barbara Kral- Pointner", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "Sebastian Havervall", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "Louisa Goumidi", - "author_inst": "Aix-Marseille Univ, INSERM, INRAE, C2VN, - Hopitaux de Marseille." - }, - { - "author_name": "Maria Farm", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "Gaelle Munsch", - "author_inst": "University of Bordeaux, Inserm" - }, - { - "author_name": "Marine Germain", - "author_inst": "University of Bordeaux, Inserm" - }, - { - "author_name": "Philip Smith", - "author_inst": "Karolinska Institute and Karolinska University Hospital" - }, - { - "author_name": "Mun-Gwan Hong", - "author_inst": "Science for Life Laboratory, KTH Royal Institute of Technology" - }, - { - "author_name": "Pierre Suchon", - "author_inst": "Aix-Marseille Univ, INSERM, INRAE- Hopitaux de Marseille" - }, - { - "author_name": "Clement Naudin", - "author_inst": "Science for Life Laboratory, KTH Royal Institute of Technology," - }, - { - "author_name": "Anne Boland", - "author_inst": "Universite Paris-Saclay" - }, - { - "author_name": "David M Smadja", - "author_inst": "Universite de Paris" - }, - { - "author_name": "Margareta Holmstrom", - "author_inst": "Karolinska University Hospital" - }, - { - "author_name": "Maria Magnusson", - "author_inst": "Karolinska Institute and Karolinska University Hospital" - }, - { - "author_name": "Angela Silveira", - "author_inst": "Karolinska Institutet and Karolinska University Hospital" - }, - { - "author_name": "Mathias Uhlen", - "author_inst": "KTH - Royal Institute of Technology" - }, - { - "author_name": "Thomas Renne", - "author_inst": "University Medical Centre Hamburg-Eppendorf" - }, - { - "author_name": "Angel Martinez-Perez", - "author_inst": "Research Institute Hospital de la Santa Creu" - }, - { - "author_name": "Joseph Emmerich", - "author_inst": "University of Paris Cite" - }, - { - "author_name": "Jean-Fran\u00e7ois Deleuze", - "author_inst": "Centre national de recherche en g\u00e9nomique humaine" - }, - { - "author_name": "Jovan Antovic", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "Alice Assinger", - "author_inst": "Medical University of Vienna" - }, - { - "author_name": "Jose Manuel Soria Fernandez", - "author_inst": "Hospital de la Santa Creu i Sant Pau." - }, - { - "author_name": "Charlotte Thalin", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Jochen M Schwenk", - "author_inst": "KTH" - }, - { - "author_name": "Juan Carlos Souto Andres", - "author_inst": "Hospital de la Santa Creu i Sant Pau." - }, - { - "author_name": "Pierre-Emmanuel Morange", - "author_inst": "Aix-Marseille University" - }, - { - "author_name": "Lynn M Butler", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "David Alexandre Tregouet", - "author_inst": "University of Bordeaux, Inserm" - }, - { - "author_name": "Jacob Odeberg", - "author_inst": "SciLifeLab KTH" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2022.04.19.22274026", "rel_title": "A Platform for Data-centric, Continuous Epidemiological Analyses", @@ -321932,6 +323217,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.04.19.22274050", + "rel_title": "The impact of community asymptomatic rapid antigen testing on COVID-19 hospital admissions: a synthetic control study", + "rel_date": "2022-04-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.19.22274050", + "rel_abs": "ObjectiveTo analyse the impact on hospital admissions for COVID-19 of large-scale, voluntary, public open access rapid testing for SARS-CoV-2 antigen in Liverpool (UK) between 6th November 2020 and 2nd January 2021.\n\nDesignSynthetic control analysis comparing hospital admissions for small areas in the intervention population to a group of control areas weighted to be similar in terms of prior COVID-19 hospital admission rates and socio-demographic factors.\n\nInterventionCOVID-SMART (Systematic Meaningful Asymptomatic Repeated Testing), a national pilot of large-scale, voluntary rapid antigen testing for people without symptoms of COVID-19 living or working in the City of Liverpool, deployed with the assistance of the British Army from the 6th November 2020 in an unvaccinated population. This pilot informed the UK roll-out of SARS-CoV-2 antigen rapid testing, and similar policies internationally.\n\nMain outcome measureWeekly COVID-19 hospital admissions for neighbourhoods in England.\n\nResultsThe intensive introduction of COVID-SMART community testing was associated with a 43% (95% confidence interval: 29% to 57%) reduction in COVID-19 hospital admissions in Liverpool compared to control areas for the initial period of intensive testing with military assistance in national lockdown from 6th November to 3rd December 2020. A 25% (11% to 35%) reduction was estimated across the overall intervention period (6th November 2020 to 2nd January 2021), involving fewer testing centres, before Englands national roll-out of community testing, after adjusting for regional differences in Tiers of COVID-19 restrictions from 3rd December 2020 to 2nd January 2021.\n\nConclusionsThe worlds first voluntary, city-wide SARS-CoV-2 rapid antigen testing pilot in Liverpool substantially reduced COVID-19 hospital admissions. Large scale asymptomatic rapid testing for SARS-CoV-2 can help reduce transmission and prevent hospital admissions.\n\nSummary boxO_ST_ABSWhat is already known on this topicC_ST_ABS- Previous studies on managing the spread of SARS-CoV-2 have identified asymptomatic transmission as significant challenges for controlling the pandemic.\n- Along with non-pharmaceutical measures, many countries rolled out population-based asymptomatic testing programmes to further limit transmission.\n- Evidence is required on whether large scale voluntary testing of communities for COVID-19 reduces severe disease, by breaking chains of transmission.\n\n\nWhat this study adds- The findings of this study suggest that large scale rapid antigen testing of communities for SARS-CoV-2, within an agile local public health campaign, can reduce transmission and prevent hospital admissions.\n- The results indicate that policy makers should integrate such testing into comprehensive, local public health programmes targeting high risk groups, supporting those required to isolate and adapting promptly to prevailing biological, behavioural and environmental circumstances.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Xingna Zhang", + "author_inst": "UNIVERSITY OF LIVERPOOL" + }, + { + "author_name": "Ben Barr", + "author_inst": "Department of Public Health, Policy & Systems, University of Liverpool, Liverpool, UK" + }, + { + "author_name": "Mark Green", + "author_inst": "Department of Geography & Planning, University of Liverpool, Liverpool, UK" + }, + { + "author_name": "David Hughes", + "author_inst": "Department of Health Data Science, University of Liverpool, Liverpool, UK" + }, + { + "author_name": "Matthew Ashton", + "author_inst": "Director of Public Health, Liverpool City Council, Liverpool, UK" + }, + { + "author_name": "Dimitrios Charalampopoulos", + "author_inst": "Department of Public Health, Policy & Systems, University of Liverpool, Liverpool, UK" + }, + { + "author_name": "Marta Garcia-Finana", + "author_inst": "Department of Health Data Science, University of Liverpool, Liverpool, UK" + }, + { + "author_name": "Iain Buchan", + "author_inst": "Department of Public Health, Policy & Systems, University of Liverpool, Liverpool, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.04.19.22274047", "rel_title": "COVID-19 outcomes by cancer status, type, treatment, and vaccination", @@ -325011,85 +326343,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.04.18.22273978", - "rel_title": "Effectiveness of BBIBP-CorV, BNT162b2 and mRNA-1273 vaccines against hospitalisations among children and adolescents during the Omicron outbreak in Argentina", - "rel_date": "2022-04-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.18.22273978", - "rel_abs": "BackgroundAlthough paediatric clinical presentations of COVID-19 are usually less severe than in adults, serious illness and death have occurred. Many countries started the vaccination rollout of children in 2021; still, information about effectiveness in the real-world setting is scarce. The aim of our study was to evaluate vaccine effectiveness (VE) against COVID-19-associated-hospitalisations in the 3-17-year population during the Omicron outbreak.\n\nMethodsWe conducted a retrospective cohort study including individuals aged 3-17 registered in the online vaccination system of the Buenos Aires Province, Argentina. mRNA-1273 and BNT162b2 were administered to 12-17-year subjects; and BBIBP-CorV to 3-11- year subjects. Vaccinated group had received a two-dose scheme by 12/1/2021. Unvaccinated group did not receive any COVID-19 vaccine between 12/14/2021-3/9/2022, which was the entire monitoring period. Vaccine effectiveness (VE) against COVID-19-associated hospitalisations was calculated as (1-OR) x100.\n\nFindingsBy 12/1/2021, 1,536,435 individuals aged 3-17 who had received zero or two doses of SARS-CoV-2 vaccines were included in this study. Of the latter, 1,440,389 were vaccinated and 96,046 not vaccinated. VE were 78{middle dot}0% [68{middle dot}7-84{middle dot}2], 76{middle dot}4%[62{middle dot}9-84{middle dot}5] and 80{middle dot}0%[64{middle dot}3-88{middle dot}0] for the entire cohort, 3-11 subgroup and 12-17 subgroup, respectively. VE for the entire population was 82{middle dot}7% during the period of Delta and Omicron overlapping circulation and decreased to 67{middle dot}7% when Omicron was the only variant present.\n\nInterpretationThis report provides evidence of high vaccine protection against associated-hospitalisations in the paediatric population during the Omicron outbreak but suggests a decrease of protection when Omicron became predominant. Application of a booster dose in children aged 3-11 warrants further consideration.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThere is limited evidence on the effectiveness of vaccines in the pediatric population, particularly in children aged 3-11 years after the SARS-CoV-2 B.1.1.529 (Omicron) variants emergence.\n\nWe searched preprint and peer-reviewed published articles in PubMed, medRxiv, and SSRN for observational studies, with no language restrictions, using the term \"COVID-19 OR SARS-CoV-2\" AND \"vaccine effectiveness\" OR \"vaccine impact\" AND \"children\" OR \"pediatric\" AND \"Omicron\" published between December 1, 2021, and April 1, 2022. We found 4 studies that included subjects in the 3-17-year population who received a two-dose-scheme of any of the available vaccines-according to each countrys authorisation. Three studies were from the US; two were test-negative-case-control studies and one was a retrospective non-peer-reviewed cohort study. The reported vaccine effectiveness (VE) for 2-doses of BNT162b2-mRNA (Pfizer-BioNTech) in preventing hospitalisations during Omicron predominance was 48-78%; and it was 40-92% for 5-11 and 12-17-year subgroups, respectively. The fourth was a cohort study still in preprint form conducted in Chile and utilized an inactivated vaccine, CoronaVac (SinoVac), widely used in Latin-America. VE for two doses of CoronaVac in the 3-5-year subgroup against hospitalisations was 64% and 69% against ICU admissions.\n\nAdded value of this studyUp to date, there are no published studies about the effectiveness of the BBIBP-CorV vaccine against hospitalisation in the pediatric population. Additionally, there are no real-world studies from low and middle-income countries about VE in the 12-17 aged population during the Omicron outbreak.\n\nThis study shows that VE after 14 days or more from two-dose-scheme was 78{middle dot}0% [68{middle dot}7-84{middle dot}2], 76{middle dot}4% [62{middle dot}9-84{middle dot}5] and 80{middle dot}0% [64{middle dot}3-88{middle dot}0] for the 3-17-year entire group, and for 3-11-year (BBIBP-CorV) and 12-17-year (mRNA vaccines) subgroups, respectively. VE for the 3-17-year entire group was 82{middle dot}7% during the period of Delta and Omicron overlapping circulation and decreased to 67{middle dot}7% when Omicron was the only variant present. These effects were consistent across all subgroups.\n\nImplications of all the available evidenceOur results provide evidence of high vaccine protection against COVID-19 associated-hospitalisations in the pediatric population during the Omicron outbreak, but suggest a decrease of protection when Omicron became predominant. Application of a booster dose in children aged 3-11 warrants further consideration.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Soledad Estrella Gonzalez", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Santiago Olszevicki", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Alejandra Gaiano", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Ana Nina Varela Baino", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Lorena Regairaz", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Martin Salazar", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Santiago Pesci", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Lupe Marin", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Veronica Gonzalez", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Teresa Varela", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Leticia Ceriani", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Enio Garcia", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Nicolas Kreplak", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Alexia Navarro", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Elisa Estenssoro", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Franco L. Marsico", - "author_inst": "Calculus Institute, University of Buenos Aires" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.18.22271936", "rel_title": "Anti-nucleocapsid antibodies following SARS-CoV-2 infection in the blinded phase of the mRNA-1273 Covid-19 vaccine efficacy clinical trial", @@ -325282,6 +326535,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2022.04.18.22273992", + "rel_title": "An Evaluation of Prospective COVID-19 Modeling: From Data to Science Translation", + "rel_date": "2022-04-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.18.22273992", + "rel_abs": "BackgroundInfectious disease modeling can serve as a powerful tool for science-based management of outbreaks, providing situational awareness and decision support for policy makers. Predictive modeling of an emerging disease is challenging due to limited knowledge on its epidemiological characteristics. For COVID-19, the prediction difficulty was further compounded by continuously changing policies, varying behavioral responses, poor availability and quality of crucial datasets, and the variable influence of different factors as the pandemic progresses. Due to these challenges, predictive modeling for COVID-19 has earned a mixed track record.\n\nMethodsWe provide a systematic review of prospective, data-driven modeling studies on population-level dynamics of COVID-19 in the US and conduct a quantitative assessment on crucial elements of modeling, with a focus on the aspects of modeling that are critical to make them useful for decision-makers. For each study, we documented the forecasting window, methodology, prediction target, datasets used, geographic resolution, whether they expressed quantitative uncertainty, the type of performance evaluation, and stated limitations. We present statistics for each category and discuss their distribution across the set of studies considered. We also address differences in these model features based on fields of study.\n\nFindingsOur initial search yielded 2,420 papers, of which 119 published papers and 17 preprints were included after screening. The most common datasets relied upon for COVID-19 modeling were counts of cases (93%) and deaths (62%), followed by mobility (26%), demographics (25%), hospitalizations (12%), and policy (12%). Our set of papers contained a roughly equal number of short-term (46%) and long-term (60%) predictions (defined as a prediction horizon longer than 4 weeks) and statistical (43%) versus compartmental (47%) methodologies. The target variables used were predominantly cases (89%), deaths (52%), hospitalizations (10%), and Rt (9%). We found that half of the papers in our analysis did not express quantitative uncertainty (50%). Among short-term prediction models, which can be fairly evaluated against truth data, 25% did not conduct any performance evaluation, and most papers were not evaluated over a timespan that includes varying epidemiological dynamics. The main categories of limitations stated by authors were disregarded factors (39%), data quality (28%), unknowable factors (26%), limitations specific to the methods used (22%), data availability (16%), and limited generalizability (8%). 36% of papers did not list any limitations in their discussion or conclusion section.\n\nInterpretationPublished COVID-19 models were found to be consistently lacking in some of the most important elements required for usability and translation, namely transparency, expressing uncertainty, performance evaluation, stating limitations, and communicating appropriate interpretations. Adopting the EPIFORGE 2020 guidelines would address these shortcomings and improve the consistency, reproducibility, comparability, and quality of epidemic forecasting reporting. We also discovered that most of the operational models that have been used in real-time to inform decision-making have not yet made it into the published literature, which highlights that the current publication system is not suited to the rapid information-sharing needs of outbreaks. Furthermore, data quality was identified to be one of the most important drivers of model performance, and a consistent limitation noted by the modeling community. The US public health infrastructure was not equipped to provide timely, high-quality COVID-19 data, which is required for effective modeling. Thus, a systematic infrastructure for improved data collection and sharing should be a major area of investment to support future pandemic preparedness.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Kristen Nixon", + "author_inst": "Johns Hopkins University, Center for Systems Science and Engineering" + }, + { + "author_name": "Sonia Jindal", + "author_inst": "Johns Hopkins University, Center for Systems Science and Engineering" + }, + { + "author_name": "Felix Parker", + "author_inst": "Johns Hopkins University, Center for Systems Science and Engineering" + }, + { + "author_name": "Nicholas G Reich", + "author_inst": "University of Massachusetts - Amherst, School of Public Health and Health Sciences" + }, + { + "author_name": "Elizabeth C Lee", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Shaun Truelove", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Lauren Gardner", + "author_inst": "Johns Hopkins University, Center for Systems Science and Engineering" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.04.19.22273034", "rel_title": "Pathogen- and type-specific changes in invasive bacterial disease epidemiology during the first year of the COVID-19 pandemic in the Netherlands", @@ -326665,29 +327961,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.17.22273854", - "rel_title": "Characterization of SARS-CoV-2 vaccine waning in Mexico", - "rel_date": "2022-04-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.17.22273854", - "rel_abs": "1.We use survival analysis to analyze the decay in the protection induced by eight vaccines using data from 44, 006 patients from the IMSS public health system in Mexico, including only previously vaccinated, confirmed SARS-CoV-2 positive with a PCR test. We analyze three groupings: all data, complete vs. incomplete dose and less than 60 years or older. We found that a Weibull distribution fits very well the complete dose data. Only three vaccines still had 30% of their initial strength after 32 weeks. In two-dose vaccines, we found that the average protection time of a complete dose increases 2 to 3 times compared to that of an incomplete dose.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "CARLOS M HERNANDEZ-SUAREZ", - "author_inst": "Universidad Francisco Gavidia" - }, - { - "author_name": "Efren Murillo-Zamora", - "author_inst": "Instituto Mexicano del Seguro Social" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.18.22273961", "rel_title": "Clonal diversity determines persistence of SARS-CoV-2 epitope-specific T cell response", @@ -326888,6 +328161,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.04.08.22273602", + "rel_title": "Three-dose mRNA-1273 vaccination schedule: sufficient antibody response in majority of immunocompromised hematology patients", + "rel_date": "2022-04-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.08.22273602", + "rel_abs": "ImportanceIn patients with hematologic malignancies, the immunogenicity of the standard 2-dose mRNA-1273 coronavirus disease 19 (COVID-19) vaccination schedule is often insufficient due to underlying disease and current or recent therapy.\n\nObjectiveTo determine whether a 3rd mRNA-1273 vaccination raises antibody concentrations in immunocompromised hematology patients to levels obtained in healthy individuals after the standard 2-dose mRNA-1273 vaccination schedule.\n\nDesignProspective observational cohort study.\n\nSettingFour academic hospitals in the Netherlands.\n\nParticipants584 evaluable immunocompromised hematology patients, all grouped in predefined cohorts spanning the spectrum of hematologic malignancies.\n\nExposureOne additional vaccination with mRNA-1273 5 months after completion of the standard 2-dose mRNA-1273 vaccination schedule.\n\nMain Outcomes and MeasuresSerum IgG antibodies to spike subunit 1 (S1) antigens prior to and 4 weeks after each vaccination, and pseudovirus neutralization of wildtype, delta and omicron variants in a subgroup of patients.\n\nResultsIn immunocompromised hematology patients, a 3rd mRNA-1273 vaccination led to median S1 IgG concentrations comparable to concentrations obtained by healthy individuals after the 2-dose mRNA-1273 schedule. The rise in S1 IgG concentration after the 3rd vaccination was most pronounced in patients with a recovering immune system, but potent responses were also observed in patients with persistent immunodeficiencies. Specifically, patients with myeloid malignancies or multiple myeloma, and recipients of autologous or allogeneic hematopoietic cell transplantation (HCT) reached median S1 IgG concentrations similar to those obtained by healthy individuals after a 2-dose schedule. Patients on or shortly after rituximab therapy, CD19-directed chimeric antigen receptor T cell therapy recipients, and chronic lymphocytic leukemia patients on ibrutinib were less or unresponsive to the 3rd vaccination. In the 27 patients who received cell therapy between the 2nd and 3rd vaccination, S1 antibodies were preserved, but a 3rd mRNA-1273 vaccination did not significantly enhance S1 IgG concentrations except for multiple myeloma patients receiving autologous HCT. A 3rd vaccination significantly improved neutralization capacity per antibody.\n\nConclusions and RelevanceThe primary schedule for immunocompromised patients with hematologic malignancies should be supplemented with a delayed 3rd vaccination. B cell lymphoma patients and allogeneic HCT recipients need to be revaccinated after treatment or transplantation.\n\nTrial RegistrationEudraCT 2021-001072-41\n\nKey pointsO_ST_ABSQuestionC_ST_ABSCan a 3rd mRNA-1273 vaccination improve COVID-19 antibody concentrations in immunocompromised hematology patients to levels similar to healthy adults after the standard 2-dose mRNA-1273 schedule?\n\nFindingsIn this prospective observational cohort study that included 584 immunocompromised hematology patients, a 3rd mRNA-1273 vaccination significantly improved SARS-CoV-2 antibody concentrations to levels not significantly different from those obtained by healthy individuals after the standard 2-dose mRNA-1273 vaccination schedule. Pseudovirus neutralization capacity per antibody of wild type virus and variants of concern also significantly improved.\n\nMeaningThe primary COVID-19 vaccination schedule for immunocompromised patients with hematologic malignancies should be supplemented with a delayed 3rd vaccination.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Sabine Haggenburg", + "author_inst": "Department of Hematology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands; Amsterdam institute for Infection and Immunity, Amsterdam " + }, + { + "author_name": "Quincy Hofsink", + "author_inst": "Department of Hematology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands; Amsterdam institute for Infection and Immunity, Amsterdam " + }, + { + "author_name": "Birgit I. Lissenberg-Witte", + "author_inst": "Department of Epidemiology and Data Science, Amsterdam UMC location Vrije Universiteit, Amsterdam, The Netherlands" + }, + { + "author_name": "Annoek E.C. Broers", + "author_inst": "Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands" + }, + { + "author_name": "Jaap A. van Doesum", + "author_inst": "Department of Hematology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands" + }, + { + "author_name": "Rob S. van Binnendijk", + "author_inst": "Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands" + }, + { + "author_name": "Gerco den Hartog", + "author_inst": "Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands" + }, + { + "author_name": "Michel S. Bhoekhan", + "author_inst": "Department of Hematology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands; Amsterdam institute for Infection and Immunity, Amsterdam " + }, + { + "author_name": "Nienke J.E. Haverkate", + "author_inst": "Amsterdam institute for Infection and Immunity, Amsterdam UMC, Amsterdam, The Netherlands; Department of Experimental Immunology, Amsterdam UMC location Univers" + }, + { + "author_name": "Judith A. Burger", + "author_inst": "Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands" + }, + { + "author_name": "Joey H. Bouhuijs", + "author_inst": "Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands" + }, + { + "author_name": "Gaby P. Smits", + "author_inst": "Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands" + }, + { + "author_name": "Dorine Wouters", + "author_inst": "Central Diagnostic Laboratory, Amsterdam UMC, Amsterdam, The Netherlands" + }, + { + "author_name": "Ester M.M. van Leeuwen", + "author_inst": "Amsterdam institute for Infection and Immunity, Amsterdam UMC, Amsterdam, The Netherlands; Department of Experimental Immunology, Amsterdam UMC location Univers" + }, + { + "author_name": "Hetty J. Bontkes", + "author_inst": "Laboratory Medical Immunology, Amsterdam UMC, Amsterdam, The Netherlands" + }, + { + "author_name": "Neeltje A. Kootstra", + "author_inst": "Amsterdam institute for Infection and Immunity, Amsterdam UMC, Amsterdam, The Netherlands; Department of Experimental Immunology, Amsterdam UMC location Univers" + }, + { + "author_name": "Sonja Zweegman", + "author_inst": "Department of Hematology, Amsterdam UMC location Vrije Universiteit, Amsterdam, The Netherlands; Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherla" + }, + { + "author_name": "Arnon P. Kater", + "author_inst": "Department of Hematology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands; Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, The Net" + }, + { + "author_name": "Mirjam H.M. Heemskerk", + "author_inst": "Department of Hematology, Leiden UMC, Leiden, The Netherlands" + }, + { + "author_name": "Kaz Groen", + "author_inst": "Department of Hematology, Amsterdam UMC location Vrije Universiteit, Amsterdam, The Netherlands" + }, + { + "author_name": "Tom van Meerten", + "author_inst": "Department of Hematology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands" + }, + { + "author_name": "Pim G.N.J. Mutsaers", + "author_inst": "Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands" + }, + { + "author_name": "Tim Beaumont", + "author_inst": "Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands" + }, + { + "author_name": "Marit J. van Gils", + "author_inst": "Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands" + }, + { + "author_name": "Abraham Goorhuis", + "author_inst": "Department of Infectious Diseases, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands" + }, + { + "author_name": "Caroline E. Rutten", + "author_inst": "Department of Hematology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands" + }, + { + "author_name": "Mette D. Hazenberg", + "author_inst": "Department of Hematology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands; Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, The Net" + }, + { + "author_name": "Inger S. Nijhof", + "author_inst": "Department of Hematology, Amsterdam UMC location Vrije Universiteit, Amsterdam, The Netherlands; Department of Internal Medicine-Hematology, St. Antonius Hospit" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2022.04.17.22273938", "rel_title": "Permissive Omicron breakthrough infections in individuals with binding or neutralizing antibodies to ancestral SARS-CoV-2", @@ -328455,41 +329855,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.08.22273513", - "rel_title": "SARS-CoV-2 spike 340 and 337 mutations in Omicron variants are selected after Sotrovimab infusion in immunocompromised patients", - "rel_date": "2022-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.08.22273513", - "rel_abs": "After monoclonal antibody sotrovimab implementation, Rockett et al have warned on March 9th about two resistant mutations in the spike at position 337 and 340 occurring within the first week in four immunocompromised patients infected by a Delta variant and resulting in viable infection up to 25 days. As sotrovimab is currently the only effective treatment against BA.1 lineage of Omicron variant, we investigated the presence of these mutations in our 22,908 Omicron sequences performed from December 2021 to March 2022.\n\nAmong 25 Omicron sequences with S:337 and S:340 substitutions, 9 were reported in six patients who had available clinical data and a follow up. All were immunicompromised, and presented a rapid selection of these mutations after sotrovimab monotherapy infusion.\n\nWith these findings, we underscore that although these mutations are rare, they have been exclusively reported in immunocompromised patients treated with sotrovimab. We urge to consider monoclonal antibody as monotherapy in immunocompromised patients as a risk for escape mutants selection.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "gregory destras", - "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Hospices Civils de Lyon, France" - }, - { - "author_name": "antonin bal", - "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Hospices Civils de Lyon, France" - }, - { - "author_name": "bruno simon", - "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Hospices Civils de Lyon, France" - }, - { - "author_name": "bruno lina", - "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Hospices Civils de Lyon, France" - }, - { - "author_name": "laurence josset", - "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Hospices Civils de Lyon, France" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.08.22273532", "rel_title": "Heterologous Gam-COVID-Vac (Sputnik V) / mRNA-1273 (Moderna) vaccination induces a stronger humoral response than homologous Sputnik V in a real-world data analysis", @@ -328646,6 +330011,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.04.07.22273549", + "rel_title": "Dose-response modelling of endemic coronavirus and SARS-CoV-2: human challenge trials reveal the individual variation in susceptibility", + "rel_date": "2022-04-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.07.22273549", + "rel_abs": "We propose a mathematical framework to analyze and interpret the outcomes of human challenge trials. We present plausible infection risks with HCoV-229E and SARS-CoV-2 over a wide range of infectious dose, and suggest ways to improve the design of future trials and to translate its outcomes to the general population.\n\nOne sentence summaryWe rephrase dose-response models in terms of heterogeneity in susceptibility in order to present the possible range of infection risks for endemic coronaviruses and SARS-CoV-2", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Fuminari Miura", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Don Klinkenberg", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Jacco Wallinga", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.04.12.22273589", "rel_title": "Profile of Brazilian inpatients with COVID-19 vaccine breakthrough infection and risk factors for unfavorable outcome", @@ -329945,121 +331337,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2022.04.14.22272888", - "rel_title": "Anti-inflammatory therapy with nebulised dornase alfa in patients with severe COVID-19 pneumonia", - "rel_date": "2022-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.14.22272888", - "rel_abs": "BackgroundCell-free (cf)-DNA, from cellular sources, including Neutrophil Extracellular Traps (NETs), is found in the circulation of COVID-19 patients and may contribute to immune dysregulation. This study determined whether pulmonary administration of the endonuclease, dornase alfa, reduced systemic inflammation by degrading local and systemic cf-DNA.\n\nMethodsEligible patients were randomized (3:1) to receive twice-daily nebulised dornase alfa in addition to best available care (BAC) or BAC alone for seven days or until discharge. A 2:1 ratio of matched contemporary controls (CC) provided additional comparators. The primary endpoint was improvement in C-reactive protein (CRP) over time, analysed using a repeated-measures mixed model, adjusted for baseline factors.\n\nResultsBetween June 2020-October 2021 we recruited 39 evaluable patients: 30 randomised to dornase alfa; 9 randomised to BAC; with 60 CC. Dornase alfa reduced CRP by 33% compared to BAC. Least squares (LS) mean post-dexamethasone CRP fell from 101.9mg/L to 23.23 mg/L in the BAC+ dornase alfa group versus a fall from 99.5mg/L to 34.82 mg/L in the BAC group at 7 days; P=0.01. This effect of dornase alfa on CRP was confirmed with subgroup and sensitivity analyses. Dornase alfa increased the chance of live discharge by 63% (HR 1.63, 95% CI 1.01 to 2.61, P=0.03), increased lymphocyte counts (LSmean 1.08 vs 0.87, P=0.02) and reduced circulating cf-DNA and the coagulopathy marker D-dimer (LS mean: 570.78 vs 1656.96 g/mL, P=0.004). Dornase alfa was well-tolerated.\n\nConclusionsWe provide proof-of-concept evidence that dornase alfa reduces pathogenic inflammation in hospitalised patients with COVID-19 pneumonia.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Joanna Porter", - "author_inst": "UCL Respiratory, University College London, UK" - }, - { - "author_name": "Jamie Inshaw", - "author_inst": "Exploristics, Belfast, N. Ireland" - }, - { - "author_name": "Vincente Joel Solis", - "author_inst": "University College London Hospitals NHS Trust, London, UK" - }, - { - "author_name": "Emma Denneny", - "author_inst": "University College London Hospitals NHS Trust, London, UK" - }, - { - "author_name": "Rebecca Evans", - "author_inst": "University College London Hospitals NHS Trust, London, UK" - }, - { - "author_name": "Mia I. Temkin", - "author_inst": "Antimicrobial Defence lab, The Francis Crick Institute, London, UK" - }, - { - "author_name": "Nathalia De Vasconcelos", - "author_inst": "Antimicrobial Defence lab, The Francis Crick Institute, London, UK" - }, - { - "author_name": "Iker Valle Aramburu", - "author_inst": "Antimicrobial Defence lab, The Francis Crick Institute, London, UK" - }, - { - "author_name": "Dennis Hoving", - "author_inst": "Antimicrobial Defence lab, The Francis Crick Institute, London, UK" - }, - { - "author_name": "Donna Basire", - "author_inst": "UCL Respiratory, University College London, UK" - }, - { - "author_name": "Tracey Crissell", - "author_inst": "University College London Hospitals NHS Trust, London, UK" - }, - { - "author_name": "Jesusa Guinto", - "author_inst": "University College London Hospitals NHS Trust, London, UK" - }, - { - "author_name": "Alison Webb", - "author_inst": "University College London Hospitals NHS Trust, London, UK" - }, - { - "author_name": "Hanif Esmail", - "author_inst": "National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK" - }, - { - "author_name": "Victoria Johnston", - "author_inst": "National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK" - }, - { - "author_name": "Anna Last", - "author_inst": "Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Thomas Rampling", - "author_inst": "National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK" - }, - { - "author_name": "Elisa Theresa Helbig", - "author_inst": "Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany" - }, - { - "author_name": "Lena Lippert", - "author_inst": "Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany" - }, - { - "author_name": "Florian Kurth", - "author_inst": "Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany" - }, - { - "author_name": "Bryan Williams", - "author_inst": "National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK" - }, - { - "author_name": "Aiden Flynn", - "author_inst": "Exploristics, Belfast, N. Ireland" - }, - { - "author_name": "Pauline Lukey", - "author_inst": "Target to Treatment Consulting Ltd, Stevenage, UK" - }, - { - "author_name": "Veronique Birault", - "author_inst": "Translation, The Francis Crick Institute, London, UK" - }, - { - "author_name": "Venizelos Papayannopoulos", - "author_inst": "Antimicrobial Defence lab, The Francis Crick Institute, London, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.13.22273835", "rel_title": "Evaluation of machine learning for predicting COVID-19 outcomes from a national electronic medical records database", @@ -330268,6 +331545,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.04.07.22273168", + "rel_title": "Development of highly specific singleplex and multiplex real-time reverse transcription PCR assays for the identification of SARS-CoV-2 Omicron BA.1, BA.2 and Delta variants", + "rel_date": "2022-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.07.22273168", + "rel_abs": "The Omicron variant of SARS-CoV-2 (B.1.1.529), first identified during November 2021, is rapidly spreading throughout the world, replacing the previously dominant Delta variant. Omicron has a high number of mutations in the spike gene, some of which are associated with greatly increased transmissibility and immune evasion. The BA.1 sublineage has been most prevalent but there is recent evidence that the BA.2 sublineage is increasing in proportion in many countries. Genome sequencing is the gold standard for Omicron identification but is relatively slow, resource intensive, of limited capacity and often unavailable. We therefore developed a simple, rapid reverse transcription PCR (RT-PCR) method for sensitive and specific detection of the Omicron variant, including both the BA.1 and BA.2 sublineages. The assay targets a total of 5 nucleotide mutations in the receptor binding domain of the spike gene that give rise to 4 amino acid substitutions at G339D, S371L, S373P and S375F. The forward primer was designed as a double-mismatch allele specific primer (DMAS) with an additional artificial mismatch located four nucleotides from the 3 end to enhance binding specificity. Assay specificity was confirmed by testing a wide range of previously-sequenced culture-derived viral isolates and clinical samples including the Alpha, Beta and Delta variants and wild type SARS-CoV-2. Respiratory syncytial virus and influenza A were also tested. The assay can be run in singleplex format, or alternatively as a multiplex RT-PCR to enable Omicron and Delta variants to be detected and distinguished within the same reaction by means of probes labelled with different fluorescent dyes. Sublineages BA.1 and BA.2 can be differentiated if required. The methods presented here can readily be established in any PCR laboratory and should provide valuable support for epidemiologic surveillance of Omicron infections, particularly in those regions that lack extensive sequencing facilities.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jeremy A Garson", + "author_inst": "University College London" + }, + { + "author_name": "Samuel Badru", + "author_inst": "Imperial College London" + }, + { + "author_name": "Anjna Badhan", + "author_inst": "Imperial College London" + }, + { + "author_name": "Simon Dustan", + "author_inst": "Imperial College London" + }, + { + "author_name": "Richard S Tedder", + "author_inst": "Kings College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.04.13.486321", "rel_title": "Relative infectivity of the SARS-CoV-2 Omicron variant in human alveolar cells", @@ -331630,73 +332942,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.12.487379", - "rel_title": "Evolution of nasal and olfactory infection characteristics of SARS-CoV-2 variants", - "rel_date": "2022-04-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.12.487379", - "rel_abs": "SARS-CoV-2 infection of the upper airway and the subsequent immune response are early, critical factors in COVID-19 pathogenesis. By studying infection of human biopsies in vitro and in a hamster model in vivo, we demonstrated a transition in tropism from olfactory to respiratory epithelium as the virus evolved. Analyzing each variants revealed that SARS-CoV-2 WA1 or Delta infects a proportion of olfactory neurons in addition to the primary target sustentacular cells. The Delta variant possesses broader cellular invasion capacity into the submucosa, while Omicron displays longer retention in the sinonasal epithelium. The olfactory neuronal infection by WA1 and the subsequent olfactory bulb transport via axon is more pronounced in younger hosts. In addition, the observed viral clearance delay and phagocytic dysfunction in aged olfactory mucosa is accompanied by a decline of phagocytosis related genes. Furthermore, robust basal stem cell activation contributes to neuroepithelial regeneration and restores ACE2 expression post-infection. Together, our study characterized the nasal tropism of SARS-CoV-2 strains, immune clearance, and regeneration post infection. The shifting characteristics of viral infection at the airway portal provides insight into the variability of COVID-19 clinical features and may suggest differing strategies for early local intervention.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Mengfei Chen", - "author_inst": "Johns Hopkins University-School of Medicine" - }, - { - "author_name": "Andrew Pekosz", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Jason Villano", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Wenjuan Shen", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Ruifeng Zhou", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Heather Kulaga", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Zhexuan Li", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Sarah E. Beck", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Kenneth W Witwer", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Joseph Mankowski", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Murugappan Ramanathan Jr.", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Nicholas Rowan", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Andrew Lane", - "author_inst": "Johns Hopkins University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "pathology" - }, { "rel_doi": "10.1101/2022.04.12.487988", "rel_title": "An ACAT inhibitor regulates SARS-CoV-2 replication and antiviral T cell activity", @@ -332069,6 +333314,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.04.12.488042", + "rel_title": "The SARS-CoV-2 receptor-binding domain facilitates neutrophil transepithelial migration and nanoparticle uptake in the mice airways", + "rel_date": "2022-04-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.12.488042", + "rel_abs": "SARS-CoV-2-induced infection is still dangerous. Mouse models are convenient to the investigation of virus-activated immune response mechanisms. However, mice are not proper model organisms to study COVID-19 due to decreased interaction affinity between the SARS-CoV-2 receptor-binding domain (RBD) and mouse angiotensin-converting enzyme 2 (ACE2) compared with human ACE2. In the present study, we propose a mouse model that allows estimating the influence of SARS-CoV-2 on the immune system. To mimic the effects of RBD- ACE2 high-affinity interaction, mice received the ACE2 inhibitor MLN-4760. To simulate virus loading, we applied 100 nm particles suspended in the solution of RBD via the oropharyngeal route to mice. In this model, MLN-4760 application enhanced neutrophil egress from the bone marrow to the bloodstream and RBD attracted neutrophils to the luminal side of the conducting airway epithelium. By contrast, inert 100 nm particles were not potent to stimulate neutrophil recruitment to the conducting airway mucosa. Using this model, and by altering the dosage of the ACE2 inhibitor, nanoparticles, and RBD, one can adapt it to investigate different COVID-19 states characterized with mild or severe airway inflammation.\n\nStatementThis study presents a mouse model that allows estimating the influence of SARS-CoV-2 on the immune system and investigates immune cell-model virus particle interactions in the conducting airway mucosa.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Elena L Bolkhovitina", + "author_inst": "Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences" + }, + { + "author_name": "Julia D Vavilova", + "author_inst": "Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences" + }, + { + "author_name": "Andrey O Bogorodskiy", + "author_inst": "Moscow Institute of Physics and Technology" + }, + { + "author_name": "Yuliya A Zagryadskaya", + "author_inst": "Moscow Institute of Physics and Technology" + }, + { + "author_name": "Ivan S Okhrimenko", + "author_inst": "Moscow Institute of Physics and Technology" + }, + { + "author_name": "Alexander M Sapozhnikov", + "author_inst": "Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences" + }, + { + "author_name": "Valentin I Borshchevskiy", + "author_inst": "Moscow Institute of Physics and Technology" + }, + { + "author_name": "Marina A Shevchenko", + "author_inst": "Shemyakin and OvchinnikovInstitute of Bioorganic Chemistry, Russian Academy of Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.04.11.487970", "rel_title": "Discrimination of SARS-CoV-2 Omicron sub-lineages BA.1 and BA.2 using a high-resolution melting-based assay: A pilot study", @@ -333193,33 +334485,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.04.09.487739", - "rel_title": "Disrupting ACE2 Dimerization Mitigates the Infection by SARS-COV-2", - "rel_date": "2022-04-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.09.487739", - "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic has caused over 6 million death and 460 million reported cases globally. More effective antiviral medications are needed to curb the continued spread of this disease. The infection by SARS-COV-2 virus is initiated via the interaction between the receptor binding domain (RBD) of the viral glycoprotein Spike (S protein) and the N-term peptidase domain (PD) of the angiotensin-converting enzyme 2 (ACE2) expressed on host cell membrane. ACE2 forms protein homodimer primarily through its ferredoxin-like fold domain (aka. Neck-domain). We investigated whether the dimerization of ACE2 receptor plays a role in SARS-COV-2 virus infection. We report here that the ACE2 receptor dimerization enhances the recognition of SARS-COV-2 S protein. A 43 amino acid peptide based on the N-term of Neck-domain could block the ACE2 dimerization and the interaction between RBD and ACE2, and mitigate the SARS-COV-2/host cell interaction. Our study illustrated a new route to develop potential therapeutics for the prevention and treatment of SARS-COV-2 viral infection.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jiaqi Zhu", - "author_inst": "University of Connecticut" - }, - { - "author_name": "Yue Su", - "author_inst": "University of Connecticut" - }, - { - "author_name": "Young Tang", - "author_inst": "University of Connecticut" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2022.04.11.487882", "rel_title": "Receptor binding domain of SARS-CoV-2 is a functional \u03b1v-integrin agonist", @@ -333412,6 +334677,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.04.08.22273608", + "rel_title": "Outpatient and Home Pulmonary Rehabilitation Program Post COVID-19: A study protocol for clinical trial", + "rel_date": "2022-04-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.08.22273608", + "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) is a widespread, highly contagious inflammatory process that causes respiratory, physical and psychological dysfunction. COVID-19 mainly affects the respiratory system and evolves in the acute phase from mild cases with common symptoms, such as fever, cough, and fatigue, to the moderate-to-severe form, causing massive alveolar damage resulting in dyspnea and hypoxemia that can rapidly progress to pneumonia, and acute respiratory distress syndrome. The acute form usually causes severe pulmonary sequelae such as pulmonary fibrosis or progression to organ failure, leading to worsening metabolic dysfunction and/or death.\n\nPurposeTo verify the effects of an outpatient and home pulmonary rehabilitation program (PRP) on clinical symptoms, pulmonary function, physical activity level, functional status, autonomic activity, peripheral muscle strength, static and functional balance, functional mobility, anxiety and depression, post-traumatic stress, health-related quality of life, and survival of patients with sequelae from COVID-19.\n\nMethodsThis study will be a cohort, parallel, two-arm multicentric study, to be carried out in three clinical centers, with blind evaluation, with 06 weeks of training and follow-up. This study was designed according to the recommendations of the CONSORT statement. To be involved in this clinical study, according to the inclusion criteria, women and men aged between 16 and 75 years affected by COVID-19. The proposed PRP is based on the guidelines recommended by the Global Initiative for Chronic Obstructive Lung Disease and, consists of a combination of aerobic and muscle strengthening exercises, lasting six weeks, with a frequency of three times a week.\n\nDiscussionIn patients infected with COVID-19 with persistent symptoms and sequelae, PRP mainly seeks to improve dyspnea, relieve anxiety and depression, prevent, and reduce complications and/or dysfunctions, reduce morbidity and mortality, and improve health-related quality of life.\n\nTrial registrationThis study was registered at clinicaltrials.gov (ID: COVID-19 PULMONARY REHAB NCT04982042).", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Luis V F Oliveira", + "author_inst": "Evangelical University of Goi\u00e1s - UniEVANG\u00c9LICA" + }, + { + "author_name": "Miri\u00e3 C Oliveira", + "author_inst": "Evangelical University of Goi\u00e1s - UniEVANG\u00c9LICA" + }, + { + "author_name": "Maria Eduarda M Lino", + "author_inst": "Evangelical University of Goias - UniEVAGELICA" + }, + { + "author_name": "Maril\u00facia M Carrijo", + "author_inst": "Evangelical University of Goias: UniEVANGELICA" + }, + { + "author_name": "Jo\u00e3o Pedro R Afonso", + "author_inst": "Evangelical University of Goias: UniEVANGELICA" + }, + { + "author_name": "Ricardo S Moura", + "author_inst": "Evangelical University of Goias: UniEVANGELICA" + }, + { + "author_name": "Let\u00edcia S Galv\u00e3o", + "author_inst": "Evangelical University of Goias: UniEVANGELICA" + }, + { + "author_name": "Elis\u00e2ngela R P P\u00f3voa", + "author_inst": "Evangelical University of Goias: UniEVANGELICA" + }, + { + "author_name": "Luis Filipe R J Oliveira", + "author_inst": "Evangelical University of Goias: UniEVANGELICA" + }, + { + "author_name": "Bianca M Reis", + "author_inst": "Evangelical University of Goias: UniEVANGELICA" + }, + { + "author_name": "Raphael H C O Diniz", + "author_inst": "Evangelical University of Goias: UniEVANGELICA" + }, + { + "author_name": "Rubens R Bernardes", + "author_inst": "Evangelical University of Goias: UniEVANGELICA" + }, + { + "author_name": "Jean C Coutinho", + "author_inst": "Evangelical University of Goi\u00e1s - UniEVANG\u00c9LICA" + }, + { + "author_name": "Anderson S Silva", + "author_inst": "Faculty of Medical Sciences of Santa Casa of Sao Paulo Department of Collective Health: Faculdade de Ciencias Medicas da Santa Casa de Sao Paulo Departamento de" + }, + { + "author_name": "Daniela R P Fonseca", + "author_inst": "Evangelical University of Goias: UniEVANGELICA" + }, + { + "author_name": "Adriano L Fonseca", + "author_inst": "Evangelical University of Goias: UniEVANGELICA" + }, + { + "author_name": "Dante B Santos", + "author_inst": "Evangelical University of Goias - UniEVANGELICA" + }, + { + "author_name": "Guilherme P Modesto", + "author_inst": "Evangelical University of Goi\u00e1s - UniEVANG\u00c9LICA" + }, + { + "author_name": "Vinicius Z Maldaner", + "author_inst": "Evangelical University of Goias - UniEVANGELICA" + }, + { + "author_name": "Irans\u00e9 Oliveira-Silva", + "author_inst": "Evangelical University of Goias - UniEVANG\u00c9LICA" + }, + { + "author_name": "Rodrigo A B L Martins", + "author_inst": "Evangelical University of Goi\u00e1s - UniEVANG\u00c9LICA" + }, + { + "author_name": "Patr\u00edcia S L L Martins", + "author_inst": "Evangelical University of Goi\u00e1s - UniEVANG\u00c9LICA" + }, + { + "author_name": "Claudia S Oliveira", + "author_inst": "Evangelical University of Goi\u00e1s - UniEVANG\u00c9LICA" + }, + { + "author_name": "Renata K Palma", + "author_inst": "Universidad Francisco de Vitoria" + }, + { + "author_name": "Gerson Cipriano Junior", + "author_inst": "Evangelical University of Goi\u00e1s - UniEVANG\u00c9LICA" + }, + { + "author_name": "Rodolfo P Vieira", + "author_inst": "Evangelical University of Goi\u00e1s - UniEVANG\u00c9LICA" + }, + { + "author_name": "Larissa R Alves", + "author_inst": "Evangelical University of Goias - UniEVANGELICA" + }, + { + "author_name": "Giuseppe Insalaco", + "author_inst": "National Research Council - CNR, Palermo (SI), Italy" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "rehabilitation medicine and physical therapy" + }, { "rel_doi": "10.1101/2022.04.06.22273526", "rel_title": "Psychosocial predictors of COVID-19 vaccine uptake among pregnant women: a cross-sectional study in Greece", @@ -334891,101 +336283,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.04.06.487394", - "rel_title": "Prime-pull immunization of mice with a BcfA-adjuvanted vaccine elicits mucosal immunity and prevents SARS CoV-2 infection and pathology", - "rel_date": "2022-04-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.06.487394", - "rel_abs": "Vaccines against SARS-CoV-2 that induce mucosal immunity capable of preventing infection and disease remain urgently needed. We show that intramuscular priming of mice with an alum and BcfA-adjuvanted Spike subunit vaccine, followed by a BcfA-adjuvanted mucosal booster, generated Th17 polarized tissue resident CD4+ T cells, and mucosal and serum antibodies. The serum antibodies efficiently neutralized SARS-CoV-2 and its Delta variant, suggesting cross-protection against a recent variant of concern (VOC). Immunization with this heterologous vaccine prevented weight loss following challenge with mouse-adapted SARS-CoV-2 and reduced viral replication in the nose and lungs. Histopathology showed a strong leukocyte and polymorphonuclear (PMN) cell infiltrate without epithelial damage in mice immunized with BcfA-containing vaccines. In contrast, viral load was not reduced in the upper respiratory tract of IL-17 knockout mice immunized with the same formulation, suggesting that the Th17 polarized T cell responses are critical for protection. We show that vaccines adjuvanted with alum and BcfA, delivered through a heterologous prime-pull regimen, protect against SARS-CoV-2 infection without causing enhanced respiratory disease.\n\nSIGNIFICANCEThere remains a need for SARS CoV-2 booster vaccines that generate mucosal immunity and prevent transmission. We show that systemic priming followed by a mucosal booster with a BcfA-adjuvanted subunit vaccine generates neutralizing antibodies and Th17 polarized systemic and tissue-resident immune responses that provide sterilizing immunity against wildtype SARS CoV-2, and a variant of concern. Importantly, in contrast to alum alone, the addition of BcfA prevents respiratory pathology. These results suggest that a BcfA-adjuvanted mucosal booster may elicit mucosal immunity in individuals previously immunized systemically with approved vaccines. This foundational study in mice sets the stage for testing our vaccine regimen in larger animal models as a booster vaccine.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Mohamed M. Shamseldin", - "author_inst": "Ohio State University" - }, - { - "author_name": "Ashley Zani", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Adam Kenney", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Jack Evans", - "author_inst": "Ohio State University" - }, - { - "author_name": "Cong Zeng", - "author_inst": "Ohio State University" - }, - { - "author_name": "Kaitlin A. Read", - "author_inst": "Ohio State University" - }, - { - "author_name": "Kyle Caution", - "author_inst": "Ohio State University" - }, - { - "author_name": "Jesse M. Hall", - "author_inst": "Ohio State University" - }, - { - "author_name": "Jessica M. Brown", - "author_inst": "Ohio State University" - }, - { - "author_name": "Gilian Gunsch", - "author_inst": "Ohio State University" - }, - { - "author_name": "Kara N. Corps", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Supranee Chaitwatponsakom", - "author_inst": "Ohio State University" - }, - { - "author_name": "Mahesh KC", - "author_inst": "Ohio State University" - }, - { - "author_name": "Mijia Lu", - "author_inst": "Ohio State University" - }, - { - "author_name": "Rajendar Deora", - "author_inst": "The Ohio State University College of Medicine" - }, - { - "author_name": "Jianrong Li", - "author_inst": "Ohio State University" - }, - { - "author_name": "Kenneth J. Oestreich", - "author_inst": "Ohio State University" - }, - { - "author_name": "Shan-Lu Liu", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Jacob S. Yount", - "author_inst": "Ohio State University" - }, - { - "author_name": "Purnima Dubey", - "author_inst": "The Ohio State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.04.07.487489", "rel_title": "Antibody Resistance of SARS-CoV-2 Omicron BA.1, BA.1.1, BA.2 and BA.3 Sub-lineages", @@ -335250,6 +336547,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.06.22273202", + "rel_title": "Prediction of deterioration from COVID-19 in patients in skilled nursing facilities using wearable and contact-free devices: a feasibility study", + "rel_date": "2022-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.06.22273202", + "rel_abs": "Background and RationaleApproximately 35% of all COVID-19 deaths occurred in Skilled Nursing Facilities (SNFs). In a healthy general population, wearables have shown promise in providing early alerts for actionable interventions during the pandemic. We tested this promise in a cohort of SNFs patients diagnosed with COVID-19 and admitted for post-acute care under quarantine. We tested if 1) deployment of wearables and contact-free biosensors is feasible in the setting of SNFs and 2) they can provide early and actionable insights into deterioration.\n\nMethodsThis prospective clinical trial has been IRB-approved (NCT04548895). We deployed two commercially available devices detecting continuously every 2-3 minutes heart rate (HR), respiratory rate (RR) and uniquely providing the following biometrics: 1) the wrist-worn bracelet by Biostrap yielded continuous oxygen saturation (O2Sat), 2) the under-mattress ballistocardiography sensor by Emfit tracked in-bed activity, tossing, and sleep disturbances. Patients also underwent routine monitoring by staff every 2-4 h. For death outcomes, cases are reported due to the small sample size. For palliative care versus at-home discharges, we report mean{+/-}SD at p<0.05.\n\nResultsFrom 12/2020 - 03/2021, we approached 26 PCR-confirmed SarsCoV2-positive patients at two SNFs: 5 declined, 21 were enrolled into monitoring by both sensors (female=13, male=8; age 77.2{+/-}9.1). We recorded outcomes as discharged to home (8, 38%), palliative care (9, 43%) or death (4, 19%). The O2Sat threshold of 91% alerted for intervention. Biostrap captured hypoxic events below 91% nine times as often as the routine intermittent pulse oximetry. In the patient deceased, two weeks prior we observed a wide range of O2Sat values (65-95%) captured by the Biostrap device and not noticeable with the routine vital sign spot checks. In this patient, the Emfit sensor yielded a markedly reduced RR (7/min) in contrast to 18/min from two routine spot checks performed in the same period of observation as well as compared to the seven patients discharged home over a total of 86 days of monitoring (RR 19{+/-} 4). Among the patients discharged to palliative care, a total of 76 days were monitored, HR did not differ compared to the patients discharged home (68{+/-}8 vs 70{+/-}7 bpm). However, we observed a statistically significant reduction of RR at 16{+/-}4/min as well as the variances in RR (10{+/-}6 vs 19{+/-}4/min vs16{+/-}13) and activity of palliative care patients vs. patients discharged home.\n\nConclusion/DiscussionWe demonstrate that wearables and under-mattress sensors can be integrated successfully into the SNF workflows and are well tolerated by the patients. Moreover, specific early changes of oxygen saturation fluctuations and other biometrics herald deterioration from COVID-19 two weeks in advance and evaded detection without the devices. Wearable devices and under-mattress sensors in SNFs hold significant potential for early disease detection.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sabine Von Preyss-Friedman", + "author_inst": "Avalon Healthcare" + }, + { + "author_name": "Linda Emmet", + "author_inst": "Avalon Healthcare" + }, + { + "author_name": "Dree Deckert", + "author_inst": "Avalon Healthcare" + }, + { + "author_name": "Dennis A.B. David", + "author_inst": "Health Stream Analytics" + }, + { + "author_name": "Heikki Raisanen", + "author_inst": "Emit Ltd" + }, + { + "author_name": "Kevin Longoria", + "author_inst": "Biostrap" + }, + { + "author_name": "Willem Gielen", + "author_inst": "Biostrap" + }, + { + "author_name": "Martin Gerbert Frasch", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.04.06.22273516", "rel_title": "Impact of the COVID-19 epidemic on mortality in rural coastal Kenya", @@ -336693,109 +338037,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.04.06.487325", - "rel_title": "Delta-Omicron recombinant SARS-CoV-2 in a transplant patient treated with Sotrovimab", - "rel_date": "2022-04-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.06.487325", - "rel_abs": "BackgroundThe emergence of recombinant viruses is a threat to public health. Recombination of viral variants may combine variant-specific features that together catalyze viral escape from treatment or immunity. The selective advantages of recombinant SARS-CoV-2 isolates over their parental lineages remain unknown.\n\nMethodsMulti-method amplicon and metagenomic sequencing of a clinical swab and the in vitro grown virus allowed for high-confidence detection of a novel recombinant variant. Mutational, phylogeographic, and structural analyses determined features of the recombinant genome and spike protein. Neutralization assays using infectious as well as pseudotyped viruses and point mutants thereof defined the recombinants sensitivity to a panel of monoclonal antibodies and sera from vaccinated and/or convalescent individuals.\n\nResultsA novel Delta-Omicron SARS-CoV-2 recombinant was identified in an unvaccinated, immunosuppressed kidney transplant recipient treated with monoclonal antibody Sotrovimab. The recombination breakpoint is located in the spike N-terminal domain, adjacent to the Sotrovimab quaternary binding site, and results in a 5-Delta AY.45 and a 3-Omicron BA.1 mosaic spike protein. Delta and BA.1 are sensitive to Sotrovimab neutralization, whereas the Delta-Omicron recombinant is highly resistant to Sotrovimab, both with and without the RBD resistance mutation E340D.\n\nConclusionsRecombination between circulating SARS-CoV-2 variants can functionally contribute to immune escape. It is critical to validate phenotypes of mosaic viruses and monitor immunosuppressed COVID-19 patients treated with monoclonal antibodies for the selection of recombinant and immune escape variants. (Funded by NYU, the National Institutes of Health, and others)", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Ralf Duerr", - "author_inst": "New York University - School of Medicine" - }, - { - "author_name": "Hao Zhou", - "author_inst": "Department of Microbiology, NYU Grossman School of Medicine" - }, - { - "author_name": "Takuya Tada", - "author_inst": "Department of Microbiology, NYU Grossman School of Medicine" - }, - { - "author_name": "Dacia Dimartino", - "author_inst": "NYU Langone Health" - }, - { - "author_name": "Christian Marier", - "author_inst": "NYU Langone Health" - }, - { - "author_name": "Paul Zappile", - "author_inst": "NYU Langone Health" - }, - { - "author_name": "Guiqing Wang", - "author_inst": "NYU Langone Health" - }, - { - "author_name": "Jonathan Plitnick", - "author_inst": "NY State Department of Health" - }, - { - "author_name": "Sara Griesemer", - "author_inst": "NY State Department of Health" - }, - { - "author_name": "Roxie C. Girardin", - "author_inst": "University at Albany, SUNY" - }, - { - "author_name": "Jessica Machowski", - "author_inst": "Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, Albany, NY" - }, - { - "author_name": "Sean Bialosuknia", - "author_inst": "Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, Albany, NY" - }, - { - "author_name": "Erica Lasek-Nesselquist", - "author_inst": "NY State Department of Health, Wadsworth Center" - }, - { - "author_name": "Samuel L Hong", - "author_inst": "Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium" - }, - { - "author_name": "Guy Baele", - "author_inst": "Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium" - }, - { - "author_name": "Meike Dittman", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Mila Brum Ortigoza", - "author_inst": "New York University School of Medicine" - }, - { - "author_name": "Prithiv J. Prasad", - "author_inst": "New York University School of Medicine" - }, - { - "author_name": "Kathleen McDonough", - "author_inst": "Wadsworth Center, NYSDOH" - }, - { - "author_name": "Nathaniel Landau", - "author_inst": "Department of Microbiology, NYU Grossman School of Medicine" - }, - { - "author_name": "Kirsten St. George", - "author_inst": "Wadsworth Center - NYSDOH" - }, - { - "author_name": "Adriana Heguy", - "author_inst": "New York University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.04.06.487306", "rel_title": "An Ultralong Bovine CDRH3 that Targets a Conserved, Cryptic Epitope on SARS-CoV and SARS-CoV-2", @@ -337008,6 +338249,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.04.22273330", + "rel_title": "Effectiveness of a nation-wide COVID-19 vaccination program in Mexico", + "rel_date": "2022-04-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.04.22273330", + "rel_abs": "BACKGROUNDVaccination has been effective in ameliorating the impact of COVID-19. However, estimation of vaccine effectiveness (VE) is still unavailable for some widely used vaccines and underrepresented groups. Here, we report on the effectiveness of a nation-wide COVID-19 vaccination program in Mexico.\n\nMETHODSWe used a test-negative design within a national COVID-19 surveillance system to assess VE of the BNT162b2, mRNA-12732, Gam-COVID-Vac, Ad5-nCoV, Ad26.COV2.S, ChAdOx1 and CoronaVac vaccines, against SARS-CoV-2 infection, COVID-19 related hospitalization and death for adults [≥]18 years in Mexico. VE was estimated using Cox proportional hazard models considering time-varying vaccination status in partial and fully vaccinated individuals compared to unvaccinated adults, adjusted by age, sex, comorbidities and municipality. We also estimated VE for adults [≥]60 years, for cases with diabetes and comparing periods with predominance of variants B.1.1.519 and B.1.617.2.\n\nRESULTSWe assessed 793,487 vaccinated compared to 4,792,338 unvaccinated adults between December 24th, 2020, and September 27th, 2021. VE against SARS-CoV-2 infection was highest for fully vaccinated individuals with mRNA-12732 (91.5%, 95%CI 90.3-92.4) and Ad26.COV2.S (82.2%, 95%CI 81.4-82.9), whereas for COVID-19 related hospitalization were BNT162b2 (84.3%, 95%CI 83.6-84.9) and Gam-COVID-Vac (81.4% 95%CI 79.5-83.1) and for mortality BNT162b2 (89.8%, 95%CI 89.2-90.2) and mRNA-12732 (93.5%, 95%CI 86.0-97.0). VE for all evaluated vaccines was reduced for adults [≥]60 years, people with diabetes, and in periods of Delta variant predominance.\n\nCONCLUSIONSAll evaluated vaccines were effective against SARS-CoV-2 infection and COVID-19 related hospitalization and death. Mass vaccination campaigns with multiple vaccine products are feasible and effective to maximize vaccination coverage.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Omar Yaxmehen Bello-Chavolla", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Neftali Eduardo Antonio-Villa", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Sergio I. Vald\u00e9s-Ferrer", + "author_inst": "Instituto Nacional De Ciencias Medicas y Nutricion" + }, + { + "author_name": "Carlos A. Ferm\u00edn-Mart\u00ednez", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Luisa Fernandez-Chirino", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Daniel Ram\u00edrez-Garc\u00eda", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Javier Mancilla-Galindo", + "author_inst": "Facultad de Medicina, Universidad Nacional Autonoma de Mexico" + }, + { + "author_name": "Ashuin Kammar-Garc\u00eda", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Jos\u00e9 Alberto \u00c1vila-Funes", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Clemente Humberto Z\u00fa\u00f1iga-Gil", + "author_inst": "Hospital General de Tijuana" + }, + { + "author_name": "Miguel Garc\u00eda-Grimshaw", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Santa Elizabeth Ceballos-Liceaga", + "author_inst": "Direccion General de Epidemiologia, Secretaria de Salud" + }, + { + "author_name": "Guillermo Carbajal-Sandoval", + "author_inst": "Direccion General de Epidemiologia, SecretarIa de Salud." + }, + { + "author_name": "Jos\u00e9 Antonio Montes-Gonz\u00e1lez", + "author_inst": "Direccion General de Epidemiologia, SecretarIa de Salud." + }, + { + "author_name": "Christian Arturo Zaragoza-Jim\u00e9nez", + "author_inst": "Direccion General de Epidemiologia, SecretarIa de Salud." + }, + { + "author_name": "Gabriel Garc\u00eda-Rodr\u00edguez", + "author_inst": "Direccion General de Epidemiologia, SecretarIa de Salud." + }, + { + "author_name": "Ricardo Cort\u00e9s-Alcal\u00e1", + "author_inst": "Direccion General de Epidemiologia, SecretarIa de Salud." + }, + { + "author_name": "Gustavo Reyes-Ter\u00e1n", + "author_inst": "Comision Coordinadora de Institutos Nacionales de Salud y Hospitales de Alta Especialidad." + }, + { + "author_name": "Hugo L\u00f3pez-Gatell", + "author_inst": "Subsecretaria de Prevencion y Promocion de la Salud, Secretaria de Salud." + }, + { + "author_name": "Luis Miguel Gutierrez-Robledo", + "author_inst": "Instituto Nacional de Geriatria" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.03.29.22271489", "rel_title": "Linking private health sector to public COVID-19 response in Kisumu, Kenya: Lessons Learnt", @@ -338439,73 +339775,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.03.30.22273194", - "rel_title": "Safety and Efficacy of Dupilumab for the Treatment of Hospitalized Patients with Moderate to Severe COVID 19: A Phase IIa Trial", - "rel_date": "2022-04-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.30.22273194", - "rel_abs": "BackgroundA profound need remains to develop further therapeutics for treatment of those hospitalized with COVID-19. Based on data implicating the type 2 cytokine interleukin (IL)-13 as a significant factor leading to critical COVID-19, this trial was designed to assess dupilumab, a monoclonal antibody that blocks IL-13 and IL-4 signaling, for treatment of inpatients with COVID-19.\n\nMethodsWe conducted a phase IIa randomized double-blind placebo-controlled trial to assess the safety and efficacy of dupilumab plus standard of care versus placebo plus standard of care in mitigating respiratory failure and death in those hospitalized with COVID-19. Subjects were followed prospectively for 60 days. The primary endpoint was the proportion of patients alive and free of invasive mechanical ventilation at 28 days.\n\nFindingsForty eligible subjects were enrolled from June to November of 2021. There was no difference in adverse events nor in ventilator free survival at day 28 between study arms. However, for the secondary endpoint of mortality at day 60, subjects randomized to dupilumab had a higher survival rate compared to the placebo group (89.5% vs 76.2%, adjusted HR 0.05, 95% CI: 0.0-0.72, p=0.03). There were fewer subjects admitted to the ICU in the dupilumab group compared to placebo (33.3% vs 66.7%; adjusted HR 0.44, 95% CI: 0.09-2.09, p=0.30). Lastly, we saw downstream evidence of IL-4 and IL-13 signaling blockade in the dupilumab group through analysis of immune biomarkers over time.\n\nInterpretationDupilumab was well tolerated and improved 60-day survival in patients hospitalized with moderate to severe COVID-19.\n\nTrial RegistrationThis trial is registered with ClinicalTrials.gov, NCT04920916.\n\nFundingVirginia Biosciences Health Research Corporation, PBM C19, Henske Family Foundation, National Institutes of Health, National Cancer Institute", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Jennifer Sasson", - "author_inst": "University of Virginia" - }, - { - "author_name": "Alexandra N Donlan", - "author_inst": "University of Virginia" - }, - { - "author_name": "Jennie Z Ma", - "author_inst": "University of Virginia" - }, - { - "author_name": "Heather Haughey", - "author_inst": "University of Virginia" - }, - { - "author_name": "Rachael Coleman", - "author_inst": "University of Virginia" - }, - { - "author_name": "Uma Nayak", - "author_inst": "University of Virginia" - }, - { - "author_name": "Amy J. Mathers", - "author_inst": "University of Virginia" - }, - { - "author_name": "Sylvain Laverdure", - "author_inst": "Frederick National Laboratory" - }, - { - "author_name": "Robin Dewar", - "author_inst": "Frederick National Laboratory" - }, - { - "author_name": "Patrick E. H. Jackson", - "author_inst": "University of Virginia" - }, - { - "author_name": "Scott K. Heysell", - "author_inst": "University of Virginia" - }, - { - "author_name": "Jeffrey M. Sturek", - "author_inst": "University of Virginia" - }, - { - "author_name": "William Petri", - "author_inst": "University of Virginia" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.03.22272610", "rel_title": "Cardiac impairment in Long Covid 1-year post-SARS-CoV-2 infection", @@ -338714,6 +339983,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.04.22273385", + "rel_title": "Significant impacts of the COVID-19 pandemic on race/ethnic differences in USA mortality", + "rel_date": "2022-04-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.04.22273385", + "rel_abs": "The COVID-19 pandemic triggered declines in life expectancy at birth around the world. The United States of America (USA) was hit particularly hard among high income countries. Early data from the USA showed that these losses varied greatly by race/ethnicity in 2020, with Hispanic and Black Americans suffering much larger losses in life expectancy compared to white people. We add to this research by examining trends in lifespan inequality, average years of life lost, and the contribution of specific causes of death and ages to race/ethnic life expectancy disparities in the USA from 2010 to 2020. We find that life expectancy in 2020 fell more for Hispanic and Black males (4.5 years and 3.6 years, respectively) compared to white males (1.5 years). These drops nearly eliminated the previous life expectancy advantage for the Hispanic compared to white population, while dramatically increasing the already large gap in life expectancy between Black and white people. While the drops in life expectancy for the Hispanic population were largely attributable to official COVID-19 deaths, Black Americans additionally saw increases in cardiovascular disease and \"deaths of despair\" over this period. In 2020, lifespan inequality increased slightly for Hispanic and white populations, but decreased for Black people, reflecting the younger age pattern of COVID-19 deaths for Hispanic people. Overall, the mortality burden of the COVID-19 pandemic hit race/ethnic minorities particularly hard in the USA, underscoring the importance of the social determinants of health during a public health crisis.\n\nSignificance statementPublic interest in social and health inequalities is increasing. We examine the impact of COVID-19 on mortality in the USA across racial/ethnic groups and present four key findings. First, all groups suffered sizable life-expectancy losses and increases in years of life lost. Mortality from cardiovascular diseases, \"deaths of despair\", and COVID-19 explained most of these losses. Second, working-age mortality accounted for substantial life-expectancy losses, especially among Hispanic males. Third, lifespan inequality increased for Hispanic and white people, but decreased slightly for Black people. Fourth, the pandemic shifted racial/ethnic mortality differentials in favor of white people: narrowing the Hispanic advantage and widening the Black disadvantage. Our results provide a comprehensive assessment of mortality trends to inform policies targeting inequalities.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jose Manuel Aburto", + "author_inst": "University of Oxford" + }, + { + "author_name": "Andrea M Tilstra", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ginevra Floridi", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jennifer Beam Dowd", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.04.04.22273372", "rel_title": "The trustworthiness and impact of trial preprints for COVID-19 decision-making: A methodological study", @@ -340461,57 +341761,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.30.22273203", - "rel_title": "COVID-19 vaccination coverage by company size and the effects of socioeconomic factors and workplace vaccination in Japan: a cohort study", - "rel_date": "2022-04-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.30.22273203", - "rel_abs": "BackgroundVaccination is considered the most effective control measure against COVID-19. Vaccine hesitancy and equitable vaccine allocation are important challenges to disseminating developed vaccines. To promote COVID-19 vaccination coverage, the government of Japan established the workplace vaccination program. However, while it appears that the program was effective in overcoming vaccine hesitancy, the program may have hindered the equitable allocation of vaccines because it mainly focused on employees of large companies. We investigated the relationship between company size and COVID-19 vaccination completion status of employees and the impact of the workplace vaccination program on this relationship.\n\nMethodsWe conducted an internet-based prospective cohort study from December 2020 (baseline) to December 2021. The data were collected using a self-administered questionnaire survey. Briefly, 27,036 workers completed the questionnaire at baseline and 18,560 at follow-up. After excluding ineligible respondents, we finally analyzed the data from 15,829 participants. At baseline, the participants were asked about the size of the company they worked for, and at follow-up they were asked about the month in which they received their second COVID-19 vaccine dose and the availability of a company-arranged vaccination opportunity.\n\nResultsIn each month throughout the observation period, the odds of having received a second COVID-19 vaccine dose were significantly lower for small-company employees than for large-company employees in the sex- and age-adjusted model. This difference decreased after adjusting for socioeconomic factors, and there was no significant difference after adjusting for the availability of a company-arranged vaccination opportunity.\n\nConclusionsThe workplace vaccination program implemented in Japan to control the COVID-19 pandemic may have been effective in overcoming vaccine hesitancy in workers; however, it may have caused an inequitable allocation of vaccines between companies of different sizes. Because people who worked for small companies were less likely to be vaccinated, it will be necessary to enhance support of vaccination for this population in the event of future infectious disease outbreaks.\n\nTrial registrationNot applicable.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Koji Mori", - "author_inst": "InstitUniversity of Occupational and Environmental Health, Japan," - }, - { - "author_name": "Takahiro Mori", - "author_inst": "Department of Occupational Health Practice and Management, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Jap" - }, - { - "author_name": "Tomohisa Nagata", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Hajime Ando", - "author_inst": "Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health" - }, - { - "author_name": "Ayako Hino", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Seiichiro Tateishi", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Mayumi Tsuji", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Keiji Muramatsu", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Yoshihisa Fujino", - "author_inst": "University of Occupational and Environmental Health, Japan" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.27.22271628", "rel_title": "Spatial prediction of COVID-19 pandemic dynamics in the United States", @@ -340816,6 +342065,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.29.22272714", + "rel_title": "Immunogenicity of Pfizer-BioNTech COVID-19 mRNA Primary Vaccination Series in Recovered Individuals Depends on Symptoms at Initial Infection.", + "rel_date": "2022-04-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.29.22272714", + "rel_abs": "ImportancePublic health vaccination recommendations for COVID-19 primary series and boosters in previously infected individuals differ worldwide. As infection with SARS-CoV-2 is often asymptomatic, it remains to be determined if vaccine immunogenicity is comparable in all previously infected subjects. We present detailed immunological evidence to clarify the requirements for one-or two-dose primary vaccination series for naturally primed individuals.\n\nObjectiveEvaluate the immune response to COVID-19 mRNA vaccines in healthcare workers (HCWs) who recovered from a SARS-CoV-2 infection.\n\nDesignMulticentric observational prospective cohort study of HCWs with a PCR-confirmed SARS-CoV-2 infection designed to evaluate the dynamics of T and B cells immune responses to primary infection and COVID-19 mRNA vaccination over 12 months.\n\nParticipantsUnvaccinated HCWs with PCR-confirmed SARS-CoV-2 infection were selected based on the presence or absence of symptoms at infection and serostatus at enrollment. Age- and sex-matched adults not infected with SARS-CoV-2 prior to vaccination were included as naive controls.\n\nExposureVaccination with Pfizer BioNTech BNT162b2 mRNA vaccine.\n\nMain Outcome(s) and Measure(s)Immunity score (zero to three), before and after vaccination, based on anti-RBD IgG ratio, serum capacity to neutralize live virus and IFN-{gamma} secretion capacity in response to SARS-CoV-2 peptide pools above the positivity threshold for each of the three assays. We compared the immunity score between groups based on subjects symptoms at diagnosis and/or serostatus prior to vaccination.\n\nResultsNone of the naive participants (n=14) showed a maximal immunity score of three following one dose of vaccine compared to 84% of the previously infected participants (n=55). All recovered individuals who did not have an immunity score of three were seronegative prior to vaccination, and 67% had not reported symptoms resulting from their initial infection. Following one dose of vaccine, their immune responses were comparable to naive individuals, with significantly weaker responses than those who were symptomatic during infection.\n\nConclusions and RelevanceIndividuals who did not develop symptoms during their initial SARS-CoV-2 infection and were seronegative prior to vaccination present immune responses comparable to that of naive individuals. These findings highlight the importance of administering the complete two-dose primary regimen and following boosters of mRNA vaccines to individuals who experienced asymptomatic SARS-CoV-2 infection.\n\nKEY POINTS\n\nQuestionIs a single dose of COVID-19 mRNA vaccine sufficient to induce robust immune responses in individuals with prior SARS-CoV-2 infection?\n\nFindingsIn this cohort of 55 health care workers previously infected with SARS-CoV-2, we show that the absence of symptoms during initial infection and negative serostatus prior to vaccination predict the strength of immune responses to COVID-19 mRNA vaccine. Lack of symptoms and a negative serostatus prior to vaccination leads to immune responses comparable to naive individuals.\n\nMeaningOur results support a two-dose primary series requirement for any individual with prior history of asymptomatic SARS-CoV-2 infection.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Sabryna Nantel", + "author_inst": "Sainte-Justine University Hospital and Research Center" + }, + { + "author_name": "Benoite Bourdin", + "author_inst": "Sainte-Justine University Hospital and Research Center" + }, + { + "author_name": "Kelsey Adams", + "author_inst": "Sainte-Justine University Hospital and Research Center" + }, + { + "author_name": "Julie Carbonneau", + "author_inst": "Infectious Disease Research Center" + }, + { + "author_name": "Henintsoa Rabezanaha", + "author_inst": "Infectious Disease Research Center" + }, + { + "author_name": "Marie-Eve Hamelin", + "author_inst": "Infectious Disease Research Center" + }, + { + "author_name": "Deirdre McCormack", + "author_inst": "Sainte-Justine University Hospital and Research Center" + }, + { + "author_name": "Patrice Savard", + "author_inst": "Montreal University Hospital and Research Center" + }, + { + "author_name": "Yves Longtin", + "author_inst": "Jewish General Hospital" + }, + { + "author_name": "Matthew Cheng", + "author_inst": "McGill University Health Center" + }, + { + "author_name": "Gaston DeSerres", + "author_inst": "Laval University Research Center" + }, + { + "author_name": "Jacques Corbeil", + "author_inst": "Laval University Research Center" + }, + { + "author_name": "Vladimir Gilca", + "author_inst": "Laval University Research Center" + }, + { + "author_name": "Mariana Baz", + "author_inst": "Infectious Disease Research Center" + }, + { + "author_name": "Guy Boivin", + "author_inst": "Infectious Disease Research Center" + }, + { + "author_name": "Caroline Quach", + "author_inst": "Sainte-Justine University Hospital and Research Center" + }, + { + "author_name": "Helene Decaluwe", + "author_inst": "Sainte-Justine University Hospital and Research Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.30.22273190", "rel_title": "Lessons from a pandemic", @@ -342239,93 +343571,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2022.04.01.486695", - "rel_title": "Omicron breakthrough infection drives cross-variant neutralization and memory B cell formation", - "rel_date": "2022-04-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.01.486695", - "rel_abs": "Omicron is the evolutionarily most distinct SARS-CoV-2 variant (VOC) to date and displays multiple amino acid alterations located in neutralizing antibody sites of the spike (S) protein. We report here that Omicron breakthrough infection in BNT162b2 vaccinated individuals results in strong neutralizing activity not only against Omicron, but also broadly against previous SARS-CoV-2 VOCs and against SARS-CoV-1. We found that Omicron breakthrough infection mediates a robust B cell recall response, and primarily expands preformed memory B cells that recognize epitopes shared broadly by different variants, rather than inducing new B cells against strictly Omicron-specific epitopes. Our data suggest that, despite imprinting of the immune response by previous vaccination, the preformed B cell memory pool has sufficient plasticity for being refocused and quantitatively remodeled by exposure to heterologous S protein, thus allowing effective neutralization of variants that evade a previously established neutralizing antibody response.\n\nOne Sentence SummaryBreakthrough infection in individuals double- and triple-vaccinated with BNT162b2 drives cross-variant neutralization and memory B cell formation.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Jasmin Quandt", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Alexander Muik", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Nadine Salisch", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Bonny Gaby Lui", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Sebastian Lutz", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Kimberly Krueger", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Ann-Kathrin Wallisch", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Petra Adams-Quack", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Maren Bacher", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Andrew Finlayson", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Orkun Ozhelvaci", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Isabel Vogler", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Katharina Grikscheit", - "author_inst": "Goethe University Frankfurt" - }, - { - "author_name": "Sebastian Hoehl", - "author_inst": "Goethe University Frankfurt" - }, - { - "author_name": "Udo Goetsch", - "author_inst": "Health Protection Authority, City of Frankfurt" - }, - { - "author_name": "Sandra Ciesek", - "author_inst": "Goethe Universtiy Frankfurt" - }, - { - "author_name": "Oezlem Tuereci", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Ugur Sahin", - "author_inst": "BioNTech SE" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.03.30.486345", "rel_title": "Ancestral origins are associated with SARS-CoV-2 susceptibility and protection in a Florida patient population", @@ -342514,6 +343759,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.03.30.486461", + "rel_title": "Methylene blue, Mycophenolic acid, Posaconazole, and Niclosamide inhibit SARS-CoV-2Omicron variant BA.1 infection of human airway epithelial explant cultures", + "rel_date": "2022-03-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.30.486461", + "rel_abs": "Sublineages of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) Omicron variants continue to amass mutations in the spike (S) glycoprotein, which leads to immune evasion and rapid spread of the virus across the human population. Here we demonstrate the susceptibility of the Omicron variant BA.1 (B.1.1.529.1) to four repurposable drugs, Methylene blue (MB), Mycophenolic acid (MPA), Posaconazole (POS), and Niclosamide (Niclo) in post-exposure treatments of primary human airway cell cultures. MB, MPA, POS, and Niclo are known to block infection of human nasal and bronchial airway epithelial explant cultures (HAEEC) with the Wuhan strain, and four variants of concern (VoC), Alpha (B.1.1.7), Beta (B.1.351), Gamma (B.1.1.28), Delta (B.1.617.2) (1, 2). Our results not only show broad anti-coronavirus effects of MB, MPA, POS and Niclo, but also demonstrate that the Omicron variant BA.1 (B.1.1.529.1) sheds infectious virus from HAEEC over at least 15 days, and maintains both intracellular and extracellular viral genomic RNA without overt toxicity, suggesting viral persistence. The data underscore the broad effects of MB, MPA, POS, and Niclo against SARS-CoV-2 and the currently circulating VoC, and reinforce the concept of repurposing drugs in clinical trials against COVID-19.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Romain Volle", + "author_inst": "University of Zurich" + }, + { + "author_name": "Luca Murer", + "author_inst": "University of Zurich" + }, + { + "author_name": "Anthony Petkidis", + "author_inst": "University of Zurich" + }, + { + "author_name": "Vardan Andriasyan", + "author_inst": "University of Zurich" + }, + { + "author_name": "Alessandro Savi", + "author_inst": "University of Zurich" + }, + { + "author_name": "Cornelia Bircher", + "author_inst": "University of Zurich" + }, + { + "author_name": "Nicole Meili", + "author_inst": "University of Zurich" + }, + { + "author_name": "Lucy Fisher", + "author_inst": "University of Zurich" + }, + { + "author_name": "Daniela Policarpo Sequeira", + "author_inst": "University of Zurich" + }, + { + "author_name": "Daniela Katharina Mark", + "author_inst": "University of Zurich" + }, + { + "author_name": "Alfonso Gomez Gonzalez", + "author_inst": "University of Zurich" + }, + { + "author_name": "Urs F Greber", + "author_inst": "University of Zurich" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.03.30.486313", "rel_title": "Identification of C270 as a novel site for allosteric modulators of SARS-CoV-2 papain-like protease", @@ -344329,29 +345637,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.03.30.22273165", - "rel_title": "Effect of COVID-19 vaccination on menstrual periods in a prospectively recruited cohort", - "rel_date": "2022-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.30.22273165", - "rel_abs": "COVID-19 vaccination protects against the potentially serious consequences of SARS-CoV2 infection, but some people have been hesitant to receive the vaccine because of reports that it could affect menstrual bleeding. To determine whether this occurs, we prospectively recruited a cohort of 79 individuals, each of whom recorded details of at least three consecutive menstrual cycles, during which time they each received at least one dose of COVID-19 vaccine. We find that either dose of the COVID-19 vaccine is associated with a delay to the subsequent period in spontaneously cycling participants (2.3 days after dose 1; 1.3 days after dose 2) but this change rapidly reverses. No change to timing was detected in those on hormonal contraception. We detected no change in menstrual flow associated with either dose of the vaccine, in either spontaneously cycling participants or those on hormonal contraception. We detected no association between menstrual changes and other commonly-reported side effects of vaccination, such as sore arm, fever and fatigue.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ee Von Woon", - "author_inst": "Imperial College London" - }, - { - "author_name": "Victoria Male", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "sexual and reproductive health" - }, { "rel_doi": "10.1101/2022.03.29.486331", "rel_title": "Genetic surveillance of SARS-CoV-2 Mpro reveals high sequence and structural conservation prior to the introduction of protease inhibitor Paxlovid", @@ -344576,6 +345861,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.27.22273000", + "rel_title": "Nationwide Effectiveness of First and Second SARS-CoV2 Booster Vaccines during the Delta and Omicron Pandemic Waves in Hungary (HUN-VE 2 Study)", + "rel_date": "2022-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.27.22273000", + "rel_abs": "BackgroundIn Hungary, the pandemic waves in late 2021 and early 2022 were dominated by the Delta and Omicron SARS-CoV-2 variants, respectively. Booster vaccines were offered with one or two doses for the vulnerable population during these periods.\n\nMethods and FindingsThe nationwide HUN-VE 2 study examined the effectiveness of primary immunization, single booster, and double booster vaccination in the prevention of Covid-19 related mortality during the Delta and Omicron waves, compared to an unvaccinated control population without prior SARS-CoV-2 infection during the same study periods.\n\nThe risk of Covid-19 related death was 55% lower during the Omicron vs. Delta wave in the whole study population (n=9,569,648 and n=9,581,927, respectively; rate ratio [RR]: 0.45, 95% confidence interval [CI]: 0.44-0.48). During the Delta wave, the risk of Covid-19 related death was 74% lower in the primary immunized population (RR: 0.26; 95% CI: 0.25-0.28) and 96% lower in the booster immunized population (RR: 0.04; 95% CI: 0.04-0.05), vs. the unvaccinated control group. During the Omicron wave, the risk of Covid-19 related death was 40% lower in the primary immunized population (RR: 0.60; 95% CI: 0.55-0.65) and 82% lower in the booster immunized population (RR: 0.18; 95% CI: 0.16-0.2) vs. the unvaccinated control group. The double booster immunized population had a 93% lower risk of Covid-19 related death compared to those with only one booster dose (RR: 0.07; 95% CI. 0.01-0.46). The benefit of the second booster was slightly more pronounced in older age groups.\n\nConclusionsThe HUN-VE 2 study demonstrated the significantly lower risk of Covid-19 related mortality associated with the Omicron vs. Delta variant and confirmed the benefit of single and double booster vaccination against Covid-19 related death. Furthermore, the results showed the additional benefit of a second booster dose in terms of SARS-CoV-2 infection and Covid-19 related mortality.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Zoltan Kiss", + "author_inst": "Second Department of Medicine and Nephrology-Diabetes Center, University of Pecs Medical School, Pecs, Hungary" + }, + { + "author_name": "Istvan Wittmann", + "author_inst": "Second Department of Medicine and Nephrology-Diabetes Center, University of Pecs Medical School, Pecs, Hungary" + }, + { + "author_name": "Lorinc Polivka", + "author_inst": "Department of Pulmonology, Semmelweis University, Budapest, Hungary" + }, + { + "author_name": "Gyorgy Surjan", + "author_inst": "Ministry of Human Resources, Budapest, Hungary" + }, + { + "author_name": "Orsolya Surjan", + "author_inst": "Department of Deputy Chief Medical Officer II., National Public Health Center, Budapest, Hungary" + }, + { + "author_name": "Zsofia Barcza", + "author_inst": "Syntesia Medical Communications Ltd., Budapest, Hungary" + }, + { + "author_name": "Gergo Attila Molnar", + "author_inst": "Second Department of Medicine and Nephrology-Diabetes Center, University of Pecs Medical School, Pecs, Hungary" + }, + { + "author_name": "David Nagy", + "author_inst": "Department of Pulmonology, Semmelweis University, Budapest, Hungary" + }, + { + "author_name": "Veronika Muller", + "author_inst": "Department of Pulmonology, Semmelweis University, Budapest, Hungary" + }, + { + "author_name": "Krisztina Bogos", + "author_inst": "Department of Pulmonology, National Koranyi Institute of Pulmonology, Budapest, Hungary" + }, + { + "author_name": "Peter Nagy", + "author_inst": "National Institute of Oncology, Budapest, Hungary" + }, + { + "author_name": "Istvan Kenessey", + "author_inst": "National Institute of Oncology, Budapest, Hungary and Cancer Surveillance Branch, International Agency for Research on Cancer, Lyon, France" + }, + { + "author_name": "Andras Weber", + "author_inst": "National Institute of Oncology, Budapest, Hungary; and Cancer Surveillance Branch, International Agency for Research on Cancer, Lyon, France" + }, + { + "author_name": "Mihaly Palosi", + "author_inst": "National Health Insurance Fund, Budapest, Hungary" + }, + { + "author_name": "Janos Szlavik", + "author_inst": "South-Pest Hospital Centre - National Institute for Infectology and Haematology, Budapest, Hungary" + }, + { + "author_name": "Zsuzsa Schaff", + "author_inst": "2nd Department of Pathology, Semmelweis University, Budapest, Hungary" + }, + { + "author_name": "Zoltan Szekanecz", + "author_inst": "Department of Rheumatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary" + }, + { + "author_name": "Cecilia Muller", + "author_inst": "Department of Chief Medical Officer, National Public Health Center, Budapest, Hungary" + }, + { + "author_name": "Miklos Kasler", + "author_inst": "Ministry of Human Resources, Budapest, Hungary" + }, + { + "author_name": "Zoltan Voko", + "author_inst": "Center for Health Technology Assessment, Semmelweis University; and Syreon Research Institute, Budapest, Hungary" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.30.22273175", "rel_title": "SARS-CoV-2 Omicron neutralization and risk of infection among elderly after a booster dose of Pfizer vaccine", @@ -347035,85 +348415,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2022.03.26.485903", - "rel_title": "The interplay between lncRNAs, RNA-binding proteins and viral genome during SARS-CoV-2 infection reveals strong connections with regulatory events involved in RNA metabolism and immune response.", - "rel_date": "2022-03-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.26.485903", - "rel_abs": "Viral infections are complex processes based on an intricate network of molecular interactions. The infectious agent hijacks components of the cellular machinery for its profit, circumventing the natural defense mechanisms triggered by the infected cell. The successful completion of the replicative viral cycle within a cell depends on the function of viral components versus the cellular defenses. Non-coding RNAs (ncRNAs) are important cellular modulators, either promoting or preventing the progression of viral infections. Among these ncRNAs, the long non-coding RNA (lncRNA) family is especially relevant due to their intrinsic functional properties and ubiquitous biological roles. Specific lncRNAs have been recently characterized as modulators of the cellular response during infection of human host cells by single stranded RNA viruses. However, the role of host lncRNAs in the infection by human RNA coronaviruses such as SARS-CoV-2 remains uncharacterized. In the present work, we have performed a transcriptomic study of a cohort of patients with different SARS-CoV-2 viral load. Our results revealed the existence of a SARS-CoV-2 infection-dependent pattern of transcriptional up-regulation in which specific lncRNAs are an integral component. To determine the role of these lncRNAs, we performed a functional correlation analysis complemented with the study of the validated interactions between lncRNAs and RNA-binding proteins (RBPs). This combination of in silico functional association studies and experimental evidence allowed us to identify a lncRNA signature composed of six elements - NRIR, BISPR, MIR155HG, FMR1-IT1, USP30-AS1, and U62317.2 - associated with the regulation of SARS-CoV-2 infection. We propose a competition mechanism between the viral RNA genome and the regulatory lncRNAs in the sequestering of specific RBPs that modulates the interferon response and the regulation of RNA surveillance by nonsense-mediated decay (NMD).\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC=\"FIGDIR/small/485903v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (46K):\norg.highwire.dtl.DTLVardef@4368c9org.highwire.dtl.DTLVardef@1948201org.highwire.dtl.DTLVardef@e31fd9org.highwire.dtl.DTLVardef@1400805_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical abstractModel of interactions among lncRNA and cognate RNA-binding proteins in SARS-CoV-2 infection. According to our model, the viral genome can establish direct interactions with three core proteins (DDX3X, UPF1 and IGF2BP2) involved in mRNA metabolism and regulation of the interferon response, which are also components of a SARS-CoV-2 lncRNA-centered regulatory network. The competition between viral RNA and lncRNAs could act as a counteracting factor for the normal function of homeostatic lncRNA-centered regulatory networks, contributing to viral progression and replication. Black arrows depict physical interactions between network components; red arrows represent functional relationships.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Francisco J. Enguita", - "author_inst": "Instituto de Medicina Molecular Joao Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal." - }, - { - "author_name": "Ana Lucia Leitao", - "author_inst": "MEtRICs, Department of Sciences and Technology of Biomass, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Port" - }, - { - "author_name": "J Tyson McDonald", - "author_inst": "Department of Radiation Medicine, Georgetown University School of Medicine, Washington, DC 20007, USA." - }, - { - "author_name": "Viktorija Zaksas", - "author_inst": "Center for Translational Data Science, Biological Sciences Division, The University of Chicago, Chicago, IL 60615, USA." - }, - { - "author_name": "Saswati Das", - "author_inst": "Department of Biochemistry, Atal Bihari Vajpayee Institute of Medical Sciences & Dr Ram Manohar Lohia Hospital, New Delhi-110001, India" - }, - { - "author_name": "Diego Galeano", - "author_inst": "Facultad de Ingenieria, Universidad Nacional de Asuncion, San Lorenzo, Central, Paraguay" - }, - { - "author_name": "Deanne Taylor", - "author_inst": "Department of Biomedical and Health Informatics, The Children Hospital of Philadelphia, Philadelphia, PA 19104, USA" - }, - { - "author_name": "Eve Syrkin Wurtele", - "author_inst": "Bioinformatics and Computational Biology Program, Center for Metabolic Biology, Department of Genetics, Development and Cell Biology, Iowa State University, Ame" - }, - { - "author_name": "Amanda Saravia-Butler", - "author_inst": "Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA" - }, - { - "author_name": "Stephen B. Baylin", - "author_inst": "Johns Hopkins School of Medicine, Baltimore, MD 21287, USA" - }, - { - "author_name": "Robert Meller", - "author_inst": "Neuroscience Institute, Department of Neurobiology/ Department of Pharmacology and Toxicology, Morehouse School of Medicine, Atlanta, GA 30310, USA." - }, - { - "author_name": "D. Marshall Porterfield", - "author_inst": "Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA" - }, - { - "author_name": "Douglas C. Wallace", - "author_inst": "Center for Mitochondrial and Epigenomic Medicine, Children Hospital of Philadelphia, Philadelphia, PA 19104, USA" - }, - { - "author_name": "Jonathan C. Schisler", - "author_inst": "McAllister Heart Institute, Department of Pharmacology, and Department of Pathology and Lab Medicine, The University of North Carolina at Chapel Hill, NC 27599," - }, - { - "author_name": "Christopher E. Mason", - "author_inst": "Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Afshin Beheshti", - "author_inst": "KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.03.25.485832", "rel_title": "A SARS-CoV-2 Spike Ferritin Nanoparticle Vaccine is Protective and Promotes a Strong Immunological Response in the Cynomolgus Macaque Coronavirus Disease 2019 (COVID-19) Model", @@ -347442,6 +348743,109 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.03.26.485922", + "rel_title": "Unique molecular signatures sustained in circulating monocytes and regulatory T cells in Convalescent COVID-19 patients", + "rel_date": "2022-03-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.26.485922", + "rel_abs": "Over two years into the COVID-19 pandemic, the human immune response to SARS-CoV-2 during the active disease phase has been extensively studied. However, the long-term impact after recovery, which is critical to advance our understanding SARS-CoV-2 and COVID-19-associated long-term complications, remains largely unknown. Herein, we characterized multi-omic single-cell profiles of circulating immune cells in the peripheral blood of 100 patients, including covenlesent COVID-19 and sero-negative controls. The reduced frequencies of both short-lived monocytes and long-lived regulatory T (Treg) cells are significantly associated with the patients recovered from severe COVID-19. Consistently, sc-RNA seq analysis reveals seven heterogeneous clusters of monocytes (M0-M6) and ten Treg clusters (T0-T9) featuring distinct molecular signatures and associated with COVID-19 severity. Asymptomatic patients contain the most abundant clusters of monocyte and Treg expressing high CD74 or IFN-responsive genes. In contrast, the patients recovered from a severe disease have shown two dominant inflammatory monocyte clusters with S100 family genes: S100A8 & A9 with high HLA-I whereas S100A4 & A6 with high HLA-II genes, a specific non-classical monocyte cluster with distinct IFITM family genes, and a unique TGF-{beta} high Treg Cluster. The outpatients and seronegative controls share most of the monocyte and Treg clusters patterns with high expression of HLA genes. Surprisingly, while presumably short-ived monocytes appear to have sustained alterations over 4 months, the decreased frequencies of long-lived Tregs (high HLA-DRA and S100A6) in the outpatients restore over the tested convalescent time (>= 4 months). Collectively, our study identifies sustained and dynamically altered monocytes and Treg clusters with distinct molecular signatures after recovery, associated with COVID-19 severity.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Andrew D. Hoffmann", + "author_inst": "Northwestern University" + }, + { + "author_name": "Sam Weinberg", + "author_inst": "Northwestern University" + }, + { + "author_name": "Suchitra Swaminathan", + "author_inst": "Northwestern University" + }, + { + "author_name": "Shuvam Chaudhuri", + "author_inst": "Northwestern University" + }, + { + "author_name": "Hannah Mubarak", + "author_inst": "Northwestern University" + }, + { + "author_name": "Matthew Schipma", + "author_inst": "Northwestern University" + }, + { + "author_name": "Chengsheng Mao", + "author_inst": "Northwestern University" + }, + { + "author_name": "Xinkun Wang", + "author_inst": "Northwestern University" + }, + { + "author_name": "Lamiaa El-Shennawy", + "author_inst": "Northwestern University" + }, + { + "author_name": "Nurmaa Dashzeveg", + "author_inst": "Northwestern University" + }, + { + "author_name": "Juncheng Wei", + "author_inst": "Northwestern University" + }, + { + "author_name": "Paul Mehl", + "author_inst": "Northwestern University" + }, + { + "author_name": "Laura Shihadah", + "author_inst": "Northwestern University" + }, + { + "author_name": "Ching Man Wai", + "author_inst": "Northwestern University" + }, + { + "author_name": "Carolina Ostiguin", + "author_inst": "Northwestern University" + }, + { + "author_name": "Yuzhi Jia", + "author_inst": "Northwestern University" + }, + { + "author_name": "Neale Wang", + "author_inst": "Northwestern University" + }, + { + "author_name": "Yuan Luo", + "author_inst": "Northwestern University" + }, + { + "author_name": "Alexis Demonbreun", + "author_inst": "Northwestern University" + }, + { + "author_name": "Michael Ison", + "author_inst": "Northwestern University" + }, + { + "author_name": "Huiping Liu", + "author_inst": "Northwestern University" + }, + { + "author_name": "Deyu Fang", + "author_inst": "Northwestern university" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.03.25.485875", "rel_title": "Mosaic RBD nanoparticles protect against multiple sarbecovirus challenges in animal models", @@ -349177,41 +350581,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.25.22272946", - "rel_title": "Understanding the role of mask-wearing during COVID-19 on the island of Ireland", - "rel_date": "2022-03-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.25.22272946", - "rel_abs": "BackgroundNon-pharmaceutical interventions (NPI) play a key role in managing epidemics, yet it is challenging to evaluate their impacts on disease spread and outcomes.\n\nMethodsTo estimate the effect of a mask-wearing intervention to mitigate the spread of SARS-CoV-2 on the island of Ireland, we focused on the potential for interindividual infectious contact over time as the outcome. This is difficult to measure directly; in a companion paper we estimated it using a multi-strain epidemiological model. We used data on mask-wearing and mobility in both Northern Ireland (NI) and the Republic of Ireland (ROI) to predict independently the estimated infectious contact over time. We made counterfactual predictions of infectious contact rates and hospitalisations under a hypothetical intervention where 90% of the population were wearing masks during early 2020, when in reality few people were wearing masks in public; this was mandated in both jurisdictions on 10th August 2020.\n\nResultsThere were 1601 hospitalisations with COVID-19 in NI between 12th March and 10th August 2020, and 1521 in ROI between 3rd April and 10th August 2020. Under the counterfactual mask-wearing scenario, we estimated 512 (95% CI 400, 730) hospitalisations in NI, and 344 (95% CI 266, 526) in ROI, during the same periods.\n\nConclusionsWe have estimated a large effect of population mask-wearing on COVID-19 hospitalisations. This could be partly due to other factors that were also changing over time.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Nicola Fitz-Simon", - "author_inst": "National University of Ireland Galway" - }, - { - "author_name": "John Ferguson", - "author_inst": "NUI Galway" - }, - { - "author_name": "Alberto Alvarez", - "author_inst": "NUI Galway" - }, - { - "author_name": "Mircea T. Sofonea", - "author_inst": "Univ. Montpellier" - }, - { - "author_name": "Tsukushi Kamiya", - "author_inst": "College de France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.24.22272854", "rel_title": "Vaccine effectiveness with BNT162b2 (Comirnaty, Pfizer-BioNTech) vaccine against reported SARS-CoV-2 Delta and Omicron infection among adolescents, Norway, August 2021 to January 2022", @@ -349384,6 +350753,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.25.22272949", + "rel_title": "Risk factors and preventive interventions for post Covid-19 condition: systematic reviews", + "rel_date": "2022-03-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.25.22272949", + "rel_abs": "BackgroundThe Covid-19 outbreak has presented many challenges to governments and healthcare systems, including observations of symptoms that persist beyond acute infection labelled as post Covid-19 condition.\n\nObjectivesTo systematically identify and synthesize evidence around pre-existing and clinical risk factors for post Covid-19 condition (occurring [≥]12 weeks after positive test/symptom onset) (KQ1), and interventions during the acute and post-acute phases of the illness that could potentially prevent post Covid-19 condition (KQ2).\n\nMethodsWe searched Medline and Embase (Jan 2021-Aug 12 2021 [KQ1], and Jan 2020-Jul 28, 2021 [KQ2]), Clinicaltrials.gov, organizational websites, and reference lists of included studies and relevant systematic reviews. Two investigators independently reviewed abstracts and full-text articles against a priori inclusion criteria, and disagreements were resolved through discussion or by consulting a third reviewer. One investigator abstracted data and assessed risk of bias using design-specific criteria, and a second investigator checked data abstraction and assessments for completeness and accuracy. Meta-analysis was performed when there was sufficient clinical and methodological similarity in an exposure-outcome comparison, based on prespecified variables. We assessed the certainty of evidence using the Grading of Recommendations, Assessment, Development and Evaluation approach (GRADE). A relative effect/association of 0.75-1.49 was considered as \"little-to-no\", whereas 0.50-0.74/1.5-1.99 was \"small-to-moderate\" and <0.50/ [≥]2.00 was \"large\" for fewer/benefit or more/harm, respectively\n\nResultsFrom 4,672 (KQ1) and 3,781 (KQ2) citations we included 17 and 18 studies, though 4 studies were included for both KQs. We found small-to-moderate associations between female sex and higher non-recovery, fatigue, and dyspnea (moderate certainty). Severe or critical acute-phase Covid-19 severity (versus not) has probably (moderate certainty) a large association with increased cognitive impairment, a small-to-moderate association with more non-recovery, and a little-to-no association with dyspnea. There may be (low certainty) large associations between hospitalization during the acute illness and increased non-recovery, increased dyspnea, and reduced return to work. There may be small-to-moderate associations between several other risk factors and post Covid-19 condition outcomes, including age [≥]60 versus <60 (functional incapacity), non-White people (lower return to work), children age >6 versus <2 years (non-recovery), having [≥]1 versus no comorbidities (non-recovery), chronic pulmonary disease (fatigue), rheumatologic disorder (depression/anxiety), and chronic obstructive pulmonary disease or hypertension (cognitive impairment). Several other risk factors had low certainty for little-to-no association with one or more outcomes (e.g. diabetes, cardiovascular disease) or very low certainty. Interventions to prevent post Covid-19 condition included medications (standard and traditional/ayurvedic), stem cell therapy, rehabilitation or similar therapies, and screening/referrals at either acute phase (symptom onset to 4 weeks) or early post-acute phase (4-8 week), with short (12-16 weeks) or longer (>16 weeks) follow-up for outcomes. We are very uncertain about the effects of preventive interventions, mainly due to risk of bias, inconsistency/lack of consistency (single studies), and in some cases imprecision.\n\nConclusionsGuidelines in relation to surveillance, screening services, and other services such as access to sickness and disability benefits, might need to focus on females and those with previously severe Covid-19 illness. Interventions targeting fatigue, dyspnea, and cognitive impairment (especially in those who had severe Covid-19) may be good to prioritize for development and evaluation to provide evidence on their effects. Inputs from patients and primary care providers should be taken into account when developing new care pathways and some tailoring to individual needs will likely be paramount. Continuous assessment of the rapidly emerging evidence is important to better shape our understanding as the body of evidence grows. Sufficiently powered prospective trials of preventive interventions are warranted.\n\nPROSPERO registrationCRD42021270354", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jennifer Pillay", + "author_inst": "University of Alberta" + }, + { + "author_name": "Sholeh Rahman", + "author_inst": "University of Alberta" + }, + { + "author_name": "Samantha Guitard", + "author_inst": "University of Alberta" + }, + { + "author_name": "Aireen Wingert", + "author_inst": "University of Alberta" + }, + { + "author_name": "Lisa Hartling", + "author_inst": "University of Alberta" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.25.22272942", "rel_title": "Estimating time-dependent infectious contact: a multi-strain epidemiological model of SARS-CoV-2 on the island of Ireland", @@ -350695,77 +352099,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.21.22272480", - "rel_title": "Altered microRNA expression in severe COVID-19: potential prognostic and pathophysiological role", - "rel_date": "2022-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.21.22272480", - "rel_abs": "BackgroundThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is ongoing. The pathophysiology of SARS-CoV-2 infection is beginning to be elucidated but the role of microRNAs (miRNAs), small non-coding RNAs that regulate gene expression, remains incompletely understood. They play a role in the pathophysiology of viral infections with potential use as biomarkers. The objective of this study was to identify miRNAs as biomarkers of severe COVID-19 and to analyze their role in the pathophysiology of SARS-CoV-2 infection.\n\nMethodsmiRNA expression was measured in nasopharyngeal swabs from 20 patients with severe COVID-19, 21 patients with non-severe COVID-19 and 20 controls. Promising miRNAs to differentiate non-severe from severe COVID-19 patients were identified by differential expression analysis and sparse Partial Least Squares-Discriminant Analysis (sPLS-DA). ROC analysis, target prediction, GO enrichment and pathway analysis were used to analyze the role and the pertinence of these miRNAs in severe COVID-19.\n\nResultsThe number of expressed miRNAs was lower in severe COVID-19 patients compared to non-severe COVID-19 patients and controls. Among the differentially expressed miRNAs between severe COVID-19 and controls, 5 miRNAs were also differentially expressed between severe and non-severe COVID-19. sPLS-DA analysis highlighted 8 miRNAs, that allowed to discriminate the severe and non-severe COVID-19 cases. Target and functional analysis revealed enrichment for genes involved in viral infections and the cellular response to infection as well as one miRNA, hsa-miR-15b-5p, that targeted the SARS-CoV-2 RNA.\n\nThe comparison of results of differential expression analysis and discriminant analysis revealed three miRNAs, namely hsa-miR-125a-5p, hsa-miR-491-5p and hsa-miR-200b-3p. These discriminated severe from non-severe cases with areas under the curve ranging from 0.76 to 0.80.\n\nConclusionsOur analysis of miRNA expression in nasopharyngeal swabs revealed several miRNAs of interest to discriminate severe and non-severe COVID-19. These miRNAs represent promising biomarkers and possibly targets for antiviral or anti-inflammatory treatment strategies.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Nathalie Garnier", - "author_inst": "Lille University" - }, - { - "author_name": "Kato Pollet", - "author_inst": "Lille University" - }, - { - "author_name": "Marie Fourcot", - "author_inst": "Lille University" - }, - { - "author_name": "Morgan Caplan", - "author_inst": "CHU Lille" - }, - { - "author_name": "Guillemette Marot", - "author_inst": "University Lille" - }, - { - "author_name": "Julien Goutay", - "author_inst": "CHU Lille" - }, - { - "author_name": "Julien Labreuche", - "author_inst": "CHU Lille" - }, - { - "author_name": "Fabrice Soncin", - "author_inst": "Inserm" - }, - { - "author_name": "Rabah Boukherroub", - "author_inst": "University Lille" - }, - { - "author_name": "Didier Hober", - "author_inst": "Lille University" - }, - { - "author_name": "- Lille COVID Research Network (LICORNE)", - "author_inst": "-" - }, - { - "author_name": "Sabine Szunerits", - "author_inst": "University of Lille" - }, - { - "author_name": "Julien Poissy", - "author_inst": "Lille University" - }, - { - "author_name": "Ilka Engelmann", - "author_inst": "CHU Lille" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.21.22272673", "rel_title": "Sequential appearance and isolation of a SARS-CoV-2 recombinant between two major SARS-CoV-2 variants in a chronically infected immunocompromised patient", @@ -350934,6 +352267,69 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.03.22.485323", + "rel_title": "Intranasal Nanoemulsion Adjuvanted S-2P Vaccine Demonstrates Protection in Hamsters and Induces Systemic, Cell-Mediated and Mucosal Immunity in Mice", + "rel_date": "2022-03-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.22.485323", + "rel_abs": "With the rapid progress made in the development of vaccines to fight the SARS-CoV-2 pandemic, almost >90% of vaccine candidates under development and a 100% of the licensed vaccines are delivered intramuscularly (IM). While these vaccines are highly efficacious against COVID-19 disease, their efficacy against SARS-CoV-2 infection of upper respiratory tract and transmission is at best temporary. Development of safe and efficacious vaccines that are able to induce robust mucosal and systemic immune responses are needed to control new variants. In this study, we have used our nanoemulsion adjuvant (NE01) to intranasally (IN) deliver stabilized spike protein (S-2P) to induce immunogenicity in mouse and hamster models. Data presented demonstrate the induction of robust immunity in mice resulting in 100% seroconversion and protection against SARS-CoV-2 in a hamster challenge model. There was a significant induction of mucosal immune responses as demonstrated by IgA- and IgG-producing memory B cells in the lungs of animals that received intranasal immunizations compared to an alum adjuvanted intramuscular vaccine. The efficacy of the S-2P/NE01 vaccine was also demonstrated in an intranasal hamster challenge model with SARS-CoV-2 and conferred significant protection against weight loss, lung pathology, and viral clearance from both upper and lower respiratory tract. Our findings demonstrate that intranasal NE01-adjuvanted vaccine promotes protective immunity against SARS-CoV-2 infection and disease through activation of three arms of immune system: humoral, cellular, and mucosal, suggesting that an intranasal SARS-CoV-2 vaccine may play a role in addressing a unique public health problem and unmet medical need.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Shyamala Ganesan", + "author_inst": "BlueWillow Biologics" + }, + { + "author_name": "Hugo Acosta", + "author_inst": "BlueWillow Biologics" + }, + { + "author_name": "Chris Brigolin", + "author_inst": "BlueWillow Biologics" + }, + { + "author_name": "Kallista Orange", + "author_inst": "BlueWillow Biologics" + }, + { + "author_name": "Kevin Trabbic", + "author_inst": "BlueWillow Biologics" + }, + { + "author_name": "Charles Chen", + "author_inst": "Medigen Vaccine Biologics Corporation and University of Philadelphia" + }, + { + "author_name": "Chia-En Lien", + "author_inst": "Medigen" + }, + { + "author_name": "Yi-Jiun Lin", + "author_inst": "Medigen Vaccine Biologics Corporation" + }, + { + "author_name": "Meei-Yun Lin", + "author_inst": "Medigen Vaccine Biologics Corporation" + }, + { + "author_name": "Ya-Shan Chuang", + "author_inst": "Medigen Vaccine Biologics Corporation" + }, + { + "author_name": "Ali Fattom", + "author_inst": "Avicenna Biologics Consultant" + }, + { + "author_name": "Vira Bitko", + "author_inst": "BlueWillow Biologics" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.03.22.485230", "rel_title": "A self-amplifying RNA vaccine against COVID-19 with long-term room-temperature stability", @@ -352721,117 +354117,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.22.22272745", - "rel_title": "Effect of prior infection, vaccination, and hybrid immunity against symptomatic BA.1 and BA.2 Omicron infections and severe COVID-19 in Qatar", - "rel_date": "2022-03-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.22.22272745", - "rel_abs": "BACKGROUNDProtection offered by five different forms of immunity, combining natural and vaccine immunity, was investigated against SARS-CoV-2 Omicron symptomatic BA.1 infection, symptomatic BA.2 infection, BA.1 hospitalization and death, and BA.2 hospitalization and death, in Qatar, between December 23, 2021 and February 21, 2022.\n\nMETHODSSix national, matched, test-negative case-control studies were conducted to estimate effectiveness of BNT162b2 (Pfizer-BioNTech) vaccine, mRNA-1273 (Moderna) vaccine, natural immunity due to prior infection with pre-Omicron variants, and hybrid immunity from prior infection and vaccination.\n\nRESULTSEffectiveness of only prior infection against symptomatic BA.2 infection was 46.1% (95% CI: 39.5-51.9%). Effectiveness of only two-dose BNT162b2 vaccination was negligible at -1.1% (95% CI: -7.1-4.6), but nearly all individuals had received their second dose several months earlier. Effectiveness of only three-dose BNT162b2 vaccination was 52.2% (95% CI: 48.1-55.9%). Effectiveness of hybrid immunity of prior infection and two-dose BNT162b2 vaccination was 55.1% (95% CI: 50.9-58.9%). Effectiveness of hybrid immunity of prior infection and three-dose BNT162b2 vaccination was 77.3% (95% CI: 72.4-81.4%). Meanwhile, prior infection, BNT162b2 vaccination, and hybrid immunity all showed strong effectiveness >70% against any severe, critical, or fatal COVID-19 due to BA.2 infection. Similar levels and patterns of effectiveness were observed for BA.1 and for the mRNA-1273 vaccine.\n\nCONCLUSIONSThere are no discernable differences in the effects of prior infection, vaccination, and hybrid immunity against BA.1 versus BA.2. Hybrid immunity resulting from prior infection and recent booster vaccination confers the strongest protection against either subvariant. Vaccination enhances protection of those with a prior infection.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Heba N. Altarawneh", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Hiam Chemaitelly", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Houssein Ayoub", - "author_inst": "Qatar University" - }, - { - "author_name": "Patrick Tang", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "Mohammad R. Hasan", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "HADI M. YASSINE", - "author_inst": "Qatar University" - }, - { - "author_name": "Hebah A. Al-Khatib", - "author_inst": "Qatar University" - }, - { - "author_name": "Maria K. Smatti", - "author_inst": "Qatar University" - }, - { - "author_name": "Peter Coyle", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Zaina Al-Kanaani", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Einas Al-Kuwari", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Andrew Jeremijenko", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Anvar Hassan Kaleeckal", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Ali Nizar Latif", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Riyazuddin Mohammad Shaik", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Hanan F. Abdul-Rahim", - "author_inst": "Qatar University" - }, - { - "author_name": "Gheyath Nasrallah", - "author_inst": "Qatar University" - }, - { - "author_name": "Mohamed Ghaith Al-Kuwari", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Adeel A Butt", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Hamad Eid Al-Romaihi", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Mohamed H. Al-Thani", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Abdullatif Al-Khal", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Roberto Bertollini", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Laith J Abu-Raddad", - "author_inst": "Weill Cornell Medicine-Qatar" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.21.22272722", "rel_title": "The dramatic surge of excess mortality in the United States between 2017 and 2021", @@ -353128,6 +354413,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2022.03.22.22272748", + "rel_title": "Venous Thromboembolism in Ambulatory Covid-19 patients: Clinical and Genetic Determinants", + "rel_date": "2022-03-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.22.22272748", + "rel_abs": "BackgroundSubstantial evidence suggests that severe Covid-19 leads to an increased risk of Venous Thromboembolism (VTE). We aimed to quantify the risk of VTE associated with ambulatory Covid-19, study the potential protective role of vaccination, and establish key clinical and genetic determinants of post-Covid VTE.\n\nMethodsWe analyzed a cohort of ambulatory Covid-19 patients from UK Biobank, and compared their 30-day VTE risk with propensity-score-matched non-infected participants. We fitted multivariable models to study the associations between age, sex, ethnicity, socio-economic status, obesity, vaccination status and inherited thrombophilia with post-Covid VTE.\n\nResultsOverall, VTE risk was nearly 20-fold higher in Covid-19 vs matched non-infected participants (hazard ratio [HR] 19.49, 95% confidence interval [CI] 11.50 to 33.05). However, the risk was substantially attenuated amongst the vaccinated (HR: 2.79, 95% CI 0.82 to 9.54). Older age, male sex, and obesity were independently associated with higher risk, with adjusted HRs of 2.00 (1.61 to 2.47) per 10 years, 1.66 (1.28 to 2.15), and 1.85 (1.29 to 2.64), respectively. Further, inherited thrombophilia led to an HR 2.05, 95% CI 1.15 to 3.66.\n\nConclusionsAmbulatory Covid-19 was associated with a striking 20-fold increase in incident VTE, but no elevated risk after breakthrough infection in the fully vaccinated. Older age, male sex, and obesity were clinical determinants of Covid-19-related VTE. Additionally, inherited thrombophilia doubled risk further, comparable to the effect of 10-year ageing. These findings reinforce the need for vaccination, and call for targeted strategies to prevent VTE during outpatient care of Covid-19.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Junqing Xie", + "author_inst": "Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Albert Prats-Uribe", + "author_inst": "Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Qi Feng", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Yunhe Wang", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Dipender Gill", + "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK 2. Genetics Department, Novo Nordisk Research Ce" + }, + { + "author_name": "Roger Paredes", + "author_inst": "Infectious Diseases Department & irsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Catalonia, Spain" + }, + { + "author_name": "DANIEL PRIETO-ALHAMBRA", + "author_inst": "Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, United Kingdom" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.21.485184", "rel_title": "Rapid genotyping of viral samples using Illumina short-read sequencing data", @@ -354751,33 +356079,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2022.03.20.22272664", - "rel_title": "An umbrella review and meta-analysis of the use of renin-angiotensin system drugs and COVID-19 outcomes: what do we know so far?", - "rel_date": "2022-03-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.20.22272664", - "rel_abs": "BackgroundsEvidence from several meta-analyses are still controversial about the effects of angiotensin-converting enzyme inhibitors (ACEIs)/angiotensin-receptor blockers (ARBs) on COVID-19 outcomes.\n\nPurposeUmbrella review of systematic reviews/meta-analysis to provide comprehensive assessment of the effect of ACEIs/ARBs on COVID-19 related outcomes by summarising the currently available evidence.\n\nData SourceMedline (OVID), Embase, Scopus, Cochrane library and medRxiv from inception to 1st February 2021.\n\nStudy SelectionSystematic reviews with meta-analysis that evaluated the effect of ACEIs/ARBs on COVID-19 related clinical outcomes\n\nData ExtractionTwo reviewers independently extracted the data and assessed studies risk of bias using AMSTAR 2 Critical Appraisal Tool.\n\nData SynthesisPooled estimates were combined using the random-effects meta-analyses model including several sub-group analyses. Overall, 47 reviews were eligible for inclusion. Out of the nine COVID-19 outcomes evaluated, there was significant associations between ACEIs/ARBs use and each of death (OR=0.80, 95%CI=0.75-0.86; I2=51.9%), death/ICU admission as composite outcome (OR=0.86, 95%CI=0.80-0.92; I2=43.9%), severe COVID-19 (OR=0.86, 95%CI=0.78-0.95; I2=68%), and hospitalisation (OR=1.23, 95%CI=1.04-1.46; I2= 76.4%). The significant reduction in death/ICU admission, however, was higher among studies which presented adjusted measure of effects (OR=0.63, 95%CI=0.47-0.84) and were of moderate quality (OR=0.74, 95%CI=0.63-0.85).\n\nLimitationsThe effect of unmeasured confounding could not be ruled out. Only 21.3% (n=10) of the studies were of moderate quality.\n\nConclusionCollective evidence from observational studies indicate a good quality evidence on the significant association between ACEIs/ARBs use and reduction in death and death/ICU admission, but poor-quality evidence on both reducing severe COVID-19 and increasing hospitalisation. Our findings further support the current recommendations of not discontinuing ACEIs/ARBs therapy in patients with COVID-19.\n\nRegistrationThe study protocol was registered in PROSPERO (CRD42021233398).\n\nFunding SourceNone", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Amanj Kurdi", - "author_inst": "University of Strathclyde" - }, - { - "author_name": "Natalie Weir", - "author_inst": "University of Strathclyde" - }, - { - "author_name": "Tanja Mueller", - "author_inst": "University of Strathclyde" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2022.03.19.22272644", "rel_title": "More severe pneumonitis in children predicts the need for admission and elevation of some but not all markers of severe Covid-19.", @@ -355054,6 +356355,125 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.03.17.22272008", + "rel_title": "A SARS-CoV-2 negative antigen rapid diagnostic in RT-qPCR positive samples correlates with a low likelihood of infectious viruses in the nasopharynx.", + "rel_date": "2022-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.17.22272008", + "rel_abs": "SARS-CoV-2 transmission occurs even among fully vaccinated individuals; thus, prompt identification of infected patients is central to control viral circulation. Antigen rapid diagnostic tests (Ag-RDT) are highly specific, but sensitivity is variable.Discordant RT-qPCR vs Ag-RDT results are reported, raising the question of whether negative Ag-RDT in positive RT-qPCR samples could imply the absence of infectious viruses. To study the relationship between a negative Ag-RDT results with virological, molecular, and serological parameters, we selected a cross sectional and a follow-up dataset and analyzed virus culture, subgenomic RNA quantification, and sequencing to determine infectious viruses and mutations. We demonstrated that a positive SARS-CoV-2 Ag-RDT result correlates with the presence of infectious virus in nasopharyngeal samples. A decrease in sgRNA detection together with an expected increase in detectable anti-S and anti-N IgGs was verified in negative Ag-RDT / positive RT-qPCR samples. The data clearly demonstrates the less likelihood of a negative Ag-RDT sample to harbor infectious SARS-CoV-2 and consequently with a lower transmissible potential.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Isadora Alonso Correa", + "author_inst": "UFRJ" + }, + { + "author_name": "Debora Souza Faffe", + "author_inst": "Federal University of Rio de Janeiro" + }, + { + "author_name": "Rafael de Mello Galiez", + "author_inst": "Federal University of Rio de Janeiro" + }, + { + "author_name": "Cassia Cristina Alves Goncalves", + "author_inst": "Hospital Universitario Gaffree e Guinle" + }, + { + "author_name": "Richard Maia", + "author_inst": "UFRJ" + }, + { + "author_name": "Gustavo Peixoto da Silva", + "author_inst": "UFRJ" + }, + { + "author_name": "Filipe Romero Rebello Moreira", + "author_inst": "UFRJ" + }, + { + "author_name": "Diana Mariani", + "author_inst": "UFRJ" + }, + { + "author_name": "Mariana Freire Campos", + "author_inst": "UFRJ" + }, + { + "author_name": "Isabela Leitao Carvalho", + "author_inst": "UFRJ" + }, + { + "author_name": "M Romario Matos de Souza", + "author_inst": "UFRJ" + }, + { + "author_name": "Marcela Sabino Cunha", + "author_inst": "UFRJ" + }, + { + "author_name": "Erica Ramos dos Santos Nascimento", + "author_inst": "Federal University of Rio de Janeiro" + }, + { + "author_name": "Liane de Jesus Ribeiro", + "author_inst": "UFRJ" + }, + { + "author_name": "Thais Felix Cordeiro da Cruz", + "author_inst": "UFRJ" + }, + { + "author_name": "Cintia Policarpo", + "author_inst": "UFRJ" + }, + { + "author_name": "Luis Gonzales", + "author_inst": "Abbott" + }, + { + "author_name": "Mary A Rodgers", + "author_inst": "Abbott Laboratories" + }, + { + "author_name": "Michael Berg", + "author_inst": "Abbott" + }, + { + "author_name": "Roy Vijesurier", + "author_inst": "Abbott" + }, + { + "author_name": "Gavin A Cloherty", + "author_inst": "Abbott Labs" + }, + { + "author_name": "John HAckett", + "author_inst": "Abbott" + }, + { + "author_name": "Orlando Costa Ferreira Junior", + "author_inst": "Federal University of Rio de Janeiro" + }, + { + "author_name": "Terezinha Marta Pereira Pinto Castineiras", + "author_inst": "UFRJ" + }, + { + "author_name": "AMILCAR TANURI", + "author_inst": "UFRJ" + }, + { + "author_name": "Luciana Costa", + "author_inst": "UFRJ" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.17.22272574", "rel_title": "Maternal Antibody Response and Transplacental Transfer Following SARS-CoV-2 Infection or Vaccination in Pregnancy", @@ -356757,37 +358177,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.16.22272508", - "rel_title": "COVID-19 Disease Model with Reservoir of Infection : Cleaning Surfaces and Wearing Masks Strategies", - "rel_date": "2022-03-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.16.22272508", - "rel_abs": "We propose an epidemic model in which all diseases are transmitted by direct transmission (infectives to susceptibles) and indirect transmission which occurs through shedding of virus by infectives and acquisition by susceptibles. The model takes into account the effect of latency period and time needed for a susceptible to become infective by indirect contact. Under the certain assumptions, the basic reproduction number of the model is identified from the direct and indirect basic reproduction numbers. The main goal is to analyse the asymptotic behaviours, global stability, bifurcation and to detecte the most sensitive parameters. Numerical simulations are carried out to illustrate the theoretical part.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Najm Fatiha", - "author_inst": "Ibn Tofail University" - }, - { - "author_name": "M. A. Aziz Alaoui", - "author_inst": "Le Havre University" - }, - { - "author_name": "Ahmed Aghriche", - "author_inst": "Ibn Tofail University" - }, - { - "author_name": "Yafia Radouane", - "author_inst": "Ibn Tofail University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.16.22271100", "rel_title": "Effectiveness of whole virus COVID-19 vaccine at protecting health care personnel against SARS-CoV-2 infections in Lima, Peru", @@ -357028,6 +358417,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.17.22272389", + "rel_title": "Suppression of de novo antibody responses against SARS-CoV2 and the Omicron variant after mRNA vaccination and booster in patients with B cell malignancies undergoing active treatment, but maintenance of pre-existing antibody levels against endemic viruses.", + "rel_date": "2022-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.17.22272389", + "rel_abs": "The impact of SARS-CoV2 vaccination in cancer patients remains incompletely understood given the heterogeneity of cancer and cancer therapies. We assessed vaccine-induced antibody response to the SARS-CoV2 Omicron (B.1.1.529) variant in 57 patients with B cell malignancies with and without active B cell-targeted therapy. Ancestral- and Omicron-reactive antibody levels were determined by ELISA and neutralization assays. In over one third of vaccinated patients at the pre-booster timepoint, there were no ELISA-detectable antibodies against either the ancestral strain or Omicron variant. The lack of vaccine-induced antibodies was predominantly in patients receiving active therapy such as anti-CD20 monoclonal antibody (mAb) or Brutons tyrosine kinase inhibitors (BTKi). While booster immunization was able to induce detectable antibodies in a small fraction of seronegative patients, the benefit was disproportionately evident in patients not on active therapy. Importantly, in patients with post-booster ELISA-detectable antibodies, there was a positive correlation of antibody levels against the ancestral strain and Omicron variant. Booster immunization increased overall antibody levels, including neutralizing antibody titers against the ancestral strain and Omicron variant; however, predominantly in patients without active therapy. Furthermore, ancestral strain neutralizing antibody titers were about 5-fold higher in comparison with those to Omicron, suggesting that even with booster administration, there may be reduced protection against the Omicron variant. Interestingly, in almost all patients regardless of active therapy, including those unable to generate detectable antibodies against SARS-CoV2 spike, we observed comparable levels of EBV, influenza, and common cold coronavirus reactive antibodies demonstrating that B cell-targeting therapies primarily impair de novo but not pre-existing antibody levels. These findings suggest that patients with B cell malignancies on active therapy may be at disproportionately higher risk to new versus endemic viral infection and suggest utility for vaccination prior to B cell-targeted therapy.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Joseph Azar", + "author_inst": "The Ohio State University" + }, + { + "author_name": "John P. Evans", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Madison Sikorski", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Karthik Chakravarthy", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Selah McKenney", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Ian Carmody", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Cong Zeng", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Rachael Teodorescu", + "author_inst": "The Ohio State University" + }, + { + "author_name": "No Joon Song", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Jamie Hamon", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Donna Bucci", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Maria Velegraki", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Chelsea Bolyard", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Kevin P Weller", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Sarah Reisinger", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Seema A Bhat", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Kami J Maddocks", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Richard J Gumina", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Anastasia N. Vlasova", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Eugene M Oltz", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Linda J Saif", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Dongjun Chung", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Jennifer A Woyach", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Peter G Shields", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Shan-Lu Liu", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Zihai Li", + "author_inst": "The Ohio State university" + }, + { + "author_name": "Mark P Rubinstein", + "author_inst": "The Ohio State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.17.22272446", "rel_title": "Founder effect contributes to the unique pattern of SARS-CoV-2 variant B.1.1.519 emergence in Alaska", @@ -358487,53 +359999,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.03.15.22272438", - "rel_title": "COVID-19 Vaccine Hesitancy among Marginalized Populations in the U.S. and Canada: Protocol for a Scoping Review", - "rel_date": "2022-03-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.15.22272438", - "rel_abs": "IntroductionDespite the development of safe and highly efficacious COVID-19 vaccines, extensive barriers to vaccine deployment and uptake threaten the effectiveness of vaccines in controlling the pandemic. Notably, marginalization produces structural and social inequalities that render certain populations disproportionately vulnerable to COVID-19 incidence, morbidity, and mortality, and less likely to be vaccinated. The purpose of this scoping review is to provide a comprehensive overview of definitions/conceptualizations, elements, and determinants of COVID-19 vaccine hesitancy among marginalized populations in the U.S. and Canada.\n\nMaterials and MethodsThe proposed scoping review follows the framework outlined by Arksey and OMalley, and further developed by the Joanna Briggs Institute. It will comply with reporting guidelines from the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). The overall research question is: What are the definitions/conceptualizations and factors associated with vaccine hesitancy in the context of COVID-19 vaccines among adults from marginalized populations in the U.S. and Canada. Search strategies will be developed using controlled vocabulary and selected keywords, and customized for relevant databases, in collaboration with a research librarian. The results will be analyzed and synthesized quantitatively (i.e., frequencies) and qualitatively (i.e., thematic analysis) in relation to the research questions, guided by a revised WHO Vaccine Hesitancy Matrix.\n\nDiscussionThis scoping review will contribute to honing and advancing the conceptualization of COVID-19 vaccine hesitancy and broader elements and determinants of underutilization of COVID-19 vaccination among marginalized populations, identify evidence gaps, and support recommendations for research and practice moving forward.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Peter A Newman", - "author_inst": "University of Toronto" - }, - { - "author_name": "Luke Reid", - "author_inst": "University of Toronto" - }, - { - "author_name": "Suchon Tepjan", - "author_inst": "VOICES-Thailand Foundation" - }, - { - "author_name": "Sophia Fantus", - "author_inst": "The University of Texas Arlington School of Social Work" - }, - { - "author_name": "Kate Allan", - "author_inst": "University of Toronto" - }, - { - "author_name": "Thabani Nyoni", - "author_inst": "University of Toronto" - }, - { - "author_name": "Adrian Guta", - "author_inst": "University of Windsor" - }, - { - "author_name": "Charmaine C Williams", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.03.15.484467", "rel_title": "A conserved immune trajectory of recovery in hospitalized COVID-19 patients", @@ -358830,6 +360295,53 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.03.15.22272432", + "rel_title": "Comorbidities Diminish the Likelihood of Seropositivity After SARS-CoV-2 Vaccination", + "rel_date": "2022-03-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.15.22272432", + "rel_abs": "BackgroundThe impact of chronic health conditions (CHC) on serostatus post-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination is unknown.\n\nMethodsWe assessed serostatus post-SARS-CoV-2 vaccination among fully vaccinated adult residents of Jefferson County, Kentucky, USA from April 2021 through August 2021. Serostatus was determined by qualitative analysis of SARS-CoV-2 specific Spike IgG antibodies via enzyme-linked immunoassay (ELISA) in peripheral blood samples.\n\nResultsOf the 5,178 fully vaccinated participants, 51 were seronegative and 5,127 were seropositive. Chronic kidney disease (CKD) and autoimmune disease showed highest association with negative serostatus in fully vaccinated individuals. The absence of any CHC was strongly associated with positive serostatus. The risk of negative serostatus increased as the total number of pre-existing CHCs increased. Similarly, use of 2 or more CHC related medications was associated with seronegative status.\n\nConclusionsPresence of any CHC, especially CKD or autoimmune disease, increased the likelihood of seronegative status among individuals who were fully vaccinated to SAR-CoV-2. This risk increased with a concurrent increase in number of comorbidities, especially with multiple medications. Absence of any CHC was protective and increased the likelihood of a positive serological response. These results will help develop appropriate guidelines for booster doses and targeted vaccination programs.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Alok R Amraotkar", + "author_inst": "University of Louisville School of Medicine" + }, + { + "author_name": "Adrienne M Bushau-Sprinkle", + "author_inst": "Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville School of Medicine, University of Louisville, Louisvill" + }, + { + "author_name": "Rachel J Keith", + "author_inst": "Division of Environmental Medicine, Christina Lee Brown Envirome Institute, University of Louisville School of Medicine, Louisville, KY" + }, + { + "author_name": "Krystal T Hamorsky", + "author_inst": "Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville School of Medicine, University of Louisville, Louisvill" + }, + { + "author_name": "Kenneth Edward Palmer", + "author_inst": "Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville School of Medicine, University of Louisville, Louisvill" + }, + { + "author_name": "Hong Gao", + "author_inst": "Division of Environmental Medicine, Christina Lee Brown Envirome Institute, University of Louisville School of Medicine, Louisville, KY" + }, + { + "author_name": "Shesh N Rai", + "author_inst": "Biostatistics and Informatics Facility, Centre for Integrative Environmental Research Sciences, University of Louisville, Louisville, KY, 40202, USA" + }, + { + "author_name": "Aruni Bhatnagar", + "author_inst": "Division of Environmental Medicine, Christina Lee Brown Envirome Institute, University of Louisville School of Medicine, Louisville, KY" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2022.03.15.22272448", "rel_title": "Impact of COVID-19 on Life Expectancy among Native Americans", @@ -360273,77 +361785,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.03.10.22271304", - "rel_title": "ACE2 gene expression and inflammatory conditions in periodontal microenvironment of COVID-19 patients with and without diabetes evaluated by qPCR", - "rel_date": "2022-03-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.10.22271304", - "rel_abs": "ObjectiveChronic periodontitis has been proposed to be linked to coronavirus disease (COVID-19) on the basis of its inflammation mechanism. We aimed to evaluate this association by investigating the expression of Angiotensin Converting Enzyme-2 (ACE2) in periodontal compartments, which contain dysbiosis-associated pathogenic bacteria, and how it can be directly or indirectly involved in exacerbating inflammation in periodontal tissue.\n\nMaterial and MethodsThis observational clinical study included 23 adult hospitalized patients admitted to Universitas Indonesia Hospital with PCR-confirmed COVID-19, while 6 non-COVID-19 participants come to periodontal clinic were included as control. Using real time-PCR (qPCR) and gingival crevicular fluids (GCF) samples from COVID-19 patients with and without diabetes and periodontitis, we assessed the mRNA expression of angiotensin-converting enzyme 2 (ACE2), IL-6, IL-8, complement C3, and LL-37 as well as the relative proportion of Porphyromonas gingivalis, Fusobacterium nucleatum, and Veillonella parvula to represent the dysbiosis condition in periodontal microenvironment. All analyses were performed to determine their relationship.\n\nResultsACE2 mRNA expression was detected in the GCF of periodontitis-COVID-19 patients with and without diabetes. However, only periodontitis-COVID-19 patients with diabetes showed a positive relationship between ACE2 expression and inflammatory conditions in the periodontal microenvironment. In addition, the interplay between pro-inflammatory cytokine (IL-6) and complement C3 could be used as a predictor of the severity of periodontal inflammation in COVID-19 patients with diabetes.\n\nConclusionThe study data show that the SARS-CoV-2 entry gene is expressed in the GCF of patients with COVID-19, and its expression correlates with inflammatory markers.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Boy M Bachtiar", - "author_inst": "Department of Oral Biology and Oral Science Research Center, Faculty of Dentistry Universitas Indonesia, Indonesia." - }, - { - "author_name": "EndangW W Bachtiar", - "author_inst": "Department of Oral Biology and Oral Science Research Center, Faculty of Dentistry Universitas Indonesia, Indonesia." - }, - { - "author_name": "Hari Sunarto", - "author_inst": "Department of Periodontology, Faculty of Dentistry, Universitas Indonesia, Indonesia." - }, - { - "author_name": "Yuniarti Soeroso", - "author_inst": "Department of Periodontology, Faculty of Dentistry, Universitas Indonesia, Indonesia." - }, - { - "author_name": "Benso Sulijaya", - "author_inst": "Department of Periodontology, Faculty of Dentistry, Universitas Indonesia, Indonesia." - }, - { - "author_name": "Citra F Theodorea", - "author_inst": "Department of Oral Biology and Oral Science Research Center, Faculty of Dentistry Universitas Indonesia, Indonesia." - }, - { - "author_name": "Irandi P Pratomo", - "author_inst": "Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Indonesia, Indonesia; Pulmonology and Respiratory Medicine Staff Group - CO" - }, - { - "author_name": "Yudhistira", - "author_inst": "Clinical Pathology Medicine Staff Group, Universitas Indonesia Hospital." - }, - { - "author_name": "Ardiana Kusumaningrum", - "author_inst": "Department of Microbiology, Faculty of Medicine, Universitas Indonesia;Clinical Microbiology Medicine Staff Group, Universitas Indonesia Hospital." - }, - { - "author_name": "Defi Efendi", - "author_inst": "Department of Pediatric Nursing, Faculty of Nursing Universitas Indonesia, and Neonatal Intensive Care Unit, Universitas Indonesia Hospital, Depok, Indonesia" - }, - { - "author_name": "Efa Apriyanti", - "author_inst": "Department of Pediatric Nursing, Faculty of Nursing Universitas Indonesia, and Paediatric Intensive Care Unit, Universitas Indonesia Hospital." - }, - { - "author_name": "Astri Deviana", - "author_inst": "Oral Biology Laboratory Faculty of Dentistry, Universitas Indonesia, Indonesia." - }, - { - "author_name": "Nastiti R Utami", - "author_inst": "Oral Biology Laboratory Faculty of Dentistry, Universitas Indonesia, Indonesia." - }, - { - "author_name": "Anissa D Andriyani", - "author_inst": "Oral Biology Laboratory Faculty of Dentistry, Universitas Indonesia, Indonesia." - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "dentistry and oral medicine" - }, { "rel_doi": "10.1101/2022.03.10.22272193", "rel_title": "Presence of Mediastinal Lymphadenopathy in Hospitalized Covid-19 Patients in a Tertiary Care Hospital in Pakistan - A cross-sectional study", @@ -360540,6 +361981,105 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.03.13.484037", + "rel_title": "A broad and potent neutralization epitope in SARS-related coronaviruses", + "rel_date": "2022-03-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.13.484037", + "rel_abs": "Many neutralizing antibodies (nAbs) elicited to ancestral SARS-CoV-2 through natural infection and vaccination generally have reduced effectiveness to SARS-CoV-2 variants. Here we show therapeutic antibody ADG20 is able to neutralize all SARS-CoV-2 variants of concern (VOCs) including Omicron (B.1.1.529) as well as other SARS-related coronaviruses. We delineate the structural basis of this relatively escape-resistant epitope that extends from one end of the receptor binding site (RBS) into the highly conserved CR3022 site. ADG20 can then benefit from high potency through direct competition with ACE2 in the more variable RBS and interaction with the more highly conserved CR3022 site. Importantly, antibodies that are able to target this site generally neutralize all VOCs, albeit with reduced potency against Omicron. Thus, this highly conserved and vulnerable site can be exploited for design of universal vaccines and therapeutic antibodies.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Meng Yuan", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Xueyong Zhu", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Wan-ting He", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Panpan Zhou", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Chengzi I Kaku", + "author_inst": "Adimab, LLC" + }, + { + "author_name": "Tazio Capozzola", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Connie Y Zhu", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Xinye Yu", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Hejun Liu", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Wenli Yu", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Yuanzi Hua", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Henry Tien", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Linghang Peng", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Ge Song", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Christopher Cottrell", + "author_inst": "The Scripps Reaserch Institutte" + }, + { + "author_name": "William R Schief", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "David Nemazee", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Laura M Walker", + "author_inst": "Adimab" + }, + { + "author_name": "Raiees Andrabi", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Dennis Burton", + "author_inst": "Scripps Institute" + }, + { + "author_name": "Ian A Wilson", + "author_inst": "The Scripps Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.03.14.22272273", "rel_title": "Understanding adherence to self-isolation in the first phase of COVID-19 response", @@ -361999,29 +363539,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.11.22272263", - "rel_title": "Surveillance of COVID-19 cases associated with dental settings using routine health data from the East of Scotland with a description of efforts to break chains of transmission from October 2020 to December 2021.", - "rel_date": "2022-03-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.11.22272263", - "rel_abs": "IntroductionDental settings have been considered high risk setting s for COVID-19. A Dental Public Health Team in South East Scotland have worked to risk assess the situation timeously to break chains of transmission.\n\nAimTo present routine data produced from a contact tracing service for COVID-19 cases in the dental setting with a focus on transmission.\n\nDesignObservational retrospective analysis of a routine data set of COVID-19 cases associated with a dental setting reported via the national contact tracing system for two health board areas in the east of Scotland.\n\nMethodsCOVID-19 cases were confirmed by PCR testing. Descriptive statistics are used to summarise the data collected over a 13-month period (Oct 2020-Dec 2021). A narrative presents themes identified during contact tracing that led to transmission within a dental setting and includes a case study.\n\nResultsA total of 811 incidents are included. No evidence of staff to patient transmission or vice versa was found in this study. Staff to staff transmission occurred in non-clinical areas contributing to 33% of total staff cases.\n\nConclusionTransmission of COVID-19 in a dental setting in the context of this study appears to be confined to non-clinical areas. Future pandemic plans should include tools to aid with implementation of guidance in non-clinical areas.\n\nIn brief pointsO_LIOutbreaks of COVID-19 in a dental setting appear to be confined to the non-clinical areas of dental practices.\nC_LIO_LIWe have found no evidence of staff to patient transmission or vice versa using our contact tracing methods.\nC_LIO_LIFuture pandemic preparedness would benefit from including current quality improvement tools to aid with implementation of new standard operating procedures and other regularly changing guidance.\nC_LI", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Niall Mc Goldrick", - "author_inst": "NHS Fife" - }, - { - "author_name": "Emma O'Keefe", - "author_inst": "NHS Fife" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "dentistry and oral medicine" - }, { "rel_doi": "10.1101/2022.03.11.22271912", "rel_title": "External validation of risk scores to predict in-hospital mortality in patients hospitalized due to coronavirus disease 2019.", @@ -362238,6 +363755,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.03.11.22272282", + "rel_title": "Development and Implementation of a Simple and Rapid Extraction-Free Saliva SARS-CoV-2 RT-LAMP Workflow for Workplace Surveillance", + "rel_date": "2022-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.11.22272282", + "rel_abs": "Effective management of the COVID-19 pandemic requires widespread and frequent testing of the population for SARS-CoV-2 infection. Saliva has emerged as an attractive alternative to nasopharyngeal samples for surveillance testing as it does not require specialized personnel or materials for its collection and can be easily provided by the patient. We have developed a simple, fast, and sensitive saliva-based testing workflow that requires minimal sample treatment and equipment. After sample inactivation, RNA is quickly released and stabilized in an optimized buffer, followed by reverse transcription loop-mediated isothermal amplification (RT-LAMP) and detection of positive samples using a colorimetric and/or fluorescent readout. The workflow was optimized using 1,670 negative samples collected from 172 different individuals over the course of 6 months. Each sample was spiked with 50 copies/L of inactivated SARS-CoV-2 virus to monitor the efficiency of viral detection. Using pre-defined clinical samples, the test was determined to be 100% specific and 97% sensitive, with a limit of detection comparable to commercially available RT-qPCR-based diagnostics. The method was successfully implemented in a CLIA laboratory setting for workplace surveillance and reporting. From April 2021-February 2022, more than 30,000 self-collected samples from 755 individuals were tested and 85 employees tested positive mainly during December and January, consistent with high infections rates in Massachusetts and nationwide. The rapid identification and isolation of infected individuals with trace viral loads before symptom onset minimized viral spread in the workplace.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Zhiru Li", + "author_inst": "New England Biolabs" + }, + { + "author_name": "Jacqueline L Bruce", + "author_inst": "New England Biolabs" + }, + { + "author_name": "Barry Cohen", + "author_inst": "New England Biolabs" + }, + { + "author_name": "Caileigh V Cunningham", + "author_inst": "New England Biolabs" + }, + { + "author_name": "William E Jack", + "author_inst": "New England Biolabs" + }, + { + "author_name": "Katell Kunin", + "author_inst": "New England Biolabs" + }, + { + "author_name": "Bradley W Langhorst", + "author_inst": "New England Biolabs" + }, + { + "author_name": "Jacob Miller", + "author_inst": "New England Biolabs" + }, + { + "author_name": "Reynes A Moncion", + "author_inst": "New England Biolabs" + }, + { + "author_name": "Catherine B Poole", + "author_inst": "New England Biolabs" + }, + { + "author_name": "Prem K Premsrirut", + "author_inst": "Mirimus Inc" + }, + { + "author_name": "Guoping Ren", + "author_inst": "New England Biolabs" + }, + { + "author_name": "Richard J Roberts", + "author_inst": "New England Biolabs" + }, + { + "author_name": "Nathan A Tanner", + "author_inst": "New England Biolabs" + }, + { + "author_name": "Yinhua Zhang", + "author_inst": "New England Biolabs" + }, + { + "author_name": "Clotilde K.S. Carlow", + "author_inst": "New England Biolabs" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.11.22272185", "rel_title": "SEROLOGICAL TESTING OF BLOOD DONORS TO CHARACTERISE THE IMPACT OF COVID-19 IN MELBOURNE, AUSTRALIA, 2020", @@ -363957,53 +365553,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2022.03.09.22272160", - "rel_title": "Cross-sector Decision Landscape in Response to COVID-19: A Qualitative Analysis of North Carolina Decision-Makers", - "rel_date": "2022-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.09.22272160", - "rel_abs": "ContextThe COVID-19 pandemic response has demonstrated the interconnectedness of individuals, organizations, and other entities jointly contributing to the production of community health. This response has involved stakeholders from numerous sectors who have been faced with new decisions, objectives, and constraints.\n\nObjectiveWe aimed to examine the cross-sector organizational decision landscape that formed in response to the COVID-19 pandemic.\n\nDesignWe applied a systems approach to the qualitative analysis of semi-structured interviews on the cross-sector, organizational response to the COVID-19 pandemic. We analyzed transcribed interviews using conventional content analysis to synthesize key themes.\n\nSettingSemi-structured interviews were conducted via secure, video-conferencing platform between October 2020 and January 2021.\n\nParticipantsForty-four state and local decision-makers representing organizations from nine sectors in North Carolina participated.\n\nMain Outcome MeasuresWe defined the decision landscape as including decision-maker roles, key decisions, and inter-relationships involved in producing community health.\n\nResultsDecision-maker roles were characterized by underlying tensions between balancing organizational mission with employee/community health and navigating organizational versus individual responsibility for reducing transmission. Key Decisions fell into several broad categories, including how to translate public health guidance into practice; when to institute, and subsequently loosen, public health restrictions; and how to address downstream social and economic impacts of public health restrictions. Lastly, given limited and changing information, as well as limited resources and expertise, the COVID-19 response required cross-sector collaboration, which was commonly coordinated by local health departments.\n\nConclusionsBy documenting the local, cross-sector decision landscape that formed in response to COVID-19, we illuminate the impacts different organizations may have on information/misinformation, prevention behaviors, and, ultimately, health. Public health researchers and practitioners must understand, and work within, this complex decision landscape when responding to COVID-19 and future community health challenges.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Caitlin B Biddell", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Karl Johnson", - "author_inst": "University of North Carolina Gillings School of Global Public Health" - }, - { - "author_name": "Mehul D Patel", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Raymond Smith", - "author_inst": "East Carolina University" - }, - { - "author_name": "Hillary K. Hecht", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Maria E. Mayorga", - "author_inst": "North Carolina State University" - }, - { - "author_name": "Julie L Swann", - "author_inst": "North Carolina State University" - }, - { - "author_name": "Kristen Hassmiller Lich", - "author_inst": "University of North Carolina at Chapel Hill" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.03.10.22272081", "rel_title": "Interstitial lung damage following COVID-19 hospitalisation: an interim analysis of the UKILD Post-COVID study.", @@ -364564,6 +366113,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.03.09.22272171", + "rel_title": "Vaccine-induced antibody level predicts the clinical course of breakthrough infection of COVID-19 caused by delta and omicron variants: a prospective observational cohort study", + "rel_date": "2022-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.09.22272171", + "rel_abs": "BackgroundOmicron variant viruses spread rapidly, even in individuals with high vaccination rates. This study aimed to determine the utility of the antibody against the spike protein level as a predictor of the disease course of COVID-19 in vaccinated patients.\n\nMethodsBetween 11 December 2021 and 10 February 2022, we performed a prospective observational cohort study in South Korea, which included patients infected with delta -and -omicron variants. Multivariable logistic regression analysis to determine the association between antibody levels and the outcomes was conducted.The relationship between antibody levels and cycle threshold (Ct) values was confirmed using a generalised linear model.\n\nResultsFrom 106 vaccinated patients (39 delta and 67 omicron), the geometric mean titres of antibodies in patients withfever ([≥]37.5 {degrees}C), hypoxia ([≤]94% of SpO2), pneumonia, C-reactive protein (CRP) elevation (>8 mg/L), or lymphopenia (<1,100 cells/L) were 1,201.5 U/mL, 98.8 U/mL, 774.1 U/mL, 1,335.1 U/mL, and 1,032.2 U/mL, respectively. Increased antibody levels were associated with a decrease in the fever occurrence (adjusted odds ratio [aOR], 0.23; 95% confidence interval [CI], 0.12-0.51), hypoxia (aOR, 0.23; 95% CI, 0.08-0.7), CRP elevation (aOR, 0.52; 95% CI, 0.29-0.0.94), and lymphopenia (aOR, 0.57; 95% CI, 0.33-0.98). Ct values showed a positive correlation between antibody levels (P =0.02).\n\nConclusionAntibody levels are predictive of the clinical course of COVID-19 in vaccinated patients with delta and omicron variant infections. Our data highlight the need for concentrated efforts to monitor patients with SARS-CoV-2 infection who are at risk of low antibody levels.\n\nSummaryIn this prospective observation cohort study, antibody level predicts clinical course of breakthrough infection of COVID-19. Fever (aOR 0.23[0.12-0.51], hypoxia (aOR 0.23[0.08-0.7]), CRP elevation(aOR 0.52[0.29-0.0.94] and lymphopenia (aOR 0.57[0.33-0.98]) were inversely correlated with antibody levels.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Min Hyung Kim", + "author_inst": "Yonsei University, college of medicine" + }, + { + "author_name": "Yooju Nam", + "author_inst": "Yonsei University College of Medicine" + }, + { + "author_name": "Nak-Hoon Son", + "author_inst": "Keimyung University" + }, + { + "author_name": "Namwoo Heo", + "author_inst": "Yonsei University College of Medicine" + }, + { + "author_name": "Bongyoung Kim", + "author_inst": "Hanyang University College of Medicine" + }, + { + "author_name": "Eawha Kang", + "author_inst": "Yonsei University College of Medicine" + }, + { + "author_name": "Areum Shin", + "author_inst": "Yonsei University College of Medicine" + }, + { + "author_name": "Andrew Jihoon Yang", + "author_inst": "Yonsei University College of Medicine" + }, + { + "author_name": "Yoon Soo Park", + "author_inst": "Yonsei University College of Medicine" + }, + { + "author_name": "Heejung Kim", + "author_inst": "Yonsei University College of Medicine" + }, + { + "author_name": "Taeyoung Kyong", + "author_inst": "Yonsei University College of Medicine" + }, + { + "author_name": "Yong Chan Kim", + "author_inst": "Yonsei University College of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.09.22272168", "rel_title": "Long COVID and its associated factors among COVID survivors in the community from a middle-income country: an online cross-sectional study", @@ -366299,45 +367911,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.03.08.22272111", - "rel_title": "Risk Perceptions and Private Protective Behaviors: Evidence from COVID-19 Pandemic", - "rel_date": "2022-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.08.22272111", - "rel_abs": "We analyze data from a survey we administered during the COVID-19 pandemic to investigate the relationship between peoples subjective beliefs about risks and their private protective behaviors. On average, people substantially overestimate the absolute level of risk associated with economic activity, but have correct signals about their relative risk. Subjective risk beliefs are predictive of changes in economic activities independently of government policies. Government mandates restricting economic behavior, in turn, attenuate the relationship between subjective risk beliefs and protective behaviors.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "M. Kate Bundorf", - "author_inst": "Duke University" - }, - { - "author_name": "Jill DeMatteis", - "author_inst": "Westat" - }, - { - "author_name": "Grant Miller", - "author_inst": "Stanford University" - }, - { - "author_name": "Maria Polyakova", - "author_inst": "Stanford University" - }, - { - "author_name": "Jialu Streeter", - "author_inst": "Stanford University" - }, - { - "author_name": "Jonathan Wivagg", - "author_inst": "Westat" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2022.03.09.22271788", "rel_title": "Comparison of influenza and COVID-19-associated hospitalizations among children < 18 years old in the United States - FluSurv-NET (October-April 2017-2021) and COVID-NET (October 2020-September 2021)", @@ -366738,6 +368311,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.08.22271822", + "rel_title": "Selection of optimum formulation of RBD-based protein sub-unit covid19 vaccine (Corbevax) based on safety and immunogenicity in an open-label, randomized Phase-1 and 2 clinical studies", + "rel_date": "2022-03-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.08.22271822", + "rel_abs": "BackgroundWe present the data from an open-label study involved in the selection of optimum formulation of RBD-based protein sub-unit COVID-19 vaccine.\n\nMethodsThe randomized Phase-1/2 trial followed by a Phase-2 trial was carried out to assess safety and immunogenicity of different formulation of COVID-19 vaccine (Corbevax) and select an optimum formulation for a phase 3 study. Healthy adults without a history of Covid-19 vaccination or SARS-CoV-2 infection, were enrolled.\n\nFindingsLow incidence of adverse events were reported post-vaccination of different Corbevax formulations and majority were mild in nature and no Grade-3 or serious adverse events were observed. All formulations in Phase-1/2 study showed similar profile of humoral and cellular immune-response with higher response associated with increasing CpG1018 adjuvant content at same RBD protein content. Hence, high concentration of CpG1018 was tested in phase-2 study, which showed significant improvement in immune-responses in terms of anti-RBD-IgG concentrations, anti-RBD-IgG1 titers, nAb-titers and cellular immune-responses while maintaining the safety profile. Interestingly, binding and neutralizing antibody titers were persisted consistently till 6 months post second vaccine dose.\n\nInterpretationsCorbevax was well tolerated with no observed safety concerns. Neutralizing antibody titers were suggestive of high vaccine effectiveness compared with human convalescent plasma or protective thresholds observed during vaccine efficacy trials of other COVID-19 vaccines. The study was prospectively registered with clinical trial registry of India-CTRI/2021/06/034014 and CTRI/2020/11/029032.\n\nFundingBill & Melinda Gates Foundation, BIRAC-division of Department of Biotechnology, Govt of India, and the Coalition for Epidemic Preparedness Innovations funded the study.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Subhash Thuluva", + "author_inst": "Biological E. Limited" + }, + { + "author_name": "Vikram Paradkar", + "author_inst": "Biological E Limited" + }, + { + "author_name": "Kishore Turaga", + "author_inst": "Biological E Limited" + }, + { + "author_name": "Subbareddy Gunneri", + "author_inst": "Biological E Limited" + }, + { + "author_name": "Vijay Yerroju", + "author_inst": "Biological E Limited" + }, + { + "author_name": "Rammohanreddy Mogulla", + "author_inst": "Biological E Limited" + }, + { + "author_name": "Mahesh Kyasani", + "author_inst": "Biological E Limited" + }, + { + "author_name": "Senthilkumar Manoharan", + "author_inst": "Biological E Limited" + }, + { + "author_name": "Guruprasad R Medigeshi", + "author_inst": "Translational Health Science and Technology Institute" + }, + { + "author_name": "JANMEJAY Singh", + "author_inst": "Translational Health Science and Technology Institute" + }, + { + "author_name": "Heena Shaman", + "author_inst": "Translational Health Science and Technology Institute" + }, + { + "author_name": "Chandramani Singh", + "author_inst": "All India Institute of Medical Sciences" + }, + { + "author_name": "Venkateshwar Rao A", + "author_inst": "St. Theresa Hospital, Hyderabad" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.09.483630", "rel_title": "Differential Activity of Repurposed Drugs as Receptor Binding Domain Antagonists for Omicron and Native Strains of SarsCov2", @@ -368213,37 +369853,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.03.05.22271959", - "rel_title": "13 cis retinoic acid improved the outcomes of COVID-19 patients. A randomized clinical trial", - "rel_date": "2022-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.05.22271959", - "rel_abs": "The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected over 100 million people causing over 2.4 million deaths over the world, and it is still expanding. Given the urgency of the COVID-19 pandemic, the clinical investigation of approved drugs is a promising alternative to find a timely effective treatment. In this randomized trial, we investigated the activity of both oral and aerosolized 13 cis retinoic acid in the treatment of SARS-COV-2 added to standard of care treatment in patients with COVID-19 versus standard of care treatment alone. This was a randomized controlled trial conducted at Kafrelsheikh Universitys Quarantine Hospitals, Egypt. After obtaining informed consent, forty patients with a confirmed diagnosis of COVID-19 were enrolled in the study. They were randomly assigned to one of two groups: Group I; 20 patients received aerosolized and oral 13 cis retinoic acid plus standard of care treatment (13 cis RA group) and Group II; 20 patients received only standard care treatment as a control group. The two groups were age and gender matched. There was no statistically significant difference between them in any of the baseline characteristics or laboratory parameters. The results showed that there was a high significant difference between the two groups regarding intensive care unit (ICU) admission, mortality and improvement (P<0.05). Only 10.52 % of patients in the 13 cis retinoic acid group needed ICU admission compared to 28.57 % in the control arm. There was no mortality in the 13 cis retinoic acid group, whereas about 14.35% were died in the group II. All patients who received 13 cis retinoic acid noticed a high improvement (P<0.001), and the mean value for clinical improvement was 16.3{+/-}4.5 days. There was no significant difference regarding the laboratory parameters before and after 14 days of treatment in the group of patients received the standard of care treatment (P=0.66). Univariate logistic regression analysis showed overall mortality was significantly related to the patients age, serum ferritin, C-reactive protein, oxygen saturation, the presence of diabetes mellitus, obesity, and abdominal pain. We conclude that 13 cis retinoic acid is a promising drug in the treatment of patients with COVID-19 infection, when added to the standard of care treatment.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Mahmoud R Elkazzaz", - "author_inst": "Kafr-elsheikh University College of Medicine" - }, - { - "author_name": "Yousry Esam-Eldin Abo-Amer", - "author_inst": "Hepatology,Gastroenterology and Infectious Diseases Department, Mahala Hepatology Teaching Hospital, Egypt" - }, - { - "author_name": "Amr Ahmed", - "author_inst": "Ministry of Health" - }, - { - "author_name": "Tamer Hayadar", - "author_inst": "Internal Medicine Department, Faculty of Medicine , Kafrelshiekh University, Egypt" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2022.03.06.22271809", "rel_title": "Defining factors that influence vaccine-induced, cross-variant neutralizing antibodies for SARS-CoV-2 in Asians", @@ -368524,6 +370133,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.05.483104", + "rel_title": "Characterization of Hydrophobic Interactions of SARS-CoV-2 and MERS-CoV Spike Protein Fusion Peptides Using Single Molecule Force Measurements", + "rel_date": "2022-03-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.05.483104", + "rel_abs": "We address the challenge of understanding how hydrophobic interactions are encoded by fusion peptide sequences within coronavirus (CoV) spike proteins. Within the fusion peptides of SARS-CoV-2 and MERS-CoV, a largely conserved peptide sequence called FP1 (SFIEDLLFNK and SAIEDLLFDK in SARS-2 and MERS, respectively) has been proposed to play a key role in encoding hydrophobic interactions that drive viral-host cell membrane fusion. While a non-polar triad (LLF) is common to both FP1 sequences, and thought to dominate the encoding of hydrophobic interactions, FP1 from SARS and MERS differ in two residues (Phe 2 versus Ala 2 and Asn 9 versus Asp 9, respectively). Here we explore if single molecule force measurements can quantify hydrophobic interactions encoded by FP1 sequences, and then ask if sequence variations between FP1 from SARS and MERS lead to significant differences in hydrophobic interactions. We find that both SARS-2 and MERS wild-type FP1 generate measurable hydrophobic interactions at the single molecule level, but that SARS-2 FP1 encodes a substantially stronger hydrophobic interaction than its MERS counterpart (1.91 {+/-} 0.03 nN versus 0.68 {+/-} 0.03 nN, respectively). By performing force measurements with FP1 sequences with single amino acid substitutions, we determine that a single residue mutation (Phe 2 versus Ala 2) causes the almost threefold difference in the hydrophobic interaction strength generated by the FP1 of SARS-2 versus MERS, despite the presence of LLF in both sequences. Infrared spectroscopy and circular dichroism measurements support the proposal that the outsized influence of Phe 2 versus Ala 2 on the hydrophobic interaction arises from variation in the secondary structure adopted by FP1. Overall, these insights reveal how single residue diversity in viral fusion peptides, including FP1 of SARS-CoV-2 and MERS-CoV, can lead to substantial changes in intermolecular interactions proposed to play a key role in viral fusion, and hint at strategies for regulating hydrophobic interactions of peptides in a range of contexts.\n\nSIGNIFICANCEFusion of coronaviruses (CoVs) and host cells is mediated by the insertion of the fusion peptide (FP) of the viral spike protein into the host cell membrane. Hydrophobic interactions between FPs with their host cell membranes regulate the viral membrane fusion process and are key to determining infection ability. However, it is not fully understood how the amino acid sequences in FPs mediate hydrophobic interactions. We use single-molecule force measurements to characterize hydrophobic interactions of FPs from SARS-CoV-2 and MERS-CoV. Our findings provide insight into the mechanisms by which the amino acid composition of FPs encodes hydrophobic interactions and their implications for fusion activity critical to the spread of infection.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Cindy Qiu", + "author_inst": "Cornell University" + }, + { + "author_name": "Gary Whittaker", + "author_inst": "Cornell University" + }, + { + "author_name": "Samuel H Gellman", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Susan Daniel", + "author_inst": "Cornell University" + }, + { + "author_name": "Nicholas L Abbott", + "author_inst": "Cornell University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.03.04.483019", "rel_title": "Soluble P2X7 receptor is elevated in the plasma of COVID-19 patients and correlates with disease severity", @@ -370063,57 +371707,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.06.22271974", - "rel_title": "Competitive fitness of emerging SARS-CoV-2 variants is linked to their Distinctiveness relative to preceding lineages from that region", - "rel_date": "2022-03-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.06.22271974", - "rel_abs": "The COVID-19 pandemic has seen the persistent emergence of immune-evasive SARS-CoV-2 variants under the selection pressure of natural and vaccination-acquired immunity. However, it is currently challenging to quantify how immunologically distinct a new variant is compared to all the prior variants to which a population has been exposed. Here we define Distinctiveness of SARS-CoV-2 sequences based on a proteome-wide comparison with all prior sequences from the same geographical region. We observe a correlation between Distinctiveness relative to contemporary sequences and future change in prevalence of a newly circulating lineage (Pearson r = 0.75), suggesting that the Distinctiveness of emergent SARS-CoV-2 lineages is associated with their competitive fitness. We further show that the average Distinctiveness of sequences belonging to a lineage, relative to the Distinctiveness of other sequences that occur at the same place and time (n = 944 location/time data points), is predictive of future increases in prevalence (AUC = 0.88, 0.86-0.90 95% confidence interval). By assessing the Delta variant in India versus Brazil, we show that the same lineage can have different Distinctiveness-contributing positions in different geographical regions depending on the other variants that previously circulated in those regions. Finally, we find that positions that constitute epitopes contribute disproportionately (20-fold higher than the average position) to Distinctiveness. Overall, this study suggests that real-time assessment of new SARS-CoV-2 variants in the context of prior regional herd exposure via Distinctiveness can augment genomic surveillance efforts.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Michiel JM Niesen", - "author_inst": "nference" - }, - { - "author_name": "Karthik Murugadoss", - "author_inst": "nference" - }, - { - "author_name": "Patrick J Lenehan", - "author_inst": "nference" - }, - { - "author_name": "Aron Marchler-Bauer", - "author_inst": "National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH)" - }, - { - "author_name": "Jiyao Wang", - "author_inst": "National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH)" - }, - { - "author_name": "Ryan Connor", - "author_inst": "National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH)" - }, - { - "author_name": "J Rodney Brister", - "author_inst": "National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH)" - }, - { - "author_name": "AJ Venkatakrishnan", - "author_inst": "nference" - }, - { - "author_name": "Venky Soundararajan", - "author_inst": "nference" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.03.04.22271706", "rel_title": "Remdesivir for the treatment of patients hospitalized with COVID-19 receiving supplemental oxygen: a targeted literature review and meta-analysis", @@ -370290,6 +371883,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2022.03.03.22271793", + "rel_title": "Reasons underlying the intention to vaccinate children aged 5-11 against COVID-19: A cross-sectional study of parents in Israel, November 2021", + "rel_date": "2022-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.03.22271793", + "rel_abs": "Vaccination is a key tool to mitigate impacts of the COVID-19 pandemic. In Israel, COVID-19 vaccines became available to adults in December 2020 and to 5-11-year-old children in November 2021. Ahead of the vaccine roll-out in children, we aimed to determine whether surveyed parents intended to vaccinate their children and describe reasons for their intentions. We collected information on parental socio-demographic characteristics, COVID-19 vaccine history, intention to vaccinate their children against COVID-19, and reasons for parental decisions using an anonymous online survey. We identified associations between parental characteristics and plans to vaccinate children using a logistic regression model and described reasons for intentions to vaccinate or not. Parental non-vaccination and having experienced major vaccination side effects were strongly associated with non-intention to vaccinate their children (OR 0.09 and 0.18 respectively, p<0.001). Parents who were younger, lived in the socio-economically deprived periphery, and belonged to the Arab population had lower intentions to vaccinate their children. Reasons for non-intention to vaccinate included concerns about vaccine safety and efficacy (53%, 95%CI 50-56) and the belief that COVID-19 is a mild disease (73%, 95%CI 73-79), while a frequent motive for vaccination was the return to normal social and educational life (89%, 95%CI 87-91). Understanding rationales for COVID-19 vaccine rejection or acceptance, as well as parental demographic data, can pave the way for intentional educational campaigns to encourage not only vaccination against COVID-19, but also regular childhood vaccine programming.\n\nHighlightsO_LIParental intention to vaccinate children aged 5-11 is much lower than vaccine coverage in parental age groups\nC_LIO_LIBeing unvaccinated and having experienced side effects following vaccination were the greatest negative predictors in parents of intention to vaccinate their children\nC_LIO_LIParents were more likely to accept a COVID-19 vaccine for their children to allow them to return to daily social life and to ensure economic security in the family\nC_LIO_LIParents were more likely to reject a COVID-19 vaccination for health reasons such as safety concerns or due the belief that COVID-19 was a mild disease in children\nC_LI", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Nicole Morozov", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Amiel A Dror", + "author_inst": "Galilee Medical Center, Azrieli Faculty of Medicine Bar-Ilan University" + }, + { + "author_name": "Amani Daoud", + "author_inst": "Department of Otolaryngology, Head and Neck Surgery, Galilee Medical Center; Azrieli Faculty of Medicine, Bar-Ilan University" + }, + { + "author_name": "Netanel Eisenbach", + "author_inst": "Department of Otolaryngology, Head and Neck Surgery, Galilee Medical Center; Azrieli Faculty of Medicine, Bar-Ilan University" + }, + { + "author_name": "Edward Kaykov", + "author_inst": "Azrieli Faculty of Medicine, Bar-Ilan University; Geriatric Medicine Department, Galilee Medical Center" + }, + { + "author_name": "Masad Barhoum", + "author_inst": "Azrieli Faculty of Medicine, Bar-Ilan University; Galilee Medical Center" + }, + { + "author_name": "Tsvi Sheleg", + "author_inst": "Azrieli Faculty of Medicine, Bar-Ilan University; Galilee Medical Center" + }, + { + "author_name": "Eyal Sela", + "author_inst": "Department of Otolaryngology, Head and Neck Surgery, Galilee Medical Center, Nahariya, Israel; Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel" + }, + { + "author_name": "Michael Edelstein", + "author_inst": "Bar Ilan University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.03.22271831", "rel_title": "Zonal Model of Aerosol Persistence in ICUs: Utilization of Time and Space-resolved Sensor Network", @@ -371793,25 +373437,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.03.02.22271656", - "rel_title": "Analyzing county-wide trends in Tennessee Covid-19 rates, Median Household Income, and Presence of Hospital", - "rel_date": "2022-03-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.02.22271656", - "rel_abs": "The Covid-19 pandemic has caused millions of deaths and infections worldwide. Recent studies suggest that Covid-19 may be disproportionately affecting certain groups. The Tennessee Department of Health regularly publishes data on Covid infections and vaccinations. This data alongside data published from the 2010 census was used to analyze trends in Covid-19 rates for the State of Tennessee. The census data for the average household income of each county was cross-referenced with the covid data. A positive correlation between population of the county and the number of new cases reported on January 3rd, 2022, appeared when observing the data. A regression analysis (ANOVA) revealed that the data on population and covid rate was significant (P-value: 2.69E-10). The results from comparing the covid rates in a county with a hospital and a county without a hospital seemed to be the most significant. The data reported by the Sycamore institute on the Tennessee counties without a hospital was used to identify trends unique to these counties. The counties lacking a hospital were compared with counties with a similar population. 7 hospital-less counties were used for comparison, 6 counties (Fayette, Grainger, Haywood, Chester, Sequatchie, Clay) reported a greater number of cases than counties of a similar population. Of the 20 counties lacking a hospital, 16 fell within the bottom 50% of median household incomes, with 9 in the bottom 25% and 4 in the bottom 10%. Healthcare sites in rural areas may lack fundamental infrastructure. These areas may require unique interventions to address the healthcare concerns present.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Viraj Vipul Brahmbhatt", - "author_inst": "Union College" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.03.01.22271611", "rel_title": "Predicting missed health care visits during the COVID-19 pandemic using machine learning methods: Evidence from 55,500 individuals from 28 European Countries", @@ -371980,6 +373605,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.03.22271769", + "rel_title": "The Coronavirus Calendar (CoronaCal): a Simplified SARS-CoV-2 Test System for Sampling and Retrospective Analysis", + "rel_date": "2022-03-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.03.22271769", + "rel_abs": "BackgroundThe testing of saliva samples for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA has become a useful and common method to diagnose coronavirus disease 2019 (Covid-19). However, there are limited examples of serial testing with correlated clinical metadata, especially in the outpatient setting.\n\nMethodWe developed a method to collect serial saliva samples on ordinary white printer paper, which can be subsequently analyzed for the presence of SARS-CoV-2 RNA using established polymerase chain reaction (PCR) procedures. The collection systems consisted of a biological diary (CoronaCal) where subjects dab their saliva onto ovals printed onto paper. The dried samples are covered with a sticker that includes a symptom checklist to create a biological diary. Each sheet of letter paper can accommodate up to 14 serial samples.\n\nResultsIn a pilot study, ten subjects used CoronaCals for durations of nine to 44 days. SARS-CoV-2 RNA was extracted and detected in CoronaCals from nine of nine people with either Covid-19 symptoms or exposure to someone with Covid-19, and in zero of one asymptomatic person. The CoronaCals were stored for up to 70 days at room temperature during collection and then frozen for up to four months before analysis, suggesting that SARS-CoV-2 RNA is stable once dried onto paper. Interestingly, the temporal pattern of symptoms was not well correlated with SARS-CoV-2 RNA in serial daily collections for up to 44 days. In addition, SARS-CoV-2 positivity was discontinuous over time in most cases but persisted for up to 24 days.\n\nConclusionsWe conclude that sampling of saliva on simple paper CoronaCals may provide a useful method to study the natural history and epidemiology of Covid-19. The CoronaCal collection and testing method we developed is also easy to implement, inexpensive, non-invasive, and scalable. More broadly, the approach can be used to archive biological samples for retrospective analysis to deepen epidemiological understanding during viral disease outbreaks and to provide information about the natural history of emerging infections.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "David S Thaler", + "author_inst": "Biozentrum, University of Basel" + }, + { + "author_name": "Thomas P Sakmar", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Thomas Huber", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Karin C Aberg", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Manija A Kazmi", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Jordan M Mattheisen", + "author_inst": "Rockefeller University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.02.22271771", "rel_title": "Effects of BA.1/BA.2 subvariant, vaccination, and prior infection on infectiousness of SARS-CoV-2 Omicron infections", @@ -373867,41 +375531,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.01.22271685", - "rel_title": "Patients with CLL have similar high risk of death upon the omicron variant of COVID-19 as previously during the pandemic.", - "rel_date": "2022-03-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.01.22271685", - "rel_abs": "Previous studies have shown that patients with chronic lymphocytic leukemia (CLL) and coronavirus disease 2019 (COVID-19) have high mortality rates. The omicron variant has been reported to give milder disease in the general population, but outcomes of infections with the omicron variant among immunocompromised patients have not previously been reported. In a population-based cohort we assessed rates of hospitalizations, ICU-admissions, and 30-day all-cause mortality among all patients with CLL from Eastern Denmark testing positive for severe adult respiratory syndrome coronavirus 2 (SARS-CoV-2) in time periods before and after dominance of the omicron variant. Rates of hospitalizations and ICU-admissions declined significantly, whereas 30-day mortality remained as high as 23% in the period with dominance of the omicron sublineage BA.2 variant. Thus, patients with CLL in general and in particular those above 70 years of age with one or more comorbidities should be considered for closer monitoring and pre-emptive antiviral therapy upon a positive SARS-CoV-2 test.\n\nKey pointsO_LIThe omicron variant of COVID-19 leads to high fatality rates in CLL, despite milder disease in the background population\nC_LIO_LIPatients with CLL who test positive for SARS-CoV-2 in the era of the omicron variant should be considered for pre-emptive antiviral therapy\nC_LI\n\nExplanation of noveltyThe omicron variant has been reported to give milder disease in the general population, but outcomes of infections with the omicron variant among immunocompromised patients have not previously been reported. These population-based data on outcome for patients with CLL upon infection with the omicron variant of SARS-CoV-2 warrants closer monitoring and pre-emptive antiviral therapy upon a positive SARS-CoV-2 test for patients with CLL.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Carsten Utoft Niemann", - "author_inst": "Rigshospitalet" - }, - { - "author_name": "Caspar da Cunha-Bang", - "author_inst": "Rigshospitalet" - }, - { - "author_name": "Marie Helleberg", - "author_inst": "Rigshospitalet" - }, - { - "author_name": "Sisse Rye Ostrowski", - "author_inst": "Rigshospitalet" - }, - { - "author_name": "Christian Brieghel", - "author_inst": "Rigshospitalet" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2022.02.28.22271591", "rel_title": "Ammonium Sulfate Addition Reduces the Need for Guanidinium Isothiocyanate in the Denaturing Transport Medium Used for SARS-COV-2 RNA Detection", @@ -374210,6 +375839,161 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.01.22271662", + "rel_title": "High Viral Specific Antibody Convalescent Plasma Effectively Neutralizes SARS-CoV-2 Variants of Concern", + "rel_date": "2022-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.01.22271662", + "rel_abs": "The ongoing evolution of SARS-Co-V2 variants to omicron severely limits available effective monoclonal antibody therapies. Effective drugs are also supply limited. Covid-19 convalescent plasma (CCP) qualified for high antibody levels effectively reduces immunocompetent outpatient hospitalization. The FDA currently allows outpatient CCP for the immunosuppressed. Viral specific antibody levels in CCP can range ten-to hundred-fold between donors unlike the uniform viral specific monoclonal antibody dosing. Limited data are available on the efficacy of polyclonal CCP to neutralize variants. We examined 108 pre-delta/pre-omicron donor units obtained before March 2021, 20 post-delta COVID-19/post-vaccination units and one pre-delta/pre-omicron hyperimmunoglobulin preparation for variant specific virus (vaccine-related isolate (WA-1), delta and omicron) neutralization correlated to Euroimmun S1 IgG antibody levels. We observed a 2-to 4-fold and 20-to 40-fold drop in virus neutralization from SARS-CoV-2 WA-1 to delta or omicron, respectively. CCP antibody levels in the upper 10% of the 108 donations as well as 100% of the post-delta COVID-19/post-vaccination units and the hyperimmunoglobulin effectively neutralized all three variants. High-titer CCP neutralizes SARS-CoV-2 variants despite no previous donor exposure to the variants.\n\nKey pointsAll of the post-delta COVID-19/post vaccination convalescent plasma effectively neutralizes the omicron and delta variants.\n\nHigh-titer CCP and hyperimmunoglobulin neutralizes SARS-CoV-2 variants despite no previous donor exposure to the variants.", + "rel_num_authors": 35, + "rel_authors": [ + { + "author_name": "Maggie Li", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Evan J Beck", + "author_inst": "NIAID" + }, + { + "author_name": "Oliver Laeyendecker", + "author_inst": "NIAID & JHMI" + }, + { + "author_name": "Yolanda J Eby", + "author_inst": "JHU" + }, + { + "author_name": "Aaron AR Tobian", + "author_inst": "Johns Hopkins Hospital" + }, + { + "author_name": "Patrizio Caturegli", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Camille Wouters", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Greg Chiklis", + "author_inst": "MRN Diagnostics, LLC Franklin, MA" + }, + { + "author_name": "William Block", + "author_inst": "Blood Centers of America, West Warwick, RI" + }, + { + "author_name": "Robert McKie", + "author_inst": "Innovative Transfusion Medicine, Coral Springs, FL" + }, + { + "author_name": "Michael Joyner", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Timothy D Wiltshire", + "author_inst": "Mayo Clinic, Rochester" + }, + { + "author_name": "Allan B Dietz", + "author_inst": "Mayo Clinic Rochester" + }, + { + "author_name": "Thomas J Gniadek", + "author_inst": "Northshore University Health System" + }, + { + "author_name": "Arell Shapiro", + "author_inst": "Hoag Hospital Newport Beach" + }, + { + "author_name": "Anusha Yarava", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Karen Lane", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Daniel F Hanley", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Evan M M Bloch", + "author_inst": "Johns Hopkins Medicine" + }, + { + "author_name": "Shmuel Shoham", + "author_inst": "The Johns Hopkins Hospital, , MD" + }, + { + "author_name": "Edward Cachay", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Barry R Meisenberg", + "author_inst": "Luminis Health-Anne Arundel Medical Center" + }, + { + "author_name": "Moises Huaman", + "author_inst": "University of Cincinnati" + }, + { + "author_name": "Yuriko Fukuta", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Bela Patel", + "author_inst": "University of Texas Health Science Center" + }, + { + "author_name": "Sonya L Heath", + "author_inst": "University of Alabama in Birmingham" + }, + { + "author_name": "Adam C. Levine", + "author_inst": "Brown University" + }, + { + "author_name": "James H Paxton", + "author_inst": "Wayne State University" + }, + { + "author_name": "Anjan Shweta", + "author_inst": "University of Miami, Miller School of Medicine" + }, + { + "author_name": "Jonathan Gerber", + "author_inst": "University of Massachusetts Chan Medical School" + }, + { + "author_name": "Kelly A Gebo", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Arturo Casadevall", + "author_inst": "Johns Hopkins School of Public Health" + }, + { + "author_name": "Andrew Pekosz", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "David J Sullivan", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "- COVID-19 Serologic Studies Consortium (CSSC)", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.01.22271202", "rel_title": "Longitudinal monitoring of SARS-CoV-2 neutralizing antibody titers and its impact on employee personal wellness decisions", @@ -375905,73 +377689,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.26.22271509", - "rel_title": "Effect of booster vaccination against Delta and Omicron variants in Iceland", - "rel_date": "2022-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.26.22271509", - "rel_abs": "By the end of July 2021, the majority of the Icelandic population had received vaccination against COVID-19. In mid-July a wave of SARS-CoV-2 infections, dominated by the delta variant, spread through the population, followed by an omicron wave in December. A booster vaccination campaign was initiated to curb the spread of the virus. We estimated the risk of infection for different vaccine combinations using vaccination data from 276,028 persons and 963,557 qPCR tests for 277,687 persons. We measured anti-Spike-RBD antibody levels and ACE2-Spike binding inhibitory activity in 371 persons who received one of four recommended vaccination schedules with or without an mRNA vaccine booster. Overall, we found different antibody levels and inhibitory activity between recommended vaccination schedules, which was reflected in the observed risk of SARS-CoV-2 infections. We observed an increased protection following mRNA boosters, against both omicron and delta variant infections, although BNT162b2 boosters provided greater protection against omicron than mRNA-1273 boosters.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Gudmundur L Norddahl", - "author_inst": "deCODE genetics/Amgen, Inc" - }, - { - "author_name": "Pall Melsted", - "author_inst": "deCODE genetics/Amgen; School of Engineering and Natural Sciences, University of Iceland" - }, - { - "author_name": "Kristbjorg Gunnarsdottir", - "author_inst": "deCODE genetics/Amgen, Inc" - }, - { - "author_name": "Gisli H Halldorsson", - "author_inst": "deCODE genetics/Amgen, Inc" - }, - { - "author_name": "Thorunn A Olafsdottir", - "author_inst": "deCODE genetics/Amgen, Inc" - }, - { - "author_name": "Arnaldur Gylfason", - "author_inst": "deCODE genetics/Amgen, Inc" - }, - { - "author_name": "Mar Kristjansson", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Olafur T Magnusson", - "author_inst": "deCODE genetics/Amgen, Inc" - }, - { - "author_name": "Patrick Sulem", - "author_inst": "deCODE genetics/Amgen, Inc" - }, - { - "author_name": "Daniel F Gudbjartsson", - "author_inst": "deCODE genetics/Amgen, Inc; School of Engineering and Natural Sciences, University of Iceland" - }, - { - "author_name": "Unnur Thorsteinsdottir", - "author_inst": "deCODE genetics/Amgen, Inc; Faculty of Medicine, School of Health Sciences, University of Iceland" - }, - { - "author_name": "Ingileif Jonsdottir", - "author_inst": "deCODE genetics/Amgen, Inc" - }, - { - "author_name": "Kari Stefansson", - "author_inst": "deCODE genetics/Amgen, Inc; Faculty of Medicine, School of Health Sciences, University of Iceland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.02.27.22271579", "rel_title": "Vaccine hesitancy strongly correlates with COVID-19 deaths underreporting", @@ -376100,6 +377817,65 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2022.02.28.482377", + "rel_title": "Sleep and circadian rhythm disruption alters the lung transcriptome to predispose to viral infection", + "rel_date": "2022-03-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.28.482377", + "rel_abs": "Sleep and circadian rhythm disruption (SCRD), as encountered during shift work, increases the risk of respiratory viral infection including SARS-CoV-2. However, the mechanism(s) underpinning higher rates of respiratory viral infection following SCRD remain poorly characterised. To address this, we investigated the effects of acute sleep deprivation on the mouse lung transcriptome. Here we show that sleep deprivation profoundly alters the transcriptional landscape of the lung, causing the suppression of both innate and adaptive immune systems, disrupting the circadian clock, and activating genes implicated in SARS-CoV-2 replication, thereby generating a lung environment that promotes viral infection and associated disease pathogenesis. Our study provides a mechanistic explanation of how SCRD increases the risk of respiratory viral infections including SARS-CoV-2 and highlights therapeutic avenues for the prevention and treatment of COVID-19.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Lewis Taylor", + "author_inst": "University of Oxford" + }, + { + "author_name": "Felix von Lendenfeld", + "author_inst": "University of Oxford" + }, + { + "author_name": "Anna Ashton", + "author_inst": "University of Oxford" + }, + { + "author_name": "Harshmeena Sanghani", + "author_inst": "University of Oxford" + }, + { + "author_name": "Eric Tam", + "author_inst": "University of Oxford" + }, + { + "author_name": "Laura Usselmann", + "author_inst": "University of Warwick" + }, + { + "author_name": "Maria Verennetikova", + "author_inst": "University of Warwick" + }, + { + "author_name": "Robert Dallmann", + "author_inst": "University of Warwick" + }, + { + "author_name": "Jane McKeating", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sridhar Vasudevan", + "author_inst": "University of Oxford" + }, + { + "author_name": "Aarti Jagannath", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2022.03.01.481391", "rel_title": "Omicron-specific mRNA vaccine elicits potent immune responses in mice, hamsters, and nonhuman primates", @@ -377631,69 +379407,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.19.22271227", - "rel_title": "Assessment of indoor biological air quality at a mass gathering event in an unimproved exhibition facility during the COVID-19 pandemic using a novel air sampling technology.", - "rel_date": "2022-02-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.19.22271227", - "rel_abs": "The objective was to evaluate the determination of biomarkers of air quality during a mass gathering event at a convention center using a novel air sampling device, AirAnswers(R). This sampler has previously only been used in smaller locations. Here it was run at five crowded locations within the exhibit area for the four days duration of a trade show. The AirAnswers(R) device uses electro-kinetic flow to sample air at high rates and capture bio-aerosols on grounded electrodes in assayable form. Cartridges were removed from the devices and immediately conveyed to the Inspirotec facility in North Chicago, where assays were performed.\n\nBiomarkers determined were for allergens and molds previously described for this system. Testing for a new marker, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA was also included. The method was validated by determination of capture efficiency with reference to an impinger sampler in a Class III controlled environment chamber. Average capture efficiency for triplicate runs was 14%. One SARS-CoV-2 positive sample as found at the registration area, which was physically separate from the main exhibit area.\n\nCat allergen Fel d 1was found in four of the locations, dog allergen Can f 1 at two. The airborne biomarker of mold proliferation, (1[->]3)-{beta}-D-Glucan, was above the assay range in all locations. The widespread presence of this mold marker could be accounted for by signs of water leakage. A generic 18S RNA marker for mold was developed and similarly showed the presence of mold in all locations, as was a genus marker for penicillium. A species marker for Cladosporium cladosporioides was in two locations. Species markers for Eurotium amstelodami and Trichoderma viride were each in a single location.\n\nThe main findings were of the widespread presence of mold markers, and the sporadic appearance of SARS-CoV-2. Masking was recommended but not enforced.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Julian Gordon", - "author_inst": "Inspirotec Inc" - }, - { - "author_name": "Osama Abdullah", - "author_inst": "Inspirotec Inc" - }, - { - "author_name": "Rachel Reboulet", - "author_inst": "Inspirotec Inc" - }, - { - "author_name": "kara Hanson", - "author_inst": "Inspirotec Inc" - }, - { - "author_name": "Christine Sadowski", - "author_inst": "Formerly Inspirotec Inc" - }, - { - "author_name": "Hunter Rennels", - "author_inst": "Inspirotec Inc" - }, - { - "author_name": "Steve Kuemmerle", - "author_inst": "Inspirotec Inc" - }, - { - "author_name": "Richard Tuttle", - "author_inst": "MRI-Global" - }, - { - "author_name": "Kristen Solocinski", - "author_inst": "MRI-Global" - }, - { - "author_name": "Brittany Knight", - "author_inst": "MRI-Global" - }, - { - "author_name": "Jacob Wilkinson", - "author_inst": "MRI-Global" - }, - { - "author_name": "Gavin Macgregor-Skinner", - "author_inst": "Global Biorisk Advisory Council" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.25.22271529", "rel_title": "Study on the usefulness of Direct Saliva sample Collection (DiSC) by polyester swab", @@ -377942,6 +379655,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2022.02.28.22270796", + "rel_title": "Real-world Effectiveness of Casirivimab and Imdevimab in Patients With COVID-19 in the Ambulatory Setting: An Analysis of Two Large US National Claims Databases", + "rel_date": "2022-02-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.28.22270796", + "rel_abs": "Background\n\nIn a phase III clinical trial, casirivimab and imdevimab (CAS+IMD) reduced the composite endpoint of COVID-19-related hospitalizations or all-cause mortality in outpatients at risk of severe disease. This study assessed real-world effectiveness of CAS+IMD.\n\nMethods\n\nData from Optum(R) Clinformatics(R) Data Mart (CDM) and IQVIA Pharmetrics Plus (PMTX+) were used to identify patients diagnosed with COVID-19 in ambulatory settings between December 2020 and March 2021 (PMTX+) and June 2021 (CDM), and either treated with CAS+IMD or untreated but treatment-eligible under Emergency Use Authorization. CAS+IMD-treated patients were matched to untreated patients and followed up to 30 days for the outcome of all-cause mortality or COVID-19-related hospitalizations (CDM) and COVID-19-related hospitalizations (PMTX+). Kaplan-Meier estimators were used to calculate outcome risks; Cox proportional-hazard models estimated adjusted hazard ratios (aHR) with 95% confidence intervals (CI).\n\nResults\n\nFor CDM, 1116 CAS+IMD-treated patients were matched to 5294 untreated patients; for PMTX+, 3280 CAS+IMD-treated patients were matched to 16,284 untreated patients. The 30-day outcome risk was 2.1% and 5.3% in treated and untreated cohorts, respectively (CDM), and the 30-day risk of COVID-19-related hospitalization was 1.9% and 4.8%, respectively (PMTX+); translating to a 61% lower adjusted outcome risk (CDM aHR 0.39 (95% CI 0.26-0.60; PMTX+ aHR 0.39 (95% CI 0.30-0.51). The benefit of treatment was maintained across multiple subgroups of high-risk patients; earlier intervention was associated with improved outcomes.\n\nConclusions\n\nThis real-world study further supports randomized clinical trial findings that treatment with CAS+IMD reduces the risk of hospitalization and mortality in patients infected with susceptible variants.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Wenhui Wei", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Dana Murdock", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Jessica J. Jalbert", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Vera Mastey", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Robert J. Sanchez", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Boaz Hirshberg", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "David M. Weinreich", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Mohamed Hussein", + "author_inst": "Regeneron Pharmaceuticals, Inc." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.28.22271627", "rel_title": "Oropharyngeal Microbiome Profiled at Admission is Predictive of the Need for Respiratory Support Among COVID-19 Patients", @@ -379309,37 +381069,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.02.25.481957", - "rel_title": "A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F", - "rel_date": "2022-02-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.25.481957", - "rel_abs": "The SARS-CoV-2 Omicron sub-variants BA.1 and BA.2 have become the dominant variants worldwide due to enhanced transmissibility and immune evasion. In response to the rise of BA.1 and BA.2, two recent studies by Liu et al. and Iketani et al. provide a detailed analysis of loss of therapeutic antibody potency through evaluation of escape by pseudotyped viruses harboring BA.1 and BA.2 receptor binding domain (RBD) point mutations. Surprisingly, Liu et al. and Iketani et al. observed a profoundly broad escape effect for the individual mutations S371L and S371F. This result cannot be explained by known escape mechanisms of the SARS-CoV-2 RBD, and conflicts with existing computational and experimental escape measurements for S371 mutations performed on monomeric RBD. Through an examination of these conflicting datasets and a structural analysis of the antibodies assayed by Liu et al. and Iketani et al., we propose a mechanism to explain S371L/F escape according to a perturbation of spike trimer conformational dynamics that has not yet been described for any SARS-CoV-2 escape mutation. The proposed mechanism is relevant to Omicron and future variant surveillance as well as therapeutic antibody design.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Nathaniel L Miller", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Thomas Clark", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Rahul Raman", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Ram Sasisekharan", - "author_inst": "Massachusetts Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.02.25.481997", "rel_title": "Adenosine A2A Receptor (A2AR) agonists improve survival in K28-hACE2 mice following SARS CoV-2 infection", @@ -379540,6 +381269,41 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.02.25.481941", + "rel_title": "Follow-up investigation and detailed mutational characterization of the SARS-CoV-2 Omicron variant lineages (BA.1, BA.2, BA.3 and BA.1.1)", + "rel_date": "2022-02-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.25.481941", + "rel_abs": "Aided by extensive protein mutations, the SARS-CoV-2 Omicron (B.1.1.529) variant overtook the previously dominant Delta variant and rapidly spread around the world. It was shown to exhibit significant resistance to current vaccines and evasion from neutralizing antibodies. It is therefore critical to investigate the Omicron mutations trajectories. In this study, a literature search of published articles and SARS-CoV-2 databases was conducted, We explored the full list of mutations in Omicron BA.1, BA.1.1, BA.2, and BA.3 lineages. We described in detail the prevalence and occurrence of the mutations across variants, and how Omicron differs from them. We used GISAID as our primary data source, which provides open-access to genomics data of the SARS-CoV-2 virus, in addition to epidemiological and geographical data. We examined how these mutations interact with each other, their co-occurrence and clustering. Our study offers for the first time a comprehensive description of all mutations with a focus on non-spike mutations and demonstrated that mutations in regions other than the Spike (S) genes are worth investigating further. Our research established that the Omicron variant has retained some mutations reported in other SARS-CoV-2 variants, yet many of its mutations are extremely rare in other variants and unique to Omicron. Some of these mutations have been linked to the transmissibility and immune escape of the virus, and indicate a significant shift in SARS-CoV-2 evolution. The most likely theories for the evolution of the Omicron variant were also discussed.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Qussai Abbas", + "author_inst": "SCAMT Institute, ITMO University" + }, + { + "author_name": "Alexey V Kusakin", + "author_inst": "SCAMT Institute, ITMO University" + }, + { + "author_name": "Kinda Sharrouf", + "author_inst": "SCAMT Institute, ITMO University" + }, + { + "author_name": "Susan Jyakhwo", + "author_inst": "SCAMT Institute, ITMO University" + }, + { + "author_name": "Aleksey S Komissarov", + "author_inst": "SCAMT Institute, ITMO University" + } + ], + "version": "1", + "license": "cc_no", + "type": "confirmatory results", + "category": "genetics" + }, { "rel_doi": "10.1101/2022.02.25.22271501", "rel_title": "Impact of Omicron variant on the response to SARS-CoV-2 mRNA vaccination in multiple myeloma and monoclonal gammopathies", @@ -381163,41 +382927,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.02.21.22271309", - "rel_title": "Association of Workload and Practice of Respectful Maternity Care Among the Healthcare Providers, Before and During the COVID-19 Pandemic in South Western Nepal: A Cross-Sectional Study", - "rel_date": "2022-02-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.21.22271309", - "rel_abs": "IntroductionRespectful maternity care is an approach that involves respecting womens belief, choices, emotions, and dignity during the childbirth process. As the workload among maternity care workforce affects intrapartum quality care, respectful maternity care might have also been affected, particularly during the pandemic. Thus, this study was conducted to examine the association between workload among healthcare providers and their practice of respectful maternity care, before and during the pandemic.\n\nMethodsA cross-sectional study was conducted in South Western Nepal. A total of 267 healthcare providers from 78 birthing centers were included. Data collection was done through telephone interviews. The exposure variable was workload among the healthcare providers, and the outcome variable was respectful maternity care practice before and during the COVID-19 pandemic. Multilevel mixed-effect linear regression was used to examine the association.\n\nResultsThe median client-provider ratio before and during the pandemic was 21.7 and 13.0, respectively. The mean score of respectful maternity care practice was 44.5 (SD 3.8) before the pandemic, which was decreased to 43.6 (SD 4.5) during the pandemic. Client-provider ratio was negatively associated with respectful maternity care practice for both times; before (Coef. -5.16; 95% CI -8.41 to -1.91) and during (Coef. -7.47; 95% CI -12.72 to -2.23) the pandemic.\n\nConclusionsWhile a higher client-provider was associated with a lower respectful maternity care practice score both before and during the COVID-19 pandemic, the coefficient was larger during the pandemic. Therefore, workload among the healthcare providers should be considered before the implementation of respectful maternity care, and more attention should be given during the pandemic.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Alpha Pokharel", - "author_inst": "Green Tara Nepal" - }, - { - "author_name": "Junko Kiriya", - "author_inst": "The University of Tokyo Graduate School of Medicine Faculty of Medicine: Tokyo Daigaku Daigakuin Igakukei Kenkyuka Igakubu" - }, - { - "author_name": "Akira Shibanuma", - "author_inst": "The University of Tokyo Graduate School of Medicine Faculty of Medicine: Tokyo Daigaku Daigakuin Igakukei Kenkyuka Igakubu" - }, - { - "author_name": "Ram Silwal", - "author_inst": "The University of Tokyo Graduate School of Medicine Faculty of Medicine: Tokyo Daigaku Daigakuin Igakukei Kenkyuka Igakubu" - }, - { - "author_name": "Masamine Jimba", - "author_inst": "The University of Tokyo Graduate School of Medicine Faculty of Medicine: Tokyo Daigaku Daigakuin Igakukei Kenkyuka Igakubu" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2022.02.22.22270091", "rel_title": "Abdominal Imaging Associates Body Composition with COVID-19 Severity", @@ -381386,6 +383115,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.22.22271359", + "rel_title": "Gestational SARS-CoV-2 infection is associated with placental expression of immune and trophoblast genes", + "rel_date": "2022-02-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.22.22271359", + "rel_abs": "IntroductionMaternal SARS-CoV-2 infection during pregnancy is associated with adverse pregnancy outcomes and can have effects on the placenta, even in the absence of severe disease or vertical transmission to the fetus. This study aimed to evaluate histopathologic and molecular effects in the placenta after SARS-CoV-2 infection during pregnancy.\n\nMethodsWe performed a study of 45 pregnant participants from the Generation C prospective cohort study at the Mount Sinai Health System in New York City. We compared histologic features and the expression of 48 immune and trophoblast genes in placentas delivered from 15 SARS-CoV-2 IgG antibody positive and 30 IgG SARS-CoV-2 antibody negative mothers. Statistical analyses were performed using Fishers exact tests, Spearman correlations and linear regression models.\n\nResultsThe median gestational age at the time of SARS-CoV-2 IgG serology test was 35 weeks. Two of the IgG positive participants also had a positive RT-PCR nasal swab at delivery. 82.2% of the infants were delivered at term ([≥]37 weeks), and gestational age at delivery did not differ between the SARS-CoV-2 antibody positive and negative groups. No significant differences were detected between the groups in placental histopathology features. Differential expression analyses revealed decreased expression of two trophoblast genes (PSG3 and CGB3) and increased expression of three immune genes (CXCL10, TLR3 and DDX58) in placentas delivered from SARS-CoV-2 IgG positive participants.\n\nDiscussionSARS-CoV-2 infection during pregnancy is associated with gene expression changes of immune and trophoblast genes in the placenta at birth which could potentially contribute to long-term health effects in the offspring.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Corina Lesseur", + "author_inst": "Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Rebecca H Jessel", + "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai." + }, + { + "author_name": "Sophie Ohrn", + "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Yula Ma", + "author_inst": "Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Qian Li", + "author_inst": "Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Fumiko Dekio", + "author_inst": "Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Rachel I Brody", + "author_inst": "Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "James G Wetmur", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Frederieke A.J. Gigase", + "author_inst": "Department of Psychiatry, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Molly Lieber", + "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Whitney Lieb", + "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jezelle Lynch", + "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Omara Afzal", + "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Erona Ibroci", + "author_inst": "Department of Psychiatry, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Anna-Sophie Rommel", + "author_inst": "Department of Psychiatry, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Teresa Janevic", + "author_inst": "Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Joanne Stone", + "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Elizabeth A Howell", + "author_inst": "Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Romeo R Galang", + "author_inst": "CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Siobhan M Dolan", + "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Veerle Bergink", + "author_inst": "Department of Psychiatry, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Lotje D De Witte", + "author_inst": "Department of Psychiatry, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jia Chen", + "author_inst": "Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "sexual and reproductive health" + }, { "rel_doi": "10.1101/2022.02.22.22270838", "rel_title": "Three-month follow-up of heterologous vs homologous third vaccination in kidney transplant recipients", @@ -382677,57 +384513,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2022.02.22.22271342", - "rel_title": "Impact of BNT162b2 mRNA Vaccination on the Development of Short and Long-term Vaccine-Related Adverse Events in Inflammatory Bowel Disease: A Multi-Center Prospective Study", - "rel_date": "2022-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.22.22271342", - "rel_abs": "IntroductionSARS-CoV-2 vaccination has been effective in protecting against severe COVID-19 infections and related mortality. It is recommended for all individuals including patients with inflammatory bowel disease (IBD). However, safety data is lacking in this group of patients. Therefore, we aim to evaluate the short- and long-term vaccine related adverse events (AEs) in patients with IBD.\n\nMethodThis is a prospective, observational cohort study investigating short- and long-term AEs related to BNT162b2 vaccine in patients with IBD (study group) after first and second dose compared to healthy participants (study group). Patients were recruited at the time of attendance to clinic or infusion rooms. Short term (<3 weeks) localized and systemic AEs were assessed via questionnaire. Follow-up phone-based survey was made to collect data on long term (up to 24 weeks) AEs.\n\nResultsA total of 408 patients answered the questionnaires, 204 patients in each group, the study and control group. No serious adverse events were reported in either the study nor the control group after the first or the second dose. Participants in the control group reported more frequent pain at the injection site than those in the study group after the first dose (58 (57%) vs 38 (37%) respectively, P-value= 0.005). After the second dose, tiredness was reported more frequently in the control group [49 (48%)] compared to the study group [25 (24%), (P-value<0.001)]. At 20-24 weeks post vaccination, 386 out of 408 (94.6%) patients were willing to participate in the follow-up phone based questionnaire (196 (96.1%) in the study group vs 190 (93.1%) in the control group). In both groups, none of the patients reported local, systemic or severe adverse events (0 out of 386) at week 20-244 post second dose.\n\nConclusionThe BNT162b2 vaccine is safe in patients with IBD. No severe or long-term adverse events were reported in our study. The frequency of local and systemic adverse events after the second dose was generally higher among healthy participants compared to patients with IBD. Further studies including a larger cohort with longer follow-up duration are needed to assess for possible rare adverse events.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Mohammad Shehab", - "author_inst": "Mubarak Hospital" - }, - { - "author_name": "Fatema Alrashed", - "author_inst": "Kuwait University" - }, - { - "author_name": "Israa Abdullah", - "author_inst": "Kuwait Hospital" - }, - { - "author_name": "Ahmad Alfadhli", - "author_inst": "Mubarak Hospital" - }, - { - "author_name": "Hamad Ali", - "author_inst": "Kuwait University" - }, - { - "author_name": "Mohamed Abu-farha", - "author_inst": "Dasman Diabetes Institute" - }, - { - "author_name": "Arshad Channanath", - "author_inst": "Dasman Diabetes Institute" - }, - { - "author_name": "Jehad Abubaker", - "author_inst": "Dasman Diabetes Institute" - }, - { - "author_name": "Fahd Al-Mulla", - "author_inst": "Dasman Diabetes Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2022.02.21.22271127", "rel_title": "Favourable vaccine-induced SARS-CoV-2 specific T cell response profile in patients undergoing immune-modifying therapies", @@ -382956,6 +384741,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.02.21.481345", + "rel_title": "Mucosal Immunization of Cynomolgus Macaques with Adenoviral Vector Vaccine Elicits Neutralizing Nasal and Serum Antibody to Several SARS-CoV-2 Variants", + "rel_date": "2022-02-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.21.481345", + "rel_abs": "The emergence of SARS-CoV-2 variants continues to be a major obstacle for controlling the global pandemic. Despite the currently authorized SARS-CoV-2 vaccines ability to reduce severe disease and hospitalization, new immunization strategies are needed that enhance mucosal immune responses, inhibit community transmission, and provide protection against emerging variants. We have developed a mucosally delivered, non-replicating recombinant adenovirus vector (rAd5) vaccine, that has proven efficacy in the clinic against other respiratory viruses [1]. Here we evaluated the immunogenicity of three candidate SARS-CoV-2 vaccines in cynomolgus macaques that contained spike (S) and/or nucleocapsid (N) from either the Wuhan or the beta variant to select a candidate for future clinical development. Mucosal immunization with the Wuhan specific S vaccine (ED90) induced significant cross-reactive serum IgG responses against to Wuhan, beta, gamma and delta lineages, and generated substantial serum neutralizing activity. In nasal samples, ED90 immunization induced 1000-fold increases in IgA to all variants of concern tested and had neutralizing activity against Wuhan and delta. While immunization with the beta specific vaccine (ED94) enhanced IgG and IgA responses to homologous beta variant S and RBD, this approach resulted in less cross-reactive responses to other variants in the serum and nasal passages compared to ED90. As ED90 immunization induced the most robust cross-reactive systemic and mucosal antibody responses, this candidate was chosen for future clinical development.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Becca A Flitter", + "author_inst": "Vaxart Inc." + }, + { + "author_name": "Colin A Lester", + "author_inst": "Vaxart Inc." + }, + { + "author_name": "Sarah N Tedjakusuma", + "author_inst": "Vaxart Inc." + }, + { + "author_name": "Emery G Dora", + "author_inst": "Vaxart Inc." + }, + { + "author_name": "Nadine Peinovich", + "author_inst": "Vaxart Inc." + }, + { + "author_name": "Mario Cortese", + "author_inst": "Vaxart Inc." + }, + { + "author_name": "Clarissa I Martinez", + "author_inst": "Vaxart Inc." + }, + { + "author_name": "Clara B Jegede", + "author_inst": "Vaxart Inc." + }, + { + "author_name": "Elena D Neuhaus", + "author_inst": "Vaxart Inc." + }, + { + "author_name": "Sean N Tucker", + "author_inst": "Vaxart Inc" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.02.21.481262", "rel_title": "Serological screening in wild ruminants in Germany, 2021/22: No evidence of SARS-CoV-2, bluetongue virus or pestivirus spread but high seroprevalences against Schmallenberg virus", @@ -384590,45 +386430,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2022.02.18.22271191", - "rel_title": "Childhood Trauma Exposure Increases Long COVID Risk", - "rel_date": "2022-02-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.18.22271191", - "rel_abs": "BackgroundA proportion of those who contract COVID-19 will develop long COVID (i.e., symptoms that persist for three months or more). Childhood trauma contributes to a pro-inflammatory state in adulthood evidenced by high morbidity and early mortality, but it has not yet been investigated as a risk factor for long COVID.\n\nMethodsParticipants (N=338) completed online measures of premorbid health, COVID-19 positivity, symptoms, recovery, depression, anxiety, and post-traumatic stress disorder (PTSD). Questionnaires about childhood and recent traumatic experiences were completed by half of the sample (N=162).\n\nResultsFifty-three percent of participants developed long COVID, of whom over 60% endorsed exercise intolerance and protracted myalgias, headaches, brain fog, and shortness of breath. Participants who experienced at least one childhood traumatic event were 3-fold more likely to develop the syndrome (OR=3.11, 95% CI, 1.49 to 6.48), while risk was nearly 6-fold increased for two or more events (OR=5.67, CI, 2.44 to 13.13). Regression models showed childhood trauma (OR=5.32, CI, 1.44 to 19.68), older age (OR=1.11, CI, 1.06 to 1.16), female sex (OR=4.02, CI, 1.34 to 12.12), along with chest pain (OR=8.77, CI, 2.80 to 27.43), brain fog (OR=3.33, CI, 1.16 to 9.57) and phantosmia (OR=5.90, CI, 1.40 to 24.86) during acute illness accurately classified long COVID status in 87% of participants.\n\nInterpretationsEarly adversity is a risk-factor for long COVID, likely due to altered immune response, central sensitization, and peripheral dysfunction. Childhood trauma, a crucial social determinant of health, should be routinely assessed in COVID-19 survivors and may aid in determining prognosis.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Alicia W. Villanueva van den Hurk", - "author_inst": "University of Dayton" - }, - { - "author_name": "Cady Ujvari", - "author_inst": "University of Dayton" - }, - { - "author_name": "Noah Greenspan", - "author_inst": "Pulmonary Wellness Foundation; Pulmonary Wellness COVID Rehabilitation and Recovery Center" - }, - { - "author_name": "Dolores Malaspina", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Xavier F. Jimenez", - "author_inst": "Zucker School of Medicine at Hofstra University; Long Island Jewish Medical Center/Northwell Health" - }, - { - "author_name": "Julie Walsh-Messinger", - "author_inst": "University of Dayton" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.21.22271298", "rel_title": "Effectiveness of Covid-19 vaccines against symptomatic and asymptomatic SARS-CoV-2 infections in an urgent care setting", @@ -385037,6 +386838,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.02.21.22271299", + "rel_title": "Psychological and financial impacts of COVID-19-related travel measures: An international cross-sectional study", + "rel_date": "2022-02-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.21.22271299", + "rel_abs": "BackgroundThe impact of COVID-19 international travel restrictions has to date, not been fully explored, and with the ongoing threat that new variants could potentially restrict movement further, it is important to consider the impacts that travel restrictions have on community members. This study aimed to evaluate the psychological and financial impact of COVID-19 travel restrictions on those separated from their partners or immediate families, as well as temporary visa holders who were unable to migrate.\n\nMethodsBetween 4 November 2021 to 1 December 2021, we executed a cross-sectional online survey targeting three specific groups; (1) those stranded from their partners; (2) those stranded from immediate families; and (3) temporary visa holders unable to migrate or cross international borders. We collected data on respondents demographic profile; the nature of COVID-19-related travel impacts; depression, anxiety, and stress levels (using the validated DASS-21); and finally, data on respondents financial, employment and accommodation situation.\n\nResults1363 respondents located globally completed the survey. 71.2% reported financial stress, 76.8% ([Formula], SD=5.94) reported moderate-to-extremely severe depression, 51.6% ([Formula], SD=5.49) moderate-to-extremely severe anxiety, and 62.6% ([Formula], SD=5.55) moderate-to-extremely severe stress levels. Statistically significant factors associated with moderate-to-extremely severe depression, anxiety, and stress included being female, chronic illness, and experiencing financial stress. Employment during COVID-19 - specifically essential services workers or unemployed - was associated with higher levels of anxiety and stress, with only essential workers being a predictor of higher stress severity. Factors that provided psychological protection included being older and having children.\n\nConclusionThis study is one of the first to explore the impact COVID-19-related international travel restrictions have had on the financial status and psychological health of affected individuals. It highlights the significant human cost associated with the restrictions and identifies psychologically vulnerable populations. These results will help the design of targeted health and social policy responses.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Pippa McDermid", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Soumya Sooppiyaragath", + "author_inst": "Independent Research Psychologist" + }, + { + "author_name": "Adam Craig", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Meru Sheel", + "author_inst": "University of Sydney" + }, + { + "author_name": "Katrina Blazek", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Siobhan Talty", + "author_inst": "Freelance Monitoring, Evaluation, Accountability and Learning Technical Advisor" + }, + { + "author_name": "Holly Seale", + "author_inst": "University of New South Wales" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.02.21.22271289", "rel_title": "Breakthrough SARS-CoV-2 infections in immune mediated disease patients undergoing B cell depleting therapy", @@ -386732,85 +388576,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, - { - "rel_doi": "10.1101/2022.02.17.22270679", - "rel_title": "Evolutionary Trajectories of SARS-CoV-2 Alpha and Delta Variants in White-Tailed Deer in Pennsylvania", - "rel_date": "2022-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.17.22270679", - "rel_abs": "Introductory paragraphThe SARS-CoV-2 pandemic likely began by viral spillover from animals to humans1-3; today multiple animal species are known to be susceptible to infection4-8. White-tailed deer, Odocoileus virginianus are infected in North America at substantial levels9-11, and genomic data suggests that a variant in deer may have spilled back to humans12,13. Here we characterize SARS-CoV-2 in deer from Pennsylvania (PA) sampled during fall and winter 2021. Of 123 nasal swab samples analyzed by RT-qPCR, 20 (16.3%) were positive for SARS-CoV-2. Seven whole-genome sequences were obtained, together with six more partial spike sequences. These annotated as alpha and delta variants, the first reported observations of these lineages in deer, documenting multiple new jumps from humans to deer. The alpha lineage persisted in deer after its displacement by delta in humans, and deer-derived alpha variants diverged significantly from those in humans, consistent with a distinctive evolutionary trajectory in deer.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Andrew D Marques", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Scott Sherrill-Mix", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "John Everett", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Hriju Adhikari", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Shantan Reddy", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Julie C Ellis", - "author_inst": "Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, PA 19348" - }, - { - "author_name": "Haley Zeliff", - "author_inst": "Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, PA 19348" - }, - { - "author_name": "Sabrina S Greening", - "author_inst": "Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, PA 19348" - }, - { - "author_name": "Carolyn C Cannuscio", - "author_inst": "Leonard Davis Institute of Health Economics, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Katherine M Strelau", - "author_inst": "Leonard Davis Institute of Health Economics, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Ronald G Collman", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Brendan J Kelly", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Kyle G Rodino", - "author_inst": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Frederic D Bushman", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Roderick B Gagne", - "author_inst": "Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, PA 19348" - }, - { - "author_name": "Eman Anis", - "author_inst": "Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, PA 19348" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.19.22271221", "rel_title": "Risk of SARS-CoV-2 reinfection 18 months after primary infection: population-level observational study.", @@ -387039,6 +388804,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.17.22271057", + "rel_title": "Autoantibodies linked to autoimmune diseases associate with COVID-19 outcomes", + "rel_date": "2022-02-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.17.22271057", + "rel_abs": "The SARS-CoV-2 infection is associated with increased levels of autoantibodies targeting immunological proteins such as cytokines and chemokines. Reports further indicate that COVID-19 patients may develop a wide spectrum of autoimmune diseases due to reasons not fully understood. Even so, the landscape of autoantibodies induced by SARS-CoV-2 infection remains uncharted territory. To gain more insight, we carried out a comprehensive assessment of autoantibodies known to be linked to diverse autoimmune diseases observed in COVID-19 patients, in a cohort of 248 individuals, of which171 were COVID-19 patients (74 with mild, 65 moderate, and 32 with severe disease) and 77were healthy controls. Dysregulated autoantibody serum levels, characterized mainly by elevated concentrations, occurred mostly in patients with moderate or severe COVID-19 infection, and was accompanied by a progressive disruption of physiologic IgG and IgA autoantibody signatures. A similar perturbation was found in patients with anosmia. Notably, autoantibody levels often accompanied anti-SARS-CoV-2 antibody concentrations, being both indicated by random forest classification as strong predictors of COVID-19 outcome, together with age. Moreover, higher levels of autoantibodies (mainly IgGs) were seen in the elderly with severe disease compared with young COVID-19 patients with severe disease. These findings suggest that the SARS-CoV-2 infection induces a broader loss of self-tolerance than previously thought, providing new ideas for therapeutic interventions.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Gabriela Crispim Baiocchi", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Aristo Vojdani", + "author_inst": "Department of Immunology, Immunosciences Laboratory, Inc., Los Angeles, CA, United States" + }, + { + "author_name": "Avi Z Rosenberg", + "author_inst": "Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA" + }, + { + "author_name": "Elroy Vojdani", + "author_inst": "Regenera Medical 11860 Wilshire Blvd., Ste. 301, Los Angeles, CA 90025 USA" + }, + { + "author_name": "Gilad Halpert", + "author_inst": "Ariel University, Israel" + }, + { + "author_name": "Yuri Ostrinski", + "author_inst": "Ariel University, Israel" + }, + { + "author_name": "Israel Zyskind", + "author_inst": "Department of Pediatrics, NYU Langone Medical Center, New York, NY, USA" + }, + { + "author_name": "Igor Salerno Filgueiras", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Lena F. Schimke", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Alexandre H. C. Marques", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Lasse M. Giil", + "author_inst": "Department of Internal Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway" + }, + { + "author_name": "Yael Bublil Lavi", + "author_inst": "Department of Chemistry Ben Gurion University Beer-Sheva, 84105, Israel" + }, + { + "author_name": "Jonathan I. Silverberg", + "author_inst": "Department of Dermatology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA" + }, + { + "author_name": "Jason Zimmerman", + "author_inst": "Maimonides Medical Center, Brooklyn, NY, USA" + }, + { + "author_name": "Dana Ashley Hill", + "author_inst": "ResourcePath, Sterling, VA" + }, + { + "author_name": "Amanda Thornton", + "author_inst": "ResourcePath, Sterling, VA" + }, + { + "author_name": "Myungjin Kim", + "author_inst": "Data Science Initiative at Brown University, Providence, RI, USA" + }, + { + "author_name": "Roberta De Vito", + "author_inst": "Department of Biostatistics and the Data Science Initiative at Brown University, Providence, RI, USA" + }, + { + "author_name": "Dennyson Leandro M. Fonseca", + "author_inst": "Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Desiree Rodrigues Placa", + "author_inst": "Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Paula Paccielli Freire", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Niels Olsen Saraiva Camara", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Vera Lucia Garcia Calich", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Harald Heidecke", + "author_inst": "CellTrend Gesellschaft mit beschrankter Haftung (GmbH), Luckenwalde, Germany" + }, + { + "author_name": "Miriam T. Lattin", + "author_inst": "Department of Biology, Yeshiva University, Manhatten, NY, USA" + }, + { + "author_name": "Hans D. Ochs", + "author_inst": "Department of Pediatrics, University of Washington School of Medicine, and Seattle Children's Research Institute, Seattle, WA, USA" + }, + { + "author_name": "Gabriela Riemekasten", + "author_inst": "Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lubeck, Lubeck, Germany" + }, + { + "author_name": "Howard Amital", + "author_inst": "Department of Medicine B, Sheba Medical Center, Tel Hashomer, Israel" + }, + { + "author_name": "Otavio Cabral Marques", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Yehuda Shoenfeld", + "author_inst": "Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2022.02.17.22271099", "rel_title": "Timeliness of reporting of SARS-CoV-2 seroprevalence results and their utility for infectious disease surveillance", @@ -388458,125 +390358,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.16.22270842", - "rel_title": "The SARS-CoV2 envelope is distinct from host membranes, exposes pro-coagulant lipids, and can be inactivated in vivo by surfactant-containing oral rinses.", - "rel_date": "2022-02-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.16.22270842", - "rel_abs": "The lipid envelope of SARS-CoV2 is an essential component of the virus, however its molecular composition is unknown. Addressing this knowledge gap could support the design of anti-viral agents, and further understanding of viral interaction with extracellular host proteins, infectivity, pathogenicity, and innate immune system clearance. Lipidomics analysis of SARS-CoV2 particles generated from Vero or A549 cells revealed that the virus envelope comprised mainly of phospholipids (PL), primarily phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylinositol (PI), with very little cholesterol, sphingolipids or other lipids, indicating significant differences from host membranes. Unlike healthy cellular membranes, procoagulant aminoPL (aPL), specifically PE and phosphatidylserine (PS), were present on the external side at levels far exceeding those seen on activated platelets. As a result, purified virions directly promoted coagulation. To investigate whether these differences enabled the viral envelope to be selectively targeted at relevant sites in vivo, we tested whether non-toxic oral rinses containing lipid disrupting chemicals could reduce viral infectivity. Products containing PL-disrupting surfactant solutions (cetylpyridinium chloride (CPC) or ethyl lauroyl arginate) met EN14476 virucidal standards in vitro, however products containing essential oils, PVP-I, or Chlorhexidine did not, nor did rinses containing components that altered the critical micelle concentration of CPC. This result was recapitulated in vivo, where a 30-second oral rinse with CPC-mouthwash eliminated live virus in the oral cavity of COVID19 patients for at least 1hr, while PVP-Iodine and saline mouthwashes were ineffective. Thus, the SARS-CoV2 lipid envelope is distinct from the host plasma membrane which may enable design of selective anti-viral approaches, it exposes PE and PS which may influence thrombosis, pathogenicity, and inflammation, and can be selectively targeted in vivo by specific oral rinses.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Zack Saud", - "author_inst": "Cardiff University" - }, - { - "author_name": "Victoria J Tyrrell", - "author_inst": "Cardiff University" - }, - { - "author_name": "Andreas Zaragkoulias", - "author_inst": "Cardiff University" - }, - { - "author_name": "Majd B Protty", - "author_inst": "Cardiff University" - }, - { - "author_name": "Evelina Statkute", - "author_inst": "Cardiff University" - }, - { - "author_name": "Anzelika Rubina", - "author_inst": "Cardiff University" - }, - { - "author_name": "Kirsten Bentley", - "author_inst": "Cardiff University" - }, - { - "author_name": "Daniel A White", - "author_inst": "Cardiff University" - }, - { - "author_name": "Patricia Dos Santos Rodrigues", - "author_inst": "Cardiff University" - }, - { - "author_name": "Robert C Murphy", - "author_inst": "University of Colorado Denver" - }, - { - "author_name": "Harald Kofeler", - "author_inst": "Medical University of Graz" - }, - { - "author_name": "William J Griffiths", - "author_inst": "Swansea University" - }, - { - "author_name": "Jorge Alvarez-Jarreta", - "author_inst": "European Bioinformatics Institute" - }, - { - "author_name": "Richard William Brown", - "author_inst": "Cardiff and Vale University Health Board" - }, - { - "author_name": "Robert G Newcombe", - "author_inst": "Cardiff University" - }, - { - "author_name": "James Heyman", - "author_inst": "Cardiff and Vale University Health Board" - }, - { - "author_name": "Manon Pritchard", - "author_inst": "Cardiff University" - }, - { - "author_name": "Robert WJ Mcleod", - "author_inst": "Cardiff University" - }, - { - "author_name": "Arvind Arya", - "author_inst": "Betsi Cadwaladr University Health Board" - }, - { - "author_name": "Ceri-Ann Lynch", - "author_inst": "Cwm Taf University Health Board" - }, - { - "author_name": "David Owens", - "author_inst": "Cardiff and Vale University Health Board" - }, - { - "author_name": "Vince Jenkins", - "author_inst": "Cardiff and Vale University Health Board" - }, - { - "author_name": "Niklaas J Buurma", - "author_inst": "Cardiff University" - }, - { - "author_name": "Valerie B O'Donnell", - "author_inst": "Cardiff University" - }, - { - "author_name": "David W Thomas", - "author_inst": "Cardiff University" - }, - { - "author_name": "Richard J Stanton", - "author_inst": "Cardiff University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.15.22270954", "rel_title": "Validation of the RT-LAMP assay in a large cohort of nasopharyngeal swab samples shows that it is a useful screening method for detecting SARS-CoV-2 and its VOC variants", @@ -388837,6 +390618,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, + { + "rel_doi": "10.1101/2022.02.14.22270925", + "rel_title": "Modeling COVID-19 disease processes by remote elicitation of causal Bayesian networks from medical experts", + "rel_date": "2022-02-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.14.22270925", + "rel_abs": "BackgroundCOVID-19 is a new multi-organ disease, caused by the SARS-CoV-2 virus, resulting in considerable worldwide morbidity and mortality. While many recognized pathophysiological mechanisms are involved, their exact causal relationships remain opaque. A better understanding is needed for predicting their progression, targeting therapeutic approaches, and improving patient outcomes. While many mathematical causal models describe COVID-19 epidemiology, none have been developed for its pathophysiology. The viruss rapid and extensive spread and therapeutic responses made this particularly difficult. Initially, no large patient datasets were publicly available, and their data remains limited. The medical literature was flooded with unfiltered, technical and sometimes conflicting pre-review reports. Clinicians in many countries had little time for academic consultations, and in-person meetings were unsafe.\n\nMethods and FindingsIn early 2020, we began a major project to develop causal models of the pathophysiological processes underlying the diseases clinical manifestations. We used Bayesian network (BN) models, because they provide both powerful tools for calculation and clear maps of probabilistic causal influence between semantically meaningful variables, as directed acyclic graphs (DAGs). Hence, they can incorporate expert opinion and numerical data, and produce explainable results. Dynamic causal BNs, which represent successive \"time slices\" of the system, can capture feedback loops and long-term disease progression.\n\nTo obtain the likely causal structures, we used extensive elicitation of expert opinion in structured online sessions. Centered in Australia, with its exceptionally low COVID-19 burden, we managed to obtain many consultation hours. Groups of clinical and other subject matter specialists, all independent volunteers, were enlisted to filter, interpret and discuss the literature and develop a current consensus. We aimed to capture the experts understanding, so we encouraged discussion and inclusion of theoretically salient latent (i.e., unobservable) variables, documented supporting literature while noting controversies, and allowed experts to propose mechanisms by extrapolation from other diseases. Intermediary experts with some combined expertise facilitated the exchange of knowledge to BN modelers and vice versa. Our method was iterative and incremental: we systematically refined and checked the group output with one-on-one follow-up meetings with the original and new experts to validate previous results. In total, 35 experts contributed 126 face-to-face hours, and could review our products.\n\nConclusionsOur method demonstrates and describes an improved procedure for developing BNs via expert elicitation, which can be implemented rapidly by other teams modeling emergent complex phenomena. The results presented are two key models, for the initial infection of the respiratory tract and the possible progression to complications, as causal DAGs and BNs with corresponding verbal descriptions, dictionaries and sources. These are the first published causal models of COVID-19 pathophysiology, with three anticipated applications: (i) making expert knowledge freely available in a readily understandable and updatable form; (ii) guiding design and analysis of observational and clinical studies, by identifying potential mediators, confounders, and modifiers of treatment effects; (iii) developing and validating parameterized automated tools for causal reasoning and decision support, in clinical and policy settings. We are currently developing such tools for the initial diagnosis, resource management, and prognosis of COVID-19, parameterized using the ISARIC and LEOSS databases.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Steven Mascaro", + "author_inst": "Faculty of Information Technology, Monash University" + }, + { + "author_name": "Yue Wu", + "author_inst": "School of Public Health, University of Sydney" + }, + { + "author_name": "Owen Woodberry", + "author_inst": "Faculty of Information Technology, Monash University" + }, + { + "author_name": "Erik P Nyberg", + "author_inst": "Faculty of Information Technology, Monash University" + }, + { + "author_name": "Ross Pearson", + "author_inst": "Faculty of Information Technology, Monash University" + }, + { + "author_name": "Jessica A Ramsay", + "author_inst": "Telethon Kids Institute" + }, + { + "author_name": "Ariel Mace", + "author_inst": "Department of General Paediatrics, Perth Children's Hospital" + }, + { + "author_name": "David Foley", + "author_inst": "Microbiology, PathWest Laboratory Medicine" + }, + { + "author_name": "Tom Snelling", + "author_inst": "School of Public Health, University of Sydney" + }, + { + "author_name": "Ann E Nicholson", + "author_inst": "Faculty of Information Technology, Monash University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.16.480801", "rel_title": "A natural broad-spectrum inhibitor of enveloped virus entry, effective against SARS-CoV-2 and Influenza A Virus in preclinical animal models.", @@ -390268,93 +392104,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2022.02.11.22270775", - "rel_title": "Favipiravir, lopinavir-ritonavir or combination therapy (FLARE): a randomised, double blind, 2x2 factorial placebo-controlled trial of early antiviral therapy in COVID-19", - "rel_date": "2022-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.11.22270775", - "rel_abs": "BackgroundEarly antiviral treatment is effective for COVID-19 but currently available agents are expensive. Favipiravir is routinely used in many countries, but efficacy is unproven. Antiviral combinations have not been systematically studied. We aimed to evaluate the effect of favipiravir, lopinavir-ritonavir or the combination of both agents on SARS-CoV-2 viral load trajectory when administered early.\n\nMethodsWe conducted a Phase 2, proof of principle, randomised, placebo-controlled, 2x2 factorial, double-blind trial of outpatients with early COVID-19 (within 7 days of symptom onset) at two sites in the United Kingdom. Participants were randomised using a centralised online process to receive: favipiravir (1800mg twice daily on Day 1 followed by 400mg four times daily on Days 2-7) plus lopinavir-ritonavir (400mg/100mg twice daily on Day 1, followed by 200mg/50mg four times daily on Days 2-7); favipiravir plus lopinavir-ritonavir placebo; lopinavir-ritonavir plus favipiravir placebo; or both placebos. The primary outcome was SARS-CoV-2 viral load at Day 5, accounting for baseline viral load. ClinicalTrials{middle dot}gov: NCT04499677.\n\nFindingsBetween 6 October 2020 and 4 November 2021, we recruited 240 participants. For the favipiravir+lopinavir-ritonavir, favipiravir+placebo, lopinavir-ritonavir+placebo and placebo-only arms, we recruited 61, 59, 60 and 60 participants and analysed 55, 56, 55 and 58 participants respectively who provided viral load measures at Day 1 and Day 5. In the primary analysis, the mean viral load in the favipiravir+placebo arm had decreased by 0.57 log10 (95% CI -1.21 to 0.07, p=0.08) and in the lopinavir-ritonavir+placebo arm by 0.18 log10 (95% CI -0.82 to 0.46, p=0.58) more than in the placebo arm at Day 5. There was no significant interaction between favipiravir and lopinavir-ritonavir (interaction coefficient term: 0.59 log10, 95% CI -0.32 to 1.50, p=0.20). More participants had undetectable virus at Day 5 in the favipiravir+placebo arm compared to placebo only (46.3% vs 26.9%, odds ratio (OR): 2.47, 95% CI 1.08 to 5.65; p=0.03). Adverse events were observed more frequently with lopinavir-ritonavir, mainly gastrointestinal disturbance. Favipiravir drug levels were lower in the combination arm than the favipiravir monotherapy arm.\n\nInterpretationAt the current doses, no treatment significantly reduced viral load in the primary analysis. Favipiravir requires further evaluation with consideration of dose escalation. Lopinavir-ritonavir administration was associated with lower plasma favipiravir concentrations.\n\nFundingLifeArc, UK.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "David M Lowe", - "author_inst": "University College London" - }, - { - "author_name": "Li-An K Brown", - "author_inst": "University College London" - }, - { - "author_name": "Kashfia Chowdhury", - "author_inst": "University College London" - }, - { - "author_name": "Stephanie Davey", - "author_inst": "Royal Free London NHS Foundation Trust" - }, - { - "author_name": "Philip Yee", - "author_inst": "Royal Free London NHS Foundation Trust" - }, - { - "author_name": "Felicia Ikeji", - "author_inst": "University College London" - }, - { - "author_name": "Amalia Ndoutoumou", - "author_inst": "University College London" - }, - { - "author_name": "Divya Shah", - "author_inst": "Great Ormond Street Hospital NHS Foundation Trust" - }, - { - "author_name": "Alexander Lennon", - "author_inst": "Great Ormond Street Hospital NHS Foundation Trust" - }, - { - "author_name": "Abhulya Rai", - "author_inst": "Great Ormond Street Hospital NHS Foundation Trust" - }, - { - "author_name": "Akosua A Agyeman", - "author_inst": "University College London" - }, - { - "author_name": "Anna Checkley", - "author_inst": "University College London Hospitals NHS Foundation Trust" - }, - { - "author_name": "Nicola Longley", - "author_inst": "University College London Hospitals NHS Foundation Trust" - }, - { - "author_name": "Hakim-Moulay Dehbi", - "author_inst": "University College London" - }, - { - "author_name": "Nick Freemantle", - "author_inst": "University College London" - }, - { - "author_name": "Judith Breuer", - "author_inst": "University College London" - }, - { - "author_name": "Joseph F Standing", - "author_inst": "University College London" - }, - { - "author_name": "- FLARE Investigators", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.13.22270755", "rel_title": "Co-infection with SARS-COV-2 Omicron and Delta Variants Revealed by Genomic Surveillance", @@ -390631,6 +392380,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.08.22270635", + "rel_title": "Surveillance of Myopericarditis following COVID-19 Booster Dose Vaccination in a Large Integrated Health System", + "rel_date": "2022-02-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.08.22270635", + "rel_abs": "PurposeThe risk of myopericarditis following COVID-19 booster vaccination has not been extensively evaluated. We provide a timely case ascertainment of myocarditis following COVID-19 booster vaccine in individuals age 18-39 years from an integrated health system.\n\nMethodsWe studied a cohort of 65,785 Kaiser Permanente (KP) Northwest Health Plan members aged 18-39 years who received a COVID-19 vaccine booster at least 5 months following completion of the primary series. We identified cases of myopericarditis by searching the electronic health record for the National Center for Health Statistics (NCHS) text label for myocarditis or pericarditis diagnosis codes in all inpatient and outpatient encounters through January 18th 2022. The cohort was followed for 21 days after their booster. We excluded anyone with a documented diagnosis of myocarditis or pericarditis before their first COVID-19 vaccination. Two physicians independently reviewed the identified patient records and applied the CDC myocarditis and pericarditis surveillance case definition to classify records as confirmed, probable or excluded based on the prior published definition.\n\nResultsOur method identified 6 patients who met the confirmed or probable CDC case definition for acute myocarditis or pericarditis within 21 days of COVID-19 booster dose among 65,785 eligible members. Four cases occurred in 27,253 men. Overall, we estimated 9.1 cases (exact 95% CI 3.4 to 19.9) of post-booster myopericarditis per 100,000 booster doses given. In men, we estimated 14.7 cases (exact 95% CI 4.0 to 37.6) per 100,000 booster doses given.\n\nConclusionWe identified a rate of 9.1 cases of myopericarditis per 100,000 COVID-19 booster doses which is higher than prior estimates reported by the Vaccine Adverse Event Reporting System (VAERS). Myopericarditis occurs following COVID-19 booster vaccine and may be underreported by current surveillance methods. High sensitivity of these case estimates is essential when modeling risk and benefit for sequential COVID-19 vaccinations for the general population.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Katie A Sharff", + "author_inst": "Kaiser Permanente Northwest" + }, + { + "author_name": "David M Dancoes", + "author_inst": "Kaiser Permanente Northwest" + }, + { + "author_name": "Jodi L Longueil", + "author_inst": "Kaiser Permanente Northwest" + }, + { + "author_name": "Paul F Lewis", + "author_inst": "Kaiser Permanente Northwest" + }, + { + "author_name": "Eric S Johnson", + "author_inst": "Kaiser Permanente Northwest" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.11.480131", "rel_title": "Omicron-Based Vaccine Candidate Elicits Potent Neutralizing Antibodies in the Animal Model", @@ -392518,85 +394302,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.14.22270965", - "rel_title": "Experiences of the physicians in the largest COVID-19 dedicated hospital of Bangladesh about COVID-19 and its aftermath", - "rel_date": "2022-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.14.22270965", - "rel_abs": "BackgroundThe doctors and the other health care workers are the first-line fighters against COVID-19. This study aims to identify the prevalence, risk factors, clinical severity of COVID-19 infection among the doctors working in the COVID unit. We also analyzed the hospital data for admission and RT-PCR positivity among the physicians.\n\nMethodsIt was a cross-sectional survey and review of the hospital database. We surveyed from September 2021 to October 2021 and explored the hospital data from march 2020 to September 2021.We included 342 physicians for analysis in the survey. We reviewed hospital data of 1578 total admitted patients and 336 RT-PCR test positive physicians for analyzing the hospital admission rate, the positivity rate for COVID-19 among the physicians and the other patients in the different COVID-19 surges.\n\nFindingsIn this study, we demonstrated the physicians sufferings during the pandemic era. We have observed four surges in the hospital admission and RT-PCR for COVID-19 positivity rate among the physicians and the general population. The physicians experienced a similar surge in the hospital admission and positivity rate to the general population. The hospital admission was lower in the fourth surge among the physicians than the general population. The positivity rate was higher in the first, second and third surge among the physicians. In the survey, a total of 146(42%) respondents had COVID-19 infection, and among them, 50(34.2%) had re-detectable positive SARS-CoV-2 infection. Most of them experienced mild (77[52.7%]) to moderate (41[28.1%]) symptoms. Increasing age (OR, 95%CI, p-value; 1.15, 1.05-1.25, 0.002), male sex (OR, 95%CI, p-value; 5.8, 3.2-9.8, <0.001), and diabetes (OR, 95%CI, p-value; 25.6, 2-327.2, 0.01) were the risk factor of having COVID-19. Female sex and diabetes were the risk factors for re-detectable positive SARS-CoV-2 infection. (OR, 95%CI, p-value; 0.24, 0.09-0.67, 0.006; 44, 8.9-218.7, <0.001 respectively). Most respondents suffered for 7-14 days. Total 98(67%) suffered from post-COVID fatigue.\n\nConclusionsThe physicians observed four surges in hospital admission and COVID-19 positivity rate. A significant number of the COVID-warrior became positive for SARS-CoV-2, had re-detectable positive SARS-CoV-2 infection, and suffered in the post-COVID-19 state.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Reaz Mahmud", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Sultana Shahana Banu", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Nusrat Sultana", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Farhana Binte Monayem", - "author_inst": "Sarkari Karmachari Hospital" - }, - { - "author_name": "Ponkaj Kanti Datta", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Mohammad Mahfuzul Hoque", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "S.M. Habibur Rahman Habib", - "author_inst": "DNCC dedicated COVID-19 Hospital" - }, - { - "author_name": "Joynal Abedin", - "author_inst": "DNCC dedicated COVID-19 Hospital" - }, - { - "author_name": "Md. Fakhrul Islam", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Md. Arifuzzaman", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Md Khairul Islam", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Sudip Ranjan Deb", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Ahmed Hossain Chowdhury", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Kazi Gias Uddin Ahmed", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Md. Titu Miah", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Md. Mujibur Rahman", - "author_inst": "Bangabandhu Sheikh Mujib Medical University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.14.22270845", "rel_title": "Quantitative, multiplexed, targeted proteomics for ascertaining variant specific SARS-CoV-2 antibody response", @@ -392921,6 +394626,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.14.22270930", + "rel_title": "Determinants of antibody responses to two doses of ChAdOx1 nCoV-19 or BNT162b2 and a subsequent booster dose of BNT162b2 or mRNA-1273: population-based cohort study (COVIDENCE UK)", + "rel_date": "2022-02-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.14.22270930", + "rel_abs": "BackgroundAntibody responses to SARS-CoV-2 vaccination vary for reasons that remain poorly understood.\n\nMethodsWe tested for presence of combined IgG, IgA and IgM (IgGAM) anti-spike antibodies before and after administration of two doses of ChAdOx1 nCoV-19 (ChAdOx1, Oxford-AstraZeneca) or BNT162b2 (Pfizer-BioNTech) in UK adults participating in a population-based longitudinal study who received their first dose of vaccine from December 15, 2020 to July 10, 2021. Information on sixty-six potential sociodemographic, behavioural, clinical, pharmacological and nutritional determinants of serological response to vaccination was captured using serial online questionnaires. We used logistic regression to estimate multivariable-adjusted odds ratios (aORs) for associations between independent variables and risk of seronegativity following two vaccine doses. Participants who were seronegative after receiving two vaccine doses were offered an additional antibody test following subsequent administration of a booster dose of BNT162b2 or mRNA-1273 (Moderna) from September 23 to December 12, 2021.\n\nFindingsSerology results following two vaccine doses were available for 9,101 participants, of whom 5,770 (63.4%) received ChAdOx1 and 3,331 (36.6%) received BNT162b2. Anti-spike IgGAM was undetectable in 378 (4.2%) participants at a median of 8.6 weeks (IQR 6.4-10.7 weeks) after their second dose of vaccine. Seronegativity following two doses of SARS-CoV-2 vaccination was associated with administration of ChAdOx1 vs BNT162b2 (aOR 7.03, 95% CI 4.39-11.24), shorter interval between first and second vaccine doses (aOR 2.37, 1.06-5.26, for <6 weeks vs >10 weeks; aOR 1.59, 1.18-2.13, for 6-10 weeks vs >10 weeks), poorer self-assessed general health (aOR 3.33, 1.49-7.46, for poor vs excellent), immunodeficiencies (aOR 6.75, 2.63-17.35) and prescription of systemic immunosuppressants (aOR 3.76, 2.44-5.78). By contrast, pre-vaccination SARS-CoV-2 seropositivity (aOR 0.16, 0.04-0.70, for symptomatic seropositives vs seronegatives) and supplemental vitamin D intake (aOR 0.73, 0.53-0.99) were associated with reduced risk of post-vaccination seronegativity. 247/378 (65.3%) of participants who were seronegative after two doses of ChAdOx1 vs BNT162b2 provided a third sample at a median of 7.8 weeks (IQR 5.8-10.4) after receiving a booster dose of BNT162b2 or mRNA-1273: eight (3.2%) of them remained seronegative after three vaccine doses, all of whom either had a primary immunodeficiency or were taking systemic immunosuppressant drugs.\n\nInterpretationWe identify multiple determinants of antibody responses to two doses of ChAdOx1 or BNT162b2, many of which are potentially modifiable. Booster doses of BNT162b2 or mRNA-1273 were highly effective in achieving seroconversion in those who failed to mount antibody responses following two doses of ChAdOx1 or BNT162b2.\n\nStudy registrationhttps://clinicaltrials.gov/ct2/show/NCT04330599\n\nFundingBarts Charity, Fischer Family Trust, The Exilarchs Foundation, DSM Nutritional Products, Health Data Research UK\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, medRxiv, and Google Scholar for papers published from January 1, 2020, to February 1, 2022, using the search terms (antibody OR humoral OR serologic* OR immunogenic*) AND (SARS-CoV-2 vaccine OR ChAdOx1 or BNT162b2 coronavirus), with no language restrictions. Population-based studies investigating multiple potential determinants of vaccine immunogenicity in people with known pre-vaccination SARS-CoV-2 serostatus are lacking.\n\nAdded value of this studyThis large population-based study, conducted in a population with known pre-vaccination SARS-CoV-2 serostatus, examines a comprehensive range of potential sociodemographic, behavioural, clinical, pharmacological and nutritional determinants of antibody responses to administration of two major SARS-CoV-2 vaccines (i.e., ChAdOx1 or BNT162b2), many of which have not previously been investigated. It is also the first population-based study to characterise antibody responses to booster doses of SARS-CoV-2 vaccines in adults who were seronegative after their primary course of vaccination.\n\nImplications of all the available evidenceIncreased risk of seronegativity following two doses of SARS-CoV-2 vaccines was associated with administration of ChAdOx1 vs BNT162b2, shorter interval between first and second vaccine doses, poorer self-assessed general health, immunocompromise and SARS-CoV-2 seronegativity pre-vaccination. Regular intake of vitamin D supplements was associated with reduced risk of post-vaccination seronegativity. Randomised controlled trials are now needed to test for causality. Booster doses of BNT162b2 or mRNA-1273 were highly effective in achieving seroconversion in the majority of people who failed to mount antibody responses following a primary course of vaccination, the few exceptions being a subset of those with primary immunodeficiency or systemic immunosuppressant drugs.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "David A Jolliffe", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Sian E Faustini", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Hayley Holt", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Natalia Perdek", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Sheena Maltby", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Mohammad Talaei", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Matthew Greenig", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Giulia Vivaldi", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Florence Tydeman", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Jane Symons", + "author_inst": "Jane Symons Media" + }, + { + "author_name": "Gwyneth A Davies", + "author_inst": "Swansea University" + }, + { + "author_name": "Ronan Lyons", + "author_inst": "Swansea University" + }, + { + "author_name": "Frank Kee", + "author_inst": "Queen's University Belfast" + }, + { + "author_name": "Aziz Sheikh", + "author_inst": "Edinburgh University" + }, + { + "author_name": "Seif O Shaheen", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Alex Richter", + "author_inst": "University of Birminghan" + }, + { + "author_name": "Adrian R Martineau", + "author_inst": "Queen Mary University of London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.14.22270940", "rel_title": "Ethnic differences in COVID-19 mortality in the second and third waves of the pandemic in England during the vaccine roll-out: a retrospective, population-based cohort study", @@ -394596,25 +396384,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.11.22270841", - "rel_title": "Underdispersion in the reported Covid-19 case and death numbers may suggest data manipulations", - "rel_date": "2022-02-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.11.22270841", - "rel_abs": "We suggest a statistical test for underdispersion in the reported Covid-19 case and death numbers, compared to the variance expected under the Poisson distribution. Screening all countries in the World Health Organization (WHO) dataset for evidence of underdispersion yields 21 country with statistically significant underdispersion. Most of the countries in this list are known, based on the excess mortality data, to strongly undercount Covid deaths. We argue that Poisson underdispersion provides a simple and useful test to detect reporting anomalies and highlight unreliable data.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Dmitry Kobak", - "author_inst": "Tuebingen University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.11.22270854", "rel_title": "Persistence of SARS-CoV-2 immunity, Omicron's footprints, and projections of epidemic resurgences in South African population cohorts.", @@ -394843,6 +396612,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2022.02.10.22270805", + "rel_title": "Adequacy of serial self-performed SARS-CoV-2 rapid antigen-detection testing for longitudinal mass screening in the workplace", + "rel_date": "2022-02-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.10.22270805", + "rel_abs": "ImportanceLongitudinal mass testing using rapid antigen detection tests (RADT) for serial screening of asymptomatic persons has been proposed for preventing SARS-CoV-2 community transmission. The feasibility of this strategy relies on implementation of accurate self-performed RADT testing where people live, work, or attend school.\n\nObjectiveTo quantify the adequacy of serial self-performed SARS-CoV-2 RADT testing in the workplace, in terms of the frequency of correct execution of procedural steps and accurate interpretation of the range of possible RADT results. We compared results using the instructions provided by the manufacturer to those with modified instructions that were informed by the most frequent or most critical errors we observed.\n\nDesignRepeated cross-sectional, diagnostic accuracy study performed prospectively in the field.\n\nSettingBusinesses in Montreal, Quebec, Canada, with at least 2 active cases of SARS-CoV-2 infection.\n\nParticipantsUntrained, asymptomatic persons in their workplace, not meeting Public Health quarantine criteria.\n\nExposuresA Modified Quick Reference Guide compared to the original manufacturers instructions.\n\nMain Outcome(s) and Measure(s)The difference in the proportions of correctly performed procedural steps, and the difference in proportions of correctly interpreted RADT proficiency panel results. The secondary outcome, among subjects with two self-testing visits, compared the second to the first self-test visit using the same measures.\n\nResultsOverall, 1892 tests were performed among 647 subjects. For self-test visit 1, significantly better accuracy in test interpretation was observed using the Modified Quick Reference Guide for weak positive (55.6% vs. 12.3%; 43.3 percentage point improvement, 95% confidence interval [CI] 33.0%-53.8%), positive (89.6% vs. 51.5%; 38.1% difference, 95%CI 28.5%-47.5%), strong positive (95.6% vs. 84.0%; 11.6% improvement, 95%CI 6.8%-16.3%) and invalid (87.3% vs. 77.3%; 10.0% improvement, 95%CI 3.8%-16.3%) tests. Use of the modified guide was associated with smaller, statistically significant, improvements on self-test visit 2. For procedural steps identified as critical for the validity of test results, adherence to procedural testing steps did not differ meaningfully according to instructions provided or reader experience.\n\nConclusions and RelevanceLongitudinal mass RADT testing for SARS-CoV-2 can be accurately self-performed in an intended-use setting; this work provides evidence for how to optimise performance.\n\nKey PointsO_ST_ABSQuestioC_ST_ABSDo untrained users correctly perform and interpret the results of SARS-CoV-2 rapid antigen detection tests (RADT) in the workplace, and how can their performance be optimised?\n\nFindingsIn this prospective field evaluation of self-performed SARS-CoV-2 RADT in an intended-use setting, we found that the accuracy of RADT interpretation was poor when the manufacturers instructions were used. A Modified Quick Reference Guide yielded significantly better user performance.\n\nMeaningLongitudinal mass RADT testing for SARS-CoV-2 can be accurately self-performed in an intended-use setting; this work provides evidence for how to optimise performance.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jesse Papenburg", + "author_inst": "Montreal Children's Hospital" + }, + { + "author_name": "Jonathon R. Campbell", + "author_inst": "McGill University" + }, + { + "author_name": "Chelsea Caya", + "author_inst": "McGill Interdisciplinary Initiative in Infection and Immunity" + }, + { + "author_name": "Cynthia Dion", + "author_inst": "McGill Interdisciplinary Initiative in Infection and Immunity" + }, + { + "author_name": "Rachel Corsini", + "author_inst": "McGill Interdisciplinary Initiative in Infection and Immunity" + }, + { + "author_name": "Matthew Cheng", + "author_inst": "McGill University Health Centre" + }, + { + "author_name": "Dick Menzies", + "author_inst": "McGill University" + }, + { + "author_name": "Cedric P Yansouni", + "author_inst": "McGill University Health Centre" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.12.22270851", "rel_title": "Empirical evidence of transmission over a school-household network for SARS-CoV-2; exploration of transmission pairs stratified by primary and secondary school.", @@ -396189,61 +398005,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2022.02.09.479786", - "rel_title": "Predicting Epitope Candidates for SARS-CoV-2", - "rel_date": "2022-02-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.09.479786", - "rel_abs": "Epitopes are short amino acid sequences that define the antigen signature to which an antibody binds. In light of the current pandemic, epitope analysis and prediction is paramount to improving serological testing and developing vaccines. In this paper, we leverage known epitope sequences from SARS-CoV, SARS-CoV-2 and other Coronaviridae and use those known epitopes to identify additional antigen regions in 62k SARS-CoV-2 genomes. Additionally, we present epitope distribution across SARS-CoV-2 genomes, locate the most commonly found epitopes, discuss where epitopes are located on proteins, and how epitopes can be grouped into classes. We also discuss the mutation density of different regions on proteins using a big data approach. We find that there are many conserved epitopes between SARS-CoV-2 and SARS-CoV, with more diverse sequences found in Nucleoprotein and Spike Glycoprotein.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Akshay Agarwal", - "author_inst": "IBM Research" - }, - { - "author_name": "Kristen L. Beck", - "author_inst": "IBM Research" - }, - { - "author_name": "Sara Capponi", - "author_inst": "IBM Research" - }, - { - "author_name": "Mark Kunitomi", - "author_inst": "IBM Research" - }, - { - "author_name": "Gowri Nayar", - "author_inst": "IBM Research" - }, - { - "author_name": "Edward Seabolt", - "author_inst": "IBM Research" - }, - { - "author_name": "Gandhar Mahadeshwar", - "author_inst": "IBM Research" - }, - { - "author_name": "Simone Bianco", - "author_inst": "IBM Almaden Research Center" - }, - { - "author_name": "Vandana Mukherjee", - "author_inst": "IBM Research" - }, - { - "author_name": "James Kaufman", - "author_inst": "IBM Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.02.10.479867", "rel_title": "Lyophilized mRNA-lipid nanoparticles vaccine with long-term stability and high antigenicity against SARS-CoV-2", @@ -396664,6 +398425,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.02.10.479924", + "rel_title": "SARS-CoV-2 Nsp1 N-terminal and linker regions as a platform for host translational shutoff", + "rel_date": "2022-02-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.10.479924", + "rel_abs": "In the early stages of SARS-CoV-2 infection, non-structural protein 1 (Nsp1) inhibits the innate immune response by inserting its C-terminal helices into the mRNA entry channel of the ribosome and promoting mRNA degradation. Nevertheless, the mechanism by which Nsp1 achieves host translational shutoff while allowing for viral protein synthesis remains elusive. We set out to characterize the interactome of full-length Nsp1 and its topology by crosslinking mass spectrometry in order to investigate the role of the N-terminal domain and linker regions in host translational shutoff. We find that these regions are in contact with 40S proteins lining the mRNA entry channel and detect a novel interaction with the G subunit of the eIF3 complex. The crosslink-derived distance restraints allowed us to derive an integrative model of full-length Nsp1 on the 40S subunit, reporting on the dynamic interface between Nsp1, the ribosome and the eIF3 complex. The significance of the Nsp1-eIF3G interaction is supported by further evidence that Nsp1 predominantly binds to 40-43S complexes. Our results point towards a mechanism by which Nsp1 is preferentially recruited to canonical initiation complexes, leading to subsequent mRNA degradation.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Andrea Graziadei", + "author_inst": "TU Berlin" + }, + { + "author_name": "Fabian Schildhauer", + "author_inst": "TU Berlin" + }, + { + "author_name": "Christian Spahn", + "author_inst": "Institue of Medical Physiscs and Biophysics, Charite-Universitatmedizin Berlin" + }, + { + "author_name": "Matthew L. Kraushar", + "author_inst": "Max Planck Institute for Molecular Genetics" + }, + { + "author_name": "Juri Rappsilber", + "author_inst": "TU Berlin" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2022.02.09.479842", "rel_title": "The rise and fall of SARS-CoV-2 variants and the emergence of competing Omicron lineages", @@ -398219,49 +400015,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.02.08.479664", - "rel_title": "SARS-CoV-2 ORF6 disrupts innate immune signalling by inhibiting cellular mRNA export", - "rel_date": "2022-02-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.08.479664", - "rel_abs": "SARS-CoV-2 is a betacoronavirus and the etiological agent of COVID-19, a devastating infectious disease. Due to its far-reaching effect on human health, there is an urgent and growing need to understand the viral molecular biology of SARS-CoV-2 and its interaction with the host cell. SARS-CoV-2 encodes 9 predicted accessory proteins, which are presumed to be dispensable for in vitro replication, most likely having a role in modulating the host cell environment to aid viral replication. Here we show that the ORF6 accessory protein interacts with cellular Rae1 to inhibit cellular protein production by blocking mRNA export. We utilised cell fractionation coupled with mRNAseq to explore which cellular mRNA species are affected by ORF6 expression and show that ORF6 can inhibit the export of many mRNA including those encoding antiviral factors such as IRF1 and RIG-I. We also show that export of these mRNA is blocked in the context of SARS-CoV-2 infection. Together, our studies identify a novel mechanism by which SARS-CoV-2 can manipulate the host cell environment to supress antiviral responses, providing further understanding to the replication strategies of a virus that has caused an unprecedented global health crisis.\n\nAuthor SummarySARS-CoV-2 is the virus responsible for the current COVID-19 pandemic. Coronaviruses, like SARS-CoV-2, replicate their genome in the cytoplasm of the host cell by hijacking the cellular machinery. In addition to structural proteins and viral enzymes, SARS-CoV-2 encodes 9 accessory proteins. Although these are not required for in vitro replication, they are thought to modulate the host cell environment to favour viral replication. In this work, we show that the ORF6 accessory protein can supress cellular protein production by blocking mRNA nuclear export through interacting with the cellular protein Rae1, a known mRNA export factor. We also investigated which cellular mRNAs were retained in the nucleus when ORF6 was overexpressed. Interestingly, we found that ORF6 inhibited the export of many different mRNAs, including those encoding antiviral factors, like IRF1 and RIG-I, even in the absence of stimulation by interferon. Importantly, we found that the export of these mRNAs was similarly affected in the context of SARS-CoV-2 infection. Therefore, we believe we have identified a novel mechanism that SARS-CoV-2 uses to suppress antiviral responses in order to make the cell more permissive to infection.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ross Hall", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Anabel Gued\u00e1n", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Melvyn W. Yap", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "George R. Young", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Ruth Harvey", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Jonathan P. Stoye", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Kate N. Bishop", - "author_inst": "The Francis Crick Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.02.08.479661", "rel_title": "N-acylethanolamine acid amide hydrolase is a novel target for drugs against SARS-CoV-2 and Zika virus", @@ -398638,6 +400391,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.09.22270633", + "rel_title": "Increasing viral transmission paradoxically reduces progression rates to severe COVID-19 during endemic transition", + "rel_date": "2022-02-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.09.22270633", + "rel_abs": "Natural infection with SARS-CoV-2 or vaccination induces virus-specific immunity protecting hosts from infection and severe disease. While the infection-preventing immunity gradually declines, the severity-reducing immunity is relatively well preserved. Here, based on the different longevity of these distinct immunities, we develop a mathematical model to estimate courses of endemic transition of COVID-19. Our analysis demonstrates that high viral transmission unexpectedly reduces the rates of progression to severe COVID-19 during the course of endemic transition despite increased numbers of infection cases. Our study also shows that high viral transmission amongst populations with high vaccination coverages paradoxically accelerates the endemic transition of COVID-19 with reduced numbers of severe cases. These results provide critical insights for driving public health policies in the era of living with COVID-19.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Hyukpyo Hong", + "author_inst": "Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea" + }, + { + "author_name": "Ji Yun Noh", + "author_inst": "Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea" + }, + { + "author_name": "Hyojung Lee", + "author_inst": "Department of Statistics, Kyungpook National University, Daegu, Republic of Korea" + }, + { + "author_name": "Sunhwa Choi", + "author_inst": "Division of Fundamental Research on Public Agenda, National Institute for Mathematical Sciences, Daejeon, Republic of Korea" + }, + { + "author_name": "Boseung Choi", + "author_inst": "Division of Big Data Science, Korea University, Sejong, Republic of Korea" + }, + { + "author_name": "Jae Kyoung Kim", + "author_inst": "Dept. of Mathematical Sciences, KAIST" + }, + { + "author_name": "Eui-Cheol Shin", + "author_inst": "Korea Advanced Institute of Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.02.08.22270674", "rel_title": "Trajectories of Neurological Recovery 12 Months after Hospitalization for COVID-19: A Prospective Longitudinal Study", @@ -400401,125 +402197,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.07.22270020", - "rel_title": "Post-marketing active surveillance of myocarditis and pericarditis following vaccination with COVID-19 mRNA vaccines in persons aged 12-39 years in Italy: a multi-database, self-controlled case series study", - "rel_date": "2022-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270020", - "rel_abs": "ObjectivesTo investigate the association between SARS-CoV-2 mRNA vaccines, BNT162b2 and mRNA-1273, and myocarditis/pericarditis.\n\nDesignSelf-Controlled Case Series study (SCCS) using national data on COVID-19 vaccination and emergency care/hospital admissions.\n\nSettingItalian Regions (Lombardia, Friuli Venezia Giulia, Veneto, Lazio).\n\nParticipants2,861,809 individuals, aged 12-39 years, vaccinated with the first doses of mRNA vaccines (2,405,759 BNT162b2 and 456,050 mRNA-1273) between 27 December 2020 and 30 September 2021.\n\nMain outcome measuresFirst diagnosis of myocarditis/pericarditis within the study period. The incidence of events in the exposure risk periods (0-21 days from the vaccination day, subdivided in three equal intervals) for first and second dose was compared with baseline period. The SCCS model was fitted using conditional Poisson regression to estimate Relative Incidences (RI) and Excess of Cases (EC) per 100,000 vaccinated by dose, age, gender and brand.\n\nResultsDuring the study period, 441 participants aged 12-39 years developed myocarditis/pericarditis (346 BNT162b2 and 95 mRNA-1273). During the 21-day risk interval there were 114 cases of myocarditis/pericarditis (74 BNT162b2 and 40 mRNA-1273) corresponding to a RI of 1.27 (0.87-1.85) and 2.16 (1.50-3.10) after first and second dose, respectively.\n\nAn increased risk of myocarditis/pericarditis at [0-7) days was observed after first [RI=6.55; 95% Confidence Interval (2.73-15.72); EC per 100,000 vaccinated=2.0 (1.5-2.3)] and second dose [RI=7.59 (3.26-17.65); EC=5.5 (4.4-5.9)] of mRNA-1273 and after second dose of BNT162b2 [RI=3.39 (2.02-5.68); EC=0.8 (0.6-1.0)]. In males, an increased risk at [0-7) days was observed after first [RI=12.28, 4.09-36.83; EC=3.8 (3.1-4.0)] and second dose [RI=11.91 (3.88-36.53); EC=8.8 (7.2-9.4)] of mRNA-1273 and after second dose of BNT162b2 [RI=3.45 (1.78-6.68); EC=1.0 (0.6-1.2)]. In females, an increased risk at [0-7) days was observed after second dose of BNT162b2 [RI=3.38 (1.47-7.74); EC=0.7 (0.3-0.9)]. At [0-7) days an increased risk following second dose of BNT162b2 was observed in the 12-17 years old [RI=5.74, (1.52-21.72); EC=1.7 (0.7-1.9)] and in 18-29 years old [RI=4.02 (1.81-8.91); EC=1.1 (0.6-1.3)]. At [0-7) days an increased risk after first [RI=7.58 (2.62-21.94); EC=3.5 (2.4-3.8)] and second [RI=9.58 (3.32-27.58); EC=8.3 (6.7-9.2)] dose of mRNA-1273 was found in 18-29 years old and after first dose in 30-39 years old [RI=6.57 (1.32-32.63); EC=1.0 (0.3-1.1)].\n\nConclusionsThis population-based study indicates that mRNA vaccines were associated with myocarditis/pericarditis in the population younger than 40 years, whereas no association was observed in older subjects. The risk increased after the second dose and in the youngest for both vaccines, remained moderate following vaccination with BNT162b2, while was higher in males following vaccination with mRNA-1273. The public health implication of these findings should be weighed in the light of the overall efficacy and safety profile of both vaccines.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Marco Massari", - "author_inst": "National Centre for Drug Research and Evaluation, Istituto Superiore di Sanit\u00e0 (National Institute of Health), Rome, Italy" - }, - { - "author_name": "Stefania Spila-Alegiani", - "author_inst": "National Centre for Drug Research and Evaluation, Istituto Superiore di Sanit\u00e0 (National Institute of Health), Rome, Italy" - }, - { - "author_name": "Cristina Morciano", - "author_inst": "National Centre for Drug Research and Evaluation, Istituto Superiore di Sanit\u00e0 (National Institute of Health), Rome, Italy" - }, - { - "author_name": "Matteo Spuri", - "author_inst": "Department of Infectious Diseases, Istituto Superiore di Sanit\u00e0 (National Institute of Health), Rome, Italy" - }, - { - "author_name": "Pasquale Marchione", - "author_inst": "Department of post-marketing surveillance, Agenzia Italiana del Farmaco (Italian Medicines Agency), Rome, Italy" - }, - { - "author_name": "Patrizia Felicetti", - "author_inst": "Department of post-marketing surveillance, Agenzia Italiana del Farmaco (Italian Medicines Agency), Rome, Italy" - }, - { - "author_name": "Valeria Belleudi", - "author_inst": "Department of Epidemiology ASL Roma, Lazio Regional Health Service, Rome, Italy" - }, - { - "author_name": "Francesca Romana Poggi", - "author_inst": "Department of Epidemiology ASL Roma, Lazio Regional Health Service, Rome, Italy" - }, - { - "author_name": "Marco Lazzeretti", - "author_inst": "Business Intelligence, Data Science e Data Analysis, ARIA SpA, Milan, Italy" - }, - { - "author_name": "Michele Ercolanoni", - "author_inst": "Business Intelligence, Data Science e Data Analysis, ARIA SpA, Milan, Italy" - }, - { - "author_name": "Elena Clagnan", - "author_inst": "ARCS Azienda Regionale di Coordinamento per la Salute, Udine, Italy" - }, - { - "author_name": "Emanuela Bovo", - "author_inst": "Veneto Tumour Registry, Azienda Zero, Padova, Italy" - }, - { - "author_name": "Gianluca Trifir\u00f2", - "author_inst": "Department of Diagnostics and Public Health, University of Verona, Verona, Italy" - }, - { - "author_name": "Ugo Moretti", - "author_inst": "Department of Diagnostics and Public Health, University of Verona, Verona, Italy" - }, - { - "author_name": "Giuseppe Monaco", - "author_inst": "Department of Health of Lombardy Region, Epidemiology Observatory, Milan, Italy" - }, - { - "author_name": "Olivia Leone", - "author_inst": "Department of Health of Lombardy Region, Epidemiology Observatory, Milan, Italy" - }, - { - "author_name": "Roberto Da Cas", - "author_inst": "National Centre for Drug Research and Evaluation, Istituto Superiore di Sanit\u00e0 (National Institute of Health), Rome, Italy" - }, - { - "author_name": "Fiorella Petronzelli", - "author_inst": "Department of post-marketing surveillance, Agenzia Italiana del Farmaco (Italian Medicines Agency), Rome, Italy" - }, - { - "author_name": "Loriana Tartaglia", - "author_inst": "Department of post-marketing surveillance, Agenzia Italiana del Farmaco (Italian Medicines Agency), Rome, Italy" - }, - { - "author_name": "Nadia Mores", - "author_inst": "Institute of Pharmacology, Pharmacovigilance, Policlinico Universitario A. Gemelli, Catholic University of Sacred Heart, Rome, Italy" - }, - { - "author_name": "Giovanna Zanoni", - "author_inst": "Immunology Unit, University Hospital, Verona, Italy" - }, - { - "author_name": "Paola Rossi", - "author_inst": "Direzione centrale salute, politiche sociali e disabilita, Friuli Venezia Giulia Region, Trieste, Italy" - }, - { - "author_name": "Sarah Samez", - "author_inst": "Centro Regionale di Farmacovigilanza, Friuli Venezia Giulia Region, Trieste, Italy" - }, - { - "author_name": "Cristina Zappetti", - "author_inst": "Direzione centrale salute, politiche sociali e disabilita, Friuli Venezia Giulia Region, Trieste, Italy" - }, - { - "author_name": "Anna Rosa Marra", - "author_inst": "Department of post-marketing surveillance, Agenzia Italiana del Farmaco (Italian Medicines Agency), Rome, Italy" - }, - { - "author_name": "Francesca Menniti-Ippolito", - "author_inst": "National Centre for Drug Research and Evaluation, Istituto Superiore di Sanit\u00e0 (National Institute of Health), Rome, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.02.07.22270596", "rel_title": "Role of Covid vaccine in determining ICU admission and death due to Covid -19 in Tamil Nadu", @@ -400764,6 +402441,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.08.479543", + "rel_title": "Spike Protein-independent Attenuation of SARS-CoV-2 Omicron Variant in Laboratory Mice", + "rel_date": "2022-02-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.08.479543", + "rel_abs": "Despite being more transmissible, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant was found to cause milder diseases in laboratory animals, often accompanied by a lower viral load compared to previous variants of concern. This study revealed the structural basis for a robust interaction between the receptor binding domain of the Omicron spike protein and mouse ACE2. Pseudovirus bearing the Omicron spike protein efficiently utilized mouse ACE2 for entry. By comparing viral load and disease severity among laboratory mice infected by a natural Omicron variant or recombinant ancestral viruses bearing either the entire Omicron Spike or only the N501Y/Q493R mutations in its spike, we found that mutations outside the spike protein in the Omicron variant may be responsible for the observed lower viral load. Together, our results indicated that a post-entry block to the Omicron variant exists in laboratory mice.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Shufeng Liu", + "author_inst": "FDA" + }, + { + "author_name": "Prabhuanand Selvaraj", + "author_inst": "FDA" + }, + { + "author_name": "Kotou Sangare", + "author_inst": "FDA" + }, + { + "author_name": "Binquan Luan", + "author_inst": "IBM Research Center" + }, + { + "author_name": "Tony T Wang", + "author_inst": "U.S. Food and Drug Administration" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.02.07.479352", "rel_title": "A highly attenuated SARS-CoV-2 related pangolin coronavirus variant has a 104nt deletion at the 3'-terminus untranslated region", @@ -402535,41 +404247,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2022.02.05.22270416", - "rel_title": "Characteristics and preparedness for COVID-19 outbreaks of Australian residential aged care facilities: A cross-sectional survey", - "rel_date": "2022-02-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.05.22270416", - "rel_abs": "ObjectiveTo provide an overview of Australian residential aged care facilities (RACFs) COVID-19 outbreak preparedness and responses, 12 months after the pandemic began in early 2020.\n\nMethodsA cross-sectional survey of RACF managers was conducted as part of an overview of COVID-19 experience during 2020. Survey questions were based on findings of previous outbreak reviews.\n\nResultsComparison with available data from the Australian Institute for Health and Welfare suggested that survey respondents (n=331) were a representative sample. Almost all RACFs had outbreak management plans, including provision for a surge workforce. However, anticipated staff replacements fell short of those often required during outbreaks. Staff of most (83%) RACFs had completed online infection control training, and a smaller proportion (73%) face-to-face training, by the time of the survey. Exploratory analyses to identify RACF characteristics associated with increased outbreak risk found a strong association with location in Victoria (adjusted risk ratio [aRR] 12.8) where most community transmission occurred during 2020. The only other association was an increased risk in facilities where all staff had not completed face-to-face infection control training (aRR 2.1). Respondents ranked leadership and management; planning and preparation; and infection control as the top three of seven critical lines of defence against COVID-19.\n\nConclusionSurvey results suggest that, in early 2021, most Australian RACFs were better prepared for the ongoing risk of COVID-19 than in 2020. Continued implementation of the Aged Care Royal Commissions recommendations is needed to ensure the aged care sector is prepared for future infectious disease emergencies.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Gwendolyn L Gilbert", - "author_inst": "Sydney Institute for Infectious Diseases, The University of Sydney" - }, - { - "author_name": "Jenna Smith", - "author_inst": "Sydney Health Literacy Lab, Sydney School of Public Health, The University of Sydney" - }, - { - "author_name": "Erin Cvejic", - "author_inst": "Sydney School of Public Health, The University of Sydney" - }, - { - "author_name": "Alan Lilly", - "author_inst": "Australian Catholic University" - }, - { - "author_name": "Kirsten McCaffery", - "author_inst": "Sydney Health Literacy Lab, Sydney School of Public Health, The University of Sydney" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2022.02.06.22270482", "rel_title": "Early genomic, epidemiological, and clinical description of the SARS-CoV-2 Omicron variant in Mexico City", @@ -402918,6 +404595,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.05.22270481", + "rel_title": "Limitations of molecular and antigen test performance for SARS-CoV-2 in symptomatic and asymptomatic COVID-19 contacts", + "rel_date": "2022-02-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.05.22270481", + "rel_abs": "ObjectivesCOVID-19 has brought unprecedented attention to the crucial role of diagnostics in pandemic control. We compared SARS-CoV-2 test performance by sample type and modality in close contacts of SARS-CoV-2 cases.\n\nMethodsClose contacts of SARS-CoV-2 positive individuals were enrolled after informed consent. Clinician-collected nasopharyngeal (NP) swabs in viral transport media (VTM) were tested with a nucleic acid test (NAT). NP VTM and self-collected passive drool were tested using the PerkinElmer real-time reverse transcription PCR (RT-PCR) assay. For the first 4 months of study, mid-turbinate swabs were tested using the BD Veritor rapid antigen test. NAT positive NP samples were tested for infectivity using a VeroE6TMPRSS2 cell culture model.\n\nResultsBetween November 17, 2020, and October 1, 2021, 235 close contacts of SARS-CoV-2 cases were recruited, including 95 with symptoms (82% symptomatic for <5 days) and 140 asymptomatic individuals. NP swab reference tests were positive for 53 (22.6%) participants; 24/50 (48%) were culture positive. PerkinElmer testing of NP and saliva samples identified an additional 28 (11.9%) SARS-CoV-2 cases who tested negative by clinical NAT. Antigen tests performed for 99 close contacts showed 83% positive percent agreement (PPA) with reference NAT among early symptomatic persons, but 18% PPA in others; antigen tests in 8 of 11 (72.7%) culture-positive participants were positive.\n\nConclusionsContacts of SARS-CoV-2 cases may be falsely negative early after contact, which more sensitive platforms may identify. Repeat or serial SARS-CoV-2 testing with both antigen and molecular assays may be warranted for individuals with high pretest probability for infection.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Matthew L Robinson", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Agha Mirza", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Nicholas Gallagher", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Alec Boudreau", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Lydia Garcia", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Tong Yu", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Julie Norton", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Chun Huai Luo", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Abigail Conte", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Ruifeng Zhou", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Kim Kafka", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Justin Hardick", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "David D McManus", + "author_inst": "T.H. Chan Medical School" + }, + { + "author_name": "Laura L Gibson", + "author_inst": "T.H. Chan Medical School" + }, + { + "author_name": "Andrew Pekosz", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Heba Mostafa", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Yukari C Manabe", + "author_inst": "Johns Hopkins University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.06.22270565", "rel_title": "Cumulative seroprevalence among healthcare workers after the first wave of the COVID-19 pandemic in El Salvador, Central America.", @@ -404805,89 +406565,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.04.22270087", - "rel_title": "ARTIFICIAL INTELLIGENCE TOOLS FOR EFFECTIVE MONITORING OF POPULATION AT DISTANCE DURING COVID-19 PANDEMIC. RESULTS FROM AN ITALIAN PILOT FEASIBILITY STUDY (RICOVAI-19 STUDY).", - "rel_date": "2022-02-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.04.22270087", - "rel_abs": "In order to reduce the burden on healthcare systems and in particular to support an appropriate way to the Emergency Department (ED) access, home tele-monitoring patients was strongly recommended during the COVID-19 pandemic. Furthermore, paper from numerous groups has shown the potential of using data from wearable devices to characterize each individuals unique baseline, identify deviations from that baseline suggestive of a viral infection, and to aggregate that data to better inform population surveillance trends. However, no evidence about usage of Artificial Intelligence (AI) applicatives on digitally data collected from patients and doctors exists. With a growing global population of connected wearable users, this could potentially help to improve the earlier diagnosis and management of infectious individuals and improving timeliness and precision of tracking infectious disease outbreaks.\n\nDuring the study RICOVAI-19 (RICOVero ospedaliero con strumenti di Artificial Intelligence nei pazienti con COVid-19) performed in the Marche Region, Italy, we evaluated 129 subjects monitored at home in a six-months period between March 22, 2021 and October 22, 2021. During the monitoring, personal on demand health technologies were used to collect clinical and vital data in order to feed the database and the machine learning engine. The AI output resulted in a clinical stability index (CSI) which enables the system to deliver suggestions to the population and doctors about how intervene.\n\nResults showed the beneficial influence of CSI for predicting clinical classes of subjects and identifying who of them need to be admitted at ED. The same pattern of results was confirming the alert included in the decision support system in order to request further testing or clinical information in some cases.\n\nIn conclusion, our study does support a high impact of AI tools on COVID-19 outcomes to fight this pandemic by driving new approaches to public awareness.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Marco Mazzanti", - "author_inst": "Barts Heart Centre Foundation Trust, Cardiac Imaging Department, London, United Kngdom" - }, - { - "author_name": "Aldo Salvi", - "author_inst": "Dipartimento di Emergenza, Medicina Interna, di urgenza e subintensiva, SOD Pronto Soccorso e OBI, Ospedali Riuniti, Ancona, Italy" - }, - { - "author_name": "Stefania Giacomini", - "author_inst": "General Physician, Medicina Generale di territorio, Azienda sanitaria Unica Regionale (ASUR), Offagna (Ancona), Italy" - }, - { - "author_name": "Elisabetta Perazzini", - "author_inst": "General Physician, Medicina Generale di territorio, Azienda sanitaria Unica Regionale (ASUR), Offagna (Ancona), Italy" - }, - { - "author_name": "Cinzia Nitti", - "author_inst": "Medicina di urgenza e subintensiva, SOD Pronto Soccorso e OBI, Ospedali Riuniti, Ancona, Italy" - }, - { - "author_name": "Susanna Contucci", - "author_inst": "Pronto Soccorso e OBI, Ospedali Riuniti, Ancona, Italy" - }, - { - "author_name": "Massimo D'Angelo", - "author_inst": "AI for Health, Almawave S.p.A., Rome, Italy" - }, - { - "author_name": "Danilo Ballanti", - "author_inst": "AI for Health, Almawave S.p.A., Rome, Italy" - }, - { - "author_name": "Domenico Ursino", - "author_inst": "Computer Engineering, Rector's delegate for ICT services DII, Universita' Politecnica delle Marche, Ancona, Italy" - }, - { - "author_name": "Matteo Marcosignori", - "author_inst": "Pronto Soccorso e OBI, Ospedali Riuniti, Ancona, Italy" - }, - { - "author_name": "Raniero Romagnoli", - "author_inst": "AI for Health, Almawave S.p.A., Rome, Italy" - }, - { - "author_name": "Marcello Tavio", - "author_inst": "Divisione di Malattie Infettive, Ospedali Riuniti, Ancona, Italy" - }, - { - "author_name": "Andrea Giacometti", - "author_inst": "Clinica di Malattie Infettive, Universita' Politecnica delle Marche, Ancona, Italy" - }, - { - "author_name": "Serena Tomassetti", - "author_inst": "Pronto Soccorso e OBI, Ospedali Riuniti, Ancona, Italy" - }, - { - "author_name": "Riccardo Bonazzi", - "author_inst": "Medical Division, Vivisol srl, Milan, Italy" - }, - { - "author_name": "Matteo Maccioni", - "author_inst": "Ehealth Engineering Lab, Aditech-Adilife srl, Ancona, Italy" - }, - { - "author_name": "Lina Zuccatosta", - "author_inst": "Divisione di Pneumologia, Ospedali Riuniti, Ancona, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.05.22269021", "rel_title": "Wastewater Surveillance of U.S. Coast Guard Installations and Seagoing Military Vessels to Mitigate the Risk of COVID-19 Outbreaks", @@ -405192,6 +406869,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.02.02.22270324", + "rel_title": "SARS-CoV-2 and influenza co-infection throughout the COVID-19 pandemic: An assessment of co-infection rates and cohort characterization", + "rel_date": "2022-02-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.02.22270324", + "rel_abs": "BackgroundCase reports of patients infected with COVID-19 and influenza virus (\"flurona\") have raised questions around the prevalence and clinical significance of these reports.\n\nMethodsEpidemiological data from the HHS Protect Public Data Hub was analyzed to show trends in SARS-CoV-2 and influenza co-infection-related hospitalizations in the United States in relation to SARS-CoV-2 and influenza strain data from NCBI Virus and FluView. In addition, we retrospectively analyzed all cases of PCR-confirmed SARS-CoV-2 across the Mayo Clinic Enterprise from January 2020 to January 2022 and identified cases of influenza co-infections within two weeks of PCR-positive diagnosis date. Using a cohort from the Mayo Clinic with joint PCR testing data, we estimated the expected number of co-infection cases given the background prevalences of COVID-19 and influenza during the Wuhan (Original), Alpha, Delta, and Omicron waves of the pandemic.\n\nFindingsConsidering data from all states of the United States using HHS Protect Public Data Hub, hospitalizations due to influenza co-infection with SARS-CoV-2 were seen to be highest in January 2022 compared to all previous months during the COVID-19 pandemic. Among 171,639 SARS-CoV-2-positive cases analyzed at Mayo Clinic between January 2020 and January 2022, only 73 cases of influenza co-infection were observed. Identified coinfected patients were relatively young (mean age: 28.4 years), predominantly male, and had few comorbidities. During the Delta era (June 16, 2021 to December 13, 2021), there were 9 lab-confirmed co-infection cases observed compared to 13.9 expected cases (95% CI: [12.7, 15.2]), and during the Omicron era (December 14, 2021 to January 17, 2022), there were 54 lab-confirmed co-infection cases compared to 80.9 expected cases (95% CI: [76.6, 85.1]).\n\nConclusionsReported co-infections of SARS-CoV-2 and influenza are rare. These co-infections have occurred throughout the COVID-19 pandemic and their prevalence can be explained by background rates of COVID-19 and influenza infection. Preliminary assessment of longitudinal EHR data suggests that most co-infections so far have been observed among relatively young and healthy patients. Further analysis is needed to assess the outcomes of \"flurona\" among subpopulations with risk factors for severe COVID-19 such as older age, obesity, and immunocompromised status.\n\nSignificance StatementReports of COVID-19 and influenza co-infections (\"flurona\") have raised concern in recent months as both COVID-19 and influenza cases have increased to significant levels in the US. Here, we analyze trends in co-infection cases over the course of the pandemic to show that these co-infection cases are expected given the background prevalences of COVID-19 and influenza independently. In addition, from an initial analysis of these co-infection cases which have been observed at the Mayo Clinic, we find that these co-infection cases are extremely rare and have mostly been observed in relatively young, healthy patients.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Colin Pawlowski", + "author_inst": "Nference" + }, + { + "author_name": "Eli Silvert", + "author_inst": "Nference" + }, + { + "author_name": "John C. O'Horo", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Patrick J. Lenehan", + "author_inst": "Nference" + }, + { + "author_name": "Douglas W Challener", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Esteban Gnass", + "author_inst": "Nference" + }, + { + "author_name": "Karthik Murugadoss", + "author_inst": "Nference" + }, + { + "author_name": "Jason Ross", + "author_inst": "Nference" + }, + { + "author_name": "Leigh Speicher", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Holly Geyer", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Aiveliagaram J Venkatakrishnan", + "author_inst": "Nference" + }, + { + "author_name": "Andrew Badley", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Venky Soundararajan", + "author_inst": "Nference" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.05.478644", "rel_title": "A scalable pipeline for SARS-CoV-2 replicon construction based on de-novo synthesis", @@ -406875,41 +408619,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.03.22269712", - "rel_title": "Comparative evaluation of oral lesions: Tale - the Covid 19 Tells", - "rel_date": "2022-02-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.03.22269712", - "rel_abs": "Introduction & ObjectivesThe COVID-19 pandemic has been raging across the globe since early January 2020. India has reported over 27 million cases and more than 3, 00,000 deaths. This study was planned to analyze the differences in demographic, clinical features and oral manifestations of COVID 19 patients hospitalized during COVID-19 pandemic.\n\nMethodsThis observational pilot study had total 36 participants, 12 each of mild, moderate and severe RT-PCR positive COVID cases hospitalized during COVID 19 pandemic. All demographic, clinical features, treatment details and oral manifestations were noted from first day of admission to hospital till treatment completion with follow up of minimum 7 days.\n\nResultsMean age of the patients was 39.44 {+/-}9.13 years with M: F ratio of 5:4. Most common clinical presentation was fever, shortness of breath and treatment involved was symptomatic with supplemental oxygen & mechanical ventilation. Most common oral site involved was tongue & oral lesions observed were herpes labialis, mucositis, burning sensation, dryness of oral cavity, angular chelitis, aphthous ulcers, geographic tongue, fissuring of tongue, candidiasis, coated tongue, sublingual varicosity, & scalloped tongue.\n\nInterpretation and ConclusionAll demographic, clinical and oral manifestations were significantly different in mild, moderate and severe cases of covid hospitalized patients. Though clinical symptoms were improved, oral lesions were worsened. Oral Lesions seen in covid patients were associated with multiple drug therapy for illness along with poor oral hygiene, but further etiology for lesions needs to be evaluated. Sublingual varicosity was observed in our hospitalised covid patients, but large sample observation is required for confirmation of findings and may be an early oral feature for covid detection. Prevention is always better than cure, so all patients positive for Covid should have a full mouth examination. Oral health should be priority during overall management of COVID patients and dentists should be a part of Covid management team.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Rashmi P. Bhavasar", - "author_inst": "K.M.SHAH DENTAL COLLEGE AND HOSPITAL, SUMANDEEP VIDYAPEETH DEEMED TO BE UNIVERSITY, PIPARIA, VADODARA, GUJARAT." - }, - { - "author_name": "Namratha A Ajith", - "author_inst": "K M SHAH DENTAL COLLEGE AND HOSPITAL, SUMANDEEP DEEMED TO BE UNIVERSITY, VADODARA, GUJARAT, INDIA" - }, - { - "author_name": "Rahul Prakash Bhavasar", - "author_inst": "Dr. Ulhas Patil Medical College and Hospital, Jalgaon, Maharashtra, India" - }, - { - "author_name": "Arti Dhawal", - "author_inst": "SBSK&MIRC, Dhiraj Hospital, Sumandeep Vidyapeeth Deemed to be University, Vadodara, Gujarat" - }, - { - "author_name": "Vivek Vaswani", - "author_inst": "SBKS&MIRC, Dhiraj Hospital, Sumandeep Vidyapeeth Deemed to be University, Vadodara, Gujarat" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "dentistry and oral medicine" - }, { "rel_doi": "10.1101/2022.02.02.22269952", "rel_title": "Serious hospital events following symptomatic infection with Sars-CoV-2 Omicron and Delta variants: an exposed-unexposed cohort study in December 2021 from the COVID-19 surveillance databases in France", @@ -407130,6 +408839,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2022.02.02.22270278", + "rel_title": "Working from home due to the COVID-19 pandemic abolished the sleep disturbance vulnerability of late chronotypes relieving their predisposition to depression", + "rel_date": "2022-02-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.02.22270278", + "rel_abs": "Background and aimsEveningness is distinctively associated with sleep disturbances and depression symptoms due to the misalignment between biological and social clock. The widespread imposition of remote working due to the COVID-19 pandemic allowed a more flexible sleep schedule. This scenario could promote sleep and mental health of evening-type subjects. We investigated the effect of working from home on sleep quality/quantity and insomnia symptoms within the morningness-eveningness continuum, and its indirect repercussions on depressive symptomatology.\n\nMethods610 Italian office workers (mean age {+/-} standard deviation, 35.47 {+/-} 10.17 yrs) and 265 remote workers (40.31 {+/-} 10.69 yrs) participated in a web-based survey during the second contagion wave of COVID-19 (28 November-11 December 2020). We evaluated chronotype, sleep quality/duration, insomnia, and depression symptoms through validated questionnaires. Three moderated mediation models were performed, testing the mediation effect of sleep variables on the association between morningness-eveningness continuum and depression symptoms, with working modality (office vs. remote working) as moderator of the relationship between chronotype and sleep variables.\n\nResultsRemote working led to delayed bedtime and get-up time. Working modality moderated the chronotype effect on sleep variables, as eveningness was related to worse sleep disturbances and shorter sleep duration only among the office workers. Working modality moderated the mediation of sleep variables between chronotype and depression. The above mediation vanished among remote workers.\n\nConclusionsRemote working strikingly abolished the vulnerability to sleep problems of evening-type subjects, relieving their predisposition to depressive symptomatology. A working environment complying with individual circadian preferences might ensure an adequate sleep quantity/quality to late chronotypes, promoting their mental health.\n\nStatement of SignificanceThe present study is the first to evaluate the different effect of pandemic-related remote working on sleep health/habits depending on the chronotype. We found longer sleep duration and improved sleep disturbances among evening-type subjects when working from home. This outcome could be ascribable to a better alignment between the endogenous circadian phase and the working schedule, as remote workers reported later bedtimes and get-up times. Moreover, we showed how improved sleep weakened the susceptibility to depressive symptomatology of evening-type people, highlighting an intriguing implication of working remotely on mental health in this category. Morningness-eveningness predisposition should be considered when designing remote working policies, in order to promote sleep and mental health of late chronotypes during the pandemic emergency, as well as in the post-covid era.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Federico Salfi", + "author_inst": "University of L'Aquila" + }, + { + "author_name": "Aurora D'Atri", + "author_inst": "University of L'Aquila" + }, + { + "author_name": "Giulia Amicucci", + "author_inst": "\"Sapienza\"University of Rome" + }, + { + "author_name": "Lorenzo Viselli", + "author_inst": "University of L'Aquila" + }, + { + "author_name": "Maurizio Gorgoni", + "author_inst": "\"Sapienza\" University of Rome" + }, + { + "author_name": "Serena Scarpelli", + "author_inst": "\"Sapienza\" University of Rome" + }, + { + "author_name": "Valentina Alfonsi", + "author_inst": "\"Sapienza\" University of Rome" + }, + { + "author_name": "Michele Ferrara", + "author_inst": "University of L'Aquila" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2022.02.03.22270311", "rel_title": "Psychological, endocrine and polygenic predictors of emotional well-being during the COVID-19 pandemic", @@ -408809,65 +410565,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.02.22270295", - "rel_title": "Real-life performance of a COVID-19 rapid antigen detection test targeting the SARS-CoV-2 nucleoprotein for diagnosis of COVID-19 due to the Omicron variant", - "rel_date": "2022-02-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.02.22270295", - "rel_abs": "ObjectivesIt has been suggested that rapid antigen detection assays (RADT) may perform suboptimally in terms of sensitivity for the diagnosis of SARS-CoV-2 Omicron variant infection. To address this issue, we conducted a prospective study in primary health centers to evaluate the clinical performance of the Panbio COVID-19 Ag Rapid Test Device in nasopharyngeal specimens (NP) carried out at the point of care.\n\nMethodsWe recruited 244 patients (median age, 40 years; range 2-96; 141 female) with clinical suspicion of COVID-19 (232 adults and 12 children). 228/244 patients had been fully vaccinated (two doses) with licensed COVID-19 vaccines prior to recruitment. Most patients (222/244) were SARS-CoV-2 naive prior to enrollment. Patients were tested by RT-PCR and RADT within 5 days since symptoms onset.\n\nResults126 patients (51.6%) tested positive by both RT-PCR and RADT, 90 patients (36.8%) returned negative results by both assays and 28 patients (11.4%) yielded discordant results (RT-PCR+/RADT-). No patients tested RT-PCR-/RADT+. Overall specificity and sensitivity of RADT was 100% (95% CI, 95.9-100%) and 81.8% (95% CI, 75-87.1%) respectively. The sensitivity of the assay increased from 79.6% (95% CI, 66.4-88.5) when considering specimens collected at days 0-1 after symptoms onset, to 86.4% (95% CI, 66.7-95.3) when grouping the specimens obtained on days 4-5.\n\nConclusionThe Panbio COVID-19 Ag Rapid Test Device perform well ([≥]80% sensitivity) as a point-of-care test for early diagnosis of COVID-19 due to the Omicron variant in primary healthcare centers.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Paul de Michelena", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "Ignacio Torres", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "Angela Ramos-Garcia", - "author_inst": "Health Care center Benimaclet, Health Department Clinico-Malvarrosa, Valencia, Spain." - }, - { - "author_name": "Victoria Gosalbes", - "author_inst": "Health Care center Salvador Pau, Health Department Clinico-Malvarrosa, Valencia, Spain." - }, - { - "author_name": "Nadia Ruiz", - "author_inst": "Health Care center Serreria, Health Department Clinico-Malvarrosa, Valencia, Spain." - }, - { - "author_name": "Ana Sanmartin", - "author_inst": "Primary Health Directorate, Health Department Clinico-Malvarrosa, Valencia, Spain." - }, - { - "author_name": "Pilar Botija", - "author_inst": "Primary Health Directorate, Health Department Clinico-Malvarrosa, Valencia, Spain." - }, - { - "author_name": "Sandrine Puojois", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "Dixie Huntley", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "Eliseo Albert", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "David Navarro", - "author_inst": "Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.01.22270285", "rel_title": "Association study of HLA with the kinetics of SARS-CoV-2 spike specific IgG antibody responses to BNT162b2 mRNA vaccine", @@ -409160,6 +410857,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.01.22269931", + "rel_title": "High Rates of Rapid Antigen Test Positivity After 5 Days of Isolation for COVID-19", + "rel_date": "2022-02-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.01.22269931", + "rel_abs": "BackgroundThe emergence of the highly transmissible COVID-19 variant, omicron, has resulted in high numbers of breakthrough infections, including among healthcare workers (HCW). Recent CDC recommendations now allow healthcare workers to return to work after day 5 if symptoms have improved, without a requirement for a negative rapid antigen test (RAT).\n\nMethodsFully vaccinated and non-immunocompromised HCW at a large, urban, academic medical center who tested positive for COVID-19 starting in late December, 2021 (when omicron was the predominant circulating strain) were allowed to return to work early if all symptoms had resolved excepting mild, intermittent cough and/or lingering loss of taste/smell, provided a rapid antigen test was negative upon return. Those with negative tests were allowed to return to work with the stipulations that they wear an N95 at all times and take breaks and eat meals apart from others. Those with positive tests on first attempt could return 24-48 hours later to test again for as many days as needed to achieve a negative result or until they completed 10 days of restriction from work.\n\nResultsBetween January 2, 2022 and January 12, 2022 there were 309 total RAT done on 260 separate HCW on day 5-10 of illness. Overall, 43% (134 of 309) of all RAT were positive between days 5-10. The greatest percent positive RAT was noted among HCW returning for their first test on day 6 (58%). The rate of positivity was greatest (58%) among HCW returning for their first test on day 6. HCW returning on day 8 and 9 were less likely to have a positive test (26%, 19/74). In RAT positive HCW returning for their first test on days 5 or 6 (and for which line intensity was recorded) 49% (25/51) were recorded as having the darkest intensity on their RAT. HCW who test positive on their first test most often remained positive on their second test, with 56% of second tests, aggregated across all days 6-10, remaining positive. Over all first tests performed on days 5-10, boosted HCW were nearly twice as likely to test RAT positive: 53% (75 out of 141) of boosted HCW tested positive.\n\nDiscussionMore than 40% of vaccinated HCW who felt well enough to work still had positive RAT tests when presenting for a first test between days 5 and 10. Boosted individuals were nearly 3x as likely to result positive on day 5, their first day eligible for return, and [~]2x as likely to result positive on first RAT overall. New guidance provides clearance to exit isolation after 5 days from symptom onset, without the need for a negative rapid antigen test to exit, as long as symptoms are beginning to resolve. Per CDC, the guidance was driven by prior studies, mostly collected before Omicron and before most people were vaccinated or infected, that reported on symptom onset beginning one or more days after peak virus loads. In such an instance, where isolation based on symptom onset often did not begin until peak virus load was already attained, then release from isolation at 5 days would be appropriate. However, reports showing much earlier onset of symptoms, coupled with our own results here demonstrate that the relationship between symptom onset and peak virus load has changed, and 5 days from symptom onset may no longer be an appropriate window to end isolation without a negative rapid antigen test to support safe exit.\n\nConclusionThese results indicate that a substantial proportion of individuals with COVID-19 are likely still contagious after day 5 of illness regardless of symptom status. Early liberation from isolation should be undertaken only with the understanding that inclusion of individuals on day 6-10 of illness in community or work settings may increase the risk of COVID-19 spread to others which, in turn, may undermine the intended benefits to staffing by resulting in more sick workers.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Emily M Landon", + "author_inst": "University of Chicago" + }, + { + "author_name": "Allison H Bartlett", + "author_inst": "University of Chicago" + }, + { + "author_name": "Rachel Marrs", + "author_inst": "University of Chicago Medicine" + }, + { + "author_name": "Caroline Guenette", + "author_inst": "University of Chicago Medicine" + }, + { + "author_name": "Stephen G Weber", + "author_inst": "University of Chicago" + }, + { + "author_name": "Michael J Mina", + "author_inst": "eMed" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.31.478564", "rel_title": "ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes using Short Read Data", @@ -410603,49 +412339,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2022.01.31.478460", - "rel_title": "A Genetically Encoded BRET-based SARS-CoV-2 Mpro Protease Activity Sensor", - "rel_date": "2022-02-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.31.478460", - "rel_abs": "The SARS-CoV-2 main protease, Mpro, is critical for its replication and is an appealing target for designing anti-SARS-CoV-2 agents. In this regard, a number of assays have been developed based on its cleavage sequence preferences to monitor its activity. These include the usage of Fluorescence Resonance Energy Transfer (FRET)-based substrates in vitro and a FlipGFP reporter, one which fluoresces after Mpro-mediated cleavage, in live cells. Here, we have engineered a pair of genetically encoded, Bioluminescence Resonance Energy Transfer (BRET)-based sensors for detecting SARS-CoV-2 Mpro proteolytic activity in living host cells as well as in vitro assays. The sensors were generated by sandwiching Mpro N-terminal autocleavage sites, either AVLQSGFR (short) or KTSAVLQSGFRKME (long), in between the mNeonGreen and nanoLuc proteins. Co-expression of the sensor with the Mpro in live cells resulted in its cleavage in a dose- and time-dependent manner while mutation of the critical C145 residue (C145A) in Mpro completely abrogated the sensor cleavage. Importantly, the BRET-based sensors displayed increased sensitivities and specificities as compared to the recently developed FlipGFP-based Mpro sensor. Additionally, the sensors recapitulated the inhibition of Mpro by the well-characterized pharmacological agent GC376. Further, in vitro assays with the BRET-based Mpro sensors revealed a molecular crowding-mediated increase in the rate of Mpro activity and a decrease in the inhibitory potential of GC376. The sensor developed here will find direct utility in studies related to drug discovery targeting the SARS-CoV-2 Mpro and functional genomics application to determine the effect of sequence variation in Mpro.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Anupriya M Geethakumari", - "author_inst": "Hamad Bin Khalifa University" - }, - { - "author_name": "Wesam S Ahmed", - "author_inst": "Hamad Bin Khalifa University" - }, - { - "author_name": "Saad H Rasool", - "author_inst": "Hamad Bin Khalifa University" - }, - { - "author_name": "Asma H Fatima", - "author_inst": "Hamad Bin Khalifa University" - }, - { - "author_name": "S M Nasir Uddin", - "author_inst": "Hamad Bin Khalifa University" - }, - { - "author_name": "Mustapha H Aouida", - "author_inst": "Hamad Bin Khalifa University" - }, - { - "author_name": "Kabir H Biswas", - "author_inst": "Hamad Bin Khalifa University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2022.01.30.478380", "rel_title": "Using Unassigned NMR Chemical Shifts to Model RNA Secondary Structure", @@ -410934,6 +412627,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.01.30.22270125", + "rel_title": "Web and social media searches highlight menstrual irregularities as a global concern in COVID-19 vaccinations", + "rel_date": "2022-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.30.22270125", + "rel_abs": "BackgroundDelineation of public concerns that prevent vaccine compliance is a major step in generating assurances and enhancing the success of COVID-19 prevention programs. We therefore sought to identify public concerns associated with COVID-19 vaccines, as reflected by web and social media searches, with a focus on menstrual irregularities.\n\nMethodsWe used trajectory analyses of web and social media search data in combination with global COVID-19 data to reveal time-dependent correlations between vaccination rates and the relative volume of vaccine and period related searches.\n\nResultsA surge of period and vaccine related Google searches followed the introduction of Covid vaccines around the world, and the commencement of vaccination programs in English speaking countries and across the United States. The relative volume of searches such as \"Covid vaccine menstrual irregularities\", \"Covid vaccine menstrual period\", \"Pfizer vaccine menstruation\", and \"Moderna vaccine menstruation\" was each significantly correlated with vaccination rates (Spearman r = 0.42-0.88, P = 4.33 x 10-34-1.55 x 10-5), and significantly different before and after the introduction of COVID vaccines (Mann-Whitney P = 2.00 x 10-21-7.10 x 10-20). TikTok users were more engaged in period problems in 2021 than ever before.\n\nConclusionsInternational, national, and state-level correlations between COVID-19 vaccinations and online activity demonstrate a global major concern of vaccine-related menstrual irregularities. Whether it is a potential side effect or an unfounded worry, monitoring of web and social media activity could reveal the public perception of COVID-19 prevention efforts, which could then be directly addressed and translated into insightful public health strategies.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Ariel Katz", + "author_inst": "Ben-Gurion University of the Negev" + }, + { + "author_name": "Yoav Tepper", + "author_inst": "Unaffiliated" + }, + { + "author_name": "Ohad Birk", + "author_inst": "Ben-Gurion University of the Negev" + }, + { + "author_name": "Alal Eran", + "author_inst": "Ben-Gurion University of the Negev" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2022.01.31.22270015", "rel_title": "Emergency department utilization and hospitalizations for ambulatory care sensitive conditions among unattached people actively seeking a primary care provider during the COVID-19 pandemic: a retrospective cohort study", @@ -412633,29 +414357,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.01.30.22269992", - "rel_title": "\"Populist Attitude and Conspiracist beliefs contribution to the overconfidence about the risk of Covid-19: implications for Preventive Health Behaviors\"", - "rel_date": "2022-01-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.30.22269992", - "rel_abs": "Populism and Conspiracy beliefs seem to represent the zeitgeist of people depending on fast and simple information retrieved through social media. The Covid-19 emergency has simply catalyzed this process, not without consequences. Supported by literature review, we hypothesize that the higher the populist attitude the higher the tendency in believing in conspiracies, and that both higher populist attitudes and conspiracist beliefs may induce people in underestimating health related risks that may be reflected in a lowered tendency in adopting preventive health behaviors against Covid-19 spread. Data collected during the quarantine (December 2020, March 2021) mainly supported our hypotheses. Results are discussed in accord with the dramatic consequences it may have overconfidence in undermining the adoption of preventive health behaviors.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Agnese Giuliani", - "author_inst": "Sapienza University of Rome: Universita degli Studi di Roma La Sapienza" - }, - { - "author_name": "Fabio Presaghi", - "author_inst": "Sapienza University of Rome: Universita degli Studi di Roma La Sapienza" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.01.29.22269971", "rel_title": "Estimating COVID-19 Vaccination Effectiveness Using Electronic Health Records of an Academic Medical Center in Michigan", @@ -412764,6 +414465,93 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2022.01.30.478159", + "rel_title": "An intranasal lentiviral booster broadens immune recognition of SARS-CoV-2 variants and reinforces the waning mRNA vaccine-induced immunity that it targets to lung mucosa", + "rel_date": "2022-01-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.30.478159", + "rel_abs": "As the COVID-19 pandemic continues and new SARS-CoV-2 variants of concern emerge, the adaptive immunity initially induced by the first-generation COVID-19 vaccines wains and needs to be strengthened and broadened in specificity. Vaccination by the nasal route induces mucosal humoral and cellular immunity at the entry point of SARS-CoV-2 into the host organism and has been shown to be the most effective for reducing viral transmission. The lentiviral vaccination vector (LV) is particularly suitable for this route of immunization because it is non-cytopathic, non-replicative and scarcely inflammatory. Here, to set up an optimized cross-protective intranasal booster against COVID-19, we generated an LV encoding stabilized Spike of SARS-CoV-2 Beta variant (LV::SBeta-2P). mRNA vaccine-primed and -boosted mice, with waning primary humoral immunity at 4 months post-vaccination, were boosted intranasally with LV::SBeta-2P. Strong boost effect was detected on cross-sero-neutralizing activity and systemic T-cell immunity. In addition, mucosal anti-Spike IgG and IgA, lung resident B cells, and effector memory and resident T cells were efficiently induced, correlating with complete pulmonary protection against the SARS-CoV-2 Delta variant, demonstrating the suitability of the LV::SBeta-2P vaccine candidate as an intranasal booster against COVID-19.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Benjamin Vesin", + "author_inst": "TheraVectys" + }, + { + "author_name": "Jodie Lopez", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Amandine Noirat", + "author_inst": "TheraVectys" + }, + { + "author_name": "Pierre Authi\u00e9", + "author_inst": "TheraVectys" + }, + { + "author_name": "Ingrid Fert", + "author_inst": "TheraVectys" + }, + { + "author_name": "Fabien Le Chevalier", + "author_inst": "TheraVectys" + }, + { + "author_name": "Fanny Moncoq", + "author_inst": "TheraVectys" + }, + { + "author_name": "Kirill Nemirov", + "author_inst": "TheraVectys" + }, + { + "author_name": "Catherine Blanc", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Cyril Planchais", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Hugo Mouquet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Fran\u00e7oise Guinet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "David Hardy", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Christiane Gerke", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Fran\u00e7ois Anna", + "author_inst": "TheraVectys" + }, + { + "author_name": "Maryline Bourgine", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Laleh MAJLESSI", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Pierre Charneau", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.01.30.478305", "rel_title": "Combating the SARS-CoV-2 Omicron variant with non-Omicron neutralizing antibodies", @@ -414303,77 +416091,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.28.22270005", - "rel_title": "Development and External Validation of a Mixed-Effects Deep Learning Model to Diagnose COVID-19 from CT Imaging", - "rel_date": "2022-01-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.28.22270005", - "rel_abs": "ObjectivesTo develop and externally geographically validate a mixed-effects deep learning model to diagnose COVID-19 from computed tomography (CT) imaging following best practice guidelines and assess the strengths and weaknesses of deep learning COVID-19 diagnosis.\n\nDesignModel development and external validation with retrospectively collected data from two countries.\n\nSettingHospitals in Moscow, Russia, collected between March 1, 2020, and April 25, 2020. The China Consortium of Chest CT Image Investigation (CC-CCII) collected between January 25, 2020, and March 27, 2020.\n\nParticipants1,110 and 796 patients with either COVID-19 or healthy CT volumes from Moscow, Russia, and China, respectively.\n\nMain outcome measuresWe developed a deep learning model with a novel mixed-effects layer to model the relationship between slices in CT imaging. The model was trained on a dataset from hospitals in Moscow, Russia, and externally geographically validated on a dataset from a consortium of Chinese hospitals. Model performance was evaluated in discriminative performance using the area under the receiver operating characteristic (AUROC), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). In addition, calibration performance was assessed using calibration curves, and clinical benefit was assessed using decision curve analysis. Finally, the models decisions were assessed visually using saliency maps.\n\nResultsExternal validation on the large Chinese dataset showed excellent performance with an AUROC of 0.936 (95%CI: 0.910, 0.961). Using a probability threshold of 0.5, the sensitivity, specificity, NPV, and PPV were 0.753 (0.647, 0.840), 0.909 (0.869, 0.940), 0.711 (0.606, 0.802), and 0.925 (0.888, 0.953), respectively.\n\nConclusionsDeep learning can reduce stress on healthcare systems by automatically screening CT imaging for COVID-19. However, deep learning models must be robustly assessed using various performance measures and externally validated in each setting. In addition, best practice guidelines for developing and reporting predictive models are vital for the safe adoption of such models.\n\nStatementsThe authors do not own any of the patient data, and ethics approval was not needed. The lead author affirms that this manuscript is an honest, accurate, and transparent account of the study being reported, that no important aspects of the study have been omitted, and that any discrepancies from the study as planned (and, if relevant, registered) have been explained. Patients and the public were not involved in the study.\n\nFundingThis study was funded by EPSRC studentship (No. 2110275), EPSRC Impact Acceleration Account (IAA) funding, and Amazon Web Services.\n\nSummaryO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIDeep learning can diagnose diseases from imaging data automatically\nC_LIO_LIMany studies using deep learning are of poor quality and fail to follow current best practice guidelines for the development and reporting of predictive models\nC_LIO_LICurrent methods do not adequately model the relationship between slices in CT volumetric data\nC_LI\n\nWhat this study addsO_LIA novel method to analyse volumetric imaging data composed of slices such as CT images using deep learning\nC_LIO_LIModel developed following current best-practice guidelines for the development and reporting of prediction models\nC_LI", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Joshua Bridge", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Yanda Meng", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Wenyue Zhu", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Thomas Fitzmaurice", - "author_inst": "Liverpool Heart and Chest Hospital NHS Foundation Trust" - }, - { - "author_name": "Caroline McCann", - "author_inst": "Liverpool Heart and Chest Hospital NHS Foundation Trust" - }, - { - "author_name": "Cliff Addison", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Manhui Wang", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Cristin Merritt", - "author_inst": "Alces Flight Limited" - }, - { - "author_name": "Stu Franks", - "author_inst": "Alces Software Limited" - }, - { - "author_name": "Maria Mackey", - "author_inst": "Amazon Web Services" - }, - { - "author_name": "Steve Messenger", - "author_inst": "Amazon Web Services" - }, - { - "author_name": "Renrong Sun", - "author_inst": "Hubei University of Chinese Medicine" - }, - { - "author_name": "Yitian Zhao", - "author_inst": "Ningbo Institute of Materials Technology and Engineering" - }, - { - "author_name": "Yalin Zheng", - "author_inst": "University of Liverpool" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.29.22270066", "rel_title": "Evaluation of the systemic and mucosal immune response induced by COVID-19 and the BNT162b2 mRNA vaccine for SARS-CoV-2", @@ -414578,6 +416295,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2022.01.27.22269512", + "rel_title": "Investigation of air change rate and aerosol behavior during an outbreak of COVID-19 in a geriatric care facility", + "rel_date": "2022-01-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.27.22269512", + "rel_abs": "BackgroundVentilation plays an important role in controlling aerosol transmission of coronavirus disease (COVID-19), and mass transmission of COVID- 19 has been reported in poorly ventilated areas.\n\nObjectiveA real-world mass infection outbreak which occurred in an elderly nursing home, in Miyagi Prefecture, Japan, was simulated experimentally and numerically to investigate the controlling factors and quantify the effectiveness of various natural ventilation settings by means of air change rate (ACR).\n\nMethodsUsing the CO2 tracer gas method, the ACR values at the time of the outbreak were estimated to be 2.0-6.2 h-1 in rooms in the facility. Furthermore, a low-cost intervention of opening windows improved the ventilation frequency by a factor of 1.48-5.74. This implies that advective fluid flows are the key in the spread of high CO2 concentration zones. A numerical simulation was performed to obtain spatio-temporal evolution on such high CO2 concentration zones under similar conditions to the present experiment.\n\nResultsThe results showed that ventilation was significantly dependent on the window opening conditions in all rooms (p-values ranging from 0.001 to 0.03 for all the rooms). In contrast, there was no significant dependence on the location of the sensor in any of the areas. Development of high CO2 concentration zones occurs in the first few minutes. Furthermore, the leading edge of such zones towards the common room yields a relatively high fluid velocity, suggesting that the large-scale advective flow dictates the spread of such high CO2 concentration zones.\n\nConclusionsThe present results suggest that secondary infections could occur due to the aerosol advection driven by such large-scale flows, even when the building design adheres the ventilation guidelines. In elderly care facilities, open architectural spaces are recommended to realize quality of life and monitor residents. However, management is required to reduce the downwind infection risk from aerosols and ACR.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Yo Ishigaki", + "author_inst": "University of Electro-Communications" + }, + { + "author_name": "Shinji Yokogawa", + "author_inst": "Info-powered Energy System Research Center (iPERC), The University of Electro-communications" + }, + { + "author_name": "Yuki Minamoto", + "author_inst": "School of Engineering, Tokyo Institute of Technology" + }, + { + "author_name": "Akira Saito", + "author_inst": "Miyagi Anti-Tuberculosis Association" + }, + { + "author_name": "Hiroko Kitamura", + "author_inst": "Occupational Health Training Center, University of Occupational and Environmental Health" + }, + { + "author_name": "Yuto Kawauchi", + "author_inst": "Graduate School of Informatics and Engineering, The University of Electro-communications" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2022.01.29.22270064", "rel_title": "The Correlation Between Brain Performance Capacity and COVID-19: A Cross-sectional Survey and Canonical Correlation Analysis", @@ -416113,65 +417869,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.01.24.22269745", - "rel_title": "Cardiovascular, respiratory and functional effects of tele-supervised home-based exercise training in individuals recovering from COVID-19 hospitalization: A randomized clinical trial", - "rel_date": "2022-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.24.22269745", - "rel_abs": "Our aim was to test the hypothesis that tele-supervised home-based exercise training (exercise) is an effective strategy for improving cardiovascular, respiratory, and functional capacity parameters in individuals that were hospitalized due to coronavirus disease 2019 (COVID-19). Thirty-two individuals (52 {+/-} 10 years; 17F) randomly assigned to exercise (N = 12) and control groups (N = 20), had their anthropometric (weight, body mass index), hemodynamic (brachial and central blood pressure), vascular (arterial stiffness), ventilatory (pulmonary function and respiratory muscle strength), and functional parameters (handgrip strength, five-time sit to stand [FTSTS], timed up and go test [TUG] and six-minute walking test [6MWT]) assessed at baseline (30 to 45 days of hospital discharged) and after 12 weeks of follow-up. Both groups similarly increased (P < 0.001) forced vital capacity (absolute and % of predicted), forced expiratory volume in the first second (absolute and % of predicted), and handgrip strength during follow-up. However, only exercise group reduced carotid-femoral pulse wave velocity (-2.0 {+/-} 0.6 m/s, P = 0.048), and increased (P < 0.05) resting oxygen saturation (1.9 {+/-} 0.6 %), mean inspiratory pressure (24.7 {+/-} 7.1 cmH2O), mean expiratory pressure (20.3 {+/-} 5.8 cmH2O) and % of predicted mean expiratory pressure (14 {+/-} 22 %) during follow-up. No significant changes were found in any other variable during follow-up. Present findings suggest that tele-supervised home-based exercise training can a potential adjunct therapeutic to rehabilitate individuals that were hospitalized due to COVID-19.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Vanessa Teixeira do Amaral", - "author_inst": "Unesp" - }, - { - "author_name": "Ariane Aparecida Viana", - "author_inst": "Unesp" - }, - { - "author_name": "Alessandro Domingues Heubel", - "author_inst": "Ufscar" - }, - { - "author_name": "Stephanie Nogueira Linares", - "author_inst": "Ufscar" - }, - { - "author_name": "Bruno Martinelli", - "author_inst": "UNISAGRADO" - }, - { - "author_name": "Pedro Henrique Camprigher Witzler", - "author_inst": "Unesp" - }, - { - "author_name": "Gustavo Yudi Orikassa de Oliveira", - "author_inst": "Unesp" - }, - { - "author_name": "Gabriel de Souza Zanini", - "author_inst": "Unesp" - }, - { - "author_name": "Audrey Borghi Silva", - "author_inst": "Ufscar" - }, - { - "author_name": "Renata Goncalves Mendes", - "author_inst": "Ufscar" - }, - { - "author_name": "Emmanuel Gomes Ciolac", - "author_inst": "Unesp" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "rehabilitation medicine and physical therapy" - }, { "rel_doi": "10.1101/2022.01.27.22269909", "rel_title": "How dangerous is omicron and how effective are vaccinations?", @@ -416404,6 +418101,197 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.01.26.477915", + "rel_title": "Breadth of SARS-CoV-2 Neutralization and Protection Induced by a Nanoparticle Vaccine", + "rel_date": "2022-01-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.26.477915", + "rel_abs": "Coronavirus vaccines that are highly effective against SARS-CoV-2 variants are needed to control the current pandemic. We previously reported a receptor-binding domain (RBD) sortase A-conjugated ferritin nanoparticle (RBD-scNP) vaccine that induced neutralizing antibodies against SARS-CoV-2 and pre-emergent sarbecoviruses and protected monkeys from SARS-CoV-2 WA-1 infection. Here, we demonstrate SARS-CoV-2 RBD-scNP immunization induces potent neutralizing antibodies in non-human primates (NHPs) against all eight SARS-CoV-2 variants tested including the Beta, Delta, and Omicron variants. The Omicron variant was neutralized by RBD-scNP-induced serum antibodies with a mean of 10.6-fold reduction of ID50 titers compared to SARS-CoV-2 D614G. Immunization with RBD-scNPs protected NHPs from SARS-CoV-2 WA-1, Beta, and Delta variant challenge, and protected mice from challenges of SARS-CoV-2 Beta variant and two other heterologous sarbecoviruses. These results demonstrate the ability of RBD-scNPs to induce broad neutralization of SARS-CoV-2 variants and to protect NHPs and mice from multiple different SARS-related viruses. Such a vaccine could provide the needed immunity to slow the spread of and reduce disease caused by SARS-CoV-2 variants such as Delta and Omicron.", + "rel_num_authors": 44, + "rel_authors": [ + { + "author_name": "Dapeng Li", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " + }, + { + "author_name": "David R Martinez", + "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA" + }, + { + "author_name": "Alexandra Sch\u00e4fer", + "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA" + }, + { + "author_name": "Haiyan Chen", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA" + }, + { + "author_name": "Maggie Barr", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA" + }, + { + "author_name": "Laura L Sutherland", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA" + }, + { + "author_name": "Esther Lee", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA" + }, + { + "author_name": "Robert Parks", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA" + }, + { + "author_name": "Dieter Mielke", + "author_inst": "Department of Surgery, Duke University, Durham, NC 27710, USA" + }, + { + "author_name": "Whitney Edwards", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA" + }, + { + "author_name": "Amanda Newman", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA" + }, + { + "author_name": "Kevin W Bock", + "author_inst": "Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Beth" + }, + { + "author_name": "Mahnaz Minai", + "author_inst": "Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Beth" + }, + { + "author_name": "Bianca M Nagata", + "author_inst": "Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Beth" + }, + { + "author_name": "Matthew Gagne", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20814, USA" + }, + { + "author_name": "Daniel Douek", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20814, USA" + }, + { + "author_name": "C Todd DeMarco", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " + }, + { + "author_name": "Thomas N Denny", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " + }, + { + "author_name": "Thomas H Oguin III", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " + }, + { + "author_name": "Alecia Brown", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA" + }, + { + "author_name": "Wes Rountree", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " + }, + { + "author_name": "Yunfei Wang", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " + }, + { + "author_name": "Katayoun Mansouri", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " + }, + { + "author_name": "Robert J Edwards", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " + }, + { + "author_name": "Guido Ferrari", + "author_inst": "Department of Surgery, Duke University, Durham, NC 27710, USA" + }, + { + "author_name": "Gregory D Sempowski", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " + }, + { + "author_name": "Amanda Eaton", + "author_inst": "Department of Surgery, Duke University, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA" + }, + { + "author_name": "Juanjie Tang", + "author_inst": "Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration, Silver Spring, MD 20871, USA." + }, + { + "author_name": "Derek W Cain", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " + }, + { + "author_name": "Sampa Santra", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA 02215, USA." + }, + { + "author_name": "Norbert Pardi", + "author_inst": "Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA." + }, + { + "author_name": "Drew Weissman", + "author_inst": "Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA." + }, + { + "author_name": "Mark Tomai", + "author_inst": "Corporate Research Materials Lab, 3M Company, St Paul, MN 55144, USA." + }, + { + "author_name": "Christopher Fox", + "author_inst": "Infectious Disease Research Institute, Seattle, WA 98102, USA." + }, + { + "author_name": "Ian N Moore", + "author_inst": "Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Beth" + }, + { + "author_name": "Hanne Andersen", + "author_inst": "BIOQUAL, Rockville, MD 20850, USA" + }, + { + "author_name": "Mark G Lewis", + "author_inst": "BIOQUAL, Rockville, MD 20850, USA" + }, + { + "author_name": "Hana Golding", + "author_inst": "Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration, Silver Spring, MD 20871, USA." + }, + { + "author_name": "Surender Khurana", + "author_inst": "Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration, Silver Spring, MD 20871, USA." + }, + { + "author_name": "Robert Seder", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20814, USA" + }, + { + "author_name": "Ralph S Baric", + "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA" + }, + { + "author_name": "David C Montefiori", + "author_inst": "Department of Surgery, Duke University, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA" + }, + { + "author_name": "Kevin O Saunders", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA; Departme" + }, + { + "author_name": "Barton F Haynes", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.01.25.22269827", "rel_title": "SARS-CoV-2 seroprevalence in children, parents and school personnel from June 2020 to April 2021: cohort study of 55 schools in Switzerland", @@ -418135,49 +420023,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2022.01.27.22269961", - "rel_title": "A Micronized Electrostatic Precipitator Respirator Effectively Removes Ambient SARS-CoV-2 Bioaerosols", - "rel_date": "2022-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.27.22269961", - "rel_abs": "RationaleInhalation of ambient SARS-CoV-2-containing bioaerosols leads to infection and pandemic airborne transmission in susceptible populations. Filter-based respirators effectively reduce exposure but complicate normal respiration through breathing zone pressure differential and are therefore impractical for long-term use.\n\nObjectivesWe tested the comparative effectiveness of a prototyped micronized electrostatic precipitator (mEP) to a filter-based respirator (N95) in the removal of viral bioaerosols from a simulated inspired air stream.\n\nMethodsEach respirator was tested within a 16-liter environmental chamber housed within a Class III biological safety cabinet within biosafety level 3 containment. SARS-CoV-2 containing bioaerosols were generated into the chamber, drawn by vacuum through each respirator, and physical particle removal and viral genomic RNA were measured distal to the breathing zone of each device.\n\nMeasurement and Main ResultsThe mEP respirator removed particles (96.5{+/-}0.4%) approximating efficiencies of the N95 (96.9{+/-}0.6%). The mEP respirator similarly decreased SARS-CoV-2 viral RNA (99.792%) when compared to N95 removal (99.942%) as a function of particle removal from the airstream distal to the breathing zone of each respirator.\n\nConclusionsThe mEP respirator approximated performance of a filter-based N95 respirator for particle removal and viral RNA as a constituent of the SARS-CoV-2 bioaerosols generated for this evaluation. In practice, the mEP respirator would provide equivalent protection from ambient infectious bioaerosols as the N95 respirator without undue pressure drop to the wearer, thereby facilitating long-term use in an unobstructed breathing configuration.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Rachel K Redmann", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Brandon J Beddingfield", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Skye Spencer", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Nicole R Chirichella", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Julian Henley", - "author_inst": "Henley Ion, Inc." - }, - { - "author_name": "Wes Hager", - "author_inst": "Phase Three Product Development" - }, - { - "author_name": "CHAD J ROY", - "author_inst": "Tulane University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.27.22269299", "rel_title": "Detection of SARS-CoV-2 Omicron, Delta, Alpha and Gamma variants using a rapid antigen test", @@ -418386,6 +420231,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.26.22269540", + "rel_title": "Impact of voluntary risk-mitigation behaviour on transmission of the Omicron SARS-CoV-2 variant in England", + "rel_date": "2022-01-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.26.22269540", + "rel_abs": "BackgroundThe Omicron variant of SARS-CoV-2 infection poses substantial challenges to public health. In England, \"plan B\" mitigation measures were introduced in December 2021 including increased home working and face coverings in shops, but stopped short of restrictions on social contacts. The impact of voluntary risk mitigation behaviours on future SARS-CoV-2 burden is unknown.\n\nMethodsWe developed a rapid online survey of risk mitigation behaviours during the winter 2021 festive period and deployed in two longitudinal cohort studies in the UK (Avon Longitudinal Study of Parents and Children (ALSPAC) and TwinsUK/Covid Symptom Study (CSS) Biobank) in December 2021. Using an individual-based, probabilistic model of COVID-19 transmission between social contacts with SARS-CoV-2 Omicron variant parameters and realistic vaccine coverage in England, we describe the potential impact of the SARS-CoV-2 Omicron wave in England in terms of the effective reproduction number and cumulative infections, hospital admissions and deaths. Using survey results, we estimated in real-time the impact of voluntary risk mitigation behaviours on the Omicron wave in England, if implemented for the entire epidemic wave.\n\nResultsOver 95% of survey respondents (NALSPAC=2,686 and NTwins=6,155) reported some risk mitigation behaviours, with vaccination and using home testing kits reported most frequently. Less than half of those respondents reported that their behaviour was due to \"plan B\". We estimate that without risk mitigation behaviours, the Omicron variant is consistent with an effective reproduction number between 2.5 and 3.5. Due to the reduced vaccine effectiveness against infection with the Omicron variant, our modelled estimates suggest that between 55% and 60% of the English population could be infected during the current wave, translating into between 15,000 and 46,000 cumulative deaths, depending on assumptions about vaccine effectiveness. We estimate that voluntary risk reduction measures could reduce the effective reproduction number to between 1.8 and 2.2 and reduce the cumulative number of deaths by up to 24%.\n\nConclusionsWe conclude that voluntary measures substantially reduce the projected impact of the SARS-CoV-2 Omicron variant, but that voluntary measures alone would be unlikely to completely control transmission.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Ellen Brooks-Pollock", + "author_inst": "University of Bristol" + }, + { + "author_name": "Kate Northstone", + "author_inst": "University of Bristol" + }, + { + "author_name": "Lorenzo Pellis", + "author_inst": "The University of Manchester" + }, + { + "author_name": "Francesca Scarabel", + "author_inst": "University of Manchester" + }, + { + "author_name": "Amy C Thomas", + "author_inst": "University of Bristol" + }, + { + "author_name": "Emily J Nixon", + "author_inst": "University of Bristol" + }, + { + "author_name": "David A Matthews", + "author_inst": "University of Bristol" + }, + { + "author_name": "Vicky Bower", + "author_inst": "King's College London" + }, + { + "author_name": "Maria-Paz Garcia", + "author_inst": "King's College London" + }, + { + "author_name": "Claire J Steves", + "author_inst": "King's College London" + }, + { + "author_name": "Nicholas J Timpson", + "author_inst": "University of Bristol" + }, + { + "author_name": "Leon Danon", + "author_inst": "Department of Engineering Mathematics, University of Bristol, UK." + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.27.22269902", "rel_title": "Anatomy of Covid outbreak of vaccinated: An observational case-control study of Covid breakthrough infections in medical college students at Rural Medical College, India", @@ -420045,189 +421953,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.17.22269242", - "rel_title": "Efficacy and Safety of a Plant-Based Virus-Like Particle Vaccine for COVID-19 Adjuvanted with AS03", - "rel_date": "2022-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.17.22269242", - "rel_abs": "BackgroundSeveral COVID-19 vaccines are currently being deployed but supply constraints, concerns over durability of immune responses, solidifying vaccine hesitancy/resistance and vaccine efficacy in the face of emerging variants mean that new vaccines continue to be needed to fight the ongoing pandemic. The vaccine described here is an enveloped, coronavirus-like particle produced in plants (CoVLP) that displays the prefusion-stabilized spike (S) glycoprotein of SARS-CoV-2 (ancestral Wuhan strain) and is adjuvanted with AS03 (CoVLP+AS03).\n\nMethodsThis Phase 3 randomized, observer-blind, placebo-controlled trial was conducted at 85 centers in Argentina, Brazil, Canada, Mexico, the UK, and the USA. Adults [≥]18 years of age including those at high risk for COVID-19 complications were randomly assigned 1:1 to receive two intramuscular injections of CoVLP (3.75 g) adjuvanted with AS03 or placebo, 21 days apart. The primary efficacy endpoint was prevention of symptomatic ([≥] 1 symptom), PCR-confirmed SARS-CoV-2 infection with onset at least 7 days after the second injection and was triggered by the identification of [≥]160 virologically-confirmed cases. Tolerability and safety of CoVLP+AS03 were also determined.\n\nResultsA total of 24,141 volunteers were randomly assigned 1:1 to receive vaccine or placebo (N= 12,074 and 12,067, respectively: median age 29, range 18 to 86 years). Overall, 83% received both doses. 14.8% were SARS-CoV-2 seropositive at baseline. Symptomatic SARS-CoV-2 infection was confirmed in 165 study participants in the intention to treat (ITT) set and 157 in the per-protocol population (PP) set. Of the 157 in the PP set, 118 COVID-19 cases were in the placebo group and 39 COVID-19 cases were in the CoVLP+AS03 group for an overall vaccine efficacy (VE) of 71.0% (95% confidence interval (CI) 58.6, 80.0). Moderate-to-severe COVID-19 occurred in 8 and 32 participants in the CoVLP+AS03 and placebo groups, respectively: VE 78.1% (95% CI: 53.9, 90.5) in the PP set overall and 84.5% (95% CI: 62.0, 94.7) in those seronegative at recruitment.\n\nTo date, 100% of the sequenced strains (122/165 cases: 73.39%) were variants, dominated by Delta (45.9%) and Gamma (43.4%) strains. Vaccine efficacy by variant was 75.3% (95% CI 52.8, 87.9) against Delta and 88.6% (95% CI 74.6, 95.6) against Gamma. Cross-protection was also observed against Alpha, Lambda and Mu variants; although fewer cases were identified, all were in the placebo group. At diagnosis, viral loads in the CoVLP+AS03 breakthrough cases were >100-fold lower than in the placebo cases. Reactogenicity data for solicited adverse events (AEs) was analysed for a subset (N=4,136 in vaccine arm and N=3,683 for placebo) of participants. Reactogenicity was mostly mild to moderate, and transient, and occurred more frequently in the CoVLP+AS03 group. The safety analysis set used for unsolicited AE assessment comprised 24,076 participants who received at least one study injection: 12,036 received CoVLP+AS03 and 12,040 received placebo. All serious adverse events were assessed as unrelated, except two events reported in the same subject in the placebo group. No significant imbalance or safety concern was noted in medically attended AEs (MAAEs), adverse event of special interest (AESIs), AEs leading to withdrawal, deaths, or adverse events potentially associated with currently authorized vaccines.\n\nConclusionsThe CoVLP+AS03 vaccine candidate conferred an efficacy of 71.0% in preventing symptomatic SARS-CoV-2 infection caused by a spectrum of variants. Vaccine efficacy of 78.1% was observed against moderate and severe disease, while variant-specific efficacy ranged from 75.3% to 100%. Markedly lower viral loads in the CoVLP+AS03 group at the time of diagnosis suggests a significant virologic impact of vaccination even in the breakthrough cases. CoVLP+AS03 vaccine candidate was well tolerated, and no safety concerns were identified during the study. If approved by regulators, this more traditional protein+adjuvant vaccine produced using the novel plant-based platform may be able to make an important contribution to the global struggle against the increasingly complex family of SARS-CoV-2 viruses (Funded by Medicago with grants from the governments of Quebec and Canada; NCT04636697).", - "rel_num_authors": 42, - "rel_authors": [ - { - "author_name": "Karen Joyce Hager", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Gonzalo P\u00e9rez Marc", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr. Cosme Argerich, Buenos Aires, Argentina" - }, - { - "author_name": "Philipe Gobeil", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Ricardo Sobhie Diaz", - "author_inst": "Paulista School of Medicine, Federal University of Sao Paulo, Brazil, and Azidus Brasil Pesquisa e Desenvolvimento Ltda, Valinhos Sao Paulo, Brazil" - }, - { - "author_name": "Gretchen Heizer", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Conrado Llapur", - "author_inst": "Clinica Mayo de UMCB SRL, San Miguel de Tucuman Tucuman, Argentina" - }, - { - "author_name": "Alexander I. Makarkov", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Eduardo Vasconcellos", - "author_inst": "Instituto de Pesquisas Clinicas L2IP, Complexo Medico Hospitalar, DF, Brazil" - }, - { - "author_name": "Stephane Pillet", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Fernando Riera", - "author_inst": "Sanatorio Allende, Av. Hipolito Yrigoyen 384, Cordoba, Cordoba 5000, Argentina" - }, - { - "author_name": "Kapil Bhutada", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Priscila Geller Wolff", - "author_inst": "IBPClin Instituto Brasil de Pequisa Clinica, Gloria, Rio de Janeiro RJ, Brazil" - }, - { - "author_name": "Garry Wallace", - "author_inst": "Dawson Clinical Research Inc., Ontario, Canada" - }, - { - "author_name": "Hessam Aazami", - "author_inst": "Hope Clinical, California, United States" - }, - { - "author_name": "Christine E Jones", - "author_inst": "Clinical and Experimental Sciences, University of Southampton and NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospita" - }, - { - "author_name": "Fernando P. Polack", - "author_inst": "Fundacion INFANT, Buenos Aires, Argentina" - }, - { - "author_name": "Judith Atkins", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Iohann Boulay", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Jiwanjeet Dhaliwall", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Nathalie Charland", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Manon Couture", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Julia Jiang-Wright", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Nathalie Landry", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Sophie Lapointe", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Aur\u00e9lien Lorin", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Asif Mahmood", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Lawrence H Moulton", - "author_inst": "Department of International health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA" - }, - { - "author_name": "Emmy Pahmer", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Julie Parent", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Pooja Saxena", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Annie Seguin", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Luan Tran", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Thomas Breuer", - "author_inst": "GlaxoSmithKline Vaccines, Wavre, Belgium" - }, - { - "author_name": "Maria Angeles Ceregido", - "author_inst": "GlaxoSmithKline Vaccines, Wavre, Belgium" - }, - { - "author_name": "Marguerite Koutsoukos", - "author_inst": "GlaxoSmithKline Vaccines, Wavre, Belgium" - }, - { - "author_name": "Francois Roman", - "author_inst": "GlaxoSmithKline Vaccines, Wavre, Belgium" - }, - { - "author_name": "Junya Namba", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Marc-Andr\u00e9 D'Aoust", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Sonia Trepanier", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Yosuke Kimura", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "- The CoVLP Study Team", - "author_inst": "-" - }, - { - "author_name": "Brian J Ward", - "author_inst": "Medicago Inc. and Research Institute of the McGill University Health Center, Montreal, QC, Canada" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.25.22269670", "rel_title": "TNF\u03b1-producing CD4+ T cells dominate the SARS-CoV-2-specific T cell response in COVID-19 outpatients and are associated with durable antibodies", @@ -420556,6 +422281,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "transplantation" }, + { + "rel_doi": "10.1101/2022.01.25.22269804", + "rel_title": "Comparison of vaccine effectiveness against the Omicron (B.1.1.529) variant in patients receiving haemodialysis", + "rel_date": "2022-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.25.22269804", + "rel_abs": "BackgroundEmerging data suggest a reduction in SARS-CoV-2 vaccine effectiveness against Omicron SARS-CoV-2 infection. There is also evidence to show that Omicron is less pathogenic than previous variants. For clinically vulnerable populations, a less pathogenic variant may still have significant impact on morbidity and mortality. Herein we assess the clinical impact of Omicron infection, and vaccine effectiveness, in an in-centre haemodialysis (IC-HD) population.\n\nMethodsOne thousand, one hundred and twenty-one IC-HD patients were included in the analysis, all patients underwent weekly screening for SARS-CoV-2 infection via RT-PCR testing between 1st December 2021 and 16th January 2022. Screening for infection via weekly RT-PCR testing and 3-monthly serological assessment started prior to the vaccine roll out in 2020.\n\nResultsOmicron infection was diagnosed in 145/1121 (12.9%) patients over the study period, equating to an infection rate of 3.1 per 1000 patient days. Vaccine effectiveness (VE) against Omicron infection in patients who had received a booster vaccine was 58 (23-75)%, p=0.002; VE was seen in patients who received either ChAdOx1, VE of 47(2-70)%, p=0.034, or BNT162b2, VE of 66 (36-81)%, p=0.0005, as their first two doses. No protection against infection was seen in patients who were partially vaccinated (2-doses), p=0.83. Prior infection was associated with reduced likelihood of Omicron infection, HR 0.69 (0.50-0.96), p=0.0289. Four (2.8%) patients died within 28 days of infection diagnosis, with no excess mortality was seen in patients with infection.\n\nConclusion3-doses of SARS-CoV-2 vaccines are required in ICHD to provide protection against Omicron infection.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Katrina Spensley", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Sarah Gleeson", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Paul Martin", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Tina Thomson", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Candice L Clarke", + "author_inst": "Imperial College London" + }, + { + "author_name": "Graham Pickard", + "author_inst": "Department of Infection and Immunity Sciences, Northwest London Pathology NHS Trust" + }, + { + "author_name": "David C Thomas", + "author_inst": "Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London" + }, + { + "author_name": "Stephen P McAdoo", + "author_inst": "Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London" + }, + { + "author_name": "Paul Randell", + "author_inst": "Department of Infection and Immunity Sciences, Northwest London Pathology NHS Trust" + }, + { + "author_name": "Peter Kelleher", + "author_inst": "Department of Infectious Diseases, Imperial College London" + }, + { + "author_name": "Rachna Bedi", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Liz Lightstone", + "author_inst": "Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London" + }, + { + "author_name": "Maria Prendecki", + "author_inst": "Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London" + }, + { + "author_name": "Michelle Willicombe", + "author_inst": "Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2022.01.26.22269788", "rel_title": "Adverse events following COVISHIELD (ChAdOx1nCoV-19) vaccination among health care workers in Sri Lanka; a multi-centre cross sectional survey", @@ -422179,41 +423975,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2022.01.24.22269741", - "rel_title": "The Choice of Response Alternatives in COVID-19 Social Science Surveys", - "rel_date": "2022-01-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.24.22269741", - "rel_abs": "Social science research is key for understanding and for predicting compliance with COVID-19 guidelines, and much of this research relies on survey data. While much focus is on the survey question stems, less is on the response alternatives presented that both constrain responses and convey information about the assumed expectations of the survey designers. The focus here is on the choice of response alternatives for the types of behavioral frequency questions used in many COVID-19 and other health surveys. We examine issues with two types of response alternatives. The first are vague quantifiers, like \"rarely\" and frequently.\" Using data from 30 countries from the Imperial COVID data hub, we show that the interpretation of these vague quantifiers (and their translations) depends on the norms in that country. If the mean amount of hand washing in your country is high, it is likely \"frequently\" corresponds to a higher numeric value for hand washing than if the mean in your country is low. The second type are precise numeric response alternatives and they can also be problematic. Using a US survey, respondents were randomly allocated to receive either response alternatives where most of the scale corresponds to low frequencies or where most of the scale corresponds to high frequencies. Those given the low frequency set provided lower estimates of the health behaviors. The choice of response alternatives for behavioral frequency questions can affect the estimates of health behaviors. How the response alternatives mold the responses should be taken into account for epidemiological modeling. We conclude with some recommendations for response alternatives for health behavioral frequency questions in surveys.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Daniel Wright", - "author_inst": "UNLV: University of Nevada Las Vegas" - }, - { - "author_name": "Sarah M Wolff", - "author_inst": "UNLV: University of Nevada Las Vegas" - }, - { - "author_name": "Rusi Jaspal", - "author_inst": "University of Brighton" - }, - { - "author_name": "Julie Barnett", - "author_inst": "University of Bath - Oakfield Campus: University of Bath" - }, - { - "author_name": "Glynis Breakwell", - "author_inst": "University of Bath - Oakfield Campus: University of Bath" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.24.477469", "rel_title": "Design of immunogens for eliciting antibody responses that may protect against SARS-CoV-2 variants", @@ -422466,6 +424227,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.21.477288", + "rel_title": "Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail", + "rel_date": "2022-01-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.21.477288", + "rel_abs": "The SARS-CoV-2 receptor-binding domain (RBD) E406W mutation abrogates neutralization mediated by the REGEN-CoV therapeutic monoclonal antibody (mAb) COVID-19 cocktail and the cilgavimab (AZD1061) mAb. Here, we show that this residue substitution remodels the ACE2-binding site allosterically, thereby dampening receptor recognition severely and altering the epitopes recognized by these three mAbs. Although vaccine-elicited neutralizing antibody titers are decreased similarly against the E406 mutant and the Delta or Epsilon variants, broadly neutralizing sarbecovirus mAbs, including a clinical mAb, inhibit the E406W spike mutant.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Amin Addetia", + "author_inst": "University of Washington" + }, + { + "author_name": "Young-Jun Park", + "author_inst": "University of Washington" + }, + { + "author_name": "Tyler Starr", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Allison J Greaney", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Kaitlin Sprouse", + "author_inst": "University of Washington" + }, + { + "author_name": "John E Bowen", + "author_inst": "University of Washington" + }, + { + "author_name": "Sasha W Tiles", + "author_inst": "University of Washington" + }, + { + "author_name": "Wesley C Van Voorhis", + "author_inst": "University of Washington" + }, + { + "author_name": "Jesse D Bloom", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Davide Corti", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Alexandra C Walls", + "author_inst": "University of Washington" + }, + { + "author_name": "David Veesler", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.01.24.477502", "rel_title": "Template-based design of peptides to inhibit SARS-CoV-2 RNA-dependent RNA polymerase complexation.", @@ -423961,61 +425785,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.18.22269433", - "rel_title": "Risk factors for developing symptomatic COVID-19 in older residents of nursing homes: A hypothesis-generating observational study", - "rel_date": "2022-01-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.18.22269433", - "rel_abs": "BackgroundCOVID-19 pandemic has had a major impact on society, including on residents of nursing homes (NH), who have a higher risk of complications and mortality due their physical and intellectual disabilities.\n\nAimTo identify which risk factors associated with developing COVID-19 infection with symptoms in institutionalized older people.\n\nMethodsA 1-year longitudinal multicenter study was conducted in 5 NH during the period December 2019 to March 2021. The inclusion criteria used were residents aged 65 years or over, living in the NH permanently, with a diagnostic test for COVID-19 confirmed by reverse transcription polymerase chain reaction and/or serological test. The main variable was symptomatic COVID-19, with at least one of the following symptoms (fever, respiratory difficulties, cough, diarrhea, sudden urinary incontinence and disorientation or delirium). Three assessments were performed: baseline, six and twelve months follow-up. Descriptive and bivariate analysis (calculating relative risk-RR) were performed, considering a 95% confidence level and a statistically significant p <0.05.\n\nResultsOf the total sample of 78 individuals who tested positive for COVID-19, mean age 84.6 years (SD={+/-}7.8), 62 (79.5%) were female; 40 (51.3%) participants presented with COVID-19 symptoms. Living in a private NH (RR=3.6, 95% CI [1.2-11.0], p=0.023) and having suffered a stroke (RR=4.1, 95% CI [1.1-14.7], p=0.033) were positively associated with developing COVID-19 infection with symptoms.\n\nConclusionsHaving suffered a stroke and living permanently in a private health care facility were positively associated with symptomatic COVID-19 in this sample of institutionalized older people.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Eduard Minobes-Molina", - "author_inst": "University of Vic - Central University of Catalonia: Universitat de Vic - Universitat Central de Catalunya" - }, - { - "author_name": "Anna Escrib\u00e0-Salvans", - "author_inst": "University of Vic - Central University of Catalonia: Universitat de Vic - Universitat Central de Catalunya" - }, - { - "author_name": "Sandra Rierola-Fochs", - "author_inst": "University of Vic - Central University of Catalonia: Universitat de Vic - Universitat Central de Catalunya" - }, - { - "author_name": "Pau Farr\u00e9s-Godayol", - "author_inst": "University of Vic - Central University of Catalonia: Universitat de Vic - Universitat Central de Catalunya" - }, - { - "author_name": "M\u00edriam Molas-Tuneu", - "author_inst": "University of Vic - Central University of Catalonia: Universitat de Vic - Universitat Central de Catalunya" - }, - { - "author_name": "Dyego Leandro Bezerra de Souza", - "author_inst": "Federal University of Rio Grande do Norte: Universidade Federal do Rio Grande do Norte" - }, - { - "author_name": "Dawn A Skelton", - "author_inst": "Glasgow Caledonian University" - }, - { - "author_name": "Ester Goutan-Roura", - "author_inst": "University of Vic - Central University of Catalonia: Universitat de Vic - Universitat Central de Catalunya" - }, - { - "author_name": "Daniel Alonso-Masmitj\u00e0", - "author_inst": "University of Vic - Central University of Catalonia: Universitat de Vic - Universitat Central de Catalunya" - }, - { - "author_name": "Javier Jerez-Roig", - "author_inst": "University of Vic - Central University of Catalonia: Universitat de Vic - Universitat Central de Catalunya" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "geriatric medicine" - }, { "rel_doi": "10.1101/2022.01.20.477164", "rel_title": "Severe acute respiratory disease in American mink (Neovison vison) experimentally infected with SARS-CoV-2", @@ -424276,6 +426045,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.22.477073", + "rel_title": "Bacteriophage-derived dsRNA exerts anti-SARS-CoV-2 activity in vitro and in Golden Syrian hamsters in vivo", + "rel_date": "2022-01-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.22.477073", + "rel_abs": "PurposeBacteriophage-derived dsRNA, also known as Larifan, is nationally well-known broad-spectrum antiviral medication. The goal of this study was to ascertain the antiviral activity of Larifan against the novel SARS-CoV-2.\n\nMethodsThe antiviral activity of Larifan against SARS-CoV-2 in vitro was measured in human lung adenocarcinoma (Calu3) and primary human small airway epithelial cells (HSAEC) using cytopathic effect assay, viral RNA copy number detection by digital droplet PCR (ddPCR) and infectious virus titration in cells supernatants in Vero E6 cells by end-point titration method. The antiviral effect of Larifan in vivo was detected in SARS-CoV-2 infection model in Golden Syrian hamsters. Larifan (5 mg/kg) was administered either subcutaneously or intranasally twice before and after virus infection with a 24-hour interval between doses. The viral RNA copies and infectious virus titre were detected in animal lungs at day three and five post-infection using ddPCR and end-point titration in Vero E6 cells, respectively. Histopathology of lungs was analysed as well.\n\nResultsLarifan inhibited SARS-CoV-2 replication in Calu3 cells both after the drug addition pre- and post-infection with a substantial drop in the supernatant viral RNA copy numbers from eight (p = 0.0013) to twenty (p = 0.0042) times, respectively. Similarly, infectious virus titre in Vero E6 cells dropped by 3.6log10 TCID50 and 2.8log10 TCID50 after the drug addition pre- and post-infection, respectively. In HSAEC, Larifan inhibited SARS-CoV-2 replication at the similar level. Larifan also markedly reduced virus numbers in the lungs of infected hamsters (p = 0.0032) both at day three and five post-infection with a more pronounced effect after intranasal administration reaching a drop by 2.7log10 at day three and 2.0log10 at day five. The administration of Larifan also reduced the amount of infections virus titer in lungs (p = 0.0039) by 4.3log10 TCID50 and 2.8log10 TCID50 at day three and five post-infection, respectively. Improvements in the infection-induced pathological lesion severity in the lungs of animals treated with Larifan were also demonstrated by histological analyses.\n\nConclusionsThe inhibition of SARS-CoV-2 replication in vitro and the reduction of the viral load in the lungs of infected hamsters treated with Larifan alongside the improved lung histopathology, suggests a potential use of Larifan in controlling the COVID-19 disease in humans.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Kristine Vaivode", + "author_inst": "Latvian Biomedical Research and Study Centre" + }, + { + "author_name": "Irina Verhovcova", + "author_inst": "Latvian Biomedical Research and Study Centre" + }, + { + "author_name": "Dace Skrastina", + "author_inst": "Latvian Biomedical Research and Study Centre" + }, + { + "author_name": "Ramona Petrovska", + "author_inst": "Latvian Biomedical Research and Study Centre" + }, + { + "author_name": "Madara Kreismane", + "author_inst": "Latvian Biomedical Research and Study Centre" + }, + { + "author_name": "Diara Lapse", + "author_inst": "Latvian Biomedical Research and Study Centre" + }, + { + "author_name": "Diana Rubene", + "author_inst": "Latvian Biomedical Research and Study Centre" + }, + { + "author_name": "Zane Kalnina", + "author_inst": "Latvian Biomedical Research and Study Centre" + }, + { + "author_name": "Dace Pjanova", + "author_inst": "Latvian Biomedical Research and Study Centre" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.01.21.477298", "rel_title": "The N764K and N856K mutations in SARS-CoV-2 Omicron S protein generate potential cleavage sites for SKI-1/S1P protease", @@ -425647,49 +427467,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.21.22269671", - "rel_title": "Impact of COVID-19 symptoms on social aspects of life of female long haulers: A qualitative study", - "rel_date": "2022-01-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.21.22269671", - "rel_abs": "IntroductionPersistent COVID-19 symptoms (long COVID) may bring numerous challenges to long haulers social lives. Women may have to endure more profound impacts given their social roles and existing structural inequality. This study aims to explore the impacts of long COVID on various aspects of social life among female long haulers.\n\nMethodsWe conducted 15 semi-structured interviews with female long haulers in the United States purposely recruited from Facebook groups, Slack groups, and organization websites. The interviews were audio recorded after appropriate consent and transcribed verbatim. Inductive approach was applied in thematic analysis, which consists of six stages: becoming familiar with data, developing initial codes, extracting themes, refining themes, labeling themes, and reporting. The MAXQDA software was used in data analysis.\n\nResultsPersistent COVID-19 symptoms negatively affected female long haulers social lives in many aspects including physical function, financial security, social relationship, conflict of social roles, and social stigma. Physical limitations changed their body image. Social isolation and work-family conflicts caused huge stress. They experienced internalization of stigma and job insecurities. Shifting to new methods of communication, especially social media may buffer the negative effects of social isolation because of long COVID.\n\nConclusionExisting policies and intervention programs need to be adapted to address the challenges and barriers that long haulers face in returning to normal social life, especially for females. Tailored social life-related recommendations and social support are needed for female long haulers.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Atefeh Aghaei", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Ran Zhang", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Slone Taylor", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Cheuk Chi Tam", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Chih-Hsiang Yang", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Xiaoming Li", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Shan Qiao", - "author_inst": "University of South Carolina" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.01.18.22269467", "rel_title": "The Effects of Messaging on Expectations and Understanding of Long COVID: An Online Randomised Trial", @@ -425974,6 +427751,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.17.22269394", + "rel_title": "Effectiveness of mRNA COVID-19 vaccines against symptomatic SARS-CoV-2 infections during the Delta variant epidemic in Japan: Vaccine Effectiveness Real-time Surveillance for SARS-CoV-2 (VERSUS)", + "rel_date": "2022-01-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.17.22269394", + "rel_abs": "BackgroundAlthough high vaccine effectiveness of messenger RNA (mRNA) coronavirus disease 2019 (COVID-19) vaccines was reported in studies in several countries, data is limited from Asian countries, especially against the Delta (B.1.617.2) variant.\n\nMethodsWe conducted a multicenter test-negative case-control study in patients aged [≥]16 visiting hospitals or clinics with signs or symptoms consistent with COVID-19 from July 1 to September 30, 2021, when the Delta variant was dominant ([≥]90% of severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2] infections) nationwide in Japan. Vaccine effectiveness of BNT162b2 or mRNA-1273 against symptomatic SARS-CoV-2 infections was evaluated. Waning immunity among patients aged 16 to 64 was also assessed.\n\nResultsWe enrolled 1936 patients, including 396 test-positive cases and 1540 test-negative controls for SARS-CoV-2. The median age was 49 years, 53.4% were male, and 34.0% had underlying medical conditions. Full vaccination (receiving two doses [≥]14 days before symptom onset) was received by 6.6% of cases and 38.8% of controls. Vaccine effectiveness of full vaccination against symptomatic SARS-CoV-2 infections was 88.7% (95% confidence interval [CI], 78.8-93.9) among patients aged 16 to 64 and 90.3% (95% CI, 73.6-96.4) among patients aged [≥]65. Among patients aged 16 to 64, vaccine effectiveness within one to three months after full vaccination was 91.8% (95% CI, 80.3-96.6), and was 86.4% (95% CI, 56.9-95.7) within four to six months.\n\nConclusionsmRNA COVID-19 vaccines had high effectiveness against symptomatic SARS-CoV-2 infections in Japan during July 1 to September 30, 2021, when the Delta variant was dominant nationwide.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Haruka Maeda", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Nobuo Saito", + "author_inst": "Department of Microbiology, Faculty of Medicine, Oita University, Oita, Japan" + }, + { + "author_name": "Ataru Igarashi", + "author_inst": "Unit of Public Health and Preventive Medicine, Yokohama City University School of Medicine, Kanagawa, Japan; Department of Health Economics and Outcomes Researc" + }, + { + "author_name": "Masayuki Ishida", + "author_inst": "Chikamori Hospital, Kochi, Japan" + }, + { + "author_name": "Kazuya Suami", + "author_inst": "Nagoya Ekisaikai Hospital, Aichi, Japan" + }, + { + "author_name": "Ai Yagiuchi", + "author_inst": "Nagoya Ekisaikai Hospital, Aichi, Japan" + }, + { + "author_name": "Yuya Kimura", + "author_inst": "Saiseikai Kurihashi Hospital, Saitama, Japan" + }, + { + "author_name": "Masaru Komino", + "author_inst": "Saiseikai Kurihashi Hospital, Saitama, Japan" + }, + { + "author_name": "Hiromi Arai", + "author_inst": "Saiseikai Kurihashi Hospital, Saitama, Japan" + }, + { + "author_name": "Toru Morikawa", + "author_inst": "Nara City Hospital, Nara, Japan" + }, + { + "author_name": "Iori Motohashi", + "author_inst": "Kawasaki Municipal Tama Hospital, Kanagawa, Japan" + }, + { + "author_name": "Rei Miyazawa", + "author_inst": "Kawasaki Municipal Tama Hospital, Kanagawa, Japan" + }, + { + "author_name": "Tetsu Moriyama", + "author_inst": "Moriyama Memorial Hospital, Tokyo, Japan" + }, + { + "author_name": "Hiroshi Kamura", + "author_inst": "Loco Clinic Nakameguro, Tokyo, Japan" + }, + { + "author_name": "Mayumi Terada", + "author_inst": "Nijigaoka Hospital, Nagasaki, Japan" + }, + { + "author_name": "Osamu Kuwamitsu", + "author_inst": "Gohongi Clinic, Tokyo, Japan" + }, + { + "author_name": "Tomoichiro Hayakawa", + "author_inst": "Hayakawa Internal Medicine Clinic, Fukuoka, Japan" + }, + { + "author_name": "Eiichiro Sando", + "author_inst": "Kita-Fukushima Medical Center, Fukushima, Japan; Fukushima Medical University, Fukushima, Japan" + }, + { + "author_name": "Yasuji Ohara", + "author_inst": "Takagi Hospital, Aichi, Japan" + }, + { + "author_name": "Osamu Teshigawara", + "author_inst": "Mizuho Street Clinic, Aichi, Japan" + }, + { + "author_name": "Motoi Suzuki", + "author_inst": "Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan" + }, + { + "author_name": "Konosuke Morimoto", + "author_inst": "Department of Respiratory Infections, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.21.22269658", "rel_title": "Modelling Quarantine Effects on SARS-CoV-2 Epidemiological Dynamics in Chilean Communes and their Relationship with the Social Priority Index", @@ -427665,33 +429545,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.19.22269572", - "rel_title": "Monitoring SARS-CoV-2 genome evolution in a localized population", - "rel_date": "2022-01-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.19.22269572", - "rel_abs": "Despite seminal advances towards understanding its infection mechanism, SARS-CoV-2 continues to cause significant morbidity and mortality worldwide. Though mass immunization programs have been implemented in several countries, the viral transmission cycle has shown a continuous progression in the form of multiple waves. A constant change in the frequencies of dominant viral lineages, arising from the accumulation of nucleotide variations (NVs) through favourable selection, is understandably expected to be a major determinant of disease severity and possible vaccine escape. Indeed, worldwide efforts have been initiated to identify specific virus lineage(s) and/or NVs that may cause a severe clinical presentation or facilitate vaccination breakthrough. Since host genetics is expected to play a major role in shaping virus evolution, it is imperative to study role of genome-wide SARS-CoV-2 NVs across various populations. In the current study, we analysed the whole genome sequence of 3543 SARS-CoV-2 infected samples obtained from the state of Telangana, India (including 210 from our previous study), collected over an extended period from April, 2020 to October, 2021. We present a unique perspective on the evolution of prevalent virus lineages and NVs during this time period. We also highlight presence of specific NVs likely to be associated favourably with samples classified as vaccination breakthroughs. Finally, we report genome-wide intra-host variations (iSNVs) at novel genomic positions. The results presented here provide critical insights into virus evolution over an extended time period within a geographically restricted area and pave the way to rigorously investigate the role of specific NVs in vaccination breakthroughs.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Asmita Gupta", - "author_inst": "Centre for DNA Fingerprinting and Diagnostics" - }, - { - "author_name": "Reelina Basu", - "author_inst": "Centre for DNA Fingerprinting and Diagnostics" - }, - { - "author_name": "Murali Dharan Bashyam", - "author_inst": "Centre for DNA Fingerprinting and Diagnostics (CDFD)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.19.22269510", "rel_title": "Microbial GWAS studies revealing combinations of Omicron RBD mutations existed and may contribute to antibody evasion and ACE2 binding", @@ -427960,6 +429813,41 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2022.01.21.477194", + "rel_title": "ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads", + "rel_date": "2022-01-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.21.477194", + "rel_abs": "SummaryViral sequence data from clinical samples frequently contain human contamination, which must be removed prior to sharing for legal and ethical reasons. To enable host read removal for SARS-CoV-2 sequencing data on low-specification laptops, we developed ReadItAndKeep, a fast lightweight tool for Illumina and nanopore data that only keeps reads matching the SARS-CoV-2 genome. Peak RAM usage is typically below 10MB, and runtime less than one minute. We show that by excluding the polyA tail from the viral reference, ReadItAndKeep prevents bleed-through of human reads, whereas mapping to the human genome lets some reads escape. We believe our test approach (including all possible reads from the human genome, human samples from each of the 26 populations in the 1000 genomes data, and a diverse set of SARS-CoV-2 genomes) will also be useful for others.\n\nAvailability and implementationReadItAndKeep is implemented in C++, released under the MIT license, and available from https://github.com/GenomePathogenAnalysisService/read-it-and-keep.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Martin Hunt", + "author_inst": "European Bioinformatics Institute" + }, + { + "author_name": "Jeremy Swann", + "author_inst": "University of Oxford" + }, + { + "author_name": "Bede Constantinides", + "author_inst": "University of Oxford" + }, + { + "author_name": "Philip W Fowler", + "author_inst": "University of Oxford" + }, + { + "author_name": "Zamin Iqbal", + "author_inst": "European Bioinformatics Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.01.21.22269322", "rel_title": "Combination of Spironolactone and Sitagliptin Improves Clinical Outcomes of Outpatients with COVID-19: An Observational Study", @@ -429399,93 +431287,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.18.22269200", - "rel_title": "Infection and transmission risks in schools and contribution to the COVID-19 pandemic in Germany - a retrospective observational study using nation-wide and regional health and education agency notification data", - "rel_date": "2022-01-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.18.22269200", - "rel_abs": "IntroductionCurrently, information on infection and transmission risks of students and teachers in schools, the effect of infection control measures for schools as well as the contribution of schools to the overall population transmission of SARS-CoV-2 in Germany are limited to regional data sets restricted to short phases of the pandemic.\n\nMethodsWe used German federal state (NUTS-2) and county (NUTS-3) data from national and regional public health and education agencies to assess infection risk and secondary attack rates (SARs) from March 2020 to October 2021 in Germany. We used multiple regression analysis and infection dynamic modelling, accounting for urbanity, socioeconomic factors, local population infection dynamics and age-specific underdetection to investigate the effects of infection control measures.\n\nResultsWe included (1) nation-wide NUTS-2 level data from calendar weeks (W) 46-50/2020 and W08-40/2021 with 304676 infections in students and 32992 in teachers; (2) NUTS-3 level data from W09-25/2021 with 85788 student and 9427 teacher infections and (3) detailed data from 5 regions covering W09/2020 to W27/2021 with 12814 infections, 43238 contacts and 4165 secondary cases for students (for teachers 14801, 5893 and 472 respectively).\n\nIn counties with mandatory surgical mask wearing during class in all schools infection risk of students and teachers was reduced by 56/100.000 persons per 14 days and by 30% and 24% relative to the population respectively. Overall contribution to population infections of contacts in school settings was 2-13%. It was lowest during school closures and vacation and highest during normal presence class intervals. Infection risk for students increased with age and was similar to or lower than the population risk during second and third waves in Germany and higher in summer 2021. Infection risk of teachers was higher than the population during the second wave and similar or lower thereafter with stricter measures in place. SARs for students and staff were below 5% in schools throughout the study period. SARs in households more than doubled from 14% W21-39/2020 to 29-33% in W08-23/2021. Most contacts were reported for schools, yet most secondary cases originated in households. In schools, staff predominantly infected staff and students predominantly infected students.\n\nConclusionOpen schools under hygiene measures and testing strategies contribute up to 13% of nation-wide infections in Germany and as little as 2% during vacations/school closures. Tighter infection control measures stabilised school SARs whilst household SARs more than doubled as more transmissible variants became prevalent in Germany. Mandatory mask wearing during class in all school types effectively reduces secondary transmission in schools, as do reduced attendance class models.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Torben Heinsohn", - "author_inst": "Helmholtz Centre for Infection Research" - }, - { - "author_name": "Berit Lange", - "author_inst": "Helmholtz Centre for Infection Research: Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Patrizio Vanella", - "author_inst": "Helmholtz Centre for Infection Research: Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Isti Rodiah", - "author_inst": "Helmholtz Centre for Infection Research: Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Stephan Gl\u00f6ckner", - "author_inst": "Helmholtz Centre for Infection Research: Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Alexander Joachim", - "author_inst": "University Hospital Cologne: Uniklinik Koln" - }, - { - "author_name": "Dennis Becker", - "author_inst": "Public Health Department Konstanz" - }, - { - "author_name": "Tobias Br\u00e4ndle", - "author_inst": "Agency for Schools and Vocational Training Hamburg" - }, - { - "author_name": "Stephan Dhein", - "author_inst": "Public Health Department Altenburger Land" - }, - { - "author_name": "Stephan Ehehalt", - "author_inst": "Public Health Department Stuttgart" - }, - { - "author_name": "Mira Fries", - "author_inst": "Public Health Department Cologne" - }, - { - "author_name": "Annette Galante-Gottschalk", - "author_inst": "Public Health Department Stuttgart" - }, - { - "author_name": "Stefanie Jehnichen", - "author_inst": "Public Health Department Konstanz" - }, - { - "author_name": "Sarah Kolkmann", - "author_inst": "Public Health Department Altenburger Land" - }, - { - "author_name": "Annelene Kossow", - "author_inst": "Public Health Department Cologne" - }, - { - "author_name": "Martin Hellmich", - "author_inst": "University of Cologne: Universitat zu Koln" - }, - { - "author_name": "J\u00f6rg D\u00f6tsch", - "author_inst": "University Hospital Cologne: Uniklinik Koln" - }, - { - "author_name": "G\u00e9rard Krause", - "author_inst": "Helmholtz Centre for Infection Research: Helmholtz-Zentrum fur Infektionsforschung GmbH" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.01.21.22269636", "rel_title": "Using Survey Data to Estimate the Impact of the Omicron Variant on Vaccine Efficacy against COVID-19 Infection", @@ -429726,6 +431527,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.19.476893", + "rel_title": "NRP1 and furin as putative mediators of SARS-CoV-2 entry into human brain cells", + "rel_date": "2022-01-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.19.476893", + "rel_abs": "COVID-19 has prominent neurological manifestations including psychiatric symptoms, indicating significant synaptic pathology. Surprisingly, existing evidence suggests negligible expression of the key SARS-CoV-2 host cell entry mediators ACE2 and TMPRSS2 in human brain, which complicates understanding of the pathomechanisms of the neuropsychiatric manifestations in COVID-19. Recent studies suggested that an alternative host-cell entry receptor, NRP1, can mediate entry of furin cleaved SARS-CoV-2 spike proteins into the host cells. However, the role of NRP1 and furin in mediating SARS-CoV-2 entry in human brain cells has been least explored and remains a lacuna in the literature. We performed an in silico analysis of the transcriptomic and proteomic expressions of SARS-CoV-2 host-cell entry receptors and associated tissue proteases in human brain tissue, using the publically available databases. Based on the expression analysis, SARS-CoV-2 entry in human brain cells is likely to be mediated through NRP1 and furin.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC=\"FIGDIR/small/476893v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (38K):\norg.highwire.dtl.DTLVardef@1c818baorg.highwire.dtl.DTLVardef@1cf7c0corg.highwire.dtl.DTLVardef@d92e19org.highwire.dtl.DTLVardef@61866a_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ashutosh Kumar", + "author_inst": "Department of Anatomy, All India Institute of Medical Sciences (AIIMS), Patna, India" + }, + { + "author_name": "Ravi K. Narayan", + "author_inst": "Department of Anatomy, Dr. B.C. Roy Multispeciality Medical Research Center, Indian Institute of Technology, Kharagpur, India" + }, + { + "author_name": "Sujeet Kumar", + "author_inst": "Centre for Proteomics and Drug Discovery, Amity Institute of Biotechnology, Amity University, Maharashtra, India" + }, + { + "author_name": "Vikas Pareek", + "author_inst": "Center for Cognitive and Brain Sciences, Indian Institute of Technology, Gandhinagar, Gujarat, India" + }, + { + "author_name": "Chiman Kumari", + "author_inst": "Department of Anatomy, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India" + }, + { + "author_name": "Rakesh K. Jha", + "author_inst": "Department of Anatomy, All India Institute of Medical Sciences (AIIMS), Patna, India" + }, + { + "author_name": "Pranav Prasoon", + "author_inst": "Pittsburgh Center for Pain Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2022.01.19.476892", "rel_title": "Molecular basis of broad neutralization against SARS-CoV-2 variants including Omicron by a human antibody", @@ -431453,105 +433297,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2022.01.15.22269335", - "rel_title": "Retention of Neutralizing response against SARS-CoV-2 Omicron variant in Sputnik V vaccinated individuals", - "rel_date": "2022-01-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.15.22269335", - "rel_abs": "The new variant Omicron (B.1.1.529) of SARS-CoV-2, first identified in November 2021, is rapidly spreading all around the world. The Omicron becomes the dominant variant of SARS-CoV-2. There are many ongoing studies evaluating the effectiveness of existing vaccines. Studies on neutralizing activity of vaccinated sera against Omicron variant are currently being carried out in many laboratories.\n\nIn this study, we have shown the neutralizing activity of sera against SARS-CoV-2 Omicron (B.1.1.529) variant compared to the reference Wuhan D614G (B.1) variant in individuals vaccinated with 2 doses of Sputnik V or BNT162b2 in different time points up to 6 months after vaccination. We performed analysis on sample pools with comparable NtAb to Wuhan D614G variant. The decrease in neutralizing antibody (NtAb) to the Omicron variant was 8.1 folds for group of Sputnik V-vaccinated and 21.4 folds for group of BNT162b2-vaccinated. Analysis showed that 74.2% of Sputnik V- and 56.9% of BNT162b2-vaccinated sera had detectable NtAb to SARS-CoV-2 Omicron variant.\n\nThe decrease in NtAb to SARS-CoV-2 Omicron variant compared to Wuhan variant has been shown for many COVID-19 vaccines in use, with some showing no neutralization at all. Today the necessity of third booster vaccination is obvious. And the most effective approach, already shown in several studies, is the use of heterologous booster vaccination pioneered in COVID-19 vaccines by Sputnik V.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Daniele Lapa", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Daria Grousova", - "author_inst": "Gamaleya NRCEM" - }, - { - "author_name": "Giulia Matusali", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Silvia Meschi", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Francesca Colavita", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Aurora Bettini", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Giulia Gramigna", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Massimo Francalancia", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Anna Rosa Garbuglia", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Enrico Girardi", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Vincenzo Puro", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Andrea Antinori", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Anna Kovyrshina", - "author_inst": "Gamaleya NRCEM" - }, - { - "author_name": "Inna Dolzhikova", - "author_inst": "Gamaleya NRCEM" - }, - { - "author_name": "Dmitry Shcheblyakov", - "author_inst": "Gamaleya NRCEM" - }, - { - "author_name": "Amir Tukhvatulin", - "author_inst": "Gamaleya NRCEM" - }, - { - "author_name": "Olga Zubkova", - "author_inst": "Gamaleya NRCEM" - }, - { - "author_name": "Denis Logunov", - "author_inst": "Gamaleya NRCEM" - }, - { - "author_name": "Boris Naroditsky", - "author_inst": "Gamaleya NRCEM" - }, - { - "author_name": "Francesco Vaia", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Alexander Gintsburg", - "author_inst": "Gamaleya NRCEM" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.18.476863", "rel_title": "SARS-CoV-2 Delta variant induces enhanced pathology and inflammatory responses in K18-hACE2 mice", @@ -431816,6 +433561,113 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.01.14.475727", + "rel_title": "Obesity associated with attenuated tissue immune cell responses in COVID-19", + "rel_date": "2022-01-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.14.475727", + "rel_abs": "Obesity is common and associated with more severe COVID-19, proposed to be in part related to an adipokine-driven pro-inflammatory state. Here we analysed single cell transcriptomes from bronchiolar lavage in three adult cohorts, comparing obese (Ob, body mass index (BMI) >30m2) and non-obese (N-Ob, BMI <30m2). Surprisingly, we found that Ob subjects had attenuated lung immune/inflammatory responses in SARS-CoV-2 infection, with decreased expression of interferon (IFN), IFN{gamma} and tumour necrosis factor (TNF) alpha response gene signatures in almost all lung epithelial and immune cell subsets, and lower expression of IFNG and TNF in specific lung immune cells. Analysis of peripheral blood immune cells in an independent adult cohort showed a similar, but less marked, reduction in type I IFN and IFN{gamma} response genes, as well as decreased serum IFN, in Ob patients with SARS-CoV-2. Nasal immune cells from Ob children with COVID-19 also showed reduced enrichment of IFN and IFN{gamma} response genes. Altogether, these findings show blunted tissue immune responses in Ob COVID-19 patients, with clinical implications.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Shuang Andrew Guo", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Georgina S Bowyer", + "author_inst": "University of Cambridge" + }, + { + "author_name": "John Robert Ferdinand", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Mailis Maes", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Zewen K Tuong", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Eleanor Gilman", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Rik G. H. Lindeboom", + "author_inst": "Wellcome Sanger Institute" + }, + { + "author_name": "Masahiro Yoshida", + "author_inst": "University College London" + }, + { + "author_name": "Kaylee Worlock", + "author_inst": "University College London" + }, + { + "author_name": "Hudaa Gopee", + "author_inst": "Newcastle University" + }, + { + "author_name": "Emily Stephenson", + "author_inst": "Newcastle University" + }, + { + "author_name": "Paul A Lyons", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Kenneth G. C. Smith", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Muzlifah Haniffa", + "author_inst": "Newcastle University" + }, + { + "author_name": "Kerstin B Meyer", + "author_inst": "Wellcome Sanger Institute" + }, + { + "author_name": "Marko Z Nikolic", + "author_inst": "University College London" + }, + { + "author_name": "Richard G Wunderink", + "author_inst": "Northwestern University" + }, + { + "author_name": "Alexander V Misharin", + "author_inst": "Northwestern University" + }, + { + "author_name": "Gordon Dougan", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Vilas Navapurkar", + "author_inst": "Cambridge University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Sarah A Teichmann", + "author_inst": "Wellcome Sanger Institute" + }, + { + "author_name": "Andrew Conway Morris", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Menna R Clatworthy", + "author_inst": "University of Cambridge" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.01.15.476426", "rel_title": "ASGR1 is a candidate receptor for SARS-CoV-2 that promotes infection of liver cells", @@ -433318,85 +435170,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.16.22269146", - "rel_title": "Development and validation of the Symptom Burden Questionnaire\u2122 for Long COVID: a Rasch analysis", - "rel_date": "2022-01-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.16.22269146", - "rel_abs": "ObjectiveTo describe the development and initial validation of a novel patient-reported outcome measure of Long COVID symptom burden, the Symptom-Burden Questionnaire for Long COVID (SBQ-LC).\n\nMethod and FindingsThis multi-phase, prospective mixed-methods study took place between April and August 2021 in the United Kingdom (UK). A conceptual framework and initial item pool were developed from published systematic reviews. Further concept elicitation and content validation was undertaken with adults with lived experience (n = 13) and clinicians (n = 10), and face validity was confirmed by the Therapies for Long COVID Study Patient and Public Involvement group (n = 25). The draft SBQ-LC was field tested by adults with self-reported Long COVID recruited via social media and international Long COVID support groups (n = 274). Thematic analysis of interview and survey transcripts established content validity and informed construction of the draft questionnaire. Rasch analysis of field test data guided item and scale refinement and provided evidence of the final SBQ-LCs measurement properties. The Rasch-derived SBQ-LC is composed of 17 independent scales with promising psychometric properties. Respondents rate symptom burden during the past 7-days using a dichotomous response or 4-point rating scale. Each scale provides coverage of a different symptom domain and returns a summed raw score that may be converted to a linear (0 - 100) score. Higher scores represent higher symptom burden.\n\nConclusionsThe SBQ-LC is a comprehensive patient-reported assessment of Long COVID symptom burden developed using modern psychometric methods. It measures symptoms of Long COVID important to individuals with lived experience and may be used to evaluate the impact of interventions and inform best practice in clinical management.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Sarah E Hughes", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Shamil Haroon", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Anuradhaa Subramanian", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Christel McMullan", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Olalekan L Aiyegbusi", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Grace M Turner", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Louise Jackson", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Elin Haf Davies", - "author_inst": "Aparito Limited" - }, - { - "author_name": "Chris Frost", - "author_inst": "Aparito Limited" - }, - { - "author_name": "Gary McNamara", - "author_inst": "Aparito Limited" - }, - { - "author_name": "Gary Price", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Karen Matthews", - "author_inst": "Patient and Public Involvement, Therapies for Long COVID (TLC) study, University of Birmingham" - }, - { - "author_name": "Jennifer Camaradou", - "author_inst": "Patient and Public Involvement, Therapies for Long COVID (TLC) study, University of Birmingham" - }, - { - "author_name": "Jane Ormerod", - "author_inst": "Patient and Public Involvement, Therapies for Long COVID (TLC) study, University of Birmingham" - }, - { - "author_name": "Anita Walker", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Melanie J Calvert", - "author_inst": "University of BIrmingham" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2022.01.17.22269412", "rel_title": "EFCAB4B (CRACR2A) genetic variants associated with COVID-19 fatality", @@ -433601,6 +435374,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.14.22269303", + "rel_title": "Development of an effective immune response in adults with Down Syndrome after SARS-CoV-2 vaccination", + "rel_date": "2022-01-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.14.22269303", + "rel_abs": "Immune dysregulation in individuals with Down syndrome (DS) leads to an increased risk for hospitalization and death due to COVID-19 and may impair the generation of protective immunity after vaccine administration. The cellular and humoral responses of 55 DS patients who received a complete SARS-CoV-2 vaccination regime at one to three (V1) and six (V2) months were characterised. SARS-CoV-2-reactive CD4+ and CD8+ T lymphocytes with a predominant Th1 phenotype were observed at V1, and increased at V2. Likewise, a sustained increase of SARS-CoV-2-specific circulating Tfh (cTfh) cells was observed one to three months after vaccine administration. Specific IgG antibodies against SARS-CoV-2 S protein were detected in 96% and 98% of subjects at V1 and V2, respectively, though IgG titers decreased significantly between both timepoints.\n\nSUMMARYThe work shows the cellular and humoral responses to SARS-CoV-2 vaccination of individuals with Down syndrome (DS) after one to three (V1) and six (V2) months. An effective immune response after six months was observed in 98% of DS individuals.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Laura Esparcia-Pinedo", + "author_inst": "Immunology Department, Hospital Universitario de La Princesa; Instituto de Investigacion Sanitaria Princesa; Madrid, Spain" + }, + { + "author_name": "Ayla Yarci-Carrion", + "author_inst": "Microbiology Department, Hospital Universitario de La Princesa, Instituto de Investigacion Sanitaria Princesa, Madrid, Spain" + }, + { + "author_name": "Gloria Mateo-Jimenez", + "author_inst": "Fundacion de Investigacion Biomedica del Hospital Universitario de La Princesa, Instituto de Investigacion Sanitaria Princesa, Madrid, Spain" + }, + { + "author_name": "Noelia Ropero", + "author_inst": "Immunology Department, Hospital Universitario de La Princesa, Instituto de Investigacion Sanitaria Princesa, Madrid, Spain" + }, + { + "author_name": "Laura Gomez-Cabanas", + "author_inst": "Biobanco, Fundacion de Investigacion del Hospital Universitario de La Princesa, Instituto de Investigacion Sanitaria Princesa, Madrid, Spain" + }, + { + "author_name": "Angel Lancho-Sanchez", + "author_inst": "Biobanco, Fundacion de Investigacion del Hospital Universitario de La Princesa, Instituto de Investigacion Sanitaria Princesa, Madrid, Spain" + }, + { + "author_name": "Enrique Martin-Gayo", + "author_inst": "Immunology Department, Hospital Universitario de La Princesa, Instituto de Investigacion Sanitaria Princesa; Department of Medicine, School of Medicine, Univers" + }, + { + "author_name": "Francisco Sanchez-Madrid", + "author_inst": "Immunology Department, Hospital Universitario de La Princesa; Instituto de Investigacion Sanitaria Princesa; Department of Medicine, School of Medicine, Univers" + }, + { + "author_name": "Fernando Moldenhauer", + "author_inst": "Internal Medicine Department, Hospital Universitario de La Princesa, Instituto de Investigacion Sanitaria Princesa, Madrid, Spain" + }, + { + "author_name": "Ainhoa Gutierrez-Cobos", + "author_inst": "Microbiology Department, Hospital Universitario de La Princesa; Instituto de Investigacion Sanitaria Princesa; Madrid, Spain" + }, + { + "author_name": "Diego Real de Asua", + "author_inst": "Internal Medicine Department, Hospital Universitario de La Princesa; Instituto de Investigacion Sanitaria Princesa; Department of Medicine, School of Medicine, " + }, + { + "author_name": "Arantzazu Alfranca", + "author_inst": "Immunology Department, Hospital Universitario de La Princesa; Instituto de Investigacion Sanitaria La Princesa; Medicine Department, Scool of Medicine, Universi" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.15.22269231", "rel_title": "A prospective, single-center study to evaluate the clinical performance of Meril ABFind in individuals vaccinated against COVID-19", @@ -434848,65 +436684,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2022.01.13.22269244", - "rel_title": "Prognostic Value of Serum/Plasma Neurofilament Light Chain for COVID-19 Associated Mortality", - "rel_date": "2022-01-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.13.22269244", - "rel_abs": "Given the continued spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), early predictors of coronavirus disease 19 (COVID-19) mortality might improve patients outcomes. Increased levels of circulating neurofilament light chain (NfL), a biomarker of neuro-axonal injury, have been observed in patients with severe COVID-19. We investigated whether NfL provides non-redundant clinical value to previously identified predictors of COVID-19 mortality.\n\nWe measured serum or plasma NfL concentrations in a blinded fashion in 3 cohorts totaling 338 COVID-19 patients. In cohort 1, we found significantly elevated NfL levels only in critically ill COVID-19 patients compared to healthy controls. Longitudinal cohort 2 data showed that NfL is elevated late in the course of the disease, following two other prognostic markers of COVID-19: decrease in absolute lymphocyte count (ALC) and increase in lactate dehydrogenase (LDH). Significant correlations between LDH and ALC abnormalities and subsequent rise of NfL implicate multi-organ failure as a likely cause of neuronal injury at the later stages of COVID-19. Addition of NfL to age and gender in cohort 1 significantly improved the accuracy of mortality prediction and these improvements were validated in cohorts 2 and 3.\n\nIn conclusion, although substantial increase in serum/plasma NfL reproducibly enhances COVID-19 mortality prediction, NfL has clinically meaningful prognostic value only close to death, which may be too late to alter medical management. When combined with other prognostic biomarkers, rising longitudinal NfL measurements triggered by LDH and ALC abnormalities would identify patients at risk of COVID-19 associated mortality who might still benefit from escalated care.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Ruturaj Masvekar", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "Peter Kosa", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "Kimberly Jin", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "Kerry Dobbs", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "Michael A Stack", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "Riccardo Castagnoli", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "Virginia Quaresima", - "author_inst": "ASST Spedali Civili di Brescia, Brescia, Italy" - }, - { - "author_name": "Helen C Su", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "Luisa Imberti", - "author_inst": "ASST Spedali Civili di Brescia, Brescia, Italy" - }, - { - "author_name": "Luigi Daniele Notarangelo", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "Bibiana Bielekova", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2022.01.13.21268270", "rel_title": "Health and Economic Consequences of Universal Paid Sick Leave Policies During the COVID-19 Pandemic", @@ -435259,6 +437036,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.14.22268821", + "rel_title": "The risk of SARS-CoV-2 Omicron variant emergence in low and middle-income countries (LMICs)", + "rel_date": "2022-01-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.14.22268821", + "rel_abs": "We estimated the probability of undetected emergence of the SARS-CoV-2 Omicron variant in 25 low and middle-income countries (LMICs) prior to December 5, 2021. In nine countries, the risk exceeds 50%; in Turkey, Pakistan and the Philippines, it exceeds 99%. Risks are generally lower in the Americas than Europe or Asia.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Kaiming Bi", + "author_inst": "University of Texas" + }, + { + "author_name": "Jose Luis Herrera-Diestra", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Yuan Bai", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Zhanwei Du", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Lin Wang", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Graham Gibson", + "author_inst": "The University of Texas at Austin," + }, + { + "author_name": "Maureen Johnson-Leon", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "Spencer Fox", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "Lauren Ancel Meyers", + "author_inst": "The University of Texas at Austin" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.13.22268861", "rel_title": "SARS-CoV-2 Omicron Neutralization After Heterologous Vaccine Boosting", @@ -437098,133 +438926,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2022.01.12.22269133", - "rel_title": "Humoral and T-cell immune response after three doses of mRNA SARS-CoV-2 vaccines in fragile patients: the Italian VAX4FRAIL study", - "rel_date": "2022-01-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.12.22269133", - "rel_abs": "BackgroundPatients with solid or hematological tumors, neurological and immune-inflammatory disorders represent potentially fragile subjects with increased risk to experience severe COVID-19 and inadequate response to SARS-CoV2 vaccination.\n\nMethodsWe designed a prospective Italian multicentric study to assess humoral and T-cell response to SARS-CoV2 vaccination in patients (n=378) with solid tumors (ST), hematological malignancies (HM), neurological (ND) and immuno-rheumatological diseases (ID). The immunogenicity of primary vaccination schedule and of the booster dose were analyzed.\n\nResultsOverall, patient seroconversion rate after two doses was 62.1%. A significant lower rate was observed in HM (52.4%) and ID (51.9%) patients compared to ST (95.6%) and ND (70.7%); a lower median level of antibodies was detected in HM and ID versus the others (p<0.0001). A similar rate of patients with a positive SARS-CoV2 T-cell response was observed in all disease groups, with a higher level observed in the ND group. The booster dose improved humoral responses in all disease groups, although with a lower response in HM patients, while the T-cell response increased similarly in all groups. In the multivariable logistic model, the independent predictors for seroconversion were disease subgroups, type of therapies and age. Notably, the ongoing treatment known to affect the immune system was associated with the worst humoral response to vaccination (p<0.0001), but had no effects on the T-cell responses.\n\nConclusionsImmunosuppressive treatment more than disease type per se is a risk factor for low humoral response after vaccination. The booster dose can improve both humoral and T-cell response.\n\nArticles main point- Lower rate of seroconversion was observed in fragile patients as compared to healthy controls\n- The booster dose improves humoral and T-cell response in all fragile patient groups\n- Immunosuppressive treatment was associated with the worst humoral response to vaccination, but had no effects on T-cell responses.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Paolo Corradini", - "author_inst": "Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Italy; University of Milan, Italy" - }, - { - "author_name": "Chiara Agrati", - "author_inst": "INMI L Spallanzani" - }, - { - "author_name": "Giovanni Apolone", - "author_inst": "Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Italy" - }, - { - "author_name": "Alberto Mantovani", - "author_inst": "Istituto Clinico Humanitas / Humanitas University" - }, - { - "author_name": "Diana Giannarelli", - "author_inst": "Istituto Nazionale Tumori Regina Elena IRCCS - IFO, Rome, Italy" - }, - { - "author_name": "Vincenzo Marasco", - "author_inst": "Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Italy; University of Milan, Italy" - }, - { - "author_name": "Veronica Bordoni", - "author_inst": "INMI L Spallanzani" - }, - { - "author_name": "Alessandra Sacchi", - "author_inst": "INMI L Spallanzani" - }, - { - "author_name": "Giulia Matusali", - "author_inst": "INMI L Spallanzani" - }, - { - "author_name": "Carlo Salvarani", - "author_inst": "INMI L Spallanzani" - }, - { - "author_name": "Pier Luigi Zinzani", - "author_inst": "Azienda Ospedaliero Universitaria di Bologna IRCCS, Italy; University of Bologna, Italy" - }, - { - "author_name": "Renato Mantegazza", - "author_inst": "Fondazione IRCCS Isitituto Neurologico Carlo Besta, Milano, Italy" - }, - { - "author_name": "Fabrizio Tagliavini", - "author_inst": "Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy" - }, - { - "author_name": "Maria Teresa Lupo Stanghellini", - "author_inst": "IRCCS San Raffaele Scientific Institute, Milano, Italy" - }, - { - "author_name": "Fabio Ciceri", - "author_inst": "IRCSS San Raffaele Scientific Institute, Milano, Italy" - }, - { - "author_name": "Silvia Damian", - "author_inst": "Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Italy" - }, - { - "author_name": "Antonio Uccelli", - "author_inst": "University of Genoa, Genoa, Italy; IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy" - }, - { - "author_name": "Daniela Fenoglio", - "author_inst": "IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy; University of Genoa, Italy" - }, - { - "author_name": "Nicola Silvestris", - "author_inst": "IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy; University of Bari Aldo Moro, Bari, Italy" - }, - { - "author_name": "Fausto Baldanti", - "author_inst": "Fondazione IRCCS Policlinico San Matteo; University of Pavia, Pavia, Italy" - }, - { - "author_name": "Giulia Piaggio", - "author_inst": "National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO), Rome, Italy" - }, - { - "author_name": "Gennaro Ciliberto", - "author_inst": "National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO), Rome, Italy" - }, - { - "author_name": "Aldo Morrone", - "author_inst": "San Gallicano Dermatological Institute IRCCS, Rome, Italy" - }, - { - "author_name": "Franco Locatelli", - "author_inst": "IRCCS Ospedale Pediatrico Bambino Gesu; University La Sapienza, Rome, Italy" - }, - { - "author_name": "Valentina Sinno", - "author_inst": "Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Italy" - }, - { - "author_name": "Maria Rescigno", - "author_inst": "Humanitas University" - }, - { - "author_name": "Massimo Costantini", - "author_inst": "Azienda USL-IRCCS Reggio Emilia" - }, - { - "author_name": "- VAX4FRAIL Study Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2022.01.12.476120", "rel_title": "An antibody targeting the N-terminal domain of SARS-CoV-2 disrupts the spike trimer", @@ -437593,6 +439294,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, + { + "rel_doi": "10.1101/2022.01.11.22269070", + "rel_title": "Diminished capacities to make treatment decision for COVID-19 vaccination in schizophrenia", + "rel_date": "2022-01-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.11.22269070", + "rel_abs": "Recent evidence suggests that schizophrenia patients are at high risk for severe COVID-19 and should be prioritized for vaccination. However, impaired decision-making capacities could negatively affect the uptake of COVID-19 vaccination in this population. Competence to consent to COVID-19 vaccination was assessed in 80 outpatients with schizophrenia. Using the MacArthur Competence Assessment Tool for Treatment, 56.3% of the sample were classified as having diminished mental capacity. Poor performance was associated with lower vaccination rates, poorer cognition and higher level of psychotic symptoms. Developing interventions for enhancing informed consent for vaccination is urgent within this population.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Stephane Raffard", + "author_inst": "Laboratoire Esylon, UM3 & Service Universitaire Psychiatrie Adulte CHU Montpellier, France" + }, + { + "author_name": "Sophie Bayard", + "author_inst": "Laboratoire Epsylon, EA 4556, University Montpellier 3, Montpellier, France" + }, + { + "author_name": "Margot Eisenblaetter", + "author_inst": "Laboratoire Epsylon, EA 4556, University Montpellier 3, France" + }, + { + "author_name": "Philippe Tattard", + "author_inst": "Service Universitaire de Psychiatrie Adulte, CHU Montpellier, Montpellier, France" + }, + { + "author_name": "Jerome Attal", + "author_inst": "Service Universitaire de PsychiatrieAdulte, CHU Montpellier, Montpellier, France" + }, + { + "author_name": "Yasmine Laraki", + "author_inst": "Service Universitaire de PsychiatrieAdulte, CHU Montpellier, Montpellier, France" + }, + { + "author_name": "Delphine Capdevielle", + "author_inst": "Service Universitaire de PsychiatrieAdulte, CHU de Montpellier, Montpellier, France" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2022.01.11.21268036", "rel_title": "Screening for SARS-CoV-2 persistence in Long COVID patients using sniffer dogs and scents from axillary sweats samples", @@ -439132,41 +440876,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2022.01.09.22268984", - "rel_title": "Household secondary attack rates of SARS-CoV-2 by variant and vaccination status: an updated systematic review and meta-analysis", - "rel_date": "2022-01-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.09.22268984", - "rel_abs": "We previously reported a household secondary attack rate (SAR) for SARS-CoV-2 of 18.9% through June 17, 2021. To examine how emerging variants and increased vaccination have affected transmission rates, we searched PubMed from June 18, 2021, through January 7, 2022. Meta-analyses used generalized linear mixed models to obtain SAR estimates and 95%CI, disaggregated by several covariates. SARs were used to estimate vaccine effectiveness based on the transmission probability for susceptibility (VES,p), infectiousness (VEI,p), and total vaccine effectiveness (VET,p). Household SAR for 27 studies with midpoints in 2021 was 35.8% (95%CI, 30.6%-41.3%), compared to 15.7% (95%CI, 13.3%-18.4%) for 62 studies with midpoints through April 2020. Household SARs were 38.0% (95%CI, 36.0%-40.0%), 30.8% (95%CI, 23.5%-39.3%), and 22.5% (95%CI, 18.6%-26.8%) for Alpha, Delta, and Beta, respectively. VEI,p, VES,p, and VET,p were 56.6% (95%CI, 28.7%-73.6%), 70.3% (95%CI, 59.3%-78.4%), and 86.8% (95%CI, 76.7%-92.5%) for full vaccination, and 27.5% (95%CI, -6.4%-50.7%), 43.9% (95%CI, 21.8%-59.7%), and 59.9% (95%CI, 34.4%-75.5%) for partial vaccination, respectively. Household contacts exposed to Alpha or Delta are at increased risk of infection compared to the original wild-type strain. Vaccination reduced susceptibility to infection and transmission to others.\n\nSummaryHousehold secondary attack rates (SARs) were higher for Alpha and Delta variants than previous estimates. SARs were higher to unvaccinated contacts than to partially or fully vaccinated contacts and were higher from unvaccinated index cases than from fully vaccinated index cases.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Zachary J. Madewell", - "author_inst": "Department of Biostatistics, University of Florida, Gainesville, FL" - }, - { - "author_name": "Yang Yang", - "author_inst": "Department of Biostatistics, University of Florida, Gainesville, FL" - }, - { - "author_name": "Ira M. Longini Jr.", - "author_inst": "Department of Biostatistics, University of Florida, Gainesville, FL" - }, - { - "author_name": "M. Elizabeth Halloran", - "author_inst": "Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Biostatistics, University of Washington, Seattle, WA" - }, - { - "author_name": "Natalie E. Dean", - "author_inst": "Department of Biostatistics, University of Florida, Gainesville, FL" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.01.10.22269002", "rel_title": "Cardiopulmonary imaging utilization and findings among hospitalized COVID-19 patients in Latin America (From RIMAC: Registry IMAging Cardiopulmonary among hospitalized COVID-19 patients in LATAM)", @@ -439535,6 +441244,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.11.22269017", + "rel_title": "Healthcare workers' views on mandatory SARS-CoV-2 vaccination in the United Kingdom: findings from the UK-REACH prospective longitudinal cohort study", + "rel_date": "2022-01-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.11.22269017", + "rel_abs": "BackgroundSeveral countries now have mandatory SARS-CoV-2/COVID-19 vaccination for healthcare workers (HCWs) or the general population. HCWs views on this are largely unknown.\n\nMethodsWe administered an online questionnaire to 17891 United Kingdom (UK) HCWs in Spring 2021 as part of the United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers (UK-REACH) nationwide prospective cohort study. We categorised responses to a free-text question \"What should society do if people dont get vaccinated against COVID-19?\" using content analysis. We collapsed categories into a binary variable: favours mandatory vaccination or not and used logistic regression to calculate its demographic predictors, and occupational, health and attitudinal predictors adjusted for demographics.\n\nFindingsOf 5633 questionnaire respondents, 3235 answered the freetext question; 18% (n=578) of those favoured mandatory vaccination but the most frequent suggestion was education (32%, n=1047). Older HCWs, HCWs vaccinated against influenza (OR 1.48; 95%CI 1.10 - 1.99, vs none) and with more positive vaccination attitudes generally (OR 1.10; 95%CI 1.06 - 1.14) were more likely to favour mandatory vaccination (OR 1.26; 95%CI 1.17 - 1.37, per decade increase), whereas female HCWs (OR= 0.80, 95%CI 0.65 - 0.99, vs male), Black HCWs (OR= 0.48, 95%CI 0.26 - 0.87, vs White), those hesitant about COVID-19 vaccination (OR= 0.56; 95%CI 0.43 - 0.71, vs not hesitant), in an Allied Health Profession (OR 0.67; 95%CI 0.51 - 0.88, vs Medical), or who trusted their organisation (OR 0.78; 95%CI 0.63 - 0.96) were less likely to.\n\nInterpretationOnly one in six of the HCWs in this large, diverse, UK-wide sample favoured mandatory vaccination. Building trust, educating and supporting HCWs who are hesitant about vaccination may be more acceptable, effective and equitable.\n\nFundingMRC-UK Research and Innovation grant (MR/V027549/1) and the Department of Health and Social Care via the National Institute for Health Research.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Katherine Woolf", + "author_inst": "University College London" + }, + { + "author_name": "Mayuri Gogoi", + "author_inst": "University of Leicester" + }, + { + "author_name": "Christopher A Martin", + "author_inst": "University of Leicester; University Hospitals of Leicester NHS Trust" + }, + { + "author_name": "Padmasayee Panineni", + "author_inst": "London North West University Healthcare NHS Trust" + }, + { + "author_name": "Susie Lagrata", + "author_inst": "University College London Hospitals NHS Foundation Trust" + }, + { + "author_name": "Laura B Nellums", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Chris McManus", + "author_inst": "University College London" + }, + { + "author_name": "Anna L Guyatt", + "author_inst": "University of Leicester" + }, + { + "author_name": "Carl Melbourne", + "author_inst": "University of Leicester" + }, + { + "author_name": "Luke Bryant", + "author_inst": "University of Leicester" + }, + { + "author_name": "Amit Gupta", + "author_inst": "Oxford University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Catherine John", + "author_inst": "University of Leicester" + }, + { + "author_name": "Sue Carr", + "author_inst": "General Medical Council; University Hospitals Leicester NHS Trust" + }, + { + "author_name": "Martin D Tobin", + "author_inst": "University of Leicester" + }, + { + "author_name": "Sandra Simpson", + "author_inst": "Nottinghamshire Healthcare NHS Foundation Trust" + }, + { + "author_name": "Bindu Gregary", + "author_inst": "Royal Preston Hospital" + }, + { + "author_name": "Avinash Aujayeb", + "author_inst": "Northumbria Specialist Emergency Care Hospital." + }, + { + "author_name": "Stephen Zingwe", + "author_inst": "Berkshire Healthcare NHS Foundation Trust." + }, + { + "author_name": "Rubina Reza", + "author_inst": "Derbyshire Healthcare NHS Foundation Trust" + }, + { + "author_name": "Laura J Gray", + "author_inst": "University of Leicester" + }, + { + "author_name": "Kamlesh Khunti", + "author_inst": "University of Leicester" + }, + { + "author_name": "Manish Pareek", + "author_inst": "University of Leicester; University Hospitals of Leicester NHS Trust" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.10.22269007", "rel_title": "EFFECT OF FULL VACCINATION AND POST-COVID OLFACTORY DYSFUNCTION IN RECOVERED COVID-19 PATIENT. A RETROSPECTIVE LONGITUDINAL STUDY WITH PROPENSITY MATCHING.", @@ -441038,37 +442850,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.08.22268920", - "rel_title": "Estimation of the test to test distribution as a proxy for generation interval distribution for the Omicron variant in England", - "rel_date": "2022-01-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.08.22268920", - "rel_abs": "BackgroundEarly estimates from South Africa indicated that the Omicron COVID-19 variant may be both more transmissible and have greater immune escape than the previously dominant Delta variant. The rapid turnover of the latest epidemic wave in South Africa as well as initial evidence from contact tracing and household infection studies has prompted speculation that the generation time of the Omicron variant may be shorter in comparable settings than the generation time of the Delta variant.\n\nMethodsWe estimated daily growth rates for the Omicron and Delta variants in each UKHSA region from the 23rd of November to the 23rd of December 2021 using surveillance case counts by date of specimen and S-gene target failure status with an autoregressive model that allowed for time-varying differences in the transmission advantage of the Delta variant where the evidence supported this. By assuming a gamma distributed generation distribution we then estimated the generation time distribution and transmission advantage of the Omicron variant that would be required to explain this time varying advantage. We repeated this estimation process using two different prior estimates for the generation time of the Delta variant first based on household transmission and then based on its intrinsic generation time.\n\nResultsVisualising our growth rate estimates provided initial evidence for a difference in generation time distributions. Assuming a generation time distribution for Delta with a mean of 2.5-4 days (90% credible interval) and a standard deviation of 1.9-3 days we estimated a shorter generation time distribution for Omicron with a mean of 1.5-3.2 days and a standard deviation of 1.3-4.6 days. This implied a transmission advantage for Omicron in this setting of 160%-210% compared to Delta. We found similar relative results using an estimate of the intrinsic generation time for Delta though all estimates increased in magnitude due to the longer assumed generation time.\n\nConclusionsWe found that a reduction in the generation time of Omicron compared to Delta was able to explain the observed variation over time in the transmission advantage of the Omicron variant. However, this analysis cannot rule out the role of other factors such as differences in the populations the variants were mixing in, differences in immune escape between variants or bias due to using the test to test distribution as a proxy for the generation time distribution.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Sam Abbott", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Katharine Sherratt", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Moritz Gerstung", - "author_inst": "German Cancer Research Centre DKFZ" - }, - { - "author_name": "Sebastian Funk", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.08.22268950", "rel_title": "Modelling COVID-19 Vaccine Breakthrough Infections in Highly Vaccinated Israel - the effects of waning immunity and third vaccination dose", @@ -441309,6 +443090,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dentistry and oral medicine" }, + { + "rel_doi": "10.1101/2022.01.05.22268617", + "rel_title": "Durability and cross-reactivity of SARS-CoV-2 mRNA vaccine in adolescent children", + "rel_date": "2022-01-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.05.22268617", + "rel_abs": "Emergent SARS-CoV-2 variants and waning humoral immunity in vaccinated individuals have resulted in increased infections and hospitalizations. Children are not spared from infection nor complications of COVID-19, and the recent recommendation for boosters in individuals ages 12 years or older calls for broader understanding of the adolescent immune profile after mRNA vaccination. We tested the durability and cross-reactivity of anti-SARS-CoV-2 serologic responses over a six-month time course in vaccinated adolescents against the SARS-CoV-2 wild type and Omicron antigens. Serum from 77 adolescents showed that anti-Spike antibodies wane significantly over 6 months. After completion of a two-vaccine series, cross-reactivity against Omicron-specific receptor-binding domain (RBD) was seen. Evidence of waning mRNA-induced vaccine immunity underscores vulnerabilities in long-term pediatric protection against SARS-CoV-2 infection, while cross-reactivity highlights the additional benefits of vaccination. Characterization of adolescent immune signatures post-vaccination will inform guidance on vaccine platforms and timelines, and ultimately optimize immunoprotection of children.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Madeleine Burns", + "author_inst": "MGH" + }, + { + "author_name": "Brittany Boribong", + "author_inst": "MGH" + }, + { + "author_name": "Yannic Bartsch", + "author_inst": "Ragon Institute" + }, + { + "author_name": "Maggie Loiselle", + "author_inst": "MGH" + }, + { + "author_name": "Jameson Davis", + "author_inst": "MGH" + }, + { + "author_name": "Rosiane Lima", + "author_inst": "MGH" + }, + { + "author_name": "Andrea Edlow", + "author_inst": "MGH" + }, + { + "author_name": "Alessio Fasano", + "author_inst": "MGH" + }, + { + "author_name": "Galit Alter", + "author_inst": "Ragon Institute" + }, + { + "author_name": "Lael Yonker", + "author_inst": "MGH" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.09.22268969", "rel_title": "Omicron Impact in India: An Early Analysis of the Ongoing COVID-19 Third Wave", @@ -442927,65 +444763,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.07.22268869", - "rel_title": "BNT162b2 post-exposure-prophylaxis against COVID-19", - "rel_date": "2022-01-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.07.22268869", - "rel_abs": "BackgroundDuring the COVID-19 pandemic, post-exposure-prophylaxis is not a practice. Following exposure, only patient isolation is imposed. Moreover, no therapeutic prevention approach is applied. We asked whether evidence exists for reduced mortality rate following post-exposure-prophylaxis.\n\nMethodsTo estimate the effectiveness of post-exposure-prophylaxis, we obtained data from the Israeli Ministry of Health (MoH) registry. The study population consisted of Israeli residents aged 12 years and older, identified for the first time as PCR-positive for SARS-CoV-2, between December 20th, 2020 (the beginning of the vaccination campaign) and October 7th, 2021. We compared \"recently injected\" patients - that proved PCR-positive on the same day or on one of the five consecutive days after first vaccination (representing an unintended post-exposure-prophylaxis), to unvaccinated control group.\n\nResultsAmong Israeli residents identified PCR-positive for SARS-CoV-2, 11,690 were found positive on the day they received their first vaccine injection (BNT162b2) or on one of the 5 days thereafter. In patients over 65 years, 143 deaths occurred among 1413 recently injected (10.12%) compared to 280 deaths among the 1413 unvaccinated (19.82%), odd ratio (OR) 0.46 (95% confidence interval (CI), 0.36 to 0.57; P<0.001). The most significant reduction in the death toll was observed among the 55 to 64 age group, with 8 deaths occurring among the 1322 recently injected (0.61%) compared to 43 deaths among the 1322 unvaccinated control (3.25%), OR 0.18 (95% CI, 0.07 to 0.39; P<0.001).\n\nConclusionPost-exposure-prophylaxis is effective against death in COVID-19 infection.\n\nIsraeli MoH Registry NumberHMO-0372-20", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Zohar Shemuelian", - "author_inst": "Goldyne Savad Institute of Gene and Cell Therapy, Hadassah Hebrew University Hospital, Jerusalem Israel" - }, - { - "author_name": "Yehuda Warszawer", - "author_inst": "Goldyne Savad Institute of Gene and Cell Therapy, Hadassah Hebrew University Hospital, Jerusalem Israel" - }, - { - "author_name": "Omri Or", - "author_inst": "Goldyne Savad Institute of Gene and Cell Therapy, Hadassah Hebrew University Hospital, Jerusalem Israel" - }, - { - "author_name": "Sagit Arbel-Alon", - "author_inst": "The Ministry of Welfare and Social Affairs, Chief Physician, Government of Israel, Jerusalem, Israel" - }, - { - "author_name": "Hilla Giladi", - "author_inst": "Goldyne Savad Institute of Gene and Cell Therapy, Hadassah Hebrew University Hospital, Jerusalem Israel" - }, - { - "author_name": "Meytal Avgil Tsadok", - "author_inst": "TIMNA-Israel Ministry of Health's Big Data Platform, Ministry of Health, Jerusalem, Israel" - }, - { - "author_name": "Roy Cohen", - "author_inst": "TIMNA-Israel Ministry of Health's Big Data Platform, Ministry of Health, Jerusalem, Israel" - }, - { - "author_name": "Galit Shefer", - "author_inst": "TIMNA-Israel Ministry of Health's Big Data Platform, Ministry of Health, Jerusalem, Israel" - }, - { - "author_name": "Antonello Maruotti", - "author_inst": "Department Law, Economics, Politics and Modern Languages, Libera Universita' Maria SS Assunta, Rome, Italy" - }, - { - "author_name": "Giovanna Jona Lasinio", - "author_inst": "Depertment of Statistical Sciences, University of Rome La Sapienza" - }, - { - "author_name": "Eithan Galun", - "author_inst": "Goldyne Savad Institute of Gene and Cell Therapy, Hadassah Hebrew University Hospital, Jerusalem Israel" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.05.22268777", "rel_title": "Persistence of immunity and impact of a third (booster) dose of an inactivated SARS-CoV-2 vaccine, BBV152; a phase 2, double-blind, randomised controlled trial", @@ -443366,6 +445143,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2022.01.06.21268555", + "rel_title": "VarLOCK - sequencing independent, rapid detection of SARS-CoV-2 variants of concern for point-of-care testing, qPCR pipelines and national wastewater surveillance", + "rel_date": "2022-01-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.06.21268555", + "rel_abs": "The COVID-19 pandemic continues to pose a threat to the general population. The ongoing vaccination programs provide protection to individuals and facilitate the opening of society and a return to normality. However, emergent and existing SARS-CoV-2 variants capable of evading the immune system endanger the efficacy of the vaccination strategy. To preserve the efficacy of SARS-CoV-2 vaccination globally, aggressive and effective surveillance for known and emerging SARS-CoV-2 Variants of Concern (VOC) is required. Rapid and specific molecular diagnostics can provide speed and coverage advantages compared to genomic sequencing alone, benefitting the public health response and facilitating VOC containment. In this work, we expand the recently developed SARS-CoV-2 CRISPR-Cas detection technology (SHERLOCK) to allow rapid and sensitive discrimination of VOCs, that can be used at point of care and/or implemented in the pipelines of small or large testing facilities, and even determine proportion of VOCs in pooled population-level wastewater samples. This technology aims to complement the ongoing sequencing efforts to allow facile and, crucially, rapid identification of individuals infected with VOCs to help break infection chains. Here, we show the optimisation of our VarLOCK assays (Variant-specific SHERLOCK) for multiple specific mutations in the S gene of SARS-CoV-2 and validation with samples from the Cardiff University Testing Service. We also show the applicability of VarLOCK to national wastewater surveillance of SARS-CoV-2 variants. In addition, we show the rapid adaptability of the technique for new and emerging VOCs such as Omicron.\n\nShort abstractThe COVID-19 pandemic continues to pose a threat as emergent and existing SARS-CoV-2 variants endanger the efficacy of the vaccination strategy. Rapid surveillance for known and emerging SARS-CoV-2 Variants of Concern (VOC) would be assisted by effective molecular diagnostics procedures. Here we develop the recent SARS-CoV-2 CRISPR-Cas detection technology (SHERLOCK) for rapid and sensitive discrimination of VOCs to complement sequencing and allow rapid identification of individuals infected with VOC. We show our assays can be implemented with test samples in the pipelines of large testing facilities, as well as determine the proportion of VOCs in pooled population level wastewater samples and has potential applicability at point of care. We demonstrate the optimisation of new VarLOCK assays (Variant-specific SHERLOCK) for multiple specific mutations in the S gene of SARS-CoV-2 and validate these with samples from the Cardiff University Testing Service, as well as the applicability of VarLOCK to national-level wastewater surveillance of SARS-CoV-2 variants. We also demonstrate the rapid adaptability of the technique for new and emerging VOCs such as Omicron.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Xinsheng Nan", + "author_inst": "Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK" + }, + { + "author_name": "Sven Hoehn", + "author_inst": "Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK" + }, + { + "author_name": "Patrick Hardinge", + "author_inst": "Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK" + }, + { + "author_name": "Shrinivas N Dighe", + "author_inst": "Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK" + }, + { + "author_name": "John Ukeri", + "author_inst": "Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff, CF10 3NB, UK" + }, + { + "author_name": "Darius Pease", + "author_inst": "COVID-19 screening service, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK" + }, + { + "author_name": "Joshua Griffin", + "author_inst": "COVID-19 screening service, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK" + }, + { + "author_name": "Jessica I Warrington", + "author_inst": "Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK and Midatech Pharma (Wales) Ltd, 1 Caspian Po" + }, + { + "author_name": "Zack Saud", + "author_inst": "Infection & Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK" + }, + { + "author_name": "Emma Hottinger", + "author_inst": "COVID-19 screening service, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK" + }, + { + "author_name": "Gordon Webster", + "author_inst": "Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK" + }, + { + "author_name": "David L Jones", + "author_inst": "Bangor University" + }, + { + "author_name": "Peter Kille", + "author_inst": "Cardiff University" + }, + { + "author_name": "Andrew Weightman", + "author_inst": "Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK" + }, + { + "author_name": "Richard Stanton", + "author_inst": "Infection & Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK" + }, + { + "author_name": "Oliver K Castell", + "author_inst": "Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff, CF10 3NB, UK" + }, + { + "author_name": "James AH Murray", + "author_inst": "Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK" + }, + { + "author_name": "Tomasz Piotr Jurkowski", + "author_inst": "Cardiff University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.07.475406", "rel_title": "Comprehensive analysis of disease pathology in immunocompetent and immunocompromised hamster models of SARS-CoV-2 infection", @@ -444749,33 +446613,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.03.22268663", - "rel_title": "The Governance of Pandemics in Primary Health Care: The Governance Strategies Adopted by Health Facility Governing Committees in Times of COVID Pandemic in Tanzania", - "rel_date": "2022-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.03.22268663", - "rel_abs": "The governance of COVID 19 in Lower and Middle-Income Countries (LMICs) is very critical for curbing its effects. However, it is unknown what governance strategies are adopted by Health Facility Governing Committees (HFGCs) s as a response to the pandemic. We employed an exploratory qualitative design to study the governance strategies adopted by HFGCs during the COVID19. Since COVID 19 is new, an inductive approach was used as it involves analyzing collected data with little or no predetermined theory for the study. A purposive sampling technique was employed in which multistage clustered sampling was used to select regions, councils, health facilities and respondents. In-depth interviews with HFGCs chairpersons and Focus Group Discussions with members of HFGCs were used to collect data. The data were analyzed based on the themes which emerged during data collection. We found five governance strategies that were found to be commonly adopted by many HFGCs which are financial allocation, re-planing, mobilization of resources, community sensitization and mobilization of stakeholders. however, these governance structures were not all adopted by all HFGCs. The HFGCs slowly adopted governance strategies in the times of COVID 19 pandemics because were unprepared. Despite being empowered by the Direct Health Facility Financing, still, the newest of the COVID 19 has been a challenge to many HFGCs. This calls for urgent capacity building for governance institutions on how to deal will pandemics in primary health facilities.\n\nKey Questions Box O_TEXTBOXKey Questions\n\nWhat is Already Known?[tpltrtarr] Governance of pandemics is very critical for minimizing its effects\n[tpltrtarr]Government in Lower and Middle-Income Countries (LMICs) reacted differently to bring the COVID 19 pandemic under control\n[tpltrtarr]Little is known on the governance strategies adopted by Health Facility Governing Committees (HFGCs) to control COVID 19 at the primary health care facilities in LMICs\n\n\nWhat are the new findings?[tpltrtarr] HFGCs response to the COVID 19 is mixed as some HFGCs were so active and others were so slowly in instituting governance strategies to combat the pandemic\n[tpltrtarr]The common governance strategies adopted were financial allocation, re-planning, embolization of resources, community sensitization and stakeholders mobilization\n[tpltrtarr]HFGCs in LMICs were not well prepared for the pandemic at the community level\n\n\nWhat do new findings imply?[tpltrtarr] Capacitated HFGCs in both soft and hard aspects cornerstone for effective governance of the pandemics in primary health care\n[tpltrtarr]Preparedness of pandemics in LMICs needs to go beyond upper-level governance structures\n\n\nC_TEXTBOX", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Anosisye Mwandulusya Kesale", - "author_inst": "Mzumbe University" - }, - { - "author_name": "Christopher Mahonge", - "author_inst": "Sokoine University of Agriculture" - }, - { - "author_name": "Mikidadi Muhanga", - "author_inst": "Sokoine University of Agriculture" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2022.01.05.22268808", "rel_title": "Adherence of SARS-CoV-2 delta variant to surgical mask and N95 respirators", @@ -444975,6 +446812,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2022.01.06.22268835", + "rel_title": "An integrated lab-on-a-chip device for RNA extraction, amplification and CRISPR-Cas12a-assisted detection for COVID-19 screening in resource-limited settings", + "rel_date": "2022-01-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.06.22268835", + "rel_abs": "In response to the ongoing COVID-19 pandemic and disparities of vaccination coverage in low- and middle-income countries, it is vital to adopt a widespread testing and screening programme, combined with contact tracing, to monitor and effectively control the infection dispersion in areas where medical resources are limited. This work presents a lab-on-a-chip platform, namely \"IFAST-CRISPR\", as an affordable, rapid and high-precision molecular diagnostic means for SARS-CoV-2 detection. The herein proposed \"sample-to-answer\" platform integrates RNA extraction, amplification and CRISPR-Cas-based detection with lateral flow readout in one device. The microscale dimensions of the device containing immiscible liquids, coupled with the use of silica paramagnetic beads and GuHCl, streamline sample preparation, including RNA concentration, extraction and purification, in 15 min with minimal hands-on steps. By combining RT-LAMP with CRISPR-Cas12 assays targeting the nucleoprotein (N) gene, visual identification of [≥] 470 copies mL-1 genomic SARS-CoV-2 samples was achieved in 45 min, with no cross-reactivity towards HCoV-OC43 nor H1N1. On-chip assays showed the ability to isolate and detect SARS-CoV-2 from 1,000 genome copies mL-1 of replication-deficient viral particles in 1 h. This simple, affordable and integrated platform demonstrated a visual, faster, and yet specificity and sensitivity-comparable alternative to the costly gold-standard RT-PCR assay, requiring only a simple heating source. Further investigations on multiplexing and direct interfacing of the accessible Swan-brand cigarette filter for saliva sample collection could provide a complete work flow for COVID-19 diagnostics from saliva samples suitable for low-resource settings.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Bongkot Ngamsom", + "author_inst": "University of Hull" + }, + { + "author_name": "Alexander Iles", + "author_inst": "University of Hull" + }, + { + "author_name": "Moses Kamita", + "author_inst": "Mount Kenya University" + }, + { + "author_name": "Racheal Kimani", + "author_inst": "Mount Kenya University" + }, + { + "author_name": "Pablo Rodriguez-Mateos", + "author_inst": "University of Hull" + }, + { + "author_name": "Mary Mungai", + "author_inst": "Kenya Medical Research Institute" + }, + { + "author_name": "Charlotte E. Dyer", + "author_inst": "University of Hull" + }, + { + "author_name": "Cheryl Walter", + "author_inst": "University of Hull" + }, + { + "author_name": "Jesse Gitaka", + "author_inst": "Mount Kenya University" + }, + { + "author_name": "Nicole Pamme", + "author_inst": "Stockholm University: Stockholm, Sweden" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.05.22268788", "rel_title": "High Sensitivity and NPV for BinaxNOW Rapid Antigen Test in Children at a Mass Testing Site During Prevalent Delta Variant", @@ -446474,65 +448366,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.01.04.475015", - "rel_title": "SARS-CoV-2 Infection of Microglia Elicits Pro-inflammatory Activation and Apoptotic Cell Death", - "rel_date": "2022-01-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.04.475015", - "rel_abs": "Accumulating evidence suggests that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes various neurological symptoms in coronavirus disease 2019 (COVID-19) patients. The most dominant immune cells in the brain are microglia. Yet, the relationship between neurological manifestations, neuroinflammation, and host immune response of microglia to SARS-CoV-2 has not been well characterized. Here, we report that SARS-CoV-2 can directly infect human microglia, eliciting M1-like pro-inflammatory responses, followed by cytopathic effects. Specifically, SARS-CoV-2 infected human microglial clone 3 (HMC3), leading to inflammatory activation and cell death. RNA-seq analysis also revealed that ER stress and immune responses were induced in the early and apoptotic processes in the late phase of viral infection. SARS-CoV-2-infected HMC3 showed the M1 phenotype and produced pro-inflammatory cytokines such as interleukin (IL)-1{beta}, IL-6, and tumour necrosis factor (TNF-), but not the anti-inflammatory cytokine IL-10. After this pro-inflammatory activation, SARS-CoV-2 infection promoted both intrinsic and extrinsic death receptor-mediated apoptosis in HMC3. Using K18-hACE2 transgenic mice, murine microglia were also infected by intranasal inoculation of SARS-CoV-2. This infection induced the acute production of pro-inflammatory microglial IL-6 and TNF- and provoked a chronic loss of microglia. Our findings suggest that microglia are potential mediators of SARS-CoV-2-induced neurological problems and, consequently, can be targets of therapeutic strategies against neurological diseases in COVID-19 patients.\n\nIMPORTANCERecent studies reported neurological manifestations and complications in COVID-19 patients, which are associated with neuroinflammation. As microglia are the dominant immune cells in brains, it needs to be elucidate the relationship between neuroinflammation and host immune response of microglia to SARS-CoV-2. Here, we suggest that SARS-CoV-2 can directly infect human microglia with cytopathic effect (CPE) using human microglial clone 3 (HMC3). The infected microglia were promoted to pro-inflammatory activation following apoptotic cell death. This pro-inflammatory activation was accompanied by the high production of pro-inflammatory cytokines, and led to neurotoxic-M1 phenotype polarization. In vivo, murine microglia were infected and produced pro-inflammatory cytokines and provoked a chronic loss using K18-hACE2 mice. Thus, our data present that SARS-CoV-2-infected microglia are potential mediators of neurological problems in COVID-19 patients. In addition, HMC3 cells are susceptible to SARS-CoV-2 and exhibit the CPE, which can be further used to investigate cellular and molecular mechanisms of neuroinflammation reported in COVID-19 patients.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Gi Uk Jeong", - "author_inst": "Korea Research Institute of Chemical Technology" - }, - { - "author_name": "Jaemyun Lyu", - "author_inst": "Arontier Co., Ltd." - }, - { - "author_name": "Kyun-Do Kim", - "author_inst": "Korea Research Institute of Chemical Technology" - }, - { - "author_name": "Young Cheul Chung", - "author_inst": "Korea Institute of Toxicology" - }, - { - "author_name": "Gun Young Yoon", - "author_inst": "Korea Research Institute of Chemical Technology" - }, - { - "author_name": "Sumin Lee", - "author_inst": "Korea Research Institute of Chemical Technology" - }, - { - "author_name": "Insu Hwang", - "author_inst": "Korea Research Institute of Chemical Technology" - }, - { - "author_name": "Won-Ho Shin", - "author_inst": "Korea Institute of Toxicology" - }, - { - "author_name": "Junsu Ko", - "author_inst": "Arontier Co., Ltd." - }, - { - "author_name": "June-Yong Lee", - "author_inst": "Yonsei University" - }, - { - "author_name": "Young-Chan Kwon", - "author_inst": "Korea Research Institute of Chemical Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.01.04.474979", "rel_title": "SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein", @@ -446733,6 +448566,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2022.01.04.22268742", + "rel_title": "COVID-19-Associated Hospitalizations Among Children Less Than 12 Years of Age in the United States", + "rel_date": "2022-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.04.22268742", + "rel_abs": "ObjectivesTo describe the characteristics, healthcare resource use and costs associated with initial hospitalization and readmissions among pediatric patients with COVID-19 in the US.\n\nMethodsHospitalized pediatric patients, 0-11 years of age, with a primary or secondary discharge diagnosis code for COVID-19 (ICD-10 code U07.1) were selected from 1 April 2020 through 30 September 2021 in the US Premier Healthcare Database Special Release (PHD SR). Patient characteristics, hospital length of stay (LOS), in-hospital mortality, hospital costs, hospital charges, and COVID-19-associated readmission outcomes were evaluated and stratified by age groups (0-4, 5-11), four COVID-19 disease progression states based on intensive care unit (ICU) and invasive mechanical ventilation (IMV) usage, and three sequential calendar periods. Sensitivity analyses were performed using the US HealthVerity claims database and restricting the analyses to primary discharge code.\n\nResultsAmong 4,573 hospitalized pediatric patients aged 0-11 years, 68.0% were 0-4 years and 32.0% were 5-11 years, with a mean (median) age of 3.2 (1) years; 56.0% were male, and 67.2% were covered by Medicaid. Among the overall study population, 25.7% had immunocompromised condition(s), 23.1% were admitted to the ICU and 7.3% received IMV. The mean (median) hospital LOS was 4.3 (2) days, hospital costs and charges were $14,760 ($6,164) and $58,418 ($21,622), respectively; in-hospital mortality was 0.5%. LOS, costs, charges, and in-hospital mortality increased with ICU admission and/or IMV usage. In total, 2.1% had a COVID-19-associated readmission. Study outcomes appeared relatively more frequent and/or higher among those 5-11 than those 0-4. Results using the HealthVerity data source were generally consistent with main analyses.\n\nLimitationsThis retrospective administrative database analysis relied on coding accuracy and inpatient admissions with validated hospital costs.\n\nConclusionsThese findings underscore that children aged 0-11 years can experience severe COVID-19 illness requiring hospitalization and substantial hospital resource use, further supporting recommendations for COVID-19 vaccination.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Manuela Di Fusco", + "author_inst": "Pfizer Inc., New York, NY" + }, + { + "author_name": "Shailja Vaghela", + "author_inst": "HealthEcon Consulting, Inc." + }, + { + "author_name": "Mary M Moran", + "author_inst": "Pfizer Inc., Collegeville, PA" + }, + { + "author_name": "Jay Lin", + "author_inst": "Novosys Health, Green Brook, NJ" + }, + { + "author_name": "Jessica E Atwell", + "author_inst": "Pfizer Inc., New York, NY" + }, + { + "author_name": "Deepa Malhotra", + "author_inst": "Pfizer Inc., New York, NY" + }, + { + "author_name": "Thomas Scassellati Sforzolini", + "author_inst": "Pfizer Inc., New York, NY" + }, + { + "author_name": "Alejandro Cane", + "author_inst": "Pfizer Inc., New York, NY" + }, + { + "author_name": "Jennifer L Nguyen", + "author_inst": "Pfizer Inc., New York, NY" + }, + { + "author_name": "Leah J McGrath", + "author_inst": "Pfizer Inc., New York, NY" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2022.01.05.475095", "rel_title": "Structure-based identification of naphthoquinones and derivatives as novel inhibitors of main protease Mpro and papain-like protease PLpro of SARS-CoV-2", @@ -448320,117 +450208,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.01.04.474908", - "rel_title": "Maternal cytokine response after SARS-CoV-2 infection during pregnancy", - "rel_date": "2022-01-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.04.474908", - "rel_abs": "ObjectiveDysregulation of the immune system during pregnancy is associated with adverse pregnancy outcomes. Recent studies report cytokine changes during the acute phase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We examine whether there is a lasting association between SARS-CoV-2 infection during pregnancy and peripheral blood cytokine levels.\n\nStudy designWe conducted a case-control study at the Mount Sinai health system in NYC including 100 SARS-CoV-2 IgG antibody positive people matched to 100 SARS-CoV-2 IgG antibody negative people on age, race/ethnicity, parity, and insurance status. Blood samples were collected at a median gestational age of 34 weeks. Levels of 14 cytokines were measured.\n\nResultsIndividual cytokine levels and cytokine cluster Eigenvalues did not differ significantly between groups, indicating no persisting maternal cytokine changes after SARS-CoV-2 infection during pregnancy.\n\nConclusionOur findings suggest that the acute inflammatory response after SARS-CoV-2 infection may be restored to normal values during pregnancy.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Frederieke A.J. Gigase", - "author_inst": "Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Nina M. Molenaar", - "author_inst": "Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Roy D. Missall", - "author_inst": "Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Anna-Sophie Rommel", - "author_inst": "Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Whitney Lieb", - "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Erona Ibroci", - "author_inst": "Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Sophie Ohrn", - "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Jezelle Lynch", - "author_inst": "Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Florian Krammer", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Rachel Brody", - "author_inst": "Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Rebecca H. Jessel", - "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Rhoda S. Sperling", - "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Corina Lesseur", - "author_inst": "Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Francesco Callipari", - "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Romeo R. Galang", - "author_inst": "CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA" - }, - { - "author_name": "Margaret C. Snead", - "author_inst": "CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA" - }, - { - "author_name": "Teresa Janevic", - "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Joanne Stone", - "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Elizabeth A. Howell", - "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Jia Chen", - "author_inst": "Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Victor J.M. Pop", - "author_inst": "Department of Clinical and Medical Psychology, Tilburg University, Tilburg, The Netherlands" - }, - { - "author_name": "Siobhan M. Dolan", - "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Veerle Bergink", - "author_inst": "Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Lotje D. De Witte", - "author_inst": "Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.01.04.474803", "rel_title": "A synthetic bispecific antibody capable of neutralizing SARS-CoV-2 Delta and Omicron", @@ -448723,6 +450500,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.30.474592", + "rel_title": "The runaway evolution of SARS-CoV-2 leading to the highly evolved Delta strain", + "rel_date": "2022-01-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.30.474592", + "rel_abs": "In new epidemics after the host shift, the pathogens may experience accelerated evolution driven by novel selective pressures. When the accelerated evolution enters a positive feedback loop with the expanding epidemics, the pathogens runaway evolution may be triggered. To test this possibility in COVID-19, we analyze the extensive databases and identify 5 major waves of strains, one replacing the previous one in 2020 - 2021. The mutations differ entirely between waves and the number of mutations continues to increase, from 3-4 to 21-31. The latest wave is the Delta strain which accrues 31 new mutations to become highly prevalent. Interestingly, these new mutations in Delta strain emerge in multiple stages with each stage driven by 6 - 12 coding mutations that form a fitness group. In short, the evolution of SARS-CoV-2 from the oldest to the youngest wave, and from the earlier to the later stages of the Delta wave, is a process of acceleration with more and more mutations. The global increase in the viral population size (M(t), at time t) and the mutation accumulation (R(t)) may have indeed triggered the runaway evolution in late 2020, leading to the highly evolved Alpha and then Delta strain. To suppress the pandemic, it is crucial to break the positive feedback loop between M(t) and R(t), neither of which has yet to be effectively dampened by late 2021. New waves beyond Delta, hence, should not be surprising.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Yongsen Ruan", + "author_inst": "Sun Yat-sen University, Guangzhou" + }, + { + "author_name": "Mei Hou", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Xiaolu Tang", + "author_inst": "Peking University" + }, + { + "author_name": "Xionglei He", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Xuemei Lu", + "author_inst": "Kunming Institute of Zoology" + }, + { + "author_name": "Jian Lu", + "author_inst": "Peking University" + }, + { + "author_name": "Chung-I Wu", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Haijun Wen", + "author_inst": "Sun Yat-sen University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2021.12.28.21268460", "rel_title": "Comparison of infectious SARS-CoV-2 from the nasopharynx of vaccinated and unvaccinated individuals", @@ -450354,57 +452178,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.30.474610", - "rel_title": "Robust expansion of phylogeny for fast-growing genome sequence data", - "rel_date": "2022-01-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.30.474610", - "rel_abs": "Massive sequencing of SARS-CoV-2 genomes has led to a great demand for adding new samples to a reference phylogeny instead of building the tree from scratch. To address such challenge, we proposed an algorithm TIPars by integrating parsimony analysis with pre-computed ancestral sequences. Compared to four state-of-the-art methods on four benchmark datasets (SARS-CoV-2, Influenza virus, Newcastle disease virus and 16S rRNA genes), TIPars achieved the best performance in most tests. It took only 21 seconds to insert 100 SARS-CoV-2 genomes to a 100k-taxa reference tree using near 1.4 gigabytes of memory. Its efficient and accurate phylogenetic placements and incrementation for phylogenies with highly similar and divergent sequences suggest that it will be useful in a wide range of studies including pathogen molecular epidemiology, microbiome diversity and systematics.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Yongtao Ye", - "author_inst": "The University of Hong Kong, Laboratory of Data Discovery for Health Limited" - }, - { - "author_name": "Marcus Shum", - "author_inst": "The University of Hong Kong, Laboratory of Data Discovery for Health Limited" - }, - { - "author_name": "Joseph Tsui", - "author_inst": "The University of Hong Kong, Laboratory of Data Discovery for Health Limited" - }, - { - "author_name": "Guangchuang Yu", - "author_inst": "Southern Medical University" - }, - { - "author_name": "David Smith", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Huachen Zhu", - "author_inst": "The University of Hong Kong, Laboratory of Data Discovery for Health Limited, Joint Institute of Virology (Shantou University/The University of Hong Kong), EKIH" - }, - { - "author_name": "Joseph Wu", - "author_inst": "The University of Hong Kong, Laboratory of Data Discovery for Health Limited" - }, - { - "author_name": "Yi Guan", - "author_inst": "The University of Hong Kong, Laboratory of Data Discovery for Health Limited, Joint Institute of Virology (Shantou University/The University of Hong Kong), EKIH" - }, - { - "author_name": "Tommy Tsan-Yuk Lam", - "author_inst": "The University of Hong Kong, Laboratory of Data Discovery for Health Limited, Joint Institute of Virology (Shantou University/The University of Hong Kong), EKIH" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.12.30.474580", "rel_title": "SARS-CoV-2 entry sites are present in all structural elements of the human glossopharyngeal and vagal nerves: clinical implications", @@ -450693,6 +452466,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.12.30.21268495", + "rel_title": "Comparison of outcomes from COVID infection in pediatric and adult patients before and after the emergence of Omicron", + "rel_date": "2022-01-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.30.21268495", + "rel_abs": "BackgroundThe Omicron SARS-CoV-2 variant is rapidly spreading in the US since December 2021 and is more contagious than earlier variants. Currently, data on the severity of the disease caused by the Omicron variant compared with the Delta variant is limited. Here we compared 3-day risks of emergency department (ED) visit, hospitalization, intensive care unit (ICU) admission, and mechanical ventilation in patients who were first infected during a time period when the Omicron variant was emerging to those in patients who were first infected when the Delta variant was predominant.\n\nMethodThis is a retrospective cohort study of electronic health record (EHR) data of 577,938 first-time SARS-CoV-2 infected patients from a multicenter, nationwide database in the US during 9/1/2021-12/24/2021, including 14,054 who had their first infection during the 12/15/2021-12/24/2021 period when the Omicron variant emerged (\"Emergent Omicron cohort\") and 563,884 who had their first infection during the 9/1/2021-12/15/2021 period when the Delta variant was predominant (\"Delta cohort\"). After propensity-score matching the cohorts, the 3-day risks of four outcomes (ED visit, hospitalization, ICU admission, and mechanical ventilation) were compared. Risk ratios, and 95% confidence intervals (CI) were calculated.\n\nResultsOf 14,054 patients in the Emergent Omicron cohort (average age, 36.4 {+/-} 24.3 years), 27.7% were pediatric patients (<18 years old), 55.4% female, 1.8% Asian, 17.1% Black, 4.8% Hispanic, and 57.3% White. The Emergent Omicron cohort differed significantly from the Delta cohort in demographics, comorbidities, and socio-economic determinants of health. After propensity-score matching for demographics, socio-economic determinants of health, comorbidities, medications and vaccination status, the 3-day risks in the Emergent Omicron cohort outcomes were consistently less than half those in the Delta cohort: ED visit: 4.55% vs. 15.22% (risk ratio or RR: 0.30, 95% CI: 0.28-0.33); hospitalization: 1.75% vs. 3.95% (RR: 0.44, 95% CI: 0.38-0.52]); ICU admission: 0.26% vs. 0.78% (RR: 0.33, 95% CI:0.23-0.48); mechanical ventilation: 0.07% vs. 0.43% (RR: 0.16, 95% CI: 0.08-0.32). In children under 5 years old, the overall risks of ED visits and hospitalization in the Emergent Omicron cohort were 3.89% and 0.96% respectively, significantly lower than 21.01% and 2.65% in the matched Delta cohort (RR for ED visit: 0.19, 95% CI: 0.14-0.25; RR for hospitalization: 0.36, 95% CI: 0.19-0.68). Similar trends were observed for other pediatric age groups (5-11, 12-17 years), adults (18-64 years) and older adults ([≥] 65 years).\n\nConclusionsFirst time SARS-CoV-2 infections occurring at a time when the Omicron variant was rapidly spreading were associated with significantly less severe outcomes than first-time infections when the Delta variant predominated.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Lindsey Wang", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Nathan A Berger", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Pamela B davis", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "David C Kaelber", + "author_inst": "MetroHealth System" + }, + { + "author_name": "Nora D Volkow", + "author_inst": "National Institute on Drug Addiction" + }, + { + "author_name": "Rong Xu", + "author_inst": "Case Western Reserve University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.01.22268615", "rel_title": "Preserved recognition of Omicron Spike following COVID-19 mRNA vaccination in pregnancy", @@ -452468,53 +454280,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.31.21268583", - "rel_title": "From Delta to Omicron: analysing the SARS-CoV-2 epidemic in France using variant-specific screening tests (September 1 to December 18, 2021)", - "rel_date": "2022-01-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.31.21268583", - "rel_abs": "We analysed 131,478 SARS-CoV-2 variant screening tests performed in France from September 1st to December 18, 2021. Tests consistent with the presence of the Omicron variant exhibit significantly higher cycle threshold Ct values, which could indicate lower amounts of virus genetic material. We estimate that the transmission advantage of the Omicron variant over the Delta variant is +105% (95% confidence interval: 96-114%). Based on these data, we use mechanistic mathematical modelling to explore scenarios for early 2022.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Mircea T. Sofonea", - "author_inst": "Univ. Montpellier" - }, - { - "author_name": "Benedicte Roquebert", - "author_inst": "Cerba Laboratory" - }, - { - "author_name": "Vincent Foulongne", - "author_inst": "CHU de Montpellier" - }, - { - "author_name": "Laura Verdurme", - "author_inst": "CERBA Laboratory" - }, - { - "author_name": "Sabine Trombert-Paolantoni", - "author_inst": "CERBA Laboratory" - }, - { - "author_name": "Mathilde Roussel", - "author_inst": "CERBA Laboratory" - }, - { - "author_name": "Stephanie Haim-Boukobza", - "author_inst": "CERBA Laboratory" - }, - { - "author_name": "Samuel Alizon", - "author_inst": "CNRS" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.31.21268596", "rel_title": "Social isolation and psychological distress among southern US college students in the era of COVID-19", @@ -452775,6 +454540,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.30.21268553", + "rel_title": "Performance of COVIDSeq and Swift normalase amplicon SARS-CoV-2 panels for SARS-CoV-2 Genomes Sequencing: Practical Guide and Combining FASTQ Strategy", + "rel_date": "2022-01-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.30.21268553", + "rel_abs": "The whole genomic sequencing (WGS) of SARS-CoV-2 has been performed extensively and is playing a crucial role in fighting against COVID-19 pandemic. Obtaining sufficient WGS data from clinical samples is often challenging especially from the samples with low viral load. We evaluated two SARS-CoV-2 sequencing protocols for their efficiency/accuracy and limitations. Sequence coverage of >95% was obtained by Swift normalase amplicon SARS-CoV-2 panels (SNAP) protocol for all the samples with Ct [≤] 35 and by COVIDSeq protocol for 97% of samples with Ct [≤] 30. Sample RNA quantitation obtained using digital PCR provided more precise cutoff values. The quantitative digital PCR cutoff values for obtaining 95% coverage are 10.5 copies/L for SNAP protocol and 147 copies/L for COVIDSeq protocol. Combining FASTQ files obtained from 2 protocols improved the outcome of sequence analysis by compensating for missing amplicon regions. This process resulted in an increase of sequencing coverage and lineage call precision.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Hosoon Choi", + "author_inst": "Central Texas Veterans Healthcare System" + }, + { + "author_name": "Munok Hwang", + "author_inst": "Central Texas Veterans Health Care System" + }, + { + "author_name": "Dhammika Navarathna", + "author_inst": "Central Texas Veterans Healthcare System" + }, + { + "author_name": "Jing Xu", + "author_inst": "Central Texas Veterans Healthcare System" + }, + { + "author_name": "Janell Lukey", + "author_inst": "Central Texas Veterans Health Care System" + }, + { + "author_name": "Chetan Jinadatha", + "author_inst": "Central Texas Veterans Health Care System" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.28.21268481", "rel_title": "Vaccination-infection interval determines cross-neutralization potency to SARS-CoV-2 Omicron after breakthrough infection by other variants", @@ -454522,45 +456326,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2021.12.29.474469", - "rel_title": "Unsupervised genome-wide cluster analysis: nucleotide sequences of the omicron variant of SARS-CoV-2 are similar to sequences from early 2020", - "rel_date": "2021-12-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.29.474469", - "rel_abs": "The GISAID database contains more than 1,000,000 SARS-CoV-2 genomes, including sequences of the recently discovered SARS-CoV-2 omicron variant and of prior SARS-CoV-2 strains that have been collected from patients around the world since the beginning of the pandemic. We applied unsupervised cluster analysis to the SARS-CoV-2 genomes, assessing their similarity at a genome-wide level based on the Jaccard index and principal component analysis. Our analysis results show that the omicron variant sequences are most similar to sequences that have been submitted early in the pandemic around January 2020. Furthermore, the omicron variants in GISAID are spread across the entire range of the first principal component, suggesting that the strain has been in circulation for some time. This observation supports a long-term infection hypothesis as the omicron strain origin.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Georg Hahn", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Sanghun Lee", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Dmitry Prokopenko", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Surender Khurana", - "author_inst": "US Food and Drug Administration" - }, - { - "author_name": "Scott T. Weiss", - "author_inst": "Harvard Medical School, Harvard University, Boston, MA 02115, USA" - }, - { - "author_name": "Christoph Lange", - "author_inst": "Harvard School of Public Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.12.30.474453", "rel_title": "Preserved T cell reactivity to the SARS-CoV-2 Omicron variant indicates continued protection in vaccinated individuals.", @@ -454949,6 +456714,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.12.28.21268398", + "rel_title": "mRNA Booster Vaccines Elicit Strong Protection Against SARS-CoV-2 Omicron Variant in Cancer Patients", + "rel_date": "2021-12-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.28.21268398", + "rel_abs": "Following its emergence in late November of 2020, the SARS-CoV-2 Omicron (B.1.1.529) variant has caused major global public health concerns. We recently demonstrated that in healthy adults the Omicron variant exhibits strong resistance to immunity induced by two doses of the mRNA vaccines, but a booster mRNA vaccine dose can provide strong protection against Omicron. However, it is currently unknown how well these mRNA vaccine boosters protect immunocompromised groups, including cancer patients, from the Omicron variant. Here we show that (1) neutralizing antibody (nAb) titers against the Delta and Omicron variants in cancer patients after two-dose mRNA vaccines are 4.2-fold and 21.3-fold lower, respectively, compared to the ancestral D614G, and (2) nAb titers against the Delta and Omicron variants in boosted cancer patients are 3.6-fold and 5.1-fold lower, respectively, compared to D614G. Our findings highlight the effectiveness and need for booster vaccination strategies in immunocompromised groups including cancer patients to protect from the Omicron variant.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Cong Zeng", + "author_inst": "OSU" + }, + { + "author_name": "John P. Evans", + "author_inst": "OSU" + }, + { + "author_name": "Karthik Chakravarthy", + "author_inst": "OSU" + }, + { + "author_name": "Panke Qu", + "author_inst": "OSU" + }, + { + "author_name": "Sarah Reisinger", + "author_inst": "OSUMC" + }, + { + "author_name": "No joon Song", + "author_inst": "OSUMC" + }, + { + "author_name": "Mark Rubinstein", + "author_inst": "OSUMC" + }, + { + "author_name": "Peter G Shields", + "author_inst": "OSUMC" + }, + { + "author_name": "Zihai Li", + "author_inst": "OSUMC" + }, + { + "author_name": "Shan-Lu Liu", + "author_inst": "The Ohio State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2021.12.22.21268218", "rel_title": "Soluble immune checkpoints are dysregulated in COVID-19 and heavy alcohol users with HIV infection", @@ -456636,53 +458456,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.12.27.21268462", - "rel_title": "Evolution of COVID-19 Health Disparities in Arizona", - "rel_date": "2021-12-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.27.21268462", - "rel_abs": "ObjectiveCOVID-19 burdens are disproportionally high in underserved and vulnerable groups in Arizona. As the pandemic progresses, it is unclear if the disparities have evolved. In this study, we aim to elicit the dynamic landscape of COVID-19 disparities at the community level and identify newly emerged vulnerable subpopulations.\n\nMaterials and MethodsWe compiled biweekly COVID-19 case counts of 274 zip code tabulation areas (ZCTAs) in Arizona from October 21, 2020, to November 25, 2021, during which the COVID-19 growth rate has changed significantly. Within each growth period, we detected health disparities by testing associations between the growth rate of COVID-19 cases in a ZCTA and the population composition of race/ethnicity, income, employment, and age. We then compared the associations between periods to discover temporal patterns of health disparities.\n\nResultsHigh percentage of Latinx or Black residents, high poverty rate, and young median age were risk factors of high cumulative COVID-19 case counts in a ZCTA. However, the impact of these factors on the growth rate of new COVID-19 cases varied. While high percentage of Black residents and young median age remained as risk factors of fast COVID-19 growth rate, high poverty rate became a protective factor. The association between the percentage of Latinx residents and the COVID-19 growth rate converted from positive to negative during summer 2021. The unemployment rate emerged as a new risk factor of fast COVID-19 growth rate after September 2021. Based on these findings, we identified 37 ZCTAs that are highly vulnerable to fast escalation of COVID-19 cases.\n\nDiscussion and ConclusionAs the pandemic progresses, disadvantaged communities continue suffering from escalated risk of COVID-19 infection. But the vulnerabilities have evolved. While the disparities related to Latinx ethnicity improved gradually, those related to Black ethnicity and young communities aggravated. The struggle of financially disadvantaged communities continued, although the burden had shifted from those living under the poverty line to those with a high unemployment rate. It is necessary to adjust current resource allocations and design and deploy new interventions to address emerging needs.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Felix L Shen", - "author_inst": "Paradise Valley High School" - }, - { - "author_name": "Jingmin Shu", - "author_inst": "Arizona State University" - }, - { - "author_name": "Matthew Lee", - "author_inst": "Arizona State University" - }, - { - "author_name": "Hyunsung Oh", - "author_inst": "Arizona State University" - }, - { - "author_name": "Flavio Marsiglia", - "author_inst": "Arizona State University" - }, - { - "author_name": "Ming Li", - "author_inst": "University of Arizona" - }, - { - "author_name": "George Runger", - "author_inst": "Arizona State University" - }, - { - "author_name": "Li Liu", - "author_inst": "Arizona State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.12.28.21268472", "rel_title": "Neutralizing antibody responses to SARS-CoV-2: a population based seroepidemiological analysis in Delhi, India", @@ -456883,6 +458656,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.27.21268424", + "rel_title": "Waning of SARS-CoV-2 booster viral-load reduction effectiveness", + "rel_date": "2021-12-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.27.21268424", + "rel_abs": "The BNT162b2 COVID-19 vaccine has been shown to reduce viral load of breakthrough infections (BTIs), an important factor affecting infectiousness. This viral-load protective effect has been waning with time post the second vaccine and later restored with a booster shot. It is currently unclear though for how long this regained effectiveness lasts. Analyzing Ct values of SARS-CoV-2 qRT-PCR tests of over 22,000 infections during a Delta-variant-dominant period in Israel, we found that this viral-load reduction effectiveness significantly declines within months post the booster dose. Adjusting for age, sex and calendric date, Ct values of RdRp gene initially increased by 2.7 [CI: 2.3-3.0] relative to unvaccinated in the first month post the booster dose, yet then decayed to a difference of 1.3 [CI: 0.7-1.9] in the second month and became small and insignificant in the third to fourth months. The rate and magnitude of this post-booster decline in viral-load reduction effectiveness mirror those observed post the second vaccine. These results suggest rapid waning of the boosters effectiveness in reducing infectiousness, possibly affecting community-level spread of the virus.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Matan Levine-Tiefenbrun", + "author_inst": "Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel. Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel." + }, + { + "author_name": "Idan Yelin", + "author_inst": "Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel" + }, + { + "author_name": "Hillel Alapi", + "author_inst": "Maccabitech, Maccabi Health Services, Tel Aviv, Israel" + }, + { + "author_name": "Esma Herzel", + "author_inst": "Maccabitech, Maccabi Health Services, Tel Aviv, Israel" + }, + { + "author_name": "Jacob Kuint", + "author_inst": "Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel. Maccabitech, Maccabi Health Services, Tel Aviv, Israel." + }, + { + "author_name": "Gabriel Chodick", + "author_inst": "Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel. Maccabitech, Maccabi Health Services, Tel Aviv, Israel." + }, + { + "author_name": "Sivan Gazit", + "author_inst": "Maccabitech, Maccabi Health Services, Tel Aviv, Israel" + }, + { + "author_name": "Tal Patalon", + "author_inst": "Maccabitech, Maccabi Health Services, Tel Aviv, Israel" + }, + { + "author_name": "Roy Kishony", + "author_inst": "Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel. Faculty of Computer Science, Technion - Israel Institute of Technology, Haifa, Is" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.27.21268309", "rel_title": "Replacement of the Gamma by the Delta variant in Brazil: impact of lineage displacement on the ongoing pandemic", @@ -458782,41 +460606,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.12.27.474315", - "rel_title": "Peptide-based epitope design on non-structural proteins of SARS-CoV-2", - "rel_date": "2021-12-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.27.474315", - "rel_abs": "The SARS-CoV-2 virus has caused the severe pandemic, COVID19 and since then its been critical to produce a potent vaccine to prevent the quick transmission and also to avoid alarming deaths. Among all type of vaccines peptide based epitope design tend to outshine with respect to low cost production and more efficacy. Therefore, we started with obtaining the necessary protein sequences from NCBI database of SARS-CoV-2 virus and filtered with respect to antigenicity, virulency, pathogenicity and non-homologous nature with human proteome using different available online tools and servers. The promising proteins was checked for containing common B and T-cell epitopes. The structure for these proteins were modeled from I-TASSER server followed by its refinement and validation. The predicted common epitopes were mapped on modeled structures of proteins by using Pepitope server. The surface exposed epitopes were docked with the most common allele DRB1*0101 using the GalaxyPepDock server. The epitopes, ELEGIQYGRS from Leader protein (NSP1), YGPFVDRQTA from 3c-like proteinase (nsp5), DLKWARFPKS from NSP9 and YQDVNCTEVP from Surface glycoprotein (spike protein) are the epitopes which has more hydrogen bonds. Hence these four epitopes could be considered as a more promising epitopes and these epitopes can be used for future studies.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Swathika RS", - "author_inst": "SCBT, SASTRA University" - }, - { - "author_name": "Vimal S", - "author_inst": "SCBT, SASTRA University" - }, - { - "author_name": "Bhagya Shree E", - "author_inst": "SCBT, SASTRA University" - }, - { - "author_name": "Elakkiya Elumalai", - "author_inst": "Center for Bioinformatics, Pondicherry University" - }, - { - "author_name": "Krishna Kant Gupta", - "author_inst": "SCBT, SASTRA University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.12.27.474273", "rel_title": "Structures of the Omicron Spike trimer with ACE2 and an anti-Omicron antibody", @@ -459229,6 +461018,97 @@ "type": "new results", "category": "physiology" }, + { + "rel_doi": "10.1101/2021.12.25.474113", + "rel_title": "Clinical grade ACE2 effectively inhibits SARS-CoV-2 Omicron infections", + "rel_date": "2021-12-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.25.474113", + "rel_abs": "The recent emergence of the SARS-CoV-2 variant Omicron has caused considerable concern due to reduced vaccine efficacy and escape from neutralizing antibody therapeutics. Omicron is spreading rapidly around the globe and is suspected to account for most new COVID-19 cases in several countries, though the severity of Omicron-mediated disease is still under debate. It is therefore paramount to identify therapeutic strategies that inhibit the Omicron SARS-CoV-2 variant. Here we report using 3D structural modelling that Spike of Omicron can still associate with human ACE2. Sera collected after the second mRNA-vaccination did not exhibit a protective effect against Omicron while strongly neutralizing infection of VeroE6 cells with the reference Wuhan strain, confirming recent data by other groups on limited vaccine and convalescent sera neutralization efficacy against Omicron. Importantly, clinical grade recombinant human soluble ACE2, a drug candidate currently in clinical development, potently neutralized Omicron infection of VeroE6 cells with markedly enhanced potency when compared to reference SARS-CoV-2 isolates. These data show that SARS-CoV-2 variant Omicron can be readily inhibited by soluble ACE2, providing proof of principle of a viable and effective therapeutic approach against Omicron infections.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Vanessa Monteil", + "author_inst": "Karolinska Instituet" + }, + { + "author_name": "Stephanie Devignot", + "author_inst": "Karolinska Institute and Karolinska University Hospital, Unit of Clinical Microbiology, Stockholm, Sweden" + }, + { + "author_name": "Jonas Klingstroem", + "author_inst": "Karolinska Institute and Karolinska University Hospital, Unit of Clinical Microbiology, Stockholm, Sweden" + }, + { + "author_name": "Charlotte Thalin", + "author_inst": "Department of Clinical Sciences, Karolinska Institute Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Max J Kellner", + "author_inst": "Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria" + }, + { + "author_name": "Wanda Christ", + "author_inst": "Karolinska Institute and Karolinska University Hospital, Unit of Clinical Microbiology, Stockholm, Sweden" + }, + { + "author_name": "Sebastian Havervall", + "author_inst": "Department of Clinical Sciences, Karolinska Institute Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Stefan Mereiter", + "author_inst": "Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria" + }, + { + "author_name": "Sylvia Knapp", + "author_inst": "Medical University Vienna" + }, + { + "author_name": "Nuria Montserrat", + "author_inst": "IBEC" + }, + { + "author_name": "Benedict Braunsfeld", + "author_inst": "Institute for Molecular Modelling and Simulation, University of Natural Resources and Life Sciences (BOKU), Austria" + }, + { + "author_name": "Ivona Kozieradzki", + "author_inst": "Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada" + }, + { + "author_name": "Omar Hasan Ali", + "author_inst": "Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada" + }, + { + "author_name": "Astrid Hagelkrueys", + "author_inst": "Institute of Molecular Biotechnology (IMBA)" + }, + { + "author_name": "Johannes Stadlmann", + "author_inst": "BOKU - University of Natural Rescources and Life Sciences, Vienna" + }, + { + "author_name": "Chris Oostenbrink", + "author_inst": "University of Natural Resources and Life Sciences" + }, + { + "author_name": "Gerald Wirnsberger", + "author_inst": "Apeiron Biologics" + }, + { + "author_name": "Josef M Penninger", + "author_inst": "IMBA, Vienna, Austria & UBC, Department of Medical Genetics, Vancouver, Canada" + }, + { + "author_name": "Ali Mirazimi", + "author_inst": "Karolinska Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.12.24.474095", "rel_title": "Early Computational Detection of Potential High Risk SARS-CoV-2 Variants", @@ -461384,49 +463264,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2021.12.22.21268127", - "rel_title": "Humoral and cellular immune responses to SARS CoV-2 vaccination in Persons with Multiple Sclerosis and NMOSD patients receiving immunomodulatory treatments", - "rel_date": "2021-12-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268127", - "rel_abs": "BackgroundVaccination against SARS CoV-2 results in excellent personal protection against a severe course of COVID19. In persons with Multiple Sclerosis (PwMS) vaccination efficacy may be reduced by immunomodulatory medications.\n\nObjectiveTo assess the vaccination induced cellular and humoral immune response in PwMS receiving disease modifiying therapies.\n\nMethodsIn a monocentric observational study on PwMS and patients with Neuromyelitis optica we quantified the cellular and humoral immune responses to SARS CoV-2.\n\nResultsPwMS receiving Glatirameracetate, Interferon-{beta}, Dimethylfumarate, Cladribine or Natalalizumab had intact humoral and cellular immune responses following vaccination against SARS CoV-2. B-cell depleting therapies reduced B-cell responses but did not affect T cell responses. S1P inhibitors strongly reduced humoral and cellular immune responses.\n\nThere was a good agreement between the Interferon gamma release assay and the T-SPOT assay used to measure viral antigen induced T-cell responses.\n\nConclusionThis study demonstrates that S1P inhibitors impair the cellular and humoral immune response in SARS CoV-2 vaccination, whereas patients receiving B-cell depleting therapies mount an intact cellular immune response. These data can support clinicians in counselling their PwMS and NMOSD patients during the COVID 19 pandemic.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Henry Bock", - "author_inst": "Carl-Thiem Klinikum Cottbus" - }, - { - "author_name": "Thomas Juretzek", - "author_inst": "Carl-Thiem Klinkum Cottbus" - }, - { - "author_name": "Robert Handreka", - "author_inst": "Carl-Thiem Klinikum Cottbus" - }, - { - "author_name": "Johanna Ruhnau", - "author_inst": "Universitity Medicine Greifswald" - }, - { - "author_name": "Karl Reuner", - "author_inst": "Carl-Thiem Klinkum Cottbus" - }, - { - "author_name": "Heidrun Peltroche", - "author_inst": "Carl-Thiem Klinkum Cottbus" - }, - { - "author_name": "Alexander Dressel", - "author_inst": "Carl Thiem Klinikum" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2021.12.20.21268066", "rel_title": "Persisting Chemosensory Impairments in 366 Healthcare Workers Following COVID-19: An 11-Month Follow-up.", @@ -461615,6 +463452,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.26.21268414", + "rel_title": "Interpretable and Predictive Deep Modeling of the SARS-CoV-2 Spike Protein Sequence", + "rel_date": "2021-12-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.26.21268414", + "rel_abs": "As the COVID-19 pandemic continues, the SARS-CoV-2 virus continues to rapidly mutate and change in ways that impact virulence, transmissibility, and immune evasion. Genome sequencing is a critical tool, as other biological techniques can be more costly, time-consuming, and difficult. However, the rapid and complex evolution of SARS-CoV-2 challenges conventional sequence analysis methods like phylogenetic analysis. The virus picks up and loses mutations independently in multiple subclades, often in novel or unexpected combinations, and, as for the newly emerged Omicron variant, sometimes with long explained branches. We propose interpretable deep sequence models trained by machine learning to complement conventional methods. We apply Transformer-based neural network models developed for natural language processing to analyze protein sequences. We add network layers to generate sample embeddings and sequence-wide attention to interpret models and visualize multiscale patterns. We demonstrate and validate our framework by modeling SARS-CoV-2 and coronavirus taxonomy. We then develop an interpretable predictive model of disease severity that integrates SARS-CoV-2 spike protein sequence and patient demographic variables, using publicly available data from the GISAID database. We also apply our model to Omicron. Based on knowledge prior to the availability of empirical data for Omicron, we predict: 1) reduced neutralization antibody activity (15-50 fold) greater than any previously characterized variant, varying between Omicron sublineages, and 2) reduced risk of severe disease (by 35-40%) relative to Delta. Both predictions are in accord with recent epidemiological and experimental data.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Bahrad A Sokhansanj", + "author_inst": "Drexel University" + }, + { + "author_name": "Zhengqiao Zhao", + "author_inst": "Drexel University" + }, + { + "author_name": "Gail L Rosen", + "author_inst": "Drexel University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.21.21268203", "rel_title": "Home Monitoring for Fever: An Inexpensive Screening Method to Prevent Household Spread of COVID-19", @@ -463234,49 +465098,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.24.21268370", - "rel_title": "A novel methodology for the synchronous collection and multimodal visualisation of continuous neurocardiovascular and neuromuscular physiological data in adults with long COVID", - "rel_date": "2021-12-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.24.21268370", - "rel_abs": "Reports suggest that adults with post-COVID-19 syndrome or long COVID may be affected by orthostatic intolerance syndromes, with autonomic nervous system dysfunction as a possible causal factor of neurocardiovascular instability (NCVI). Long COVID can also manifest as prolonged fatigue, which may be linked to neuromuscular function impairment (NMFI). The current clinical assessment for NCVI monitors neurocardiovascular performance upon the application of orthostatic stressors such as an active (i.e. self-induced) stand or a passive (tilt table) standing test. Lower limb muscle contractions may be important in orthostatic recovery via the skeletal muscle pump. In this study, adults with long COVID were assessed with a protocol that, in addition to the standard NCVI tests, incorporated simultaneous lower limb muscle monitoring for NMFI assessment. To accomplish such an investigation, a wide range of continuous non-invasive biomedical technologies were employed, including digital artery photoplethysmography for the extraction of cardiovascular signals, near-infrared spectroscopy for the extraction of regional tissue oxygenation in brain and muscle, and electromyography for assessment of timed muscle contractions in the lower limbs. With the novel technique described and exemplified in this paper, we were able to integrate signals from all instruments used in the assessment in a precisely synchronized fashion. We demonstrate that it is possible to visualize the interactions between all different physiological signals during the combined NCVI/NMFI assessment. Multiple counts of evidence were collected, which can capture the dynamics between skeletal muscle contractions and neurocardiovascular responses. The proposed multimodal data visualization can offer an overview of the functioning of the muscle pump during both supine rest and orthostatic recovery and can conduct comparison studies with signals from multiple participants at any given time in the assessment. This could help researchers and clinicians generate and test hypotheses based on the multimodal inspection of raw data, in long COVID and other clinical cohorts.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Feng Xue", - "author_inst": "Trinity College Dublin" - }, - { - "author_name": "Ann Monaghan", - "author_inst": "Trinity College Dublin" - }, - { - "author_name": "Glenn Jennings", - "author_inst": "Trinity College Dublin" - }, - { - "author_name": "Lisa Byrne", - "author_inst": "St. James' Hospital, Dublin" - }, - { - "author_name": "Tim Foran", - "author_inst": "St. James' Hospital, Dublin" - }, - { - "author_name": "Eoin Duggan", - "author_inst": "Trinity College Dublin" - }, - { - "author_name": "Roman Romero-Ortuno", - "author_inst": "Trinity College Dublin" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2021.12.23.21268276", "rel_title": "Risk of myocarditis following sequential COVID-19 vaccinations by age and sex", @@ -463441,6 +465262,37 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.12.23.474050", + "rel_title": "SARS-CoV-2 comes up with a perfect recipe for disaster: Each mutation plays a specific role in the evolution of variants of concern", + "rel_date": "2021-12-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.23.474050", + "rel_abs": "Multiple mutations have been seen to undergo convergent evolution in SARS-CoV-2 variants of concern. One such evolution occurs in Beta, Gamma, and Omicron variants at three amino acid positions K417, E484, and N501 in the receptor binding domain of the spike protein. We examined the physical mechanisms underlying the convergent evolution of three mutations K417T/E484K/N501Y by delineating the individual and collective effects of mutations on binding to angiotensin converting enzyme 2 receptor, immune escape from neutralizing antibodies, protein stability and expression. Our results show that each mutation serves a distinct function that improves virus fitness supporting its positive selection, even though individual mutations have deleterious effects that make them prone to negative selection. Compared to the wild-type, K417T escapes Class 1 antibodies, has increased stability and expression; however, it has decreased receptor binding. E484K escapes Class 2 antibodies; however, it has decreased receptor binding, stability and expression. N501Y increases receptor binding; however, has decreased stability and expression. When these mutations come together, the deleterious effects are mitigated due to the presence of compensatory effects. Triple mutant K417T/E484K/N501Y has increased receptor binding, escapes both Class 1 and Class 2 antibodies, and has similar stability and expression as that of the wild-type. These results show the implications of presence of multiple mutations on virus evolution that enhance viral fitness on different fronts by balancing both positive and negative selection and improves the chances of selection of mutations together.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Vaibhav Upadhyay", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Casey Patrick", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Alexandra Lucas", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Krishna Mallela", + "author_inst": "University of Colorado Anschutz Medical Campus" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.12.23.473930", "rel_title": "Human KIR+CD8+ T cells target pathogenic T cells in Celiac disease and are active in autoimmune diseases and COVID-19", @@ -465100,49 +466952,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.23.21268352", - "rel_title": "Early Treatment with fluvoxamine among patients with COVID-19: a cost-consequence model", - "rel_date": "2021-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21268352", - "rel_abs": "BackgroundThree randomized trials have been conducted indicating a clinical benefit of early treatment with fluvoxamine versus placebo for adults with symptomatic COVID-19. We assessed the cost-consequences associated with the use of this early treatment in outpatient populations.\n\nMethodsUsing results from the three completed trials of fluvoxamine vs. placebo for the treatment of COVID-19, we performed a meta-analysis. We conducted a cost-consequence analysis using a decision-model to assess the health system benefits of the avoidance of progression to severe COVID-19. Outcomes of relevance to resource planning decisions in the US and elsewhere, including costs and days of hospitalization avoided, were reported. We constructed a decision-analytic model in the form of a decision tree to evaluate two treatment strategies for high-risk patients with confirmed, symptomatic COVID-19, from the perspective of a third-party payer:(1) treatment with a 10-day course of fluvoxamine (100mg twice daily); (2) current standard-of-care; (3) molnupiravir 5-day course. We used a time horizon of 28 days.\n\nResultsAdministration of fluvoxamine to symptomatic outpatients with COVID-19 at high-risk of developing progression to severe COVID-19 complications is substantially cost-saving in the US, in the amount of $232 per eligible patient, and saves an average of 0.15 hospital days per patient treated is likely to be similarly beneficial in other settings. Fluvoxamine is cost saving in locations where total hospital costs are >$738. Molnupiravir had an additional cost to the healthcare system of $404 per patient treated.\n\nConclusionsFluvoxamine is cost-saving for COVID-19 outpatient therapy.\n\nFundingFastGrants and Rainwater Charitable Foundation", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Fergal P Mills", - "author_inst": "InnomarConsulting" - }, - { - "author_name": "Gilmar Reis", - "author_inst": "CardResearch" - }, - { - "author_name": "Kristian Thorlund", - "author_inst": "McMaster University" - }, - { - "author_name": "Jamie I Forrest", - "author_inst": "Platform Life Sciences" - }, - { - "author_name": "Christina M Guo", - "author_inst": "Platform Life Sciences" - }, - { - "author_name": "David R Boulware", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Edward J Mills", - "author_inst": "McMaster University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2021.12.22.21268045", "rel_title": "Essential Workers COVID-19 Vaccine Hesitancy, Misinformation and Informational Needs in the Republic of North Macedonia.", @@ -465499,6 +467308,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.23.21268319", + "rel_title": "Surveillance and correlation of SARS-CoV-2 viral RNA, antigen, virus isolation, and self-reported symptoms in a longitudinal study with daily sampling", + "rel_date": "2021-12-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21268319", + "rel_abs": "The novel coronavirus pandemic incited unprecedented demand for assays that detect viral nucleic acids, viral proteins, and corresponding antibodies. The 320 molecular diagnostics in receipt of FDA emergency use authorization mainly focus on viral detection; however, no currently approved test can be used to infer infectiousness, i.e., the presence of replicable virus. As the number of tests conducted increased, persistent SARS-CoV-2 RNA positivity by RT-PCR in some individuals led to concerns over quarantine guidelines. To this end, we attempted to design an assay that reduces the frequency of positive test results from individuals who do not shed culturable virus. We describe multiplex quantitative RT-PCR (qRT-PCR) assays that detect genomic RNA (gRNA) and subgenomic RNA (sgRNA) species of SARS-CoV-2, including spike (S), nucleocapsid (N), membrane (M), envelope (E), and ORF8. The absolute copy number of each RNA target was determined in longitudinal specimens from a household transmission study. Calculated viral RNA levels over the 14-day follow up period were compared with antigen testing and self-reported symptoms to characterize the clinical and molecular dynamics of infection and infer predictive values of these qRT-PCR assays relative to culture isolation. When detection of sgS RNA was added to the CDC 2019-Novel Coronavirus Real-Time RT-PCR Diagnostic Panel, we found a qRT-PCR positive result was 98% predictive of a positive culture (negative predictive value was 94%). Our findings suggest sgRNA presence correlates with active infection, may help identify individuals shedding culturable virus, and that similar multiplex assays can be adapted to current and future variants.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Gaston Bonenfant", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Jessica Deyoe", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Terianne Wong", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Carlos G. Grijalva", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "H. Keipp Talbot", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Natasha Halasa", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "James Chappell", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Dan Cui", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Norman Hassell", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Natalie J. Thornburg", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Melissa A. Rolfes", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "David Wentworth", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Bin Zhou", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.22.473478", "rel_title": "Accelerating manufacturing to start large-scale supply of a new adenovirus-vectored vaccine within 100 days", @@ -467097,117 +468973,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.12.21.473594", - "rel_title": "Construction of a potent pan-vaccine based on the evolutionary tendency of SARS-CoV-2 spike protein.", - "rel_date": "2021-12-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.21.473594", - "rel_abs": "SARS-CoV-2 continued to spread globally along with different variants. Here, we systemically analyzed viral infectivity and immune-resistance of SARS-CoV-2 variants to explore the underlying rationale of viral mutagenesis. We found that the Beta variant harbors both high infectivity and strong immune resistance, while the Delta variant is the most infectious with only a mild immune-escape ability. Remarkably, the Omicron variant is even more immune-resistant than the Beta variant, but its infectivity increases only in Vero E6 cells implying a probable preference for the endocytic pathway. A comprehensive analysis revealed that SARS-CoV-2 spike protein evolved into distinct evolutionary paths of either high infectivity plus low immune resistance or low infectivity plus high immune resistance, resulting in a narrow spectrum of the current single-strain vaccine. In light of these findings and the phylogenetic analysis of 2674 SARS-CoV-2 S-protein sequences, we generated a consensus antigen (S6) taking the most frequent mutations as a pan-vaccine against heterogeneous variants. As compared to the ancestry SWT vaccine with significantly declined neutralizations to emerging variants, the S6 vaccine elicits broadly neutralizing antibodies and full protections to a wide range of variants. Our work highlights the importance and feasibility of a universal vaccine strategy to fight against antigen drift of SARS-CoV-2.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Yongliang Zhao", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Wenjia Ni", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Simeng Liang", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Lianghui Dong", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Min Xiang", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Zeng Cai", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University," - }, - { - "author_name": "Danping Niu", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Qiuhan Zhang", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Dehe Wang", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Yucheng Zheng", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Zhen Zhang", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Dan Zhou", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Wenhua Guo", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Yongbing Pan", - "author_inst": "Wuhan Institute of Biological Products Co. Ltd." - }, - { - "author_name": "Xiaoli Wu", - "author_inst": "Wuhan Institute of Biological Products Co. Ltd." - }, - { - "author_name": "Yimin Yang", - "author_inst": "Wuhan Institute of Biological Products Co. Ltd." - }, - { - "author_name": "Zhaofei Jing", - "author_inst": "Wuhan Institute of Biological Products Co. Ltd." - }, - { - "author_name": "Yongzhong Jiang", - "author_inst": "Hubei Provincial Center for Diseases Control and Prevention" - }, - { - "author_name": "- SARS-CoV-2 Vaccine Task Force Group", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University," - }, - { - "author_name": "Yu Chen", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University," - }, - { - "author_name": "Huan Yan", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University," - }, - { - "author_name": "Yu Zhou", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University," - }, - { - "author_name": "Ke Xu", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University," - }, - { - "author_name": "Ke Lan", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University," - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.12.20.473471", "rel_title": "Nucleocapsid 203 mutations enhance SARS-CoV-2 immune evasion", @@ -467456,6 +469221,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.12.22.21268226", + "rel_title": "A systematic review of observational methods used to quantify personal protective behaviours among members of the public during the COVID-19 pandemic, and the concordance between observational and self-report measures in infectious disease health protection", + "rel_date": "2021-12-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268226", + "rel_abs": "ObjectivesTo assess the quantity and quality of studies using an observational measure of behaviour during the COVID-19 pandemic, and to narratively describe the association between self-report and observational data for behaviours relevant to controlling an infectious disease outbreak.\n\nDesignSystematic review and narrative synthesis of observational studies.\n\nData sourcesWe searched Medline, Embase, PsychInfo, Publons, Scopus and the Public Health England behavioural science LitRep database from inception to 17th September 2021 for relevant studies.\n\nStudy selectionWe included studies which collected observational data of at least one of three health protective behaviours (hand hygiene, face covering use and maintaining physical distance from others ( social distancing)) during the COVID-19 pandemic. Studies where observational data were compared to self-report data in relation to any infectious disease were also included.\n\nData extraction and synthesisWe evaluated the quality of studies using the NIH quality assessment scale for observational studies, extracted data on sample size, setting and adherence to health protective behaviours, and synthesized results narratively.\n\nResultsOf 27,279 published papers on COVID-19 relevant health protective behaviours that included one or more terms relating to hand hygiene, face covering and social distancing, we identified 48 studies that included an objective observational measure. Of these, 35 assessed face covering use, 17 assessed hand hygiene behaviour and seven assessed physical distancing. The general quality of these studies was good. When expanding the search to all infectious diseases, we included 21 studies that compared observational versus self-report data. These almost exclusively studied hand hygiene. The difference in outcomes was striking, with self-report over-estimating observed adherence by up to a factor of five in some settings. In only four papers did self-report match observational data in any domains.\n\nConclusionsDespite their importance in controlling the pandemic, we found remarkably few studies assessing protective behaviours by observation, rather than self-report, though these studies tended to be of reasonably good quality. Observed adherence tends to be substantially lower than estimates obtained via self-report. Accurate assessment of levels of personal protective behaviour, and evaluation of interventions to increase this, would benefit from the use of observational methods.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Rachel Davies", + "author_inst": "King's College London" + }, + { + "author_name": "Fiona Mowbray", + "author_inst": "King's College London" + }, + { + "author_name": "Alex F Martin", + "author_inst": "King's College London" + }, + { + "author_name": "Louise E Smith", + "author_inst": "King's College London" + }, + { + "author_name": "G James Rubin", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.23.21268314", "rel_title": "Seroconversion rate after primary vaccination with two doses of BNT162b2 versus mRNA-1273 in solid organ transplant recipients: a systematic review and meta-analysis", @@ -469727,49 +471527,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.16.473063", - "rel_title": "Passage of SARS-CoV-2 in cells expressing human and mouse ACE2 selects for mouse-adapted and ACE2-independent viruses", - "rel_date": "2021-12-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.16.473063", - "rel_abs": "Human ACE2 (hACE2) is the key cell attachment and entry receptor for SARS-CoV-2, with the original SARS-CoV-2 isolates unable to use mouse ACE2 (mACE2). Herein we describe a new system for generating mouse-adapted SARS-CoV-2 in vitro by serial passaging virus in co-cultures of cell lines expressing hACE2 and mACE2. Mouse-adapted viruses emerged with up to five amino acid changes in the spike protein, all of which have been seen in human isolates. Mouse-adapted viruses replicated to high titers in C57BL/6J mouse lungs and nasal turbinates, and caused severe lung histopathology. One mouse-adapted virus was also able to replicate efficiently in ACE2-negative cell lines, with ACE2-independent entry by SARS-CoV-2 representing a new biology for SARS-CoV-2 that has potential widespread implications for disease and intervention development.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Kexin Yan", - "author_inst": "QIMR Berghofer Medical Research Institute" - }, - { - "author_name": "Troy Dumenil", - "author_inst": "QIMR Berghofer Medical Research Institute" - }, - { - "author_name": "Bing Tang", - "author_inst": "QIMR Berghofer Medical Research Institute" - }, - { - "author_name": "Thuy T Le", - "author_inst": "QIMR Berghofer Medical Research Institute" - }, - { - "author_name": "Cameron Bishop", - "author_inst": "QIMR Berghofer Medical Research Institute" - }, - { - "author_name": "Andreas Suhrbier", - "author_inst": "QIMR Berghofer Medical Research Institute" - }, - { - "author_name": "Daniel J Rawle", - "author_inst": "QIMR Berghofer Medical Research Institute" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.12.19.21268042", "rel_title": "Government messaging about COVID-19 vaccination in Canada and Australia: a Narrative Policy Framework study", @@ -469994,6 +471751,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.19.21268069", + "rel_title": "Mutational analysis of SARS-CoV-2. ORF8 and the evolution of the Delta and Omicron variants.", + "rel_date": "2021-12-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.19.21268069", + "rel_abs": "SARS-CoV-2 the virus responsible for the current pandemic. This virus is continually evolving, adapting to both innate and acquired immune responses and therapeutic drugs. Therefore, it is important to understand how the virus evolving to design the appropriate therapeutic and vaccine in preparation for future variants. Here, we used the online SARS-CoV-2 databases, Nextstrain and Ourworld, to map the evolution and epidemiology of the virus. We identified 30 high entropy residues which underwent a progressive evolution to arrive at the current dominant variant - Delta variant. The virus underwent mutational waves with the first wave made up of structural proteins important in its infectivity and the second wave made up of the ORFs important for its contagion. The most important driver of the second wave is ORF8 mutations at residue 119 and 120. Further mutations of these two residues are creating new clades that are offshoots from the Delta backbone. More importantly the further expansion of the S protein in the Omicron variant is now followed with the acquisition of ORF8 mutations 119 and 120. These findings demonstrate how SARS-CoV-2 mutates and points to two evolutionary paths; 1) Mutational expansion on the Delta backbone among the ORFs and 2) Mutational expansion of the S protein on other backbone follow with mutational wave among the ORFs. Both are happening at the same time right now with the Omicron variant early in the first wave to follow with a more aggressive second wave of mutations.\n\nHIGHLIGHTSMutational waves in the evolution of SARS-CoV-2. S protein as the driver of the first wave improving the minimum inhaled viral load required to cause infection and ORF8 mutations 119 and 120 as the driver of the second mutational wave to improve the Contagion Airborne Transmission value.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Gopika Trieu", + "author_inst": "Oncotelic" + }, + { + "author_name": "Vuong N Trieu", + "author_inst": "Oncotelic" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.20.21268048", "rel_title": "Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-CoV-2 virus-like particles", @@ -471916,57 +473696,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.17.21267362", - "rel_title": "The role of airborne transmission in a large single source outbreak of SARS-CoV-2 in a Belgian nursing home in 2020", - "rel_date": "2021-12-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.17.21267362", - "rel_abs": "ObjectivesTo better understand the conditions which have led to one of the largest COVID-19 outbreaks in Belgian nursing homes in 2020.\n\nSettingA nursing home in Flanders, Belgium, which experienced a massive outbreak of COVID-19 after a cultural event. An external volunteer who dressed as a legendary figure visited consecutively the 4 living units and tested positive for SARS-CoV-2 the next day. Within days, residents started to display symptoms and the outbreak spread rapidly within the nursing home.\n\nMethodsWe interviewed key informants and collected standardized data from all residents retrospectively. A batch of 115 positive samples with a Ct value of <37 by qRT-PCR were analysed using whole-genome sequencing. Six months after the outbreak, ventilation assessment of gathering rooms in the nursing home was done using a tracer gas test with calibrated CO2 sensors.\n\nResultsTimeline of diagnoses and symptom onsets clearly pointed to the cultural event as the start of the outbreak, with the volunteer as index case. The genotyping of positive samples depicted the presence of one large cluster, suggesting a single source outbreak.\n\nThe global attack rate among residents was 77% with a significant association between infection and presence at the event. Known risk factors such as short distance to or physical contact with the volunteer, and wearing of a mask during the event were not associated with early infection. The ventilation assessment showed a high background average CO2 level in four main rooms varying from 657 ppm to 846 ppm.\n\nConclusionsOur investigation shows a rapid and widespread single source outbreak of SARS-CoV-2 in a nursing home, in which airborne transmission was the most plausible explanation for the massive intra-facility spread. Our results underscore the importance of ventilation and air quality for the prevention of future outbreaks in closed facilities.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Bea Vuylsteke", - "author_inst": "Institute of Tropical Medicine" - }, - { - "author_name": "Lize Cuypers", - "author_inst": "Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, 3000 Leuven, Belgium" - }, - { - "author_name": "Guy Baele", - "author_inst": "Department of Microbiology and Immunology, Rega Institute, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium" - }, - { - "author_name": "Marianne Stranger", - "author_inst": "Air Quality Measurements, Health Unit, VITO NV, 2400 Mol, Belgium" - }, - { - "author_name": "Sarah Lima Paralovo", - "author_inst": "Air Quality Measurements, Health Unit, VITO NV, 2400 Mol, Belgium" - }, - { - "author_name": "Emmanuel Andre", - "author_inst": "Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, 3000 Leuven, Belgium" - }, - { - "author_name": "Joke Dirks", - "author_inst": "Artsenpraktijk Mol, 2400 Mol" - }, - { - "author_name": "Piet Maes", - "author_inst": "Department of Microbiology and Immunology, Rega Institute, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium" - }, - { - "author_name": "Marie Laga", - "author_inst": "Department of Public Health, Institute of Tropical Medicine, 2000 Antwerp, Belgium" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.18.21267628", "rel_title": "RESISTANCE CONFERRING MUTATIONS IN SARS-CoV-2 DELTA FOLLOWING SOTROVIMAB INFUSION", @@ -472215,6 +473944,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.19.21268070", + "rel_title": "Effectiveness of different booster regimens for preventing infection and adverse outcomes in Puerto Rico", + "rel_date": "2021-12-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.19.21268070", + "rel_abs": "Recent laboratory and observational studies have demonstrated that the COVID-19 vaccine effectiveness wanes over time. In response, several jurisdictions have authorized the administration of booster doses. Since August 13, 2021, Puerto Rico has administered 540,140 booster shots. We used data collected and made public by the Puerto Rico Department of Health (PRDH) to evaluate the effectiveness of four different booster regimens at preventing SARS-CoV-2 laboratory confirmed infections and adverse COVID-19 outcomes. Specifically, we analyzed data from all 115,995 SARS-CoV-2 infections occurring since the vaccination process commenced on December 15, 2020. We combined vaccination status, SARS-CoV-2 test results, and COVID-19 hospitalizations and deaths data, and fit a statistical model that adjusted for time-varying incidence rates and age group, to estimate time-varying vaccine effectiveness against infection and adverse outcomes. We find that, after 6 months, the mRNA-1273 and BNT162b2 effectiveness against infection wanes substantially to 61% (58%-63%) and 36% (34%-39%), respectively, while the Ad26.COV2.S wanes to 35% (31%-39%) after two months. However, after a booster shot of the corresponding initial vaccine manufacturer, effectiveness increased to 87% (83%-91%) and 82% (79%-85%) for mRNA-1273 and BNT162b2, respectively. The effectiveness for Ad26.COV2.S followed by either a mRNA-1273 or BNT162b2 booster increased to 88% (71%-100%), substantially higher than 65% (59%-70%), the peak effectiveness reached with just one shot. We also found that heterologous booster regimens restored effectiveness. Furthermore, we did not observe waning after two months of the booster shot. Finally, we found that all booster regimens provided increased protection against COVID-19 hospitalizations and deaths. Code and data to reproduce the analyses are provided here: https://github.com/rafalab/booster-eff-pr.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Rafael A Irizarry", + "author_inst": "Dana-Farber Cancer Institute" + }, + { + "author_name": "Monica M Robles Fontan", + "author_inst": "CDC Foundation-Puerto Rico Department of Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.20.21268095", "rel_title": "Worldwide clustering and infection cycles as universal features of multiscale stochastic processes in the SARS-CoV-2 pandemic", @@ -473826,33 +475578,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.16.473030", - "rel_title": "Modeling the dynamics of within-host viral infection and evolution predicts quasispecies distributions and phase boundaries separating distinct classes of infections", - "rel_date": "2021-12-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.16.473030", - "rel_abs": "We use computational modeling to study within-host viral infection and evolution. In our model, viruses exhibit variable binding to cells, with better infection and replication countered by a stronger immune response and a high rate of mutation. By varying host conditions (permissivity to viral entry T and immune clearance intensity A) for large numbers of cells and viruses, we study the dynamics of how viral populations evolve from initial infection to steady state and obtain a phase diagram of the range of cell and viral responses. We find three distinct replicative strategies corresponding to three physiological classes of viral infections: acute, chronic, and opportunistic. We show similarities between our findings and the behavior of real viral infections such as common flu, hepatitis, and SARS-CoV-2019. The phases associated with the three strategies are separated by a phase transition of primarily first order, in addition to a crossover region. Our simulations also reveal a wide range of physical phenomena, including metastable states, periodicity, and glassy dynamics. Lastly, our results suggest that the resolution of acute viral disease in patients whose immunity cannot be boosted can only be achieved by significant inhibition of viral infection and replication.\n\nAuthor summaryVirus, in particular RNA viruses, often produce offspring with slightly altered genetic composition. This process occurs both across host populations and within a single host over time. Here, we study the interactions of viruses with cells inside a host over time. In our model, the viruses encounter host cell defenses characterized by two parameters: permissivity to viral entry T and immune response A). The viruses then mutate upon reproduction, eventually resulting in a distribution of related viral types termed a quasi-species distribution. Across varying host conditions (T, A), three distinct viral quasi-species types emerge over time, corresponding to three classes of viral infections: acute, chronic and opportunistic. We interpret these results in terms of real viral types such as common flu, hepatitis, and also SARS-CoV-2019. Analysis of viral of viral mutant populations over a wide range of permissivity and immunity, for large numbers of cells and viruses, reveals phase transitions that separate the three classes of viruses, both in the infection-cycle dynamics and at steady state. We believe that such a multiscale approach for the study of within-host viral infections, spanning individual proteins to collections of cells, can provide insight into developing more effective therapies for viral disease.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Greyson R Lewis", - "author_inst": "UCSF Biophysics Graduate Group" - }, - { - "author_name": "Wallace F Marshall", - "author_inst": "UCSF, Center for Cellular Construction, Chan Zuckerberg Biohub" - }, - { - "author_name": "Barbara A Jones", - "author_inst": "IBM Research - Almaden" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.12.17.473179", "rel_title": "Disrupted Peyer's patch microanatomy in COVID-19 including germinal centre atrophy independent of local virus", @@ -474125,6 +475850,109 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.12.17.473170", + "rel_title": "Structure prediction of the druggable fragments in SARS-CoV-2 untranslated regions", + "rel_date": "2021-12-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.17.473170", + "rel_abs": "The outbreak of the COVID-19 pandemic has led to intensive studies of both the structure and replication mechanism of SARS-CoV-2. In spite of some secondary structure experiments being carried out, the 3D structure of the key function regions of the viral RNA has not yet been well understood. At the beginning of COVID-19 breakout, RNA-Puzzles community attempted to envisage the three-dimensional structure of 5'- and 3'-Un-Translated Regions (UTRs) of the SARS-CoV-2 genome. Here, we report the results of this prediction challenge, presenting the methodologies developed by six participating groups and discussing 100 RNA 3D models (60 models of 5'-UTR and 40 of 3'-UTR) predicted through applying both human experts and automated server approaches. We describe the original protocol for the reference-free comparative analysis of RNA 3D structures designed especially for this challenge. We elaborate on the deduced consensus structure and the reliability of the predicted structural motifs. All the computationally simulated models, as well as the development and the testing of computational tools dedicated to 3D structure analysis, are available for further study.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Julita Gumna", + "author_inst": "Institute of Bioorganic Chemistry, Polish Academy of Sciences" + }, + { + "author_name": "Maciej Antczak", + "author_inst": "Institute of Computing Science, Poznan University of Technology" + }, + { + "author_name": "Ryszard Walenty Adamiak", + "author_inst": "Institute of Bioorganic Chemistry, Polish Academy of Sciences" + }, + { + "author_name": "Janusz Marek Bujnicki", + "author_inst": "Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw" + }, + { + "author_name": "Shi-Jie Chen", + "author_inst": "Department of Physics, Department of Biochemistry, and Institute of Data Science and Informatics, University of Missouri-Columbia" + }, + { + "author_name": "Feng Ding", + "author_inst": "Department of Physics and Astronomy, Clemson University" + }, + { + "author_name": "Pritha Ghosh", + "author_inst": "Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw" + }, + { + "author_name": "Jun Li", + "author_inst": "Department of Physics, Department of Biochemistry, and Institute of Data Science and Informatics, University of Missouri-Columbia" + }, + { + "author_name": "Sunandan Mukherjee", + "author_inst": "Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw" + }, + { + "author_name": "Chandran Nithin", + "author_inst": "Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw" + }, + { + "author_name": "Katarzyna Pachulska-Wieczorek", + "author_inst": "Institute of Bioorganic Chemistry, Polish Academy of Sciences" + }, + { + "author_name": "Almudena Ponce-Salvatierra", + "author_inst": "Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw" + }, + { + "author_name": "Mariusz Popenda", + "author_inst": "Institute of Bioorganic Chemistry, Polish Academy of Sciences" + }, + { + "author_name": "Joanna Sarzynska", + "author_inst": "Institute of Bioorganic Chemistry, Polish Academy of Sciences" + }, + { + "author_name": "Tomasz Wirecki", + "author_inst": "Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw" + }, + { + "author_name": "Dong Zhang", + "author_inst": "Department of Physics, Department of Biochemistry, and Institute of Data Science and Informatics, University of Missouri-Columbia" + }, + { + "author_name": "Sicheng Zhang", + "author_inst": "Department of Physics, Department of Biochemistry, and Institute of Data Science and Informatics, University of Missouri-Columbia" + }, + { + "author_name": "Tomasz Zok", + "author_inst": "Institute of Computing Science, Poznan University of Technology" + }, + { + "author_name": "Eric Westhof", + "author_inst": "CNRS Institute of Molecular and Cellular Biology, University of Strasbourg" + }, + { + "author_name": "Marta Szachniuk", + "author_inst": "Institute of Computing Science, Poznan University of Technology" + }, + { + "author_name": "Zhichao Miao", + "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute" + }, + { + "author_name": "Agnieszka Rybarczyk", + "author_inst": "Institute of Computing Science, Poznan University of Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.12.17.472912", "rel_title": "Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic.", @@ -475476,53 +477304,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.17.21267996", - "rel_title": "Antibody Responses to 3rd Dose mRNA Vaccines in Nursing Home and Assisted Living Residents", - "rel_date": "2021-12-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.17.21267996", - "rel_abs": "A comparison of SARS-CoV-2 wild-type and the beta variant virus neutralization capacity between 2 and 3 mRNA vaccine series in nursing home residents, and between nursing home and assisted living residents strongly supports 3rd dose vaccine recommendations, and equivalent polices for nursing homes and assisted living settings. Findings suggest that residents mount a robust humoral response to a 3rd mRNA vaccination, and have greater neuralization capacity compared to a 2 dose series.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ali Zhang", - "author_inst": "Michael G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada" - }, - { - "author_name": "Jessica A Breznik", - "author_inst": "McMaster Immunology Research Centre, McMaster University Hamilton, ON, Canada" - }, - { - "author_name": "Rumi Clare", - "author_inst": "Department of Medicine, Michael G. DeGroote School of Medicine McMaster University Hamilton, ON, Canada" - }, - { - "author_name": "Ishac Nazy", - "author_inst": "Department of Medicine, Michael G. DeGroote School of Medicine McMaster University Hamilton, ON, Canada" - }, - { - "author_name": "Matthew S Miller", - "author_inst": "Michael G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada" - }, - { - "author_name": "Dawn M.E. Bowdish", - "author_inst": "McMaster Immunology Research Centre, McMaster University Hamilton, ON, Canada" - }, - { - "author_name": "Andrew P Costa", - "author_inst": "Department of Health Research Methods Evidence, and Impact, McMaster University Hamilton, Canada" - }, - { - "author_name": "- COVID-in-LTC Study Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.15.472838", "rel_title": "A third vaccination with a single T cell epitope protects against SARS-CoV-2 infection in the absence of neutralizing antibodies", @@ -475783,6 +477564,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2021.12.16.21267934", + "rel_title": "Predictors of SARS-CoV-2 infection in a multi-ethnic cohort of United Kingdom healthcare workers: a prospective nationwide cohort study (UK-REACH)", + "rel_date": "2021-12-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.16.21267934", + "rel_abs": "IntroductionHealthcare workers (HCWs), particularly those from ethnic minority groups, have been shown to be at disproportionately higher risk of infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) compared to the general population. However, there is insufficient evidence on how demographic and occupational factors influence infection risk among ethnic minority HCWs.\n\nMethodsWe conducted a cross-sectional analysis using data from the United Kingdom Research study into Ethnicity And COVID-19 Outcomes in Healthcare workers (UK-REACH) cohort study. We used logistic regression to examine associations of demographic, household and occupational predictor variables with SARS-CoV-2 infection (defined by PCR, serology or suspected COVID-19) in a diverse group of HCWs.\n\nResults2,496 of the 10,772 HCWs (23.2%) who worked during the first UK national lockdown in March 2020 reported previous SARS-CoV-2 infection. In an adjusted model, demographic and household factors associated with increased odds of infection included younger age, living with other key workers and higher religiosity. Important occupational risk factors associated with increased odds of infection included attending to a higher number of COVID-19 positive patients (aOR 2.49, 95%CI 2.03-3.05 for [≥]21 patients per week vs none), working in a nursing or midwifery role (1.35, 1.15- 1.58, compared to doctors), reporting a lack of access to personal protective equipment (1.27, 1.15 - 1.41) and working in an ambulance (1.95, 1.52-2.50) or hospital inpatient setting (1.54, 1.37 - 1.74). Those who worked in Intensive Care Units were less likely to have been infected (0.76, 0.63-0.90) than those who did not. Black HCWs were more likely to have been infected than their White colleagues, an effect which attenuated after adjustment for other known predictors.\n\nConclusionsWe identified key sociodemographic and occupational risk factors associated with SARS-CoV-2 infection amongst UK HCWs, and have determined factors that might contribute to a disproportionate odds of infection in HCWs from Black ethnic groups. These findings demonstrate the importance of social and occupational factors in driving ethnic disparities in COVID-19 outcomes, and should inform policies, including targeted vaccination strategies and risk assessments aimed at protecting HCWs in future waves of the COVID-19 pandemic.\n\nTrial registrationISRCTN 11811602", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Christopher A Martin", + "author_inst": "University of Leicester" + }, + { + "author_name": "Daniel Pan", + "author_inst": "University of Leicester" + }, + { + "author_name": "Carl Melbourne", + "author_inst": "University of Leicester" + }, + { + "author_name": "Lucy Teece", + "author_inst": "University of Leicester" + }, + { + "author_name": "Avinash Aujayeb", + "author_inst": "Northumbria Specialist Emergency Care Hospital" + }, + { + "author_name": "Rebecca F Baggaley", + "author_inst": "University of Leicester" + }, + { + "author_name": "Luke Bryant", + "author_inst": "University of Leicester" + }, + { + "author_name": "Sue Carr", + "author_inst": "General Medical Council" + }, + { + "author_name": "Bindu Gregary", + "author_inst": "Royal Preston Hospital" + }, + { + "author_name": "Amit Gupta", + "author_inst": "Oxford University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Anna Louise Guyatt", + "author_inst": "University of Leicester" + }, + { + "author_name": "Catherine John", + "author_inst": "University of Leicester" + }, + { + "author_name": "Chris McManus", + "author_inst": "University College London" + }, + { + "author_name": "Joshua Nazareth", + "author_inst": "University of Leicester" + }, + { + "author_name": "Laura B Nellums", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Rubina Reza", + "author_inst": "Derbyshire Healthcare NHS Foundation Trust" + }, + { + "author_name": "Sandra Simpson", + "author_inst": "Nottinghamshire Healthcare NHS Foundation Trust" + }, + { + "author_name": "Martin D Tobin", + "author_inst": "University of Leicester" + }, + { + "author_name": "Katherine Woolf", + "author_inst": "University College London" + }, + { + "author_name": "Stephen Zingwe", + "author_inst": "Berkshire Healthcare NHS Foundation Trust" + }, + { + "author_name": "Kamlesh Khunti", + "author_inst": "University of Leicester" + }, + { + "author_name": "Keith R Abrams", + "author_inst": "University of Warwick" + }, + { + "author_name": "Laura J Gray", + "author_inst": "University of Leicester" + }, + { + "author_name": "Manish Pareek", + "author_inst": "University of Leicester" + }, + { + "author_name": "- UK-REACH Study Collaborative Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.16.21267912", "rel_title": "Prolonged Detection of SARS CoV2 RNA in Extracellular Vesicles in Nasal Swab RT-PCR Negative Patients", @@ -477566,57 +479462,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.17.21267655", - "rel_title": "Presentation, characteristics, treatments and outcomes of mechanically ventilated patients with COVID-19 in Bulgaria", - "rel_date": "2021-12-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.17.21267655", - "rel_abs": "BackgroundThe first surge of coronavirus disease 2019 (COVID-19) cases in Bulgaria occurred in the fall of 2020. Here we describe the clinical presentation, patient characteristics, treatments and outcomes of mechanically ventilated COVID-19 patients in a newly formed COVID-19 ICU at a tertiary cardiac center in Sofia, Bulgaria.\n\nMethodsThis is a retrospective observational study of mechanically ventilated COVID-19 patients admitted to Sveta Ekaterina University Hospital in Sofia, Bulgaria, between November 4th, 2020 and January 6th, 2021. Data were collected from electronic and written patient records and charts.\n\nResultsWe identified 38 critical care patients admitted with respiratory failure and treated with mechanical ventilation at our COVID-19 ICU during this period. The median age was 66 (IQR 57-76, range 27-89) and 74% were male. Most patients, 36 (95%), had at least one comorbidity. The most common comorbidities were hypertension, valvular heart disease, ischemic heart disease and diabetes mellitus. Overall, 27 (71%) patients had a concomitant cardiac disease other than hypertension and 24% were recent cardiac surgical patients. Inotropic support was required in 29 (76%) patients, renal replacement therapy in 12 (32%) patients and prone positioning and ECMO were used in 5 (13%) and 2 (5%) patients respectively. The median duration of mechanical ventilation was 7.5 (IQR 5-14) days overall and 9 (IQR 6-13) days for survivors. At 30-days 28 (74%) of patients had died. Overall, 32 (84%) patients died in hospital and only 6 (16%) patients were discharged home.\n\nConclusionsDuring the first major surge of COVID-19 cases in Bulgaria, despite the wave arriving later than in other countries, the healthcare system was largely unprepared. In our setting, mortality in mechanically ventilated patients was very high at 84%. Several factors might have contributed to these results, namely the predominance of cardiovascular comorbidities in our patient population, the strained ICU capacity and the lack of medical personnel.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Neda Bakalova", - "author_inst": "Sveta Ekaterina University Hospital" - }, - { - "author_name": "Ivats Natsev", - "author_inst": "Sveta Ekaterina University Hospital" - }, - { - "author_name": "Hristo Damov", - "author_inst": "Sveta Ekaterina University Hospital" - }, - { - "author_name": "Irina Yatsenko", - "author_inst": "Sveta Ekaterina University Hospital" - }, - { - "author_name": "Stefanija Jovinska", - "author_inst": "Sveta Ekaterina University Hospital" - }, - { - "author_name": "Rostislav Enev", - "author_inst": "Sveta Ekaterina University Hospital" - }, - { - "author_name": "Mikhail Cholakov", - "author_inst": "Sveta Ekaterina University Hospital" - }, - { - "author_name": "Filip Abedinov", - "author_inst": "Sveta Ekaterina University Hospital" - }, - { - "author_name": "Denitza Kalendjieva", - "author_inst": "Sveta Ekaterina University Hospital" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2021.12.16.472920", "rel_title": "Amyloidogenesis of SARS-CoV-2 Spike Protein", @@ -477789,6 +479634,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.14.21267800", + "rel_title": "A Cloth Facemask Causes No Major Respiratory or Cardiovascular Perturbations during Moderate to Heavy Exercise", + "rel_date": "2021-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267800", + "rel_abs": "ObjectivesTo investigate whether wearing a cloth facemask could affect physiological and perceptual responses to exercise at distinct exercise intensities in non-trained men and women.\n\nMethodsIn a crossover design, participants (17 men and 18 women) underwent a progressive square-wave test at four intensities (i. at 80% of the ventilatory anerobic threshold [80%VAT]; ii. at VAT; iii. at the respiratory compensation point [RCP]; iv. at exercise peak [Peak] to exhaustion), with or without a triple-layered cloth mask (Mask or No-Mask). Several physiological, metabolic and perceptual measures were analyzed.\n\nResultsMask reduced inspiratory capacity at all exercise intensities vs. No-Mask (p<0.0001), irrespective of sex. Mask reduced respiratory frequency vs. No-Mask (p=0.001) at Peak (-8.3 breaths{middle dot}min-1; CI: -5.8, -10.8), RCP (-6.9 breaths{middle dot}min-1; CI: -4.6, -9.2) and VAT (-6.5 breaths{middle dot}min-1; CI: -4.1, -8.8), but not at Baseline or at 80%VAT. Mask also reduced tidal volume (p<0.0001) at both RCP (-0.5L; CI: -0.3, -0.6) and Peak (-0.8L; CI: -0.6, -0.9), but not at Baseline, 80%VAT or VAT. Shallow breathing index was increased with Mask at Peak compared to No-Mask (11.3; CI: 7.5, 15.1), but not at any other intensities. Mask did not change heart rate, lactate, ratings of perceived exertion, blood pressure or oxygen saturation.\n\nConclusionsWearing a cloth facemask during exercise at moderate to heavy intensities is unlikely to incur significant respiratory or cardiovascular changes, irrespective of sex. These data can inform new exercise recommendations for health during the COVID-19 pandemic and debunk unfounded allegations of harmful effects of masks during exercise. ClinicalTrials.gov: NCT04887714\n\nWhat are the new findings?{checkmark} Using a progressive square-wave test, we showed that wearing a cloth facemask during exercise increased breathing difficulty, but this was dependent upon the exercise intensity.\n{checkmark}Respiratory variables (e.g., inspiratory capacity, respiratory frequency, shallow breathing index) were affected at higher rather than lower intensities.\n{checkmark}Mask wearing did not change heart rate, lactate, ratings of perceived exertion, blood pressure or oxygen saturation at any exercise intensity.\n{checkmark}There were no substantial sex differences on the effects of mask wearing during exercise.\n\n\nHow might it impact on clinical practice in the future?{checkmark} These data can debunk unfounded allegations on harmful effects of masks during exercise, and help inform new exercise recommendations for health during the COVID-19 pandemic, particularly where facemasks remain necessary.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Natalia Mendes Guardieiro", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Gabriel Barreto", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Felipe Miguel Marticorena", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Tamires Nunes Oliveira", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Luana Farias de Oliveira", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Ana Lucia de Sa Pinto", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Danilo Marcelo Leite do Prado", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Bryan Saunders", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Bruno Gualano", + "author_inst": "University of Sao Paulo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "sports medicine" + }, { "rel_doi": "10.1101/2021.12.14.21267806", "rel_title": "REACT-1 round 15 final report: Increased breakthrough SARS-CoV-2 infections among adults who had received two doses of vaccine, but booster doses and first doses in children are providing important protection", @@ -479240,33 +481136,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.12.14.21267742", - "rel_title": "Impact of Population Mixing Between a Vaccinated Majority and Unvaccinated Minority on Disease Dynamics. Implications for SARS-CoV-2", - "rel_date": "2021-12-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267742", - "rel_abs": "BackgroundThe speed of vaccine development has been a singular achievement during the SARS-CoV-2 pandemic, though uptake has not been universal. Vaccine opponents often frame their opposition in terms of the rights of the unvaccinated. Our objective was to explore the impact of mixing of vaccinated and unvaccinated populations on risk among vaccinated individuals.\n\nMethodsWe constructed a simple Susceptible-Infectious-Recovered (SIR) compartmental model of a respiratory infectious disease with two connected sub-populations: vaccinated individuals and unvaccinated individuals. We simulated a spectrum of patterns of mixing between vaccinated and unvaccinated groups that ranged from random mixing to like-with-like mixing (complete assortativity), where individuals preferentially have contact with others with the same vaccination status. We evaluated the dynamics of an epidemic within each subgroup, and in the population as a whole.\n\nResultsThe relative risk of infection was markedly higher among unvaccinated individuals than among vaccinated individuals. However, the contact-adjusted contribution of unvaccinated individuals to infection risk during the epidemic was disproportionate, with unvaccinated individuals contributing to infections among the vaccinated at a rate higher than would have been expected based on contact numbers alone. As assortativity increased, attack rates among the vaccinated decreased, but the contact-adjusted contribution to risk among vaccinated individuals derived from contact with unvaccinated individuals increased.\n\nInterpretationWhile risk associated with avoiding vaccination during a virulent pandemic accrues chiefly to the unvaccinated, the choices of unvaccinated individuals impact the health and safety of vaccinated individuals in a manner disproportionate to the fraction of unvaccinated individuals in the population.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ashleigh Tuite", - "author_inst": "University of Toronto" - }, - { - "author_name": "Afia Amoako", - "author_inst": "University of Toronto" - }, - { - "author_name": "David Fisman", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.14.21267199", "rel_title": "The COVID-19 pandemic amplified long-standing racial disparities in the United States criminal justice system", @@ -479815,6 +481684,165 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.15.21267805", + "rel_title": "Booster of mRNA-1273 Vaccine Reduces SARS-CoV-2 Omicron Escape from Neutralizing Antibodies", + "rel_date": "2021-12-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.15.21267805", + "rel_abs": "The Omicron variant of SARS-CoV-2 is raising concerns because of its increased transmissibility and potential for reduced susceptibility to antibody neutralization. To assess the potential risk of this variant to existing vaccines, serum samples from mRNA-1273 vaccine recipients were tested for neutralizing activity against Omicron and compared to neutralization titers against D614G and Beta in live virus and pseudovirus assays. Omicron was 41-84-fold less sensitive to neutralization than D614G and 5.3-7.4-fold less sensitive than Beta when assayed with serum samples obtained 4 weeks after 2 standard inoculations with 100 {micro}g mRNA-1273. A 50 {micro}g boost increased Omicron neutralization titers and may substantially reduce the risk of symptomatic vaccine breakthrough infections.", + "rel_num_authors": 36, + "rel_authors": [ + { + "author_name": "Nicole Doria-Rose", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Xiaoying Shen", + "author_inst": "DUKE UNIVERSITY MEDICAL CENTER" + }, + { + "author_name": "Stephen D Schmidt", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Sijy O'Dell", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Charlene McDanal", + "author_inst": "Duke University Medical Center" + }, + { + "author_name": "Wenhong Feng", + "author_inst": "Duke University Medical Center" + }, + { + "author_name": "Jin Tong", + "author_inst": "Duke University Medical Center" + }, + { + "author_name": "Amanda Eaton", + "author_inst": "Duke University Medical Center" + }, + { + "author_name": "Maha Maglinao", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Haili Tang", + "author_inst": "Duke University Medical Center" + }, + { + "author_name": "Kelly E Manning", + "author_inst": "Emory University" + }, + { + "author_name": "Venkata-Viswanadh Edara", + "author_inst": "Emory University" + }, + { + "author_name": "Linlin Lai", + "author_inst": "Emory University" + }, + { + "author_name": "Madison Ellis", + "author_inst": "Emory University" + }, + { + "author_name": "Kathryn Moore", + "author_inst": "Emory University" + }, + { + "author_name": "Katharine Floyd", + "author_inst": "Emory University" + }, + { + "author_name": "Stephanie L Foster", + "author_inst": "Emory University" + }, + { + "author_name": "Robert L Atmar", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Kirsten E Lyke", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Tongqing Zhou", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Lingshu Wang", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "yi Zhang", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Martin R Gaudinski", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Walker P Black", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Ingelise Gordon", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Mercy Guech", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Julie E Ledgerwood", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "John N Misasi", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Alicia Widge", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Paul C Roberts", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "John Beigel", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Bette Korber", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Rolando Pajon", + "author_inst": "Moderna Inc." + }, + { + "author_name": "John R Mascola", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Mehul S Suthar", + "author_inst": "Emory University" + }, + { + "author_name": "David C Montefiori", + "author_inst": "Duke University Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.14.472513", "rel_title": "Metalloproteinase-dependent and TMPRSS2-independnt cell surface entry pathway of SARS-CoV-2 requires the furin-cleavage site and the S2 domain of spike protein", @@ -481485,121 +483513,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.12.15.21267834", - "rel_title": "Comparison of the Immunogenicity of five COVID-19 vaccines in Sri Lanka", - "rel_date": "2021-12-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.15.21267834", - "rel_abs": "We assessed antibody responses 3 months post-vaccination in those who received mRNA-1273 (n=225), Sputnik V (n=128) or the first dose of Gam-COVID-Vac (n=184) and compared the results with previously reported data of Sinopharm and AZD1222 vaccinees. 99.5% of Moderna >94% of AZD1222 or Sputnik V, 72% to 76% of Gam-COVID-Vac (first dose) and 38.1% to 68.3% of Sinopharm vaccinees had ACE2 blocking antibodies above the positive threshold. The ACE2 blocking antibody levels were highest to lowest was Moderna > Sputnik V/ AZD1222 (had equal levels)> first dose of Gam-COVID-Vac > Sinopharm. All Moderna recipients had antibodies above the positive threshold to the ancestral (WT), B.1.1.7, B.1.351.1 and 80% positivity rate for B.1.617.2. Positivity rates of Sputnik V vaccinees for WT and variants, were higher than AZD1222 vaccinees, while Sinopharm vaccinees had the lowest positivity rates (<16.7%). These findings highlight the need for further studies to understand the effects on clinical outcomes.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Chandima Jeewandara", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Inoka Aberathna", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Saubhagya Danasekara", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Laksiri Gomes", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Suranga Fernando", - "author_inst": "Ministry of Health, Sri Lanka" - }, - { - "author_name": "Dinuka Guruge", - "author_inst": "Colombo Municipal Council, Colombo, Sri Lanka." - }, - { - "author_name": "Thushali Ranasinghe", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Banuri Gunasekara", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Achala Kamaladasa", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Heshan Kuruppu", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Gayasha Somathilaka", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Jeewantha Jayamali", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Deshni Jayathilaka", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Helanka Wijayathilake", - "author_inst": "Ministry of Health, Sri Lanka" - }, - { - "author_name": "Pradeep Pushpakumara", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Michael Harvie", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Thashmi Nimasha", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Shiromi de Silva", - "author_inst": "Colombo Municipal Council, Colombo, Sri Lanka" - }, - { - "author_name": "Ruwan Wijayamuni", - "author_inst": "Colombo Municipal Council, Colombo, Sri Lanka." - }, - { - "author_name": "Lisa Schimanski", - "author_inst": "Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.\"" - }, - { - "author_name": "Pramila Rijal", - "author_inst": "Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK." - }, - { - "author_name": "Jack Tan", - "author_inst": "Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK." - }, - { - "author_name": "Alain Townsend", - "author_inst": "University of Oxford" - }, - { - "author_name": "Graham Ogg", - "author_inst": "MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK." - }, - { - "author_name": "Gathsaurie Neelika Malavige", - "author_inst": "University of Sri Jayewardenepura" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.12.14.21267460", "rel_title": "Differential Risk of SARS-CoV-2 Infection by Occupation: Evidence from the Virus Watch prospective cohort study in England and Wales", @@ -481892,6 +483805,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.12.14.21267818", + "rel_title": "Performances of community pharmacists and community pharmacies during COVID-19 outbreak: a cross-sectional study", + "rel_date": "2021-12-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267818", + "rel_abs": "BackgroundCommunity pharmacists can play an important role in the management of coronavirus disease-19 (COVID-19) outbreak by providing pharmaceutical care and education services. In addition to providing drug-related services, community pharmacies must take measures to reduce the risk of COVID-19 transmission to customers and technicians in pharmacy. Therefore, a study was designed to assess community pharmacists performance and community pharmacies preparedness during COVID-19 outbreak.\n\nMaterials & MethodsA cross-sectional study was conducted in Kerman, Iran. A 20-item checklist consisting of nine items assessing the practice of pharmacists regarding use of personal protective equipment (PPE) and education of people about routes of transmission, prophylaxis and treatment of COVID-19 and eleven items evaluating the adherence of pharmacies to principles of reducing the risk of COVID-19 transmission in public places was used.\n\nResultsOf 95 enrolled pharmacists, 55 (57.9%) were female and 78.9% had work experience [≤] 10 years. More than 90% of pharmacists used appropriate PPE and provided information about medications for prevention and treatment of COVID-19 and routs of its transmission to the pharmacy customers. Phone consultation was done by 71.6% of pharmacists. Concerning the preparedness of pharmacies, 92% of personnel used PPE, and hand sanitizers were available in 89.5% of pharmacies. However, a clear sheet was not placed at counters in the majority of pharmacies, and home delivery services were not provided by most pharmacies.\n\nConclusionsThe practice of most community pharmacists was acceptable. However, stricter measures should be taken to diminish the probability of COVID-19 transmission in community pharmacies.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Afsaneh Sadeghinejad", + "author_inst": "Kerman University of Medical Sciences" + }, + { + "author_name": "Naemeh Nikvarz", + "author_inst": "Kerman University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2021.12.14.21267713", "rel_title": "Transmission of SARS-CoV-2 by children and young people in households and schools: a meta-analysis of population-based and contact-tracing studies", @@ -483751,49 +485687,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.13.21267657", - "rel_title": "Simple decision rules to predict local surges in COVID-19 hospitalizations during the winter and spring of 2022", - "rel_date": "2021-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.13.21267657", - "rel_abs": "Low rates of vaccination, emergence of novel variants of SARS-CoV-2, and increasing transmission relating to seasonal changes leave many U.S. communities at risk for surges of COVID-19 during the winter and spring of 2022 that might strain hospital capacity, as in previous waves. The trajectories of COVID-19 hospitalizations during this period are expected to differ across communities depending on their age distributions, vaccination coverage, cumulative incidence, and adoption of risk mitigating behaviors. Yet, existing predictive models of COVID-19 hospitalizations are almost exclusively focused on national- and state-level predictions. This leaves local policymakers in urgent need of tools that can provide early warnings about the possibility that COVID-19 hospitalizations may rise to levels that exceed local capacity. In this work, we develop simple decision rules to predict whether COVID-19 hospitalization will exceed the local hospitalization capacity within a 4- or 8-week period if no additional mitigating strategies are implemented during this time. These decision rules use real-time data related to hospital occupancy and new hospitalizations associated with COVID-19, and when available, genomic surveillance of SARS-CoV-2. We showed that these decision rules present reasonable accuracy, sensitivity, and specificity (all [≥]80%) in predicting local surges in hospitalizations under numerous simulated scenarios, which capture substantial uncertainties over the future trajectories of COVID-19 during the winter and spring of 2022. Our proposed decision rules are simple, visual, and straightforward to use in practice by local decision makers without the need to perform numerical computations.\n\nSignificance StatementIn many U.S. communities, the risk of exceeding local healthcare capacity during the winter and spring of 2022 remains substantial since COVID-19 hospitalizations may rise due to seasonal changes, low vaccination coverage, and the emergence of new variants of SARS-CoV-2, such as the omicron variant. Here, we provide simple and easy-to-communicate decision rules to predict whether local hospital occupancy is expected to exceed capacity within a 4- or 8-week period if no additional mitigating measures are implemented. These decision rules can serve as an alert system for local policymakers to respond proactively to mitigate future surges in the COVID-19 hospitalization and minimize risk of overwhelming local healthcare capacity.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Reza Yaesoubi", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Shiying You", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Qin Xi", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Nicolas A Menzies", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Ashleigh Tuite", - "author_inst": "University of Toronto Dalla Lana School of Public Health" - }, - { - "author_name": "Yonatan Grad", - "author_inst": "Harvard T. H. Chan School of Public Health" - }, - { - "author_name": "Joshua A Salomon", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.12.21267681", "rel_title": "COVID-19 in French Nursing Homes during the Second Pandemic Wave: A Mixed-Methods Cross-Sectional Study", @@ -483986,6 +485879,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.14.472240", + "rel_title": "In silico evidence of superantigenic features in ORF8 protein from COVID-19", + "rel_date": "2021-12-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.14.472240", + "rel_abs": "Very early on COVID-19 pandemic outbreak, it was noted that the some of the virus-induced clinical conditions resembled features of toxaemia caused by the toxic shock syndrome toxin type 1, which is a soluble superantigen produced by Staphylococcus aureus. Among all SARS proteins, the ORF8 protein from SARS-2 virus is significantly different from other known SARS-like coronaviruses, and therefore could exhibit unique pathogenic properties. We assess if ORF8 protein bears super antigenic features using in silico tools. We show that ORF8 has properties of an extracellular soluble protein and shares a significant degree of amino acid sequence identity with toxic shock syndrome toxin. Besides, docking and binding affinity analyses between monomeric and homodimeric ORF-8 with V{beta} 2.1 and TRBV11-2 reveal strong interaction and high binding affinity. ORF8-TRBV11-2 strong interaction can contribute to the observed clonal expansion of that chain during COVID-19-associated multisystem inflammatory syndrome. Taken together, the evidence presented here supports the hypothesis that ORF8 protein from SARS-2 bears super antigenic properties.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Guillermo Gomez-Icazbalceta", + "author_inst": "Xanthu Bioresearch Center. Medellin, Antioquia. Colombia" + }, + { + "author_name": "Zubair Hussain", + "author_inst": "National Institute for Biotechnology and Genetic Engineering. Faisalabad, Punjab. Pakistan" + }, + { + "author_name": "Marcela Velez-Alavez", + "author_inst": "VELKOVET Veterinary Research Center. Mexico City. Mexico" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.13.21267670", "rel_title": "Third BNT162b2 vaccination neutralization of SARS-CoV-2 Omicron infection", @@ -485645,65 +487565,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.10.21267613", - "rel_title": "The impact of remote home monitoring of people with COVID-19 using pulse oximetry: a national population and observational study.", - "rel_date": "2021-12-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.10.21267613", - "rel_abs": "BackgroundRemote home monitoring of people testing positive for COVID-19 using pulse oximetry was implemented across England during the Winter of 2020/21 to identify falling blood oxygen saturation levels at an early stage. This was hypothesised to enable earlier hospital admission, reduce the need for intensive care and improve survival. This study is an evaluation of the clinical effectiveness of the pre-hospital monitoring programme, COVID oximetry @home (CO@h).\n\nMethodsWe analysed relationships at a geographical area level between the extent to which people aged 65 or over were enrolled onto the programme and outcomes over the period between November 2020 to February 2021\n\nFindingsFor every 10% increase in coverage of the programme, mortality was reduced by 2% (95% confidence interval: -4% to 1%), admissions increased by 3% (-1% to 7%), in-hospital mortality fell by 3% (-8% to 3%) and lengths of stay increased by 1{middle dot}8% (-1{middle dot}2% to 4{middle dot}9%). None of these results are statistically significant.\n\nInterpretationThere are several possible explanations for our findings. One is that the CO@h did not have the hypothesised impact. Another is that the low rates of enrolment and incomplete data in many areas reduced the chances of detecting any impact that may have existed. Also, CO@h has been implemented in many different ways across the country and these may have had varying levels of effect.\n\nFundingThis is independent research funded by the National Institute for Health Research, Health Services & Delivery Research programme (RSET Project no. 16/138/17; BRACE Project no. 16/138/31) and NHSEI. NJF is an NIHR Senior Investigator. The views expressed in this publication are those of the authors and not necessarily those of the National Institute for Health Research or the Department of Health and Social Care.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSExisting evidence before this study and the search strategy used to obtain this evidence has been published previously by the authors in a systematic review. Previous quantitative studies have assessed remote oximetry monitoring services for COVID-19 patients mostly at individual sites and focussed on their safety. However, their effectiveness has been little studied. This may reflect the challenges of identifying reliable counterfactuals during a rapidly evolving pandemic.\n\nAdded value of this studyThis study is part of a wider mixed methods evaluation that followed the rapid implementation of remote monitoring across the English NHS during the Winter of 2020/21. It adds to the evidence of the effectiveness of such programmes at a national level.\n\nImplications of the available evidenceThere is some existing evidence that remote monitoring of COVID-19 patients can be locally effective although we have not been able to replicate such findings at a wider level. Missing data and lower coverage of the service than expected may have influenced our results, and the effectiveness of some local programmes could have been lost among the analysis of national data. Future implementation requires better data collection strategies which could be focussed within fewer local areas, and effective learning from areas that have achieved better population coverage.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Christopher Sherlaw-Johnson", - "author_inst": "Nuffield Trust" - }, - { - "author_name": "Theo Georghiou", - "author_inst": "Nuffield Trust" - }, - { - "author_name": "Steve Morris", - "author_inst": "Cambridge University" - }, - { - "author_name": "Nadia Crellin", - "author_inst": "Nuffield Trust" - }, - { - "author_name": "Ian Litchfield", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Efthalia Massou", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Manbinder Sidhu", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Sonila Tomini", - "author_inst": "University College London" - }, - { - "author_name": "Cecilia Vindrola-Padros", - "author_inst": "University College London" - }, - { - "author_name": "Holly Walton", - "author_inst": "University College London" - }, - { - "author_name": "Naomi Fulop", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.11.21267259", "rel_title": "Time-Varying Mortality Risk Suggests Increased Impact of Thrombosis in Hospitalized Covid-19 Patients", @@ -485968,6 +487829,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.12.11.21267652", + "rel_title": "Symptoms persisting after hospitalization for COVID-19: 12 months interim results of the COFLOW study", + "rel_date": "2021-12-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.11.21267652", + "rel_abs": "IntroductionA large proportion of patients experiences a wide range of sequelae after acute COVID-19 infection, especially after severe illness. The long-term health sequelae need to be assessed. Our objective was to longitudinally assess persistence of symptoms and clusters of symptoms up to 12 months after hospitalization for COVID-19, and to assess determinants of the main persistent symptoms.\n\nMethodsIn this multicenter prospective cohort study patients with COVID-19 are followed up for 2 years with measurements at 3, 6, 12, and 24 months after hospital discharge. Here, we present interim results regarding persistent symptoms up to 12 months. Symptoms were clustered into physical, respiratory, cognitive and fatigue symptoms.\n\nResultsWe included 492 patients; mean age was 60.2{+/-}10.7 years, 335 (68.1%) males, median length of hospital stay 11 (6.0-27.0) days. At 3 months after discharge 97.0% of the patients had at least 1 persisting symptom, this declined to 95.5% and 92.0% at 6 and 12 months, respectively (p=0.010). Muscle weakness, exertional dyspnea, fatigue, and memory and concentration problems were the most prevalent symptoms with rates over 50% during follow-up. Over time, muscle weakness, hair loss, and exertional dyspnea decreased significantly (p<0.001), while other symptoms, such as fatigue, concentration and memory problems, anosmia, and ageusia persisted. Symptoms from the physical and respiratory cluster declined significantly over time, in contrast to symptoms from the fatigue and cognitive clusters. Female gender was the most important predictor of persistent symptoms and co-occurrence of symptoms from all clusters. Shorter hospital stay and treatment with steroids were related with decreased muscle weakness; comorbidity and being employed were related with increased fatigue; and shorter hospital stay and comorbidity were related with memory problems.\n\nConclusionThe majority of patients experienced COVID-19 sequelae up to 12 months after hospitalization. Whereas physical and respiratory symptoms showed slow gradual decline, fatigue and cognitive symptoms did not evidently resolve over time. This finding stresses the importance of finding the underlying causes and effective treatments for post-COVID condition, beside adequate COVID-19 prevention.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Martine Bek", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Julia C Berentschot", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Majanka Heijenbrok", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Susanne Huijts", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Michel E van Genderen", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Johan H Vlake", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Jasper van Bommel", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Joachim G.J.V. Aerts", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Gerard M Ribbers", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Rita J.G. van den Berg", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Merel E Hellemons", + "author_inst": "Erasmus MC" + }, + { + "author_name": "- CO-FLOW collaboration Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.12.12.21267518", "rel_title": "Immunogenic epitope panel for accurate detection of non-cross-reactive T cell response to SARS-CoV-2", @@ -487511,93 +489435,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.08.21267452", - "rel_title": "Accuracy and usability of saliva and nasal rapid antigen self-testing for detection of SARS-CoV-2 infection in the general population: a head-to-head comparison", - "rel_date": "2021-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.08.21267452", - "rel_abs": "BackgroundSARS-CoV-2 self-tests may lower the threshold of testing and produce a result quickly. This could support the early detection of infectious cases and reduce further community transmission. However, the diagnostic accuracy of (unsupervised) self-testing with rapid antigen diagnostic tests (Ag-RDTs) is mostly unknown. We therefore conducted a large-scale head-to-head comparison of the diagnostic accuracy of a self-performed SARS-CoV-2 saliva and nasal Ag-RDT, each compared to a molecular reference test, in the general population in the Netherlands.\n\nMethodsIn this cross-sectional study we consecutively included individuals aged 16 years and older presenting for SARS-CoV-2 testing at three Dutch public health service test sites irrespective of their indication for testing, vaccination status, and symptomatology. Participants were sampled for molecular testing at the test site and received two self-tests (the Hangzhou AllTest saliva self-test and the SD Biosensor nasal self-test by Roche Diagnostics) to perform at home within a few hours without knowledge of their molecular test result. Information on presence and type of symptoms, user experiences, and results of both self-tests were collected via an online questionnaire. For each self-test, sensitivity, specificity, positive and negative predictive values were determined with molecular testing as reference standard.\n\nFindingsThe SARS-CoV-2 molecular reference test positivity rate was 6.5% in the 2,819 participants. Overall sensitivities with 95% confidence intervals were 46.7% (85/182; 39.3%-54.2%) for the saliva Ag-RDT, and 68.9% (124/180; 61.6%-75.6%) for the nasal Ag-RDT. With a viral load cut-off ([≥]5.2 log10 SARS-CoV-2 E-gene copies/mL) as a proxy of infectiousness, sensitivities increased to 54.9% (78/142; 46.4%-63.3%) for the saliva Ag-RDT and 83.9% (120/143; 76.9%-89.5%) for the nasal Ag-RDT.\n\nFor the nasal Ag-RDT, sensitivities were 78.5% [71.1%-84.8%] and 22.6% [9.6%-41.1%] in those with and without symptoms at the time of sampling, which increased to 90.4% (113/125; 83.8%-94.9%) and 38.9% (7/18; 17.3%-64.3%) after applying the viral load cut-off. In those with and without prior confirmed SARS-CoV-2, sensitivities were 36.8% [19/372; 16.3%-61.6%] and 72.7% [161/2437; 65.1%-79.4%] for the nasal Ag-RDT, which increased to 100% (7/7; 59.0%-100%) and 83.1% (113/126; 75.7%-89.0%) after applying the viral load cut-off.\n\nThe diagnostic accuracy of the nasal Ag-RDT did not differ by COVID-19 vaccination status, sex, and age. Specificities were >99%, positive predictive values >70% and negative predictive values >95%, for the saliva Ag-RDT, and >99%, >90%, and >95% for the nasal Ag-RDT, respectively, in most analyses.\n\nInterpreting the results was considered (very) easy for both self-tests.\n\nInterpretationThe Hangzhou AllTest self-performed saliva Ag-RDT is not reliable for SARS-CoV-2 infection detection overall nor in the studied subgroups. The SD Biosensor self-performed nasal Ag-RDT had high sensitivity in individuals with symptoms and in those without a prior SARS-CoV-2 infection. The overall accuracy in individuals with symptoms was comparable to that found in previous studies with professional sampling for this Ag-RDT. The extremely low sensitivity of the nasal Ag-RDT in asymptomatic individuals and in individuals who had had a prior SARS-CoV-2 infection is an important finding and warrants further investigation.\n\nFundingDutch Ministry of Health, Welfare, and Sport.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Ewoud Schuit", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Roderick P Venekamp", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Irene K Veldhuijzen", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Wouter van den Bijllaardt", - "author_inst": "Amphia Hospital" - }, - { - "author_name": "Suzan D Pas", - "author_inst": "Bravis Hospital" - }, - { - "author_name": "Joep J.J.J.M. Stohr", - "author_inst": "Amphia Hospital" - }, - { - "author_name": "Esther B Lodder", - "author_inst": "Public Health Service West-Brabant" - }, - { - "author_name": "Marloes Hellwich", - "author_inst": "Public Health Service Hart voor Brabant" - }, - { - "author_name": "Richard Molenkamp", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Zsofia Igloi", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Constantijn Wijers", - "author_inst": "Public Health Service Rotterdam-Rijnmond" - }, - { - "author_name": "Irene H Vroom", - "author_inst": "Public Health Service Rotterdam-Rijnmond" - }, - { - "author_name": "Carla R S Nagel-Imming", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Wanda G H Han", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Jan A J Kluytmans", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Susan van den Hof", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Janneke H H M Van de Wijgert", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Karel G M Moons", - "author_inst": "University Medical Center Utrecht" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.09.21267539", "rel_title": "Food for thought: Eating before saliva collection and interference with SARS-CoV-2 detection", @@ -487898,6 +489735,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.10.21267363", + "rel_title": "Exploring selection bias in COVID-19 research: Simulations and prospective analyses of two UK cohort studies", + "rel_date": "2021-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.10.21267363", + "rel_abs": "BackgroundNon-random selection into analytic subsamples could introduce selection bias in observational studies of SARS-CoV-2 infection and COVID-19 severity (e.g. including only those have had a COVID-19 PCR test). We explored the potential presence and impact of selection in such studies using data from self-report questionnaires and national registries.\n\nMethodsUsing pre-pandemic data from the Avon Longitudinal Study of Parents and Children (ALSPAC) (mean age=27.6 (standard deviation [SD]=0.5); 49% female) and UK Biobank (UKB) (mean age=56 (SD=8.1); 55% female) with data on SARS-CoV-2 infection and death-with-COVID-19 (UKB only), we investigated predictors of selection into COVID-19 analytic subsamples. We then conducted empirical analyses and simulations to explore the potential presence, direction, and magnitude of bias due to selection when estimating the association of body mass index (BMI) with SARS-CoV-2 infection and death-with-COVID-19.\n\nResultsIn both ALSPAC and UKB a broad range of characteristics related to selection, sometimes in opposite directions. For example, more educated participants were more likely to have data on SARS-CoV-2 infection in ALSPAC, but less likely in UKB. We found bias in many simulated scenarios. For example, in one scenario based on UKB, we observed an expected odds ratio of 2.56 compared to a simulated true odds ratio of 3, per standard deviation higher BMI.\n\nConclusionAnalyses using COVID-19 self-reported or national registry data may be biased due to selection. The magnitude and direction of this bias depends on the outcome definition, the true effect of the risk factor, and the assumed selection mechanism.\n\nKey messagesO_LIObservational studies assessing the association of risk factors with SARS-CoV-2 infection and COVID-19 severity may be biased due to non-random selection into the analytic sample.\nC_LIO_LIResearchers should carefully consider the extent that their results may be biased due to selection, and conduct sensitivity analyses and simulations to explore the robustness of their results. We provide code for these analyses that is applicable beyond COVID-19 research.\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Louise Amanda Claire Millard", + "author_inst": "University of Bristol" + }, + { + "author_name": "Alba Fernandez-Sanles", + "author_inst": "University of Bristol" + }, + { + "author_name": "Alice R Carter", + "author_inst": "Medical Research Council Integrative Epidemiology Unit, University of Bristol" + }, + { + "author_name": "Rachael Hughes", + "author_inst": "University of Bristol" + }, + { + "author_name": "Kate Tilling", + "author_inst": "University of Bristol" + }, + { + "author_name": "Tim P Morris", + "author_inst": "UCL" + }, + { + "author_name": "Daniel Smith", + "author_inst": "University of Bristol" + }, + { + "author_name": "Gareth J Griffith", + "author_inst": "University of Bristol" + }, + { + "author_name": "Gemma L Clayton", + "author_inst": "University of Bristol" + }, + { + "author_name": "Emily Kawabata", + "author_inst": "University of Bristol" + }, + { + "author_name": "George Davey Smith", + "author_inst": "University of Bristol" + }, + { + "author_name": "Deborah A Lawlor", + "author_inst": "University of Bristol" + }, + { + "author_name": "Maria Carolina Borges", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.09.21267571", "rel_title": "Coronavirus (COVID-19) Spike in Georgia: An Epidemiologic Study of Data, Modelling, and Policy Implications to Understand the Gender-and Race-Specific Variations", @@ -489601,61 +491505,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.12.09.21267203", - "rel_title": "Reduced Odds of SARS-CoV-2 Reinfection after Vaccination among New York City Adults, June-August 2021", - "rel_date": "2021-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.09.21267203", - "rel_abs": "BackgroundBelief in immunity from prior infection and concern that vaccines might not protect against new variants are contributors to vaccine hesitancy. We assessed effectiveness of full and partial COVID-19 vaccination against reinfection when Delta was the predominant variant in New York City.\n\nMethodsWe conducted a case-control study in which case-patients with reinfection during June 15- August 31, 2021 and control subjects with no reinfection were matched (1:3) on age, sex, timing of initial positive test in 2020, and neighborhood poverty level. Conditional logistic regression was used to calculate matched odds ratios (mOR) and 95% confidence intervals (CI).\n\nResultsOf 349,598 adult residents who tested positive for SARS-CoV-2 infection in 2020, did not test positive again >90 days after initial positive test through June 15, 2021, and did not die before June 15, 2021, 1,067 were reinfected during June 15-August 31, 2021. Of 1,048 with complete matching criteria data, 499 (47.6%) were known to be symptomatic for COVID-19-like-illness, and 75 (7.2%) were hospitalized. Unvaccinated individuals, compared with fully vaccinated individuals, had elevated odds of reinfection (mOR, 2.23; 95% CI, 1.90, 2.61), of symptomatic reinfection (mOR, 2.17; 95% CI, 1.72, 2.74), and of reinfection with hospitalization (mOR, 2.59; 95% CI, 1.43, 4.69). Partially versus fully vaccinated individuals had 1.58 (95% CI: 1.22, 2.06) times the odds of reinfection. All three vaccines authorized or approved for use in the U.S. were similarly effective.\n\nConclusionAmong adults with previous SARS-CoV-2 infection, vaccination reduced odds of reinfections when the Delta variant predominated.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Alison Levin-Rector", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Lauren Firestein", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Emily McGibbon", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Jessica Sell", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Sungwoo Lim", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Ellen H. Lee", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Don Weiss", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Anita Geevarughese", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Jane R. Zucker", - "author_inst": "New York City Department of Health and Mental Hygiene; Centers for Disease Control and Protection" - }, - { - "author_name": "Sharon K. Greene", - "author_inst": "New York City Department of Health and Mental Hygiene" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.09.21267355", "rel_title": "Estimating Active Cases of COVID-19", @@ -490000,6 +491849,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.06.21266926", + "rel_title": "Opening up safely: public health system requirements for ongoing COVID-19 management based on evaluation of Australia's surveillance system performance", + "rel_date": "2021-12-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.06.21266926", + "rel_abs": "BackgroundOngoing management of COVID-19 requires an evidence-based understanding of the performance of public health measures to date, and application of this evidence to evolving response objectives. This paper aims to define system requirements for COVID-19 management under future transmission and response scenarios, based on surveillance system performance to date.\n\nMethodsFrom 1st November 2020 to 30th June 2021 community transmission was eliminated in Australia, allowing investigation of system performance in detecting novel outbreaks, including against variants of concern (VoCs). We characterised surveillance systems in place from peer-reviewed and publicly available data, analysed the epidemiological characteristics of novel outbreaks over this period, and assessed surveillance system sensitivity and timeliness in outbreak detection. These findings were integrated with analysis of other critical COVID-19 public health measures to establish requirements for future COVID-19 management.\n\nFindingsAustralia reported 25 epidemiologically distinct outbreaks and 5 distinct clusters of cases in the study period, all linked through genomic sequencing to breaches in quarantine facilities housing international travellers. Most (21/30, 70%) were detected through testing of those with acute respiratory illness in the community, and 9 through quarantine screening. For the 21 detected in the community, the testing rate (percent of the total State population tested in the week preceding detection) was 2.07% on average, was higher for those detected while prior outbreaks were ongoing. For 17/30 with data, the delay from the primary case to detection of the index case was, on average 4.9 days, with 10 of the 17 outbreaks detected within 5 days and 3 detected after > 7days. One outbreak was preceded by an unexpected positive wastewater detection. Of the 24 outbreaks in 2021, 20 had publicly available sequencing data, all of which were VoCs. Surveillance for future VoCs using a similar strategy to that used for detecting SARS-CoV-2 to date would necessitate a 100-1,000-fold increase in capacity for genomic sequencing.\n\nInterpretationAustralias surveillance systems performed well in detecting novel introduction of SARS-CoV-2 in a period when community transmission was eliminated, introductions were infrequent and case numbers were low. Detection relied on community surveillance in symptomatic members of the general population and quarantine screening, supported by comprehensive genomic sequencing. Once vaccine coverage is maximised, the priority for future COVID-19 control will shift to detection of SARS-CoV-2 Vos associated with increased severity of disease in the vaccinated and vaccine ineligible. This will require ongoing investment in maintaining surveillance systems and testing of all international arrivals, alongside greatly increased genomic sequencing capacity. Other essential requirements for managing voices are maintaining outbreak response capacity and developing capacity to rapidly engineer, manufacture, and distribute variant vaccines at scale. The most important factor in management of COVID-19 now and into the future will continue to be how effectively governments support all sectors of the community to engage in control measures.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Kamalini Lokuge", + "author_inst": "National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia" + }, + { + "author_name": "Emily Banks", + "author_inst": "National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia" + }, + { + "author_name": "Tatum Street", + "author_inst": "National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia" + }, + { + "author_name": "Sydney Jantos", + "author_inst": "National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia" + }, + { + "author_name": "Mohana Baptista", + "author_inst": "Department of Health, Victoria, Australia" + }, + { + "author_name": "Kathryn Glass", + "author_inst": "National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.06.21262384", "rel_title": "A descriptive analysis of 2020 California Occupational Safety and Health Administration COVID-19-related complaints", @@ -491507,29 +493395,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.12.08.21267167", - "rel_title": "Access to healthcare as an important moderating variable for understanding geography of immunity levels for COVID-19 - preliminary insights from Poland", - "rel_date": "2021-12-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.08.21267167", - "rel_abs": "BackgroundBiases in COVID-19 burden and uncertainty in estimation of the corresponding epidemiologic indexes is a known and common phenomenon in infectious diseases. We investigated to what extent healthcare access (HCA) related supply/demand interfered with registered data on COVID-19 in Poland.\n\nMaterial and methodsWe run a multiple linear regression model with interactions to explain geographic variation in seroprevalence, hospitalizations (on voivodeship - NUTS-2 level) and current (beginning of the 4th wave - 15.09-21.11.2021) case notifications/crude mortality (on poviat - old NUTS-4 level). We took vaccination coverage and cumulative case notifications up to the so called 3rd wave as predictor variables and supply/demand (HCA) as moderating variables.\n\nResultsHCA with interacting terms (mainly demand) explained to the great extent the variance of current incidence and most variance of current mortality. HCA (mainly supply) is significantly moderating cumulative case notifications till the 3rd wave explaining the variance in seroprevalence and hospitalization.\n\nConclusionsSeeking causal relations between vaccination-or infection-gained immunity level and current infection dynamics could be misleading without understanding socio-epidemiologic context such as the moderating role of HCA (sensu lato). After quantification, HCA could be incorporated into epidemiologic models for improved prediction of real disease burden.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Andrzej Jarynowski", - "author_inst": "Institute for Interdisciplinary Research" - }, - { - "author_name": "Vitaly Belik", - "author_inst": "FU Berlin" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.09.21267516", "rel_title": "Changes in the trajectory of Long Covid symptoms following COVID-19 vaccination: community-based cohort study", @@ -491702,6 +493567,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.09.21267295", + "rel_title": "Population Optimally Immunized after Accounting for Type-Specific COVID-19 Vaccine Waning Intervals: State-Level Prevalence and Trends", + "rel_date": "2021-12-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.09.21267295", + "rel_abs": "BACKGROUNDCOVID-19 vaccines exhibit real-world waning effectiveness against SARS-CoV-2 infection within the first 3-6 months after a completed series. Consequently, the main metric tracked by the CDC (percent \"fully vaccinated,\" with no adjustment for booster status) has become insufficiently informative.\n\nMETHODSWe analyzed CDC daily vaccination data to quantify COVID-19 immunization status for 4 mutually-exclusive groups: (1) not immunized; (2) partially immunized (people who received the 1st dose of a 2-dose series); (3) immunized with waning immunity (previously immunized people whose booster dose is overdue); and (4) optimally immunized (people who: (a) received the Janssen vaccine <2 months ago or completed an mRNA vaccine series <6 months ago, or (b) received the Janssen vaccine >2 months ago or completed an mRNA vaccine series >6 months ago and received a booster dose.)\n\nRESULTSThe proportion of the total US population who were optimally immunized against COVID-19 fell from a high of 45.3% on July 17 to 29.4% on November 30. During November, the majority of states experienced a worsening trend in the percent of the total population who were overdue for a booster dose, including the 4 largest states, with percentage point increases of 3.5 in New York, 3.4 in California, 2.3 in Texas and 1.7 in Florida.\n\nCONCLUSIONSOur proposed classification scheme accounts for type-specific vaccine waning intervals, provides an accurate assessment of progress toward national immunization goals, and reveals the urgent need for additional public health mitigation strategies to successfully combat the COVID-19 pandemic in the United States.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Elizabeth B Pathak", + "author_inst": "Women's Institute for Independent Social Enquiry" + }, + { + "author_name": "Jason L Salemi", + "author_inst": "University of South Florida College of Public Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.08.21267494", "rel_title": "Omicron strain spreads with the doubling time of 3.2-3.6 days in South Africa province of Gauteng that achieved herd immunity to Delta variant", @@ -493025,53 +494913,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2021.12.08.21267459", - "rel_title": "Genetic overlap between idiopathic pulmonary fibrosis and COVID-19", - "rel_date": "2021-12-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.08.21267459", - "rel_abs": "Genome-wide association studies (GWAS) of coronavirus disease 2019 (COVID-19) and idiopathic pulmonary fibrosis (IPF) have identified genetic loci associated with both traits, suggesting possible shared biological mechanisms. Using updated GWAS of COVID-19 and IPF, we evaluated the genetic overlap between these two diseases and identified four genetic loci (including one novel) with likely shared causal variants between severe COVID-19 and IPF. Although there was a positive genetic correlation between COVID-19 and IPF, two of these four shared genetic loci had an opposite direction of effect. IPF-associated genetic variants related to telomere dysfunction and spindle assembly showed no association with COVID-19 phenotypes. Together, these results suggest there are both shared and distinct biological processes driving IPF and severe COVID-19 phenotypes.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Richard J Allen", - "author_inst": "University of Leicester" - }, - { - "author_name": "Beatriz Guillen-Guio", - "author_inst": "University of Leicester" - }, - { - "author_name": "Emma Croot", - "author_inst": "University of Leicester" - }, - { - "author_name": "Luke M Kraven", - "author_inst": "University of Leicester" - }, - { - "author_name": "Samuel Moss", - "author_inst": "Imperial College London" - }, - { - "author_name": "Iain Stewart", - "author_inst": "Imperial College London" - }, - { - "author_name": "R Gisli Jenkins", - "author_inst": "Imperial College London" - }, - { - "author_name": "Louise V Wain", - "author_inst": "University of Leicester" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.12.08.21266760", "rel_title": "Humoral and cellular responses to SARS-CoV-2 vaccination in patients with lymphoid malignancies", @@ -493428,6 +495269,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.08.21267353", + "rel_title": "The challenge of limited vaccine supplies: impact of prior infection on anti-spike IgG antibody trajectories after a single COVID-19 vaccination", + "rel_date": "2021-12-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.08.21267353", + "rel_abs": "Given high SARS-CoV-2 incidence, coupled with slow and inequitable vaccine roll-out, there is an urgent need for evidence to underpin optimum vaccine deployment, aiming to maximise global population immunity at speed. We evaluate whether a single vaccination in previously infected individuals generates similar initial and subsequent antibody responses to two vaccinations in those without prior infection. We compared anti-spike IgG antibody responses after a single dose of ChAdOx1, BNT162b2, or mRNA-1273 SARS-CoV-2 vaccines in the COVID-19 Infection Survey in the UK general population. In 100,849 adults who received at least one vaccination, 13,404 (13.3%) had serological and/or PCR evidence of prior infection. Prior infection significantly boosted antibody responses for all three vaccines, producing a higher peak level and longer half-life, and a response comparable to those without prior infection receiving two vaccinations. In those with prior infection, median time above the positivity threshold was estimated to last for >1 year after the first dose. Single-dose vaccination targeted to those previously infected may provide protection in populations with high rates of previous infection faced with limited vaccine supply, as an interim measure while vaccine campaigns are scaled up.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Jia Wei", + "author_inst": "University of Oxford" + }, + { + "author_name": "Philippa Matthews", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nicole Stoesser", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ian Diamond", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Ruth Studley", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Emma Rourke", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Duncan Cook", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "John Bell", + "author_inst": "University of Oxford" + }, + { + "author_name": "John Newton", + "author_inst": "Public Health England" + }, + { + "author_name": "Jeremy Farrar", + "author_inst": "Wellcome Trust" + }, + { + "author_name": "Alison Howarth", + "author_inst": "University of Oxford" + }, + { + "author_name": "Brian Marsden", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sarah Hoosdally", + "author_inst": "University of Oxford" + }, + { + "author_name": "Yvonne Jones", + "author_inst": "University of Oxford" + }, + { + "author_name": "David Stuart", + "author_inst": "University of Oxford" + }, + { + "author_name": "Derrick W Crook", + "author_inst": "NIHR Oxford Biomedical Research Centre" + }, + { + "author_name": "tim E peto", + "author_inst": "oxford university" + }, + { + "author_name": "Ann Sarah Walker", + "author_inst": "University of Oxford" + }, + { + "author_name": "David W Eyre", + "author_inst": "University of Oxford" + }, + { + "author_name": "Koen B Pouwels", + "author_inst": "University of Oxford" + }, + { + "author_name": "- COVID-19 Infection Survey team", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.07.21267204", "rel_title": "Outbreak of COVID-19 among vaccinated and unvaccinated homeless shelter residents- Sonoma County, California, July 2021", @@ -495119,73 +497059,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.07.21267293", - "rel_title": "SPECIFIC DETECTION OF SARS-COV-2 B.1.1.529 (OMICRON) VARIANT BY FOUR RT-qPCR DIFFERENTIAL ASSAYS", - "rel_date": "2021-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.07.21267293", - "rel_abs": "In this report, we describe four RT-qPCR assays that enable rapid identification of the newly emerging SARS-COV-2 Omicron (B.1.1.529) variant of concern. The assays target Omicron characteristic mutations in the nsp6 (Orf1a), spike and nucleocapsid genes. We demonstrate that the assays are straightforward to assemble and perform, are amendable for multiplexing, and may be used as a reliable first-line tool to identify B.1.1.529 suspected samples. Importantly, this is a preliminary development report. Further validation and optimization of the assays described herein will be published hereafter.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "ORAN ERSTER", - "author_inst": "Israel Central Virology laboratory" - }, - { - "author_name": "Adi Beth Din", - "author_inst": "Israel Institute for Biological Research" - }, - { - "author_name": "Hadar Asraf", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Virginia Levy", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Areej Kabat", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Batya Mannasse", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Roberto Azar", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Ohad Shifman", - "author_inst": "Israel Institute for Biological Research" - }, - { - "author_name": "shirley Lazar", - "author_inst": "Israel Institute for Biological Research" - }, - { - "author_name": "Michal Mandelboim", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel, School of Public Health, Sackler Faculty" - }, - { - "author_name": "Shay Fleishon", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Ella Mendelson", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel, School of Public Health, Sackler Faculty" - }, - { - "author_name": "Neta S Zuckerman", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.04.471153", "rel_title": "Elucidating design principles for engineering cell-derived vesicles to inhibit SARS-CoV-2 infection", @@ -495350,6 +497223,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.07.21267415", + "rel_title": "Covid-19 social distancing: when less is more", + "rel_date": "2021-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.07.21267415", + "rel_abs": "Covid-19 is the first digitally documented pandemic in history, presenting a unique opportunity to learn how to best deal with similar crises in the future. In this study we have carried out a model-based evaluation of the effectiveness of social distancing, using Austria and Slovenia as examples. Whereas the majority of comparable studies have postulated a negative relationship between the stringency of social distancing (reduction in social contacts) and the scale of the epidemic, our model has suggested a sinusoidal relationship, with tipping points at which the system changes its predominant regime from less social distancing - more cumulative deaths and infections to less social distancing - fewer cumulative deaths and infections. This relationship was found to persist in scenarios with distinct seasonal variation in transmission and limited national intensive care capabilities. In such situations, relaxing social distancing during low transmission seasons (spring and summer) was found to relieve pressure from high transmission seasons (fall and winter) thus reducing the total number of infections and fatalities. Strategies that take into account this relationship could be particularly beneficial in situations where long-term containment is not feasible.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Christian Neuwirth", + "author_inst": "Interfaculty Department of Geoinformatics - Z GIS, University of Salzburg, Salzburg, Austria" + }, + { + "author_name": "Christoph Gruber", + "author_inst": "Center for Computational Material Science, Institute of Applied Physics, Vienna University of Technology, Vienna, Austria" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.07.21267073", "rel_title": "A Scaling Law for PCR Positivity in the COVID Second Wave", @@ -497017,57 +498913,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2021.12.06.21267339", - "rel_title": "Systematic review of cardiac adverse effects in children and young people un-der 18 years of age after SARS-CoV-2 vaccination", - "rel_date": "2021-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.06.21267339", - "rel_abs": "BackgroundReports of myocarditis and pericarditis following vaccination with mRNA vaccines for SARS-CoV-2 have occurred after countries began vaccinating adolescents. We undertook a systematic review of cardiac adverse effects associated with SARS-CoV-2 vaccine in children and young people (CYP)< 18 years.\n\nMethodsSystematic review with protocol prospectively registered with PROSPERO (CRD42021275380).\n\nSix electronic databases were searched from 1 December 2019 to 14 September 2021. Eligible studies were those reporting on CYP with reported or proven myocarditis, pericarditis and/or myopericarditis associated with vaccination against SARS-CoV-2. We summarized findings across all clinical cases reported in case report / case series studies. As a number of studies reported data from two publicly available vaccine surveillance systems, we updated estimates of reporting rates for cardiac adverse events up to 31 October for the US Vaccine Adverse Event Reporting System (VAERS) and 13 November for EudraVigilance covering European Union and European Economic Area (EUEA) countries.\n\nResultsTwenty-one studies were included from 338 identified records. Seventeen were case reports/series describing a total of 127 CYP. Three studies described reporting rates from passive surveillance databases (VAERS, EudraVigilance, and the WHO VigiBase) and one described 22 cases from the US Vaccine Safety Datalink (VSD).\n\nClinical series reported that 99.2% presented with chest pain, 100% had raised troponin and 73.8% had an abnormal ECG. Cardiovascular magnetic resonance (CMR) in 91 cases identified myocardial injury in 61.5%, with 90.1% showing late gadolinium enhancement. NSAIDs were the most common treatment (76.0%).\n\nOne US dataset (VSD) estimated a significant excess of 29.6 events per million vaccine doses across both sexes and doses. There were 1129 reports of myocarditis and 358 reports of pericarditis from across the USA and EU/EEA. The VAERS reporting rate per million for myocarditis was 12.4 for boys and 1.4 for girls after the first dose, and 49.6 for boys and 6.1 for girls after the second dose. There was a marked trend for VAERS reporting to be highest soon after initiation of the vaccine schedule, suggesting reporting bias.\n\nConclusionsCardiac adverse effects are very rare after mRNA vaccination for COVID-19 in CYP <18 years. The great majority of cases are mild and self-limiting without significant treatment. No data are yet available on children under 12 years. Larger detailed longitudinal studies are urgently needed from active surveillance sources.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Joana Cruz", - "author_inst": "University College of London" - }, - { - "author_name": "Amedine Duret", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Rachel Harwood", - "author_inst": "Alder Hey in the Park" - }, - { - "author_name": "Lorna K. Fraser", - "author_inst": "Martin House Research Centre, University of York" - }, - { - "author_name": "Caroline B. Jones", - "author_inst": "Alder Hey Childrens Hospital Liverpool" - }, - { - "author_name": "Joseph Ward", - "author_inst": "UCL Great Ormond St. Institute of Child Health" - }, - { - "author_name": "Elizabeth Whittaker", - "author_inst": "Faculty of Medicine, Imperial College London" - }, - { - "author_name": "Simon E Kenny", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Russell M Vinner", - "author_inst": "UCL Great Ormond St. Institute of Child Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.12.06.21267391", "rel_title": "The Impact of Mass Exodus on the Resurgence of COVID19 Cases: Study Case of Regions in Indonesia", @@ -497216,6 +499061,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.12.01.21267121", + "rel_title": "Impact of COVID-19 on healthcare access for Australian adolescents and young adults", + "rel_date": "2021-12-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.01.21267121", + "rel_abs": "BackgroundAccess to healthcare for young people is essential to build the foundation for a healthy life. We investigated the factors associated with healthcare access by Australian young adults during and before the COVID-19 pandemic.\n\nMethodsWe included 1110 youths using two recent data collection waves from the Longitudinal Study of Australian Children (LSAC). Data were collected during COVID-19 in 2020 for Wave 9C1 and before COVID-19 in 2018 for Wave 8. The primary outcome for this study was healthcare access. Both bivariate and multivariate logistic regression models were employed to identify the factors associated with reluctance to access healthcare services during COVID-19 and pre-COVID-19 times.\n\nResultsAmong respondents, 39.6% avoided seeking health services during the first year of the COVID-19 pandemic when they needed them, which was similar to pre-COVID-19 times (41.4%). The factors most strongly impacting upon reluctance and/or barriers to healthcare access during COVID-19 were any illness or disability, and high psychological distress. In comparison, prior to the pandemic the factors which were significantly impeding healthcare access were country of birth, state of residence, presence of any pre-existing condition and psychological distress. The most common reason reported (55.9%) for avoided seeking care was that they thought the problem would go away.\n\nConclusionsA significant proportion of youths did not seek care when they felt they needed to seek care, both during and before the COVID-19 pandemic.\n\nWhat is known about the subject?O_LISome adolescents and young adults do not access healthcare when they need it.\nC_LIO_LIHealthcare access and barriers to access is best understood through a multi-system lens including policy, organisational, and individual-level factors. For instance, policy barriers (such as cost), organisational barriers (such as transportation, or difficulty accessing a timely appointment) and individual barriers (such as experiences, knowledge or beliefs).\nC_LIO_LIBarriers to care may differ for sub-groups e.g. rural\nC_LIO_LIDuring the COVID-19 pandemic, public health restrictions including the stricter \"lockdowns\" have reduced healthcare access. The burden of cases upon the healthcare system has further reduced healthcare access.\nC_LI\n\nWhat this study adds?O_LIA significant proportion of youth did not seek healthcare when they felt they needed to seek care, both before (41.4%) and during the first year of the COVID-19 pandemic (39.6%)\nC_LIO_LIYouth with a disability or chronic condition, asthma and/or psychological distress were more likely to avoid accessing healthcare during COVID-19 times.\nC_LIO_LIThe most common reason for not seeking healthcare when it was felt to be needed was because the youth thought the problem would go away (pre-COVID-19 35.7% of the sample versus during the first year of COVID-19 55.9%)\nC_LIO_LIDuring the coronavirus restriction period (\"lockdown\") the most common reason for not seeking healthcare when it was felt to be needed was because the youth did not want to visit a doctor during lockdown (21.8%) with the next most common reason being because telehealth was the only appointment option available at the time (8.4%)\nC_LI", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Md Irteja Islam", + "author_inst": "Sydney School of Public Health, Faculty of Medicine and Health, The University of Sydney, Edward Ford Building, A27 Fisher Road, NSW 2006, Australia." + }, + { + "author_name": "Joseph Freeman", + "author_inst": "Sydney School of Public Health, Faculty of Medicine and Health, The University of Sydney, Edward Ford Building, A27 Fisher Road, NSW 2006, Australia" + }, + { + "author_name": "Verity Chadwick", + "author_inst": "Royal North Shore Hospital, Reserve Rd, St Leonard's NSW, Australia" + }, + { + "author_name": "Alexandra Martiniuk", + "author_inst": "Sydney School of Public Health, Faculty of Medicine and Health, The University of Sydney, Edward Ford Building, A27 Fisher Road, NSW 2006, Australia" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2021.12.02.21267182", "rel_title": "COVID-19 infections post-vaccination by HIV status in the United States", @@ -498707,61 +500583,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.02.21267191", - "rel_title": "Prevalence of SARS-CoV-2 infection among COVID-19 RT-PCR laboratory workers in Bangladesh", - "rel_date": "2021-12-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.02.21267191", - "rel_abs": "BackgroundHealth care workers (HCWs) at the frontline are confronting a substantial risk of infection during the coronavirus disease 2019 (COVID-19) pandemic. This emerging virus created specific hazards to researchers and laboratory staff in a clinical setting, underlined by rapid and extensive worldwide transmission. This study aimed to investigate the prevalence of SARS-CoV-2 infection among COVID-19 RT-PCR laboratory health workers in Bangladesh.\n\nMaterials & MethodsThis retrospective study was conducted between October 2 to December 2, 2020. A total of 508 participants, including doctors, scientific officers, medical technologists, and cleaners working in several COVID-19 RT-PCR laboratories, were included in this study. Data were collected from each participant using a semi-structured questionnaire prepared in the format of an anonymous Google form. All participants provided informed consent. The Ethical clearance was obtained from the Institutional Ethics Review Committee of Shaheed Suhrawardy Medical College, Dhaka, Bangladesh. All statistical analyses were performed using SPSS (Statistical Package for the Social Sciences) version 25.0 software (SPSS, Inc).\n\nResultsOut of the 508 participants, 295 tested positive for SARS CoV-2 RT-PCR. Among the positive cases, 202 were men, 93 were women, with the median age of 30 years. The most positive cases were medical technologists (53.22%) followed by doctors (28.8%). Out of the 271 symptomatic positive cases, the most typical symptoms were fever (78.5%), fatigue (70%), loss of smell and taste (65%), cough (64%), and others. Hypertension, obesity, and diabetes were found in 8.8%, 8.8%, and 7.1% positive cases. A + blood group was present in 37% of the positive cases, followed by the B+ blood group (27%) and O+ blood group (25%). Inadequate supply of personal protection equipment (PPE), absence of negative pressure ventilation, laboratory contamination, and no training on molecular test methods were found in 13.8%, 67.8%, 44.7%, and 40.6% of positive cases, respectively.\n\nConclusionEvaluating the infection status of laboratory health workers is crucial for drawing attention from the public, providing practical suggestions for government agencies, and increasing protective measures for laboratory health workers.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Mohammad Jahidur Rahman Khan", - "author_inst": "Shaheed Suhrawardy Medical College" - }, - { - "author_name": "Samshad Jahan shumu", - "author_inst": "Shaheed Suhrawardy Medical College" - }, - { - "author_name": "Ruksana Raihan", - "author_inst": "US-Bangla Medical College" - }, - { - "author_name": "Nusrat Mannan", - "author_inst": "US-Bangla Medical College" - }, - { - "author_name": "Md Selim Reza", - "author_inst": "RT-PCR LAB, Bangabandhu Sheikh Mujib Medical College" - }, - { - "author_name": "Nazia Hasan Khan", - "author_inst": "United Hospital Limited" - }, - { - "author_name": "Amirul Huda Bhuiyan", - "author_inst": "Dhaka Medical College" - }, - { - "author_name": "Paroma Deb", - "author_inst": "Dhaka Medical College" - }, - { - "author_name": "Farzana Mim", - "author_inst": "Jahangirnagar University" - }, - { - "author_name": "Arifa Akram", - "author_inst": "National Institute of Laboratory Medicine and Referral Centre" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.02.21267164", "rel_title": "Estimation of heterogeneous instantaneous reproduction numbers with application to characterize SARS-CoV-2 transmission in Massachusetts counties", @@ -499038,6 +500859,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.12.02.21266871", + "rel_title": "Impact of individual-level characteristics and transmission mitigation behaviors on SARS-CoV-2 infection and seroprevalence in a large Northern California Bay Area cohort", + "rel_date": "2021-12-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.02.21266871", + "rel_abs": "Comprehensive data on transmission mitigation behaviors and both SARS-CoV-2 infection and serostatus are needed from large, community-based cohorts to identify COVID-19 risk factors and the impact of public health measures. From July 2020-March 2021, approximately 5,500 adults from the East Bay Area, California were followed over three data collection rounds to investigate the association between geographic and demographic characteristics and transmission mitigation behavior with SARS-CoV-2 prevalence. We estimated the populated-adjusted prevalence of antibodies from SARS-CoV-2 infection and COVID-19 vaccination, and self-reported COVID-19 test positivity. Population-adjusted SARS-CoV-2 seroprevalence was low, increasing from 1.03% (95% CI: 0.50-1.96) in Round 1 (July-September 2020), to 1.37% (95% CI: 0.75-2.39) in Round 2 (October-December 2020), to 2.18% (95% CI: 1.48-3.17) in Round 3 (February-March 2021). Population-adjusted seroprevalence of COVID-19 vaccination was 21.64% (95% CI: 19.20-24.34) in Round 3, with Whites having 4.35% (95% CI: 0.35-8.32) higher COVID-19 vaccine seroprevalence than non-Whites. No evidence for an association between transmission mitigation behavior and seroprevalence was observed. Despite >99% of participants reporting wearing masks, non-Whites, lower-income, and lower-educated individuals had the highest SARS-CoV-2 seroprevalence and lowest vaccination seroprevalence. Results demonstrate that more effective policies are needed to address these disparities and inequities.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Cameron Adams", + "author_inst": "Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720, USA; Division of Biostatistics, School of Public He" + }, + { + "author_name": "Mary Horton", + "author_inst": "Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720, USA; Computational Biology Graduate Group, Universi" + }, + { + "author_name": "Olivia Solomon", + "author_inst": "Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720, USA; Computational Biology Graduate Group, Universi" + }, + { + "author_name": "Marcus Wong", + "author_inst": "Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720, USA; Infectious Disease and " + }, + { + "author_name": "Sean L. Wu", + "author_inst": "Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, USA" + }, + { + "author_name": "Sophia Fuller", + "author_inst": "Division of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720, USA" + }, + { + "author_name": "Xiaorong Shao", + "author_inst": "Genetic Epidemiology and Genomics Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, 94720, USA" + }, + { + "author_name": "Indro Fedrigo", + "author_inst": "Genetic Epidemiology and Genomics Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, 94720, USA" + }, + { + "author_name": "Hong Quach", + "author_inst": "Genetic Epidemiology and Genomics Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, 94720, USA" + }, + { + "author_name": "Diana Quach", + "author_inst": "Genetic Epidemiology and Genomics Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, 94720, USA" + }, + { + "author_name": "Michelle Meas", + "author_inst": "Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720, USA" + }, + { + "author_name": "Luis Lopez", + "author_inst": "Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720, USA" + }, + { + "author_name": "Abigail Broughton", + "author_inst": "Genetic Epidemiology and Genomics Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, 94720, USA" + }, + { + "author_name": "Anna L. Barcellos", + "author_inst": "Genetic Epidemiology and Genomics Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, 94720, USA" + }, + { + "author_name": "Joan Shim", + "author_inst": "Genetic Epidemiology and Genomics Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, 94720, USA" + }, + { + "author_name": "Yusef Seymens", + "author_inst": "Genetic Epidemiology and Genomics Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, 94720, USA" + }, + { + "author_name": "Samantha Hernandez", + "author_inst": "Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720, USA" + }, + { + "author_name": "Magelda Montoya", + "author_inst": "Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720, USA" + }, + { + "author_name": "Darrell M. Johnson", + "author_inst": "University of Minnesota Genomics Center, Minneapolis, MN, 55455, USA" + }, + { + "author_name": "Kenneth Beckman", + "author_inst": "University of Minnesota Genomics Center, Minneapolis, MN, 55455, USA" + }, + { + "author_name": "Michael P. Busch", + "author_inst": "Vitalant Research Institute, San Francisco CA, 94118, USA" + }, + { + "author_name": "Josefina Coloma", + "author_inst": "Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720, USA" + }, + { + "author_name": "Joseph Lewnard", + "author_inst": "Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720, USA; Computational Biology Graduate Group, Universi" + }, + { + "author_name": "Eva Harris", + "author_inst": "Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720, USA; Infectious Disease and " + }, + { + "author_name": "Lisa F. Barcellos", + "author_inst": "Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720, USA; Computational Biology Graduate Group, Universi" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.02.21267168", "rel_title": "The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia", @@ -500393,153 +502329,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.12.01.470767", - "rel_title": "A public antibody class recognizes a novel S2 epitope exposed on open conformations of SARS-CoV-2 spike", - "rel_date": "2021-12-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.01.470767", - "rel_abs": "Delineating the origins and properties of antibodies elicited by SARS-CoV-2 infection and vaccination is critical for understanding their benefits and potential shortcomings. Therefore, we investigated the SARS-CoV-2 spike (S)-reactive B cell repertoire in unexposed individuals by flow cytometry and single-cell sequencing. We found that [~]82% of SARS-CoV-2 S-reactive B cells show a naive phenotype, which represents an unusually high fraction of total human naive B cells ([~]0.1%). Approximately 10% of these naive S-reactive B cells shared an IGHV1-69/IGKV3-11 B cell receptor pairing, an enrichment of 18-fold compared to the complete naive repertoire. A proportion of memory B cells, comprising switched ([~]0.05%) and unswitched B cells ([~]0.04%), was also reactive with S and some of these cells were reactive with ADAMTS13, which is associated with thrombotic thrombocytopenia. Following SARS-CoV-2 infection, we report an average 37-fold enrichment of IGHV1-69/IGKV3-11 B cell receptor pairing in the S-reactive memory B cells compared to the unselected memory repertoire. This class of B cells targets a previously undefined non-neutralizing epitope on the S2 subunit that becomes exposed on S proteins used in approved vaccines when they transition away from the native pre-fusion state because of instability. These findings can help guide the improvement of SARS-CoV-2 vaccines.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Mathieu Claireaux", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Tom G Caniels", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Marlon de Gast", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Julianna Han", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Denise Guerra", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Gius Kerster", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Barbera DC van Schaik", - "author_inst": "Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, " - }, - { - "author_name": "Aldo Jongejan", - "author_inst": "Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, " - }, - { - "author_name": "Angela I Schriek", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Marloes Grobben", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Philip JM Brouwer", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Karlijn van der Straten", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Yoann Aldon", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Joan Capella-Pujol", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Jonne L Snitselaar", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Wouter Olijhoek", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Aafke Aartse", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Mitch Brinkkemper", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Ilja Bontjer", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Judith A Burger", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Meliawati Poniman", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Tom PL Bijl", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Jonathan L Torres", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Jeffrey Copps", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Isabel Cuella Martin", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Steven W de Taeye", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Godelieve J de Bree", - "author_inst": "Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Infection and I" - }, - { - "author_name": "Andrew B Ward", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Kwinten Sliepen", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Antoine HC van Kampen", - "author_inst": "Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, " - }, - { - "author_name": "Perry D Moerland", - "author_inst": "Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, " - }, - { - "author_name": "Rogier W Sanders", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Marit J van Gils", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.12.01.470697", "rel_title": "Macaque-human differences in SARS-CoV-2 Spike antibody response elicited by vaccination or infection", @@ -500760,6 +502549,97 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.12.02.470978", + "rel_title": "Secreted ORF8 is a pathogenic cause of severe Covid-19 and potentially targetable with select NLRP3 inhibitors", + "rel_date": "2021-12-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.02.470978", + "rel_abs": "COVID-19 is a significant cause of morbidity and mortality in blood cancer patients, especially those on immunosuppressive therapy. Despite extensive research, the specific factor associated with SARS-CoV-2 infection that mediates the life-threatening inflammatory cytokine response in patients with severe COVID-19 remains unidentified. Herein we demonstrate that the virus-encoded Open Reading Frame 8 (ORF8) protein is abundantly secreted as a glycoprotein in vitro and in symptomatic patients with COVID-19. ORF8 specifically binds to the NOD-like receptor family pyrin domain-containing 3 (NLRP3) in CD14+ monocytes to induce a non-canonical inflammasomal response, and a canonical response when the second activation signal is present. Levels of ORF8 protein in the blood correlate with severity and disease-specific mortality in patients with acute SARS-CoV-2 infection. Furthermore, the ORF8-induced inflammasome response was readily inhibited by the NLRP3 inhibitor MCC950 in vitro. Our study identifies a dominant cause of pathogenesis, its underlying mechanism, and a potential new treatment for severe COVID-19.\n\nKey pointsO_LISecreted glycoprotein ORF8 induces monocytic pro-inflammatory cytokines involving the activation of the NLPR3 inflammasome pathway.\nC_LIO_LIORF8 is prognostically present in the blood of symptomatic patients with covid-19 and is targetable with NLRP3 inhibitor MCC-950.\nC_LI", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Xiaosheng Wu", + "author_inst": "Hematology Division, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA" + }, + { + "author_name": "Michelle K Manske", + "author_inst": "Hematology Division, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA" + }, + { + "author_name": "Gordon Ruan", + "author_inst": "Hematology Division, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA" + }, + { + "author_name": "Taylor L Witter", + "author_inst": "Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA" + }, + { + "author_name": "Kevin E Nowakowski", + "author_inst": "Hematology Division, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA" + }, + { + "author_name": "Jithma P Abeykoon", + "author_inst": "Hematology Division, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA" + }, + { + "author_name": "Xinyi Tang", + "author_inst": "Hematology Division, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA" + }, + { + "author_name": "Yue Yu", + "author_inst": "Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA" + }, + { + "author_name": "Kimberly A. Gwin", + "author_inst": "Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA" + }, + { + "author_name": "Annie Wu", + "author_inst": "Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA" + }, + { + "author_name": "Vanessa Taupin", + "author_inst": "Electron Microscopy Core, University of California San Diego, La Jolla, CA, USA" + }, + { + "author_name": "Vaishali Bhardwaj", + "author_inst": "Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA" + }, + { + "author_name": "Jonas Paludo", + "author_inst": "Hematology Division, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA" + }, + { + "author_name": "Surendra Dasari", + "author_inst": "Deoartment of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA" + }, + { + "author_name": "Haidong Dong", + "author_inst": "Department of Immunology, Mayo Clinic, Rochester, Minnsota, USA" + }, + { + "author_name": "Stephen M Ansell", + "author_inst": "Hematology Division, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA" + }, + { + "author_name": "Andrew D Badley", + "author_inst": "Division of infectious diseases, Department of Medicine, Mayo Clinic, Rochester, MN, USA" + }, + { + "author_name": "Matthew Schellenberg", + "author_inst": "Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA" + }, + { + "author_name": "Thomas E Witzig", + "author_inst": "Hematology Division, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.12.02.471028", "rel_title": "Systems immune profiling of variant-specific vaccination against SARS-CoV-2", @@ -502055,29 +503935,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.11.30.21267029", - "rel_title": "Assessment of correlations between risk factors and symptom presentation among defined at-risk groups following a confirmed COVID-19 diagnosis", - "rel_date": "2021-12-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.30.21267029", - "rel_abs": "This study analyzes the specific linkages between symptoms within individual COVID patients belonging to at-risk groups. The goal was to determine how strongly linked patient symptoms are within these at-risk groups to find any associations between factors such as comorbidities and COVID symptoms. In this study, de-identified patient data from the N3C database was utilized in order to link representative immunocompromised states with specific symptoms, and non-immunocompromised state with the same, to determine if the strength of the correlation changes for these at-risk groups. Multiple autoimmune disorders resulting in immunocompromised state were analyzed, to determine if severity of immune response and inflammatory action plays a role in any potential differences. An exploratory approach using statistical methods and visualization techniques appropriate to multidimensional data sets was taken. The identified correlations may allow pattern analysis in disease presentation specific to a given population, potentially informing pattern recognition, symptom presentation, and treatment approaches in patients with immune comorbidities.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Dylan Aidlen", - "author_inst": "Northeastern University" - }, - { - "author_name": "Jamie Henzy", - "author_inst": "Northeastern University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.12.01.21267147", "rel_title": "Comparison of Saliva and Mid-Turbinate Swabs for Detection of COVID-19", @@ -502234,6 +504091,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, + { + "rel_doi": "10.1101/2021.11.25.21266853", + "rel_title": "Digital exclusion predicts worse mental health among adolescents during COVID-19", + "rel_date": "2021-12-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.25.21266853", + "rel_abs": "BackgroundSocial isolation is strongly associated with poor mental health. The COVID-19 pandemic and ensuing social restrictions disrupted young peoples social interactions and resulted in several periods during which school closures necessitated online learning. We hypothesise that digitally excluded young people would demonstrate greater deterioration in their mental health than their digitally connected peers during this time.\n\nMethodsWe analysed representative mental health data from a sample of UK 10-15-year-olds (N = 1387); Understanding Society collected the Strengths and Difficulties Questionnaire in 2017-19 and thrice during the pandemic (July 2020, November 2020 and March 2021). We employed cross-sectional methods and longitudinal latent growth curve modelling to describe trajectories of adolescent mental health for participants with and without access to a computer or a good internet connection for schoolwork.\n\nOutcomesAdolescent mental health had a quadratic trajectory during the COVID-19 pandemic, with the highest mean Total Difficulties score around December 2020. The worsening and recovery of mental health during the pandemic was greatly pronounced among those without access to a computer, although we did not find evidence for a similar effect among those without a good internet connection.\n\nInterpretationDigital exclusion, as indicated by lack of access to a computer, is a tractable risk factor that likely compounds other adversities facing children and young people during periods of social isolation.\n\nFundingBritish Psychological Society; School of the Biological Sciences, University of Cambridge; NIHR Applied Research Centre; Medical Research Council; Economic and Social Research Council; and Emmanuel College, University of Cambridge.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Thomas Edward Metherell", + "author_inst": "Department of Psychology, University of Cambridge" + }, + { + "author_name": "Sakshi Ghai", + "author_inst": "Department of Psychology, University of Cambridge; MRC Cognition and Brain Sciences Unit" + }, + { + "author_name": "Ethan Michael McCormick", + "author_inst": "Donders Institute, Radboud University Medical Center" + }, + { + "author_name": "Tamsin Jane Ford", + "author_inst": "Department of Psychiatry, University of Cambridge" + }, + { + "author_name": "Amy Orben", + "author_inst": "MRC Cognition and Brain Sciences Unit" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.11.30.470642", "rel_title": "Variance in Variants: Propagating Genome Sequence Uncertainty into Phylogenetic Lineage Assignment", @@ -504069,237 +505961,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.11.24.469906", - "rel_title": "Differential neutralization and inhibition of SARS-CoV-2 variants by antibodies elicited by COVID-19 mRNA vaccines", - "rel_date": "2021-11-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.24.469906", - "rel_abs": "IntroductoryThe evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the emergence of many new variant lineages that have exacerbated the COVID-19 pandemic. Some of those variants were designated as variants of concern/interest (VOC/VOI) by national or international authorities based on many factors including their potential impact on vaccines. To ascertain and rank the risk of VOCs and VOIs, we analyzed their ability to escape from vaccine-induced antibodies. The variants showed differential reductions in neutralization and replication titers by post-vaccination sera. Although the Omicron variant showed the most escape from neutralization, sera collected after a third dose of vaccine (booster sera) retained moderate neutralizing activity against that variant. Therefore, vaccination remains the most effective strategy to combat the COVID-19 pandemic.", - "rel_num_authors": 54, - "rel_authors": [ - { - "author_name": "Li Wang", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Markus H Kainulainen", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Nannan Jiang", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Han Di", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Gaston Bonenfant", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Lisa Mills", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Michael Currier", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Punya Shrivastava-Ranjan", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Brenda M Calderon", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Mili Sheth", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Brian R Mann", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Jaber Hossain", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Xudong Lin", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Sandra Lester", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Elizabeth Pusch", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Joyce Jones", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Dan Cui", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Payel Chatterjee", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Harley M Jenks", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Esther Morantz", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Gloria Larson", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Masato Hatta", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Jennifer Harcourt", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Azaibi Tamin", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Yan Lin", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Ying Tao", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Kun Zhao", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Kristine Lacek", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Ashely Burroughs", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Terianne Wong", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Suxiang Tong", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "John R Barnes", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Mark W Tenforde", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Wesley H Self", - "author_inst": "Vanderbilt University, Nashville, Tennessee, USA" - }, - { - "author_name": "Nathan I Shapiro", - "author_inst": "Harvard University, Cambridge, Massachusetts, USA" - }, - { - "author_name": "Matthew C Exline", - "author_inst": "Ohio State University, Columbus, Ohio, USA" - }, - { - "author_name": "D. Clark Files", - "author_inst": "Wake Forest Baptist Medical Center, Winston-Salem, North Carolina, USA" - }, - { - "author_name": "Kevin W Gibbs", - "author_inst": "Wake Forest Baptist Medical Center, Winston-Salem, North Carolina, USA" - }, - { - "author_name": "David N Hager", - "author_inst": "Johns Hopkins University, Baltimore, Maryland, USA" - }, - { - "author_name": "Manish Patel", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Alison S Laufer Halpin", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Laura K McMullan", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Justin S Lee", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Hongjie Xia", - "author_inst": "The University of Texas Medical Branch at Galveston, Texas" - }, - { - "author_name": "Xuping Xie", - "author_inst": "The University of Texas Medical Branch at Galveston, Texas" - }, - { - "author_name": "Pei-Yong Shi", - "author_inst": "The University of Texas Medical Branch at Galveston, Texas" - }, - { - "author_name": "C. Todd Davis", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Christina F Spiropoulou", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Natalie J. Thornburg", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "M. Steven Oberste", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Vivien Dugan", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "- SSEV Bioinformatics Working Group", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "David E Wentworth", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Bin Zhou", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.11.28.468932", "rel_title": "Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography", @@ -504520,6 +506181,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.11.28.470293", + "rel_title": "Protective immunity of the primary SARS-CoV-2 infection reduces disease severity post re-infection with Delta variants in Syrian hamsters", + "rel_date": "2021-11-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.28.470293", + "rel_abs": "Delta variant has evolved to become dominant SARS-CoV-2 lineage worldwide and there are reports of secondary infections with varying severity in vaccinated and unvaccinated naturally recovered COVID-19 patients. As the protective immunity following the infection wanes within few months, studies of re-infection after prolonged duration is needed. Hence we assessed the potential of re-infection by Delta, Delta AY.1 and B.1 in COVID-19 recovered hamsters after 3 months of infection. Re-infection with Delta and B.1 variants in hamsters showed reduced viral shedding, lung pathology and lung viral load, whereas the upper respiratory tract viral load remained similar to that of first infection. The reduction in viral load and lung pathology after re-infection with Delta AY.1 variant was not marked. Further we assessed the disease characteristics of Delta AY.1 to understand whether it has any replication advantage over Delta variant and B.1 variant, an early isolate in Syrian hamsters. Body weight changes, viral load in respiratory organs, lung pathology, cytokine response and neutralizing antibody response were assessed. Delta AY.1 variant produced milder disease in comparison to Delta variant and the neutralizing response was similar against Delta, B.1 and B.1.351 variant in contrast to Delta or B.1 infected hamsters which showed a significant reduction in neutralization titres against B.1.351. Elevation of IL-6 levels was observed post infection in hamsters after primary infection. The prior infection could not produce sterilizing immunity but the protective effect was evident following reinfection. This indicates the importance of the transmission prevention efforts even after achieving herd immunity.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSSecondary infections with Delta variant are being widely reported and there are reports of increased disease severity. Delta sub lineages with K417N substitution has caused concern worldwide due to the presence of the same substitution in Beta variant, a Variant of Concern known for its immune evasion. The information on the biological characteristics of this sub lineage is also scanty.\n\nAdded value of this studyThe present study showed that the secondary infection with Delta variant does not show any evidence of increased disease severity in hamster model. Delta AY. 1 variant produces mild disease in Syrian hamsters in contrast to severe disease caused by Delta variant. Delta, B.1 and AY.1 variant infected hamster sera showed comparable cross neutralizing response against each other. In contrast to the lower neutralizing response shown by B.1 and Delta variant infected animals against B.1.351 variant, Delta AY.1 showed comparable response as that with other variants.\n\nImplications of the available evidenceSARS-CoV-2 infections do not produce sterilizing immunity but protect from developing severe disease in case of Delta variant re-infection indicating the importance of the transmission prevention efforts even after achieving herd immunity. Delta AY. 1 infection in hamsters did not show any evidence of speculated immune evasion.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Sreelekshmy Mohandas", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, Pin-411021" + }, + { + "author_name": "Pragya Yadav", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, Pin-411021" + }, + { + "author_name": "Anita Shete", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, Pin-411021" + }, + { + "author_name": "Dimpal Nyayanit", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, Pin-411021" + }, + { + "author_name": "Rajlaxmi Jain", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, Pin-411021" + }, + { + "author_name": "Gajanan N Sapkal", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, Pin-411021" + }, + { + "author_name": "Chandrasekhar Mote", + "author_inst": "Krantisinh Nana Patil College of Veterinary Science, Shirwal, Satara, Maharashtra, India Pin-400088" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.11.29.470346", "rel_title": "In silico study on the effects of disulfide bonds in ORF8 of SARS-CoV-2", @@ -505987,33 +507691,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.11.29.21266623", - "rel_title": "Transient adverse events after REGN-CoV2 administration for mild COVID-19 patients and their potential predictive factors: a single center analysis", - "rel_date": "2021-11-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.29.21266623", - "rel_abs": "BackgroundREGN-COV2, a monoclonal antibody cocktail drug against the SARS-COV-2 virus, has proven to be effective in preventing the development of severe COVID-19 and is increasingly being administered in outpatient and home settings. Adverse events such as fever and decreased oxygen saturation may occur after administration of REGN-COV2, and although these symptoms are generally mild and transient, predicting the occurrence of these adverse events is useful in developing a monitoring plan for patients.\n\nMethodsWe performed a retrospective analysis of 76 patients who received REGN-CoV2 between August and September 2021. We collected information on fever, decreased oxygen saturation requiring oxygen supplementation, and other adverse events from medical records. Patients were divided into two subgroups: those who presented with fever or oxygen desaturation and those who did not, and underlying medical conditions and laboratory data were compared between each group. The parameters that exhibited significant differences were further tested using Fishers exact test to evaluate whether appropriate thresholds could be set to distinguish the incidence group from the non-incidence group.\n\nFindingsOf the 76 patients, 47 had fever of 38.5{degrees}C or higher within 24 hours after administration, and 27 of these patients had a body temperature of 37.5{degrees}C or lower before administration. Oxygen was required in 17 cases, 7 of which required oxygen more than 24 hours after administration of REGN-COV2, and additional treatment such as dexamethasone was given as the disease progressed to moderate. Among the parameters analyzed, lymphocyte count and IFN{lambda}3 showed significant differences between the fever and non-fever groups. This was also the case in the comparison excluding patients who had fever before administration. There was also a significant difference in ferritin and CRP between the oxygen required and non-required groups. In addition to IFN{lambda}3, ferritin, and CRP, there was a significant difference in LDH between the group that required additional treatment and the group that did not. When lymphocytes count <950/{micro}L was used to predict fever, the sensitivity and specificity were 55% and 79%, respectively, with odds ratio 4.746 (95% CI: 1.666 to 14.12, p=0.004) in contingency table analysis. Similarly, when IFN{lambda}3 >5.0 was used as the cutoff, sensitivity 72%, specificity 76%, odds ratio 8.220 (2.857 to 22.22; p<0.0001).\n\nInterpretationsTransient fever and decreased oxygen saturation are common adverse events after REGN-CoV2 administration, and their occurrence correlated with the severity factor of COVID-19 itself. Evaluation of these items at the time of administration is useful not only for predicting the severity of COVID-19 but also for the development of adverse events in patients receiving REGN-CoV2.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Gen Kano", - "author_inst": "Kyoto Yamashiro General Medical Center" - }, - { - "author_name": "Kyoko Taniguchi", - "author_inst": "Kyoto Yamashiro General Medical Center" - }, - { - "author_name": "Yukiko Oue", - "author_inst": "Kyoto Yamashiro General Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.25.470044", "rel_title": "Anticipating future SARS-CoV-2 variants of concern through ab initio quantum mechanical modeling", @@ -506206,6 +507883,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.11.27.21266927", + "rel_title": "Variations of the quality of care during the COVID-19 pandemic affected the mortality rate of non-COVID patients with hip fracture", + "rel_date": "2021-11-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.27.21266927", + "rel_abs": "IntroductionAs COVID-19 roared through the world, governments worldwide enforced containment measures that affected various treatment pathways, including those for hip fracture (HF). This study aimed to measure process and outcome indicators related to the quality of care provided to non-COVID-19 elderly patients affected by HF in Emilia-Romagna, a region of Italy severely hit by the pandemic.\n\nMethodsWe collected the hospital discharge records of all patients admitted to the hospitals of Emilia-Romagna with a diagnosis of HF from January to May in the years 2019/2020. We analyzed surgery rate, surgery timeliness, length of hospital stay, timely rehabilitation, and 30-day mortality for each HF patient. We evaluated monthly data (2020 vs. 2019) with the chi-square and t-test, where appropriate. Logistic regression was used to investigate the differences in 30-day mortality.\n\nResultsOur study included 5379 patients with HF. In April and May 2020, there was a significant increase in the proportion of HF patients that did not undergo timely surgery. In March 2020, we found a significant increase in mortality (OR = 2.22). Female sex (OR = 0.52), age [≥]90 years (OR = 4.33), surgery after 48 hours (OR = 3.08) and not receiving surgery (OR = 6.19) were significantly associated with increased mortality. After adjusting for the aforementioned factors, patients hospitalized in March 2020 still suffered higher mortality (OR = 2.21).\n\nConclusionsOur results show a reduction in the overall quality of care provided to non-COVID-19 elderly patients affected by HF. The mortality rate of patients with HF increased significantly in March 2020. Patients characteristics and variations in processes of care partially explained this increase. Our analysis reveals the importance of including process and outcomes indicators, for both acute and post-acute care management issues, in emergency preparedness plans, to monitor healthcare systems capacities and capabilities.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Davide Golinelli", + "author_inst": "University of Bologna" + }, + { + "author_name": "Francesco Sanmarchi", + "author_inst": "University of Bologna" + }, + { + "author_name": "Angelo Capodici", + "author_inst": "University of Bologna" + }, + { + "author_name": "Giuorgia Gribaudo", + "author_inst": "University of Bologna" + }, + { + "author_name": "Mattia Altini", + "author_inst": "Healthcare Administration, AUSL Romagna, Ravenna, Italy" + }, + { + "author_name": "Simona Rosa", + "author_inst": "University of Bologna" + }, + { + "author_name": "Francesco Esposito", + "author_inst": "University of Bologna" + }, + { + "author_name": "Maria Pia Fantini", + "author_inst": "University of Bologna" + }, + { + "author_name": "Jacopo Lenzi", + "author_inst": "University of Bologna" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2021.11.27.21266930", "rel_title": "Dosing interval strategies for two-dose COVID-19 vaccination in 13 low- and middle-income countries of Europe: health impact modelling and benefit-risk analysis", @@ -507869,101 +509597,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.24.21266809", - "rel_title": "Pandemic inequity in a megacity: a multilevel analysis of individual, community, and health care vulnerability risks for COVID-19 mortality in Jakarta, Indonesia", - "rel_date": "2021-11-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.24.21266809", - "rel_abs": "BackgroundThe 33 recognized megacities comprise approximately 7% of the global population, yet account for 20% COVID-19 deaths. The specific inequities and other factors within megacities that affect vulnerability to COVID-19 mortality remain poorly defined. We assessed individual, community-level and health care factors associated with COVID-19-related mortality in a megacity of Jakarta, Indonesia, during two epidemic waves spanning March 2, 2020, to August 31, 2021.\n\nMethodsThis retrospective cohort included all residents of Jakarta, Indonesia, with PCR-confirmed COVID-19. We extracted demographic, clinical, outcome (recovered or died), vaccine coverage data, and disease prevalence from Jakarta Health Office surveillance records, and collected sub-district level socio-demographics data from various official sources. We used multi-level logistic regression to examine individual, community and sub-district-level health care factors and their associations with COVID-19-mortality.\n\nFindingsOf 705,503 cases with a definitive outcome by August 31, 2021, 694,706 (98{middle dot}5%) recovered and 10,797 (1{middle dot}5%) died. The median age was 36 years (IQR 24-50), 13{middle dot}2% (93,459) were <18 years, and 51{middle dot}6% were female. The sub-district level accounted for 1{middle dot}5% of variance in mortality (p<0.0001). Individual-level factors associated with death were older age, male sex, comorbidities, and, during the first wave, age <5 years (adjusted odds ratio (aOR) 1{middle dot}56, 95%CI 1{middle dot}04-2{middle dot}35; reference: age 20-29 years). Community-level factors associated with death were poverty (aOR for the poorer quarter 1{middle dot}35, 95%CI 1{middle dot}17-1{middle dot}55; reference: wealthiest quarter), high population density (aOR for the highest density 1{middle dot}34, 95%CI 1{middle dot}14-2{middle dot}58; reference: the lowest), low vaccine coverage (aOR for the lowest coverage 1{middle dot}25, 95%CI 1{middle dot}13-1{middle dot}38; reference: the highest).\n\nInterpretationIn addition to individual risk factors, living in areas with high poverty and density, and low health care performance further increase the vulnerability of communities to COVID-19-associated death in urban low-resource settings.\n\nFundingWellcome (UK) Africa Asia Programme Vietnam (106680/Z/14/Z).\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed on November 22, 2021, for articles that assessed individual, community, and healthcare vulnerability factors associated with coronavirus disease 2019 (COVID-19) mortality, using the search terms (\"novel coronavirus\" OR \"SARS-CoV-2\" OR \"COVID-19\") AND (\"death\" OR \"mortality\" OR \"deceased\") AND (\"community\" OR \"social\") AND (\"healthcare\" OR \"health system\"). The 33 recognized megacities comprise approximately 7% of the global population, yet account for 20% COVID-19 deaths. The specific inequities and other factors within megacities that affect vulnerability to COVID-19 mortality remain poorly defined. At individual-level, studies have shown COVID-19-related mortality to be associated with older age and common underlying chronic co-morbidities including hypertension, diabetes, obesity, cardiac disease, chronic kidney disease and liver disease. Only few studies from North America, and South America have reported the association between lower community-level socio-economic status and healthcare performance with increased risk of COVID-19-related death. We found no studies have been done to assess individual, community, and healthcare vulnerability factors associated with COVID-19 mortality risk, especially in lower-and middle-income countries (LMIC) where accessing quality health care services is often challenging for substantial proportions of population, due to under-resourced and fragile health systems. In Southeast Asia, by November 22, 2021, COVID-19 case fatality rate had been reported at 2{middle dot}2% (23,951/1,104,835) in Vietnam, 1{middle dot}7% (47,288/2,826,853) in Philippines, 1{middle dot}0% (20,434/2,071,009) in Thailand, 1{middle dot}2% (30,063/2,591,486) in Malaysia, 2{middle dot}4% (2,905/119,904) in Cambodia, and 0{middle dot}3% in Singapore (667/253,649). Indonesia has the highest number of COVID-19 cases and deaths in the region, reporting 3{middle dot}4% case fatality rate (143,744 /4,253,598), with the highest number of cases in the capital city of Jakarta. A preliminary analysis of the first five months of surveillance in Jakarta found that 497 of 4265 (12%) hospitalised patients had died, associated with older age, male sex; pre-existing hypertension, diabetes, or chronic kidney disease; clinical diagnosis of pneumonia; multiple (>3) symptoms; immediate intensive care unit admission, or intubation.\n\nAdded value of this studyThis retrospective population-based study of the complete epidemiological surveillance data of Jakarta during the first eighteen months of the epidemic is the largest studies in LMIC to date, that comprehensively analysed the individual, community, and healthcare vulnerability associated with COVID-19-related mortality among individuals diagnosed with PCR-confirmed COVID-19. The overall case fatality rate among general population in Jakarta was 1{middle dot}5% (10,797/705,503). Individual factors associated with risk of death were older age, male sex, comorbidities, and, during the first wave, age <5 years (adjusted odds ratio (aOR) 1{middle dot}56, 95%CI 1{middle dot}04-2{middle dot}35; reference: age 20-29 years). The risk of death was further increased for people living in sub-districts with high rates of poverty (aOR for the poorer quarter 1{middle dot}35, 95%CI 1{middle dot}17-1{middle dot}55; reference: wealthiest quarter), high population density (aOR for the highest density 1{middle dot}34, 95%CI 1{middle dot}14-2{middle dot}58), and low COVID-19 vaccination coverage (aOR for the lowest coverage 1{middle dot}25, 95%CI 1{middle dot}13-1{middle dot}38; reference: the highest).\n\nImplications of all available evidenceDifferences in socio-demographics and access to quality health services, among other factors, greatly influence COVID-19 mortality in low-resource settings. This study affirmed that in addition to well-known individual risk factors, community-level socio-demographics and healthcare factors further increase the vulnerability of communities to die from COVID-19 in urban low-resource settings. These results highlight the need for accelerated vaccine rollout and additional preventive interventions to protect the urban poor who are most vulnerable to dying from COVID-19.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Henry Surendra", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Ngabila Salama", - "author_inst": "DKI Jakarta Health Office" - }, - { - "author_name": "Karina D Lestari", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Verry Adrian", - "author_inst": "DKI Jakarta Health Office" - }, - { - "author_name": "Widyastuti Widyastuti", - "author_inst": "DKI Jakarta Health Office" - }, - { - "author_name": "Dwi Oktavia", - "author_inst": "DKI Jakarta Health Office" - }, - { - "author_name": "Rosa N Lina", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Bimandra A Djaafara", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Ihsan Fadilah", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Rahmat Sagara", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Lenny L Ekawati", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Ahmad Nurhasim", - "author_inst": "The Conversation Indonesia" - }, - { - "author_name": "Riris Andono A Ahmad", - "author_inst": "Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada" - }, - { - "author_name": "Aria Kekalih", - "author_inst": "Faculty of Medicine, Universitas Indonesia" - }, - { - "author_name": "Ari F Syam", - "author_inst": "Faculty of Medicine, Universitas Indonesia" - }, - { - "author_name": "Anuraj H Shankar", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Guy Thwaites", - "author_inst": "Oxford University Clinical Research Unit" - }, - { - "author_name": "J Kevin Baird", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Raph L Hamers", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Iqbal RF Elyazar", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.24.21266837", "rel_title": "Changes in antidepressant use in Australia: A nationwide analysis prior to and during the COVID-19 pandemic (2015-2021)", @@ -508156,6 +509789,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2021.11.24.21266824", + "rel_title": "Synergetic measures needed to control infection waves and contain SARS-CoV-2 transmission", + "rel_date": "2021-11-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.24.21266824", + "rel_abs": "BackgroundThe public and scientific discourse on how to mitigate the COVID-19 pandemic is often focused on the impact of individual protective measures, in particular on vaccination. In view of changing virus variants and conditions, however, it seems not clear if vaccination or any other protective measure alone may suffice to contain the transmission of SARS-CoV-2.\n\nMethodsHere, we investigate the effectiveness and synergies of vaccination and non-pharmaceutical interventions like masking, distancing & ventilation, testing & isolation, and contact reduction as a function of compliance in the population. Our new analysis accounts for the practical compliance in the population and for both droplet transmission and aerosol transmission.\n\nFindingsFor realistic conditions, we find that it would be difficult to contain highly contagious SARS-CoV-2 variants by any individual measure. Instead, we show how multiple synergetic measures have to be combined to reduce the effective reproduction number (Re) below unity for different basic reproduction numbers ranging from the SARS-CoV-2 ancestral strain up to measles-like values (R0 = 3 to 18). For R0 = 5 as reported for the Delta variant and [~]70% vaccination rate, the synergies of masking and distancing & ventilation with compliances around 30% appear sufficient to keep Re < 1. In combination with 2-3 tests per week, this would work also at lower vaccination rates, e.g., in schools.\n\nInterpretationIf the Omicron variant were to reach R0 = 8, it could still be contained with the synergetic measures outlined above. In case of measles-like transmissibilities (R0 = 12 to 18), higher compliances and testing rates or additional measures like general contact reductions would be required. The presented findings and approach can be used to design and communicate efficient strategies for mitigating the COVID-19 pandemic.\n\nFundingMax Planck Society.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSStudies on how to mitigate the COVID-19 pandemic are often focused on the impact of individual protective measures, in particular on vaccination. The effectiveness of non-pharmaceutical interventions (NPIs) like masking or distancing & ventilation are often under debate due to a lack of understanding of different transmission pathways (droplet versus aerosol transmission) and protective measures, in particular for the efficacy of masking and contrasting randomized trial results under different conditions (virus-limited vs. virus-rich) and at different levels of practical compliance. Thus, in view of more contagious variants such as Delta or Omicron, it is not clear if vaccination or any other protective measure alone may suffice to contain the transmission of SARS-CoV-2.\n\nAdded value of this studyOur analysis explicitly accounts for both droplet and aerosol transmission as well as for practical compliance in the population, which is the main reason for divergent results on the effectiveness of the same NPIs in different regions. This was not fully considered before and may have led to misunderstandings and misinformation about the actual effects of preventive measures. For realistic conditions, we find that it would be difficult to contain highly contagious SARS-CoV-2 variants by any individual measure. Instead, we show that combining multiple synergetic measures with realistic compliances can reduce Re below unity without lockdown.\n\nImplications of all the available evidenceOur findings and the presented scientific approach can be used to design and communicate efficient strategies for mitigating the COVID-19 pandemic for specific environments like schools as well as on a population level.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Hang Su", + "author_inst": "Max Planck Institute for Chemistry" + }, + { + "author_name": "Yafang Cheng", + "author_inst": "Max Planck Institute for Chemistry" + }, + { + "author_name": "Christian Witt", + "author_inst": "Department of Outpatient Pneumology, Charite Universitaetsmedizin Berlin, Campus Charite Mitte, Chariteplatz 1, 10117, Berlin, Germany" + }, + { + "author_name": "Nan Ma", + "author_inst": "Jinan University" + }, + { + "author_name": "Ulrich Poeschl", + "author_inst": "Max Planck Institute for Chemistry" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.22.21266522", "rel_title": "A comparison of health care use after severe COVID-19, respiratory syncytial virus, and influenza in children", @@ -509575,73 +511243,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.11.22.21266565", - "rel_title": "Impacts of vaccination and asymptomatic testing on SARS-CoV-2 transmission dynamics in a university setting", - "rel_date": "2021-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.22.21266565", - "rel_abs": "We investigate the impact of vaccination and asymptomatic testing uptake on SARS-CoV-2 transmission in a university student population using a stochastic compartmental model. We find that the magnitude and timing of outbreaks is highly variable depending on the transmissibility of the most dominant strain of SARS CoV-2 and under different vaccine uptake levels and efficacies. When delta is the dominant strain, low level interventions (no asymptomatic testing, 30% vaccinated with a vaccine that is 80% effective at reducing infection) lead to 53-71% of students become infected during the first term. Asymptomatic testing is most useful when vaccine uptake is low: when 30% of students are vaccinated, 90% uptake of asymptomatic testing leads to almost half the case numbers. With high interventions (90% using asymptomatic testing, 90% vaccinated) cumulative incidence is 7-9%, with around 80% of these cases estimated to be asymptomatic. However, under emergence of a new variant that is at least twice as transmissible as delta and with the vaccine efficacy against infection reduced to 55%, large outbreaks are likely in universities, even with very high (90%) uptake of vaccination and 100% uptake of asymptomatic testing. If vaccine efficacy against infection against this new variant is higher (70%), then outbreaks can be mitigated if there is least 50% uptake of asymptomatic testing additional to 90% uptake of vaccination. Our findings suggest that effective vaccination is critical for controlling SARS-CoV-2 transmission in university settings with asymptomatic testing ranging from additionally useful to critical, depending on effectiveness and uptake of vaccination. Other measures may be necessary to control outbreaks under the emergence of a more transmissible variant with vaccine escape.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Emily J Nixon", - "author_inst": "University of Bristol" - }, - { - "author_name": "Amy C Thomas", - "author_inst": "University of Bristol" - }, - { - "author_name": "Daniel A Stocks", - "author_inst": "University of Bristol" - }, - { - "author_name": "Antoine M. G. Barreaux", - "author_inst": "University of Bristol" - }, - { - "author_name": "Gibran Hemani", - "author_inst": "University of Bristol" - }, - { - "author_name": "Adam Trickey", - "author_inst": "University of Bristol" - }, - { - "author_name": "Rachel Kwiatkowska", - "author_inst": "University of Bristol" - }, - { - "author_name": "Josephine G Walker", - "author_inst": "University of Bristol" - }, - { - "author_name": "David Ellis", - "author_inst": "University of Bristol" - }, - { - "author_name": "Leon Danon", - "author_inst": "Department of Engineering Mathematics, University of Bristol, UK." - }, - { - "author_name": "Caroline Relton", - "author_inst": "University of Bristol" - }, - { - "author_name": "Hannah Christensen", - "author_inst": "University of Bristol" - }, - { - "author_name": "Ellen Brooks Pollock", - "author_inst": "University of Bristol" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.23.21266734", "rel_title": "Establishing and characterising large COVID-19 cohorts after mapping the Information System for Research in Primary Care in Catalonia to the OMOP Common Data Model", @@ -509878,6 +511479,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.11.23.469755", + "rel_title": "Distinct SARS-CoV-2 sensing pathways in pDCs driving TLR7-antiviral vs. TLR2-immunopathological responses in COVID-19", + "rel_date": "2021-11-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.23.469755", + "rel_abs": "Understanding the molecular pathways driving the acute antiviral and inflammatory response to SARS-CoV-2 infection is critical for developing treatments for severe COVID-19. Here we show that in COVID-19 patients, circulating plasmacytoid dendritic cells (pDCs) decline early after symptom onset and this correlated with COVID-19 disease severity. This transient depletion coincides with decreased expression of antiviral type I IFN and the systemic inflammatory cytokines CXCL10 and IL-6. Importantly, COVID-19 disease severity correlated with decreased pDC frequency in peripheral blood. Using an in vitro stem cell-based human pDC model, we demonstrate that pDCs directly sense SARS-CoV-2 and in response produce multiple antiviral (IFN and IFN{lambda}1) and inflammatory (IL-6, IL-8, CXCL10) cytokines. This immune response is sufficient to protect epithelial cells from de novo SARS-CoV-2 infection. Targeted deletion of specific sensing pathways identified TLR7-MyD88 signaling as being crucial for production of the antiviral IFNs, whereas TLR2 is responsible for the inflammatory IL-6 response. Surprisingly, we found that SARS-CoV-2 engages the neuropilin-1 receptor on pDCs to mitigate the antiviral IFNs but not the IL-6 response. These results demonstrate distinct sensing pathways used by pDCs to elicit antiviral vs. immunopathological responses to SARS-CoV-2 and suggest that targeting neuropilin-1 on pDCs may be clinically relevant for mounting TLR7-mediated antiviral protection.\n\nOne Sentence SummarypDCs sense SARS-CoV-2 and elicit antiviral protection of lung epithelial cells through TLR7, while recognition of TLR2 elicits an IL-6 inflammatory response associated with immunopathology.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC=\"FIGDIR/small/469755v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (35K):\norg.highwire.dtl.DTLVardef@fe64daorg.highwire.dtl.DTLVardef@18f4278org.highwire.dtl.DTLVardef@54de50org.highwire.dtl.DTLVardef@1cf67cb_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract:C_FLOATNO SARS-CoV-2 sensing by plasmacytoid dendritic cells.\n\nSARS-CoV-2 is internalized by pDCs via a yet unknown endocytic mechanism. The intracellular TLR7 sensor detects viral RNA and induces a signaling cascade involving MyD88-IRAK4-TRAF6 (1) to induce CXCL10 and, via IRF7 phosphorylation and translocation, inducing type I and III Interferons (2). Once secreted, type I and III IFNs initiate autocrine and paracrine signals that induce the expression of IFN stimulated genes (ISGs), thereby facilitating an antiviral response that can protect the cell against infection. However, SARS-CoV-2, has the intrinsic property to facilitate CD304 signaling, potentially by interfering with IRF7 nuclear translocation, thereby inhibiting type I IFN production and thus reducing the antiviral response generated by the pDC (4). Furthermore, the SARS-CoV-2 envelope (E) glycoprotein is sensed by the extracellular TLR2/6 heterodimer and this facilitates production of the inflammatory IL-6 cytokine (5). Illustration was created with BioRender.com\n\nC_FIG", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Renee M van der Sluis", + "author_inst": "Aarhus University" + }, + { + "author_name": "Lamin B Cham", + "author_inst": "Aarhus University Hospital" + }, + { + "author_name": "Alberg Gris Oliver", + "author_inst": "Aarhus University" + }, + { + "author_name": "Kristine Raaby Gammelgaard", + "author_inst": "Aarhus University" + }, + { + "author_name": "Jesper Geert Pedersen", + "author_inst": "Aarhus University" + }, + { + "author_name": "Manja Idorn", + "author_inst": "Aarhus University" + }, + { + "author_name": "Ulvi Ahmodov", + "author_inst": "Aarhus University" + }, + { + "author_name": "Sabina S Hernandez", + "author_inst": "Aarhus University" + }, + { + "author_name": "Ena Cemalovic", + "author_inst": "Aarhus University" + }, + { + "author_name": "Stine H Godsk", + "author_inst": "Aarhus University" + }, + { + "author_name": "Jakob Thyrsted", + "author_inst": "Aarhus University" + }, + { + "author_name": "Jesper D Gunst", + "author_inst": "Aarhus University Hospital" + }, + { + "author_name": "Silke D Nielsen", + "author_inst": "Aarhus University" + }, + { + "author_name": "Janni j Jorgensen", + "author_inst": "Aarhus University" + }, + { + "author_name": "Tobias W Bjerg", + "author_inst": "Aarhus University" + }, + { + "author_name": "Anders Laustsen", + "author_inst": "Aarhus University" + }, + { + "author_name": "Line Reinert", + "author_inst": "Aarhus University" + }, + { + "author_name": "David Olagnier", + "author_inst": "Aarhus University" + }, + { + "author_name": "Rasmus O. Bak", + "author_inst": "Aarhus University" + }, + { + "author_name": "Mads Kjolby", + "author_inst": "Aarhus University" + }, + { + "author_name": "Christian Kanstrup Holm", + "author_inst": "Aarhus University" + }, + { + "author_name": "Martin Tolstrup", + "author_inst": "Aarhus University Hospital" + }, + { + "author_name": "Soren R. Paludan", + "author_inst": "Aarhus University" + }, + { + "author_name": "lasse S Kristensen", + "author_inst": "Aarhus University" + }, + { + "author_name": "Ole S Sogaard", + "author_inst": "Aarhus University Hospital" + }, + { + "author_name": "Martin R Jakobsen", + "author_inst": "Aarhus University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.11.24.469842", "rel_title": "Single-domain antibodies efficiently neutralize SARS-CoV-2 variants of concern", @@ -511257,29 +512977,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.11.17.21266461", - "rel_title": "Space-time Classification Index for Assessing COVID-19 Hotspots", - "rel_date": "2021-11-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.17.21266461", - "rel_abs": "ObjectivesTo develop new methods to address problems associated with use of traditional measures of disease surveillance, including prevalence and positivity rates.\n\nMethodsWe use data from the public New York Times Github repository to develop a space-time classification index of COVID-19 hotspots. The Local Indicator of Spatial Association (LISA) statistic is applied to identify daily clusters of COVID-19 cases, from July 4th to July 19th.\n\nResultsThe classification index is a spatial and temporal assessment tool that seeks to incorporate temporal trends of the clusters that are \"high-high\" and \"high-low\". Two classifications support the index: severity and temporal duration. We define severity as the number of times a county is statistically significant and temporal duration captures the number of consecutive days a county is a hotspot.\n\nConclusionsThe space-time classification index provides a statistically robust measure of the spatial patterns of COVID-19 hotspots. Spatial information is not captured through measures like the positivity rate, which merely divides the number of cases by tests conducted. The index proposed in this paper can guide intervention efforts by classifying counties with six-levels of importance.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "David Haynes II", - "author_inst": "Institute for Health Informatics, University of Minnesota" - }, - { - "author_name": "Chetan Tiwari", - "author_inst": "Departments of Geosciences & Computer Science, Georgia State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.17.21266441", "rel_title": "Pausing methotrexate improves immunogenicity of COVID-19 vaccination in patients with rheumatic diseases", @@ -511608,6 +513305,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.11.21.469172", + "rel_title": "Identification of a promiscuous conserved CTL epitope within the SARS-CoV-2 spike protein", + "rel_date": "2021-11-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.21.469172", + "rel_abs": "The COVID-19 disease caused by infection with SARS-CoV-2 and its variants is devastating to the global public health and economy. To date, over a hundred COVID-19 vaccines are known to be under development and the few that have been approved to fight the disease are using the spike protein as the primary target antigen. Although virus neutralizing epitopes are mainly located within the RBD of the spike protein, the presence of T cell epitopes, particularly the CTL epitopes that are likely to be needed for killing infected cells, has received comparatively little attention. In this study, we predicted several potential T cell epitopes with web-based analytic tools, and narrowed them down from several potential MHC-I and MHC-II epitopes by ELIspot and cytolytic assays to a conserved MHC-I epitope. The epitope is highly conserved in current viral variants including the most recent Omicron and compatible with presentation by most HLA alleles worldwide. In conclusion, we identified a CTL epitope suitable for evaluating the CD8+ T cell-mediated cellular response and potentially for addition into future COVID-19 vaccine candidates to maximize CTL responses against SARS-CoV-2.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Sheng Jiang", + "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College(SHMC), Fudan University" + }, + { + "author_name": "Shuting Wu", + "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College(SHMC), Fudan University" + }, + { + "author_name": "Gan Zhao", + "author_inst": "Advaccine Biopharmaceutics (Suzhou) Co. LTD, Jiangsu Province, China." + }, + { + "author_name": "Yue He", + "author_inst": "Advaccine Biopharmaceutics (Suzhou) Co. LTD" + }, + { + "author_name": "Xinrong Guo", + "author_inst": "Colby College, Waterville, Maine, USA" + }, + { + "author_name": "Zhiyu Zhang", + "author_inst": "Advaccine Biopharmaceutics (Suzhou) Co. LTD, Jiangsu Province, China." + }, + { + "author_name": "Jiawang Hou", + "author_inst": "Advaccine Biopharmaceutics (Suzhou) Co. LTD, Jiangsu Province, China" + }, + { + "author_name": "Yuan Ding", + "author_inst": "Advaccine Biopharmaceutics (Suzhou) Co. LTD, Jiangsu Province, China." + }, + { + "author_name": "Alex Cheng", + "author_inst": "Advaccine Biopharmaceutics (Suzhou) Co. LTD, Jiangsu Province, China." + }, + { + "author_name": "Bin Wang", + "author_inst": "Fudan University Shanghai Basic Medical Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.11.21.469423", "rel_title": "Conserved recombination patterns across coronavirus subgenera", @@ -513267,73 +515019,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.17.21266499", - "rel_title": "Comprehensive genomic, immunological and clinical analysis of COVID-19 vaccine breakthrough infections: a prospective, comparative cohort study", - "rel_date": "2021-11-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.17.21266499", - "rel_abs": "ObjectivesAs the COVID-19 pandemic is still ongoing and SARS-CoV-2 variants are circulating worldwide, an increasing number of breakthrough infections have been detected despite the good efficacy of COVID-19 vaccines.\n\nMethodsA prospective, comparative cohort study was conducted in Beijing Ditan Hospital to evaluate the clinical, immunological and genomic characteristics of COVID-19 breakthrough infections. Data on 88 COVID-19 breakthrough cases (vaccinated group) and 41 unvaccinated cases (unvaccinated group) from June 1 to August 20, 2021 were extracted from a cloud database. Among these 129 COVID-19 cases, we successfully sequenced 33 whole genomes, including 16 from the vaccinated group and 17 from the unvaccinated group.\n\nResultsAsymptomatic and mild cases predominated in both groups, but 2 patients developed severe disease in the unvaccinated group. Between the two groups, the median time of viral shedding in the vaccinated group were significantly lower than those in the unvaccinated group (p = 0.003). A comparison of dynamic IgG titres of cases in the two groups indicated that IgG titres in the vaccinated group showed a significantly increasing trend (P =0.028). The CD4+T lymphocyte count was lower in the unvaccinated group, and there was a significant difference between the two groups (p=0.018). In the vaccinated group, the number of moderate cases who received Sinopharm BBIBP (42 cases) was significantly higher than those who received Sinovac Coronavac (p=0.020). Whole-genome sequencing revealed 23 cases of delta variants, including 15 patients from the vaccinated group. However, no significant difference was observed in either the RT-qPCR results or viral shedding time.\n\nConclusionsCOVID-19 vaccine breakthrough infections were mainly asymptomatic and mild, the IgG titres were significantly higher and increased rapidly, and the viral shedding was short. Delta variants may be more likely to cause breakthrough infections, and vaccination may not reduce the viral loads and shedding time.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Di Tian", - "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing, China" - }, - { - "author_name": "Yang Song", - "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China." - }, - { - "author_name": "Man Zhang", - "author_inst": "Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control (CDC), Beijing, China; Research Centre for Preve" - }, - { - "author_name": "Yang Pan", - "author_inst": "Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control (CDC), Beijing, China; Research Centre for Preve" - }, - { - "author_name": "Ziruo Ge", - "author_inst": "Emergency Department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China." - }, - { - "author_name": "Yao Zhang", - "author_inst": "Emergency Department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China." - }, - { - "author_name": "Xingxiang Ren", - "author_inst": "Emergency Department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China." - }, - { - "author_name": "Jing Wen", - "author_inst": "Emergency Department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China." - }, - { - "author_name": "Yanli Xu", - "author_inst": "Emergency Department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China." - }, - { - "author_name": "Hong Guo", - "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China." - }, - { - "author_name": "Peng Yang", - "author_inst": "Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control (CDC), Beijing, China; Research Centre for Preve" - }, - { - "author_name": "Zhihai Chen", - "author_inst": "Emergency Department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China." - }, - { - "author_name": "Wenbo Xu", - "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.20.21266644", "rel_title": "Immunogenicity of heterologous prime/boost inactivated and mRNA COVID-19 vaccine", @@ -513494,6 +515179,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2021.11.18.21266501", + "rel_title": "Risk factors for workplace bullying, severe psychological distress, and suicidal ideation during the COVID-19 pandemic: a nationwide internet survey for the general working population in Japan", + "rel_date": "2021-11-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.18.21266501", + "rel_abs": "ObjectivesThe pandemic of the new coronavirus disease (COVID-19) has created a challenging environment for workers. This study aimed to investigate the risk factors for workplace bullying and mental health outcomes during the pandemic among workers.\n\nMethodsWe conducted a nationwide online cross-sectional survey from August to September 2020 in Japan (N = 16,384). Workplace bullying was measured by one item from the Brief Job Stress Questionnaire; severe psychological distress (SPD) by K6 ([≥]13); and suicidal ideation by one item. Prevalence ratios were calculated by Poisson regression analyses adjusting for potential confounders such as gender, age, occupational characteristics, and a prior history of depression.\n\nResultsOverall, 15% of workers experienced workplace bullying, 9% had SPD, and 12% had suicidal ideation during the second and third wave of the COVID-19 pandemic in Japan. The results of this study showed men, executives, managers, and permanent employees had a higher risk of bullying compared to women or part-time workers.\n\nIncreased physical and psychological demands were common risk factors for bullying, SPD, and suicidal ideation. Newly starting working from home was a significant predictor for adverse mental health outcomes, however, it was found to be a preventive factor against workplace bullying.\n\nConclusionsThe results of this study found different high-risk groups for bullying or mental health during the pandemic. When intervening to decrease workplace bullying or mental health problems, we should focus on not only previously reported vulnerable workers but also workers who experienced a change of their working styles or job demands.\n\nKey messagesO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIWorkplace bullying is one of the severe job stressors in the workplace that cause mental health problems.\nC_LIO_LIHealth care workers, less-educated workers, and non-regular female workers have been reported to have greater psychological distress during the COVID-19 pandemic.\nC_LI\n\nWhat are the new findings?O_LIAbout 15% of workers experienced workplace bullying, 9% had SPD, and 12% had suicidal ideation during the pandemic in Japan.\nC_LIO_LIMen, executives, managers, and permanent workers had a higher risk of bullying compared to women or part-time workers.\nC_LIO_LIIncreased physical or psychological demands were common risk factors for bullying, SPD, and suicidal ideation.\nC_LIO_LIWhile newly starting working from home was a preventive factor against workplace bullying, it was found to be a significant risk factor for adverse mental health outcomes.\nC_LI\n\nHow might this impact on policy or clinical practice in the foreseeable future?O_LIThe results of this study indicate a different pattern of high-risk groups for bullying or mental health during the pandemic.\nC_LIO_LIWhen intervening to decrease workplace bullying or mental health problems, we should focus on not only previously reported vulnerable workers but also workers who experienced a change of their working styles or job demands.\nC_LI", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Kanami Tsuno", + "author_inst": "Kanagawa University of Human Services" + }, + { + "author_name": "Takahiro Tabuchi", + "author_inst": "Osaka International Cancer Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.11.19.21266537", "rel_title": "Effectiveness of Vaccination Against Reported SARS-CoV-2 Infection in United States Coast Guard Personnel Between May and August 2021: A Time-Series Analysis", @@ -514873,61 +516581,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.11.16.21266408", - "rel_title": "HLA-A*03:01 is associated with increased risk of fever, chills, and more severe reaction to Pfizer-BioNTech COVID-19 vaccination", - "rel_date": "2021-11-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.16.21266408", - "rel_abs": "COVID-19 vaccines are safe and highly effective, but some individuals experience unpleasant reactions to vaccination. As the majority of adults in the US have received a COVID-19 vaccine this year, there is an unprecedented opportunity to study the genetics of reactions to vaccination via surveys of individuals who are already part of genetic research studies. Here, we have queried 17,440 participants in the Helix DNA Discovery Project and Healthy Nevada Project about their reactions to COVID-19 vaccination. Our GWAS identifies an association between severe difficulties with daily routine after vaccination and HLA-A*03:01. This association was statistically significant only for those who received the Pfizer-BioNTech vaccine (BNT162b2; p=4.70E-11), but showed a trending association in those who received the Moderna vaccine (mRNA-1273; p=0.005) despite similar sample sizes for study. In Pfizer-BioNTech recipients, HLA-A*03:01 was associated with a two-fold increase in risk of severe vaccine reactions. The effect was consistent across ages, sexes, and whether the person had previously had a COVID-19 infection. The reactions experienced by HLA-A*03:01 carriers were driven by associations with chills, fever, fatigue, and in general feeling unwell.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Alexandre Bolze", - "author_inst": "Helix" - }, - { - "author_name": "Iva Neveux", - "author_inst": "Desert Research Institute" - }, - { - "author_name": "Kelly M Schiabor Barrett", - "author_inst": "Helix" - }, - { - "author_name": "Simon White", - "author_inst": "Helix" - }, - { - "author_name": "Magnus Isaksson", - "author_inst": "Helix" - }, - { - "author_name": "Shaun Dabe", - "author_inst": "Renown Health" - }, - { - "author_name": "William Lee", - "author_inst": "Helix" - }, - { - "author_name": "Joseph J Grzymski", - "author_inst": "Desert Research Institute" - }, - { - "author_name": "Nicole L Washington", - "author_inst": "Helix" - }, - { - "author_name": "Elizabeth T Cirulli", - "author_inst": "Helix" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.17.21266410", "rel_title": "COVID-19 management in social care in England: a systematic review of changing policies and newspaper reported staff perspectives.", @@ -515116,6 +516769,137 @@ "type": "PUBLISHAHEADOFPRINT", "category": "palliative medicine" }, + { + "rel_doi": "10.1101/2021.11.12.21265796", + "rel_title": "Transmission potential of vaccinated and unvaccinated persons infected with the SARS-CoV-2 Delta variant in a federal prison, July-August 2021", + "rel_date": "2021-11-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.12.21265796", + "rel_abs": "BackgroundThe extent to which vaccinated persons who become infected with SARS-CoV-2 contribute to transmission is unclear. During a SARS-CoV-2 Delta variant outbreak among incarcerated persons with high vaccination rates in a federal prison, we assessed markers of viral shedding in vaccinated and unvaccinated persons.\n\nMethodsConsenting incarcerated persons with confirmed SARS-CoV-2 infection provided mid-turbinate nasal specimens daily for 10 consecutive days and reported symptom data via questionnaire. Real-time reverse transcription-polymerase chain reaction (RT-PCR), viral whole genome sequencing, and viral culture was performed on these nasal specimens. Duration of RT-PCR positivity and viral culture positivity was assessed using survival analysis.\n\nResultsA total of 978 specimens were provided by 95 participants, of whom 78 (82%) were fully vaccinated and 17 (18%) were not fully vaccinated. No significant differences were detected in duration of RT-PCR positivity among fully vaccinated participants (median: 13 days) versus those not fully vaccinated (median: 13 days; p=0.50), or in duration of culture positivity (medians: 5 days and 5 days; p=0.29). Among fully vaccinated participants, overall duration of culture positivity was shorter among Moderna vaccine recipients versus Pfizer (p=0.048) or Janssen (p=0.003) vaccine recipients.\n\nConclusionsAs this field continues to develop, clinicians and public health practitioners should consider vaccinated persons who become infected with SARS-CoV-2 to be no less infectious than unvaccinated persons. These findings are critically important, especially in congregate settings where viral transmission can lead to large outbreaks.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Phillip P. Salvatore", + "author_inst": "U.S. Centers for Disease Control & Prevention" + }, + { + "author_name": "Christine C. Lee", + "author_inst": "U.S. Centers for Disease Control & Prevention" + }, + { + "author_name": "Sadia Sleweon", + "author_inst": "U.S. Centers for Disease Control & Prevention" + }, + { + "author_name": "David W. McCormick", + "author_inst": "U.S. Centers for Disease Control & Prevention" + }, + { + "author_name": "Lavinia Nicolae", + "author_inst": "U.S. Centers for Disease Control & Prevention" + }, + { + "author_name": "Kristen Knipe", + "author_inst": "U.S. Centers for Disease Control & Prevention" + }, + { + "author_name": "Thomas Dixon", + "author_inst": "Bureau of Prisons, U.S. Department of Justice" + }, + { + "author_name": "Robert Banta", + "author_inst": "Bureau of Prisons, U.S. Department of Justice" + }, + { + "author_name": "Isaac Ogle", + "author_inst": "Bureau of Prisons, U.S. Department of Justice" + }, + { + "author_name": "Cristen Young", + "author_inst": "Bureau of Prisons, U.S. Department of Justice" + }, + { + "author_name": "Charles Dusseau", + "author_inst": "Bureau of Prisons, U.S. Department of Justice" + }, + { + "author_name": "Shawn Salmonson", + "author_inst": "Bureau of Prisons, U.S. Department of Justice" + }, + { + "author_name": "Charles Ogden", + "author_inst": "Bureau of Prisons, U.S. Department of Justice" + }, + { + "author_name": "Eric Godwin", + "author_inst": "Bureau of Prisons, U.S. Department of Justice" + }, + { + "author_name": "TeCora Ballom", + "author_inst": "Bureau of Prisons, U.S. Department of Justice" + }, + { + "author_name": "Tara Ross", + "author_inst": "Bureau of Prisons, U.S. Department of Justice" + }, + { + "author_name": "Nhien Tran Wynn", + "author_inst": "U.S. Centers for Disease Control & Prevention" + }, + { + "author_name": "Ebenezer David", + "author_inst": "U.S. Centers for Disease Control & Prevention" + }, + { + "author_name": "Theresa K. Bessey", + "author_inst": "U.S. Centers for Disease Control & Prevention" + }, + { + "author_name": "Gimin Kim", + "author_inst": "U.S. Centers for Disease Control & Prevention" + }, + { + "author_name": "Suganthi Suppiah", + "author_inst": "U.S. Centers for Disease Control & Prevention" + }, + { + "author_name": "Azaibi Tamin", + "author_inst": "U.S. Centers for Disease Control & Prevention" + }, + { + "author_name": "Jennifer L. Harcourt", + "author_inst": "U.S. Centers for Disease Control & Prevention" + }, + { + "author_name": "Mili Sheth", + "author_inst": "U.S. Centers for Disease Control & Prevention" + }, + { + "author_name": "Luis Lowe", + "author_inst": "U.S. Centers for Disease Control & Prevention" + }, + { + "author_name": "Hannah Browne", + "author_inst": "U.S. Centers for Disease Control & Prevention" + }, + { + "author_name": "Jacqueline E. Tate", + "author_inst": "U.S. Centers for Disease Control & Prevention" + }, + { + "author_name": "Hannah L. Kirking", + "author_inst": "U.S. Centers for Disease Control & Prevention" + }, + { + "author_name": "Liesl M. Hagan", + "author_inst": "U.S. Centers for Disease Control & Prevention" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.18.21266558", "rel_title": "Effectiveness of digital contact tracing for COVID-19 in New South Wales, Australia", @@ -516399,29 +518183,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2021.11.17.468929", - "rel_title": "Predicting SARS-CoV-2 epitope-specific TCR recognition using pre-trained protein embeddings", - "rel_date": "2021-11-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.17.468929", - "rel_abs": "The COVID-19 pandemic is ongoing because of the high transmission rate and the emergence of SARS-CoV-2 variants. The P272L mutation in SARS-Cov-2 S-protein is known to be highly relevant to the viral escape associated with the second pandemic wave in Europe. Epitope-specific T-cell receptor (TCR) recognition is a key factor in determining the T-cell immunogenicity of a SARS-CoV-2 epitope. Although several data-driven methods for predicting epitope-specific TCR recognition have been proposed, they remain challenging owing to the enormous diversity of TCRs and the lack of available training data. Self-supervised transfer learning has recently been demonstrated to be powerful for extracting useful information from unlabeled protein sequences and increasing the predictive performance of the fine-tuned models in downstream tasks.\n\nHere, we present a predictive model based on Bidirectional Encoder Representations from Transformers (BERT), employing self-supervised transfer learning, to predict SARS-CoV-2 T-cell epitope-specific TCR recognition. The fine-tuned model showed notably high predictive performance for independent evaluation using the SARS-CoV-2 epitope-specific TCR CDR3{beta} sequence datasets. In particular, we found the proline at position 4 corresponding to the P272L mutation in the SARS-CoV-2 S-protein269-277 epitope (YLQPRTFLL) may contribute substantially to TCR recognition of the epitope through interpreting the output attention weights of our model.\n\nWe anticipate that our findings will provide new directions for constructing a reliable data-driven model to predict the immunogenic T-cell epitopes using limited training data and help accelerate the development of an effective vaccine in response to SARS-CoV-2 variants.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Youngmahn Han", - "author_inst": "Korea Institute of Science and Technology Information" - }, - { - "author_name": "Aeri Lee", - "author_inst": "BioBrain Inc" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.11.15.468720", "rel_title": "Susceptibility of sheep to experimental co-infection with the ancestral lineage of SARS-CoV-2 and its alpha variant", @@ -516714,6 +518475,45 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.11.16.468802", + "rel_title": "NUDT18 catalyzes hydrolysis of active metabolites of the antivirals Remdesivir and Ribavirin", + "rel_date": "2021-11-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.16.468802", + "rel_abs": "Remdesivir and Molnupiravir have gained considerable interest due to their activity against SARS-CoV-2. Cellular hydrolysis of their active triphosphate forms, Remdesivir-TP and Molnupiravir-TP, would decrease drug efficiency. We therefore tested Remdesivir-TP as a substrate against a panel of human hydrolases and found that NUDT18 catalyzes the hydrolysis of Remdesivir-TP. The kcat value of NUDT18 for Remdesivir-TP was determined to 2.6 s-1 and the Km value was 156 M, suggesting that NUDT18 catalyzed hydrolysis of Remdesivir-TP occurs in cells. We demonstrate that the triphosphates of the antivirals Ribavirin and Molnupiravir are hydrolyzed by NUDT18, albeit with a lower efficiency compared to Remdesivir-TP. NUDT18 also hydrolyses the triphosphates of Sofosbuvir and Aciclovir although with significantly lower activity. These results suggest that NUDT18 can act as a cellular sanitizer of modified nucleotides and may influence the antiviral efficacy of Remdesivir, Molnupiravir and Ribavirin. NUDT18 is expressed in respiratory epithelial cells and may limit the antiviral efficacy of Remdesivir and Molnupiravir against SARS-CoV2 replication by decreasing the intracellular concentration of their active metabolites at their intended site of action.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ann-Sofie Jemth", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Emma Rose Scaletti", + "author_inst": "Stockholm University" + }, + { + "author_name": "Evert Jan Homan", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Pal Stenmark", + "author_inst": "Stockholm University" + }, + { + "author_name": "Thomas Helleday", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Maurice Michel", + "author_inst": "Karolinska Institutet" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.11.17.468942", "rel_title": "IFITM dependency of SARS-CoV-2 variants of concern", @@ -518201,225 +520001,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.12.468428", - "rel_title": "#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol", - "rel_date": "2021-11-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.12.468428", - "rel_abs": "We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus ob-scure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized.\n\nACM Reference FormatAbigail Dommer1{dagger}, Lorenzo Casalino1{dagger}, Fiona Kearns1{dagger}, Mia Rosenfeld1, Nicholas Wauer1, Surl-Hee Ahn1, John Russo,2 Sofia Oliveira3, Clare Morris1, AnthonyBogetti4, AndaTrifan5,6, Alexander Brace5,7, TerraSztain1,8, Austin Clyde5,7, Heng Ma5, Chakra Chennubhotla4, Hyungro Lee9, Matteo Turilli9, Syma Khalid10, Teresa Tamayo-Mendoza11, Matthew Welborn11, Anders Christensen11, Daniel G. A. Smith11, Zhuoran Qiao12, Sai Krishna Sirumalla11, Michael OConnor11, Frederick Manby11, Anima Anandkumar12,13, David Hardy6, James Phillips6, Abraham Stern13, Josh Romero13, David Clark13, Mitchell Dorrell14, Tom Maiden14, Lei Huang15, John McCalpin15, Christo- pherWoods3, Alan Gray13, MattWilliams3, Bryan Barker16, HarindaRajapaksha16, Richard Pitts16, Tom Gibbs13, John Stone6, Daniel Zuckerman2*, Adrian Mulholland3*, Thomas MillerIII11,12*, ShantenuJha9*, Arvind Ramanathan5*, Lillian Chong4*, Rommie Amaro1*. 2021. #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy ofDeltaSARS-CoV-2 in a Respiratory Aerosol. In Supercomputing 21: International Conference for High Perfor-mance Computing, Networking, Storage, and Analysis. ACM, New York, NY, USA, 14 pages. https://doi.org/finalDOI", - "rel_num_authors": 51, - "rel_authors": [ - { - "author_name": "Abigail Dommer", - "author_inst": "UC San Diego" - }, - { - "author_name": "Lorenzo Casalino", - "author_inst": "UC San Diego" - }, - { - "author_name": "Fiona Kearns", - "author_inst": "UC San Diego" - }, - { - "author_name": "Mia Rosenfeld", - "author_inst": "UC San Diego" - }, - { - "author_name": "Nicholas Wauer", - "author_inst": "UC San Diego" - }, - { - "author_name": "Surl-Hee Ahn", - "author_inst": "UC San Diego" - }, - { - "author_name": "John Russo", - "author_inst": "OHSU" - }, - { - "author_name": "Sofia Oliveira", - "author_inst": "U Bristol" - }, - { - "author_name": "Clare Morris", - "author_inst": "UC San Diego" - }, - { - "author_name": "Anthony Bogetti", - "author_inst": "U Pittsburgh" - }, - { - "author_name": "Anda Trifan", - "author_inst": "University of Illinois at Urbana/ Champaign and Argonne National Lab" - }, - { - "author_name": "Alexander Brace", - "author_inst": "Argonne National Lab" - }, - { - "author_name": "Terra Sztain", - "author_inst": "Freie University Berlin" - }, - { - "author_name": "Austin Clyde", - "author_inst": "Argonne National Lab" - }, - { - "author_name": "Heng Ma", - "author_inst": "Argonne National Lab" - }, - { - "author_name": "Chakra Chennubhotla", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Hyungro Lee", - "author_inst": "Rutgers U" - }, - { - "author_name": "Matteo Turilli", - "author_inst": "Rutgers U" - }, - { - "author_name": "Syma Khalid", - "author_inst": "U Oxford" - }, - { - "author_name": "Teresa Tamayo-Mendoza", - "author_inst": "Entos, Inc" - }, - { - "author_name": "Matthew Welborn", - "author_inst": "Entos, Inc" - }, - { - "author_name": "Anders Christiansen", - "author_inst": "Entos, Inc" - }, - { - "author_name": "Daniel G.A. Smith", - "author_inst": "Entos, Inc" - }, - { - "author_name": "Zhuoran Qiao", - "author_inst": "Entos, Inc" - }, - { - "author_name": "Sai Krishna Sirumalla", - "author_inst": "Entos, Inc" - }, - { - "author_name": "Frederick Manby", - "author_inst": "Entos, Inc" - }, - { - "author_name": "Anima Anandkumar", - "author_inst": "California Institute of Technology & NVIDIA, Inc" - }, - { - "author_name": "David Hardy", - "author_inst": "University of Illinois at Urbana / Champaign" - }, - { - "author_name": "James Phillips", - "author_inst": "University of Illinois at Urbana / Champaign" - }, - { - "author_name": "Abraham Stern", - "author_inst": "NVIDIA Corp" - }, - { - "author_name": "Josh Romero", - "author_inst": "NVIDIA Corp" - }, - { - "author_name": "David Clark", - "author_inst": "NVIDIA Corp" - }, - { - "author_name": "Mitchell Dorrell", - "author_inst": "Pittsburgh Supercomputing Center" - }, - { - "author_name": "Tom Maiden", - "author_inst": "Pittsburgh Supercomputing Center" - }, - { - "author_name": "Lei Huang", - "author_inst": "Texas Advanced Computing Center" - }, - { - "author_name": "John McCalpin", - "author_inst": "Texas Advanced Computing Center" - }, - { - "author_name": "Christopher Woods", - "author_inst": "U Bristol" - }, - { - "author_name": "Alan Gray", - "author_inst": "NVIDIA Corp" - }, - { - "author_name": "Matt Williams", - "author_inst": "U Bristol" - }, - { - "author_name": "Bryan Barker", - "author_inst": "Oracle for Research" - }, - { - "author_name": "Harinda Rajapaksha", - "author_inst": "Oracle for Research" - }, - { - "author_name": "Richard Pitts", - "author_inst": "Oracle for Research" - }, - { - "author_name": "Tom Gibbs", - "author_inst": "NVIDIA Corp" - }, - { - "author_name": "John Stone", - "author_inst": "University of Illinois at Urbana/Champaign" - }, - { - "author_name": "Daniel Zuckerman", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Adrian Muholland", - "author_inst": "University of Bristol" - }, - { - "author_name": "Thomas Miller III", - "author_inst": "California Institute of Technology & Entos, Inc" - }, - { - "author_name": "Shantenu Jha", - "author_inst": "Rutgers University" - }, - { - "author_name": "Arvind Ramanathan", - "author_inst": "Argonne National Lab" - }, - { - "author_name": "Lillian Chong", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Rommie E Amaro", - "author_inst": "University of California San Diego" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.11.15.468283", "rel_title": "Mutagenic distinction between the receptor-binding and fusion subunits of the SARS-CoV-2 spike glycoprotein", @@ -518700,6 +520281,41 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.11.13.21266289", + "rel_title": "AI/ML Models to Aid in the Diagnosis of COVID-19 Illness from Forced Cough Vocalizations: Good Machine Learning Practice and Good Clinical Practices from Concept to Consumer for AI/ML Software Devices", + "rel_date": "2021-11-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.13.21266289", + "rel_abs": "From a comprehensive and systematic search of the relevant literature on signal data signature (SDS)-based artificial intelligence/machine learning (AI/ML) systems designed to aid in the diagnosis of COVID-19 illness, we identified the highest quality articles with statistically significant data sets for a head-to-head comparison to our own model in development. Further comparisons were made to the recently released \"Good Machine Learning Practice (GMLP) for Medical Device Development: Guiding Principles\" and, in conclusions, we proposed supplemental principles aimed at bringing AI/ML technologies in closer alignment GMLP and Good Clinical Practices (GCP).", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Karl Kelley", + "author_inst": "RAIsonance, Inc." + }, + { + "author_name": "Mona Kelley", + "author_inst": "RAIsonance, Inc." + }, + { + "author_name": "S. Caitlin Kelley", + "author_inst": "RAIsonance, inc." + }, + { + "author_name": "Allison A. Sakara", + "author_inst": "RAIsonance, Inc." + }, + { + "author_name": "Maurice A. Ramirez", + "author_inst": "RAIsonance, Inc" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.11.13.468472", "rel_title": "A live attenuated influenza virus-vectored intranasal COVID-19 vaccine provides rapid, prolonged, and broad protection against SARS-CoV-2 infection", @@ -520411,113 +522027,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.12.21266250", - "rel_title": "Protection offered by mRNA-1273 versus BNT162b2 vaccines against SARS-CoV-2 infection and severe COVID-19 in Qatar", - "rel_date": "2021-11-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.12.21266250", - "rel_abs": "BACKGROUNDGrowing evidence suggests that COVID-19 vaccines differ in effectiveness against breakthrough infection or severe COVID-19, but vaccines have yet to be investigated in controlled studies that head-to-head compare immunity of one to another. This study compared protection offered by the mRNA-1273 (Moderna) vaccine with that of the BNT162b2 (Pfizer-BioNTech) vaccine in Qatar.\n\nMETHODSIn a population of 1,531,736 vaccinated persons, two matched retrospective cohort studies were designed and used to investigate differences in mRNA-1273 and BNT162b2 vaccine protection, after the first and second doses, from December 21, 2020 to October 20, 2021.\n\nRESULTSAfter dose 1, cumulative incidence of breakthrough infection was 0.79% (95% CI: 0.75-0.83%) for mRNA-1273-vaccinated individuals and 0.86% (95% CI: 0.82-0.90%) for BNT162b2-vaccinated individuals, 21 days post-injection. Adjusted hazard ratio (AHR) for breakthrough infection was 0.89 (95% CI: 0.83-0.95; p=0.001). AHR was constant in the first two weeks at 1, but it declined to 0.67 (95% CI: 0.57-0.77; p<0.001) in the third week after dose 1. AHR for any severe, critical, or fatal COVID-19 was 0.71 (95% CI: 0.53-0.95; p=0.020). After dose 2, cumulative incidence was 0.59% (95% CI: 0.55-0.64%) for mRNA-1273-vaccinated individuals and 0.84% (95% CI: 0.79-0.89%) for BNT162b2-vaccinated individuals, 180 days post-injection. AHR for breakthrough infection was 0.69 (95% CI: 0.63-0.75; p<0.001) and was largely constant over time after dose 2. AHR for any severe, critical, or fatal COVID-19 was 0.37 (95% CI: 0.10-1.41; p=0.147).\n\nCONCLUSIONSmRNA-1273 vaccination is associated with lower SARS-CoV-2 breakthrough infection and COVID-19 hospitalization and death than BNT162b2 vaccination, but the number of hospitalizations and deaths was exceedingly small for both vaccines. Both vaccines demonstrated strikingly similar patterns of build-up of protection after the first dose and waning of protection after the second dose.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Laith J Abu-Raddad", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Hiam Chemaitelly", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Houssein H. Ayoub", - "author_inst": "Qatar University" - }, - { - "author_name": "Patrick J Tang", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "Mohammad Rubayet Hasan", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "Peter Coyle", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "HADI M. YASSINE", - "author_inst": "Qatar University" - }, - { - "author_name": "Fatiha Benslimane", - "author_inst": "Qatar University" - }, - { - "author_name": "Hebah A. Al-Khatib", - "author_inst": "Qatar University" - }, - { - "author_name": "Zaina Al-Kanaani", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Einas Al Kuwari", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Andrew Jeremijenko", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Anvar Hassan Kaleeckal", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Ali Nizar Latif", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Riyazuddin Mohammad Shaik", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Hanan F. Abdul Rahim", - "author_inst": "Qatar University" - }, - { - "author_name": "Gheyath Nasrallah", - "author_inst": "Qatar University" - }, - { - "author_name": "Mohamed Ghaith Al Kuwari", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Adeel A Butt", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Hamad Eid Al Romaihi", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Mohamed H. Al-Thani", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Abdullatif Al Khal", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Roberto Bertollini", - "author_inst": "Ministry of Public Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.10.467646", "rel_title": "Total virome characterizations of game animals in China reveals a spectrum of emerging viral pathogens", @@ -520766,6 +522275,33 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.11.10.468129", + "rel_title": "CORSID enables de novo identification of transcription regulatory sequences and genes in coronaviruses", + "rel_date": "2021-11-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.10.468129", + "rel_abs": "Genes in coronaviruses are preceded by transcription regulatory sequences (TRSs), which play a critical role in gene expression mediated by the viral RNA-dependent RNA-polymerase via the process of discontinuous transcription. In addition to being crucial for our understanding of the regulation and expression of coronavirus genes, we demonstrate for the first time how TRSs can be leveraged to identify gene locations in the coronavirus genome. To that end, we formulate the TRS AND GO_SCPLOWENEC_SCPLOW IO_SCPLOWDENTIFICATIONC_SCPLOW (TRS-GO_SCPLOWENEC_SCPLOW-ID) problem of simultaneously identifying TRS sites and gene locations in unannotated coronavirus genomes. We introduce CORSID (CORe Sequence IDentifier), a computational tool to solve this problem. We also present CORSID-A, which solves a constrained version of the TRS-GO_SCPLOWENEC_SCPLOW-ID problem, the TRS IO_SCPLOWDENTIFICATIONC_SCPLOW (TRS-ID) problem, identifying TRS sites in a coronavirus genome with specified gene annotations. We show that CORSID-A outperforms existing motif-based methods in identifying TRS sites in coronaviruses and that CORSID outperforms state-of-the-art gene finding methods in finding genes in coronavirus genomes. We demonstrate that CORSID enables de novo identification of TRS sites and genes in previously unannotated coronaviruses. CORSID is the first method to perform accurate and simultaneous identification of TRS sites and genes in coronavirus genomes without the use of any prior information.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Chuanyi Zhang", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Palash Sashittal", + "author_inst": "University of Illinois, Urbana-Champaign" + }, + { + "author_name": "Mohammed El-Kebir", + "author_inst": "University of Illinois at Urbana-Champaign" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.11.10.468168", "rel_title": "Ensemble cryo-electron microscopy reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex", @@ -522161,41 +523697,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.10.21266139", - "rel_title": "The role of antiviral treatment in curbing the COVID-19 pandemic: a modeling study.", - "rel_date": "2021-11-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.10.21266139", - "rel_abs": "Despite the development of safe and effective vaccines, effective treatments for COVID-19 disease are still urgently needed. Several antiviral drugs have shown to be effective in reducing progression of COVID-19 disease. In the present work, we use an agent-based mathematical model to assess the potential population impact of the use of antiviral treatments in four countries with different demographic structure and current levels of vaccination coverage: Kenya, Mexico, United States (US) and Belgium. We analyzed antiviral effects on reducing hospitalization and death, and potential antiviral effects on reducing transmission. For each country, we varied daily treatment initiation rate (DTIR) and antiviral effect in reducing transmission (AVT). Irrespective of location and AVT, widespread antiviral treatment of symptomatic adult infections ([≥]20% DTIR) prevented the majority of COVID-19 deaths, and recruiting 6% of all adult symptomatic infections daily reduced mortality by a third in all countries. Furthermore, our model projected that targeting antiviral treatment to the oldest age group (65 years old and older, DTIR of 20%) can prevent over 47% of deaths. Our results suggest that early antiviral treatment (as soon as possible after inception of infection) is needed to mitigate transmission, preventing 50% more infections compared to late treatment (started 3 to 5 days after symptoms onset). Our results highlight the synergistic effect of vaccination and antiviral treatment: as the vaccination rate increases, antivirals have a larger relative impact on population transmission. These results suggest that antiviral treatments can become a strategic tool that, in combination with vaccination, can significantly reduce COVID-19 hospitalizations and deaths and can help control SARS-CoV-2 transmission.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Laura Matrajt", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Elizabeth R Brown", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Myron S Cohen", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Dobromir Dimitrov", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Holly Janes", - "author_inst": "Fred Hutchinson Cancer Research Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.10.21266195", "rel_title": "Disparities in COVID-19 Fatalities among Working Californians", @@ -522544,6 +524045,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.10.468057", + "rel_title": "SARS-CoV-2 ORF8 encoded protein contains a histone mimic, disrupts chromatin regulation, and enhances replication", + "rel_date": "2021-11-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.10.468057", + "rel_abs": "SARS-CoV-2 emerged in China at the end of 2019 and caused the global pandemic of COVID-19, a disease with high morbidity and mortality. While our understanding of this new virus is rapidly increasing, gaps remain in our understanding of how SARS-CoV-2 can effectively suppress host cell antiviral responses. Recent work on other viruses has demonstrated a novel mechanism through which viral proteins can mimic critical regions of human histone proteins. Histone proteins are responsible for governing genome accessibility and their precise regulation is critical for a cells ability to control transcription and respond to viral threats. Here, we show that the protein encoded by ORF8 (Orf8) in SARS-CoV-2 functions as a histone mimic of the ARKS motif in histone 3. Orf8 is associated with chromatin, binds to numerous histone-associated proteins, and is itself acetylated within the histone mimic site. Orf8 expression in cells disrupts multiple critical histone post-translational modifications (PTMs) including H3K9ac, H3K9me3, and H3K27me3 and promotes chromatin compaction while Orf8 lacking the histone mimic motif does not. Further, SARS-CoV-2 infection in human cell lines and postmortem patient lung tissue cause these same disruptions to chromatin. However, deletion of the Orf8 gene from SARS-CoV-2 largely blocks its ability to disrupt host-cell chromatin indicating that Orf8 is responsible for these effects. Finally, deletion of the ORF8 gene affects the host-cell transcriptional response to SARS-CoV-2 infection in multiple cell types and decreases the replication of SARS-CoV-2 in human induced pluripotent stem cell-derived lung alveolar type 2 (iAT2) pulmonary cells. These findings demonstrate a novel function for the poorly understood ORF8-encoded protein and a mechanism through which SARS-CoV-2 disrupts host cell epigenetic regulation. Finally, this work provides a molecular basis for the finding that SARS-CoV-2 lacking ORF8 is associated with decreased severity of COVID-19.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "John Kee", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Samuel Thudium", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "David Renner", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Karl Glastad", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Katherine Palozola", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Zhen Zhang", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Yize Li", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Joseph Cesare", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Yemin Lan", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Rachel Truitt", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Fabian L Cardenas-Diaz", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Darrell N Kotton", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Konstantinos D Alysandratos", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Xianwen Zhang", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Xuping Xie", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Pei-Yong Shi", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Wenli Yang", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Edward Morrisey", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Benjamin A Garcia", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Shelley L Berger", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Susan R Weiss", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Erica Korb", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2021.11.11.21266189", "rel_title": "Tenofovir Disoproxil Fumarate and severity of COVID-19 in people with HIV infection", @@ -524146,53 +525750,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.05.21265970", - "rel_title": "Exploring Associations with Severe Hypoxemic Respiratory Failure in COVID-19 Patients upon Admission: A Model for Severe Hypoxemic Respiratory Failure in 329 Unvaccinated, Hospitalized COVID-19 Patients.", - "rel_date": "2021-11-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.05.21265970", - "rel_abs": "ObjectiveThe severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2) has caused a pandemic claiming more than 4 million lives worldwide. Overwhelming Coronavirus-Disease-2019 (COVID-19) respiratory failure placed tremendous demands on healthcare systems increasing the death toll. Cost-effective prognostic tools to characterize COVID-19 patients likely to progress to severe hypoxemic respiratory failure are still needed.\n\nDesignWe conducted a retrospective cohort study to develop a model utilizing demographic and clinical data collected in the first 12-hours admission to explore associations with severe hypoxemic respiratory failure in unvaccinated and hospitalized COVID-19 patients.\n\nSettingUniversity based healthcare system including 6 hospitals located in the Galveston, Brazoria and Harris counties of Texas.\n\nParticipantsAdult patients diagnosed with COVID-19 and admitted to one of six hospitals between March 19th and June 31st, 2020.\n\nPrimary outcomeThe primary outcome was defined as reaching a WHO ordinal scale between 6-9 at any time during admission, which corresponded to severe hypoxemic respiratory failure requiring high-flow oxygen supplementation or mechanical ventilation.\n\nResultsWe included 329 participants in the model cohort and 62 (18.8%) met the primary outcome. Our multivariable regression model found that lactate dehydrogenase (OR 2.36), qSOFA score (OR: 2.26), and neutrophil to lymphocyte ratio (OR:1.15) were significant predictors of severe disease. The final model showed an area under curve (AUC) of 0.84. The sensitivity analysis and point of influence analysis did not reveal inconsistencies.\n\nConclusionsOur study suggests that a combination of accessible demographic and clinical information collected on admission may predict the progression to severe COVID-19 among adult patients with mild and moderate disease. This model requires external validation prior to its use.\n\nSTRENGTHS AND LIMITATIONS OF THIS STUDY Our study utilized objective and measurable demographic and clinical information regularly available in healthcare settings even among patients unable to communicate.\n Our primary outcome corresponds to WHO ordinal score which would allow compare our results to other studies and in other settings.\n Our model could serve as an effective point of service tool during early admission to assist in clinical management and allocation of resources to unvaccinated patients.\n Our study is a retrospective study of unvaccinated COVID19 patients, and validation of our prediction model in the rest of our study population is still needed.\n In addition, testing our model in a more recent cohort after emergence of new SARS-CoV-2 variants will be needed to assess its robustness.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "John W Davis", - "author_inst": "University Of Texas Medical Branch At Galveston" - }, - { - "author_name": "Beilin Wang", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Ewa Tomczak", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Chia-Chi Fu", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Wissam Harmouch", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "David Reynoso", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Philip Keiser", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Miguel Cabada", - "author_inst": "University of Texas Medical Branch at Galveston" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.04.21265951", "rel_title": "Validation of a rapid and sensitive SARS-CoV-2 screening system developed for pandemic-scale infection surveillance", @@ -524409,6 +525966,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.11.08.21265884", + "rel_title": "Favipiravir In Adults with Moderate to Severe COVID-19: A Phase 3 Multicentre, Randomized, Double-Blind, Placebo-Controlled Trial.", + "rel_date": "2021-11-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.08.21265884", + "rel_abs": "AimTo assess the efficacy and safety of favipiravir in adults with moderate to severe coronavirus disease 2019 (COVID-19).\n\nMethodsIn this randomized, double-blind, multicenter, phase 3 trial, adults (21-80 years) with real-time reverse transcriptase polymerase chain reaction (rRT-PCR) confirmed SARS-CoV-2 infection and presenting with moderate to severe COVID-19 and requiring hospitalization were randomized 1:1 to oral favipiravir (day 1: 1800 mg BID and days 2-10: 800 mg BID) (FPV) plus standard supportive care (SoC) versus placebo plus SoC (placebo). The primary endpoint was time to resolution of hypoxia.\n\nResultsIn total, 353 patients were randomized to receive either FPV or placebo (175 and 178 in the FPV and placebo groups, respectively). Overall, 76% of the patients (240/315, 78% in FPV vs. 75% in placebo group) reached resolution of hypoxia on or before day 28. The median time to resolution of hypoxia was 7 days in the FPV group and 8 days in the placebo group. Treatment effect was not significant [Hazard ratio (HR) (95% CI): 0.991 (0.767, 1.280) (p=0.94)].\n\nPatients in the lower NEWS-2 clinical risk subgroup were more likely to achieve shorter time to resolution of hypoxia with the median time to resolution of hypoxia of 6 days in FPV and 7 days in placebo group [HR (95% CI): 1.21 (0.847, 1.731) (p=0.29)]; shorter time to hospital discharge with a median time to discharge of 8 and 10 days in the FPV and placebo group, respectively [HR (95% CI): 1.47 (1.081, 1.997) (p=0.014)]; and shorter time to improvement by 1-point improvement over baseline in WHO 10-point clinical status score with the median time to improvement by 1-point from baseline of 6 and 7 days in the FPV and placebo group, respectively [HR (95% CI): 1.16 (0.830, 1.624) (p=0.38)] than higher NEWS-2 clinical risk subgroup.\n\nTreatment emergent adverse event (TEAEs) were experienced by 62/334 (19%) patients [35/168 (21%) patients in FPV and 27/166 (16%) in placebo group]. Hyperuricaemia/increased blood uric acid was reported in 9 (3%)/2 (1%) patients [8 (5%)/1(1%) patients in FPV and 1 (1%)/1(1%) in placebo group], which were of mild intensity and transient. Overall, 36 serious adverse events (SAEs) were reported, 20 in FPV and 16 in placebo group.\n\nConclusionThe trial did not find favipiravir to be effective in moderate to severe, hospitalized COVID-19 patients; favourable clinical trends were observed in patients with lower NEWS-2 risk when early administration of favipiravir could be achieved.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Srinivas Shenoy", + "author_inst": "Dr Reddys Laboratories Limited" + }, + { + "author_name": "Sagar Munjal", + "author_inst": "Dr Reddys Laboratories Limited" + }, + { + "author_name": "Sarah Al Youha", + "author_inst": "Jaber Al-Ahmad Al-Sabah Hospital" + }, + { + "author_name": "Mohammad Alghounaim", + "author_inst": "Jaber Al Ahmad Hospital at Mishref Field Hospital" + }, + { + "author_name": "Sulaiman Almazeedi", + "author_inst": "Jaber Al-Ahmad Al-Sabah Hospital" + }, + { + "author_name": "Yousef Alshamali", + "author_inst": "Jaber Al-Ahmad Al-Sabah Hospital" + }, + { + "author_name": "Richard H Kaszynski", + "author_inst": "Emergency and Critical Care Center Tokyo Metropolitan Hiroo Hospital" + }, + { + "author_name": "Salman K Al-Sabah", + "author_inst": "Kuwait University" + }, + { + "author_name": "- Kuwait Clinical Trial Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.01.21265445", "rel_title": "Delta subvariants of SARS-COV-2 in Israel, Qatar and Bahrain: Optimal vaccination as an effective strategy to block viral evolution and control the pandemic", @@ -525704,29 +527312,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.08.21266099", - "rel_title": "A mathematical model for repetitive behaviors of Covid-19", - "rel_date": "2021-11-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.08.21266099", - "rel_abs": "Covid-19 pandemic waves have been hitting us again and again in the past couple years in many countries, while the reason why they come in such repetitive manners remains unexplained, which have brought us with lingering anxieties and economic stagnations.\n\nWe proposed a mathematical model to describe the mechanism of the repetitive appearance of the number of new cases based upon the SIQR model in which Q (quarantined infectors) were distinguished from I (un-quarantined ones). The repetitive behavior of the pandemic was simulated by an activator-inhibitor system around a fixed point in a phase space as a kind of self-organized oscillations. Periods between each wave were confirmed to be approximately similar. Repetitive behaviors were also observed in actual Covid-19 data.\n\nPractical policies and actions were discussed on the ways to effectively control the repetition of pandemic, and proactive PCR test especially after the peak-out stage is highly recommended.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Yoshiro Nishimoto", - "author_inst": "Seishin Science Club" - }, - { - "author_name": "Kenichi Inoue", - "author_inst": "Seishin Science Club" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.08.467648", "rel_title": "Phage-like particle vaccines are highly immunogenic and protect against pathogenic coronavirus infection and disease", @@ -525887,6 +527472,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.11.08.467773", + "rel_title": "A self-amplifying mRNA COVID-19 vaccine drives potent and broad immune responses at low doses that protects non-human primates against SARS-CoV-2", + "rel_date": "2021-11-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.08.467773", + "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic continues to spread globally, highlighting the urgent need for safe and effective vaccines that could be rapidly mobilized to immunize large populations. We report the preclinical development of a self-amplifying mRNA (SAM) vaccine encoding a prefusion stabilized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein and demonstrate potent cellular and humoral immune responses at low doses in mice and rhesus macaques. The homologous prime-boost vaccination regimen of SAM at 3, 10 and 30 g induced potent neutralizing antibody titers in rhesus macaques following two SAM vaccinations at all dose levels, with the 10 g dose generating geometric mean titers (GMT) 48-fold greater than the GMT of a panel of SARS-CoV-2 convalescent human sera. Spike-specific T cell responses were observed at all dose levels. SAM vaccination provided protective efficacy against SARS-CoV-2 challenge as both a homologous prime-boost and as a single boost following ChAd prime, demonstrating reduction of viral replication in both the upper and lower airways. Protection was most effective with a SAM prime-boost vaccination regimen at 10 and 30 g and with a ChAd/SAM heterologous prime-boost regimen. The SAM vaccine is currently being evaluated in clinical trials as both a homologous prime-boost regimen at low doses and as a boost following heterologous prime.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Amy R Rappaport", + "author_inst": "Gritstone bio" + }, + { + "author_name": "Sue-Jean Hong", + "author_inst": "Gritstone bio" + }, + { + "author_name": "Ciaran D Scallan", + "author_inst": "Gritstone bio" + }, + { + "author_name": "Leonid Gitlin", + "author_inst": "Gritstone bio" + }, + { + "author_name": "Arvin Akoopie", + "author_inst": "Gritstone bio" + }, + { + "author_name": "Gregory R Boucher", + "author_inst": "Gritstone bio" + }, + { + "author_name": "Milana Egorova", + "author_inst": "Gritstone bio" + }, + { + "author_name": "J Aaron Espinosa", + "author_inst": "Gritstone bio" + }, + { + "author_name": "Mario Fidanza", + "author_inst": "Gritstone bio" + }, + { + "author_name": "Melissa A Kachura", + "author_inst": "Gritstone bio" + }, + { + "author_name": "Annie Shen", + "author_inst": "Gritstone bio" + }, + { + "author_name": "Gloria Sivko", + "author_inst": "Battelle Biomedical Research Center" + }, + { + "author_name": "Anne Van Abbema", + "author_inst": "Gritstone bio" + }, + { + "author_name": "Robert L Veres", + "author_inst": "Gritstone bio" + }, + { + "author_name": "Karin Jooss", + "author_inst": "Gritstone bio" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.11.09.467911", "rel_title": "Evidence for a long-r ange RNA-RNA interaction between ORF8 and the downstream region of the Spike polybasic insertion of SARS-CoV-2", @@ -527670,61 +529330,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.08.21265888", - "rel_title": "SARS-CoV-2 Antibody Response is Associated with Age in Convalescent Outpatients", - "rel_date": "2021-11-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.08.21265888", - "rel_abs": "COVID-19 has had an unprecedented global impact on human health. Understanding the antibody memory responses to infection is one tool needed to effectively control the pandemic. Among 173 outpatients who had virologically confirmed SARS-CoV-2 infection, we evaluated serum antibody concentrations, microneutralization activity, and enumerated SARS-CoV-2 specific B cells in convalescent blood specimens. Serum antibody concentrations were variable, allowing for stratification of the cohort into high and low responders. Serum antibody concentration was positively associated with microneutralization activity and participant age, with participants under the age of 30 showing the lowest antibody level. Neither participant sex, the timing of blood sampling following the onset of illness, nor the number of SARS-CoV-2 spike protein specific B cells correlated with serum antibody concentration. These data suggest that young adult outpatients did not generate as robust antibody memory, compared with older adults. Further, serum antibody concentration or neutralizing activity trended but did not significantly correlate with the number of SARS-CoV-2 memory B cells. These findings have direct implications for public health policy and current vaccine efforts. Knowledge gained regarding antibody memory following infection will inform the need for vaccination in those previously infected and allow for a better approximation of population-wide protective immunity.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Bo Zhai", - "author_inst": "UPMC Children's Hospital of Pittsburgh" - }, - { - "author_name": "Karen Clarke", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "David L Bauer", - "author_inst": "Tulane University School of Medicine" - }, - { - "author_name": "Saran Kupul", - "author_inst": "UPMC Children's Hospital of Pittsburgh" - }, - { - "author_name": "Lucas J Schratz", - "author_inst": "UPMC Children's Hospital of Pittsburgh" - }, - { - "author_name": "M Patricia Nowalk", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Anita K McElroy", - "author_inst": "UPMC Children's Hospital of Pittsburgh" - }, - { - "author_name": "James B McLachlan", - "author_inst": "Tulane University School of Medicine" - }, - { - "author_name": "Richard K Zimmerman", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "John F Alcorn", - "author_inst": "UPMC Children's Hospital of Pittsburgh" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.04.21265780", "rel_title": "Immunogenicity and safety of the homogenous booster shot of a recombinant fusion protein vaccine (V-01) against COVID-19 in healthy adult participants primed with a two-dose regimen", @@ -527993,6 +529598,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.05.21265698", + "rel_title": "The COVID19 pandemic has changed women's experiences of pregnancy in the UK", + "rel_date": "2021-11-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.05.21265698", + "rel_abs": "IntroductionDuring the SARS-CoV-2 pandemic, maternity care has been substantially altered to reduce transmission of the SARS-CoV-2 virus. Many antenatal services are now restricted or delivered online, and visiting has been restricted during labour and in the postnatal period.\n\nMethodsWe conducted an online survey from 1st August to 31st December 2020 to investigate the experiences of women who were pregnant or breastfeeding in the UK during the SARS-CoV-2 pandemic. The survey included 55 open and closed questions and required 5 minutes to complete. We publicised the survey using social media.\n\nResultsWe received 96 responses, including 66 currently pregnant women and 22 women who were pregnant during the pandemic. The response rate was 70.1% of survey views. We found mixed experiences of the impact of the pandemic on antenatal and perinatal care, notably with some women feeling visiting restrictions were insufficient and others feeling they were too strict. Twenty-nine women received no information about COVID-19, and 6 women found it very difficult to find information. Thirty-nine women would have liked to have more information about breastfeeding after a pregnancy affected by COVID-19, and 37 women wanted more information about antibody persistence and transfer.\n\nDiscussionAdditional support is required for pregnant and lactating women during the current pandemic. Provision of information and support, including via social media, may improve womens experiences of pregnancy in the current environment.\n\nSignificanceMaternity services in the UK have been significantly restructured to prevent transmission of the SARS-CoV-2 virus, including restrictions to in-person antenatal care, and perinatal visiting. It is not fully known how these changes are perceived by pregnant and breastfeeding women.\n\nReactions to changes in antenatal care are mixed, including whether restrictions were too lenient or too strict. Most women underwent online antenatal care in addition in-person visits. Some received no information about COVID-19, and a significant proportion of women would have liked more information, particularly regarding antibody transfer and benefits of breastfeeding during the pandemic.\n\nEthical statementThis study was approved by North East - Newcastle & North Tyneside 1 Research Ethics Committee", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Sarah S Sturrock", + "author_inst": "St George's, University of London" + }, + { + "author_name": "Kim Turner", + "author_inst": "Keck School of Medicine, University of Southern California" + }, + { + "author_name": "Chelon Lee-Wo", + "author_inst": "St George's, University of London" + }, + { + "author_name": "Vanessa Greening", + "author_inst": "St George's, University of London" + }, + { + "author_name": "Asma Khalil", + "author_inst": "St George's, University of London" + }, + { + "author_name": "Paul Heath", + "author_inst": "St George's, University of London" + }, + { + "author_name": "Kirsty Le Doare", + "author_inst": "St. George's, University of London" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.04.21265945", "rel_title": "Inhaled Corticosteroids for Outpatients with Covid-19: A Meta-Analysis", @@ -529516,29 +531164,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.11.04.21265923", - "rel_title": "How Do College Students with Disabilities Feel About Taking COVID-19 Vaccines?", - "rel_date": "2021-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.04.21265923", - "rel_abs": "This survey explores attitudes of 245 currently enrolled college students with disabilities regarding their comfort taking a COVID-19 vaccine. Results suggest most college students with disabilities are willing to take a COVID-19 vaccine if their institution requires it to return to campus in subsequent semesters. However, many students with disabilities would not feel comfortable with a vaccine mandate mid-semester and would consider withdrawing, especially among older students with disabilities and first-generation college students with disabilities. Implications for postsecondary policy and leadership are addressed.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Z W. Taylor", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Chelseaia Charran", - "author_inst": "The University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2021.11.02.21265778", "rel_title": "Plasma markers of neurologic injury and systemic inflammation in individuals with self-reported neurologic post-acute sequelae of SARS-CoV-2 infection (PASC)", @@ -529783,6 +531408,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.11.02.466971", + "rel_title": "Protein arginylation is regulated during SARS-CoV-2 infection", + "rel_date": "2021-11-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.02.466971", + "rel_abs": "In 2019, the world witnessed the onset of an unprecedented pandemic. In September 2021, the infection by SARS-CoV-2 had already been responsible for the death of more than 4 million people worldwide. Recently, we and other groups discovered that SARS-CoV-2 infection induces ER-stress and activation of unfolded protein response (UPR) pathway. The degradation of misfolded/unfolded proteins is an essential element of proteostasis and occurs mainly in lysosomes or proteasomes. The N-terminal arginylation of proteins is characterized as an inducer of ubiquitination and proteasomal degradation by the N-end rule pathway. Here we present, for the first time, data on the role of arginylation during SARS-CoV-2 infection. We studied the modulation of protein arginylation in Vero CCL-81 and Calu-3 cells infected after 2h, 6h, 12h, 24h, and 48h. A reanalysis of in vivo and in vitro public omics data combined with immunoblotting was performed to measure the levels of ATE1 and arginylated proteins. This regulation is seen specifically during infections by coronaviruses. We demonstrate that during SARS-CoV-2 infection there is an increase in the expression of the ATE1 enzyme associated with regulated levels of specific arginylated proteins. On the other hand, infected macrophages showed no ATE1 regulation. An important finding revealed that modulation of the N-end rule pathway differs between different types of infected cells. We also confirmed the potential of tannic acid to reduce viral load, and furthermore, to modulate ATE1 levels during infection. In addition, the arginylation inhibitor merbromin (MER) is also capable of both reducing viral load and reducing ATE1 levels. Taken together, these data show the importance of arginylation during the progression of SARS-CoV-2 infection and open the door for future studies that may unravel the role of ATE1 and its inhibitors in pathogen infection.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Janaina Macedo-da-Silva", + "author_inst": "GlycoProteomics Laboratory, Department of Parasitology, ICB, University of Sao Paulo, Brazil" + }, + { + "author_name": "Livia Rosa-Fernandes", + "author_inst": "Laboratory of Experimental Immunoparasitology, Department of Parasitology, ICB, University of Sao Paulo, Brazil" + }, + { + "author_name": "Vinicius de Moraes Gomes", + "author_inst": "GlycoProteomics Laboratory, Department of Parasitology, ICB, University of Sao Paulo, Brazil" + }, + { + "author_name": "Veronica Feijoli Santiago", + "author_inst": "GlycoProteomics Laboratory, Department of Parasitology, ICB, University of Sao Paulo, Brazil" + }, + { + "author_name": "Catarina Maria Stanischesk Molnar", + "author_inst": "GlycoProteomics Laboratory, Department of Parasitology, ICB, University of Sao Paulo, Brazil" + }, + { + "author_name": "Bruno R Barboza", + "author_inst": "GlycoProteomics Laboratory, Department of Parasitology, ICB, University of Sao Paulo, Brazil" + }, + { + "author_name": "Edmarcia Elisa de Sousa", + "author_inst": "Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences at the University of Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Edison Luiz Durigon", + "author_inst": "Universidade de Sao Paulo Instituto de Ciencias Biomedicas" + }, + { + "author_name": "Claudio Romero Farias Marinho", + "author_inst": "Institute of Biomedical Sciences / University of Sao Paulo - USP" + }, + { + "author_name": "Carsten Wrenger", + "author_inst": "Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences at the University of Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Suely Kazue Nagahashi Marie", + "author_inst": "Laboratory of Molecular and Cellular Biology (LIM 15), Department of Neurology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, 01246903, Bra" + }, + { + "author_name": "Giuseppe Palmisano", + "author_inst": "University of Sao Paulo" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2021.11.02.463717", "rel_title": "Comparing protein-protein interaction networks of SARS-CoV-2 and (H1N1) influenza using topological features", @@ -531514,69 +533202,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.01.21265766", - "rel_title": "Interferon pathway lupus risk alleles modulate risk of death from acute COVID-19", - "rel_date": "2021-11-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.01.21265766", - "rel_abs": "Type I interferon (IFN) is critical in our defense against viral infections. Increased type I IFN pathway activation is a genetic risk factor for systemic lupus erythematosus (SLE), and a number of common risk alleles contribute to the high IFN trait. We hypothesized that these common gain-of-function IFN pathway alleles may be associated with protection from mortality in acute COVID-19. We studied patients admitted with acute COVID-19 (756 European-American and 398 African-American ancestry). Ancestral backgrounds were analyzed separately, and mortality after acute COVID-19 was the primary outcome. In European-American ancestry, we found that a haplotype of interferon regulatory factor 5 (IRF5) and alleles of protein kinase cGMP-dependent 1 (PRKG1) were associated with mortality from COVID-19. Interestingly, these were much stronger risk factors in younger patients (OR=29.2 for PRKG1 in ages 45-54). Variants in the IRF7 and IRF8 genes were associated with mortality from COVID-19 in African-American subjects, and these genetic effects were more pronounced in older subjects. Combining genetic information with blood biomarker data such as C-reactive protein, troponin, and D-dimer resulted in significantly improved predictive capacity, and in both ancestral backgrounds the risk genotypes were most relevant in those with positive biomarkers (OR for death between 14 and 111 in high risk genetic/biomarker groups). This study confirms the critical role of the IFN pathway in defense against COVID-19 and viral infections, and supports the idea that some common SLE risk alleles exert protective effects in anti-viral immunity.\n\nBackgroundWe find that a number of IFN pathway lupus risk alleles significantly impact mortality following COVID-19 infection. These data support the idea that type I IFN pathway risk alleles for autoimmune disease may persist in high frequency in modern human populations due to a benefit in our defense against viral infections.\n\nTranslational SignificanceWe develop multivariate prediction models which combine genetics and known biomarkers of severity to result in greatly improved prediction of mortality in acute COVID-19. The specific associated alleles provide some clues about key points in our defense against COVID-19.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Ilona Nln", - "author_inst": "Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Ruth Fernandez-Ruiz", - "author_inst": "Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Theresa L Wampler Muskardin", - "author_inst": "Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Jacqueline L Paredes", - "author_inst": "Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Ashira D Blazer", - "author_inst": "Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Stephanie Tuminello", - "author_inst": "Center for Human Genetics and Genomics, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Mukundan Attur", - "author_inst": "Divison of Rheumatology, Department of Medicine, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Eduardo Iturrate", - "author_inst": "Department of Medicine, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Christopher M Petrilli", - "author_inst": "Department of Medicine, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Steven B Abramson", - "author_inst": "Department of Medicine, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Aravinda Chakravarti", - "author_inst": "Center for Human Genetics and Genomics, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Timothy B Niewold", - "author_inst": "Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.11.01.21265527", "rel_title": "Effectiveness, Explainability and Reliability of Machine Meta-Learning Methods for Predicting Mortality in Patients with COVID-19: Results of the Brazilian COVID-19 Registry", @@ -532217,6 +533842,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.11.01.21265761", + "rel_title": "The Brief Observation of Symptoms of Autism (BOSA): Development of a New Adapted Assessment Measure for Remote Telehealth Administration through COVID-19 and Beyond", + "rel_date": "2021-11-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.01.21265761", + "rel_abs": "Interest in telehealth assessment for autism has increased due to COVID-19 and subsequent expansion of remote psychological services, though options that are easy for clinicians to adopt and available through the lifespan are limited. The Brief Observation of Symptoms of Autism (BOSA) provides a social context with standardized materials and activities that can be coded by clinicians trained in the Autism Diagnostic Observation Schedule (ADOS). The current project examined psychometric properties to determine optimal use for each BOSA version. Three hundred and seven participants with 453 BOSAs were included to determine best performing items for algorithms, validity, sensitivity, specificity, recommended cut-offs, and proposed ranges of concern. While preliminary, the BOSA provides a promising new option for telehealth-administered assessment for autism.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Deanna Dow", + "author_inst": "University of California, Los Angeles (UCLA) Semel Institute for Neuroscience and Human Behavior" + }, + { + "author_name": "Alison Holbrook", + "author_inst": "Simons Foundation Autism Research Initiative" + }, + { + "author_name": "Christina Toolan", + "author_inst": "University of California, Los Angeles (UCLA) Semel Institute for Neuroscience and Human Behavior" + }, + { + "author_name": "Nicole McDonald", + "author_inst": "University of California, Los Angeles (UCLA) Semel Institute for Neuroscience and Human Behavior" + }, + { + "author_name": "Kyle Sterrett", + "author_inst": "University of California, Los Angeles (UCLA) Semel Institute for Neuroscience and Human Behavior" + }, + { + "author_name": "Nicole Rosen", + "author_inst": "University of California, Los Angeles (UCLA) Semel Institute for Neuroscience and Human Behavior" + }, + { + "author_name": "So Hyun Kim", + "author_inst": "Department of Psychiatry, Weill Cornell Medical College, New York-Presbyterian Hospital" + }, + { + "author_name": "Catherine Lord", + "author_inst": "University of California, Los Angeles (UCLA) Semel Institute for Neuroscience and Human Behavior" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.11.01.21265775", "rel_title": "Using portable air purifiers to reduce airborne transmission of infectious respiratory viruses - a computational fluid dynamics study", @@ -533680,93 +535352,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2021.10.31.466677", - "rel_title": "Multiple spillovers and onward transmission of SARS-Cov-2 in free-living and captive White-tailed deer (Odocoileus virginianus)", - "rel_date": "2021-11-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.31.466677", - "rel_abs": "Many animal species are susceptible to SARS-CoV-2 and could potentially act as reservoirs, yet transmission of the virus in non-human free-living animals has not been documented. White-tailed deer (Odocoileus virginianus), the predominant cervid in North America, are susceptible to SARS-CoV-2 infection, and experimentally infected fawns can transmit the virus. To test the hypothesis that SARS-CoV-2 may be circulating in deer, we tested 283 retropharyngeal lymph node (RPLN) samples collected from 151 free-living and 132 captive deer in Iowa from April 2020 through December of 2020 for the presence of SARS-CoV-2 RNA. Ninety-four of the 283 deer (33.2%; 95% CI: 28, 38.9) samples were positive for SARS-CoV-2 RNA as assessed by RT-PCR. Notably, between November 23, 2020 and January 10, 2021, 80 of 97 (82.5%; 95% CI 73.7, 88.8) RPLN samples had detectable SARS-CoV-2 RNA by RT-PCR. Whole genome sequencing of the 94 positive RPLN samples identified 12 SARS-CoV-2 lineages, with B.1.2 (n = 51; 54.5%), and B.1.311 (n = 19; 20%) accounting for ~75% of all samples. The geographic distribution and nesting of clusters of deer and human lineages strongly suggest multiple zooanthroponotic spillover events and deer-to-deer transmission. The discovery of sylvatic and enzootic SARS-CoV-2 transmission in deer has important implications for the ecology and long-term persistence, as well as the potential for spillover to other animals and spillback into humans. These findings highlight an urgent need for a robust and proactive \"One Health\" approach to obtaining a better understanding of the ecology and evolution of SARS-CoV-2.\n\nOne-Sentence SummarySARS-CoV-2 was detected in one-third of sampled white-tailed deer in Iowa between September 2020 and January of 2021 that likely resulted from multiple human-to-deer spillover and deer-to-deer transmission events.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Suresh V Kuchipudi", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Meera Surendran-Nair", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Rachel M Ruden", - "author_inst": "Iowa State University" - }, - { - "author_name": "Michele Yon", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Ruth H Nissly", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Rahul K Nelli", - "author_inst": "Iowa State University" - }, - { - "author_name": "Lingling Li", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Bhushan M Jayarao", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Kurt Vandegrift", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Costas D Maranas", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Nicole Levine", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Katriina Willgert", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Andrew J.K Conlan", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Randall J Olsen", - "author_inst": "Houston Methodist Research Institute and Houston Methodist Hospital" - }, - { - "author_name": "James Davis", - "author_inst": "Argonne National Laboratory" - }, - { - "author_name": "James M. Musser", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Peter J Hudson", - "author_inst": "Pennsylvania State University University Park : Penn State" - }, - { - "author_name": "Vivek Kapur", - "author_inst": "Pennsylvania State University University Park : Penn State" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.10.29.466519", "rel_title": "A biosafety level 2 surrogate for studying SARS-CoV-2 survival in food processing environmental biofilms", @@ -534019,6 +535604,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.28.21265629", + "rel_title": "An Objective Search for Unrecognized Bias in Validated COVID-19 Prediction Models", + "rel_date": "2021-10-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.28.21265629", + "rel_abs": "The growing recognition of algorithmic bias has spurred discussions about fairness in artificial intelligence (AI) / machine learning (ML) algorithms. The increasing translation of predictive models into clinical practice brings an increased risk of direct harm from algorithmic bias; however, bias remains incompletely measured in many medical AI applications. Using data from over 56 thousand Mass General Brigham (MGB) patients with confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we evaluate unrecognized bias in four AI models developed during the early months of the pandemic in Boston, Massachusetts that predict risks of hospital admission, ICU admission, mechanical ventilation, and death after a SARS-CoV-2 infection purely based on their pre-infection longitudinal medical records.\n\nWe discuss that while a model can be biased against certain protected groups (i.e., perform worse) in certain tasks, it can be at the same time biased towards another protected group (i.e., perform better). As such, current bias evaluation studies may lack a full depiction of the variable effects of a model on its subpopulations.\n\nIf the goal is to make a change in a positive way, the underlying roots of bias need to be fully explored in medical AI. Only a holistic evaluation, a diligent search for unrecognized bias, can provide enough information for an unbiased judgment of AI bias that can invigorate follow-up investigations on identifying the underlying roots of bias and ultimately make a change.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Hossein Estiri", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Zachary Strasser", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Sina Rashidian", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Jeffrey Klann", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Kavishwar Wagholikar", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Thomas McCoy Jr.", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Shawn Murphy", + "author_inst": "Massachusetts General Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.10.28.21265549", "rel_title": "COVID-19 Vaccine Failure in Chronic Lymphocytic Leukemia and Monoclonal B-Lymphocytosis; Humoral and Cellular Immunity", @@ -535334,61 +536962,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2021.10.28.21265588", - "rel_title": "Designing an evidence-based Bayesian network for estimating the risk versus benefits of AstraZeneca COVID-19 vaccine", - "rel_date": "2021-10-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.28.21265588", - "rel_abs": "Uncertainty surrounding the risk of developing and dying from Thrombosis and Thromobocytopenia Syndrome (TTS) associated with the AstraZeneca (AZ) COVID-19 vaccine may contribute to vaccine hesitancy. A model is urgently needed to combine and effectively communicate the existing evidence on the risks versus benefits of the AZ vaccine. We developed a Bayesian network to consolidate the existing evidence on risks and benefits of the AZ vaccine, and parameterised the model using data from a range of empirical studies, government reports, and expert advisory groups. Expert judgement was used to interpret the available evidence and determine the structure of the model, relevant variables, data to be included, and how these data were used to inform the model.\n\nThe model can be used as a decision support tool to generate scenarios based on age, sex, virus variant and community transmission rates, making it a useful for individuals, clinicians, and researchers to assess the chances of different health outcomes. Model outputs include the risk of dying from TTS following the AZ COVID-19 vaccine, the risk of dying from COVID-19 or COVID-19-associated atypical severe blood clots under different scenarios. Although the model is focused on Australia, it can be easily adaptable to international settings by re-parameterising it with local data. This paper provides detailed description of the model-building methodology, which can used to expand the scope of the model to include other COVID-19 vaccines, booster doses, comorbidities and other health outcomes (e.g., long COVID) to ensure the model remains relevant in the face of constantly changing discussion on risks versus benefits of COVID-19 vaccination.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Helen J Mayfield", - "author_inst": "School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia" - }, - { - "author_name": "Colleen L Lau", - "author_inst": "School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia" - }, - { - "author_name": "Jane E Sinclair", - "author_inst": "School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, Brisbane, Queensland, Australia" - }, - { - "author_name": "Samuel J Brown", - "author_inst": "School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, Brisbane, Queensland, Australia" - }, - { - "author_name": "Andrew Baird", - "author_inst": "St Kilda Medical Group, St Kilda, Melbourne, Victoria, Australia" - }, - { - "author_name": "John Litt", - "author_inst": "Discipline of General Practice, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia; Scientific Advisory Committee," - }, - { - "author_name": "Aapeli Vuorinen", - "author_inst": "Data Science Institute, Columbia University, New York, New York, U.S.A." - }, - { - "author_name": "Kirsty R Short", - "author_inst": "School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, Brisbane, Queensland, Australia" - }, - { - "author_name": "Michael Waller", - "author_inst": "School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia" - }, - { - "author_name": "Kerrie Mengersen", - "author_inst": "School of Mathematical Sciences, Faculty of Science, Queensland University of Technology, Brisbane, Queensland, Australia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.29.21265248", "rel_title": "Safety and immunogenicity of a high-dose quadrivalent influenza vaccine administered concomitantly with a third dose of the mRNA-1273 SARS-CoV-2 vaccine in adults >= 65 years of age: a Phase II, open-label study", @@ -535817,6 +537390,53 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.10.26.466002", + "rel_title": "Whole-genome sequencing of Vero E6 (C1008) and comparative analysis of four Vero cell sublines", + "rel_date": "2021-10-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.26.466002", + "rel_abs": "The Vero cell line is an immortalized cell line established from kidney epithelial cells of the African green monkey. A variety of sublines have been established from the original cell line, which display different characteristics. In this study, we determined the whole-genome sequence of Vero E6 (C1008) and performed comparative analysis among Vero JCRB 0111, Vero CCL-81, Vero 76 and Vero E6. Analysis of the copy number changes and loss of heterozygosity revealed that all sublines share a large deletion and loss of heterozygosity on chromosome 12, which harbors type I interferon and CDKN2 gene clusters. We identified a substantial number of genetic differences among the sublines including single nucleotide variants, indels, and copy number variations. The spectrum of single nucleotide variants indicated a close genetic relationship between Vero JCRB0111 and Vero CCL-81, and between Vero 76 and Vero E6, and a considerable genetic gap between the former two and the latter two lines. In contrast, we confirmed the pattern of genomic integration sites of simian endogenous retroviral sequences, which was consistent among the sublines. We identified subline-specific/enriched loss of function and missense variants, which potentially contribute to the differences in response to viral infection among the Vero sublines. In particular, we focused on Vero E6-specific/enriched variants and identified four genes (IL1RAP, TRIM25, RB1CC1, and ATG2A) that contained missense variants specific or enriched in Vero E6. In addition, we found that V739I variants of ACE2, which functions as the receptor for SARS-CoV-2, were heterozygous in Vero JCRB0111, Vero CCL-81, and Vero 76; however, Vero E6 contained the allele with isoleucine, resulting from the loss of one of the X chromosomes.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Kazuhiro Konishi", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Toshiyuki Yamaji", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Chisato Sakuma", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Fumio Kasai", + "author_inst": "National Institutes of Biomedical Innovation, Health and Nutrition" + }, + { + "author_name": "Toshinori Endo", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Arihiro Kohara", + "author_inst": "National Institutes of Biomedical Innovation, Health and Nutrition" + }, + { + "author_name": "Kentaro Hanada", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Naoki Osada", + "author_inst": "Hokkaido University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2021.10.28.465226", "rel_title": "A Potential Novel COVID-19 Vaccine With RBD-HR1/HR2 Hexamer Structure", @@ -537252,77 +538872,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.25.21265166", - "rel_title": "Regional probabilistic situational awareness and forecasting of COVID-19", - "rel_date": "2021-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.25.21265166", - "rel_abs": "Mathematical models and statistical inference are fundamental for surveillance and control of the COVID-19 pandemic. Several aspects cause regional heterogeneity in disease spread. Individual behaviour, mobility, viral variants and transmission vary locally, temporally and with season, and interventions and vaccination are often implemented regionally. Therefore, we developed a new regional changepoint stochastic SEIR metapopulation model. The model is informed by real-time mobility estimates from mobile phone data, laboratory-confirmed cases, and hospitalisation incidence. To estimate locally and time-varying transmissibility, case detection probabilities, and missed imported cases, we present a new sequential Approximate Bayesian Computation method allowing inference in useful time, despite the high parametric dimension. We test our approach on Norway and find that three-week-ahead predictions are precise and well-calibrated, suitable for real-time surveillance.\n\nSignificanceWe developed a regional infectious disease spread model focussing on operational usefulness in real time. The model is informed by near real-time mobile phone mobility data, laboratory-confirmed cases, and hospitalisation incidence. The model is used to estimate reproduction numbers and provide regional predictions of future hospital beds. Regional reproduction numbers are important due spatio-temporal heterogeneity due to for example local interventions. We assume different regional reproduction numbers for different periods of the epidemic. We propose a new calibration method to estimate the reproduction numbers and other parameters of the model, tailored to handle the increasingly high dimension of parameters over time. The model has been successfully used for local situational awareness and forecasting for the Norwegian health authorities during COVID-19.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Solveig Engebretsen", - "author_inst": "SAMBA, Norwegian Computing Center" - }, - { - "author_name": "Alfonso Diz-Lois Palomares", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Gunnar \u00d8vind Isaksson R\u00f8", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Anja Br\u00e5then Kristoffersen", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Jonas Christoffer Lindstr\u00f8m", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Kenth Eng\u00f8-Monsen", - "author_inst": "Telenor Research, Telenor (Norway)" - }, - { - "author_name": "Louis Yat Hin Chan", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "\u00d8rjan Dale", - "author_inst": "Telenor (Norway)" - }, - { - "author_name": "J\u00f8rgen Eriksson Midtb\u00f8", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Kristian Lindalen-Stenerud", - "author_inst": "Telenor (Norway)" - }, - { - "author_name": "Francesco Di Ruscio", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Richard Aubrey White", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Arnoldo Frigessi", - "author_inst": "University of Oslo//Oslo University Hospital" - }, - { - "author_name": "Birgitte Freiesleben de Blasio", - "author_inst": "Norwegian Institute of Public Health/University of Oslo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.23.21265429", "rel_title": "Use of serology immunoassays for predicting SARS-CoV-2 infection: a serology-based diagnostic algorithm", @@ -537603,6 +539152,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, + { + "rel_doi": "10.1101/2021.10.23.21265421", + "rel_title": "Assessing the potential impact of immunity waning on the dynamics of COVID-19: an endemic model of COVID-19", + "rel_date": "2021-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.23.21265421", + "rel_abs": "We developed an endemic model of COVID-19 to assess the impact of vaccination and immunity waning on the dynamics of the disease. Our model exhibits the phenomenon of back-ward bifurcation and bi-stability, where a stable disease-free equilibrium co-exists with a stable endemic equilibrium. The epidemiological implication of this is that the control reproduction number being less than unity is no longer sufficient to guarantee disease eradication. We showed that this phenomenon could be eliminated by either increasing the vaccine efficacy or by reducing the disease transmission rate (adhering to non-pharmaceutical interventions). Furthermore, we numerically investigated the impacts of vaccination and waning of both vaccine-induced immunity and post-recovery immunity on the disease dynamics. Our simulation results show that the waning of vaccine-induced immunity has more effect on the disease dynamics relative to post-recovery immunity waning, and suggests that more emphasis should be on reducing the waning of vaccine-induced immunity to eradicate COVID-19.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Muhammad Rabiu Musa", + "author_inst": "university of KwaZulu-Natal" + }, + { + "author_name": "Sarafa Iyaniwura", + "author_inst": "Department of Mathematics and Institute of Applied Mathematics, University of British Columbia, Vancouver, BC, Canada." + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.10.22.21264941", "rel_title": "Access and quality of sexual and reproductive health (SRH) services in Britain during the early stages of the COVID-19 pandemic: a qualitative interview study of patient experiences", @@ -538994,81 +540566,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.23.21265402", - "rel_title": "Severity of Illness Caused by Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern in Children: A Single-Center Retrospective Cohort Study", - "rel_date": "2021-10-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.23.21265402", - "rel_abs": "BackgroundRecent surges in coronavirus 2019 disease (COVID-19) is attributed to the emergence of more transmissible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs). However, the relative severity of SARS-CoV-2 VOCs in children is unknown.\n\nMethodsThis retrospective single-center cohort study was performed at the Ann & Robert H. Lurie Childrens Hospital of Chicago, academic free-standing childrens hospital. We included all children [≤] 18 years-old diagnosed with COVID-19 between October 15th, 2020 and August 31st, 2021 and whose SARS-CoV-2 isolate was sequenced using the Illumina platform. For each patient sample, we identified the SARS-CoV-2 lineage, which was assigned to one of the following groups: Non-VOC, alpha VOC, beta VOC, gamma VOC, or delta VOC. We measured frequency of 5 markers of COVID-19 severity: hospitalization; COVID-19 pharmacologic treatment; respiratory support; intensive care unit admission; and severe disease as classified by the COVID-19 World Health Organization (WHO) Clinical Progression Scale (severe disease; score [≥] 6). A series of logistic regression models were fitted to estimate odds of each severity marker with each VOC (in comparison to non-VOCs), adjusting for COVID-19 community incidence and demographic and clinical co-variates.\n\nResultsDuring the study period, 2,025 patients tested positive for SARS-CoV-2; 1,422 (70.2%) had sufficient viral load to permit sequencing. Among the 499 (35.1%) patients whose isolate was sequenced, median (inter-quartile range) age was 7 (1,12) years; 256 (51.3%) isolates were a VOC: 96 (37.5%) alpha, 38 (14.8%) gamma, and 119 (46.5%) delta. After adjusting for age, Black race, Hispanic ethnicity, high-risk medical conditions, and COVID-19 community incidence, neither alpha nor delta was associated with severe COVID-19. Gamma was independently associated with hospitalization (OR 5.9, 95% CI 1.6-21.5, p=0.007), respiratory support (OR 8.3, 95% CI 1.5-56.3, p=0.02), and severe disease as classified by the WHO Clinical Progression Scale (OR 7.7, 95% CI 1.0-78.1, p=0.05).\n\nConclusionsCompared to non-VOC COVID-19 infections, the gamma VOC, but not the alpha or delta VOCs, was associated with increased severity. These data suggest that recent increased in pediatric COVID-19 hospitalizations are related to increased delta COVID-19 incidence rather than increased delta virulence in children.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Priya R. Edward", - "author_inst": "Ann & Robert H. Lurie Children's Hospital of Chicago" - }, - { - "author_name": "Ramon Lorenzo-Redondo", - "author_inst": "Northwestern University" - }, - { - "author_name": "Megan E. Reyna", - "author_inst": "Ann & Robert H. Lurie Childrens Hospital of Chicago" - }, - { - "author_name": "Lacy M Simons", - "author_inst": "Northwestern University" - }, - { - "author_name": "Judd F. Hultquist", - "author_inst": "Northwestern University Feinberg School of Medicine" - }, - { - "author_name": "Ami B. Patel", - "author_inst": "Ann & Robert H. Lurie Childrens Hospital of Chicago" - }, - { - "author_name": "Egon A Ozer", - "author_inst": "Northwestern University" - }, - { - "author_name": "William J Mullerr", - "author_inst": "Ann & Robert H. Lurie Childrens Hospital of Chicago" - }, - { - "author_name": "Taylor Heald-Sargent", - "author_inst": "Ann & Robert H. Lurie Childrens Hospital of Chicago" - }, - { - "author_name": "Matthew McHugh", - "author_inst": "Ann & Robert H. Lurie Childrens Hospital of Chicago" - }, - { - "author_name": "Taylor J. Dean", - "author_inst": "Northwestern University Feinberg School of Medicine," - }, - { - "author_name": "Raj M. Dalal", - "author_inst": "Northwestern University Feinberg School of Medicine," - }, - { - "author_name": "Jordan John", - "author_inst": "Northwestern University Feinberg School of Medicine," - }, - { - "author_name": "Shannon C. Manz", - "author_inst": "Northwestern University Feinberg School of Medicine" - }, - { - "author_name": "Larry K. Kociolek", - "author_inst": "Ann & Robert H. Lurie Children's Hospital of Chicago" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.25.21265493", "rel_title": "Modeling the impact of vaccination strategies for nursing homes in the context of increased SARS-CoV-2 community transmission and variants", @@ -539265,6 +540762,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2021.10.25.21265304", + "rel_title": "Effectiveness of Covid-19 Vaccines in the United States Over 9 Months: Surveillance Data from the State of North Carolina", + "rel_date": "2021-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.25.21265304", + "rel_abs": "BackgroundThe duration of protection afforded by Covid-19 vaccines in the United States is unclear. Whether the recent increase of breakthrough infections was caused by waning immunity to the primary vaccination or by emergence of new variants that are more highly transmissible is also unknown.\n\nMethodsWe extracted data on vaccination histories and clinical outcomes (Covid-19, hospitalization, death) for the period from December 13, 2020 through September 8, 2021 by linking data from the North Carolina COVID-19 Surveillance System and COVID-19 Vaccine Management System covering [~]10.6 million residents statewide. We used the Kaplan-Meier method to estimate the effectiveness of the BNT162b2 (Pfizer-BioNTech), mRNA-1273 (Moderna), and Ad26.COV2.S (Janssen) vaccines in reducing the incidence of Covid-19 over successive post-vaccination time periods, producing separate estimates for individuals vaccinated during different calendar periods. In addition, we used Cox regression with time-dependent vaccination status and time-varying hazard ratios to estimate the effectiveness of the three vaccines in reducing the hazard rates or current risks of Covid-19, hospitalization, and death, as a function of time elapsed since the first dose.\n\nResultsFor the Pfizer two-dose regimen, vaccine effectiveness in reducing the current risk of Covid-19 ramps to a peak level of 94.9% (95% confidence interval [CI], 94.5 to 95.2) at 2 months (post the first dose) and drops to 70.1% (95% CI, 68.9 to 71.2) after 7 months; effectiveness in reducing the current risk of hospitalization ramps to a peak level of 96.4% (95% CI, 94.7 to 97.5) at 2 months and remains at 87.7% (95% CI, 84.3 to 90.4) at 7 months; effectiveness in reducing the current risk of death ramps to 95.9% (95% CI, 92.9 to 97.6) at 2 months and is maintained at 88.4% (95% CI, 83.0 to 92.1) at 7 months. For the Moderna two-dose regimen, vaccine effectiveness in reducing the current risk of Covid-19 ramps to a peak level of 96.0% (95% CI, 95.6 to 96.4) at 2 months and drops to 81.9% (95% CI, 81.0 to 82.7) after 7 months; effectiveness in reducing the current risk of hospitalization ramps to a peak level of 97.5% (95% CI, 96.3 to 98.3) at 2 months and remains at 92.3% (95% CI, 89.7 to 94.3) at 7 months; effectiveness in reducing the current risk of death ramps to 96.0% (95% CI, 91.9 to 98.0) at 3 months and remains at 93.7% (95% CI, 90.2 to 95.9) at 7 months. For the Janssen one-dose regimen, effectiveness in reducing the current risk of Covid-19 ramps to a peak level of 79.0% (95% CI, 77.1 to 80.7) at 1 month and drops to 64.3% (95% CI, 62.3 to 66.1) after 5 months; effectiveness in reducing the current risk of hospitalization ramps to a peak level of 89.8% (95% CI, 78.8 to 95.1) at 2 months and stays above 80% through 5 months; effectiveness in reducing the current risk of death ramps to 89.4% (95% CI, 52.3 to 97.6) at 3 months and stays above 80% through 5 months. For all three vaccines, the ramping and waning patterns are similar for individuals who were vaccinated at different dates, and across various demographic subgroups (age, sex, race/ethnicity, geographic region, county-level vaccination rate).\n\nConclusionsThe two mRNA vaccines are remarkably effective and durable in reducing the risks of hospitalization and death. The Janssen vaccine also offers a high level of protection against hospitalization and death. The Moderna vaccine is significantly more durable than the Pfizer vaccine in reducing the risk of Covid-19. Waning vaccine effectiveness is caused primarily by declining immunity rather than emergence of new variants. It would be worthwhile to investigate the effectiveness of the Janssen vaccine as a two-dose regimen, with the second dose given approximately 1-2 months after the first dose.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Danyu Lin", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Yu Gu", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Bradford Wheeler", + "author_inst": "NCDHHS" + }, + { + "author_name": "Hayley Young", + "author_inst": "NCDHHS" + }, + { + "author_name": "Shannon Holloway", + "author_inst": "North Carolina State University" + }, + { + "author_name": "Shadia Khan Sunny", + "author_inst": "NCDHHS" + }, + { + "author_name": "Zack Moore", + "author_inst": "NCDHHS" + }, + { + "author_name": "Donglin Zeng", + "author_inst": "University of North Carolina" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.25.21265484", "rel_title": "Rapid surveillance platforms for key SARS-CoV-2 mutations in Denmark", @@ -541144,69 +542688,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2021.10.21.21265340", - "rel_title": "How different pre-existing mental disorders and their co-occurrence affects clinical outcomes of COVID-19? A study based on real-world data in the Southern United States", - "rel_date": "2021-10-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.21.21265340", - "rel_abs": "ImportanceA growing body of research focuses on the impact of pre-existing mental disorders on clinical outcomes of COVID-19 illness. Although a psychiatric history might be an independent risk factor for COVID-19 infection and mortality, no studies have systematically investigated how different clusters of pre-existing mental disorders may affect COVID-19 clinical outcomes or showed how the coexistence of mental disorder clusters is related to COVID-19 clinical outcomes.\n\nObjectiveTo explore how different pre-existing mental disorders and their co-occurrence affects COVID-19-related clinical outcomes based on real-world data.\n\nDesign, Setting, and ParticipantsUsing a retrospective cohort study design, a total of 476,775 adult patients with lab-confirmed and probable COVID-19 between March 06, 2020 and April 14, 2021 in South Carolina, United States were included in the current study. The electronic health record data of COVID-19 patients were linked to all payer-based claims data through the SC Revenue and Fiscal Affairs Office.\n\nMain Outcomes and MeasuresKey COVID-19 clinical outcomes included severity, hospitalization, and death. COVID-19 severity was defined as asymptomatic, mild, and moderate/severe. Pre-existing mental disorder diagnoses from Jan 2, 2019 to Jan 14, 2021 were extracted from the patients healthcare utilization data via ICD-10 codes. Mental disorders were categorized into internalizing disorders, externalizing disorders, and thought disorders.\n\nResultsOf the 476,775 COVID-19 patients, 55,300 had pre-existing mental disorders. There is an elevated risk of COVID-19-related hospitalization and death among participants with pre-existing mental disorders adjusting for key socio-demographic covariates (i.e., age, gender, race, ethnicity, residence, smoking). Co-occurrence of any two clusters was positively associated with COVID-19-related hospitalization and death. The odds ratio of being hospitalized was 2.50 (95%CI 2.284, 2.728) for patients with internalizing and externalizing disorders, 3.34 (95%CI 2.637, 4.228) for internalizing and thought disorders, 3.29 (95%CI 2.288, 4.733) for externalizing and thought disorders, and 3.35 (95%CI 2.604, 4.310) for three clusters of mental disorders.\n\nConclusions and RelevancePre-existing internalizing disorders, externalizing disorders, and thought disorders are positively related to COVID-19 hospitalization and death. Co-occurrence of any two clusters of mental disorders have elevated risk of COVID-19-related hospitalization and death compared to those with a single cluster.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Shan Qiao", - "author_inst": "University of South Carolina" - }, - { - "author_name": "jiajia zhang", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Shujie Chen", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Bankole Olatosi", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Suzanne Hardeman", - "author_inst": "Prisma Health (Midland), South Carolina" - }, - { - "author_name": "Meera Narasimhan", - "author_inst": "Prisma Health (Midland), South Carolina" - }, - { - "author_name": "Larisa Bruner", - "author_inst": "Department of Health and Environment Control South Carolina" - }, - { - "author_name": "Diedhiou Abdoulaye", - "author_inst": "Department of Health and Environment Control South Carolina" - }, - { - "author_name": "Cheryl L. Scott", - "author_inst": "Department of Health and Environment Control South Carolina" - }, - { - "author_name": "Ali B. Mansaray", - "author_inst": "Department of Health and Environment Control South Carolina" - }, - { - "author_name": "Sharon Weissman", - "author_inst": "University of South Carolina School of Medicine" - }, - { - "author_name": "Xiaoming Li", - "author_inst": "University of South Carolina" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.22.21265371", "rel_title": "Social mixing patterns in the UK following the relaxation of COVID-19 pandemic restrictions: a cross-sectional online survey", @@ -541411,6 +542892,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.10.21.21265349", + "rel_title": "Safety and Effectiveness of COVID-19 SPUTNIK V Vaccine in Dialysis Patients", + "rel_date": "2021-10-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.21.21265349", + "rel_abs": "Given the vulnerability of people with chronic kidney disease to COVID-19, nephrology societies have issued statements calling for prioritization of these patients for vaccination. It is not yet known whether COVID-19 vaccines confer the same high level of protection in patients with kidney disease. The aims of this study were to evaluate the safety measured by the events supposedly attributed to vaccines and the effectiveness evaluated by the presence of antibodies in dialysis patients immunized with the COVID-19 Sputnik V vaccine.\n\nMethodsmulticenter, observational and analytical study of a prospective cohort of hemodialysis patients in the Autonomous City of Buenos Aires with a vaccination plan. Patients older than 18 years on dialysis who received both components of the COVID-19 vaccine were included.\n\nResults491 patients included in the safety analysis. ESAVI with either the first or second component was detected in 186 (37.9% 95% CI 33.6%-42.34%). The effectiveness analysis measures of antibodies against SARS-Cov-2 were performed in 102 patients, 98% had positive IgG against SARS-Cov-2 antibodies 21 days after the second component .In patients with COVID-19 prior to vaccination, antibodies at day 21 after the first component reached almost the highest levels compared to those patients who did not have COVID-19, and the rise between the last measures was lower than patients without COVID-19.\n\nConclusionDialysis patients constitute a vulnerable population for SARS-Cov-2 infection, beyond the recommendations that were implemented by dialysis units, full vaccination is a priority and necessary. The Sputnik V vaccine has been shown to be safe and effective in this patient population.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Guillermo Rosa-Diez", + "author_inst": "Hospital Italiano de Buenos Aires, Nephrology, Argentina" + }, + { + "author_name": "Maria M Papaginovic-Leiva", + "author_inst": "Hospital Medico Policial Churruca Vizca, Nephrology, Argentina" + }, + { + "author_name": "Fernando Lombi", + "author_inst": "Hospital Britanico, Nephrology, Argentina" + }, + { + "author_name": "Maria S Crucelegui", + "author_inst": "Hospital Italiano de Buenos Aires, Nephrology, Argentina" + }, + { + "author_name": "Ricardo D Martinez", + "author_inst": "Hospital Medico Policial Churruca Visca, Nephrology, Argentina" + }, + { + "author_name": "Hernan Trimarchi", + "author_inst": "Hospital Britanico, Nephrology, Argentina" + }, + { + "author_name": "Ruben Schiavelli", + "author_inst": "Hospital General de Agudos Dr. Cosme Argerich, Nephrology, Argentina" + }, + { + "author_name": "Mercedes Grizzo", + "author_inst": "Hospital General de Agudos Dr. Cosme Argerich, Nephrology, Argentina" + }, + { + "author_name": "Miguel Rano", + "author_inst": "Hospital General de Agudos Dr. Cosme Argerich, Nephrology, Argentina" + }, + { + "author_name": "Ricardo M . Heguilen", + "author_inst": "Hospital General de Agudos Dr. Juan A. Fernandez, Nephrology, Argentina" + }, + { + "author_name": "Rocio A Jones", + "author_inst": "Hospital General de Agudos Dr. Juan A. Fernandez, Nephrology, Argentina" + }, + { + "author_name": "Luciana Gonzalez-Paganti", + "author_inst": "Hospital Militar Central Cirujano Mayor Dr. Cosme Argerich, Nephrology, Argentina" + }, + { + "author_name": "Matias Ferrari", + "author_inst": "Hospital Militar Central Cirujano Mayor Dr. Cosme Argerich, Nephrology, Argentina" + }, + { + "author_name": "Paula Zingoni", + "author_inst": "Operational Planning, Ministry of Health of the Government of the City of Buenos Aires, Argentina" + }, + { + "author_name": "Victoria Kjohede", + "author_inst": "INBIRS (Instituto Investigaciones Biomedicas en Retrovirus y SIDA), School of Medicine. University of Buenos Aires, Argentina" + }, + { + "author_name": "Jorge R Geffner", + "author_inst": "NBIRS (Instituto Investigaciones Biomedicas en Retrovirus y SIDA), School of Medicine. University of Buenos Aires, Argentina" + }, + { + "author_name": "Daniel Ferrante", + "author_inst": "Health Planning and Network Management Ministry of Health Buenos Aires City, Argentina" + }, + { + "author_name": "Fernan Gonzalez Bernaldo de Quiros", + "author_inst": "Minister of Health, Buenos Aires City, Argentina" + }, + { + "author_name": "Vanina Pagotto", + "author_inst": "Hospital Italiano de Buenos Aires" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2021.10.22.21265401", "rel_title": "SARS-CoV-2 Receptor Binding Domain IgG Response to AstraZeneca (AZD1222) COVID-19 Vaccination, Jamaica", @@ -543354,85 +544926,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.10.20.21265295", - "rel_title": "Predictors of SARS-CoV-2 infection following high-risk exposure: a test-negative design case-control study", - "rel_date": "2021-10-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.20.21265295", - "rel_abs": "BackgroundNon-pharmaceutical interventions (NPIs) are recommended for COVID-19 mitigation. However, the effectiveness of NPIs in preventing SARS-CoV-2 transmission remains poorly quantified.\n\nMethodsWe conducted a test-negative design case-control study enrolling cases (testing positive for SARS-CoV-2) and controls (testing negative) with molecular SARS-CoV-2 diagnostic test results reported to California Department of Public Health between 24 February-26 September, 2021. We used conditional logistic regression to assess predictors of case status among participants who reported contact with an individual known or suspected to have been infected with SARS-CoV-2 (\"high-risk exposure\") within [≤]14 days of testing.\n\nResults643 of 1280 cases (50.2%) and 204 of 1263 controls (16.2%) reported high-risk exposures [≤]14 days before testing. Adjusted odds of case status were 2.94-fold (95% confidence interval: 1.66-5.25) higher when high-risk exposures occurred with household members (vs. other contacts), 2.06-fold (1.03-4.21) higher when exposures occurred indoors (vs. not indoors), and 2.58-fold (1.50-4.49) higher when exposures lasted [≥]3 hours (vs. shorter durations) among unvaccinated and partially-vaccinated individuals; excess risk associated with such exposures was mitigated among fully-vaccinated individuals. Mask usage by participants or their contacts during high-risk exposures reduced adjusted odds of case status by 48% (8-72%). Adjusted odds of case status were 68% (32-84%) and 77% (59-87%) lower for partially- and fully-vaccinated participants, respectively, than for unvaccinated participants. Benefits of mask usage were greatest when exposures lasted [≥]3 hours, occurred indoors, or involved non-household contacts.\n\nConclusionsNPIs reduced the likelihood of SARS-CoV-2 infection following high-risk exposure. Vaccine effectiveness was substantial for partially and fully vaccinated persons.\n\nKEY POINTSO_LISARS-CoV-2 infection risk was greatest for unvaccinated participants when exposures to known or suspected cases occurred indoors or lasted [≥]3 hours.\nC_LIO_LIFace mask usage when participants were exposed to a known or suspect case reduced odds of infection by 48%.\nC_LI", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Kristin L. Andrejko", - "author_inst": "University of California at Berkeley" - }, - { - "author_name": "Jake Pry", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Jennifer F. Myers", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "John Openshaw", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "James Watt", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Nozomi Birkett", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Jennifer L DeGuzman", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Sophia S. Li", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Camilla M. Barbaduomo", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Anna T. Fang", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Vivian H. Tran", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Mahsa H. Javadi", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Paulina M. Frost", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Zheng N. Dong", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Seema Jain", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Joseph A. Lewnard", - "author_inst": "University of California Berkeley" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.21.21265216", "rel_title": "Generation time of the Alpha and Delta SARS-CoV-2 variants", @@ -543677,6 +545170,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2021.10.22.465399", + "rel_title": "Nanoviricides Platform Technology based NV-387 polymer Protects Remdesivir from Plasma-Mediated Catabolism in vitro:Importance of its increased lifetime for in vivo action", + "rel_date": "2021-10-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.22.465399", + "rel_abs": "As of today seven coronaviruses were identified to infect humans, out of which only 4 of them belongs to beta family of coronavirus, like HCoV-HKU1, SARS-CoV-2, MERS-CoV and SARS-CoV. SARS family of viruses were known to cause severe respiratory disease in humans. SARS-CoV-2 infection causes pandemic COVID-19 disease with high morbidity and mortality. Remdesivir (RDV) is the only antiviral drug so far approved for Covid-19 therapy by FDA. However its efficacy is limited in vivo due to its low stability in presence of Plasma.\n\nHere we show the stability of RDV encapsulated with our platform technology based polymer NV-387 (NV-CoV-2-R), in presence of Plasma in vitro in comparison to naked RDV when incubated in plasma. The potential use of this polymer in vivo will be discussed, here.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ashok Chakraborty", + "author_inst": "Allexcel" + }, + { + "author_name": "Anil Diwan", + "author_inst": "Nanoviricides, inc" + }, + { + "author_name": "Vinod Arora", + "author_inst": "Allexcel, Inc." + }, + { + "author_name": "Yogesh Thakur", + "author_inst": "Allexcel, Inc." + }, + { + "author_name": "Preetam Holkar", + "author_inst": "Allexcel, inc." + }, + { + "author_name": "Vijetha Chiniga", + "author_inst": "Allexcel, Inc." + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2021.10.21.21265314", "rel_title": "Autoimmune conditions following mRNA (BNT162b2) and inactivated (CoronaVac) COVID-19 vaccination: a descriptive cohort study among 1.1 million vaccinated people in Hong Kong", @@ -545175,37 +546707,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2021.10.20.21265283", - "rel_title": "Food Security Impacts of the COVID-19 Pandemic: Following a Cohort of Vermonters During the First Year", - "rel_date": "2021-10-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.20.21265283", - "rel_abs": "ObjectiveThis study assessed changes in household food insecurity throughout the first year of the COVID-19 pandemic in a cohort of Vermonters and examined the socio-demographic characteristics associated with increased odds of experiencing food insecurity during the pandemic.\n\nDesignWe conducted three online surveys with a cohort of Vermonters between March 2020 and March 2021 to collect longitudinal data on food security, food access, and job disruptions during the COVID-19 pandemic. Food security was measured using the USDA six-item module. We used t-tests and chi-square tests to determine statistically significant differences between groups and multivariate logistic regression models to determine the factors correlated with food insecurity.\n\nParticipants441 adults (18 years and older)\n\nSettingVermont, United States\n\nResultsFood insecurity rates increased significantly during the pandemic and remained above pre-pandemic levels a year after the start of the pandemic. Nearly a third (31.6%) of respondents experienced food insecurity at some point during the first year of the pandemic. Certain demographic groups were at significantly higher odds of experiencing food insecurity during the first year of the COVID-19 pandemic including households with children (OR 5.1, p < 0.01), women (OR 7.3, p < 0.05), BIPOC/Hispanic respondents (OR 10.4, p < 0.05), and households experiencing a job disruption (OR 4.6, p <0.01).\n\nConclusionThe prevalence of food insecurity increased during the first year of the COVID-19 pandemic and remained higher than pre-pandemic levels a year after the pandemic began. Odds of experiencing food insecurity during the pandemic vary based on socio-demographic factors.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ashley C McCarthy", - "author_inst": "University of Vermont" - }, - { - "author_name": "Emily H Belarmino", - "author_inst": "University of Vermont" - }, - { - "author_name": "Farryl MW Bertmann", - "author_inst": "University of Vermont" - }, - { - "author_name": "Meredith T. Niles", - "author_inst": "University of Vermont" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.10.20.21265269", "rel_title": "Effect of the third dose of BNT162b2 vaccine in quantitative SARS-CoV-2 spike 1-2 IgG antibody titers in healthcare workers", @@ -545526,6 +547027,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.19.21265062", + "rel_title": "Mutations on non-structural proteins of SARS-CoV-2 are possibly responsible for adverse clinical outcomes in a real-life practice", + "rel_date": "2021-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.19.21265062", + "rel_abs": "Among a cluster of COVID-19 cases from the end of March through April 2021 in Asahikawa, we experienced the cases in which patients manifested severe clinical symptoms compared to patients who were infected before that. A hundred three patients (age range: 65 to 89 years old) enrolled in this study were divided into two groups, group A: the patients infected from November 2020 to March 2021, and group B: the patients in this cluster population. The mortality rates were 6.1% in group A and 16.2% in group B (OR: 2.97, 95%CI: 0.65-15.38). For the severity of disease, the patients in group B required higher oxygen flow rate in early course of admission (mild; p=0.892, moderate; p=0.117, severe; p=0.029). Whole viral genome sequences revealed five non-synonymous mutations by comparison of the isolates with each group. Of these, four were on non-structural proteins (NSPs) including nsp3, 6 and 15, and one was on S protein located near the C-terminus, suggesting that the mutations on NSPs could be responsible for adverse clinical outcomes in COVID-19 patients.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Takaya Ichikawa", + "author_inst": "Division of Internal Medicine, Asahikawa City Hospital, Asahikawa, Japan" + }, + { + "author_name": "Shiho Torii", + "author_inst": "Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan" + }, + { + "author_name": "Hikoyu Suzuki", + "author_inst": "digzyme Inc., Tokyo, Japan" + }, + { + "author_name": "Akio Takada", + "author_inst": "Department of Pathology, Asahikawa City Hospital, Asahikawa, Japan" + }, + { + "author_name": "Satoshi Suzuki", + "author_inst": "Division of Internal Medicine, Asahikawa City Hospital, Asahikawa, Japan" + }, + { + "author_name": "Masahide Nakajima", + "author_inst": "Department of Pediatrics, Asahikawa City Hospital, Asahikawa, Japan" + }, + { + "author_name": "Akihito Tampo", + "author_inst": "Department of Emergency Medicine, Asahikawa City Hospital, Asahikawa, Japan" + }, + { + "author_name": "Yasutaka Kakinoki", + "author_inst": "Division of Internal Medicine, Asahikawa City Hospital, Asahikawa, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.19.21265208", "rel_title": "Airborne transmission of SARS-CoV-2 over distances greater than two metres: a rapid systematic review", @@ -547341,49 +548889,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.14.21264762", - "rel_title": "Longitudinal and comparative analysis of humoral response upon COVID-19 vaccination", - "rel_date": "2021-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.14.21264762", - "rel_abs": "The emergence of COVID-19 has led to a worldwide challenge for the rapid development of vaccines. Several types of safe and effective vaccines have been available in a time frame never seen before. Comparative studies to know the extent of protection and the immune response elicited by the different vaccines are of outstanding utility. Here, as a correlate for protection, we perform a comparative study of the humoral response to three vaccines, ChAdOx1 (Oxford-AstraZeneca), mRNA-1273 (Moderna), and BNT162b2 (Pfizer-BioNTech) by applying a flow cytometry-based highly sensitive method that we had previously developed. We have found that mRNA vaccines (mRNA-1273 and BNT162b2) induce a stronger humoral response that lasts for at least 6 months after vaccination. We also show that only one dose of BNT162b2 is enough to achieve the maximum response in seropositive pre-vaccination donors.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Salvador Romero-Pinedo", - "author_inst": "VITRO SA" - }, - { - "author_name": "Marina Quesada", - "author_inst": "VITRO SA" - }, - { - "author_name": "Stela \u00c1lvarez-Fern\u00e1ndez", - "author_inst": "VITRO SA" - }, - { - "author_name": "Asunci\u00f3n Olmo", - "author_inst": "VITRO SA" - }, - { - "author_name": "David Abia", - "author_inst": "Centro de Biolog\u00eda Molecular Severo Ochoa" - }, - { - "author_name": "Balbino Alarc\u00f3n", - "author_inst": "Centro de Biolog\u00eda Molecular Severo Ochoa" - }, - { - "author_name": "Pilar Delgado", - "author_inst": "Centro de Biolog\u00eda Molecular Severo Ochoa" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.11.21264694", "rel_title": "A cohort of 222 anti-CD20 treated patients with multiple sclerosis followed through the COVID-19 pandemic: Attenuated humoral but robust cellular immune responses after vaccination and infection", @@ -547592,6 +549097,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.10.12.21264136", + "rel_title": "Accuracy of emergency medical service telephone triage of need for an ambulance response in suspected COVID-19: An observational cohort study", + "rel_date": "2021-10-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.12.21264136", + "rel_abs": "BackgroundEmergency Medical Services (EMS) have experienced surges in demand as the COVID-19 pandemic has progressed with ambulances services in the UK declaring major incidents due to the risk of care being compromised. COVID-19 specific EMS telephone triage tools have been introduced to help manage demand. There has been no previous evaluation of the accuracy of EMS telephone triage in identifying patients with suspected COVID-19 at risk of serious adverse outcome.\n\nWe aimed to assess accuracy of EMS telephone triage in identifying patients who need an EMS response and identify factors which affect triage accuracy.\n\nMethodPatients who made an emergency call to Yorkshire Ambulance Service between 2nd April and 29th June 2020 and were assessed using an AMPDS pandemic pathway for suspected COVID-19 were linked to Office for National Statistics death registration data, hospital and general practice electronic health care data collected by NHS Digital.\n\nAccuracy of decision to dispatch an ambulance was assessed in terms of death or need for organ support at 30 days from the first 999 call. Multivariable logistic regression was used to identify factors associated with false negative and false positive triage.\n\nResultsOf 12, 653 callers included in the study population, 11.1% experienced the primary composite adverse outcome. Using the triage pathway, 16% of callers did not receive an emergency response and they had a lower risk (3.5%) of the primary outcome. Ambulances were dispatched to 4, 230 callers (33.4%) who were not subsequently conveyed to hospital and did not experience the primary outcome (false positive triage). Multivariable modelling found older age and presence of pre-existing respiratory disease were significant predictors of false positive triage.\n\nConclusionEMS telephone triage avoided 16% of calls receiving an emergency ambulance, of whom 3.5% died or needed organ support by 30 days. Telephone triage can therefore reduce the burden of EMS responses but with the cost of a small proportion of patients who do not receive an initial emergency response deteriorating. Research is needed to identify the appropriate balance between over- and under-triage", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Carl Marincowitz", + "author_inst": "Centre for Urgent and Emergency Care Research (CURE), Health Services Research School of Health and Related Research, University of Sheffield" + }, + { + "author_name": "Tony Stone", + "author_inst": "Centre for Urgent and Emergency Care Research (CURE), Health Services Research School of Health and Related Research, University of Sheffield" + }, + { + "author_name": "Madina Hasan", + "author_inst": "Centre for Urgent and Emergency Care Research (CURE), Health Services Research School of Health and Related Research, University of Sheffield" + }, + { + "author_name": "Richard Campbell", + "author_inst": "Centre for Urgent and Emergency Care Research (CURE), Health Services Research School of Health and Related Research, University of Sheffield" + }, + { + "author_name": "Peter Bath", + "author_inst": "Information School, University of Sheffield" + }, + { + "author_name": "Janette Turner", + "author_inst": "Centre for Urgent and Emergency Care Research (CURE), Health Services Research School of Health and Related Research, University of Sheffield" + }, + { + "author_name": "Richard Pilbery", + "author_inst": "Yorkshire Ambulance Service NHS Trust" + }, + { + "author_name": "Benjamin Thomas", + "author_inst": "Clinical Trials Research Unit (CTRU), Health Services Research School of Health and Related Research, University of Sheffield" + }, + { + "author_name": "Laura Sutton", + "author_inst": "Clinical Trials Research Unit (CTRU), Health Services Research School of Health and Related Research, University of Sheffield" + }, + { + "author_name": "Fiona Bell", + "author_inst": "Yorkshire Ambulance Service NHS Trust" + }, + { + "author_name": "Katie Biggs", + "author_inst": "Clinical Trials Research Unit (CTRU), Health Services Research School of Health and Related Research, University of Sheffield" + }, + { + "author_name": "Frank Hopfgartner", + "author_inst": "Information School, University of Sheffield" + }, + { + "author_name": "Suvodeep Mazumdar", + "author_inst": "Information School, University of Sheffield" + }, + { + "author_name": "Jennifer Petrie", + "author_inst": "Clinical Trials Research Unit (CTRU), Health Services Research School of Health and Related Research, University of Sheffield" + }, + { + "author_name": "Steve Goodacre", + "author_inst": "Centre for Urgent and Emergency Care Research (CURE), Health Services Research School of Health and Related Research, University of Sheffield" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2021.10.18.464900", "rel_title": "Preclinical Efficacy of IMM-BCP-01, a Highly Active Patient-Derived Anti-SARS-CoV-2 Antibody Cocktail", @@ -548962,49 +550542,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.15.21265006", - "rel_title": "Vaccine effectiveness of Ad26.COV2.S against symptomatic COVID-19 and clinical outcomes in Brazil: a test-negative study design", - "rel_date": "2021-10-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.15.21265006", - "rel_abs": "We used a test-negative design to estimate the vaccine effectiveness of Ad26.COV2.S (Janssen) against symptomatic COVID-19 and clinical outcomes in Mato-Grosso do Sul, Brazil. We analyzed 11,817 RT-PCR tests. The mean age was 37 (SD=17) years, 2,308 (20%) of individuals more or equal than 50 years and almost two-thirds of the population was Brown/Pardo. Adjusted effectiveness against symptomatic COVID-19 after 28 days of the single dose was 50.9% (95% CI, 35.5-63.0). Adjusted effectiveness against clinical outcomes was 72.9% (95% CI, 35.1-91.1) for hospitalization, 92.5% (95% CI, 54.9-99.6) for ICU admission, 88.7% (95% CI, 17.9-99.5) for mechanical ventilation and 90.5% (95% CI, 31.5-99.6) for death. Despite lacking precision on some estimates, a single dose of Ad26.COV2.S vaccine continues to protect specially for severe forms of COVID-19 in the context of new variants.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Otavio T Ranzani", - "author_inst": "Barcelona Institute for Global Health, ISGlobal, Spain / Pulmonary Division, University of Sao Paulo" - }, - { - "author_name": "Rog\u00e9rio dos Santos Leite", - "author_inst": "Secretaria Municipal de Sa\u00fade de Corumb\u00e1, Corumb\u00e1, Brazil" - }, - { - "author_name": "Larissa Domingues Castilho", - "author_inst": "Secretaria de Sa\u00fade do estado de Mato Grosso do Sul, Campo Grande, Brazil" - }, - { - "author_name": "Crhistinne Cavalheiro Maymone Gon\u00e7alves", - "author_inst": "Secretaria de Sa\u00fade do estado de Mato Grosso do Sul, Campo Grande, Brazil/ Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil" - }, - { - "author_name": "Geraldo Resende", - "author_inst": "Secretaria de Sa\u00fade do estado de Mato Grosso do Sul, Campo Grande, Brazil" - }, - { - "author_name": "Rosana Leite de Melo", - "author_inst": "Secretaria Extraordin\u00e1ria de Enfrentamento \u00e0 Covid-19, Ministerio da Sa\u00fade, Bras\u00edlia, Brazil" - }, - { - "author_name": "Julio Croda", - "author_inst": "Fiocruz Mato Grosso do Sul, Funda\u00e7\u00e3o Oswaldo Cruz, Campo Grande, Brazil/ Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil/ Department of Epidemi" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.15.21265059", "rel_title": "CoWWAn: Model-based assessment of COVID-19 epidemic dynamics by wastewater analysis", @@ -549137,6 +550674,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.14.21264992", + "rel_title": "Estimating COVID-19 Hospitalizations in the United States with surveillance data using a Bayesian Hierarchical model", + "rel_date": "2021-10-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.14.21264992", + "rel_abs": "IntroductionIn the United States, COVID-19 is a nationally notifiable disease, cases and hospitalizations are reported to the CDC by states. Identifying and reporting every case from every facility in the United States may not be feasible in the long term. Creating sustainable methods for estimating burden of COVID-19 from established sentinel surveillance systems is becoming more important. We aimed to provide a method leveraging surveillance data to create a long-term solution to estimate monthly rates of hospitalizations for COVID-19.\n\nMethodsWe estimated monthly hospitalization rates for COVID-19 from May 2020 through April 2021 for the 50 states using surveillance data from COVID-19-Associated Hospitalization Surveillance Network (COVID-NET) and a Bayesian hierarchical model for extrapolation. We created a model for six age groups (0-17, 18-49, 50-64, 65-74, 75-84, and [≥]85 years), separately. We identified covariates from multiple data sources that varied by age, state, and/or month, and performed covariate selection for each age group based on two methods, Least Absolute Shrinkage and Selection Operator (LASSO) and Spike and Slab selection methods. We validated our method by checking sensitivity of model estimates to covariate selection and model extrapolation as well as comparing our results to external data.\n\nResultsWe estimated 3,569,500 (90% Credible Interval:3,238,000 - 3,934,700) hospitalizations for a cumulative incidence of 1,089.8 (988.6 - 1,201.3) hospitalizations per 100,000 population with COVID-19 in the United States from May 2020 through April 2021. Cumulative incidence varied from 352 - 1,821per 100,000 between states. The age group with the highest cumulative incidence was aged [≥]85 years (5,583.1; 5,061.0 - 6,157.5). The monthly hospitalization rate was highest in December (183.8; 154.5 - 218.0). Our monthly estimates by state showed variations in magnitudes of peak rates, number of peaks and timing of peaks between states.\n\nConclusionsOur novel approach to estimate COVID-19 hospitalizations has potential to provide sustainable estimates for monitoring COVID-19 burden, as well as a flexible framework leveraging surveillance data.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Alexia Couture", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Danielle Iuliano", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Howard H Chang", + "author_inst": "Emory University" + }, + { + "author_name": "Neha N Patel", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Matthew Gilmer", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Molly Steele", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Fiona P Havers", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Michael Whitaker", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Carrie Reed", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.10.14.21264918", "rel_title": "Back to the medical classes-Part I- Strategy for return to the presential practices during COVID-19 pandemics in a Brazilian Medical School", @@ -550592,37 +552180,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.10.13.21264855", - "rel_title": "\"I had no life. I was only existing\". Factors shaping the mental health and wellbeing of people experiencing long Covid: a qualitative study.", - "rel_date": "2021-10-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.13.21264855", - "rel_abs": "BackgroundAround one in 10 people who have COVID-19 report persistent symptoms or long Covid. Impaired mental health and wellbeing is commonly reported including anxiety, depression and reduced quality of life. There is however, limited in-depth research exploring why mental health and wellbeing have been impacted among people experiencing long Covid.\n\nAimsTo explore factors impacting mental health and wellbeing, from the perspective of people with long Covid.\n\nMethodSemi-structured qualitative interviews that were audio-recorded and transcribed. Data were analysed using reflexive thematic analysis. 21 people with long Covid participated in the study. Participants were eligible to take part if they self-reported a positive swab test/antibody test, or one or more commonly reported COVID-19 symptoms at illness onset and experiences of one or more long Covid symptom three or more weeks following illness onset.\n\nResultsFive themes were identified across participant accounts regarding factors impacting mental health and wellbeing including i) experiences of care and understanding from others; ii) lack of service and treatment options; iii) severe disruption to daily life iv) uncertainty of illness trajectories and v) changes to identity.\n\nConclusionsPeople with long Covid experience a range of factors that negatively impact their mental health and wellbeing. Providing patient centred health services that integrate the rapidly evolving research in this area is important, as are peer support groups and supported approaches to self-management.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Alexandra Burton", - "author_inst": "University College London" - }, - { - "author_name": "Henry Aughterson", - "author_inst": "UCL" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - }, - { - "author_name": "Keir Elmslie James Philip", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.10.13.21264894", "rel_title": "Memory B cell and humoral responses elicited by Sputnik V in nai\u0308ve and COVID-19-recovered vaccine recipients", @@ -550778,6 +552335,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.13.21264932", + "rel_title": "The role of educational settings in the transmission chain of SARS-CoV-2 in 2020: a systematic review", + "rel_date": "2021-10-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.13.21264932", + "rel_abs": "BackgroundSchool closures have been used as a core Non pharmaceutical intervention during the COVID-19 pandemic, however the role of educational settings in COVID-19 transmission is still unclear.\n\nMethodsThis systematic literature review assessed studies published between December 2019 and April 1, 2021 in Medline and Embase, which included studies that assessed educational settings from approximately January 2020 to January 2021. The inclusion criteria were based on the PCC framework (P-Population, C-Concept, C-Context). The study Population was restricted to people 1-17 years old (excluding neonatal transmission), the Concept was to assess child-to-child and child-to-adult transmission, while the Context was to assess specifically educational setting transmission clusters.\n\nResultsFifteen studies met inclusion criteria, ranging from daycare centers to high schools and summer camps, while eight studies assessed the re-opening of schools in the 2020-2021 school year. In principle although there is sufficient evidence that children can both be infected by and transmit SARS-CoV-2 in school settings, the SAR remain relatively low -when NPI measures are implemented in parallel. Moreover, although the evidence was limited there was an indication that younger children may have a lower SAR than adolescents.\n\nConclusionsTransmission in educational settings in 2020 was minimal -when NPI measures were implemented in parallel. However, with an upsurge of cases related to variants of concern, continuous surveillance and assessment of the evidence is warranted to ensure the maximum protection of the health of students and the educational workforce, while also minimising the numerous negative impacts that school closures may have on children.\n\nStrengths and limitations of this studyO_LIThis study provides a rapid review of the peer-reviewed literature pertaining to SARS-CoV-2 transmission by children within educational settings.\nC_LIO_LIThe review reflects the status quo of the previous school years (January 2020 -January 2021) due to the lag time between study implementation, peer review and publication.\nC_LIO_LIThe included studies represent child-to-child transmission within the context of previous SARS-CoV-2 strains and are not directly applicable to newer variants.\nC_LI", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Constantine Vardavas", + "author_inst": "School of Medicine, University of Crete, Greece" + }, + { + "author_name": "Katerina Nikitara", + "author_inst": "University of Crete" + }, + { + "author_name": "Alexander Mathioudakis", + "author_inst": "University of Manchester" + }, + { + "author_name": "Michele Hilton-Boon", + "author_inst": "Glasgow Caledonian University" + }, + { + "author_name": "Revati Phalkey", + "author_inst": "Public Health England" + }, + { + "author_name": "Jo Leonardi-Bee", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Anastasia Pharris", + "author_inst": "European Centre for Disease Prevention and Control" + }, + { + "author_name": "Charlotte Deogan", + "author_inst": "European Centre for Disease Prevention and Control" + }, + { + "author_name": "Jonathan E. Suk", + "author_inst": "European Centre for Disease Prevention and Control" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.12.21264913", "rel_title": "Psychiatric Manifestations and Associated Risk Factors among Hospitalized Patients with COVID-19 in Edo State, Nigeria.", @@ -552685,73 +554293,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.12.21264860", - "rel_title": "SARS-CoV-2 vaccine antibody response and breakthrough infections in patients receiving dialysis", - "rel_date": "2021-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.12.21264860", - "rel_abs": "BackgroundPatients receiving dialysis are a sentinel population for groups at high risk for death and disability from COVID-19. Understanding correlates of protection post-vaccination can inform immunization and mitigation strategies.\n\nMethodsMonthly since January 2021, we tested plasma from 4791 patients receiving dialysis for antibodies to the receptor-binding domain (RBD) of SARS-CoV-2 using a high-throughput assay. We qualitatively assessed the proportion without a detectable RBD response and among those with a response, semiquantitative median IgG index values. Using a nested case-control design, we matched each breakthrough case to five controls by age, sex, and vaccination-month to determine whether peak and pre-breakthrough RBD IgG index values were associated with risk for infection post-vaccination.\n\nResultsAmong 2563 vaccinated patients, the proportion without a detectable RBD response increased from 6.6% [95% CI 5.5-8.1] in 14-30 days post-vaccination to 20.2% [95% CI 17.1-23.8], and median index values declined from 92.7 (95% CI 77.8-107.5) to 3.7 (95% CI 3.1-4.3) after 5 months. Persons with SARS-CoV-2 infection prior-to-vaccination had higher peak index values than persons without prior infection, but values equalized by 5 months (p=0.230). Breakthrough infections occurred in 56 patients, with samples collected a median of 21 days pre-breakthrough. Peak and pre-breakthrough RBD values <23 (equivalent to <506 WHO BAU/mL) were associated with higher odds for breakthrough infection (OR: 3.7 [95% CI 2.0-6.8] and 9.8 [95% CI 2.9-32.8], respectively).\n\nConclusionsThe antibody response to SARS-CoV-2 vaccination wanes rapidly, and in persons receiving dialysis, the persisting antibody response is associated with risk for breakthrough infection.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Shuchi Anand", - "author_inst": "Stanford University" - }, - { - "author_name": "Maria E Montez-Rath", - "author_inst": "Stanford University" - }, - { - "author_name": "Jialin Han", - "author_inst": "Stanford University" - }, - { - "author_name": "Pablo Garcia", - "author_inst": "Stanford University" - }, - { - "author_name": "LinaCel Cadden", - "author_inst": "Ascend Clinical Lab" - }, - { - "author_name": "Patti Hunsader", - "author_inst": "Ascend Clinical Lab" - }, - { - "author_name": "Curt Morgan", - "author_inst": "Ascend Clinical Lab" - }, - { - "author_name": "Russell Kerschmann", - "author_inst": "Ascend Clinical Lab" - }, - { - "author_name": "Paul Beyer", - "author_inst": "Ascend Clinical Lab" - }, - { - "author_name": "Mary Dittrich", - "author_inst": "US Renal Care" - }, - { - "author_name": "Geoffrey A Block", - "author_inst": "US Renal Care" - }, - { - "author_name": "Glenn M Chertow", - "author_inst": "Stanford University" - }, - { - "author_name": "Julie Parsonnet", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.11.21264869", "rel_title": "Modeling and analysis of COVID-19 infected persons during repeated waves in Japan", @@ -552964,6 +554505,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.12.21264902", + "rel_title": "COVID-19 and Mental Health: Predicted Mental Health Status is Associated with Clinical Symptoms and Pandemic-Related Psychological and Behavioral Responses", + "rel_date": "2021-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.12.21264902", + "rel_abs": "BackgroundThe COVID-19 pandemic led to dramatic threats to health and social life. Study objectives - develop a prediction model leveraging subsample of known Patient/Controls and evaluate the relationship of predicted mental health status to clinical outcome measures and pandemic-related psychological and behavioral responses during lockdown (spring/summer 2020).\n\nMethodsOnline cohort study conducted by National Institute of Mental Health Intramural Research Program. Convenience sample of English-speaking adults (enrolled 4/4-5/16/20; n=1,992). Enrollment measures: demographics, clinical history, functional status, psychiatric and family history, alcohol/drug use. Outcome measures (enrollment and q2 weeks/6 months): distress, loneliness, mental health symptoms, and COVID-19 survey. NIMH IRP Patient/Controls survey responses informed assignment of Patient Probability Scores (PPS) for all participants. Regression models analyzed the relationship between PPS and outcome measures.\n\nOutcomesMean age 46.0 ({+/-}14.7), female (82.4%), white (88.9 %). PPS correlated with distress, loneliness, depression, and mental health factors. PPS associated with negative psychological responses to COVID-19. Worry about mental health (OR 1.46) exceeded worry about physical health (OR 1.13). PPS not associated with adherence to social distancing guidelines but was with stress related to social distancing and worries about infection of self/others.\n\nInterpretationMental health status (PPS) was associated with concurrent clinical ratings and COVID-specific negative responses. A focus on mental health during the pandemic is warranted, especially among those with mental health vulnerabilities. We will include PPS when conducting longitudinal analyses of mental health trajectories and risk and resilience factors that may account for differing clinical outcomes.\n\nFundingNIMH (ZIAMH002922); NCCIH (ZIAAT000030)", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Joyce Y Chung", + "author_inst": "National Institutue of Mental Health" + }, + { + "author_name": "Alison Gibbons", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Lauren Atlas", + "author_inst": "National Center for Complementary and Integrative Health" + }, + { + "author_name": "Elizabeth Ballard", + "author_inst": "National Institute of Mental Health" + }, + { + "author_name": "Monique Ernst", + "author_inst": "National Institute of Mental Health" + }, + { + "author_name": "Shruti Japee", + "author_inst": "National Institute of Mental Health" + }, + { + "author_name": "Cristan Farmer", + "author_inst": "National Institute of Mental Health" + }, + { + "author_name": "Jacob Shaw", + "author_inst": "National Institute of Mental Health" + }, + { + "author_name": "Francisco Pereira", + "author_inst": "National Institute of Mental Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.10.13.21264961", "rel_title": "Examining the Association between the COVID-19 Pandemic and Self-Harm Death Counts in Four Canadian Provinces", @@ -554587,65 +556179,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.10.21264825", - "rel_title": "Effects of Age, Sex, Serostatus and Underlying Comorbidities on Humoral Response Post-SARS-CoV-2 Pfizer-BioNTech Vaccination: A Systematic Review", - "rel_date": "2021-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.10.21264825", - "rel_abs": "With the advent of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic, several vaccines have been developed to mitigate its spread and prevent adverse consequences of the Coronavirus Disease 2019 (COVID-19). The mRNA technology is an unprecedented vaccine, usually given in two doses to prevent SARS-CoV-2 infections. Despite effectiveness and safety, inter-individual immune response heterogeneity has been observed in recipients of mRNA-based vaccines. As a novel disease, the specific immune response mechanism responsible for warding off COVID-19 remains unclear at this point. However, significant evidence suggests that humoral response plays a crucial role in affording immunoprotection and preventing debilitating sequelae from COVID-19. As such this paper focused on the possible effects of age, sex, serostatus, and comorbidities on humoral response (i.e., total antibodies, IgG and/or IgA) of different populations post-mRNA-based Pfizer-BioNTech vaccination. A systematic search of literature was performed through PubMed, Cochrane CENTRAL, and Google Scholar. Studies were included if they reported humoral response to COVID-19 mRNA vaccines. A total of 32 studies was identified and reviewed, and the percent difference of means of reported antibody levels were calculated for comparison. Findings revealed that older individuals, the male sex, seronegativity, and those with more comorbidities mounted less humoral immune response. Given these findings, several recommendations were proposed regarding the current vaccination practices. These include giving additional doses of vaccination for immunocompromised and elderly populations. Another recommendation is conducting clinical trials in giving a combined scheme of mRNA vaccines, protein vaccines, and vector-based vaccines.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Kin Israel Notarte", - "author_inst": "Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines" - }, - { - "author_name": "Abbygail Therese Ver", - "author_inst": "Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines" - }, - { - "author_name": "Jacqueline Veronica Velasco", - "author_inst": "Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines" - }, - { - "author_name": "Adriel Pastrana", - "author_inst": "Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines" - }, - { - "author_name": "Jesus Alfonso Catahay", - "author_inst": "Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines" - }, - { - "author_name": "Gian Luca Salvagno", - "author_inst": "Service of Laboratory Medicine, Pederzoli Hospital, Peschiera del Garda, Italy" - }, - { - "author_name": "Eric Peng Huat Yap", - "author_inst": "Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore" - }, - { - "author_name": "Luis Martinez-Sobrido", - "author_inst": "Host-Pathogens Interactions and Population Health Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA" - }, - { - "author_name": "Jordi Torrelles", - "author_inst": "Host-Pathogens Interactions and Population Health Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA" - }, - { - "author_name": "Giuseppe Lippi", - "author_inst": "Section of Clinical Biochemistry, University of Verona, Verona, Italy" - }, - { - "author_name": "Brandon Michael Henry", - "author_inst": "Clinical Laboratory, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Ohio, USA" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.10.10.21264821", "rel_title": "Modelling the effect of COVID-19 mass vaccination on acute admissions in a major English healthcare system", @@ -554902,6 +556435,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.10.21264779", + "rel_title": "Genetically determined serum testosterone level and Covid-19 illness level: A mendelian randomization study", + "rel_date": "2021-10-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.10.21264779", + "rel_abs": "BackgroundIt is hypothesized that different levels of hormones especially serum testosterone level could explain the sex differences between men and women on the susceptibility and case fatality rate of COVID-19. However, traditional observational studies that support this hypothesis could not effectively establish the causal effects.\n\nObjectiveUtilizing recently published genome-wide associations studies (GWAS) on serum Testosterone level and on COVID-19 related phenotypes, we sought to assess the causality through Mendelian Randomization (MR) analyses. We further applied a suite of statistical genomics methods to further explore the biological mechanisms.\n\nResultsWe found that testosterone level is significantly associated with Covid-19 critical illness. All six MR methods yielded significant associations. There is no significant association between Testosterone and COVID-19 respiratory failure or COVID-19 susceptibility.\n\nConclusionBased on the GWAS currently available, we provide support for a causal role of Testosterone on COVID-19 critical illness.Nevertheless, we recognize that the COVID-19 susceptibility GWAS effort is still ongoing and there is no such strong locus as CCR5 for HIV discovered for COVID-19.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Juan Xiong", + "author_inst": "Shenzhen University, Shenzhen, China" + }, + { + "author_name": "Ziyong Ma", + "author_inst": "Jinan Foreign Language School, Jinan, Shandong,China" + }, + { + "author_name": "Ruicheng Miao", + "author_inst": "Shandong Experimental High School, Jinan, Shandong, China" + }, + { + "author_name": "Jie Huang", + "author_inst": "Peking University" + }, + { + "author_name": "Xue-Jun Kong", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Yifei Qu", + "author_inst": "Shandong experimental high school, Jinan, Shandong, China" + }, + { + "author_name": "Xu Yang", + "author_inst": "Shenzhen Aone Medical Laboratory, Shenzhen, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.12.464114", "rel_title": "A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy", @@ -556264,57 +557840,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.10.07.21264204", - "rel_title": "Decreased hospital visits and increased mortality rate in the emergency department during the COVID-19 pandemic: Evidence from Albania.", - "rel_date": "2021-10-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.07.21264204", - "rel_abs": "ObjectiveTo investigate the hospital visits and mortality rate during the COVID-19 in emergency department of Vlora regional hospital in Albania and to compare with the three previous years (2017-2019).\n\nData sourcesSecondary data of patients that visited emergency department of Vlora Regional hospital Albania (largest hospital in the south of the country), since January 1, 2017 till December 31, 2020.\n\nStudy DesignThis is a retrospective study. We used the hard copy of the patients health register records.\n\nExtraction methodsThe data extraction was conducted during March 2021 till June 2021. Eligible were all patients admitted and recorded in the registry of the Emergency department. The causes of admission were categorized in 14 different disease categories. All registered patient admitted to the Vlora regional hospital were included in the study. Patients that all data were not recorded and patients that data were not possible to be read were excluded.\n\nPrincipal FindingsStudy population included 44.917 patients during 2017-2020. Mean age of patients was 51.5 years, while 53.6% were females. The highest number of patients was in 2017 (n=12.407) and the lowest in 2020 (n=9.266). Increase of patients presented with cardiovascular, psychiatric and renal/urinary tract were observed in 2020 in comparison to 2019. Patients decreased over time with an average annual percent decrease of -7% (p-value=0.22). Joinpoint analysis revealed that mortality rate increased over time with an average annual percent increase of 34.3% (95% confidence interval= -42.7% to 214.8%, p-value=0.27).\n\nConclusionsDuring the study years the number of patients visiting emergency department decreased while mortality rate increased. Educating and raising awareness of patient to seek medical assistance should be a key objective of health policy makers and health personnel. A specific focus should be put on the more vulnerable (elderly and unemployed) as their health status is in higher risk.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jorgjia Bucaj", - "author_inst": "Department of Healthcare, Faculty of Health, University of Vlora, Vlora, Albania" - }, - { - "author_name": "Enkeleint A. Mechili", - "author_inst": "Department of Healthcare, Faculty of Health, University of Vlora" - }, - { - "author_name": "Petros Galanis", - "author_inst": "Faculty of Nursing, Center for Health Services Management and Evaluation, National and Kapodistrian University of Athens, Athens, Greece" - }, - { - "author_name": "Bruna Mersini", - "author_inst": "Vlora Regional Hospital, Vlora, Albania" - }, - { - "author_name": "Sonila Nika", - "author_inst": "Department of Nursing, Faculty of Health, University of Vlora, Vlora, Albania" - }, - { - "author_name": "Inis Hoxhaj", - "author_inst": "Department of Nursing, Faculty of Health, University of Vlora, Vlora, Albania" - }, - { - "author_name": "Stefano Likaj", - "author_inst": "Department of Nursing, Faculty of Health, University of Vlora, Vlora, Albania" - }, - { - "author_name": "Athina E. Patelarou", - "author_inst": "Faculty of Nursing, Hellenic Mediterranean University, Crete, Greece" - }, - { - "author_name": "Evridiki Patelarou", - "author_inst": "Faculty of Nursing, Hellenic Mediterranean University, Crete, Greece" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.10.08.21264765", "rel_title": "The impact of heating, ventilation, and air conditioning design features on the transmission of viruses, including the 2019 novel coronavirus: a systematic review of ventilation and coronavirus", @@ -556495,6 +558020,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2021.10.07.21264711", + "rel_title": "Differential anchoring effects of vaccination comparator selection: characterizing a potential bias due to healthcare utilization in COVID-19 versus influenza", + "rel_date": "2021-10-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.07.21264711", + "rel_abs": "IntroductionObservational data enables large-scale vaccine safety surveillance but requires careful evaluation of potential sources of bias. One potential source of bias is an index date selection procedure for the unvaccinated cohort or unvaccinated comparison time. Here, we evaluate different index date selection procedures for two vaccines: COVID-19 and influenza.\n\nMethodsFor each vaccine, we extracted patient baseline characteristics on the index date and up to 450 days prior and then compared them to the characteristics of the unvaccinated patients indexed on an arbitrary date or indexed on a date of a visit. Additionally, we compared vaccinated patients indexed on the date of vaccination and the same patients indexed on a prior date or visit.\n\nResultsCOVID-19 vaccination and influenza vaccination differ drastically from each other in terms of populations vaccinated and their status on the day of vaccination. When compared to indexing on a visit in unvaccinated population, influenza vaccination had markedly higher covariate proportions and COVID-19 vaccination had lower proportions of most covariates on the index date. In contrast, COVID-19 vaccination had similar covariate proportions when compared to an arbitrary date. These effects attenuated but were still present with a longer lookback period. The effect of day 0 was present even when patients served as their own controls.\n\nConclusionPatient baseline characteristics are sensitive to the choice of the index date. In vaccine safety studies, unexposed index event should represent vaccination settings. Study designs previously used to assess influenza vaccination must be reassessed for COVID-19 to account for a potentially healthier population and lack of medical activity on the day of vaccination.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Anna Ostropolets", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Patrick B Ryan", + "author_inst": "Janssen Research and Development" + }, + { + "author_name": "Martijn J Schuemie", + "author_inst": "Janssen Research and Development" + }, + { + "author_name": "George Hripcsak", + "author_inst": "Columbia University Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.07.21264713", "rel_title": "Monitoring and forecasting the COVID-19 epidemic in Moscow: model selection by balanced identification technology - version: September 2021", @@ -558222,37 +559778,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.08.21264716", - "rel_title": "COVID-19 Pandemic Impact on Sexually Transmitted Infection Testing in a College Setting", - "rel_date": "2021-10-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.08.21264716", - "rel_abs": "ObjectiveAssess the impact of the pandemic on STI (sexually transmitted infections) testing in a college health setting.\n\nDesignExploratory analysis of the number of STI tests done, positive rates for those tests and of percentage of \"compliance to follow-up\" from March to December 2020 and its comparison with historical data at the University Health Services, UW-Madison.\n\nSamplestudents STI tests during the analyzed period.\n\nMeasurementObserved (2020) vs Expected (2015-2019, average) number of STI tests, positive rate, compliance to follow-up testing for STIs.\n\nResultsThere was a significant decrease in the number of tests done and increase of positive rate when compared to historical for total sample and per sex. There was a decrease in the percentage of follow-up for the entire sample and females and an increase for males.\n\nConclusionsConsidering the three outcomes assessed, we observe an impact in STI testing during the pandemic. In concordance with national data, our analysis shows significant declines in STI testing and follow-up during 2020 compared to previous years and an increase in positivity rate. The finding of higher positivity with lower number of tests is likely due to triaging patients, facilitating testing for those at highest risk of infection.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Agustina M Marconi", - "author_inst": "UW-Madison" - }, - { - "author_name": "Elizabeth C Falk-Hanson", - "author_inst": "UW-Madison" - }, - { - "author_name": "Megan E Crass", - "author_inst": "UW-Madison" - }, - { - "author_name": "Peter Campbell", - "author_inst": "UW-Madison" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.09.21264771", "rel_title": "Taste loss as a distinct symptom of COVID-19: A systematic review and meta-analysis", @@ -558489,6 +560014,65 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.10.07.463402", + "rel_title": "Inhibition of SARS-CoV-2 spike protein palmitoylation reduces virus infectivity", + "rel_date": "2021-10-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.07.463402", + "rel_abs": "Spike glycoproteins of almost all enveloped viruses are known to undergo post-translational attachment of palmitic acid moieties. The precise role of such palmitoylation of the spike protein in membrane fusion and infection is not completely understood. Here, we report that palmitoylation of the first five cysteine residues of the c-terminal cysteine-rich domain of the SARS-CoV-2 spike are indispensable for infection and palmitoylation deficient spike mutants are defective in trimerization and subsequent membrane fusion. The DHHC9 palmitoyltransferase interacts with and palmitoylates the spike protein in the ER and Golgi, and knockdown of DHHC9 results in reduced fusion and infection of SARS-CoV-2. Two bis-piperazine backbone-based DHHC9 inhibitors inhibit SARS-CoV-2 spike protein palmitoylation and the resulting progeny virion particles released are defective in fusion and infection. This establishes these palmitoyltransferase inhibitors as potential new intervention strategies against SARS-CoV-2.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Ahmed A. Ramadan", + "author_inst": "Department of Molecular Medicine, University of South Florida, Tampa, FL 33612" + }, + { + "author_name": "Karthick Mayilsamy", + "author_inst": "Department of Molecular Medicine, University of South Florida, Tampa, FL 33612; Department of Internal Medicine, University of South Florida, Tampa, FL 33612" + }, + { + "author_name": "Andrew R. McGill", + "author_inst": "Department of Molecular Medicine, University of South Florida, Tampa, FL 33612; Department of Internal Medicine, University of South Florida, Tampa, FL 33612; D" + }, + { + "author_name": "Anandita Ghosh", + "author_inst": "Department of Molecular Medicine, University of South Florida, Tampa, FL 33612" + }, + { + "author_name": "Marc A. Giulianotti", + "author_inst": "Center for Translational Science, Florida International University, Port St. Lucie, FL 34987" + }, + { + "author_name": "Haley M. Donow", + "author_inst": "Center for Translational Science, Florida International University, Port St. Lucie, FL 34987" + }, + { + "author_name": "Shyam S. Mohapatra", + "author_inst": "Department of Molecular Medicine, University of South Florida, Tampa, FL 33612; Department of Internal Medicine, University of South Florida, Tampa, FL 33612; D" + }, + { + "author_name": "Subhra Mohapatra", + "author_inst": "Department of Molecular Medicine, University of South Florida, Tampa, FL 33612; Department of Internal Medicine, University of South Florida, Tampa, FL 33612" + }, + { + "author_name": "Bala Chandran", + "author_inst": "Department of Molecular Medicine, University of South Florida, Tampa, FL 33612" + }, + { + "author_name": "Robert J. Deschenes", + "author_inst": "Department of Molecular Medicine, University of South Florida, Tampa, FL 33612" + }, + { + "author_name": "Arunava Roy", + "author_inst": "Department of Molecular Medicine, University of South Florida, Tampa, FL 33612" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.10.07.463533", "rel_title": "Angiotensin converting enzyme 2 (ACE2) is expressed in murine cutaneous under single-cell transcriptome resolution", @@ -560268,101 +561852,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.10.05.21264559", - "rel_title": "Effectiveness and Safety of MSC Cell Therapies for Hospitalized Patients with COVID-19: A Systematic Review and Meta-analysis", - "rel_date": "2021-10-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.05.21264559", - "rel_abs": "MSC (a.k.a. mesenchymal stem cell or medicinal signaling cell) cell therapies have shown promise in decreasing mortality in ARDS and suggest benefits in treatment of COVID-19 related ARDS. We performed a meta-analysis of published trials assessing the effectiveness and adverse events (AE) of MSC cell therapy in individuals hospitalized for COVID-19. Systematic searches were performed in multiple databases through April 8th, 2021. Reports in all languages including randomized clinical trials (RCTs), comparative observational studies, and case series/case reports were included. Random effects model was used to pool outcomes from RCTs and comparative observational studies. Outcome measures included all-cause mortality, serious adverse events (SAEs), AEs, pulmonary function, laboratory and imaging findings. A total of 413 patients were identified from 25 studies, which included 8 controlled trials (3 RCTs), 5 comparative observational studies, (n=300) and 17 case-series/case reports (n=113). The patients age was 60.5 years (mean), 33.7% were women. When compared with the control group, MSC cell therapy was associated with reduction in all-cause mortality (RR=0.31, 95% CI: 0.12 to 0.75, I2=0.0%; 3 RCTs and 5 comparative observational studies, 300 patients), reduction in SAEs (IRR=0.36, 95% CI: 0.14 to 0.90, I2=0.0%; 3 RCTs and 2 comparative studies, n=219), no significant difference in AE rate. A sub-group with pulmonary function studies suggested improvement in patients receiving MSC. These findings support the potential for MSC cell therapy to decrease all-cause mortality, reduce SAEs, and improve pulmonary function compared to conventional care. Large scale double-blinded, well-powered RCTs should be conducted to further explore these results.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Wenchun Qu", - "author_inst": "Department of Pain Medicine, Mayo Clinic, Jacksonville, Florida; Center for Regenerative Medicine, Mayo Clinic, Jacksonville, Florida" - }, - { - "author_name": "Zhen Wang", - "author_inst": "Evidence-Based Practice Center, Mayo Clinic, Rochester, Minnesota; Robert D. and Patricia E. Kern Center for the Science of Health Care Delivery, Mayo Clinic, R" - }, - { - "author_name": "Erica Engelberg Cook", - "author_inst": "Department of Neuroscience, Mayo Clinic, Jacksonville, Florida" - }, - { - "author_name": "Abu Bakar Siddik", - "author_inst": "Department of Pain Medicine, Mayo Clinic, Jacksonville, Florida" - }, - { - "author_name": "Guojun Bu", - "author_inst": "Center for Regenerative Medicine, Mayo Clinic, Jacksonville, Florida; Department of Neuroscience, Mayo Clinic, Jacksonville, Florida" - }, - { - "author_name": "Julie G Allickson", - "author_inst": "Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota" - }, - { - "author_name": "Eva Kubrova", - "author_inst": "Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, Minnesota" - }, - { - "author_name": "Arnold I Caplan", - "author_inst": "Skeletal Research Center, Biology Department, Case Western Reserve University, Cleveland, Ohio" - }, - { - "author_name": "Joshua M Hare", - "author_inst": "Interdisciplinary Stem Cell Institute and Cardiology Division, Department of Medicine, University of Miami, Miller School of Medicine, Miami, Florida" - }, - { - "author_name": "Calillo Ricordi", - "author_inst": "Department of Surgery, Diabetes Research Institute and Cell Transplant Center, University of Miami Miller School of Medicine" - }, - { - "author_name": "Carl J Pepine", - "author_inst": "Division of Cardiovascular Medicine, and Center for Regenerative Medicine, University of Florida, Gainesville, Florida" - }, - { - "author_name": "Joanne Kurtzberg", - "author_inst": "Marcus Center for Cellular Cures, Duke University School of Medicine" - }, - { - "author_name": "Jorge M Pascual", - "author_inst": "Division of Pulmonary, Allergy and Sleep Medicine, Department of Medicine, Mayo Clinic, Jacksonville, Florida" - }, - { - "author_name": "Jorge M Mallea", - "author_inst": "Division of Pulmonary, Allergy and Sleep Medicine, Department of Medicine, Mayo Clinic, Jacksonville, Florida" - }, - { - "author_name": "Ricardo L Rodriguez", - "author_inst": "Co-Chair Regenerative Medicine Committee, American Society Plastic Surgeons" - }, - { - "author_name": "Tarek Nayfeh", - "author_inst": "Evidence-Based Practice Center, Mayo Clinic, Rochester, Minnesota; Robert D. and Patricia E. Kern Center for the Science of Health Care Delivery, Mayo Clinic, R" - }, - { - "author_name": "Samer Saadi", - "author_inst": "Evidence-Based Practice Center, Mayo Clinic, Rochester, Minnesota; Robert D. and Patricia E. Kern Center for the Science of Health Care Delivery, Mayo Clinic, R" - }, - { - "author_name": "Elaine M Richards", - "author_inst": "Department of Physiology and Functional Genomics, Center of Regenerative Medicine, University of Florida, Gainesville, Florida" - }, - { - "author_name": "Keith March", - "author_inst": "Division of Cardiovascular Medicine, Center for Regenerative Medicine, University of Florida, Gainesville, Florida" - }, - { - "author_name": "Fred P Sanfilippo", - "author_inst": "Department of Pathology and Laboratory Medicine, Department of Health Policy and Management, Emory University, Atlanta, Georgia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.10.05.21264597", "rel_title": "Effect of workplace infection control practices on workers' psychological distress: a large-scale cohort study during the COVID-19 second state of emergency in Japan", @@ -560575,6 +562064,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.10.06.21264535", + "rel_title": "Analytical performance of eleven SARS-CoV-2 antigen-detecting rapid tests for Delta variant", + "rel_date": "2021-10-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.06.21264535", + "rel_abs": "Global concerns arose as the emerged and rapidly spreading SARS-CoV-2 Delta variant. To date, few data on routine diagnostic performance for Delta are available. Here, we investigate the analytical performance of eleven commercially available antigen-detecting rapid diagnostic tests (Ag-RDTs) for Delta VOC in comparison with current and earlier VOCs (Alpha, Beta and Gamma) and early pandemic variant using cultured SARS-CoV-2. Comparable sensitivity was observed for Delta for the majority of Ag-RDTs.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Meriem Bekliz", + "author_inst": "Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzer" + }, + { + "author_name": "Kenneth Adea", + "author_inst": "Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzer" + }, + { + "author_name": "Manel Essaidi-Laziosi", + "author_inst": "Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzer" + }, + { + "author_name": "Camille Escadafal", + "author_inst": "FIND, the global alliance for diagnostics, Geneva, Switzerland." + }, + { + "author_name": "Jilian Sacks", + "author_inst": "FIND, the global alliance for diagnostics, Geneva, Switzerland." + }, + { + "author_name": "Laurent Kaiser", + "author_inst": "University of Geneva Hospitals" + }, + { + "author_name": "Isabella Eckerle", + "author_inst": "Geneva Centre for Emerging Viral Diseases, Geneva, Switzerland; Laboratory of Virology, Division of Laboratory Medicine, Geneva, Switzerland; Department of Micr" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.06.21264616", "rel_title": "Evolution of SARS-CoV-2 immune responses in nursing home residents following full dose of the Comirnaty COVID-19 vaccine", @@ -562502,93 +564034,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.10.06.21263384", - "rel_title": "SARS-CoV-2 RNA and antibody dynamics in a Dutch household study with dense sampling frame", - "rel_date": "2021-10-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.06.21263384", - "rel_abs": "This study investigated the dynamics of SARS-CoV-2 infection and diagnostics in household members of different ages and with different symptom severity after SARS-CoV-2 exposure during the early phase of the pandemic. Households with a SARS-CoV-2 confirmed positive case and at least one child in the Netherlands were followed for 6 weeks. Naso (NP)- and oropharyngeal (OP) swabs, oral fluid and feces specimens were analyzed for SARS-CoV-2 RNA and serum for SARS-CoV-2-specific antibodies. The dynamics of the presence of viral RNA and the serological response was modeled to determine the sampling time-frame and sample type with the highest sensitivity to confirm or reject a SARS-CoV-2 diagnosis. Transmission of SARS-CoV-2 between adults and children within a household was correlated with symptom severity of index cases. In children higher viral loads compared to adults were detected at symptom onset. Early in infection, higher viral loads were detected in NP and OP specimens, while RNA in especially feces were longer detectable. SARS-CoV-2-specific antibodies have a 90% probability of detection from 7 days (total Ig) and 18 days (IgG) since symptom onset. In conclusion this study has shown that on average, children carry higher loads of virus as compared to adults early after infection. For highest probability of detection in SARS-CoV-2 diagnostics early in infection, RT-PCR on NP and OP specimens are more sensitive than on oral fluid and feces. For SARS-CoV-2 diagnostics late after infection, RT-PCR on feces specimens and serology are more valuable.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Wanda G.H. Han", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Arno Swart", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Axel Bonacic Marinovic", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Dirk Eggink", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Johan Reimerink", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Lisa A Wijsman", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Bas van der Veer", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Sharon van den Brink", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Anne-Marie van den Brandt", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Sophie van Tol", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Gert-Jan Godeke", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Fion Brouwer", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Marieke Hoogerwerf", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "- the Dutch FFX-COVID-19 research group", - "author_inst": "" - }, - { - "author_name": "Daphne F.M. Reukers", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Nynke Rots", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Chantal Reusken", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Adam Meijer", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.02.21264267", "rel_title": "Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion", @@ -562797,6 +564242,289 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.04.21264015", + "rel_title": "Circulating proteins to predict adverse COVID-19 outcomes", + "rel_date": "2021-10-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.04.21264015", + "rel_abs": "Predicting COVID-19 severity is difficult, and the biological pathways involved are not fully understood. To approach this problem, we measured 4,701 circulating human protein abundances in two independent cohorts totaling 986 individuals. We then trained prediction models including protein abundances and clinical risk factors to predict adverse COVID-19 outcomes in 417 subjects and tested these models in a separate cohort of 569 individuals. For severe COVID-19, a baseline model including age and sex provided an area under the receiver operator curve (AUC) of 65% in the test cohort. Selecting 92 proteins from the 4,701 unique protein abundances improved the AUC to 88% in the training cohort, which remained relatively stable in the testing cohort at 86%, suggesting good generalizability. Proteins selected from different adverse COVID-19 outcomes were enriched for cytokine and cytokine receptors, but more than half of the enriched pathways were not immune-related. Taken together, these findings suggest that circulating proteins measured at early stages of disease progression are reasonably accurate predictors of adverse COVID-19 outcomes. Further research is needed to understand how to incorporate protein measurement into clinical care.", + "rel_num_authors": 67, + "rel_authors": [ + { + "author_name": "Chen-Yang Su Mr.", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Sirui Zhou", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Edgar Gonzalez-Kozlova", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Guillaume Butler-Laporte", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Elsa Brunet-Ratnasingham", + "author_inst": "Centre hospitalier de l'Universite de Montreal" + }, + { + "author_name": "Tomoko Nakanishi", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Wonseok Jeon", + "author_inst": "McGill University" + }, + { + "author_name": "David Morrison", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Laetitia Laurent", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Joanthan Afilalo", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Marc Afilalo", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Danielle Henry", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Yiheng Chen", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Julia Carrasco-Zanini", + "author_inst": "University of Cambridge School of Clinical Medicine" + }, + { + "author_name": "Yossi Farjoun", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Maik Pietzner", + "author_inst": "University of Cambridge School of Clinical Medicine" + }, + { + "author_name": "Nofar Kimchi", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Zaman Afrasiabi", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Nardin Rezk", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Meriem Bouab", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Louis Petitjean", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Charlotte Guzman", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Xiaoqing Xue", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Chris Tselios", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Branka Vulesevic", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Olumide Adeleye", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Tala Abdullah", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Noor Almamlouk", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Yara Moussa", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Chantal DeLuca", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Naomi Duggan", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Erwin Schurr", + "author_inst": "McGill University Health Centre" + }, + { + "author_name": "Nathalie Brassard", + "author_inst": "Centre hospitalier de l'Universite de Montreal" + }, + { + "author_name": "Madeleine Durand", + "author_inst": "Centre hospitalier de l'Universite de Montreal" + }, + { + "author_name": "Diane Marie Del Valle", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ryan Thompson", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Mario A. Cedillo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Eric Schadt", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Kai Nie", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Nicole W Simons", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Konstantinos Mouskas", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Nicolas Zaki", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Manishkumar Patel", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Hui Xie", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jocelyn Harris", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Robert Marvin", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Esther Cheng", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Kevin Tuballes", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Kimberly Argueta", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ieisha Scott", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "- The Mount Sinai COVID Biobank Team", + "author_inst": "" + }, + { + "author_name": "Celia M T Greenwood", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Clare Paterson", + "author_inst": "SomaLogic Inc." + }, + { + "author_name": "Michael Hinterberg", + "author_inst": "SomaLogic Inc." + }, + { + "author_name": "Claudia Langenberg", + "author_inst": "University of Cambridge School of Clinical Medicine" + }, + { + "author_name": "Vincenzo Forgetta", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Joelle Pineau", + "author_inst": "McGill University" + }, + { + "author_name": "Vincent Mooser", + "author_inst": "McGill University" + }, + { + "author_name": "Thomas Marron", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Noam Beckmann", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ephraim Kenigsberg", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Seunghee Kim-schulze", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Alexander W. Charney", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sacha Gnjatic", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Daniel E. Kaufmann", + "author_inst": "Centre hospitalier de l'Universite de Montreal" + }, + { + "author_name": "Miriam Merad", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "J Brent Richards", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.04.21264500", "rel_title": "Increase in preterm stillbirths and reduction in iatrogenic preterm births for fetal compromise: a multi-centre cohort study of COVID-19 lockdown effects in Melbourne, Australia", @@ -564336,25 +566064,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.10.03.21264494", - "rel_title": "Why a Globally Fair COVID-19 Vaccination? An Analysis based on Agent-Based Simulation", - "rel_date": "2021-10-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.03.21264494", - "rel_abs": "In this paper, an Agent-Based Model (ABM) is proposed to evaluate the impact of COVID-19 vaccination drive in different settings. The main focus is to evaluate the counter-effectiveness of disparity in vaccination drive among different regions / countries. The model proposed is simple yet novel in the sense that it captures the spatial transmission-induced activity into consideration, through which we are able to relate transmission model to the mutated variations of the virus. Some important what-if questions are asked in terms of number of deaths, and time required and percentage of population needed to be vaccinated before the pandemic is eradicate. The simulation results have revealed that it is necessary to maintain a global (rather than regional or country oriented) vaccination drive in case of a new pandemic or continual efforts against COVID-19.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Kashif Zia", - "author_inst": "Sohar University, Oman" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.02.21264454", "rel_title": "COVID-19 Vaccine: Newspaper Coverage of the side effects of the vaccine in Nigeria", @@ -564563,6 +566272,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.03.21264492", + "rel_title": "Non-pharmaceutical interventions and vaccinating school children required to contain SARS-CoV-2 Delta variant outbreaks in Australia: a modelling analysis", + "rel_date": "2021-10-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.03.21264492", + "rel_abs": "BackgroundIn countries with high COVID-19 vaccination rates the SARS-CoV-2 Delta variant has resulted in rapidly increasing case numbers. This study evaluated the use of non-pharmaceutical interventions (NPIs) coupled with alternative COVID-19 vaccination strategies to determine feasible Delta mitigation strategies for Australia. We aimed to understanding the interplay between high vaccine coverage levels and NPI physical distancing activation, and to establish the benefit of adding children and adolescents to the vaccination program. Border closure has limited SARS-CoV-2 transmission in Australia, however slow vaccination uptake resulted in Delta outbreaks in the two largest cities, and may continue once international travel resumes.\n\nMethodsAn agent-based model was used to evaluate the potential reduction in the COVID-19 health burden resulting from alternative vaccination strategies. We assumed immunity was derived from vaccination with the BNT162b2 Pfizer BioNTech vaccine. Two age-specific vaccination strategies were evaluated, age 5 and above, and 12 and above, and the health burden determined under alternative coverages, with/without activation of NPIs. Age-specific infections generated by the model, together with recent UK data, permitted reductions in the health burden to be quantified.\n\nResultsCases, hospitalisations and deaths are shown to reduce by: i) increasing coverage to include children aged 5 to 11 years, ii) activating moderate NPI measures, and/or iii) increasing coverage levels above 80%. At 80% coverage, vaccinating ages 12 plus without NPIs is predicted to give 1,162 hospitalisations; adding ages 5 and above gives 1,073 cases per million population. Activating moderate NPIs reduces hospitalisations to 705. Alternatively, increasing coverage to 90% reduces this to 684. Combining all three measures is shown to reduce cases to 398, hospitalisations to 2 and deaths to zero.\n\nConclusionsDelta variant outbreaks may be successfully managed by an achievable 80% vaccine coverage rate and moderate NPI measures, allowing schools and many workplaces to remain open. This prevents use of hard lockdown measures, and consequential economic and societal damage. Activating moderate NPIs is shown to give a similar reduction in health burden as increasing coverage of ages 12 and above to 90%. If 90% coverage cannot be achieved, including children and adolescents in the vaccination program coupled with moderate NPIs appears necessary to contain future COVID-19 Delta transmission.\n\nFundingThe authors acknowledge funding support from the Department of Health, Western Australia (Future Health Research and Innovation Fund) and the Department of Health, Queensland, Australia.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "George J Milne", + "author_inst": "University of Western Australia" + }, + { + "author_name": "Julian Carrivick", + "author_inst": "University of Western Australia" + }, + { + "author_name": "David Whyatt", + "author_inst": "University of Western Australia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.03.21264476", "rel_title": "Determination of utility of 3 minute and 6 minute walk tests in assessment of progression of mild COVID-19 infection at a tertiary hospital in North India", @@ -566162,109 +567898,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.01.21264408", - "rel_title": "Reduced amplification efficiency of the RNA-dependent-RNA-polymerase (RdRp) target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests", - "rel_date": "2021-10-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.01.21264408", - "rel_abs": "Routine SARS-CoV-2 surveillance in the Western Cape region of South Africa (January-August 2021) found a reduced PCR amplification efficiency of the RdRp gene target of the Seegene, Allplex 2019-nCoV diagnostic assay when detecting the Delta variant. We propose that this can be used as a surrogate for variant detection.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Ziyaad Valley-Omar", - "author_inst": "Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa" - }, - { - "author_name": "Kruger Marais", - "author_inst": "Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa" - }, - { - "author_name": "Arash Iranzadeh", - "author_inst": "Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa" - }, - { - "author_name": "Michelle Naidoo", - "author_inst": "Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa" - }, - { - "author_name": "Stephen Korsman", - "author_inst": "Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa" - }, - { - "author_name": "Tongai Maponga", - "author_inst": "Division of Medical Virology, Stellenbosch University, Western Cape, South Africa" - }, - { - "author_name": "Hannah Hussey", - "author_inst": "Centre Health Intelligence, Western Cape Government: Health, South Africa" - }, - { - "author_name": "Mary-Ann Davies", - "author_inst": "Centre for Infectious Disease Epidemiology and Research, School of Public health, University of Cape Town, Western Cape South Africa" - }, - { - "author_name": "Andrew Boulle", - "author_inst": "Centre for Infectious Disease Epidemiology and Research, School of Public health, University of Cape Town, Western Cape South Africa" - }, - { - "author_name": "Deelan Doolabh", - "author_inst": "Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa" - }, - { - "author_name": "Mariska Laubscher", - "author_inst": "Lancet laboratories, South Africa" - }, - { - "author_name": "JD Deetlefs", - "author_inst": "Ampath Laboratories, South Africa" - }, - { - "author_name": "Jean Maritz", - "author_inst": "PathCare Laboratories, South Africa" - }, - { - "author_name": "Lesley Scott", - "author_inst": "Research diagnostic Laboratories, School of Pathology, University of the Witwatersrand, South Africa" - }, - { - "author_name": "Nokukhanya Msomi", - "author_inst": "Discipline of Virology, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Houriiyah Tegally", - "author_inst": "KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Tulio de Oliveira", - "author_inst": "KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Jinal Bhiman", - "author_inst": "National institute for Communicable Diseases, Johannesburg, South Africa" - }, - { - "author_name": "Carolyn Williamson", - "author_inst": "Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa" - }, - { - "author_name": "Wolfgang Preiser", - "author_inst": "Division of Medical Virology, Stellenbosch University, Western Cape, South Africa" - }, - { - "author_name": "Diana Ruth Hardie", - "author_inst": "Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa" - }, - { - "author_name": "Nei-yuan Hsiao", - "author_inst": "Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.29.21264199", "rel_title": "Effectiveness of mRNA-1273 against Delta, Mu, and other emerging variants", @@ -566457,6 +568090,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.29.21264315", + "rel_title": "Characteristics associated with COVID-19 vaccination status among staff and faculty of a large, diverse University in Los Angeles.", + "rel_date": "2021-10-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.29.21264315", + "rel_abs": "ObjectiveThis study examined characteristics associated with being unvaccinated among a sample of university staff and faculty prior to university campus reopening for in-person learning in spring-summer 2021.\n\nMethodsStaff and faculty responded to an email invitation to complete an online survey. Survey questions included demographic data (race/ethnicity, age, sex), COVID-19 knowledge and behaviors, employment specific data including division and subdivision (healthcare vs. non-healthcare related division); and self-reported vaccination status. A multivariable logistic regression analysis was performed to determine significant characteristics associated with the likelihood of being unvaccinated for COVID-19.\n\nResultsParticipants identifying as Asian and Asian American, Hispanic/Latinx or Multicultural/Other had greater odds of being unvaccinated compared to Non-Hispanic White participants. Other characteristics associated with greater likelihood of being unvaccinated included working as university staff member (vs. faculty), older age, decrease in income, inability to work remotely and not traveling outside of Los Angeles area. Political affiliation as an Independent or as something else were more likely to be unvaccinated compared to participants identifying as Democrat.\n\nConclusionsFindings suggest several factors associated with racial and social disparities may delay the uptake of COVID-19 vaccination. This study highlights the need for targeted educational interventions to promote vaccination among university staff and faculty.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Michele Nicolo", + "author_inst": "University of Southern California" + }, + { + "author_name": "Eric Kawaguchi", + "author_inst": "University of Southern California" + }, + { + "author_name": "Angie Ghanem-Uzqueda", + "author_inst": "University of Southern California" + }, + { + "author_name": "Andre E Kim", + "author_inst": "University of SouthernCalifornia" + }, + { + "author_name": "Daniel Soto", + "author_inst": "University of Southern California" + }, + { + "author_name": "Sohini Deva", + "author_inst": "University of Southern California" + }, + { + "author_name": "Kush J Shanker", + "author_inst": "University of SouthernCalifornia" + }, + { + "author_name": "Christopher J Rogers", + "author_inst": "University of Southern California" + }, + { + "author_name": "Ryan Lee", + "author_inst": "University of Southern California" + }, + { + "author_name": "Yolee Casagrande", + "author_inst": "University of Southern California" + }, + { + "author_name": "Frank Gilliland", + "author_inst": "University of Southern California" + }, + { + "author_name": "Sarah Van Orman", + "author_inst": "University of Southern California" + }, + { + "author_name": "Jeffrey Klausner", + "author_inst": "University of Southern California" + }, + { + "author_name": "Andrea A.Z. Kovacs", + "author_inst": "University of Southern California" + }, + { + "author_name": "David V Conti", + "author_inst": "University of Southern California" + }, + { + "author_name": "Howard Hu", + "author_inst": "University of Southern California" + }, + { + "author_name": "Jennifer B Unger", + "author_inst": "University of Southern California" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.29.21264295", "rel_title": "Neonatal outcomes of preterm infants born during COVID-19 community lockdowns in Melbourne, Australia", @@ -567920,45 +569636,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.29.21264305", - "rel_title": "Determinants of sleep quality in adults during the COVID-19 pandemic: COVID-Inconfidentes, a population-based study", - "rel_date": "2021-09-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.29.21264305", - "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) pandemic has had a negative effect on the health and behavior of the worlds population.\n\nObjectivesTo evaluate sleep quality and its associated factors in adults during the COVID-19 pandemic in Brazil.\n\nMethodsThis is a population-based serological survey of 1762 adults collected from October to December 2020 in the Iron Quadrangle region, Brazil. To measure sleep quality, we used the Pittsburgh Sleep Quality Index questionnaire and socio-demographic, health, health related behaviors, anxiety, vitamin D, weight gain/loss, and pandemic characteristics were assessed using a structured questionnaire. Univariate and multivariate analyses were performed to identify the factors associated with sleep quality.\n\nResultsMore than half of the individuals evaluated had poor sleep quality (52.5%). In multivariate analysis, factors related to sleep quality included living alone (OR=2.36; 95%CI: 1.11-5.00), anxiety disorder (OR=2.22; 95%CI: 1.20-4.14), 5.0% weight loss during the pandemic (OR=1.66; 95%CI: 1.01-2.76), weight gain of 5.0% (OR=1.90; 95%CI: 1.08-3.34), insufficient vitamin D scenario (OR=1.47; 95%CI: 1.01-2.12), and symptoms of COVID-19 (OR=1.94; 95%CI: 1.25-3.01).\n\nConclusionsOur study revealed that more than half of the participants had poor sleep quality during the COVID-19 outbreak, and the factors associated with poor sleep quality were related to the pandemic, such as insufficient vitamin D scenario and weight change.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Luiz Antonio Alves Menezes-Junior", - "author_inst": "Federal University of Ouro Preto" - }, - { - "author_name": "Luciano Garcia Lourencao", - "author_inst": "Federal University of Rio Grande" - }, - { - "author_name": "Amanda Cristina de Souza Andrade", - "author_inst": "Federal University of Mato Grosso" - }, - { - "author_name": "Julia Cristina Cardoso Carraro", - "author_inst": "Federal University of Ouro Preto" - }, - { - "author_name": "George Luiz Lins Machado-Coelho", - "author_inst": "Federal University of Ouro Preto" - }, - { - "author_name": "Adriana Lucia Meireles", - "author_inst": "Federal Univeristy of Ouro Preto" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.30.462449", "rel_title": "Pyronaridine Protects Against SARS-CoV-2 in Mouse", @@ -568331,6 +570008,73 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.09.30.462514", + "rel_title": "Ad26.COV2.S Prevents SARS-CoV-2 Induced Pathways of Inflammation and Thrombosis in Hamsters", + "rel_date": "2021-09-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.30.462514", + "rel_abs": "Syrian golden hamsters exhibit features of severe disease after SARS-CoV-2 challenge and are therefore useful models of COVID-19 pathogenesis and prevention with vaccines. Recent studies have shown that SARS-CoV-2 infection stimulates type I interferon, myeloid, and inflammatory signatures similar to human disease, and that weight loss can be prevented with vaccines. However, the impact of vaccination on transcriptional programs associated with COVID-19 pathogenesis and protective adaptive immune responses is unknown. Here we show that SARS-CoV-2 challenge in hamsters stimulates antiviral, myeloid, and inflammatory programs as well as signatures of complement and thrombosis associated with human COVID-19. Notably, single dose immunization with Ad26.COV2.S, an adenovirus serotype 26 vector (Ad26)-based vaccine expressing a stabilized SARS-CoV-2 spike protein, prevents the upregulation of these pathways such that the gene expression profiles of vaccinated hamsters are comparable to uninfected animals. Finally, we show that Ad26.COV2.S vaccination induces T and B cell signatures that correlate with binding and neutralizing antibody responses. These data provide further insights into the mechanisms of Ad26.COV2.S based protection against severe COVID-19 in hamsters.\n\nAuthor SummaryIn this study, we show that vaccination with Ad26.COV2.S protected SARS-CoV-2 challenged hamsters from developing severe COVID-19 disease by attenuating excessive proinflammatory responses, such as IL-6 and IL-1, macrophages and neutrophils signaling. Ad26 vaccination also prevented the upregulation of pathways associated with thrombosis such coagulation and clotting cascades associated with infection, and the transcriptomic profiles of vaccinated animals were largely comparable to control uninfected hamsters. In contrast, SARS-CoV-2 challenged unvaccinated hamsters showed significant increase of these proinflammatory and prothrombotic pathways and significant weight loss compared to vaccinated hamsters.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Malika Aid", + "author_inst": "BIDMC: Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Samuel Vidal", + "author_inst": "BIDMC: Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Cesar Piedra-Mora", + "author_inst": "Tufts University" + }, + { + "author_name": "Sarah Ducat", + "author_inst": "Tufts University" + }, + { + "author_name": "Chi Chan", + "author_inst": "OHSU: Oregon Health & Science University" + }, + { + "author_name": "Stephen Bondoc", + "author_inst": "OHSU: Oregon Health & Science University" + }, + { + "author_name": "Alessandro Colarusse", + "author_inst": "University of Montreal: Universite de Montreal" + }, + { + "author_name": "Carly Starke", + "author_inst": "OHSU: Oregon Health & Science University" + }, + { + "author_name": "Michael Nekorchuk", + "author_inst": "OHSU: Oregon Health & Science University" + }, + { + "author_name": "Kathleen Busman-Sahay", + "author_inst": "OHSU: Oregon Health & Science University" + }, + { + "author_name": "Jacob Estes", + "author_inst": "OHSU: Oregon Health & Science University" + }, + { + "author_name": "Amanda Martinot", + "author_inst": "Tufts University" + }, + { + "author_name": "Dan H Barouch", + "author_inst": "Beth Israel Deaconess Medical Center" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.09.26.21263756", "rel_title": "Methods for Estimation of SARS-CoV-2 Seroprevalence and Reported COVID-19 Cases in U.S. Children, August 2020 - May 2021", @@ -569938,257 +571682,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.09.28.21264207", - "rel_title": "Durability of ChAdOx1 nCov-19 (AZD1222) vaccination in people living with HIV - responses to SARS-CoV-2, variants of concern and circulating coronaviruses", - "rel_date": "2021-09-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.28.21264207", - "rel_abs": "Duration of protection from SARS-CoV-2 infection in people with HIV (PWH) following vaccination is unclear. In a sub-study of the phase 2/3 the COV002 trial (NCT04400838), 54 HIV positive male participants on antiretroviral therapy (undetectable viral loads, CD4+ T cells >350 cells/ul) received two doses of ChAdOx1 nCoV-19 (AZD1222) 4-6 weeks apart and were followed for 6 months. Responses to vaccination were determined by serology (IgG ELISA and MesoScale Discovery (MSD)), neutralisation, ACE-2 inhibition, gamma interferon ELISpot, activation-induced marker (AIM) assay and T cell proliferation. We show that 6 months after vaccination the majority of measurable immune responses were greater than pre-vaccination baseline, but with evidence of a decline in both humoral and cell mediated immunity. There was, however, no significant difference compared to a cohort of HIV-uninfected individuals vaccinated with the same regimen. Responses to the variants of concern were detectable, although were lower than wild type. Pre-existing cross-reactive T cell responses to SARS-CoV-2 spike were associated with greater post-vaccine immunity and correlated with prior exposure to beta coronaviruses. These data support the on-going policy to vaccinate PWH against SARS-CoV-2, and underpin the need for long-term monitoring of responses after vaccination.", - "rel_num_authors": 59, - "rel_authors": [ - { - "author_name": "Ane Ogbe", - "author_inst": "University of Oxford" - }, - { - "author_name": "Matthew Pace", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mustapha Bittaye", - "author_inst": "University of Oxford" - }, - { - "author_name": "Timothy Tipoe", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sandra Adele", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jasmini Alagaratnam", - "author_inst": "Imperial College" - }, - { - "author_name": "Parvinder K. Aley", - "author_inst": "University of Oxford" - }, - { - "author_name": "M. Azim Ansari", - "author_inst": "University of Oxford" - }, - { - "author_name": "Anna Bara", - "author_inst": "Imperial College Healthcare NHS trust" - }, - { - "author_name": "Samantha Broadhead", - "author_inst": "NIHR Guys and St Thomas Biomedical Research Centre" - }, - { - "author_name": "Anthony Brown", - "author_inst": "University of Oxford" - }, - { - "author_name": "Helen Brown", - "author_inst": "University of Oxford" - }, - { - "author_name": "Wanwisa Dejnirattisai", - "author_inst": "University of Oxford" - }, - { - "author_name": "Federica Cappuccini", - "author_inst": "University of Oxford" - }, - { - "author_name": "Paola Cinardo", - "author_inst": "Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas NHS Trust, London, UK" - }, - { - "author_name": "Katie J. Ewer", - "author_inst": "University of Oxford" - }, - { - "author_name": "Henry Fok", - "author_inst": "Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas NHS Trust, London, UK" - }, - { - "author_name": "Pedro M. Folegatti", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jamie Fowler", - "author_inst": "University of Oxford" - }, - { - "author_name": "Leila Godfrey", - "author_inst": "University of Oxford" - }, - { - "author_name": "Anna L. Goodman", - "author_inst": "Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas NHS Trust, London, UK" - }, - { - "author_name": "Bethany Jackson", - "author_inst": "Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas NHS Trust, London, UK" - }, - { - "author_name": "Daniel Jenkin", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mathew Jones", - "author_inst": "University of Oxford" - }, - { - "author_name": "Stephanie Longet", - "author_inst": "University of Oxford" - }, - { - "author_name": "Rebecca Makinson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Natalie G. Marchevsky", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mathew Moncy", - "author_inst": "Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas NHS Trust, London, UK" - }, - { - "author_name": "Andrea Mazzella", - "author_inst": "Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas NHS Trust, London, UK" - }, - { - "author_name": "Yama F. Mujadidi", - "author_inst": "University of Oxford" - }, - { - "author_name": "Lucia Parolini", - "author_inst": "University of Oxford" - }, - { - "author_name": "Claire Petersen", - "author_inst": "Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK" - }, - { - "author_name": "Emma Plested", - "author_inst": "University of Oxford" - }, - { - "author_name": "Katrina M Pollock", - "author_inst": "NIHR Imperial Clinical Research Facility and NIHR Imperial Biomedical Research Centre, London, UK" - }, - { - "author_name": "Thurkka Rajeswaran", - "author_inst": "Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas NHS Trust, London, UK" - }, - { - "author_name": "Maheshi N. Ramasamy", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sarah Rhead", - "author_inst": "University of Oxford" - }, - { - "author_name": "Hannah Robinson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Nicola Robinson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sonia Serrano", - "author_inst": "NIHR Guys and St Thomas Biomedical Research Centre" - }, - { - "author_name": "Helen Stockmann", - "author_inst": "Department of HIV Medicine, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK" - }, - { - "author_name": "Tom Tipton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Anele Waters", - "author_inst": "Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas NHS Trust, London, UK" - }, - { - "author_name": "Helen Sanders", - "author_inst": "University of Oxford" - }, - { - "author_name": "Panagiota Zacharopoulou", - "author_inst": "University of Oxford" - }, - { - "author_name": "Eleanor Barnes", - "author_inst": "University of Oxford" - }, - { - "author_name": "Susanna Dunachie", - "author_inst": "University of Oxford" - }, - { - "author_name": "Philip Goulder", - "author_inst": "University of Oxford" - }, - { - "author_name": "Paul Klenerman", - "author_inst": "University of Oxford" - }, - { - "author_name": "Gavin R. Screaton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alan Winston", - "author_inst": "Imperial College London" - }, - { - "author_name": "Adrian V. S. Hill", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sarah C. Gilbert", - "author_inst": "University of Oxford" - }, - { - "author_name": "Miles Carroll", - "author_inst": "University of Oxford" - }, - { - "author_name": "Andrew J. Pollard", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sarah Fidler", - "author_inst": "Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK" - }, - { - "author_name": "Julie Fox", - "author_inst": "Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas NHS Trust, London, UK" - }, - { - "author_name": "Teresa Lambe", - "author_inst": "University of Oxford" - }, - { - "author_name": "John Frater", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "hiv aids" - }, { "rel_doi": "10.1101/2021.09.28.21264250", "rel_title": "Reduced antibody activity against SARS-CoV-2 B.1.617.2 Delta virus in serum of mRNA-vaccinated patients receiving TNF-alpha inhibitors", @@ -570593,6 +572086,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.27.21264219", + "rel_title": "Mucosal antibody response to SARS-CoV-2 in paediatric and adult patients: a longitudinal study", + "rel_date": "2021-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.27.21264219", + "rel_abs": "Conjunctival and nasal mucosal antibody responses in thirty-four paediatric and forty-seven adult COVID-19 patients were measured. The mucosal antibody was IgA dominant. In the nasal epithelial lining fluid (NELF) of asymptomatic paediatric patients, SARS-CoV-2 spike protein 1 (S1) specific immunoglobulin A (IgA) was induced early. Their plasma S1-specific IgG levels were higher than symptomatic patients. More adult with mild disease had NELF S1-specific IgA than those with severe/critical illness. Within the first week of diagnosis, higher S1-specific antibodies in NELF and plasma and lower vial loads were detected in paediatric than adult patients with mild disease. The IgA and IgG levels correlated positively with the surrogate neutralization readout. The detectable NELF neutralizing S1-specific IgA in the first week after diagnosis correlated with a rapid decline in viral load. This study highlights the effect of nasal IgA in limiting the SARS-CoV-2 replication and provides complementary information to the serum antibody measurements.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Renee Chan", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Kate C Chan", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Grace CY Lui", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Joseph GS Tsun", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Kathy YY Chan", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Jasmine SK Yip", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Shaojun Liu", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Michelle WL Yu", + "author_inst": "The Prince of Wales Hospital, Hong Kong" + }, + { + "author_name": "Rita WY Ng", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Kelvin KL Chong", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Maggie H Wang", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Paul KS Chan", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Albert M Li", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Hugh Simon Lam", + "author_inst": "The Chinese University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.28.21264266", "rel_title": "Excess Deaths associated with the COVID-19 Pandemic in Ukraine in 2020", @@ -572080,33 +573644,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.26.21264153", - "rel_title": "COVID-19 Vaccination Strategies Considering Hesitancy Using Particle-Based Epidemic Simulation", - "rel_date": "2021-09-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.26.21264153", - "rel_abs": "Vaccine hesitancy is one of the critical factors in achieving herd immunity and suppressing the COVID-19 epidemic. Many countries face this as an acute public health issue that diminishes the efficacy of their vaccination campaigns. Epidemic modeling and simulation can be used to predict the effects of different vaccination strategies. In this work, we present an open-source particle-based COVID-19 simulator with a vaccination module capable of taking into account the vaccine hesitancy of the population. To demonstrate the efficacy of the simulator, we conducted extensive simulations for the province of Lecco, Italy. The results indicate that the combination of both high vaccination rate and low hesitancy leads to faster epidemic suppression.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Aknur Karabay", - "author_inst": "Institute of Smart Systems and Artificial Intelligence" - }, - { - "author_name": "Askat Kuzdeuov", - "author_inst": "Institute of Smart Systems and Artificial Intelligence" - }, - { - "author_name": "Huseyin Atakan Varol", - "author_inst": "Institute of Smart Systems and Artificial Intelligence" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.25.21264106", "rel_title": "Functional Data Analysis: Transition from Daily Observation of COVID-19 Prevalence in France to Functional Curves", @@ -572263,6 +573800,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.09.27.21264000", + "rel_title": "Pre-pandemic SARS-CoV-2 serological reactivity in rural malaria-experienced Cambodians", + "rel_date": "2021-09-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.27.21264000", + "rel_abs": "Greater Mekong inhabitants are exposed to pathogens, zoonotic and otherwise, that may influence SARS-CoV-2 seroreactivity. A pre-pandemic (2005 to 2011) serosurvey of from 528 malaria-experienced Cambodians demonstrated higher-than-expected (up to 13.8 %) positivity of non-neutralizing IgG to SARS-CoV-2 spike and RBD antigens. These findings have implications for interpreting large-scale serosurveys.\n\nArticle Summary LineIn the pre-COVID19 pandemic years of 2005 to 2011, malaria experienced Cambodians from rural settings had higher-than-expected seroreactivity to SARS-CoV-2 spike and receptor binding domain proteins.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Jessica Manning", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Irfan Zaidi", + "author_inst": "NIAID" + }, + { + "author_name": "Chanthap Lon", + "author_inst": "NIAID" + }, + { + "author_name": "Luz Angela Rosas", + "author_inst": "NIAID" + }, + { + "author_name": "Jaekeun Park", + "author_inst": "NIAID" + }, + { + "author_name": "Aiyana Ponce", + "author_inst": "NIAID" + }, + { + "author_name": "Jennifer Bohl", + "author_inst": "NIAID" + }, + { + "author_name": "Sophana Chea", + "author_inst": "NIAID" + }, + { + "author_name": "Maria Karkanitsa", + "author_inst": "NIAID" + }, + { + "author_name": "Sokunthea Sreng", + "author_inst": "NIAID" + }, + { + "author_name": "Huy Rekol", + "author_inst": "National Center for Parasitology, Entomology and Malaria Control" + }, + { + "author_name": "Char Meng Chour", + "author_inst": "National Center for Parasitology, Entomology and Malaria Control" + }, + { + "author_name": "Dominic Esposito", + "author_inst": "Frederick National Laboratory" + }, + { + "author_name": "Jeff Taubenberger", + "author_inst": "NIAID" + }, + { + "author_name": "Matthew Memoli", + "author_inst": "NIAID" + }, + { + "author_name": "Kaitlyn E. Sadtler", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Patrick E. Duffy", + "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" + }, + { + "author_name": "Fabiano Oliveira", + "author_inst": "NIAID" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.26.21264150", "rel_title": "Changes in dispensing of medicines proposed for re-purposing in the first year of the COVID-19 pandemic in Australia", @@ -573706,109 +575330,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.09.24.21263766", - "rel_title": "The Report on China-Spain Joint Clinical Testing for Rapid COVID-19 Risk Screening by Eye-region Manifestations", - "rel_date": "2021-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.24.21263766", - "rel_abs": "BackgroundThe worldwide surge in coronavirus cases has led to the COVID-19 testing demand surge. Rapid, accurate, and cost-effective COVID-19 screening tests working at a population level are in imperative demand globally.\n\nMethodsBased on the eye symptoms of COVID-19, we developed and tested a COVID-19 rapid prescreening model using the eye-region images captured in China and Spain with cellphone cameras. The convolutional neural networks (CNNs)-based model was trained on these eye images to complete binary classification task of identifying the COVID-19 cases. The performance was measured using area under receiver-operating-characteristic curve (AUC), sensitivity, specificity, accuracy, and F1. The application programming interface was open access.\n\nFindingsThe multicenter study included 2436 pictures corresponding to 657 subjects (155 COVID-19 infection, 23{middle dot}6%) in development dataset (train and validation) and 2138 pictures corresponding to 478 subjects (64 COVID-19 infections, 13{middle dot}4%) in test dataset. The image-level performance of COVID-19 prescreening model in the China-Spain multicenter study achieved an AUC of 0{middle dot}913 (95% CI, 0{middle dot}898-0{middle dot}927), with a sensitivity of 0{middle dot}695 (95% CI, 0{middle dot}643-0{middle dot}748), a specificity of 0{middle dot}904 (95% CI, 0{middle dot}891-0{middle dot}919), an accuracy of 0{middle dot}875(0{middle dot}861-0{middle dot}889), and a F1 of 0{middle dot}611(0{middle dot}568-0{middle dot}655).\n\nInterpretationThe CNN-based model for COVID-19 rapid prescreening has reliable specificity and sensitivity. This system provides a low-cost, fully self-performed, non-invasive, real-time feedback solution for continuous surveillance and large-scale rapid prescreening for COVID-19.\n\nFundingThis project is supported by Aimomics (Shanghai) Intelligent", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Yanwei Fu", - "author_inst": "School of Data Science, Fudan University," - }, - { - "author_name": "Feng Li", - "author_inst": "Shanghai Public Health Clinical Center" - }, - { - "author_name": "Paula boned Fustel", - "author_inst": "University and Polytechnic Hospital La Fe" - }, - { - "author_name": "Lei Zhao", - "author_inst": "Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Lijie Jia", - "author_inst": "Department of Anesthesia, the International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine" - }, - { - "author_name": "Haojie Zheng", - "author_inst": "The Fifth Hospital of Shijiazhuang" - }, - { - "author_name": "Qiang Sun", - "author_inst": "Academy for Engineering & Technology, Fudan University" - }, - { - "author_name": "Shisong Rong", - "author_inst": "Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear" - }, - { - "author_name": "Haicheng Tang", - "author_inst": "Shanghai Public Health Clinical Center" - }, - { - "author_name": "Xiangyang Xue", - "author_inst": "Academy for Engineering & Technology, Fudan University" - }, - { - "author_name": "Li Yang", - "author_inst": "The Fifth Hospital of Shijiazhuang" - }, - { - "author_name": "Hong Li", - "author_inst": "Medical Examination Center,Hubei Provincial Hospital of Traditional Chinese Medicine" - }, - { - "author_name": "Jiao Xie", - "author_inst": "Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Wenxuan Wang", - "author_inst": "School of Computer Science, Fudan University" - }, - { - "author_name": "Yuan Li", - "author_inst": "The Fifth Hospital of Shijiazhuang" - }, - { - "author_name": "Wei Wang", - "author_inst": "The Fifth Hospital of Shijiazhuang" - }, - { - "author_name": "Yantao Pei", - "author_inst": "The Fifth Hospital of Shijiazhuang" - }, - { - "author_name": "JIamin Wang", - "author_inst": "The Fifth Hospital of Shijiazhuang" - }, - { - "author_name": "Xiuqi Wu", - "author_inst": "The Fifth Hospital of Shijiazhuang" - }, - { - "author_name": "Yanhua Zheng", - "author_inst": "The Fifth Hospital of Shijiazhuang" - }, - { - "author_name": "Hongxia Tian", - "author_inst": "The Fifth Hospital of Shijiazhuang" - }, - { - "author_name": "Mengwei Gu", - "author_inst": "Aimomics (Shanghai) Intelligent Technology Co., Ltd." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "ophthalmology" - }, { "rel_doi": "10.1101/2021.09.23.21264036", "rel_title": "Diagnostic Yield of Screening for SARS-CoV-2 among Patients Admitted for Alternate Diagnoses", @@ -574093,6 +575614,277 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2021.09.24.21263853", + "rel_title": "Multi-omics approach identifies novel age-, time- and treatment-related immunopathological signatures in MIS-C and pediatric COVID-19", + "rel_date": "2021-09-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.24.21263853", + "rel_abs": "Pediatric COVID-19 (pCOVID-19) is rarely severe, however a minority of SARS-CoV-2-infected children may develop MIS-C, a multisystem inflammatory syndrome with significant morbidity. In this longitudinal multi-institutional study, we used multi-omics to identify novel time- and treatment-related immunopathological signatures in children with COVID-19 (n=105) and MIS-C (n=76). pCOVID-19 was characterized by enhanced type I IFN responses, and MIS-C by type II IFN- and NF-{kappa}B dependent responses, matrisome activation, and increased levels of Spike protein. Reduced levels of IL-33 in pCOVID-19, and of CCL22 in MIS-C suggested suppression of Th2 responses. Expansion of TRBV11-2 T-cell clonotypes in MIS-C was associated with inflammation and signatures of T-cell activation, and was reversed by glucocorticoids. The association of MIS-C with the combination of HLA A*02, B*35, C*04 alleles suggests genetic susceptibility. MIS-C B cells showed higher mutation load. Use of IVIG was identified as a confounding factor in the interpretation of autoantibody levels.", + "rel_num_authors": 64, + "rel_authors": [ + { + "author_name": "Keith Sacco", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Riccardo Castagnoli", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Svetlana Vakkilainen", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Can Liu", + "author_inst": "Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA, Graduate Program in Biological Sciences, Universit" + }, + { + "author_name": "Ottavia M. Delmonte", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Cihan Oguz", + "author_inst": "NIAID Collaborative Bioinformatics Resource (NCBR), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Ian M. Kaplan", + "author_inst": "Adaptive Biotechnologies, Seattle, WA 98109, USA" + }, + { + "author_name": "Sara Alehashemi", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Peter D. Burbelo", + "author_inst": "National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA" + }, + { + "author_name": "Farzana Bhuyan", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Adriana A. de Jesus", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Kerry Dobbs", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Lindsey B. Rosen", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Aristine Cheng", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA" + }, + { + "author_name": "Elana Shaw", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Mikko S. Vakkilainen", + "author_inst": "Department of Computer Science, Aalto University, Helsinki, Finland" + }, + { + "author_name": "Francesca Pala", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Justin Lack", + "author_inst": "NIAID Collaborative Bioinformatics Resource (NCBR), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Yu Zhang", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Danielle Fink", + "author_inst": "Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA" + }, + { + "author_name": "Vasileios Oikonomou", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Andrew L. Snow", + "author_inst": "Department of Pharmacology & Molecular Therapeutics, Uniformed Services, University of the Health Sciences, Bethesda, MD 20892, USA." + }, + { + "author_name": "Clifton L. Dalgard", + "author_inst": "Department of Pharmacology & Molecular Therapeutics, Uniformed Services, University of the Health Sciences, Bethesda, MD 20892, USA." + }, + { + "author_name": "Jinguo Chen", + "author_inst": "Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), National Institutes of Health, Bethesda, MD 20892, USA" + }, + { + "author_name": "Brian A. Sellers", + "author_inst": "Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), National Institutes of Health, Bethesda, MD 20892, USA" + }, + { + "author_name": "Gina A. Montealegre Sanchez", + "author_inst": "Intramural Clinical Management and Operation Branch (ICMOB), Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Inst" + }, + { + "author_name": "Karyl Barron", + "author_inst": "Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA" + }, + { + "author_name": "Emma Rey", + "author_inst": "Facultad de Medicina Clinica Alemana Universidad del Desarrollo, Santiago, Chile" + }, + { + "author_name": "Maria Cecilia Vial", + "author_inst": "Facultad de Medicina Clinica Alemana Universidad del Desarrollo, Santiago, Chile" + }, + { + "author_name": "Maria Cecilia Poli", + "author_inst": "Facultad de Medicina Clinica Alemana Universidad del Desarrollo, Santiago, Chile; Unidad de Inmunologia y Reumatologia, Hospital de ninos Dr. Roberto del Rio, S" + }, + { + "author_name": "Amelia Licari", + "author_inst": "Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavi" + }, + { + "author_name": "Daniela Montagna", + "author_inst": "Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavi" + }, + { + "author_name": "Gian Luigi Marseglia", + "author_inst": "Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavi" + }, + { + "author_name": "Francesco Licciardi", + "author_inst": "Department of Pediatric and Public Health Sciences, Regina Margherita Children's Hospital, A.O.U. Citta Della Salute E Della Scienza Di Torino, University of Tu" + }, + { + "author_name": "Ugo Ramenghi", + "author_inst": "Department of Pediatric and Public Health Sciences, Regina Margherita Children's Hospital, A.O.U. Citta Della Salute E Della Scienza Di Torino, University of Tu" + }, + { + "author_name": "Valentina Discepolo", + "author_inst": "Department of Translational Medical Sciences, Section of Pediatrics, University of Naples Federico II, Napoli, Italy" + }, + { + "author_name": "Andrea Lo Vecchio", + "author_inst": "Department of Translational Medical Sciences, Section of Pediatrics, University of Naples Federico II, Napoli, Italy" + }, + { + "author_name": "Alfredo Guarino", + "author_inst": "Department of Translational Medical Sciences, Section of Pediatrics, University of Naples Federico II, Napoli, Italy" + }, + { + "author_name": "Eli M. Eisenstein", + "author_inst": "Department of Pediatrics, Hadassah-Hebrew University Medical Center, Mount Scopus, Jerusalem, Israel" + }, + { + "author_name": "Luisa Imberti", + "author_inst": "CREA (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy" + }, + { + "author_name": "Alessandra Sottini", + "author_inst": "CREA (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy" + }, + { + "author_name": "Andrea Biondi", + "author_inst": "Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM- Ospedale San" + }, + { + "author_name": "Sayonara Mato", + "author_inst": "Randall Children's Hospital at Legacy Emanuel, Portland, Portland, Oregon, OR 97227, USA" + }, + { + "author_name": "Dana Gerstbacher", + "author_inst": "Division of pediatric Rheumatology, Stanford Childrens Hospital, Stanford, CA 94304, USA" + }, + { + "author_name": "Meng Truong", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Michael A. Stack", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Mary Magliocco", + "author_inst": "Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA" + }, + { + "author_name": "Marita Bosticardo", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Tomoki Kawai", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Jefffrey J. Danielson", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Tyler Hulett", + "author_inst": "CDI Laboratories, Antygen Division, Baltimore, MD MD 21205, USA" + }, + { + "author_name": "Manor Askenazi", + "author_inst": "CDI Laboratories, Antygen Division, Baltimore, MD MD 21205, USA" + }, + { + "author_name": "- NIAID Immune Response to COVID Group", + "author_inst": "" + }, + { + "author_name": "- Chile MIS-C Group", + "author_inst": "" + }, + { + "author_name": "- Pavia Pediatric COVID-19 Group", + "author_inst": "" + }, + { + "author_name": "Jeffrey I Cohen", + "author_inst": "Laboratory of Infectious Diseases, National Institute of Allergy and Infectious diseases, National Institutes of Health, Bethesda, MD 20892, USA" + }, + { + "author_name": "Helen C. Su", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Douglas B. Kuhns", + "author_inst": "Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA" + }, + { + "author_name": "Michail S. Lionakis", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Thomas M. Snyder", + "author_inst": "Adaptive Biotechnologies, Seattle, WA, USA" + }, + { + "author_name": "Steven M. Holland", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "Raphaela Goldbach-Mansky", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + }, + { + "author_name": "John S. Tsang", + "author_inst": "Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA; NIH Center for Human Immunology, NIAID, NIH, Bethe" + }, + { + "author_name": "Luigi D. Notarangelo", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.24.21264045", "rel_title": "Non-invasive Vagus Nerve Stimulation for Respiratory Symptoms of COVID-19: Results From a Randomized Controlled Trial (SAVIOR I)", @@ -575528,57 +577320,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.14.21263403", - "rel_title": "Evaluation Of A New All In One Sars-Cov-2 Antigen-Detecting Rapid Diagnostic Test And Self-Test: Diagnostic Performance And Usability On Child And Adult Population", - "rel_date": "2021-09-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.14.21263403", - "rel_abs": "The control of the COVID-19 epidemics has been one of top global health priorities for the last eighteen months. To that end, more reliable and easy-to-use diagnostic tests are necessary. Young children are still not eligible to vaccination and it is important to find a way to easily test this key population regularly. With that in mind, we evaluated a new innovative easy two-step self-test named COVID-VIRO ALL IN(R) developed by AAZ that uses a sampling nasal sponge instead of a classic nasal swab. Mirroring the previous study conducted on the first generation of COVID-VIRO(R) antigenic self-test, we first performed a multicentre, prospective study on 124 adults and children, in a point-of-care setting. Sensitivity, specificity and overall acceptance of the COVID-VIRO ALL IN(R) antigen self-test compared to RT-PCR on nasopharyngeal samples were evaluated at 93.02%, 100% and 97,5%, respectively. We then performed a multicentre, prospective, usability study to evaluate the ease of use of COVID-VIRO ALL IN(R) in real life on 68 laypersons, all adults. Globally, 99% of them considered the instructions material good, 98% executed the procedure well, and all of them interpreted the results correctly. The usability was then specifically investigated on 40 children and teenagers participants, comparing both COVID-VIRO(R) first generation and the new COVID-VIRO ALL IN(R). All of them found COVID-VIRO ALL IN(R) much easier to use and much more comfortable. For young children, the COVID-VIRO ALL IN(R) self-test appears to be safer (less risk of trauma compare to nasal swabs and no liquid exposure) easier to use than classic COVID self-tests and giving immediate result which is not the case for RT-PCR done on saliva samples (currently done in routine for kids in French schools). It could be an adapted tool for future mass screening campaigns in schools or at home under adult supervision for kids from the age of 3.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "thierry prazuck", - "author_inst": "CHR Orleans" - }, - { - "author_name": "Anne Gravier", - "author_inst": "Centre gratuit d information de depistage et de diagnostic Orleans" - }, - { - "author_name": "Daniela Pires-Roteira", - "author_inst": "Centre hospitalier d Orleans, service des maladies infectieuses et tropicales" - }, - { - "author_name": "Aurelie Theillay", - "author_inst": "Centre hospitalier regional d Orleans service des maladies infectieuses et tropicales" - }, - { - "author_name": "Sandra Pallay", - "author_inst": "Centre hospitalier regional d Orleans service des maladies infectieuses et tropicales" - }, - { - "author_name": "Mathilda Colin", - "author_inst": "Centre hospitalier regional d Orleans service des maladies infectieuses et tropicales" - }, - { - "author_name": "Raphael Serreau", - "author_inst": "Service de medecine preventive Orleans metropole" - }, - { - "author_name": "Laurent Hocqueloux", - "author_inst": "Centre hospitalier regional d Orleans service des maladies infectieuses et tropicales" - }, - { - "author_name": "Nino Guy Cassuto", - "author_inst": "Laboratoires Drouot" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.26.461851", "rel_title": "Cytotoxic T-cell-based vaccine against SARS-CoV2: a hybrid immunoinformatic approach", @@ -575715,6 +577456,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.23.21264032", + "rel_title": "Modeling the transmission of the SARS-CoV-2 delta variant in a partially vaccinated population", + "rel_date": "2021-09-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.23.21264032", + "rel_abs": "In a population with ongoing vaccination, the trajectory of a pandemic is determined by how the virus spreads in unvaccinated and vaccinated individuals that exhibit distinct transmission dynamics based on different levels of natural and vaccine-induced immunity. We developed a mathematical model that considers both subpopulations and immunity parameters including vaccination rates, vaccine effectiveness, and a gradual loss of protection. The model forecasted the spread of the SARS-CoV-2 delta variant in the US under varied transmission and vaccination rates. We further obtained the control reproduction number and conducted sensitivity analyses to determine how each parameter may affect virus transmission. Our results show that a combination of strengthening vaccine-induced immunity and preventative behavioral measures will likely be required to deaccelerate the rise of infectious SARS-CoV-2 variants.\n\nOne-Sentence SummaryMathematical models considering vaccinated and unvaccinated individuals help forecast and manage the spread of new SARS-CoV-2 variants.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ugo Avila", + "author_inst": "National Autonomous University of Mexico" + }, + { + "author_name": "Eric Avila", + "author_inst": "Autonomous University of Yucatan" + }, + { + "author_name": "Kuan-lin Huang", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.22.21263976", "rel_title": "Covid-19 Per Capita Fatality Rate: A Path Analysis Model", @@ -577438,93 +579206,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.19.21263807", - "rel_title": "RNA-extraction-free diagnostic method to detect SARS-CoV-2: an assessment from two States, India", - "rel_date": "2021-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.19.21263807", - "rel_abs": "With increasing demand for large numbers of testing during COVID-19 pandemic, came alternative protocols with shortened turn-around time. We evaluated the performance of such an approach wherein 1138 consecutive clinic attendees were enrolled; 584 and 554 respectively from two independent study sites in the cities of Pune and Kolkata. Paired nasopharyngeal and oropharyngeal swabs were tested by using both reference and index methods in blinded fashion. Prior to conducting RT-PCR, swabs collected in viral transport medium (VTM) were processed for RNA extraction (reference method) and swabs collected in dry tube without VTM were incubated in Tris-EDTA-Proteinase K buffer for 30 minutes and heat inactivated at 98{degrees}C for 6 minutes (index method). Overall sensitivity and specificity of the index method were 78.9% (95% CI 71% to 86%) and 99 % (95% CI 98% to 99.6%) respectively. Agreement between the index and reference method was 96.8 % (k = 0.83, SE=0.030). The reference method exhibited enhanced detection of viral genes (E, N and RdRP) with lower Ct values compared to the index method. The index method can be used for detecting SARS-CoV-2 infection with appropriately chosen primer-probe set and heat treatment approach in pressing time; low sensitivity constrains its potential wider use.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Madhumathi Jayaprakasam", - "author_inst": "Indian Council of Medical Research (ICMR), Ansari Nagar, New Delhi-110029" - }, - { - "author_name": "Sumit Aggarwal", - "author_inst": "Indian Council of Medical Research (ICMR), Ansari Nagar, New Delhi-110029" - }, - { - "author_name": "Arati Mane", - "author_inst": "ICMR-National AIDS Research Institute (ICMR-NARI), Pune" - }, - { - "author_name": "Vandana Saxena", - "author_inst": "ICMR-National AIDS Research Institute (ICMR-NARI), Pune" - }, - { - "author_name": "Amrita Rao", - "author_inst": "ICMR-National AIDS Research Institute (ICMR-NARI), Pune" - }, - { - "author_name": "Bhaswati Bandopadhyay", - "author_inst": "School of Tropical Medicine, Kolkata" - }, - { - "author_name": "Banya Chakraborty", - "author_inst": "School of Tropical Medicine, Kolkata" - }, - { - "author_name": "Subhasish Kamal Guha", - "author_inst": "School of Tropical Medicine, Kolkata" - }, - { - "author_name": "Mekhala Taraphdar", - "author_inst": "School of Tropical Medicine, Kolkata" - }, - { - "author_name": "Alisha Acharya", - "author_inst": "School of Tropical Medicine, Kolkata" - }, - { - "author_name": "Bishal Gupta", - "author_inst": "School of Tropical Medicine, Kolkata" - }, - { - "author_name": "Sonia Deb", - "author_inst": "School of Tropical Medicine, Kolkata" - }, - { - "author_name": "Aparna Chowdhury", - "author_inst": "School of Tropical Medicine, Kolkata" - }, - { - "author_name": "Kh Jitenkumar Singh", - "author_inst": "ICMR-National Institute of Medical Statistics (NIMS-ICMR), New Delhi" - }, - { - "author_name": "Prashant Tapase", - "author_inst": "ICMR-National Institute of Medical Statistics (NIMS-ICMR), New Delhi" - }, - { - "author_name": "Ravindra M Pandey", - "author_inst": "All India Institute of Medical Sciences (AIIMS), New Delhi" - }, - { - "author_name": "Balram Bhargava", - "author_inst": "Secretary, Department of Health Research (DHR) and Director General, ICMR" - }, - { - "author_name": "Samiran Panda", - "author_inst": "Indian Council of Medical Research (ICMR), Ansari Nagar, New Delhi-110029" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.21.21263457", "rel_title": "Real-world Effectiveness of 2-dose SARS-CoV-2 Vaccination in Kidney Transplant Recipients", @@ -577689,6 +579370,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.21.21263568", + "rel_title": "Risk Factors for Low Humoral Response to BNT-162b2 In Hemodialysis Patients", + "rel_date": "2021-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.21.21263568", + "rel_abs": "IntroductionMaintenance Hemodialysis (HD) patients are at higher risk of both infection and mortality associated with the new coronavirus 2. Immunization through large-scale vaccination is the cornerstone of infection prevention in this population. This study aims to identify risk factors for low response to the BNT-162b2 (Pfizer BioNTech) vaccine in a HD cohort.\n\nMaterials and MethodsObservational prospective study of a HD group followed in a Portuguese Public Founded Hemodialysis Center who received BNT-162b2 vaccination. Specific anti-Spike IgG was evaluated as arbitrary units per milliliter (AU/mL) on two separate occasions: 3 weeks after the first dose and 3 weeks after the second. IgG titers, Non-Responders (NR), and Weak-Responders (WR) after each dose were evaluated against risk factors that included demographic, clinical and analytical variables.\n\nResultsHumoral response evaluated by IgG anti-Spike levels showed a strong correlation with Charlson comorbidity index (CCI) and intact parathormone (iPTH) after each inoculation (1st dose: {rho}=-0.64/0.54; 2nd dose: {rho}=-0.66/0.63, respectively; p<0.01 throughout). After completing both doses: 1) NR were associated with female sex (p<0.01), lower albumin and iPTH (p=0.01); 2) WR showed higher CCI, older age, lower iPTH and lower albumin (p=<0.01, p=0.03, p<0.01, p=0.05, respectively) and, consistently, associated with CCI over 8, age over 75, iPTH under 150 ng/L, female sex, dialysis vintage under 24 months and central venous catheter (CVC) over arteriovenous fistula (p=0.01, p=0.03, p<0.01, p=0.01, p=0.01, p<0.01, respectively). A binary regression model using CCI, sex (male) and CVC was statistically significant in prediction of WR after the 2nd dose with OR (95% CI): 1.81 (1.06-3.08); 0.05 (0.01-0.65); 13.55 (1.06-174.18), respectively (p=0.01).\n\nConclusionOlder age, higher CCI, lower iPTH and albumin, CVC as vascular access and recent hemodialysis initiation (less than 2 years) associate with lower response to vaccination in our study. A higher comorbidity burden is suggested as a more significant surrogate marker for low immunogenicity rather than age alone. Identifying HD patients as a population at high-risk for low response to vaccination is essential for proper policy-making, facilitating the implementation of adequate and individualized contingency protocols.\n\nWhat is already known about this subjectO_LIMaintenance hemodialysis patients have lower humoral response to BNT-162b2 COVID-19 vaccine when compared to the general population.\nC_LIO_LIMaintenance dialysis patients are at high risk of exposure to coronavirus 2 in addition to a more severe disease course.\nC_LI\n\nWhat this study addsO_LIWe suggest Charlson commorbidity index, older age, intact parathormone, central venous catheter as vascular access and lower dialysis vintage as possible surrogate markers of immunogenicity in HD patients.\nC_LIO_LIThere is a low humoral response after a single dose of the vaccine (50%) that can be increased after the second (86%).\nC_LI\n\nWhat impact this may have on practice or policyO_LIStrict Protocols for follow-up measures in HD patients, including closer humoral titers assessment, risk stratification, adequate isolation, and surveillance of symptoms might be necessary in order to improve this population survival/life expectancy.\nC_LIO_LIScreening HD patients, seroconversion rates may be improved by giving extra inoculations for patients at risk for low response.\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Rui A Duarte", + "author_inst": "Centro Hospitalar do M\u00e9dio Tejo" + }, + { + "author_name": "C\u00e1tia Figueiredo", + "author_inst": "Centro Hospitalar do M\u00e9dio Tejo" + }, + { + "author_name": "Ivan Luz", + "author_inst": "Centro Hospitalar do M\u00e9dio Tejo" + }, + { + "author_name": "Francisco Ferrer", + "author_inst": "Centro Hospitalar do M\u00e9dio Tejo" + }, + { + "author_name": "Hern\u00e2ni Gon\u00e7alves", + "author_inst": "Centro Hospitalar do M\u00e9dio Tejo" + }, + { + "author_name": "Flora Sofia", + "author_inst": "Centro Hospitalar do M\u00e9dio Tejo" + }, + { + "author_name": "Karina Lopes", + "author_inst": "Centro Hospitalar do M\u00e9dio Tejo" + }, + { + "author_name": "Ana Vila Lobos", + "author_inst": "Centro Hospitalar do M\u00e9dio Tejo" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2021.09.21.21263627", "rel_title": "The slower antibody response in myelofibrosis patients after two doses of mRNA SARS-CoV-2 vaccine calls for a third dose", @@ -578932,93 +580660,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.20.21263566", - "rel_title": "Health-care workers in gastrointestinal endoscopy are at higher risk for SARS-CoV-2 infection compared to other aerosol-generating disciplines", - "rel_date": "2021-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.20.21263566", - "rel_abs": "ObjectiveHealthcare workers (HCW) are at high risk of SARS-CoV-2 infection due to exposure to potentially infectious material, especially during aerosol-generating procedures (AGP). We aimed to investigate the prevalence of infection among HCW in medical disciplines with AGP.\n\nDesignA nationwide questionnaire-based study in in- and outpatient settings was conducted between 12/16/2020 and 01/24/2021. Data on SARS-CoV-2 infections among HCW and potential risk factors were investigated.\n\nResults2,070 healthcare facilities with 25,113 employees were included in the study. Despite a higher rate of pre-interventional testing, clinics treated three times more confirmed SARS-CoV-2 cases than private practices (28.8% vs. 88.4%, p<0.001). Overall infection rate among HCW accounted for 4.7%. Multivariate analysis revealed that ZIP-regions having comparably higher incidences were significantly associated with increased risk of infection. Furthermore, clinical setting and the GIE specialty have more than double the risk of infection (OR 2.63; 95% CI 2.501-2.817, p<0.01 and OR 2.35; 95% CI 2.245-2.498, p<0.01). The number of procedures performed per day was also significantly associated with an increased risk of infection (OR 1.01; 95% CI 1.007-1.014), p<0.01). No treatment of confirmed SARS-CoV-2 cases was tending to lower the risk of infection (OR 0.72; 95% CI 0.507-1.025, p=0.068).\n\nConclusionHCW in GIE seem to be at higher risk of infection than those in other AGP, especially in the clinical setting. Regions having comparably higher incidences as well as the number of procedures performed per day were also significantly associated with increased risk of infection.\n\nSignificance of this studyO_ST_ABSWhat is already known on this subject?C_ST_ABSHealth care workers, especially those exposed to aerosol generating procedures, are assumed to have an increased risk of SARS-CoV-2 infection. However, data confirming this are lacking, especially for the outpatient care setting.\n\nWhat are the new findings?Health care workers in gastrointestinal endoscopy have a higher risk of SARS-CoV-2-infection than in other AGPs. This risk is particularly higher\n\n- in clinical settings compared to private practices\n- in regions having comparably higher incidences\n- the more procedures are performed per day\n\n\nHow might it impact on clinical practice in the foreseeable future?Our study suggests making additional efforts to protect HCW in the gastrointestinal work field.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Christoph Roemmele", - "author_inst": "Clinic for Internal Medicine III - Gastroenterology and Infectious Diseases, University Hospital Augsburg, Stenglinstrasse 2, 86156 Augsburg, Germany" - }, - { - "author_name": "Alanna Ebigbo", - "author_inst": "Clinic for Internal Medicine III - Gastroenterology and Infectious Diseases, University Hospital Augsburg, Stenglinstrasse 2, 86156 Augsburg, Germany" - }, - { - "author_name": "Maria Kahn", - "author_inst": "Clinic for Internal Medicine III - Gastroenterology and Infectious Diseases, University Hospital Augsburg, Stenglinstrasse 2, 86156 Augsburg, Germany" - }, - { - "author_name": "Stephan Zellmer", - "author_inst": "Clinic for Internal Medicine III - Gastroenterology and Infectious Diseases, University Hospital Augsburg, Stenglinstrasse 2, 86156 Augsburg, Germany" - }, - { - "author_name": "Anna Muzalyova", - "author_inst": "Clinic for Internal Medicine III - Gastroenterology and Infectious Diseases, University Hospital Augsburg, Stenglinstrasse 2, 86156 Augsburg, Germany" - }, - { - "author_name": "Gertrud Hammel", - "author_inst": "Institute of Environmental Medicine, Helmholtz Zentrum Munich, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany" - }, - { - "author_name": "Christina Bartenschlager", - "author_inst": "Chair of Health Care Operations/Health Information Management, University Augsburg, Neusaesser Strasse 47, 86156 Augsburg, Germany" - }, - { - "author_name": "Albert Beyer", - "author_inst": "Medical Practice for Gastroenterology and Gastrointestinal Oncology, Altoetting, Germany" - }, - { - "author_name": "Jonas Rosendahl", - "author_inst": "Clinic for Internal Medicine - Gastroenterology and Pneumology, University Hospital Halle" - }, - { - "author_name": "Tilo Schlittenbauer", - "author_inst": "Department of Oral and Maxillofacial Surgery, University Hospital Augsburg, Stenglinstrasse 2, 86156 Augsburg, Germany" - }, - { - "author_name": "Johannes Zenk", - "author_inst": "Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Augsburg, Stenglinstrasse 2, 86156 Augsburg, Germany" - }, - { - "author_name": "Bilal Al-Nawas", - "author_inst": "Clinic and Polyclinic for Oral and Maxillofacial Surgery, Plastic Surgery, University Hospital Mainz, Augustusplatz 2, 55131 Mainz, Germany" - }, - { - "author_name": "Roland Frankenberger", - "author_inst": "Department for Operative Dentistry, Endodontics, and Pediatric Dentistry, Philipps University Marburg and University Hospital Giessen and Marburg, Campus Marbur" - }, - { - "author_name": "Juergen Hoffmann", - "author_inst": "Department of Oral and Maxillofacial Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany" - }, - { - "author_name": "Christoph Arens", - "author_inst": "Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany" - }, - { - "author_name": "Frank Lammert", - "author_inst": "Saarland University Medical Center" - }, - { - "author_name": "Claudia Traidl-Hoffmann", - "author_inst": "Department of Environmental Medicine, Faculty of Medicine, University of Augsburg, Neusaesser Strasse 47, 86156 Augsburg, Germany" - }, - { - "author_name": "Helmut Messmann", - "author_inst": "Clinic for Internal Medicine III - Gastroenterology and Infectious Diseases, University Hospital Augsburg, Stenglinstrasse 2, 86156 Augsburg, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2021.09.20.21263808", "rel_title": "Human Milk Antibodies Elicited by BNT162b2 Vaccination Target have reduced activity against SARS-CoV-2 Variants of Concern", @@ -579327,6 +580968,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.09.20.21263794", + "rel_title": "Development and evaluation of a machine learning-based in-hospital COvid-19 Disease Outcome Predictor (CODOP): a multicontinental retrospective study", + "rel_date": "2021-09-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.20.21263794", + "rel_abs": "BackgroundMore contagious SARS-CoV-2 virus variants, breakthrough infections, waning immunity, and sub-optimal rates of COVID-19 vaccination account for a new surge of infections leading to record numbers of hospitalizations and deaths in several European countries. This is a particularly concerning scenario for resource-limited countries, which have a lower vaccination rate and fewer clinical tools to fight against the next pandemic waves. There is an urgent need for clinically valuable, generalizable, and parsimonious triage tools assisting the appropriate allocation of hospital resources. We aimed to develop and extensively validate CODOP, a machine learning-based tool for accurately predicting the clinical outcome of hospitalized COVID-19 patients.\n\nMethodsCODOP was built using modified stable iterative variable selection and linear regression with lasso regularisation. To avoid generalization problems, CODOP was trained and tested with three time-sliced and geographically distinct cohorts encompassing 40 511 blood-based analyses of COVID-19 patients from more than 110 hospitals in Spain and the USA during 2020-21. We assessed the discriminative ability of the model using the Area Under the Receiving Operative Curve (AUROC) as well as horizon and Kaplan-Meier risk stratification analyses. To reckon the fluctuating pressure levels in hospitals through the pandemic, we offer two online CODOP calculators suited for undertriage or overtriage scenarios. We challenged their generalizability and clinical utility throughout an evaluation on a cohort of patients hospitalized in five hospitals from three Latin American countries.\n\nFindingsCODOP uses 12 clinical parameters commonly measured at hospital admission and associated with the pathophysiology of COVID-19. CODOP reaches high discriminative ability up to nine days before clinical resolution (AUROC: 0{middle dot}90-0{middle dot}96, 95% CI 0{middle dot}879-0{middle dot}970), it is well calibrated, and it enables an effective dynamic risk stratification during hospitalization. The two CODOP online calculators demonstrate their potential for triage decisions when challenged with the distinctive Latin American evaluation cohorts (73-100% sensitivity and 84-100% specificity).\n\nInterpretationThe high predictive performance of CODOP in geographically disperse patient cohorts and the easiness-of-use, strongly suggest its clinical utility as a global triage tool, particularly in resource-limited countries.\n\nFundingThe Max Planck Society.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe have searched PubMed for articles about the existence of in-hospital COVID-19 mortality predictive models, using the search terms \"coronavirus\", \"COVID-19\", \"risk\", \"death\", \"mortality\", and \"prediction\", focusing on studies published between March 1, 2020 and 31 August, 2021. The studies we identified generally used small-medium size cohorts of patients that are geographically restricted to small regions of the developed world (many times, to the same city). We havent found studies that challenged their models in extended cohorts of patients from very distinct health system populations, particularly from resource-limited countries. Further, most of the previous models are rigid by not acknowledging the fluctuating availability of hospital resources during the pandemic (e.g., beds, oxygen supply). These and other limitations have been pointed out by expert reviews indicating that published in-hospital COVID-19 mortality predictive models are subject to high risk of bias, report an over-optimistic performance, and have limited clinical value in assisting daily triage decisions. A parsimonious, accurate and extensively validated model is yet to be developed.\n\nAdded value of this studyWe analysed clinical data from different cohorts totalling 21 607 COVID-19 patients treated in more than 110 hospitals in Spain and the USA during three different pandemic waves extending from February 2020 to April 2021. The new CODOP in-hospital mortality prediction model is based on 11 blood biochemistry parameters (representing main biological pathways involved in the pathogenesis of SARS-CoV-2) plus Age, all of them commonly measured upon hospitalization. CODOP accurately predicted mortality risk up to nine days before clinical resolution (AUROC: 0{middle dot}90-0{middle dot}96, 95% CI 0{middle dot}879-0{middle dot}970), it is well calibrated, and it enables an effective dynamic risk stratification during hospitalization. We offer two online CODOP calculator subtypes (https://gomezvarelalab.em.mpg.de/codop/) tailored to overtriage and undertriage scenarios. The online calculators were able to reach the desired prediction performance in five independent evaluation cohorts gathered in hospitals of three Latin American countries from March 7th 2020 to June 7th 2021.\n\nImplications of all the available evidenceWe present here a highly accurate, parsimonious and extensively validated COVID-19 in-hospital mortality prediction model, derived from working with the largest number and the most geographically extended representation of patients and health systems to date.\n\nThe rigorous analytical methods, the generalizability of the model in distinct world regions, and its flexibility to reckon with the changing availability of hospital resources point to CODOP as a clinically useful tool potentially improving the outcome prediction and the management of COVID-19 hospitalized patients.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Riku Klen", + "author_inst": "Turku PET Centre, University of Turku, Finland" + }, + { + "author_name": "Disha Purohit", + "author_inst": "Max Planck Institute of Experimental Medicine" + }, + { + "author_name": "Ricardo Gomez-Huelgas", + "author_inst": "Internal Medicine Department, Regional University Hospital of Malaga, Biomedical Research Institute of Malaga, University of Malaga, Malaga, Spain" + }, + { + "author_name": "Jose Manuel Casas-Rojo", + "author_inst": "Internal Medicine Department, Infanta Cristina University Hospital, Parla, Madrid, Spain" + }, + { + "author_name": "Juan Miguel Anton Santos", + "author_inst": "Internal Medicine Department, Infanta Cristina University Hospital, Parla, Madrid, Spain" + }, + { + "author_name": "Jesus Millan Nunez-Cortes", + "author_inst": "Internal Medicine Department, Gregorio Maranon University Hospital, Madrid, Spain" + }, + { + "author_name": "Carlos Lumbreras", + "author_inst": "Internal Medicine Department, 12 de Octubre University Hospital, Madrid, Spain" + }, + { + "author_name": "Jose Manuel Ramos-Rincon", + "author_inst": "Internal Medicine Department, General University Hospital of Alicante, Alicante Institute for 22 Health and Biomedical Research (ISABIAL), Miguel Hernandez Elch" + }, + { + "author_name": "Pablo Young", + "author_inst": "Clinical Medicine service, Hospital Britanico of Buenos Aires, Buenos Aires, Argentina" + }, + { + "author_name": "Juan Ignacio Ramirez", + "author_inst": "Clinical Medicine service, Hospital Britanico of Buenos Aires, Buenos Aires, Argentina" + }, + { + "author_name": "Estela Edith Titto Omonte", + "author_inst": "Internal Medicine Service, Hospital Santa Cruz - Caja Petrolera de Salud, Santa Cruz de la Sierra, Bolivia" + }, + { + "author_name": "Rosmery Gross Artega", + "author_inst": "Hospital of San Juan de Dios, Epidemiology Unit, Santa Cruz, Bolivia" + }, + { + "author_name": "Magdy Teresa Canales Beltran", + "author_inst": "Instituto Hondureno of social security, Hospital Honduras Medical Centre, Tegucigalpa, Honduras" + }, + { + "author_name": "Pascual Ruben Valdez", + "author_inst": "Hospital Velez Sarsfield, Buenos Aires, Argentina" + }, + { + "author_name": "Florencia Pugliese", + "author_inst": "Hospital Velez Sarsfield, Buenos Aires, Argentina" + }, + { + "author_name": "Rosa Castagna", + "author_inst": "Hospital Velez Sarsfield, Buenos Aires, Argentina" + }, + { + "author_name": "Nico Funke", + "author_inst": "Max Planck Institute of Experimental Medicine" + }, + { + "author_name": "Benjamin Leiding", + "author_inst": "Institute for Software and Systems Engineering, TU Clausthal, Clausthal, Germany" + }, + { + "author_name": "David Gomez-Varela", + "author_inst": "Max Planck Institute of Experimental Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.09.15.21263559", "rel_title": "COVID-19 vaccine hesitancy and vaccine passports: Vaccination or restriction?", @@ -580671,49 +582403,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.14.21263300", - "rel_title": "Predictors of COVID-19 vaccine uptake in healthcare workers: a cross-sectional study in Greece", - "rel_date": "2021-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.14.21263300", - "rel_abs": "BackgroundThe role of healthcare workers (HCWs) in the general public health is crucial and their decision to vaccinate against the COVID-19 can have a positive impact on the general population facilitating widespread COVID-19 vaccine uptake.\n\nObjectiveTo estimate the uptake of a COVID-19 vaccine in HCWs and to expand our knowledge regarding the predictors of COVID-19 vaccine uptake.\n\nMethodsAn on-line cross-sectional study was conducted in Greece during August 2021. We collected socio-demographic data of HCWs and we measured attitudes towards vaccination and COVID-19, knowledge and trust. We used a convenience sample since we distributed the questionnaire through social media and e-mails.\n\nResultsStudy population included 855 HCWs. The majority of HCWs were vaccinated against the COVID-19 (91.5%). According to multivariate analysis, females, HCWs without a previous COVID-19 diagnosis, and HCWs with previous seasonal influenza vaccination history had a greater probability to take a COVID-19 vaccine. Also, increased self-perceived knowledge regarding COVID-19 and increased trust in COVID-19 vaccines and government regarding the information about the COVID-19 vaccines were associated with COVID-19 vaccine uptake. On the other hand, HCWs with more concerns about the side-effects of COVID-19 vaccination were more reluctant to take a COVID-19 vaccine.\n\nConclusionsOur study provides a timely assessment of COVID-19 vaccination status among HCWs and identifies specific factors associated with COVID-19 vaccine uptake. By understanding these factors, policy makers and scientists will be able to develop novel strategies to improve COVID-19 vaccine uptake among HCWs.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Petros A Galanis", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Ioannis Moisoglou", - "author_inst": "General Hospital of Lamia" - }, - { - "author_name": "Irene Vraka", - "author_inst": "P & A Kyriakou Children's Hospital" - }, - { - "author_name": "Olga Siskou", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Olympia Konstantakopoulou", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Aglaia Katsiroumpa", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Daphne Kaitelidou", - "author_inst": "National and Kapodistrian University of Athens" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.14.21263467", "rel_title": "Information Theoretic Model Selection for Accurately Estimating Unreported COVID-19 Infections", @@ -580986,6 +582675,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, + { + "rel_doi": "10.1101/2021.09.15.21263597", + "rel_title": "High- Versus Low-Dose Dexamethasone for the Treatment of COVID-19-related Acute Respiratory Distress Syndrome: A Multicenter and Randomized Open-label Clinical Trial", + "rel_date": "2021-09-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.15.21263597", + "rel_abs": "PurposeTo determine whether high-dose dexamethasone increases the number of ventilator-free days (VFD) among patients with acute respiratory distress syndrome due to coronavirus disease 2019 (C-ARDS)\n\nMaterialsA multicenter randomized controlled trial in adults with C-ARDS. Patients received 16 mg/d of dexamethasone intravenously for five days followed by 8 mg/d of dexamethasone for five days, or 6 mg/d of dexamethasone intravenously for 10 days.\n\nResultsData from 98 patients who received at least one dose of dexamethasone were analyzed. At 28 days after randomization, there was no difference between high- and low-dose dexamethasone groups in VFD (median, 0 d [interquartile range (IQR) 0-14 d] versus 0 d [IQR 0-1 d]; P=0.231). The cumulative hazard of successful discontinuation from mechanical ventilation was increased by the high-dose treatment (adjusted sub-distribution hazard ratio: 1.84; 95% CI: 1.31 to 2.5; P<0.001). None of the prespecified secondary and safety outcomes showed a significant difference between treatment arms.\n\nConclusionsAmong patients with C-ARDS, the use of higher doses of dexamethasone compared with the recommended low-dose treatment did not show an increase in VFD. However, the higher dose significantly improved the time required to liberate them from the ventilator\n\nClinical Trial Registered: NCT04395105", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Luis Patricio Maskin", + "author_inst": "CEMIC (Centro de Educacion Medica e Investigaciones Clinicas)" + }, + { + "author_name": "Ignacio Bonelli", + "author_inst": "CEMIC (Centro de Educacion Medica e Investigaciones Clinicas)" + }, + { + "author_name": "Gabriel Leonardo Olarte", + "author_inst": "Sanatorio Sagrado Corazon" + }, + { + "author_name": "Fernando Palizas Jr.", + "author_inst": "Clinica Bazterrica" + }, + { + "author_name": "Agostina E Velo", + "author_inst": "CEMIC (Centro de Educacion Medica e Investigaciones Clinicas)" + }, + { + "author_name": "Maria Fernanda Lurbet", + "author_inst": "CEMIC (Centro de Educacion Medica e Investigaciones Clinicas)" + }, + { + "author_name": "Pablo Lovazzano", + "author_inst": "CEMIC (Centro de Educacion Medica e Investigaciones Clinicas)" + }, + { + "author_name": "Sophia Kotsias", + "author_inst": "CEMIC (Centro de Educacion Medica e Investigaciones Clinicas)" + }, + { + "author_name": "Shiry Attie", + "author_inst": "CEMIC (Centro de Educacion Medica e Investigaciones Clinicas)" + }, + { + "author_name": "Ignacio Lopez Saubidet", + "author_inst": "CEMIC (Centro de Educacion Medica e Investigaciones Clinicas)" + }, + { + "author_name": "Natalio D Baredes", + "author_inst": "Sanatorio Sagrado Corazon" + }, + { + "author_name": "Mariano Setten", + "author_inst": "CEMIC (Centro de Educacion Medica e Investigaciones Clinicas)" + }, + { + "author_name": "Pablo Oscar Rodriguez", + "author_inst": "CEMIC (Centro de Educacion Medica e Investigaciones Clinicas)" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.09.16.21263170", "rel_title": "Characterisation of the blood RNA host response underpinning severity in COVID-19 patients", @@ -582169,73 +583925,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.09.17.21263528", - "rel_title": "Dichotomy between the humoral and cellular responses elicited by mRNA and adenoviral vector vaccines against SARS-CoV-2.", - "rel_date": "2021-09-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.17.21263528", - "rel_abs": "Protection from severe disease and hospitalization by SARS-CoV-2 vaccination has been amply demonstrated by real-world data. However, the rapidly evolving pandemic raises new concerns. One pertains efficacy of adenoviral vector-based vaccines, particularly the single-dose Ad26.COV2.S, relative to mRNA vaccines. We investigated the immunogenicity of Ad26.COV2.S and mRNA vaccines in 33 subjects vaccinated with either vaccine class five months earlier on average. After controlling for time since vaccination, Spike-binding antibody and neutralizing antibody levels were higher in the mRNA-vaccinated subjects, while no significant differences in antigen-specific B cell and T cell responses were observed between the two groups. Thus, a dichotomy exists between humoral and cellular responses elicited by the two vaccine classes. Our results have implications for the need of booster doses in vaccinated subjects and might explain the dichotomy reported between the waning protection from symptomatic infection by SARS-CoV-2 vaccination and its persisting efficacy in preventing hospitalization and death.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Rahul Ukey", - "author_inst": "PHRI, Rutgers NJMS, Newark, NJ" - }, - { - "author_name": "Natalie Bruiners", - "author_inst": "PHRI, Rutgers NJMS, Newark, NJ" - }, - { - "author_name": "Hridesh Mishra", - "author_inst": "PHRI, Rutgers NJMS, Newark,NJ" - }, - { - "author_name": "Pankaj K Mishra", - "author_inst": "PHRI, Rutgers NJMS, Newark, NJ" - }, - { - "author_name": "Deborah McCluskey", - "author_inst": "Clinical Reserach Center, Rutgers RWJMS, New Brunswick, NJ" - }, - { - "author_name": "Alberta Onyuka", - "author_inst": "Global Tuberculosis Institute, Rutgers NJMS,Newark,NJ" - }, - { - "author_name": "Fei Chen", - "author_inst": "Clinical Reserach Center, Rutgers RWJMS, New Brunswick, NJ" - }, - { - "author_name": "Abraham Pinter", - "author_inst": "Rutgers University" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute For Allergy & Immunology" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "La Jolla Institute for Allergy & Immunology" - }, - { - "author_name": "Jason Roy", - "author_inst": "Department of Biostatistics, Rutgers University School of Public Health, NJ" - }, - { - "author_name": "Sunanda Gaur", - "author_inst": "Rutgers, Robert Wood Johnson Medical School" - }, - { - "author_name": "Maria Laura Gennaro", - "author_inst": "PHRI, Rutgers NJMS, Newark, NJ" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.17.21263532", "rel_title": "Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a sixteen-week interval between doses", @@ -582528,6 +584217,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.12.21263461", + "rel_title": "Equivalency of Protection from Natural Immunity in COVID-19 Recovered Versus Fully Vaccinated Persons: A Systematic Review and Pooled Analysis", + "rel_date": "2021-09-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.12.21263461", + "rel_abs": "BACKGROUNDWe present a systematic review and pooled analysis of clinical studies to date, that (1) specifically compare the protection of natural immunity in the COVID-recovered versus the efficacy of full vaccination in the COVID-naive, and (2) the added benefit of vaccination in the COVID-recovered, for prevention of subsequent SARS-CoV-2 infection.\n\nMETHODSUsing the PRISMA 2020 guidance, we first conducted a systematic review of available literature on PubMed, MedRxIV and FDA briefings to identify clinical studies either comparing COVID vaccination to natural immunity or delineating the benefit of vaccination in recovered individuals. After assessing for eligibility, studies were qualitatively appraised and formally graded using the NOS system for observational, case-control and RCTs. Incidence rates were tabulated for the following groups: never infected (NI) and unvaccinated (UV), NI and vaccinated (V), previously infected (PI) and UV, PI and UV. Pooling was performed by grouping the RCTs and observational studies separately, and then all studies in total. Risk ratios and risk differences are reported for individual studies and pooled groups, in 1) NPI/V vs. PI/UV and 2) PI/UV vs. PI/V analysis. In addition, number needed to treat (NNT) analysis was performed for vaccination in naive and previously infected cohorts.\n\nRESULTSNine clinical studies were identified including three randomized controlled studies, four retrospective observational cohorts, one prospective observational cohort, and a case-control study. The NOS quality appraisals of these articles ranged from four to nine (out of nine stars). All of the included studies found at least statistical equivalence between the protection of full vaccination and natural immunity; and, three studies found superiority of natural immunity. Four observational studies found a statistically significant incremental benefit to vaccination in the COVID-recovered individuals. In total pooled analysis, incidence in NPI/V trended higher than PI/UV groups (RR=1.86 [95%CI 0.77-4.51], P=0.17). Vaccination in COVID-recovered individuals provided modest protection from reinfection (RR=1.82 [95%CI 1.21-2.73], P=0.004), but the absolute risk difference was extremely small (AR= 0.004 person-years [95% CI 0.001-0.007], P=0.02). The NNT to prevent one annual case of infection in COVID-recovered patients was 218, compared to 6.5 in COVID-naive patients, representing a 33.5-fold difference in benefit between the two populations.\n\nCONCLUSIONSWhile vaccinations are highly effective at protecting against infection and severe COVID-19 disease, our review demonstrates that natural immunity in COVID-recovered individuals is, at least, equivalent to the protection afforded by full vaccination of COVID-naive populations. There is a modest and incremental relative benefit to vaccination in COVID-recovered individuals; however, the net benefit is marginal on an absolute basis. COVID-recovered individuals represent a distinctly different benefit-risk calculus. Therefore, vaccination of COVID-recovered individuals should be subject to clinical equipoise and individual preference.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Mahesh B Shenai", + "author_inst": "Inova Health System" + }, + { + "author_name": "Ralph Rahme", + "author_inst": "SBH Health System" + }, + { + "author_name": "Hooman Noorchasm", + "author_inst": "American Patient Defense Union" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.09.09.21262448", "rel_title": "An Analysis of SARS-CoV-2 Vaccine Breakthrough Infections and Associated Clinical Outcomes", @@ -584199,33 +585915,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.16.460716", - "rel_title": "The supramolecular organization of SARS-CoV and SARS-CoV-2 virions revealed by coarse-grained models of intact virus envelopes", - "rel_date": "2021-09-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.16.460716", - "rel_abs": "The coronavirus disease 19 (COVID-19) pandemic is causing a global health crisis and has already caused a devastating societal and economic burden. The pathogen, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has a high sequence and architecture identity with SARS-CoV, but far more people have been infected by SARS-CoV-2. Here, combining structural data from cryo-EM and structure prediction, we constructed bottom-up Martini coarse-grained models of intact SARS-CoV and SARS-CoV-2 envelopes. Microsecond molecular dynamics simulations were performed, allowing us to explore their dynamics and supramolecular organization. Both SARS-CoV and SARS-CoV-2 envelopes present a spherical morphology with structural proteins forming multiple string-like islands in the membrane and clusters between heads of spike proteins. Critical differences between the SARS-CoV and SARS-CoV-2 envelopes are the interaction pattern between spike proteins and the flexibility of spike proteins. Our models provide structural and dynamic insights in the SARS virus envelopes, and could be used for further investigation, such as drug design, and fusion and fission processes.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Beibei Wang", - "author_inst": "Beijing Normal University" - }, - { - "author_name": "Changqing Zhong", - "author_inst": "University of Electronic Science and Technology of China" - }, - { - "author_name": "D. Peter Tieleman", - "author_inst": "University of Calgary" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.09.15.21263654", "rel_title": "Correlates of COVID-19 vaccination status among college students", @@ -584706,6 +586395,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.19.460976", + "rel_title": "Planning and Conducting an Online Conference at the time of COVID-19: Lessons Learned from EGREPA 2021", + "rel_date": "2021-09-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.19.460976", + "rel_abs": "BackgroundThis paper describes the realisation and evaluation of the EGREPA 2021 conference, in online format. As an example, and support for future conferences, the decision process to switch during the COVID-19 pandemic from onsite to online, the conception and tools, the experiences of the organisers and the feedback of the participants are described.\n\nMethodsThe CERN tool \"Indico\" served as the central conference management system including public homepage, submission and payment system, abstract review and decision platform, and conference material repository. Zoom, YouTube Live and Open Broadcaster Software (OBS) were utilised for keynotes and other presentation sessions, including livestreaming of pre-recorded presentations. Gather was implemented for poster sessions and individual meetings. An anonymous survey included Likert-type questions on acceptance and quality of the tools and instructions, open questions related to positive and negative issues, and ideas for the next online-conference.\n\nResultsThe event was evaluated well, with mostly fluently working technical solutions. A few participants indicated problems switching from YouTube to Zoom between presentations and discussions. Opinions on pre-recordings of talks were divided. Participants required more time for socialising. Guidelines and materials were mostly rated helpful.\n\nLessons LearnedSimplifying the livestreaming, presenters choice between pre-recording or presenting live, more time for socialising and breaks are discussed. Tools for conducting an online conference should be introduced to the participants in advance. Indico is rated as a very helpful tool for planning and conducting an online-conference.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Ellen Bentlage", + "author_inst": "University of Muenster, Germany" + }, + { + "author_name": "Luca Roekens", + "author_inst": "University of Muenster, Germany" + }, + { + "author_name": "Lennart Bussmann", + "author_inst": "University of Muenster, Germany" + }, + { + "author_name": "Michael Brach", + "author_inst": "University of Muenster, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2021.09.17.460777", "rel_title": "Altered fibrin clot structure contributes to thrombosis risk in severe COVID-19", @@ -586445,37 +588165,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.13.21263497", - "rel_title": "Factors Influencing The First and Second Peak of COVID-19 Global Cases: A Survival Analysis", - "rel_date": "2021-09-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263497", - "rel_abs": "ObjectivesThe number of reported cases continues to increase everyday, since the first case of COVID-19 was detected in Wuhan, China in December 2019. Using the global COVID-19 data of 188 countries extracted from the Our World in Data between January 22, 2020-January 18, 2021, this study attempts to explore the potential determinants of the number of days to reach the first and second peak of COVID-19 cases for all 188 countries.\n\nMethodsA semi-parametric Cox proportional hazard (PH) model has been used to explore the covariates that are associated with the number of days to reach the first and second peak of global COVID-19 cases.\n\nResultsAs of January 18, 2021, the first and second peak were found in 175 and 59 countries, out of 188 countries, respectively. The median number of days to hit the first peak was 60 days for countries which have median age above 40 while the median number of days to hit the second peak was 267 days for countries which have population density above 500 per square kilometer. Countries having population density between 250 and 500 were 2.25 times more likely to experience the first peak of COVID-19 cases (95% CI: 1.15-4.45, P < 0.05) than countries which have population density below 25. Countries having population density between 100 and 250 were 67% less likely to get the second peak (95% CI: 0.119-0.908, P < 0.05) compared to countries which have population density below 25. Countries having cardiovascular death rates above 350 were 2.94 times more likely to get the first peak (95% CI: 1.59-5.43, P < 0.001). In contrast, countries having diabetes prevalence rate 3 to 12 were 85% less likely to experience the second peak of COVID-19 cases (95% CI: 0.036-0.680, P < 0.05) than countries which have diabetes prevalence rate below 3. Besides, highly significant difference is found in the Kaplan-Meier plots of the number of days to reach both peaks across different categories of the countrys Human Development Index.\n\nConclusionsThe number of days to the first peak was considerably small in Asian & European countries but that to the second peak in the countries where diabetes prevalence was very higher. Countrys life expectancy had a significant effect on determining the first peak and so was the case for two other variables-the cardiovascular death rate and hospital beds per thousand. A contrast result was found for Human Development Index factor under the second peak. Additionally, it was found that the second peak was more likely to occur in more densely populated countries.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Yesar Ahmed Oshan", - "author_inst": "ISRT, University of Dhaka" - }, - { - "author_name": "Begum Zainab", - "author_inst": "ISRT, University of Dhaka" - }, - { - "author_name": "Dipankar Bandyopadhyay", - "author_inst": "Department of Biostatistics, Virginia Commonwealth University" - }, - { - "author_name": "Hasinur Rahaman Khan", - "author_inst": "University of Dhaka, Bangladesh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.13.21262182", "rel_title": "mRNA COVID-19 Vaccination and Development of CMR-confirmed Myopericarditis", @@ -586760,6 +588449,161 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.13.21263214", + "rel_title": "Detailed Overview of the Buildout and Integration of an Automated High-Throughput CLIA Laboratory for SARS-CoV-2 Testing on a Large Urban Campus", + "rel_date": "2021-09-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263214", + "rel_abs": "In 2019, the first cases of SARS-CoV-2 were detected in Wuhan, China, and by early 2020 the cases were identified in the United States. SARS-CoV-2 infections increased in the US causing many states to implement stay-at-home orders and additional safety precautions to mitigate potential outbreaks. As policies changed throughout the pandemic and restrictions lifted, there was an increase in demand for Covid-19 testing which was costly, difficult to obtain, or had long turn-around times. Some academic institutions, including Boston University, created an on-campus Covid-19 screening protocol as part of planning for the safe return of students, faculty, and staff to campus with the option for in-person classes. At BU, we stood up an automated high-throughput clinical testing lab with the capacity to run 45,000 individual tests weekly by fall of 2020, with a purpose-built clinical testing laboratory, a multiplexed RT-PCR test, robotic instrumentation, and trained CLIA certified staff. There were challenges to overcome, including the supply chain issues for PPE testing materials, and equipment that were in high demand. The Boston University Clinical Testing Laboratory was operational at the start of the fall 2020 academic year. The lab performed over 1 million SARS-CoV-2 RT-PCR tests during the 2020-2021 academic year.", + "rel_num_authors": 35, + "rel_authors": [ + { + "author_name": "Lena Landaverde", + "author_inst": "Precision Diagnostics Center, Boston University, Boston, MA; Biomedical Engineering, College of Engineering, Boston University, Boston, MA; Boston University Cl" + }, + { + "author_name": "David McIntyre", + "author_inst": "Biomedical Engineering, College of Engineering, Boston University, Boston, MA; Design, Automation, Manufacturing, and Prototyping Laboratory, Boston University," + }, + { + "author_name": "James Robson", + "author_inst": "Biomedical Engineering, College of Engineering, Boston University, Boston, MA" + }, + { + "author_name": "Dany Fu", + "author_inst": "Design, Automation, Manufacturing, and Prototyping Laboratory, Boston University, Boston, MA; Software & Application Innovation Lab, Hariri Institute for Comput" + }, + { + "author_name": "Luis Ortiz", + "author_inst": "Biomedical Engineering, College of Engineering, Boston University, Boston, MA; Design, Automation, Manufacturing, and Prototyping Laboratory, Boston University," + }, + { + "author_name": "Rita Chen", + "author_inst": "Design, Automation, Manufacturing, and Prototyping Laboratory, Boston University, Boston, MA; Electrical and Computer Engineering, Boston University, Boston, MA" + }, + { + "author_name": "Samuel M.D. Oliveira", + "author_inst": "Design, Automation, Manufacturing, and Prototyping Laboratory, Boston University, Boston, MA; Electrical and Computer Engineering, Boston University, Boston, MA" + }, + { + "author_name": "Andy Fan", + "author_inst": "Biomedical Engineering, College of Engineering, Boston University, Boston, MA" + }, + { + "author_name": "Amy Barrett", + "author_inst": "Office of the Provost, Boston University, Boston, MA" + }, + { + "author_name": "Stephen P. Burgay", + "author_inst": "Office of External Affairs, Boston University, Boston, MA" + }, + { + "author_name": "Stephen Choate", + "author_inst": "Information Services & Technology, Boston University, Boston, MA" + }, + { + "author_name": "David Corbett", + "author_inst": "Health Information Privacy Resources, Boston University, Boston, MA" + }, + { + "author_name": "Lynn Doucette-Stamm", + "author_inst": "Boston University Clinical Testing Laboratory, Boston University, Boston, MA" + }, + { + "author_name": "Kevin Gonzales", + "author_inst": "BU Healthway, Boston University, Boston, MA; Office of Research, Boston University, Boston, MA" + }, + { + "author_name": "Davidson H. Hamer", + "author_inst": "Precision Diagnostics Center, Boston University, Boston, MA; Department of Global Health, Boston University School of Public Health, Boston University, Boston, " + }, + { + "author_name": "Lilly Huang", + "author_inst": "Office of General Counsel, Boston University, Boston, MA" + }, + { + "author_name": "Shari Huval", + "author_inst": "Information Services & Technology, Boston University, Boston, MA" + }, + { + "author_name": "Christopher Knight", + "author_inst": "Information Services & Technology, Boston University, Boston, MA" + }, + { + "author_name": "Diane Lindquist", + "author_inst": "Health Privacy and Compliance, Boston University, Boston, MA" + }, + { + "author_name": "Kelly Lockard", + "author_inst": "Continuous Improvement & Data Analytics, Boston University, Boston, MA" + }, + { + "author_name": "Trevor L. Macdowell", + "author_inst": "Information Services & Technology, Boston University, Boston, MA" + }, + { + "author_name": "Elizabeth Mauro", + "author_inst": "Information Services & Technology, Boston University, Boston, MA" + }, + { + "author_name": "Colleen McGinty", + "author_inst": "Operations, Boston University, Boston, MA" + }, + { + "author_name": "Candice Miller", + "author_inst": "Boston University Clinical Testing Laboratory, Boston University, Boston, MA" + }, + { + "author_name": "Maura Monahan", + "author_inst": "Information Services & Technology, Boston University, Boston, MA" + }, + { + "author_name": "Randall Moore", + "author_inst": "Sourcing and Procurement, Boston University, Boston, MA" + }, + { + "author_name": "Judy Platt", + "author_inst": "Student Health Services, Healthway, Boston University School of Public Health, Boston, MA" + }, + { + "author_name": "Jeffery Roy", + "author_inst": "Sourcing and Procurement, Boston University, Boston, MA" + }, + { + "author_name": "Tracey Schroeder", + "author_inst": "Information Services & Technology, Boston University, Boston, MA" + }, + { + "author_name": "Dean R. Tolan", + "author_inst": "Boston University Clinical Testing Laboratory, Boston University, Boston, MA; HFI Laboratory, Boston University, Boston, MA" + }, + { + "author_name": "Ann Zaia", + "author_inst": "Occupational Health Center, Boston University, Boston, MA" + }, + { + "author_name": "Robert A. Brown", + "author_inst": "College of Engineering, Boston University, Boston, MA; Office of the President, Boston University, Boston, MA" + }, + { + "author_name": "Gloria Waters", + "author_inst": "Office of Research, Boston University, Boston, MA; College of Health and Rehabilitation Services, Sargent College, Boston University, Boston, MA" + }, + { + "author_name": "Douglas Densmore", + "author_inst": "Design, Automation, Manufacturing, and Prototyping Laboratory, Boston University, Boston, MA; Biological Design Center, Boston University, Boston, MA; Electrica" + }, + { + "author_name": "Catherine M. Klapperich", + "author_inst": "Precision Diagnostics Center, Boston University, Boston, MA; Biomedical Engineering, College of Engineering, Boston University, Boston, MA; Boston University Cl" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.09.13.21263511", "rel_title": "Using Artificial Intelligence-based models to predict the risk of Mucormycosis among COVID-19 Survivors: An Experience from India", @@ -588311,57 +590155,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2021.09.13.21263476", - "rel_title": "Association between work attendance when experiencing fever or cold symptoms and company characteristics and socioeconomic status in the COVID-19 pandemic in Japanese workers: a cross-sectional study", - "rel_date": "2021-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263476", - "rel_abs": "ObjectiveThis study investigated the association between attending work while experiencing fever or cold symptoms and workers socioeconomic background and company characteristics during the COVID-19 pandemic.\n\nMethodsA cross-sectional online survey was performed. Of a total of 33,302 participants, 3,676 workers who experienced fever or cold symptoms after April 2020 were included. The odds ratios (ORs) of attending work while sick associated with workers socioeconomic background and company characteristics were evaluated using a multilevel logistic model.\n\nResultsThe OR of attending work while sick associated with a lack of policy prohibiting workers from working when ill was 2.75 (95%CI: 2.28-3.20, P<0.001).\n\nConclusionThis study suggests that clear company policies on work and illness can be effective for preventing employees from attending work while sick.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Kazuyoshi Mizuki", - "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Makoto Okawara", - "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Ayako Hino", - "author_inst": "Department of Mental Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Hajime Ando", - "author_inst": "Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Tomohisa Nagata", - "author_inst": "Department of Occupational Health Practice and Management, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Jap" - }, - { - "author_name": "Seiichiro Tateishi", - "author_inst": "Department of Occupational Medicine, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Mayumi Tsuji", - "author_inst": "Department of Environmental Health, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Shinya Matsuda", - "author_inst": "Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Yoshihisa Fujino", - "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.09.12.21263475", "rel_title": "Spike Protein NTD mutation G142D in SARS-CoV-2 Delta VOC lineages is associated with frequent back mutations, increased viral loads, and immune evasion", @@ -588714,6 +590507,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.12.21263451", + "rel_title": "What pushed Israel out of herd immunity? Modeling COVID-19 spread of Delta and Waning immunity", + "rel_date": "2021-09-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.12.21263451", + "rel_abs": "Following a successful vaccination campaign at the beginning of 2021 in Israel, where approximately 60% of the population were vaccinated with an mRNA BNT162b2 vaccine, it seemed that Israel had crossed the herd immunity threshold (HIT). Nonetheless, Israel has seen a steady rise in COVID-19 morbidity since June 2021, reaching over 1,000 cases per million by August. This outbreak is attributed to several events that came together: the temporal decline of the vaccines effectiveness (VE); lower effectiveness of the vaccine against the current Delta (B.1.617.2) variant; highly infectiousness of Delta; and temporary halt of mandated NPIs (non-pharmaceutical interventions) or any combination of the above. Using a novel spatial-dynamic model and recent aggregate data from Israel, we examine the extent of the impact of the Delta variant on morbidity and whether it can solely explain the outbreak. We conclude that both Delta infectiousness and waning immunity could have been able to push Israel below the HIT independently, and thus, to mitigate the outbreak effective NPIs are required. Our analysis cautions countries that once vaccines will wane a highly infectious spread is expected, and therefore, the expected decline in the vaccines effectiveness in those countries should be accompanied by another vaccination campaign and effective NPIs.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Hilla De-Leon", + "author_inst": "ECT*" + }, + { + "author_name": "Dvir Aran", + "author_inst": "Technion - Israel Institute of Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.11.21263211", "rel_title": "Early immunologic response to mRNA COVID-19 vaccine in patients receiving biologics and/or immunomodulators.", @@ -590417,57 +592233,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.09.04.21262932", - "rel_title": "A Comparative Study Between Nasopharyngeal/Oropharyngeal, Faecal and Saliva Viral Shedding In Ghanaian COVID-19 Patients attending KATH from October-December, 2020", - "rel_date": "2021-09-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.04.21262932", - "rel_abs": "BackgroundDiagnostic testing for the current SARS-CoV-2 infections involves the collection and testing of invasive pharyngeal specimens by qualified Health workers. Though fully clad in personal protective equipment, the concern is that sampling in close proximity to the patient poses as a major health hazard. The present study sought to verify if saliva or faeces could become a possible surrogate for pharyngeal samples for SARS-CoV 2 testing in suspected Ghanaian COVID-19 patients.\n\nObjectivesTo ascertain if there is SARS-CoV 2 viral shedding in the saliva and faecal samples of Ghanaian COVID-19 patients, their sensitivity and specificity as compared to pharyngeal samples.\n\nMethodFifty (50) recruited COVID-19 patients who have been confirmed via RT-PCR using their nasopharyngeal/oropharyngeal samples and twenty (20) SARS-CoV 2 negative suspected patients each provided some faecal and saliva sample for RT-PCR analysis for SARS-CoV 2.\n\nResultsForty-three (43) out of the fifty (50) COVID-19 patients recruited representing 86% tested positive for SARS-CoV 2 via their saliva sample whiles all their faecal samples tested positive for SARS-CoV 2 representing 100%. The sensitivity of saliva samples was 86% whiles the specificity was 100% but the sensitivity and specificity of the faecal samples were all 100%.\n\nConclusionThere is indeed viral shedding of SARS-CoV 2 in the saliva and faeces of Ghanaian COVID-19 patients just like their counterparts in other parts of the world. Saliva and faeces could possibly become an alternative sample to the current in place of the invasive pharyngeal samples for SARS-CoV 2 testing in resource limited settings. Further research to explore this possibility at different testing sites with larger sample size is recommended.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Ernest Badu-Boateng", - "author_inst": "Komfo Anokye Teaching Hospital / Catholic University College of Ghana-Fiapre, Sunyani" - }, - { - "author_name": "Lydia Sarponmaa Asante", - "author_inst": "Catholic University College of Ghana" - }, - { - "author_name": "Albert Dompreh", - "author_inst": "Komfo Anokye Teaching Hospital" - }, - { - "author_name": "Laud Anthony Basing Wihibeturo", - "author_inst": "KNUST" - }, - { - "author_name": "Kwabena Adjei Asante", - "author_inst": "Komfo Anokye Teaching Hospital" - }, - { - "author_name": "Sylvia Karikari", - "author_inst": "Komfo Anokye Teaching Hospital" - }, - { - "author_name": "Albert Adubofour", - "author_inst": "Komfo Anokye Teaching Hospital" - }, - { - "author_name": "Chris Oppong", - "author_inst": "Komfo Anokye Teaching Hospital" - }, - { - "author_name": "Faustina Acheampong", - "author_inst": "Komfo Anokye Teaching Hospital" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.03.21262757", "rel_title": "Asymptomatic SARS-CoV-2 infection and the demography of COVID-19", @@ -590816,6 +592581,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.09.21263347", + "rel_title": "Implicit, Intrinsic, Extrinsic (or Environmental), and Host Factors Attributing the Covid-19 Pandemic. Part 2- Implicit Factor Pesticide Use: A Systematic Analysis", + "rel_date": "2021-09-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.09.21263347", + "rel_abs": "Advances in our understanding of complex COVID-19 pandemic would allow us to effectively eliminate and eradicate SARS-COV2 virus. Although tremendous amount of research devoted to the robustness across its biology, diagnostics, vaccines and treatment has exploded in the past two years. However, still science do not have robust answers for causes, for example (i) What are the reasons of non-uniform global distribution of COVID-19? (ii) Why the United States, India, and Brazil, are the first-three most affected nations?, (iii) How did Bhutan, a nation sharing a boundary with China manage nearly 0.34% infections and 3 deaths from COVID-19? Nonetheless, the biomass bistribution of biosphere report suggest more than 1550-fold larger microbial biomass involving bacteria, fungi, archaea, protists and viruses is exist in comparision to all global human population in the biosphere. The rich microbiota act a first line of defence to invade pathogens and affect us both through the environment and microbiome. Unfortunately, a role of pathogen-transmission factors viz. implicit factors (competitive microflora) is still under represented. This study is an attempt from a gold standard correlation methodology using a large pesticide use global data. The non-specific pesticides kill both pests as well as protective microbiota, resulting a loss in rich biodiversity and allow easy pathogen entry to human. Entire predictions were found consistent with the recently observed evidences. These insights enhanced scientific ability to interrogate viral epidemiology and recommended to limit pesticide use for future pandemic prevention.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Ananya Aggarwal", + "author_inst": "Graphic Era Hill University" + }, + { + "author_name": "Ragini Rai", + "author_inst": "Graphic Era Hill University" + }, + { + "author_name": "Gaurav Joshi", + "author_inst": "Graphic Era Hill University" + }, + { + "author_name": "Prashant Gahtori", + "author_inst": "Graphic Era Hill University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.14.460275", "rel_title": "SARS-CoV-2 Spike Protein Regulation of Angiotensin Converting Enzyme 2 and Tissue Renin-Angiotensin Systems: Influence of Biologic Sex", @@ -592299,65 +594095,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.06.21262027", - "rel_title": "A simple, sensitive and quantitative FACS-based test for SARS-CoV-2 serology in humans and animals", - "rel_date": "2021-09-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.06.21262027", - "rel_abs": "Serological tests are important for understanding the physiopathology and following the evolution of the Covid-19 pandemic. Assays based on flow cytometry (FACS) of tissue culture cells expressing the spike (S) protein of SARS-CoV-2 have repeatedly proven to perform slightly better than the plate-based assays ELISA and CLIA (chemiluminescent immuno-assay), and markedly better than lateral flow immuno-assays (LFIA).\n\nHere, we describe an optimized and very simple FACS assay based on staining a mix of two Jurkat cell lines, expressing either high levels of the S protein (Jurkat-S) or a fluorescent protein (Jurkat-R expressing m-Cherry, or Jurkat-G, expressing GFP, which serve as an internal negative control). We show that the Jurkat-S&R-flow test has a much broader dynamic range than a commercial ELISA test and performs at least as well in terms of sensitivity and specificity. Also, it is more sensitive and quantitative than the hemagglutination-based test HAT, which we described recently. The Jurkat-flow test requires only a few microliters of blood; thus, it can be used to quantify various Ig isotypes in capillary blood collected from a finger prick. It can be used also to evaluate serological responses in mice, hamsters, cats and dogs. Whilst the Jurkat-flow test is ill-suited and not intended for clinical use, it offers a very attractive solution for laboratories with access to tissue culture and flow cytometry who want to monitor serological responses in humans or in animals, and how these relate to susceptibility to infection, or re-infection, by the virus, and to protection against Covid-19.\n\nNoteThis manuscript has been refereed by Review Commons, and modified thanks to the comments and suggestions from two referees. Those comments, and our replies, are provided at the end of the manuscripts pdf, and can also be accessed by clicking on the box with a little green number found just above the \"Abstract \" tab in the medRXiv window.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Agnes Maurel Ribes", - "author_inst": "Centre Hospitalier Universitaire de Toulouse" - }, - { - "author_name": "Pierre Bessiere", - "author_inst": "Ecole nationale veterinaire de Toulouse" - }, - { - "author_name": "Jean-Charles Guery", - "author_inst": "Institut Toulousain des Maladies Infectieuses et Inflammatoires" - }, - { - "author_name": "Eloise Joly Featherstone", - "author_inst": "York University Hospital" - }, - { - "author_name": "Timothee Bruel", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Remy Robinot", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Olivier Schwartz", - "author_inst": "Institut Psateur" - }, - { - "author_name": "Romain Volmer", - "author_inst": "Ecole nationale veterinaire de Toulouse, France" - }, - { - "author_name": "Florence Abravanel", - "author_inst": "Institut Toulousain des Maladies Infectieuses et Inflammatoires" - }, - { - "author_name": "Jacques Izopet", - "author_inst": "Institut Toulousain des Maladies Infectieuses et Inflammatoires" - }, - { - "author_name": "Etienne Joly", - "author_inst": "IPBS, University of Toulouse, CNRS, Toulouse" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.07.21263200", "rel_title": "Distinguishing Incubation and Acute Disease Stages of Mild-to-Moderate COVID-19", @@ -592658,6 +594395,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.09.21263315", + "rel_title": "Professional practice for COVID-19 risk reduction among health care workers : a Cross-Sectional Study with Matched Case-Control Comparison", + "rel_date": "2021-09-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.09.21263315", + "rel_abs": "BackgroundHealth care workers (HCWs) are particularly exposed to COVID-19 and therefore it is paramount to study preventive measures in this population.\n\nAimTo investigate socio-demographic factors and professional practice associated with the risk of COVID-19 among HCWs in health establishments in Normandy, France\n\nMethodsA cross-sectional and 3 case-control studies were conducted in order to explore the possible risk factors that lead to SARS-CoV2 transmission within HCWs, based on an online questionnaire. The case-control studies focused on risk factors associated with care of COVID-19 patients, care of non COVID-19 patients and contacts between colleagues.\n\nFindingsAmong 2,058 respondents, respectively 1,363 (66.2%) and 695 (33.8%) in medical and medico-social establishments, 301 (14.6%) reported having been infected by SARS-CoV2. When caring for COVID-19 patients, HCWs who declared wearing respirators, either for all patient care (ORa 0.39; 95% CI: 0.29-0.51) or only when exposed to aerosol-generating procedures (ORa 0.56; 95% CI: 0.43-0.70), had a lower risk of infection compared with HCWs who declared wearing mainly surgical masks. During care of non COVID-19 patients, wearing mainly a respirator was associated with a higher risk of infection (ORa 1.84; 95% CI: 1.06-3.37). An increased risk was also found for HCWs who changed uniform in workplace changing rooms (ORa 1.93; 95% CI: 1.63-2.29).\n\nConclusionCorrect use of PPE adapted to the situation and risk level is essential in protecting HCWs against infection.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sarah WILSON", + "author_inst": "Service Hygiene Hospitaliere et de Controle des Infections, Centre Hospitalo-Universitaire, Caen F-14033, France" + }, + { + "author_name": "Audrey MOUET", + "author_inst": "Service Hygiene Hospitaliere et de Controle des Infections, Centre Hospitalo-Universitaire, Caen F-14033, France" + }, + { + "author_name": "Camille JEANNE-LEROYER", + "author_inst": "Service Hygiene Hospitaliere et de Controle des Infections, Centre Hospitalo-Universitaire, Caen F-14033, France" + }, + { + "author_name": "France BORGEY", + "author_inst": "Centre appui pour la Prevention des Infections Associees aux Soins, CPias Normandie, Centre Hospitalo-Universitaire, Caen F-14033, France" + }, + { + "author_name": "Emmanuelle ODINET-RAULIN", + "author_inst": "Agence Regionale de Sante Normandie, Caen F-14000, France" + }, + { + "author_name": "Xavier HUMBERT", + "author_inst": "Normandie Univ, UNICAEN, UFR de Sante, Departement de Medecine Generale, Caen F-14032" + }, + { + "author_name": "Simon LE HELLO", + "author_inst": "Service Hygiene Hospitaliere et de Controle des Infections, Centre Hospitalo-Universitaire, Caen F-14033, France, Groupe de Recherche sur Adaptation Microbienne" + }, + { + "author_name": "Pascal THIBON", + "author_inst": "Centre appui pour la Prevention des Infections Associees aux Soins, CPias Normandie, Centre Hospitalo-Universitaire, Caen F-14033, France" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.07.21263228", "rel_title": "Analysis of 2.1 million SARS-CoV-2 genomes identifies mutations associated with transmissibility", @@ -593801,45 +595585,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.07.21263222", - "rel_title": "Elevated plasma levels of CXCL16 in severe COVID-19 patients", - "rel_date": "2021-09-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.07.21263222", - "rel_abs": "Genome-wide association studies have recently identified 3p21.31, with lead variant pointing to the CXCR6 gene, as the strongest thus far reported susceptibility risk locus for severe manifestation of COVID-19. In order the determine its role, we measured plasma levels of Chemokine (C{square}X{square}C motif) ligand 16 (CXCL16) in the plasma of COVID-19 hospitalized patients. CXCL16 interacts with CXCR6 promoting chemotaxis or cell adhesion. The CXCR6/CXCL16 axis mediates homing of T cells to the lungs in disease and hyper-expression is associated with localised cellular injury. To characterize the CXCR6/CXCL16 axis in the pathogenesis of severe COVID-19, plasma concentrations of CXCL16 collected at baseline from 115 hospitalized COVID-19 patients participating in ODYSSEY COVID-19 clinical trial were assessed together with a set of controls. We report elevated levels of CXCL16 in a cohort of COVID-19 hospitalized patients. Specifically, we report significant elevation of CXCL16 plasma levels in association with severity of COVID-19 (as defined by WHO scale) (P-value<0.02). Our current study is the largest thus far study reporting CXCL16 levels in COVID-19 hospitalized patients (with whole-genome sequencing data available). The results further support the significant role of the CXCR6/CXCL16 axis in the immunopathogenesis of severe COVID-19 and warrants further studies to understand which patients would benefit most from targeted treatments.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "SANDRA P SMIESZEK", - "author_inst": "Vanda Pharmaceuticals Inc." - }, - { - "author_name": "Vasilios M Polymeropoulos", - "author_inst": "Vanda Pharmaceuticals Inc." - }, - { - "author_name": "Christos M Polymeropulos", - "author_inst": "Vanda Pharmaceuticals Inc." - }, - { - "author_name": "Bartloemiej P Przychodzen", - "author_inst": "Vanda Pharmaceuticals Inc." - }, - { - "author_name": "Gunther Birznieks", - "author_inst": "Vanda Pharmaceuticals Inc." - }, - { - "author_name": "Mihael M Polymeropoulos", - "author_inst": "Vanda Pharmaceuticals Inc." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.07.21263213", "rel_title": "Comprehensive Evaluation of COVID-19 Patient Short- and Long-term Outcomes: Disparities in Healthcare Utilization and Post-Hospitalization Outcomes", @@ -594144,6 +595889,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.06.21263149", + "rel_title": "Reduced magnitude and durability of humoral immune responses by COVID-19 mRNA vaccines among older adults", + "rel_date": "2021-09-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.06.21263149", + "rel_abs": "BackgroundmRNA vaccines reduce COVID-19 incidence and severity, but the durability of vaccine-induced immune responses, particularly among the elderly, remains incompletely characterized.\n\nMethodsAnti-spike RBD antibody titers, ACE2 competition and virus neutralizing activities were longitudinally assessed in 151 healthcare workers and older adults (overall aged 24-98 years) up to three months after vaccination.\n\nResultsOlder adults exhibited lower antibody responses after one and two vaccine doses for all measures. In multivariable analyses correcting for sociodemographic, chronic health and vaccine-related variables, age remained independently associated with all response outcomes. The number of chronic health conditions was additionally associated with lower binding antibody responses after two doses, and male sex with lower ACE2 competition activity after one dose. Responses waned universally at three months after the second dose, but binding antibodies, ACE2 competition and neutralizing activities remained significantly lower with age. Older adults also displayed reduced ability to block ACE2 binding by the Delta variant.\n\nConclusionsThe humoral immune response to COVID-19 mRNA vaccines is significantly weaker with age, and universally wanes over time. This will likely reduce antibody-mediated protection against SARS-CoV-2 and the Delta variant as the pandemic progresses. Older adults may benefit from additional immunizations as a priority.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Mark A. Brockman", + "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby BC, " + }, + { + "author_name": "Francis M. Mwimanzi", + "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada" + }, + { + "author_name": "Hope R. Lapointe", + "author_inst": "British Columbia Centre for Excellence in HIV/AIDS, Vancouver BC, Canada" + }, + { + "author_name": "Yurou Sang", + "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada" + }, + { + "author_name": "Olga Agafitei", + "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada" + }, + { + "author_name": "Peter Cheung", + "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver BC, Canada" + }, + { + "author_name": "Siobhan Ennis", + "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada" + }, + { + "author_name": "Kurtis Ng", + "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada" + }, + { + "author_name": "Simran Basra", + "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby BC, " + }, + { + "author_name": "Li Yi Lim", + "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada" + }, + { + "author_name": "Fatima Yaseen", + "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada" + }, + { + "author_name": "Landon Young", + "author_inst": "Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver BC, Canada" + }, + { + "author_name": "Gisele Umviligihozo", + "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada" + }, + { + "author_name": "F. Harrison Omondi", + "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver BC, Canada" + }, + { + "author_name": "Rebecca Kalikawe", + "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada" + }, + { + "author_name": "Laura Burns", + "author_inst": "Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver BC, Canada" + }, + { + "author_name": "Chanson J. Brumme", + "author_inst": "British Columbia Centre for Excellence in HIV/AIDS; Department of Medicine, University of British Columbia, Vancouver BC, Canada" + }, + { + "author_name": "Victor Leung", + "author_inst": "Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver BC, Canada; Department of Pathology and Laboratory Medicine, University of British" + }, + { + "author_name": "Julio Montaner", + "author_inst": "British Columbia Centre for Excellence in HIV/AIDS, Vancouver BC, Canada; Department of Medicine, University of British Columbia, Vancouver BC, Canada;" + }, + { + "author_name": "Daniel Holmes", + "author_inst": "Division of Medical Biochemistry, St. Paul's Hospital, Vancouver BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, V" + }, + { + "author_name": "Mari DeMarco", + "author_inst": "Division of Medical Biochemistry, St. Paul's Hospital, Vancouver BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, V" + }, + { + "author_name": "Janet Simons", + "author_inst": "Division of Medical Biochemistry, St. Paul's Hospital, Vancouver BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, V" + }, + { + "author_name": "Ralph Pantophlet", + "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby BC, " + }, + { + "author_name": "Masahiro Niikura", + "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada" + }, + { + "author_name": "Marc G. Romney", + "author_inst": "Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver BC, Canada; Department of Pathology and Laboratory Medicine, University of British" + }, + { + "author_name": "Zabrina L. Brumme", + "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver BC, Canada" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.06.21263031", "rel_title": "The efficiency of dynamic regional lockdown approach in controlling the COVID-19 epidemic. Insights from the agent-based epidemiological model for Poland", @@ -595975,173 +597839,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.03.21262551", - "rel_title": "A Learning Health System Randomized Trial of Monoclonal Antibodies for Covid-19", - "rel_date": "2021-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.03.21262551", - "rel_abs": "BackgroundNeutralizing monoclonal antibodies (mAb) targeting SARS-CoV-2 decrease hospitalization and death in patients with mild to moderate Covid-19. Yet, their clinical use is limited, and comparative effectiveness is unknown.\n\nMethodsWe present the first results of an ongoing, learning health system adaptive platform trial to expand mAb treatment to all eligible patients and evaluate the comparative effectiveness of available mAbs. The trial launched March 10, 2021. Results are reported as of June 25, 2021 due to the U.S. federal decision to pause distribution of bamlanivimab-etesevimab; patient follow-up concluded on July 23, 2021. Patients referred for mAb who met Emergency Use Authorization criteria were provided a random mAb allocation of bamlanivimab, bamlanivimab-etesevimab, or casirivimab-imdevimab with a therapeutic interchange policy. The primary outcome was hospital-free days (days alive and free of hospital) within 28 days, where patients who died were assigned -1 day. The primary analysis was a Bayesian cumulative logistic model of all patients treated at an infusion center or emergency department, adjusting for treatment location, age, sex, and time. Inferiority was defined as a 99% posterior probability of an odds ratio < 1. Equivalence was defined as a 95% posterior probability that the odds ratio is within a given bound.\n\nResultsPrior to trial launch, 3.1% (502) of 16,345 patients who were potentially eligible by an automated electronic health record (EHR) screen received mAb. During the trial period, 23.2% (1,201) of 5,173 EHR-screen eligible patients were treated, a 7.5-fold increase. After including additional referred patients from outside the health system, a total of 1,935 study patients received mAb therapy (128 bamlanivimab, 885 bamlanivimab-etesevimab, 922 casirivimab-imdevimab). Mean age ranged from 55 to 57 years, half were female (range, 53% to 54%), and 17% were Black (range, 12% to 19%). Median hospital-free days were 28 (IQR, 28 to 28) for each mAb group. Hospitalization varied between groups (bamlanivimab, 12.5%; bamlanivimab-etesevimab, 14.7%, casirivimab-imdevimab, 14.3%). Relative to casirivimab-imdevimab, the median adjusted odds ratios were 0.58 (95% credible interval (CI), 0.30 to 1.16) and 0.94 (95% CI, 0.72 to 1.24) for the bamlanivimab and bamlanivimab-etesevimab groups, respectively. These odds ratios yielded 91% and 94% probabilities of inferiority of bamlanivimab versus bamlanivimab-etesevimab and casirivimab-imdevimab respectively, and an 86% probability of equivalence between bamlanivimab-etesevimab and casirivimab-imdevimab, at the prespecified odds ratio bound of 0.25. Twenty-one infusion-related adverse events occurred in 0% (0/128), 1.4% (12/885), and 1.0% (9/922) of patients treated with bamlanivimab, bamlanivimab-etesevimab, and casirivimab-imdevimab, respectively.\n\nConclusionIn non-hospitalized patients with mild to moderate Covid-19, bamlanivimab, compared to bamlanivimab-etesevimab and casirivimab-imdevimab, resulted in 91% and 94% probabilities of inferiority with regards to odds of improvement in hospital-free days within 28 days. There was an 86% probability of equivalence between bamlanivimab-etesevimab and casirivimab-imdevimab at an odds ratio bound of 0.25. However, the trial was unblinded early due to federal distribution decisions, and no mAb met prespecified criteria for statistical inferiority or equivalence. (ClinicalTrials.gov, NCT04790786).", - "rel_num_authors": 38, - "rel_authors": [ - { - "author_name": "Erin K McCreary PharmD", - "author_inst": "Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "J Ryan Bariola MD", - "author_inst": "Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Tami Minnier MS", - "author_inst": "Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Richard J Wadas MD", - "author_inst": "Department of Emergency Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Judith A Shovel BSN", - "author_inst": "Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Debbie L Albin BS", - "author_inst": "Supply Chain Management/HC Pharmacy, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Oscar C Marroquin MD", - "author_inst": "Clinical Analytics, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Kevin E Kip PhD", - "author_inst": "Clinical Analytics, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Kevin Collins MBA", - "author_inst": "Clinical Analytics, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Mark Schmidhofer MD", - "author_inst": "Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Mary K Wisniewski MA", - "author_inst": "Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "David A Nace MD", - "author_inst": "Division of Geriatric Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA" - }, - { - "author_name": "Colleen Sullivan MHA", - "author_inst": "Clinical Research Investigation and Systems Modeling of Acute Illness (CRISMA) Center, Department of Critical Care Medicine, University of Pittsburgh School of " - }, - { - "author_name": "Meredith Axe BS", - "author_inst": "Department of Emergency Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Russell Meyer MBA", - "author_inst": "Department of Emergency Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Alexandra Weissman MD", - "author_inst": "Department of Emergency Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "William Garrard PhD", - "author_inst": "Clinical Analytics, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Octavia M Peck-Palmer PhD", - "author_inst": "Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Alan Wells MD", - "author_inst": "Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Robert D Bart MD", - "author_inst": "Health Services Division, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Anne Yang MD", - "author_inst": "Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Lindsay Berry PhD", - "author_inst": "Berry Consultants, Austin, TX, USA" - }, - { - "author_name": "Scott Berry PhD", - "author_inst": "Berry Consultants, Austin, TX, USA" - }, - { - "author_name": "Anna McGlothin PhD", - "author_inst": "Berry Consultants, Austin, TX, USA" - }, - { - "author_name": "Amy Crawford PhD", - "author_inst": "Berry Consultants, Austin, TX, USA" - }, - { - "author_name": "Tina Khadem PharmD", - "author_inst": "Health System Office of Healthcare Innovation, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Kelsey Linstrum MS", - "author_inst": "Clinical Research Investigation and Systems Modeling of Acute Illness (CRISMA) Center, Department of Critical Care Medicine, University of Pittsburgh School of " - }, - { - "author_name": "Stephanie K Montgomery MS", - "author_inst": "Clinical Research Investigation and Systems Modeling of Acute Illness (CRISMA) Center, Department of Critical Care Medicine, University of Pittsburgh School of " - }, - { - "author_name": "Daniel Ricketts MT", - "author_inst": "Clinical Research Investigation and Systems Modeling of Acute Illness (CRISMA) Center, Department of Critical Care Medicine, University of Pittsburgh School of " - }, - { - "author_name": "Jason N Kennedy MS", - "author_inst": "Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Caroline J Pidro BS", - "author_inst": "Clinical Research Investigation and Systems Modeling of Acute Illness (CRISMA) Center, Department of Critical Care Medicine, University of Pittsburgh School of " - }, - { - "author_name": "Ghady Haidar MD", - "author_inst": "Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Graham M Snyder MD", - "author_inst": "Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Bryan J McVerry MD", - "author_inst": "Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA" - }, - { - "author_name": "Christopher W Seymour MD", - "author_inst": "Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Derek C Angus MD", - "author_inst": "Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Paula L Kip PhD", - "author_inst": "Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Dave T Huang MD", - "author_inst": "Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2021.09.08.459502", "rel_title": "Digital Spatial Profiling of Collapsing Glomerulopathy", @@ -596330,6 +598027,49 @@ "type": "new results", "category": "cancer biology" }, + { + "rel_doi": "10.1101/2021.09.09.459641", + "rel_title": "Targeting Stem-loop 1 of the SARS-CoV-2 5'UTR to suppress viral translation and Nsp1 evasion", + "rel_date": "2021-09-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.09.459641", + "rel_abs": "SARS-CoV-2 is a highly pathogenic virus that evades anti-viral immunity by interfering with host protein synthesis, mRNA stability, and protein trafficking. The SARS-CoV-2 nonstructural protein 1 (Nsp1) uses its C-terminal domain to block the mRNA entry channel of the 40S ribosome to inhibit host protein synthesis. However, how SARS-CoV-2 circumvents Nsp1-mediated suppression for viral protein synthesis and if the mechanism can be targeted therapeutically remain unclear. Here we show that N- and C-terminal domains of Nsp1 coordinate to drive a tuned ratio of viral to host translation, likely to maintain a certain level of host fitness while maximizing replication. We reveal that the SL1 region of the SARS-CoV-2 5 UTR is necessary and sufficient to evade Nsp1-mediated translational suppression. Targeting SL1 with locked nucleic acid antisense oligonucleotides (ASOs) inhibits viral translation and makes SARS-CoV-2 5 UTR vulnerable to Nsp1 suppression, hindering viral replication in vitro at a nanomolar concentration. Thus, SL1 allows Nsp1 to switch infected cells from host to SARS-CoV-2 translation, presenting a therapeutic target against COVID-19 that is conserved among immune-evasive variants. This unique strategy of unleashing a virus own virulence mechanism against itself could force a critical trade off between drug resistance and pathogenicity.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Valerie Leger", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Tian-Min Fu", + "author_inst": "Ohio State University" + }, + { + "author_name": "Judy Lieberman", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Lee Gehrke", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Ming Shi", + "author_inst": "Harbin Institute of Technology" + }, + { + "author_name": "Longfei Wang", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Hao Wu", + "author_inst": "Harvard Medical School" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.09.09.459577", "rel_title": "A virus-encoded microRNA contributes to evade innate immune response during SARS-CoV-2 infection", @@ -598177,77 +599917,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.03.21262874", - "rel_title": "Detection of SARS CoV-2 contamination in the Operating Room and Birthing Room Setting: Risks to attending health care workers", - "rel_date": "2021-09-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.03.21262874", - "rel_abs": "BackgroundThe exposure risks to front-line health care workers who are in close proximity for prolonged periods of time, caring for COVID-19 patients undergoing surgery or obstetrical delivery is unclear. Understanding of sample types that may harbour virus is important for evaluating risk.\n\nObjectivesTo determine if SARS-CoV-2 viral RNA from patients with COVID-19 undergoing surgery or obstetrical care is present in: 1) the peritoneal cavity of males and females 2) the female reproductive tract, 3) the environment of the surgery or delivery suite (surgical instruments, equipment used, air or floors) and 4) inside the masks of the attending health care workers.\n\nMethodsThe presence of SARS-CoV-2 viral RNA in patient, environmental and air samples was identified by real time reverse transcriptase polymerase chain reaction (RT-PCR). Air samples were collected using both active and passive sampling techniques.\n\nResultsIn this multi-centre observational case series, 32 patients with COVID-19 underwent urgent surgery or obstetrical delivery and 332 patient and environmental samples were collected and analyzed to determine if SARS-CoV-2 RNA was present. SARS-CoV-2 RNA was detected in: 4/24(16.7%) patient samples, 5/60(8.3%) floor, 1/54(1.9%) air, 10/23(43.5%) surgical instruments/equipment, 0/24 cautery filters and 0/143 inner surface of mask samples.\n\nConclusionsWhile there is evidence of SARS-CoV-2 RNA in the surgical and obstetrical operative environment (6% of samples taken), the finding of no detectable virus inside the masks worn by the medical teams would suggest a low risk of infection for our health care workers using appropriate personal protective equipment (PPE).", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Patricia Lee", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Robert Kozak", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Nasrin Alavi", - "author_inst": "Sunnybrook Research Institute" - }, - { - "author_name": "Hamza Mbareche", - "author_inst": "Sunnybrook Research Institute" - }, - { - "author_name": "Rose Kung", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Kellie Murphy", - "author_inst": "Sinai Health System" - }, - { - "author_name": "Darian Perruzza", - "author_inst": "Sunnybrook Research Institute" - }, - { - "author_name": "Stephanie Jarvi", - "author_inst": "Sunnybrook Research Institute" - }, - { - "author_name": "Elsa Salvant", - "author_inst": "Sunnybrook Research Institute" - }, - { - "author_name": "Noor Niyar Ladhani", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Albert Yee", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Louise-Helene Gagnon", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Richard Jenkinson", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Grace Y. Liu", - "author_inst": "Sunnybrook Health Sciences Centre" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.09.02.21262599", "rel_title": "Severe COVID-19 is associated with sustained biochemical disturbances and prolonged symptomatology; A retrospective single-centre cohort study", @@ -598388,6 +600057,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.03.21263103", + "rel_title": "The prevalence of adaptive immunity to COVID-19 and reinfection after recovery, a comprehensive systematic review and meta-analysis of 12 011 447 individuals", + "rel_date": "2021-09-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.03.21263103", + "rel_abs": "ObjectivesThis study aims to estimate the prevalence and longevity of detectable SARS-CoV-2 antibodies as well as memory cells T and B after recovery. In addition, the prevalence of COVID-19 reinfection, and the preventive efficacy of previous infection with SARS-CoV-2 were investigated.\n\nMethods and analysesA synthesis of existing research was conducted. The Cochrane Library for COVID-19 resources, the China Academic Journals Full Text Database, PubMed, and Scopus as well as preprint servers were searched for studies conducted between 1 January 2020 to 1 April 2021. We included studies with the relevant outcomes of interest. All included studies were assessed for methodological quality and pooled estimates of relevant outcomes were obtained in a meta-analysis using a bias adjusted synthesis method. Proportions were synthesized with the Freeman-Tukey double arcsine transformation and binary outcomes using the odds ratio (OR). Heterogeneity between included studies was assessed using the I2 and Cochrans Q statistics and publication bias was assessed using Doi plots.\n\nResultsFifty-four studies, from 18 countries, with around 12 000 000 individuals, followed up to 8 months after recovery were included. At 6-8 months after recovery, the prevalence of SARS-CoV-2 specific immunological memory remained high; IgG - 90.4% (95%CI 72.2-99.9, I2=89.0%, 5 studies), CD4+ - 91.7% (95%CI 78.2 - 97.1, one study), and memory B cells 80.6% (95%CI 65.0-90.2, one study) and the pooled prevalence of reinfection was 0.2% (95%CI 0.0 - 0.7, I2 = 98.8, 9 studies). Individuals previously infected with SARS-CoV-2 had an 81% reduction in odds of a reinfection (OR 0.19, 95% CI 0.1 - 0.3, I2 = 90.5%, 5 studies).\n\nConclusionAround 90% of people previously infected with SARS-CoV-2 had evidence of immunological memory to SARS-CoV-2, which was sustained for at least 6-8 months after recovery, and had a low risk of reinfection.\n\nRegistrationPROSPERO: CRD42020201234\n\nWhat is already known on this topicIndividuals who recover from COVID-19 may have immunity against future infection but the proportion who develop immunity is uncertain. Further, there is uncertainty about the proportion of individuals who get reinfected with COVID-19.\n\nWhat this study addsUsing data from 54 studies with follow up time up to 8 months after recovery, during the period February 2020-February 2021, we found that, post-COVID-19, up to 90% of individuals had antibodies and memory T and B cells against SARS-CoV-2. We also found a pooled prevalence of reinfection of 0.2%, and that infection conferred an 81% decrease in odds of reinfection with SARS-CoV-2, compared to unimmunized individuals without previous COVID-19.\n\nThis review of 12 million individuals presents evidence that most individuals who recover from COVID-19 develop immunological memory to SARS-CoV-2, which was still detectable for up to 8 months. Further, reinfection after recovery from COVID-19 was rare during the first 8 months after recovery, with a prevalence below 1%, while prior infection confers protection with an odds ratio of 0.19 and a preventive efficacy of 80% at a baseline prevalence of 5% for COVID-19 in a community.\n\nImplications of all the available evidenceIndividuals with a history of COVID-19 infection have immunity against the disease for up to 8 months, although this period could be longer. These individuals could be prioritized last for COVID-19 vaccinations or considered for single dose vaccinations.\n\nStrengthsThis comprehensive review addresses key questions on prevalent immunological memory and risk of reinfection in individuals with prior confirmed COVID-19 using robust systematic review methods.\n\nLimitationsSome of the included studies which examined prevalent immunological memory were small studies which were affected by loss to follow up. The review did not examine evidence for immunity against the new divergent variants, which may be more likely to have immune evasion behaviour and may present a higher risk of reinfection. Lastly, the review did not examine the effect of the severity of COVID-19 on both immunological memory and the risk of reinfection.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Tawanda Chivese", + "author_inst": "Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar" + }, + { + "author_name": "Joshua Matizanadzo", + "author_inst": "Department of Public Health and Primary Care, Brighton and Sussex Medical School, United Kingdom" + }, + { + "author_name": "Omran Musa", + "author_inst": "Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar" + }, + { + "author_name": "George Hindy", + "author_inst": "Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar" + }, + { + "author_name": "Luis Furuya-Kanamori", + "author_inst": "UQ Centre for Clinical Research, The University of Queensland, Herston, Australia" + }, + { + "author_name": "Nazmul Islam", + "author_inst": "Department of Public Health, QU Health, Qatar University, Doha, Qatar" + }, + { + "author_name": "Rafal Al-Shebly", + "author_inst": "Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar" + }, + { + "author_name": "Rana Shalaby", + "author_inst": "Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar" + }, + { + "author_name": "Mohammad Habibullah", + "author_inst": "Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar" + }, + { + "author_name": "Talal Al-Marwani", + "author_inst": "Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar" + }, + { + "author_name": "Rizeq F Hourani", + "author_inst": "Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar" + }, + { + "author_name": "Ahmed D Nawaz", + "author_inst": "Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar" + }, + { + "author_name": "Mohammad Haider", + "author_inst": "Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar" + }, + { + "author_name": "Mohamed M Emara", + "author_inst": "Microbiology section, Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha, Qatar" + }, + { + "author_name": "Farhan Cyprian", + "author_inst": "Immunology section, Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar" + }, + { + "author_name": "Suhail A. R. Doi", + "author_inst": "Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.02.21263012", "rel_title": "Infectiousness of places: The impact of human settlement and activity space in the transmission of COVID-19", @@ -599763,69 +601511,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.01.21262540", - "rel_title": "Analysis of the Dynamics, Outcome, and Prerequisites of the first German SARS-CoV-2 Superspreading Event", - "rel_date": "2021-09-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.01.21262540", - "rel_abs": "BackgroundThe beginning of the COVID-19 pandemic was shaped by superspreading events including large-scale outbreaks. In Germany the first SARS-CoV-2 outbreak was a superspreading event in a rural area during indoor carnival festivities in February 2020.\n\nMethods51 days after the event all known participants were asked to give blood samples, pharyngeal swabs and answer a self-administered questionnaire. Metric room coordinates for all tables, seats, and ventilation-points were assessed.\n\nFindingsWe analyzed infection rates among all 411 participants, and the risk of infection in relation to various factors including age, alcohol consumption, and ventilation system. Overall, 46% (n=186/404) of the participants had been infected. We demonstrate that the spatial distribution of infected participants was associated with proximity to the ventilation system (represented as inverse distance, with Odds Ratio OR 1.39, 95% KI [0.86; 2.25]). Interestingly, the risk of infection was highly associated with age, whereby children (OR: 0.33 [0.267; 0.414]) and young adults (age 18-25) had a lower risk of infection than older participants resulting in an average infection risk increase of 28% per 10 years age difference. Behavioral differences also impacted the risk of infection including time spent outside (OR: 0.55 [0.33; 0.91]) or smoking (OR: 0.32 [0.124; 0.81]).\n\nInterpretationOur findings underline the importance of proper indoor ventilation for events in the future. The lower susceptibility for children and young adults indicates their limited involvement in superspreading events.\n\nFundingThe government of North Rhine-Westphalia (Germany) supported the study with 65,000 Euro.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThe scientific literature was searched for the term \"superspreading event AND Covid-19 OR Sars Cov 2\" and identified published papers from China, South Korea, Europe, and North America. Most researchers analyzed superspreading events within a health care setting e.g. in hospitals or nursing homes, or described the general impact of superspreading events on the global pandemic. Only a few metanalyses of transmission clusters analyzed party occasions (e.g. a nightclub in Berlin, Germany) as superspreading events. These reports describe less than 100 infections and are very limited due to missing data or reporting biases. Therefore, the ability to draw scientific conclusions is also limited. Additionally, to our knowledge, there are no studies, which investigated individual behavior, the location, and role of children during a superspreading event. The research for the study started April 2020 and was concluded in June 2021.\n\nAdded value of this studyOur report analyzes the first COVID-19 superspreading event in Germany in detail, which was not only a unique setting but also included children and adults in the same room. We demonstrate that nearly half of the participants were infected with SARS-CoV-2 and that the proximity of the seating to the ventilation system was an important risk factor for infection. The data showed that low physical distance including singing and duration of attendance at this event increased the risk of infection, while regular smoking and spending the break of the event outside lowered the risk of infection. This underlines the benefit of airing to lower the amount of both droplets and aerosols. Furthermore, we found lower infection in children than adults despite being in the same room suggesting differences in infectability in children. Indeed, we observed that an additional 10 years of age is on average associated with 28% increased risk of infection.\n\nImplications of all the available evidenceTaken together, the results demonstrate the importance of the ventilation system during superspreading events. In particular children and young adults had a lower risk of infection during the event indicating that they have a limited role during this pandemic. Overall, our data demonstrate in detail age-dependent infectability as well as highlights to understand transmission dynamics in order to improve comprehensive public health preparedness measures.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Lukas Wessendorf", - "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany, and German Center for Infection Research (DZIF), partner site Bonn-Cologne" - }, - { - "author_name": "Enrico Richter", - "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany, and German Center for Infection Research (DZIF), partner site Bonn-Cologne" - }, - { - "author_name": "Bianca Schulte", - "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany, and German Center for Infection Research (DZIF), partner site Bonn-Cologne" - }, - { - "author_name": "Ricarda Maria Schmithausen", - "author_inst": "Institute of Hygiene and Public Health, University Hospital, University of Bonn, Germany" - }, - { - "author_name": "Martin Exner", - "author_inst": "Institute of Hygiene and Public Health, University Hospital, University of Bonn, Germany" - }, - { - "author_name": "Nils Lehmann", - "author_inst": "Institute of Medical Informatics, Biometry und Epidemiology (IMIBE), University Hospital Essen, Germany" - }, - { - "author_name": "Martin Coenen", - "author_inst": "Clinical Study Core Unit, Study Center Bonn (SZB), Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Germany" - }, - { - "author_name": "Christine Fuhrmann", - "author_inst": "Clinical Study Core Unit, Study Center Bonn (SZB), Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Germany" - }, - { - "author_name": "Angelika Kellings", - "author_inst": "Clinical Study Core Unit, Study Center Bonn (SZB), Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Germany" - }, - { - "author_name": "Anika Huesing", - "author_inst": "Institute of Medical Informatics, Biometry und Epidemiology (IMIBE), University Hospital Essen, Germany" - }, - { - "author_name": "Karl-Heinz Joeckel", - "author_inst": "Institute of Medical Informatics, Biometry und Epidemiology (IMIBE), University Hospital Essen, Germany" - }, - { - "author_name": "Hendrik Streeck", - "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany, and German Center for Infection Research (DZIF), partner site Bonn-Cologne" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.01.21262990", "rel_title": "Impact and effectiveness of social distancing for COVID-19 mitigation -- A transnational and transregional study", @@ -599950,6 +601635,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.09.01.21262387", + "rel_title": "Simultaneous detection of SARS-CoV-2 RNA and host antibodies enabled by a multiplexed electrochemical sensor platform", + "rel_date": "2021-09-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.01.21262387", + "rel_abs": "The current COVID-19 pandemic highlights the continued need for rapid, accurate, and cost-effective point-of-care (POC) diagnostics that can accurately assess an individuals infection and immunity status for SARS-CoV-2. As the virus continues to spread and vaccines become more widely available, detecting viral RNA and serological biomarkers can provide critical insights into the status of infectious, previously infectious, and vaccinated individuals over time. Here, we describe an integrated, low-cost, 3D printed, lab-on-a-chip device that extracts, concentrates, and amplifies viral RNA from unprocessed patient saliva and simultaneously detects RNA and multiple host anti-SARS-CoV-2 antibodies via multiplexed electrochemical (EC) outputs in two hours. The EC sensor platform enables single-molecule CRISPR/Cas-based molecular detection of SARS-CoV-2 viral RNA as well as serological detection of antibodies against the three immunodominant SARS-CoV-2 viral antigens. This study demonstrates that microfluidic EC sensors can enable multiplexed POC diagnostics that perform on par with traditional laboratory-based techniques, enabling cheaper and more widespread monitoring of infection and immunity over time.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Devora Najjar", + "author_inst": "MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA" + }, + { + "author_name": "Joshua Rainbow", + "author_inst": "Centre for Biosensors, Bioelectronics and Biodevices (C3Bio) and Department of Electronic and Electrical Engineering, University of Bath, Bath BA2 7AY, UK" + }, + { + "author_name": "Sanjay Sarma Timilsina", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA" + }, + { + "author_name": "Pawan Jolly", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA" + }, + { + "author_name": "Helena de Puig", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA" + }, + { + "author_name": "Mohamed Yafia", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA" + }, + { + "author_name": "Nolan Durr", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA" + }, + { + "author_name": "Hani Sallum", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA" + }, + { + "author_name": "Galit Alter", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Jonathan Z. Li", + "author_inst": "Brigham and Women's Hospital, Harvard Medical School" + }, + { + "author_name": "Xu G. Yu", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA" + }, + { + "author_name": "David R. Walt", + "author_inst": "Brigham and Women's Hospital/Harvard Medical School" + }, + { + "author_name": "Joseph A. Paradiso", + "author_inst": "MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA" + }, + { + "author_name": "Pedro Estrela", + "author_inst": "Centre for Biosensors, Bioelectronics and Biodevices (C3Bio) and Department of Electronic and Electrical Engineering, University of Bath, Bath BA2 7AY, UK" + }, + { + "author_name": "James J. Collins", + "author_inst": "Institute for Medical Engineering and Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA" + }, + { + "author_name": "Donald E. Ingber", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.02.21261735", "rel_title": "A third dose of inactivated vaccine augments the potency, breadth, and duration of anamnestic responses against SARS-CoV-2", @@ -601293,89 +603057,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.08.31.21262891", - "rel_title": "Strengthening public COVID-19 response with private facilities in Kisumu, Kenya", - "rel_date": "2021-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.31.21262891", - "rel_abs": "INTRODUCTIONIn Africa almost half of healthcare services are delivered through private sector providers. These are often underused in national public health responses. In line with our previous HIV experience and to support and accelerate the public sectors COVID-19 response, we initiated a public-private project (PPP) in Kisumu County, Kenya. In this manuscript we demonstrate this PPPs performance, using COVID-19 testing as an aggregator and with semi-real time digital monitoring tools for rapid scaling of COVID-19 response.\n\nMETHODSCOVID-19 diagnostic testing formed the basis for a PPP between KEMRI, Department of Health Kisumu County, PharmAccess Foundation, and local faith-based and private healthcare facilities: COVID-Dx. COVID-Dx was implemented from June 01, 2020, to March 31, 2021 in Kisumu County, Kenya. Trained laboratory technologists in participating healthcare facilities collected nasopharyngeal and oropharyngeal samples from patients meeting the Kenyan MoH COVID-19 case definition. Samples were rapidly transported by motorbike and tested using RT-PCR at the central reference laboratory in KEMRI. Healthcare workers in participating facilities collected patient clinical data using a digitized MoH COVID-19 Case Identification Form. We shared aggregated results from these data via (semi-) live dashboards with all relevant stakeholders through their mobile phones. Statistical analyses were performed using Stata 16 to inform project processes.\n\nRESULTSNine private facilities participated in the project. A detailed patient trajectory was developed from case identification to result reporting, all steps supported by a semi-real time digital dashboard. A total of 4,324 PCR tests for SARS-CoV-2 (16%) were added to the public response, identifying 425 positives. Geo-mapped and time-tagged information on incident cases was depicted on Google maps dashboards and fed back to policymakers for informed rapid decision making. Preferential COVID-19 testing was performed on health workers at risk, with 1,009 tested (43% of all County health workforce).\n\nCONCLUSIONWe demonstrate feasibility of rapidly increasing the public health sector response to a COVID-19 epidemic outbreak in an African setting. Our PPP intervention in Kisumu, Kenya was based on a joint testing strategy and demonstrated that semi-real time digitalization of patient trajectories in the healthcare system can gain significant efficiencies, linking public and private healthcare efforts, increasing transparency, support better quality health services and informing policy makers to target interventions. This PPP has since scaled to 33 facilities in Kisumu and subsequently to 84 sites in 14 western Kenyan Counties.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Shannen van Duijn", - "author_inst": "PharmAccess Foundation Amsterdam Office, the Netherlands" - }, - { - "author_name": "Hellen C. Barsosio", - "author_inst": "Kenya Medical Research Institute (KEMRI), Center for Global Health Research (CGHR), Kisumu, Kenya" - }, - { - "author_name": "Mevis Omollo", - "author_inst": "Kenya Medical Research Institute (KEMRI), Center for Global Health Research (CGHR), Kisumu, Kenya" - }, - { - "author_name": "Emmanuel Milimo", - "author_inst": "PharmAccess Foundation Kenya Office, Kisumu, Kenya" - }, - { - "author_name": "Isdorah A. Odero", - "author_inst": "Kenya Medical Research Institute (KEMRI), Center for Global Health Research (CGHR), Kisumu, Kenya" - }, - { - "author_name": "Robert Aroka", - "author_inst": "PharmAccess Foundation Kenya Office, Kisumu, Kenya" - }, - { - "author_name": "Teresa de Sanctis", - "author_inst": "PharmAccess Foundation Amsterdam Office, the Netherlands" - }, - { - "author_name": "Alloys K Oloo", - "author_inst": "Kenya Medical Research Institute (KEMRI), Center for Global Health Research (CGHR), Kisumu, Kenya" - }, - { - "author_name": "Micah J. June", - "author_inst": "Kenya Medical Research Institute (KEMRI), Center for Global Health Research (CGHR), Kisumu, Kenya" - }, - { - "author_name": "Nathalie Houben", - "author_inst": "PharmAccess Foundation Kenya Office, Kisumu, Kenya" - }, - { - "author_name": "Charlotte Wilming", - "author_inst": "PharmAccess Foundation Amsterdam Office, the Netherlands" - }, - { - "author_name": "Kephas Otieno", - "author_inst": "Kenya Medical Research Institute (KEMRI), Center for Global Health Research (CGHR), Kisumu, Kenya" - }, - { - "author_name": "Simon Kariuki", - "author_inst": "Kenya Medical Research Institute (KEMRI), Center for Global Health Research (CGHR), Kisumu, Kenya" - }, - { - "author_name": "Simon Onsongo", - "author_inst": "Aga Khan Hospital, Kisumu" - }, - { - "author_name": "Albert Odhiambo", - "author_inst": "County Government of Kisumu, Kisumu, Kenya" - }, - { - "author_name": "Gregory Ganda", - "author_inst": "Department of Health Kisumu" - }, - { - "author_name": "Tobias Rinke de Wit", - "author_inst": "PharmAccess Foundation Amsterdam Office, the Netherlands" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.03.458829", "rel_title": "Characterization of SARS-CoV-2 variants B.1.617.1 (Kappa), B.1.617.2 (Delta) and B.1.618 on cell entry, host range, and sensitivity to convalescent plasma and ACE2 decoy receptor", @@ -601728,6 +603409,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.01.21262913", + "rel_title": "Sars-Cov-2 antibody titer 3 months post-vaccination is affected by age, gender, smoking and vitamin D.", + "rel_date": "2021-09-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.01.21262913", + "rel_abs": "ContextVaccination against Sars-Cov-2 is in full swing during COVID-19 pandemic. One of the efficient methods to evaluate response to vaccination is the assessment of humoral immunity by measuring Sars-Cov-2 antibody titer. Identification of factors that affect the humoral response is important so as to ameliorate the responses to vaccination or identify vulnerable groups that may need vaccination boosters.\n\nObjectiveWe investigated the effect of anthropometric parameters (age, BMI), smoking, diabetes, statin use hypertension and levels of 25(OH)D and DHEAS to the Sars-Cov-2 antibody titer.\n\nMethodsIn this longitudinal observational cohort study 712 subjects were tested for Sars-Cov-2 antibodies 3 months after the second dose of BNT162b2 vaccine. Multiple linear regression analysis was performed to identify which factors are associated with the antibody titer.\n\nResultsWe identified age to be negatively associated with antibody titer (p=0.0073) and male sex (p=0.0008). However, interaction of age and gender was significant (p<0.0001) highlighting the finding that only after the age of 40 years men had lower antibody levels than women. DHEAS, an aging marker, was not associated with the antibody titer. Smoking was also associated with low antibody titer (p=0.0008) while overweight or obese subjects did not have different antibody response compared to normal weight individuals. Although diabetic and hypertensive subjects trended towards lower antibody titer, this association was not statistically significant. Replete vitamin D levels were associated with higher antibody titers (p=0.00422).\n\nConclusionsAge, male sex and smoking negatively affects antibody titer while 25(OH)D is associated with increased Sars-Cov-2 antibody titers.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Anastasia Parthymou", + "author_inst": "University of Patras" + }, + { + "author_name": "Evagelia E Habeos", + "author_inst": "University of Patras" + }, + { + "author_name": "George I Habeos", + "author_inst": "University of Patras" + }, + { + "author_name": "Apostolos Deligakis", + "author_inst": "\"St Andrews\" State General Hospital, Patras" + }, + { + "author_name": "Ektoras Livieratos", + "author_inst": "University of Patras" + }, + { + "author_name": "Markos Marangos", + "author_inst": "University of Patras" + }, + { + "author_name": "Dionysios V Chartoumpekis", + "author_inst": "University of Patras" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.01.21262955", "rel_title": "Immune response elicited from heterologous SARS-CoV-2 vaccination: Sinovac (CoronaVac) followed by AstraZeneca (Vaxzevria)", @@ -603247,269 +604971,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.09.02.21262965", - "rel_title": "Whole genome sequencing identifies multiple loci for critical illness caused by COVID-19", - "rel_date": "2021-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.02.21262965", - "rel_abs": "Critical illness in COVID-19 is caused by inflammatory lung injury, mediated by the host immune system. We and others have shown that host genetic variation influences the development of illness requiring critical care1 or hospitalisation2;3;4 following SARS-Co-V2 infection. The GenOMICC (Genetics of Mortality in Critical Care) study recruits critically-ill cases and compares their genomes with population controls in order to find underlying disease mechanisms.\n\nHere, we use whole genome sequencing and statistical fine mapping in 7,491 critically-ill cases compared with 48,400 population controls to discover and replicate 22 independent variants that significantly predispose to life-threatening COVID-19. We identify 15 new independent associations with critical COVID-19, including variants within genes involved in interferon signalling (IL10RB, PLSCR1), leucocyte differentiation (BCL11A), and blood type antigen secretor status (FUT2). Using transcriptome-wide association and colocalisation to infer the effect of gene expression on disease severity, we find evidence implicating expression of multiple genes, including reduced expression of a membrane flippase (ATP11A), and increased mucin expression (MUC1), in critical disease.\n\nWe show that comparison between critically-ill cases and population controls is highly efficient for genetic association analysis and enables detection of therapeutically-relevant mechanisms of disease. Therapeutic predictions arising from these findings require testing in clinical trials.", - "rel_num_authors": 62, - "rel_authors": [ - { - "author_name": "Athanasios Kousathanas", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Erola Pairo-Castineira", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Konrad Rawlik", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Alex Stuckey", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Christopher A Odhams", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Susan Walker", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Clark D Russell", - "author_inst": "Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK" - }, - { - "author_name": "Tomas Malinauskas", - "author_inst": "Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK" - }, - { - "author_name": "Jonathan Millar", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Katherine S Elliott", - "author_inst": "Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK" - }, - { - "author_name": "Fiona Griffiths", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Wilna Oosthuyzen", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Kirstie Morrice", - "author_inst": "Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK." - }, - { - "author_name": "Sean Keating", - "author_inst": "Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK." - }, - { - "author_name": "Bo Wang", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Daniel Rhodes", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Lucija Klaric", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK." - }, - { - "author_name": "Marie Zechner", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Nick Parkinson", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Andrew D. Bretherick", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK." - }, - { - "author_name": "Afshan Siddiq", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Peter Goddard", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Sally Donovan", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "David Maslove", - "author_inst": "Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, ON, Canada." - }, - { - "author_name": "Alistair Nichol", - "author_inst": "Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland." - }, - { - "author_name": "Malcolm G Semple", - "author_inst": "NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, L" - }, - { - "author_name": "Tala Zainy", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Fiona Maleady-Crowe", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Linda Todd", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Shahla Salehi", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Julian Knight", - "author_inst": "Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK" - }, - { - "author_name": "Greg Elgar", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Georgia Chan", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Prabhu Arumugam", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Tom A Fowler", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Augusto Rendon", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Manu Shankar-Hari", - "author_inst": "Department of Intensive Care Medicine, Guy's and St. Thomas NHS Foundation Trust, London, UK." - }, - { - "author_name": "Charlotte Summers", - "author_inst": "Department of Medicine, University of Cambridge, Cambridge, UK." - }, - { - "author_name": "Charles Hinds", - "author_inst": "William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK." - }, - { - "author_name": "Peter Horby", - "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK." - }, - { - "author_name": "Danny McAuley", - "author_inst": "Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK" - }, - { - "author_name": "Hugh Montgomery", - "author_inst": "UCL Centre for Human Health and Performance, London, W1T 7HA, UK." - }, - { - "author_name": "Peter J.M. Openshaw", - "author_inst": "National Heart and Lung Institute, Imperial College London, London, UK" - }, - { - "author_name": "Yang Wu", - "author_inst": "Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia" - }, - { - "author_name": "Jian Yang", - "author_inst": "Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China" - }, - { - "author_name": "Paul Elliott", - "author_inst": "Imperial College, London" - }, - { - "author_name": "Timothy Walsh", - "author_inst": "Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK." - }, - { - "author_name": "- GenoMICC Investigators", - "author_inst": "" - }, - { - "author_name": "- 23andMe Investigators", - "author_inst": "" - }, - { - "author_name": "- Covid-19 Human Genetics Initiative", - "author_inst": "" - }, - { - "author_name": "Angie Fawkes", - "author_inst": "Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK." - }, - { - "author_name": "Lee Murphy", - "author_inst": "Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK." - }, - { - "author_name": "Kathy Rowan", - "author_inst": "Intensive Care National Audit & Research Centre, London, UK." - }, - { - "author_name": "Chris P Ponting", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK." - }, - { - "author_name": "Veronique Vitart", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK." - }, - { - "author_name": "James F Wilson", - "author_inst": "Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK." - }, - { - "author_name": "Richard H Scott", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Sara Clohisey", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Loukas Moutsianas", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Andy Law", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Mark J Caulfield", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "J. Kenneth Baillie", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2021.08.29.21262798", "rel_title": "Viral loads of Delta-variant SARS-CoV2 breakthrough infections following vaccination and booster with the BNT162b2 vaccine", @@ -603682,6 +605143,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.31.21262909", + "rel_title": "PERCOVID: A Model to Describe COVID Percolation on a Network of Social Relationships", + "rel_date": "2021-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.31.21262909", + "rel_abs": "We develop a site-bond percolation model, called PERCOVID, in order to describe the time evolution of COVID epidemics and more generally all epidemics propagating through respiratory tract in human populations. This model is based on a network of social relationships representing interconnected households experiencing governmental non-pharmaceutical interventions. The model successfully accounts for the COVID-19 epidemiological data in metropolitan France from December 2019 up to July 2021. Our model shows the impact of lockdowns and curfews, as well as the influence of the progressive vaccination campaign in order to keep COVID-19 pandemic under the percolation threshold. We illustrate the role played by the social interactions by comparing a typical scenario for the epidemic evolution in France, Germany and Italy during the first wave from January to May 2020. We investigate finally the role played by the and {delta} variants in the evolution of the epidemic in France till autumn 2021, paying particular attention to the essential role played by the vaccination. Our model predicts that the rise of the epidemic observed in July 2021 will not result in a fourth major epidemic wave in France.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Jean-Francois Mathiot", + "author_inst": "Laboratoire de Physique de Clermont" + }, + { + "author_name": "Laurent Gerbaud", + "author_inst": "Clermont Auvergne University, CHU Clermont-Ferrand, CNRS, SIGMA Clermont, Institut Pascal," + }, + { + "author_name": "Vincent J Breton", + "author_inst": "CNRS-IN2P3" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.31.21262915", "rel_title": "COVID-19 scenarios for comparing the effectiveness of age-specific vaccination regimes, exemplified for the city of Aschaffenburg (Germany)", @@ -605369,37 +606857,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.29.21262799", - "rel_title": "The emergence of SARS-CoV-2 variants of concern is driven by acceleration of the evolutionary rate", - "rel_date": "2021-08-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.29.21262799", - "rel_abs": "The ongoing SARS-CoV-2 pandemic has seen an unprecedented amount of rapidly generated genome data. These data have revealed the emergence of lineages with mutations associated to transmissibility and antigenicity, known as variants of concern (VOCs). A striking aspect of VOCs is that many of them involve an unusually large number of defining mutations. Current phylogenetic estimates of the evolutionary rate of SARS-CoV-2 suggest that its genome accrues around 2 mutations per month. However, VOCs can have around 15 defining mutations and it is hypothesised that they emerged over the course of a few months, implying that they must have evolved faster for a period of time. We analysed genome sequence data from the GISAID database to assess whether the emergence of VOCs can be attributed to changes in the evolutionary rate of the virus and whether this pattern can be detected at a phylogenetic level using genome data. We fit a range of molecular clock models and assessed their statistical fit. Our analyses indicate that the emergence of VOCs is driven by an episodic increase in the evolutionary rate of around 4-fold the background phylogenetic rate estimate that may have lasted several weeks or months. These results underscore the importance of monitoring the molecular evolution of the virus as a means of understanding the circumstances under which VOCs may emerge.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "John H Tay", - "author_inst": "Peter Doherty Institute, University of Melbourne" - }, - { - "author_name": "Ashleigh F Porter", - "author_inst": "Peter Doherty Institute, University of Melbourne" - }, - { - "author_name": "Wytamma Wirth", - "author_inst": "Peter Doherty Institute University of Melbourne" - }, - { - "author_name": "Sebastian Duchene", - "author_inst": "University of Melbourne" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.30.21262821", "rel_title": "The impact of pausing the Oxford-AstraZeneca COVID-19 vaccine on uptake in Europe: a difference-in-differences analysis", @@ -605668,6 +607125,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.29.21262512", + "rel_title": "Correlation between times to SARS-CoV-2 symptom onset and secondary transmission undermines epidemic control efforts", + "rel_date": "2021-08-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.29.21262512", + "rel_abs": "Severe acute respiratory coronavirus 2 (SARS-CoV-2) infections have been associated with substantial presymptomatic transmission, which occurs when the generation interval--the time between infection of an individual with a pathogen and transmission of the pathogen to another individual--is shorter than the incubation period--the time between infection and symptom onset. We collected a dataset of 257 SARS-CoV-2 transmission pairs in Japan and jointly estimated the mean generation interval (3.7-5.1 days) and mean incubation period (4.4-5.7 days) as well as measured their dependence (Kendalls tau of 0.4-0.6), taking into consideration demographic and epidemiological characteristics of the pairs. The positive correlation between the two parameters demonstrates that reliance on isolation of symptomatic COVID-19 cases as a focal point of control efforts is insufficient to address the challenges posed by SARS-CoV-2 transmission dynamics. Accounting for this dependence within SARS-CoV-2 epidemic models can also improve model estimates.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Natalie M Linton", + "author_inst": "Kyoto University" + }, + { + "author_name": "Andrei R. Akhmetzhanov", + "author_inst": "National Taiwan University" + }, + { + "author_name": "Hiroshi Nishiura", + "author_inst": "Kyoto University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.28.21262763", "rel_title": "Increasing incidence of parosmia and phantosmia in patients recovering from COVID-19 smell loss", @@ -607243,41 +608727,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.28.458041", - "rel_title": "Validation and invalidation of SARS-CoV-2 main protease inhibitors using the Flip-GFP and Protease-Glo luciferase assays", - "rel_date": "2021-08-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.28.458041", - "rel_abs": "SARS-CoV-2 main protease (Mpro) is one of the most extensive exploited drug targets for COVID-19. Structurally disparate compounds have been reported as Mpro inhibitors, raising the question of their target specificity. To elucidate the target specificity and the cellular target engagement of the claimed Mpro inhibitors, we systematically characterize their mechanism of action using the cell-free FRET assay, the thermal shift-binding assay, the cell lysate Protease-Glo luciferase assay, and the cell-based Flip-GFP assay. Collectively, our results have shown that majority of the Mpro inhibitors identified from drug repurposing including ebselen, carmofur, disulfiram, and shikonin are promiscuous cysteine inhibitors that are not specific to Mpro, while chloroquine, oxytetracycline, montelukast, candesartan, and dipyridamole do not inhibit Mpro in any of the assays tested. Overall, our study highlights the need of stringent hit validation at the early stage of drug discovery.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC=\"FIGDIR/small/458041v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (41K):\norg.highwire.dtl.DTLVardef@b0c310org.highwire.dtl.DTLVardef@d652deorg.highwire.dtl.DTLVardef@da8d0corg.highwire.dtl.DTLVardef@62449b_HPS_FORMAT_FIGEXP M_FIG C_FIG Flip-GFP and Protease-Glo luciferase assays, coupled with the FRET and thermal shift binding assays, were applied to validate the reported SARS-CoV-2 Mpro inhibitors.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Chunlong Ma", - "author_inst": "University of Arizona" - }, - { - "author_name": "Haozhou Tan", - "author_inst": "University of Arizona" - }, - { - "author_name": "Juliana Choza", - "author_inst": "University of Arizona" - }, - { - "author_name": "Yuying Wang", - "author_inst": "University of Arizona" - }, - { - "author_name": "Jun Wang", - "author_inst": "University of Arizona" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.08.27.21262721", "rel_title": "Short-Term Immune Response After Inactivated SARS-CoV-2 (CoronaVac, Sinovac) And ChAdOx1 nCoV-19 (Vaxzevria, Oxford-AstraZeneca) Vaccinations in Thai Health Care Workers", @@ -607674,6 +609123,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.23.21262464", + "rel_title": "Opaganib in COVID-19 pneumonia: Results of a randomized, placebo-controlled Phase 2a trial", + "rel_date": "2021-08-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.23.21262464", + "rel_abs": "BackgroundOpaganib, an oral sphingosine kinase-2 inhibitor with antiviral and anti-inflammatory properties, was shown to inhibit SARS-CoV-2 replication in vitro. We thus considered that opaganib could be beneficial for moderate to severe COVID-19 pneumonia. The objective of the study was to evaluate the effect of opaganib on supplemental oxygen requirements, time to hospital discharge and its safety in COVID-19 pneumonia hospitalized patients requiring supplemental oxygen.\n\nMethodsThis Phase 2a, randomized, double-blind, placebo-controlled study was conducted between July and December 2020 in eight sites in the USA. Forty-two enrolled patients received opaganib (n=23) or placebo (n=19) added to standard of care for up to 14 days and were followed up for 28 days after their last dose of opaganib/placebo.\n\nResultsThe relative decrease in total supplemental oxygen requirement from baseline to Day 14 was 61.6% in the opaganib versus 46.7% in the placebo arms. By Day 14, 50.0% of patients in the opaganib and 22.2% in the placebo group no longer required supplemental oxygen for at least 24 hours, while 86.4% and 55.6%, respectively, were discharged from hospital. The incidence of [≥] Grade 3 treatment-emergent adverse events was 17.4% and 33.3% in the opaganib and placebo groups, respectively. Three deaths occurred in each group.\n\nConclusionsIn this proof-of-concept study, hypoxic, hospitalized patients receiving oral opaganib required less supplementary oxygen and had earlier hospital discharge, with no safety concerns arising. These findings support further evaluation of opaganib in this population.\n\nSummaryUpon receiving opaganib, patients with COVID-19 pneumonia who were hospitalized and required supplemental oxygen showed symptomatic clinical improvement compared to placebo, with less supplemental oxygen requirement, resulting in earlier hospital discharge, and no safety concerns arising.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Kevin L Winthrop", + "author_inst": "Oregon Health & Sci. Univ., Portland, OR" + }, + { + "author_name": "Alan W Skolnick", + "author_inst": "HD Res., Houston, TX" + }, + { + "author_name": "Adnan Rafiq", + "author_inst": "Mem. Hermann Southeast Hosp., Houston, TX" + }, + { + "author_name": "Scott H Beegle", + "author_inst": "Albany Med. Coll., Albany, NY" + }, + { + "author_name": "Julian Suszanski", + "author_inst": "Henry Ford Hosp., Detroit, MI" + }, + { + "author_name": "Guenther Koehne", + "author_inst": "Miami Cancer Inst., Miami, FL" + }, + { + "author_name": "Ofra Barnett-Griness", + "author_inst": "Bioforum Ltd., Ness Ziona, Israel" + }, + { + "author_name": "Aida Bibliowicz", + "author_inst": "RedHill Biopharma Ltd., Tel-Aviv, Israel" + }, + { + "author_name": "Reza Fathi", + "author_inst": "RedHill Biopharma Ltd., Tel-Aviv, Israel" + }, + { + "author_name": "Patricia Anderson", + "author_inst": "RedHill Biopharma Ltd., Tel-Aviv, Israel" + }, + { + "author_name": "Gilead Raday", + "author_inst": "RedHill Biopharma Ltd., Tel-Aviv, Israel" + }, + { + "author_name": "Gina Eagle", + "author_inst": "G.E.T Pharma Consulting LLC, Lambertville, NJ" + }, + { + "author_name": "Vered Katz Ben-Yair", + "author_inst": "RedHill Biopharma Ltd., Tel-Aviv, Israel" + }, + { + "author_name": "Harold S Minkowitz", + "author_inst": "HD Res., Houston, TX" + }, + { + "author_name": "Mark L Levitt", + "author_inst": "Levitt Oncology Associates Ltd., Hashmonaim, Israel" + }, + { + "author_name": "Michael S Gordon", + "author_inst": "Honor Health Res. Inst., Scottsdale, AZ" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.28.21262733", "rel_title": "COVID-19 infection among health care workers: Experience in Base Hospital Wathupitiwala,Sri Lanka.", @@ -609165,73 +610693,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.26.21262697", - "rel_title": "Mental health and substance use associated with hospitalization among people with laboratory confirmed diagnosis of COVID-19 in British Columbia: a population-based cohort study", - "rel_date": "2021-08-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.26.21262697", - "rel_abs": "BackgroundThis study identified factors associated with hospital admission among people with laboratory-diagnosed COVID-19 cases in British Columbia.\n\nMethodsThis study was performed using the BC COVID-19 Cohort, which integrates data on all COVID-19 cases, hospitalizations, medical visits, emergency room visits, prescription drugs, chronic conditions and deaths. The analysis included all laboratory-diagnosed COVID-19 cases in British Columbia as of January 15th, 2021. We evaluated factors associated with hospital admission using multivariable Poisson regression analysis with robust error variance.\n\nFindingsFrom 56,874 COVID-19 cases included in the analyses, 2,298 were hospitalized. Models showed significant association of the following factors with increased hospitalization risk: male sex (adjusted risk ratio (aRR)=1.27; 95%CI=1.17-1.37), older age (p-trend <0.0001 across age groups with a graded increase in hospitalization risk with increasing age [aRR 30-39 years=3.06; 95%CI=2.32-4.03, to aRR 80+years=43.68; 95%CI=33.41-57.10 compared to 20-29 years-old]), asthma (aRR=1.15; 95%CI=1.04-1.26), cancer (aRR=1.19; 95%CI=1.09-1.29), chronic kidney disease (aRR=1.32; 95%CI=1.19-1.47), diabetes (treated without insulin aRR=1.13; 95%CI=1.03-1.25, requiring insulin aRR=5.05; 95%CI=4.43-5.76), hypertension (aRR=1.19; 95%CI=1.08-1.31), injection drug use (aRR=2.51; 95%CI=2.14-2.95), intellectual and developmental disabilities (aRR=1.67; 95%CI=1.05-2.66), problematic alcohol use (aRR=1.63; 95%CI=1.43-1.85), immunosuppression (aRR=1.29; 95%CI=1.09-1.53), and schizophrenia and psychotic disorders (aRR=1.49; 95%CI=1.23-1.82). Among women of reproductive age, in addition to age and comorbidities, pregnancy (aRR=2.69; 95%CI=1.42-5.07) was associated with increased risk of hospital admission.\n\nInterpretationOlder age, male sex, substance use, intellectual and developmental disability, chronic comorbidities, and pregnancy increase the risk of COVID-19-related hospitalization.\n\nFundingBC Centre for Disease Control, Canadian Institutes of Health Research.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSFactors such as older age, social inequities and chronic health conditions have been associated to severe COVID-19 illness. Most of the evidence comes from studies that dont include all COVID-19 diagnoses in a jurisdiction), focusing on in-hospital mortality. In addition, mental illness and substance use were not evaluated in these studies. This study assessed factors associated with hospital admission among people with laboratory-diagnosed COVID-19 cases in British Columbia.\n\nAdded value of this studyIn this population-based cohort study that included 56,874 laboratory-confirmed COVID-19 cases, older age, male sex, injection drug use, problematic alcohol use, intellectual and developmental disability, schizophrenia and psychotic disorders, chronic comorbidities and pregnancy were associated with the risk of hospitalization. Insulin-dependent diabetes was associated with higher risk of hospitalization, especially in the subpopulation younger than 40 years. To the best of our knowledge this is the first study reporting this finding, (insulin use and increased risk of COVID-19-related death has been described previously).\n\nImplications of all the available evidencePrioritization of vaccination in population groups with the above mentioned risk factors could reduce COVID-19 serious outcomes. The findings indicate the presence of the syndemic of substance use, mental illness and COVID-19, which deserve special public health considerations.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "H\u00e9ctor Alexander Vel\u00e1squez Garc\u00eda", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "James Wilton", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Kate Smolina", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Mei Chong", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Drona Rasali", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Michael Otterstatter", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Caren Rose", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Natalie Prystajecky", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Samara David", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Eleni Galanis", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Geoffrey McKee", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Mel Krajden", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Naveed Zafar Janjua", - "author_inst": "BC Centre for Disease Control" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.25.21262627", "rel_title": "History of suicide attempts and COVID-19 infection in Veterans with schizophrenia or schizoaffective disorder: effect modification by age and obesity", @@ -609696,6 +611157,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.25.21262529", + "rel_title": "Effectiveness of vaccination against symptomatic and asymptomatic SARS-CoV-2 infection: a systematic review and meta-analysis", + "rel_date": "2021-08-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.25.21262529", + "rel_abs": "OBJECTIVETo assess the effectiveness of SARS-CoV-2 vaccines in terms of prevention of disease and transmission. The evaluation was narrowed to two mRNA vaccines and two modified adenovirus vectored vaccines.\n\nMETHODSA frequentist random effects meta-analysis was carried out after data extraction. Risk of bias of the included studies was assessed using New-Castle-Ottawa Scale. The overall risk of SARS-CoV-2 infection confirmed by real time Polymerase Chain Reaction (PCR) was estimated in partially and fully vaccinated individuals. The effect size was expressed as Relative Risk (RR) and RRR (RR reduction) of SARS-CoV-2 infection after vaccination. Potential sources of heterogeneity were investigated through between-study heterogeneity analysis and subgroup meta-analysis.\n\nRESULTSThe systematic review identified 27 studies eligible for the quantitative synthesis. Partially vaccinated individuals presented a RRR=73% (95%CI=59%-83%) for any positive SARS-CoV-2 PCR (RR=0.27) and a RRR=79% (95%CI=30%-93%) for symptomatic SARS-CoV-2 PCR (RR=0.21). Fully vaccinated individuals showed a RRR=94% (95%CI=88%-98%) for any SARS-CoV-2 positive PCR (RR=0.06) compared to unvaccinated. According to the subgroup meta-analysis, full BNT162b2 vaccination protocol achieved a RRR=84%-94% against any SARS-CoV-2 positive PCR and a RRR=68%-84% against symptomatic positive PCR. The RR for any SARS-CoV-2 positive PCR remained higher within elderly groups aged [≥]69 years (RR=0.12-0.15) compared to younger individuals (RR=0.05-0.12). The RR against B.1.351 infection approached 0.40 for any positive PCR and 0.36 for symptomatic SARS-COV-2 while the RR of any B.1.1.7 infection was 0.14.\n\nCONCLUSIONThe current licensed vaccines may be transmission blocking, especially after full vaccination protocol. Given the substantial heterogeneity, results should be interpreted with caution. Subgroups meta-analyses suggested that the risk of any SARS-CoV-2 infection may be higher for non-B.1.1.7 variants and individuals aged [≥]69 years. Further data and longer follow-up are required to investigate additional sources of heterogeneity and the effectiveness of SARS-CoV-2 vaccination within population subgroups.\n\nSTRENGTHSO_LIReal-world data suggest that the current licensed vaccines may be transmission blocking, in particular after full vaccination protocol.\nC_LIO_LIThe risk of any SARS-CoV-2 infection either symptomatic or asymptomatic, may be higher for non-B.1.1.7 variants and individuals aged [≥]69 years.\nC_LI\n\nLIMITATIONSO_LIGiven the substantial heterogeneity encountered in this meta-analysis, results should be interpreted with caution\nC_LIO_LIFur ther evidence on the impact of SARS-CoV-2 variants are vital in order to monitor mutations associated with vaccine escape\nC_LI", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Angela Meggiolaro", + "author_inst": "Italian Ministry of Health, General Directorate of Prevention" + }, + { + "author_name": "Monica Sane Schepisi", + "author_inst": "Ministry of Health, General Directorate of Prevention" + }, + { + "author_name": "George Nikolaidis", + "author_inst": "IQVIA, London" + }, + { + "author_name": "Daniele Mipatrini", + "author_inst": "Ministry of Health, General Directorate of Prevention" + }, + { + "author_name": "Andrea Siddu", + "author_inst": "Italian Ministry of Health, General Directorate of Prevention" + }, + { + "author_name": "Giovanni Rezza", + "author_inst": "Italian Ministry of health, General Directorate of Prevention" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.26.21262523", "rel_title": "Association between tocilizumab, sarilumab and all-cause mortality at 28 days in hospitalized patients with COVID-19: A network meta-analysis", @@ -611387,45 +612887,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.08.24.21262580", - "rel_title": "The efficacy and safety of bamlanivimab treatment against COVID-19: A meta-analysis", - "rel_date": "2021-08-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.24.21262580", - "rel_abs": "BackgroundBamlanivimab is routinely used in the treatment of coronavirus disease 2019 (COVID-19) in worldwide. We performed a meta-analysis to investigate the efficacy and safety of bamlanivimab treatment in patients with COVID-19.\n\nMethodsWe searched articles from Web of Science, PubMed, Embase, the Cochrane Library and MedRxiv between 30 January 2020 and August 5, 2021. We selected randomized clinical trials (RCTs) and observational studies with a control group to assess the efficiency of bamlanivimab in treating patients with COVID-19.\n\nResultsOur meta-analysis retrieved 3 RCTs and 7 cohort studies including 14461 patients. Bmlanivimab may help outpatients to prevent hospitalization or emergency department visit (RR 0.41 95%CI 0.29 to 0.58), reduce ICU admission (RR 0.47 95%CI 0.23 to 0.92) and mortality (RR 0.32 95%CI 0.13 to 0.77) from the disease. The combination of bamlanivimab and etesevimab may had a greater potential for positive treatment outcome.\n\nConclusionBamlanivimab has demonstrated clinical efficacy on mild or moderate ill patients with COVID-19 to prevent hospitalization, reduce severity and mortality from the disease. Combinations of two or more monoclonal antibody increase the effect. Well-designed clinical trials to identify the clinical and biochemical characteristics in COVID-19 patients population that could benefit from bamlanivimab are warranted in the future.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSCan bamlanivimab treat COVID-19 patients? What are the factors that have great impact on the treatment outcome?\n\nFindingsIn this meta-analysis that retrieved 3 RCTs and 7 cohort studies and included 14461 adults, Bmlanivimab may help outpatients to prevent hospitalization or emergency department visit (RR 0.41 95%CI 0.29 to 0.58), reduce ICU admission (RR 0.47 95%CI 0.23 to 0.92) and mortality (RR 0.32 95%CI 0.13 to 0.77) from the disease.\n\nMeaningIn COVID-19 pandemic, the use of bamlanivimab may be warranted. Combinations of two or more monoclonal antibody increase the effect.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Huairong Xiang", - "author_inst": "second xiangya hospital central south university" - }, - { - "author_name": "Bei He", - "author_inst": "second xiangya hospital central south university" - }, - { - "author_name": "Yun Li", - "author_inst": "second xiangya hospital central south university" - }, - { - "author_name": "Xuan Cheng", - "author_inst": "second xiangya hospital central south university" - }, - { - "author_name": "Qizhi Zhang", - "author_inst": "second xiangya hospital central south university" - }, - { - "author_name": "Wenxing Peng", - "author_inst": "second xiangya hospital central south university" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2021.08.24.21262554", "rel_title": "Impact of the early stages of the COVID-19 pandemic on coverage of RMNH interventions in Ethiopia", @@ -611602,6 +613063,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.08.23.21262454", + "rel_title": "Evaluation of GENECUBE(R) HQ SARS-CoV-2 for anterior nasal samples and saliva samples with a new rapid examination protocol", + "rel_date": "2021-08-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.23.21262454", + "rel_abs": "IntroductionGENECUBE(R) is a rapid molecular identification system, and previous studies demonstrated that GENECUBE(R) HQ SARS-CoV-2 showed excellent analytical performance for the detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) with nasopharyngeal samples. However, other respiratory samples have not been evaluated.\n\nMethodsThis prospective comparison between GENECUBE(R) HQ SARS-CoV-2 and reference real-time reverse transcriptase polymerase chain reaction (RT-PCR) was performed for the detection of SARS-CoV-2 using anterior nasal samples and saliva samples. Additionally, we evaluated a new rapid examination protocol using GENECUBE(R) HQ SARS-CoV-2 for the detection of SARS-CoV-2 with saliva samples. For the rapid protocol, in the preparation of saliva samples, purification and extraction processes were adjusted, and the total process time was shortened to approximately 35 minutes.\n\nResultsFor 359 anterior nasal samples, the total-, positive-, and negative concordance of the two assays was 99.7% (358/359), 98.1% (51/52), and 100% (307/307), respectively. For saliva samples, the total-, positive-, and negative concordance of the two assays was 99.6% (239/240), 100% (56/56), and 99.5% (183/184), respectively. With the new protocol, total-, positive-, and negative concordance of the two assays was 98.8% (237/240), 100% (56/56), and 98.4% (181/184), respectively. In all discordance cases, SARS-CoV-2 was detected by additional molecular examinations.\n\nConclusionGENECUBE(R) HQ SARS-CoV-2 provided high analytical performance for the detection of SARS-CoV-2 in anterior nasal samples and saliva samples.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Asami Naito", + "author_inst": "Tsukuba i-Laboratory LLP" + }, + { + "author_name": "Yoshihiko Kiyasu", + "author_inst": "Department of Infectious Diseases, University of Tsukuba Hospital" + }, + { + "author_name": "Yusaku Akashi", + "author_inst": "Division of Infectious Diseases, Department of Medicine, Tsukuba Medical Center Hospital" + }, + { + "author_name": "Akio Sugiyama", + "author_inst": "Diagnostic System Department, TOYOBO Co., Ltd." + }, + { + "author_name": "Masashi Michibuchi", + "author_inst": "Diagnostic System Department, TOYOBO Co., Ltd." + }, + { + "author_name": "Yuto Takeuchi", + "author_inst": "Department of Infectious Diseases, University of Tsukuba Hospital" + }, + { + "author_name": "Shigeyuki Notake", + "author_inst": "Department of Clinical Laboratory, Tsukuba Medical Center Hospital" + }, + { + "author_name": "Koji Nakamura", + "author_inst": "Department of Clinical Laboratory, Tsukuba Medical Center Hospital" + }, + { + "author_name": "Hiroichi Ishikawa", + "author_inst": "Department of Respiratory Medicine, Tsukuba Medical Center Hospital" + }, + { + "author_name": "Hiromichi Suzuki", + "author_inst": "Department of Infectious Diseases, Faculty of Medicine, University of Tsukuba" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.25.21262632", "rel_title": "Longevity of SARS-CoV-2 Antibody in Health Care Workers: 6-Months Follow Up", @@ -613401,45 +614917,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.08.24.457397", - "rel_title": "Direct RNA sequencing reveals SARS-CoV-2 m6A sites and possible differential DRACH motif methylation among variants", - "rel_date": "2021-08-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.24.457397", - "rel_abs": "The causative agent of COVID-19 pandemic, the SARS-CoV-2 coronavirus, has a 29,903 bases positive-sense single-stranded RNA genome. RNAs exhibit about 100 modified bases that are essential for proper function. Among internal modified bases, the N6-methyladenosine, or m6A, is the most frequent, and is implicated in SARS-CoV-2 immune response evasion. Although the SARS-CoV-2 genome is RNA, almost all genomes sequenced so far are in fact, reverse transcribed complementary DNAs. This process reduces the true complexity of these viral genomes because incorporation of dNTPs hides RNA base modifications. Here, in this perspective paper, we present an initial exploration of the Nanopore direct RNA sequencing to assess the m6A residues in the SARS-CoV-2 sequences of ORF3a, E, M, ORF6, ORF7a, ORF7b, ORF8, N, ORF10 and the 3-untranslated region. We identified 15 m6A methylated positions, of which, 6 are in ORF N. Also, because m6A is associated with the DRACH motif, we compared its distribution in major SARS-CoV-2 variants. Although DRACH is highly conserved among variants we show that variants Beta and Eta have a fourth position C>U change in DRACH at 28,884b that could affect methylation. The Nanopore technology offers a unique opportunity for the study of viral epitranscriptomics. This technique is PCR-free and is not sequencing-by-synthesis, therefore, no PCR bias and synthesis errors are introduced. The modified bases are preserved and assessed directly with no need for chemical treatments or antibodies. This is the first report of direct RNA sequencing of a Brazilian SARS-CoV-2 sample coupled with the identification of modified bases.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Joao H. Campos", - "author_inst": "Federal University of Sao Paulo, Brazil" - }, - { - "author_name": "Juliana T. Maricato", - "author_inst": "Federal University of Sao Paulo, Brazil" - }, - { - "author_name": "Carla T. Braconi", - "author_inst": "Federal University of Sao Paulo, Brazil" - }, - { - "author_name": "Fernando Antoneli", - "author_inst": "Federal University of Sao Paulo, Brazil" - }, - { - "author_name": "Luiz Mario R. Janini", - "author_inst": "Federal University of Sao Paulo, Brazil" - }, - { - "author_name": "Marcelo RS Briones", - "author_inst": "Federal University of Sao Paulo, Brazil" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.08.23.457411", "rel_title": "Woodsmoke particulates alter expression of antiviral host response genes in human nasal epithelial cells infected with SARS-CoV-2 in a sex-dependent manner", @@ -613720,6 +615197,73 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.08.25.457699", + "rel_title": "Directing an mRNA-LNP vaccine toward lymph nodes improves humoral and cellular immunity against SARS-CoV-2", + "rel_date": "2021-08-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.25.457699", + "rel_abs": "The exploration and identification of safe and effective vaccines for the SARS-CoV-2 pandemic has captured the worlds attention and remains an ongoing issue in order to protect against emerging variants of concern (VoCs) while generating long lasting immunity. Here, we report the synthesis of a novel messenger ribonucleic acid (mRNA) encoding the spike protein in a lipid nanoparticle formulation (LNP) (STI-7264) that generates robust humoral and cellular immunity following immunization of C57Bl6 mice. In efforts to continually improve immunity, a lymphatic drug delivery device (MuVaxx) was engineered and tested to modulate immune cells at the injection site (epidermis and dermis) and draining lymph node (LN) to elicit adaptive immunity. Using MuVaxx, immune responses were elicited and maintained at a 10-fold dose reduction compared to traditional intramuscular (IM) administration as measured by anti-spike antibodies, cytokine producing CD8 T cells, and neutralizing antibodies against the Washington (Wild Type, WT) and South African (beta) variants. Remarkably, a 4-fold elevated T cell response was observed in MuVaxx administered vaccination as compared to that of IM administered vaccination. Thus, these data support further investigation into STI-7264 and lymphatic mediated delivery using MuVaxx for SARS-CoV-2 and VoCs vaccines.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "David M Francis", + "author_inst": "Sorrento Therapeutics" + }, + { + "author_name": "Runqiang Chen", + "author_inst": "Sorrento Therapeutics" + }, + { + "author_name": "Sahba Khorsandzadeh", + "author_inst": "Sorrento Therapeutics" + }, + { + "author_name": "Qidong Hu", + "author_inst": "Sorrento Therapeutics" + }, + { + "author_name": "Xiaoxuan Lyu", + "author_inst": "Sorrento Therapeutics" + }, + { + "author_name": "Hua Wang", + "author_inst": "Sorrento Therapeutics" + }, + { + "author_name": "Wan-lin Lim", + "author_inst": "Sorrento Therapeutics" + }, + { + "author_name": "Haotian Sun", + "author_inst": "Sorrento Therapeutics" + }, + { + "author_name": "Hui Xie", + "author_inst": "Sorrento Therapeutics" + }, + { + "author_name": "Namir Shaabani", + "author_inst": "Sorrento Therapeutics" + }, + { + "author_name": "Russell Ross", + "author_inst": "Sorrento Therapeutics" + }, + { + "author_name": "Brian Cooley", + "author_inst": "Sorrento Therapeutics" + }, + { + "author_name": "Henry Ji", + "author_inst": "Sorrento Therapeutics" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.08.20.21262349", "rel_title": "COVID-19 mitigation measures in primary schools and association with infection and school staff wellbeing: an observational survey linked with routine data in Wales, UK", @@ -615278,41 +616822,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.08.24.457457", - "rel_title": "Defective ORF8 dimerization in delta variant of SARS CoV2 leads to abrogation of ORF8 MHC-I interaction and overcome suppression of adaptive immune response", - "rel_date": "2021-08-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.24.457457", - "rel_abs": "In India, the breakthrough infections during second wave of COVID-19 pandemic was due to SARS-COV-2 delta variant (B.1.617.2). It was reported that majority of the infections were caused by the delta variant and only 9.8% percent cases required hospitalization whereas, only 0.4% fatality was observed. Sudden dropdown in COVID-19 infections was observed within a short timeframe, suggesting better host adaptation with evolved delta variant. Down regulation of host immune response against SARS-CoV-2 by ORF8 induced MHC-I degradation has been reported earlier. The Delta variant carried mutations (deletion) at Asp119 and Phe120 amino acids which are critical for ORF8 dimerization. The deletions of amino acids Asp119 and Phe120 in ORF8 of delta variant results in structural instability of ORF8 dimer caused by disruption of hydrogen bonding and salt bridges as revealed by structural analysis and MD simulation studies of ORF8 dimer. Further, flexible docking of wild type and mutant ORF8 dimer revealed reduced interaction of mutant ORF8 dimer with MHC-I as compared to wild type ORF8 dimer with MHC-1, thus implicating its possible role in MHC-I expression and host immune response against SARS-CoV-2. We thus propose that mutant ORF8 may not hindering the MHC-I expression thereby resulting in better immune response against SARS-CoV-2 delta variant, which partly explains the sudden drop of SARS-CoV-2 infection rate in the second wave of SARS-CoV-2 predominated by delta variant in India\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC=\"FIGDIR/small/457457v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (40K):\norg.highwire.dtl.DTLVardef@751eeaorg.highwire.dtl.DTLVardef@140b5b5org.highwire.dtl.DTLVardef@159a3a5org.highwire.dtl.DTLVardef@6c206_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Armi Chaudhari", - "author_inst": "gujarat biotechnology research center" - }, - { - "author_name": "Dr. Indira Singh", - "author_inst": "Gujarat Biotechnology Research center" - }, - { - "author_name": "Dr. Madhvi Joshi", - "author_inst": "Gujarat Biotechnology Research Centre" - }, - { - "author_name": "Dr. AMRUTLAL PATEL", - "author_inst": "Gujarat Biotechnology research center" - }, - { - "author_name": "Proff. Chaitanya Joshi", - "author_inst": "Gujarat Biotechnology research center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.08.19.21262310", "rel_title": "Predicting SARS-CoV-2 infections for children and youth with single symptom screening", @@ -615585,6 +617094,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.08.20.21262389", + "rel_title": "Model-based assessment of SARS-CoV-2 Delta variant transmission dynamics within partially vaccinated K-12 school populations", + "rel_date": "2021-08-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.20.21262389", + "rel_abs": "BackgroundWe examined school reopening policies amidst rising transmission of the highly transmissible Delta variant, accounting for vaccination among individuals aged 12 years and older, with the goal of characterizing risk to students and teachers under various within-school non-pharmaceutical interventions (NPIs) combined with specific vaccination coverage levels.\n\nMethodsWe developed an individual-based transmission model to simulate transmission of the Delta variant of SARS-CoV-2 among a synthetic population, representative of Bay Area cities. We parameterized the model using community contact rates from vaccinated households ascertained from a household survey of Bay Area families with children conducted between February - April, 2021.\n\nInterventions and outcomesWe evaluated the additional infections in students and teachers/staff resulting over a 128-day semester from in-school instruction compared to remote instruction when various NPIs (mask use, cohorts, and weekly testing of students/teachers) were implemented in schools, across various community-wide vaccination coverages (50%, 60%, 70%), and student ([≥]12 years) and teacher/staff vaccination coverages (50% - 95%). We quantified the added benefit of universal masking over masking among unvaccinated students and teachers, across varying levels of vaccine effectiveness (45%, 65%, 85%), and compared results between Delta and Alpha variant circulation.\n\nResultsThe Delta variant sharply increases the risk of within-school COVID-transmission when compared to the Alpha variant. In our highest risk scenario (50% community and within-school vaccine coverage, no within-school NPIs, and predominant circulation of the Delta variant), we estimated that an elementary school could see 33-65 additional symptomatic cases of COVID-19 over a four-month semester (depending on the relative susceptibility of children <10 years). In contrast, under the Bay Area reopening plan (universal mask use, community and school vaccination coverage of 70%), we estimated excess symptomatic infection attributable to school reopening among 2.0-9.7% of elementary students (8-36 excess symptomatic cases per school over the semester), 3.0% of middle school students (13 cases per school) and 0.4% of high school students (3 cases per school). Excess rates among teachers attributable to reopening were similar. Achievement of lower risk tolerances, such as <5 excess infections per 1,000 students or teachers, required a cohort approach in elementary and middle school populations. In the absence of NPIs, increasing the vaccination coverage of community members from 50% to 70% or elementary teachers from 70% to 95% reduced the estimated excess rate of infection among elementary school students attributable to school transmission by 24% and 41%, respectively. We estimated that with 70% coverage of the eligible community and school population with a vaccine that is [≤]65% effective, universal masking can avert more cases than masking of unvaccinated persons alone.\n\nConclusionsAmidst circulation of the Delta variant, our findings demonstrated that schools are not inherently low risk, yet can be made so with high community vaccination coverages and universal masking. Vaccination of adult community members and teachers protects unvaccinated elementary and middle school children. Elementary and middle schools that can support additional interventions, such as cohorts and testing, should consider doing so, particularly if additional studies find that younger children are equally as susceptible as adults to the Delta variant of SARS-CoV-2.\n\nLimitationsWe did not consider the effect of social distancing in classrooms, or variation in testing frequency, and considerable uncertainty remains in key transmission parameters.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Jennifer R Head", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Kristin L Andrejko", + "author_inst": "University of California at Berkeley" + }, + { + "author_name": "Justin V Remais", + "author_inst": "University of California, Berkeley" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.17.21262138", "rel_title": "Anti-PF4 levels of patients with VITT do not reduce 4 months following AZD1222 vaccination", @@ -617484,69 +619020,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.19.21262296", - "rel_title": "Assessment of inter-laboratory differences in SARS-CoV-2 consensus genome assemblies between public health laboratories in Australia", - "rel_date": "2021-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.19.21262296", - "rel_abs": "Whole-genome sequencing of viral isolates is critical for informing transmission patterns and ongoing evolution of pathogens, especially during a pandemic. However, when genomes have low variability in the early stages of a pandemic, the impact of technical and/or sequencing errors increases. We quantitatively assessed inter-laboratory differences in consensus genome assemblies of 72 matched SARS-CoV-2-positive specimens sequenced at different laboratories in Sydney, Australia. Raw sequence data were assembled using two different bioinformatics pipelines in parallel, and resulting consensus genomes were compared to detect laboratory-specific differences. Matched genome sequences were predominantly concordant, with a median pairwise identity of 99.997%. Identified differences were predominantly driven by ambiguous site content. Ignoring these produced differences in only 2.3% (5/216) of pairwise comparisons, each differing by a single nucleotide. Matched samples were assigned the same Pango lineage in 98.2% (212/216) of pairwise comparisons, and were mostly assigned to the same phylogenetic clade. However, epidemiological inference based only on single nucleotide variant distances may lead to significant differences in the number of defined clusters if variant allele frequency thresholds for consensus genome generation differ between laboratories. These results underscore the need for a unified, best-practices approach to bioinformatics between laboratories working on a common outbreak problem.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Charles S.P. Foster", - "author_inst": "School of Medical Sciences, Faculty of Medicine & Health, University of New South Wales" - }, - { - "author_name": "Sacha Stelzer-Braid", - "author_inst": "School of Medical Sciences, Faculty of Medicine & Health, University of New South Wales" - }, - { - "author_name": "Ira W. Deveson", - "author_inst": "Garvan Institute of Medical Research," - }, - { - "author_name": "Rowena A. Bull", - "author_inst": "The Kirby Institute for Infection and Immunity, University of New South Wales" - }, - { - "author_name": "Malinna Yeang", - "author_inst": "Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital" - }, - { - "author_name": "Jane Phan-Au", - "author_inst": "School of Medical Sciences, Faculty of Medicine & Health, University of New South Wales" - }, - { - "author_name": "Mariana Ruiz Silva", - "author_inst": "School of Medical Sciences, Faculty of Medicine & Health, University of New South Wales" - }, - { - "author_name": "Sebastiaan J. van Hal", - "author_inst": "NSW Health Pathology, Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital" - }, - { - "author_name": "Rebecca J. Rockett", - "author_inst": "Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital" - }, - { - "author_name": "Vitali Sintchenko", - "author_inst": "Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital" - }, - { - "author_name": "Ki Wook Kim", - "author_inst": "School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales" - }, - { - "author_name": "William D. Rawlinson", - "author_inst": "Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.17.21262165", "rel_title": "Interpreting Wastewater SARS-CoV-2 Results using Bayesian Analysis", @@ -617815,6 +619288,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.18.21262227", + "rel_title": "Modeling SARS-CoV-2 transmission at a winter destination resort region with high outside visitation", + "rel_date": "2021-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.18.21262227", + "rel_abs": "Travel destinations, particularly large resorts in otherwise small communities, risk infectious disease outbreaks from an influx of visitors who may import infections during peak seasons. The COVID-19 pandemic highlighted this risk in the context of global travel and has raised questions about appropriate interventions to curb the potential spread of infectious disease at tourist destinations. In Colorado, the initial outbreaks of SARS-CoV-2 in the state occurred in ski communities, leading to large economic losses from closures and visitor restrictions. In this study, we modeled SARS-CoV-2 transmission during the 2020-21 season in a ski region of Colorado to determine optimal combinations of intervention strategies that would keep the region below a predetermined threshold of SARS-CoV-2 infection density. This analysis used an age-stratified, deterministic SEIR compartmental model of disease transmission, calibrated to cellphone-based mobility data, to simulate infection trajectories during the winter ski season. Under three national infection levels corresponding to high, medium, and low viral importation risk, we estimated the potential impact of interventions including policy and behavior changes, visitor restriction strategies, and case investigation/contact tracing, in order to quantify the relative and absolute impacts of these interventions in the context of the COVID-19 pandemic. Our results suggest that, in the context of low viral importation risk, case investigation/contact tracing and policy and behavior changes may be sufficient to stay below predetermined infection thresholds without visitor restrictions. However, if viral importation risk is high, visitor restrictions and/or screening for infected visitors would be needed to avoid lockdown-like control scenarios and large outbreaks in tourist communities. These findings provide important guidance to tourist destinations for balancing policy impact in future infectious disease outbreaks.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Emma J Wu", + "author_inst": "Departments of Epidemiology and of Environmental & Occupational Health, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora" + }, + { + "author_name": "Jude Bayham", + "author_inst": "Colorado State University, Agricultural & Resource Economics, Fort Collins, Colorado" + }, + { + "author_name": "Elizabeth J Carlton", + "author_inst": "Department of Environmental & Occupational Health, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado" + }, + { + "author_name": "Jonathan M Samet", + "author_inst": "Departments of Epidemiology and of Environmental & Occupational Health, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora" + }, + { + "author_name": "Andrea G Buchwald", + "author_inst": "University of Maryland School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.08.16.21262100", "rel_title": "CORONAVIRUS DISEASE 2019 IN A TERTIARY PEDIATRIC CENTER IN PORTUGAL", @@ -619062,41 +620570,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.08.18.21262166", - "rel_title": "Changes in the serial interval and transmission dynamics associated with the SARS-CoV-2 Delta variant in South Korea", - "rel_date": "2021-08-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.18.21262166", - "rel_abs": "We estimated mean serial interval and superspreading potential for the predominant Delta variant of SARS-CoV-2. Mean serial intervals were similar with 3.7 and 3.5 days during early and latter periods, respectively. Furthermore, the risk of superspreading events was similar with 23% and 25% of cases seeded 80% of all transmissions.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sukhyun Ryu", - "author_inst": "Konyang University College of Medicine, South Korea" - }, - { - "author_name": "Dasom Kim", - "author_inst": "Konyang University College of Medicine, South Korea" - }, - { - "author_name": "Jun-Sik Lim", - "author_inst": "Seoul National University, South Korea" - }, - { - "author_name": "Sheikh Taslim Ali", - "author_inst": "The University of Hong Kong, China" - }, - { - "author_name": "Benjamin J Cowling", - "author_inst": "The University of Hong Kong, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.17.21262183", "rel_title": "The association between immunosuppressants use and COVID-19 adverse outcome: National COVID-19 cohort in South Korea", @@ -619337,6 +620810,69 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.08.19.457020", + "rel_title": "Platelet proteome analysis reveals an early hyperactive phenotype in SARS-CoV-2-infected humanized ACE2 mice", + "rel_date": "2021-08-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.19.457020", + "rel_abs": "Coronavirus disease-2019 (COVID-19) provokes a hypercoagulable state with increased incidence of thromboembolism and mortality. Platelets are major effectors of thrombosis and hemostasis. Suitable animal models are needed to better understand COVID-19-associated coagulopathy (CAC) and underlying platelet phenotypes. Here, we assessed K18-hACE2 mice undergoing a standardized SARS-CoV-2 infection protocol to study dynamic platelet responses via mass spectrometry-based proteomics. In total, we found significant changes in >1,200 proteins. Strikingly, protein alterations occurred rapidly by 2 days post-infection (dpi) and preceded outward clinical signs of severe disease. Pathway enrichment analysis of 2dpi platelet proteomes revealed that SARS-CoV-2 infection upregulated complement-coagulation networks (F2, F12, CFH, CD55/CD59), platelet activation-adhesion-degranulation proteins (PF4, SELP, PECAM1, HRG, PLG, vWF), and chemokines (CCL8, CXCL5, CXCL12). When mice started to lose weight at 4dpi, pattern recognition receptor signaling (RIG-I/MDA5, CASP8, MAPK3), and interferon pathways (IFIT1/IFIT3, STAT1) were predominant. Interestingly, SARS-CoV-2 spike protein in the lungs was observed by immunohistochemistry, but in platelets was undetected by proteomics. Similar to patients, K18-hACE2 mice during SARS-CoV-2 infection developed progressive lymphohistiocytic interstitial pneumonia with platelet aggregates in the lungs and kidneys. In conclusion, this model recapitulates activation of coagulation, complement, and interferon responses in circulating platelets, providing valuable insight into platelet pathology during COVID-19.\n\nKey PointsO_LISARS-CoV-2-infected humanized ACE2 mice recapitulate platelet reprogramming towards activation-degranulation-aggregation.\nC_LIO_LIComplement/coagulation pathways are dominant in platelets at 2 days post-infection (dpi), while interferon signaling is dominant at 4dpi.\nC_LI", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Saravanan Subramaniam", + "author_inst": "Pulmonary Center, Department of Medicine, School of Medicine, Boston University MA, USA" + }, + { + "author_name": "Ryan Matthew Hekman", + "author_inst": "Center for Network Systems Biology, Boston University, Boston, MA, USA" + }, + { + "author_name": "Archana Jayaraman", + "author_inst": "Pulmonary Center, Department of Medicine, School of Medicine, Boston University MA, USA" + }, + { + "author_name": "Paige Montanaro", + "author_inst": "National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA, USA; Department of Pathology and Laboratory Medicine, School of Medic" + }, + { + "author_name": "Benjamin Blum", + "author_inst": "Center for Network Systems Biology, Boston University, Boston, MA, USA" + }, + { + "author_name": "Devin Kenney", + "author_inst": "National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA, USA; Department of Microbiology, School of Medicine, Boston Universit" + }, + { + "author_name": "Maria Ericsson", + "author_inst": "Electron Microscopy Core Facility, Harvard Medical School, Boston, MA, USA" + }, + { + "author_name": "Katya Ravid", + "author_inst": "Department of Medicine, Boston University School of Medicine, Boston, MA, USA; Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, " + }, + { + "author_name": "Nicholas A Crossland", + "author_inst": "National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA, USA; National Emerging Infectious Diseases Laboratories (NEIDL), Bost" + }, + { + "author_name": "Andrew Emili", + "author_inst": "Center for Network Systems Biology, Boston University, Boston, MA, USA" + }, + { + "author_name": "Florian Douam", + "author_inst": "National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA, USA; Department of Microbiology, School of Medicine, Boston Universit" + }, + { + "author_name": "Markus Bosmann", + "author_inst": "Pulmonary Center, Department of Medicine, School of Medicine, Boston University MA, USA; National Emerging Infectious Diseases Laboratories (NEIDL), Boston Univ" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.08.20.457146", "rel_title": "SARS-CoV-2 hijacks p38\u03b2/MAPK11 to promote viral protein translation", @@ -620948,33 +622484,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.14.21257136", - "rel_title": "Worldwide association of lifestyle related factors and COVID-19 mortality", - "rel_date": "2021-08-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.14.21257136", - "rel_abs": "BackgroundSeveral lifestyle related factors such as obesity and diabetes have been identified as risk factors for Coronavirus disease 2019 (COVID-19) mortality. The objective of this study was to examine the global association between lifestyle related factors and COVID-19 mortality using data from each individual country.\n\nMethodsThe association between prevalence of seven lifestyle related factors (overweight, insufficient physical activity, smoking, type 2 diabetes, hypertension, hyperlipidemia, and age over 65) and COVID-19 mortality was assessed by linear and multivariable regression among 186 countries. The cumulative effect of lifestyle related factors on COVID-19 mortality was assessed by dividing countries into four categories according to the number of lifestyle related factors in the upper half range and comparing the mean mortality between groups.\n\nResultsIn linear regression, COVID-19 mortality was significantly associated with overweight, insufficient physical activity, hyperlipidemia, and age [≥]65. In multivariable regression, overweight and age [≥]65 demonstrated significant association with COVID-19 mortality (P = 0.0039, 0.0094). Countries with more risk factors demonstrated greater COVID-19 mortality (P for trend <0.001).\n\nConclusionLifestyle related factors, especially overweight and elderly population, were associated with increased COVID-19 mortality on a global scale. Global effort to reduce burden of lifestyle related factors along with protection and vaccination of these susceptible groups may help reduce COVID-19 mortality.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jingzhou Wang", - "author_inst": "University of Chicago" - }, - { - "author_name": "Toshiro Sato", - "author_inst": "Keio University" - }, - { - "author_name": "Atsushi NA Sakuraba", - "author_inst": "Univ of Chicago" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.16.21262036", "rel_title": "Comparison of Antibody Levels in Response to SARS-CoV-2 Infection and Vaccination Type in a Midwestern Cohort", @@ -621191,6 +622700,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.17.21260846", + "rel_title": "COVID-19 infection, hospitalisation and death Amongst People with Rare Autoimmune Rheumatic Disease in England. Results from the RECORDER Project.", + "rel_date": "2021-08-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.17.21260846", + "rel_abs": "ObjectivesTo calculate the rates of COVID-19 infection and COVID-19-related death among people with rare autoimmune rheumatic diseases (RAIRD) during the first wave of the COVID-19 pandemic in England compared to the general population.\n\nMethodsWe used Hospital Episode Statistics to identify all people alive 01 March 2020 with ICD-10 codes for RAIRD from the whole population of England. We used linked national health records (demographic, death certificate, admissions and PCR testing data) to calculate rates of COVID-19 infection and death up to 31 July 2020. Our primary definition of COVID-19-related death was mention of COVID-19 on the death certificate. General population data from Public Health England and the Office for National Statistics were used for comparison. We also describe COVID-19-related hospital admissions and all-cause deaths.\n\nResultsWe identified a cohort of 168,680 people with RAIRD, of whom 1874 (1.11%) had a positive COVID-19 PCR test. The age-standardised infection rate was 1.54 (95% CI 1.50-1.59) times higher than in the general population. 713 (0.42%) people with RAIRD died with COVID-19 on their death certificate and the age-sex-standardised mortality rate for COVID-19-related death was 2.41 (2.30 - 2.53) times higher than in the general population. There was no evidence of an increase in deaths from other causes in the RAIRD population.\n\nConclusionsDuring the first wave of COVID-19 in England, people with RAIRD had a 54% increased risk of COVID-19 infection and more than twice the risk of COVID-19-related death compared to the general population. These increases were seen despite shielding policies.\n\nKey MessagesO_LIPeople with RAIRD were at increased risk of COVID-19 infection during the first wave.\nC_LIO_LICompared to the general population, they had over twice the risk of COVID-19-related death.\nC_LIO_LIThese increased risks were seen despite shielding policies in place in England.\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Megan Rutter", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Peter C Lanyon", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Matthew J Grainge", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Richard Hubbard", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Emily Peach", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Mary Bythell", + "author_inst": "National Disease Registration Service, Public Health England" + }, + { + "author_name": "Peter Stilwell", + "author_inst": "National Disease Registration Service, Public Health England" + }, + { + "author_name": "Jeanette Ashton", + "author_inst": "National Disease Registration Service, Public Health England" + }, + { + "author_name": "Sarah Stevens", + "author_inst": "National Disease Registration Service, Public Health England" + }, + { + "author_name": "Fiona A Pearce", + "author_inst": "University of Nottingham" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.15.21262007", "rel_title": "Dynamics of seroconversion of anti-SARS-CoV-2 IgG antibodies in the Czech unvaccinated population: nationwide prospective seroconversion (PROSECO) study", @@ -622662,145 +624226,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.08.13.454991", - "rel_title": "A screening pipeline identifies a broad-spectrum inhibitor of bacterial AB toxins with cross protection against influenza A virus H1N1 and SARS-CoV-2", - "rel_date": "2021-08-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.13.454991", - "rel_abs": "A challenge for the development of host-targeted anti-infectives against a large spectrum of AB-like toxin-producing bacteria encompasses the identification of chemical compounds corrupting toxin transport through both endolysosomal and retrograde pathways. Here, we performed a high-throughput screening of small chemical compounds blocking active Rac1 proteasomal degradation triggered by the Cytotoxic Necrotizing Factor-1 (CNF1) toxin, followed by orthogonal screens against two AB toxins hijacking defined endolysosomal (Diphtheria toxin) or retrograde (Shiga-like toxin 1) pathways to intoxicate cells. This led to the identification of the molecule N-(3,3-diphenylpropyl)-1-propyl-4-piperidinamine, referred to as C910. This compound induces the swelling of EEA1-positive early endosomes, in absence of PIKfyve kinase inhibition, and disturbs the trafficking of CNF1 and the B-subunit of Shiga toxin along the endolysosomal or retrograde pathways, respectively. Together, we show that C910 protects cells against 8 bacterial AB toxins including large clostridial glucosylating toxins from Clostridium difficile. Of interest, C910 also reduced viral infection in vitro including influenza A virus subtype H1N1 and SARS-CoV-2. Moreover, parenteral administration of C910 to the mice resulted in its accumulation in lung tissues and reduced lethal influenza infection.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Yu Wu", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Nassim Mahtal", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Lea Swistak", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Sara Sagadiev", - "author_inst": "Seattle Childrens Research Institute" - }, - { - "author_name": "Mridu Acharya", - "author_inst": "Seattle Childrens Research Institute" - }, - { - "author_name": "Caroline Demeret", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Sylvie Van der Werf", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Florence Guivel-Benhassine", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Olivier Schwartz", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Serena Petracchini", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Amel Mettouchi", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Elea Paillares", - "author_inst": "Insitut Pasteur" - }, - { - "author_name": "Lucie Caramelle", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Pierre Couvineau", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Robert Thai", - "author_inst": "Univeristy Paris Saclay, CEA" - }, - { - "author_name": "Peggy Barbe", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Mathilde Keck", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Arnaud Machelart", - "author_inst": "University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille" - }, - { - "author_name": "Valentin Sencio", - "author_inst": "University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille" - }, - { - "author_name": "Francois Trottein", - "author_inst": "University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille" - }, - { - "author_name": "Martin Sachse", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Gaetan Chicanne", - "author_inst": "University Toulouse III Paul Sabatier" - }, - { - "author_name": "Bernard Payrastre", - "author_inst": "University Toulouse III Paul Sabatier" - }, - { - "author_name": "Florian Ville", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Victor Kreis", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Michel-Robert Popoff", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Ludger Johannes", - "author_inst": "Institut Curie" - }, - { - "author_name": "Jean-Christophe Cintrat", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Julien Barbier", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Daniel Gillet", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Emmanuel Lemichez", - "author_inst": "Institut Pasteur" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.08.15.456341", "rel_title": "Infection and transmission of SARS-CoV-2 and its alpha variant in pregnant white-tailed deer", @@ -622993,6 +624418,45 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2021.08.15.456422", + "rel_title": "Prediction of coronavirus 3C-like protease cleavage sites using machine-learning algorithms", + "rel_date": "2021-08-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.15.456422", + "rel_abs": "The coronavirus 3C-like (3CL) protease is a Cysteine protease. It plays an important role in viral infection and immune escape by not only cleaving the viral polyprotein ORF1ab at 11 sites, but also cleaving the host proteins. However, there is still a lack of effective tools for determining the cleavage sites of the 3CL protease. This study systematically investigated the diversity of the cleavage sites of the coronavirus 3CL protease on the viral polyprotein, and found that the cleavage motif were highly conserved for viruses in the genera of Alphacoronavirus, Betacoronavirus and Gammacoronavirus. Strong residue preferences were observed at the neighboring positions of the cleavage sites. A random forest (RF) model was built to predict the cleavage sites of the coronavirus 3CL protease based on the representation of residues at cleavage site and neighboring positions by amino acid indexes, and the model achieved an AUC of 0.96 in cross-validations. The RF model was further tested on an independent test dataset composed of cleavage sites on host proteins, and achieved an AUC of 0.88 and a prediction precision of 0.80 when considering the accessibility of the cleavage site. Then, 1,079 human proteins were predicted to be cleaved by the 3CL protease by the RF model. These proteins were enriched in pathways related to neurodegenerative diseases and pathogen infection. Finally, a user-friendly online server named 3CLP was built to predict the cleavage sites of the coronavirus 3CL protease based on the RF model. Overall, the study not only provides an effective tool for identifying the cleavage sites of the 3CL protease, but also provides insights into the molecular mechanism underlying the pathogenicity of coronaviruses.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Huiting Chen", + "author_inst": "Hunan University" + }, + { + "author_name": "Zhaozhong Zhu", + "author_inst": "Hunan Unversity" + }, + { + "author_name": "Ye Qiu", + "author_inst": "Hunan University" + }, + { + "author_name": "Xingyi Ge", + "author_inst": "Hunan University" + }, + { + "author_name": "Heping Zheng", + "author_inst": "Hunan University" + }, + { + "author_name": "Yousong Peng", + "author_inst": "Hunan University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.08.14.456353", "rel_title": "Cutting epitopes to survive: the case of lambda variant", @@ -624336,61 +625800,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.11.21261876", - "rel_title": "SARS-CoV-2 variants: levels of neutralisation required for protective immunity", - "rel_date": "2021-08-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.11.21261876", - "rel_abs": "A number of SARS-CoV-2 variants of concern (VOC) have been identified that partially escape serum neutralisation activity elicited by current vaccines. Recent studies have also shown that vaccines demonstrate reduced protection against symptomatic infection with SARS-CoV-2 variants. Here we integrate published data on in vitro neutralisation and clinical protection to understand and predict vaccine efficacy against existing SARS-CoV-2 variants. We find that neutralising activity against the ancestral SARS-CoV-2 is highly predictive of neutralisation of the VOC, with all vaccines showing a similar drop in neutralisation to the variants. Neutralisation levels remain strongly correlated with protection from infection with SARS-CoV-2 VOC (r=0.81, p=0.0005). We apply an existing model relating in vitro neutralisation to protection (parameterised on data from ancestral virus infection) and find this remains predictive of vaccine efficacy against VOC once drops in neutralisation to the VOC are taken into account. Modelling of predicted vaccine efficacy against variants over time suggests that protection against symptomatic infection may drop below 50% within the first year after vaccination for some current vaccines. Boosting of previously infected individuals with existing vaccines (which target ancestral virus) has been shown to significantly increase neutralising antibodies. Our modelling suggests that booster vaccination should enable high levels of immunity that prevent severe infection outcomes with the current SARS-CoV-2 VOC, at least in the medium term.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Deborah Cromer", - "author_inst": "Kirby Institute, University of New South Wales, Sydney, Australia" - }, - { - "author_name": "Megan Steain", - "author_inst": "School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia." - }, - { - "author_name": "Arnold Reynaldi", - "author_inst": "Kirby Institute, University of New South Wales, Sydney, Australia" - }, - { - "author_name": "Timothy E Schlub", - "author_inst": "Kirby Institute, University of New South Wales, Sydney, Australia" - }, - { - "author_name": "Adam K Wheatley", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Jennifer A Juno", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Stephen J Kent", - "author_inst": "University of Melbourne" - }, - { - "author_name": "James A Triccas", - "author_inst": "School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia." - }, - { - "author_name": "David S Khoury", - "author_inst": "Kirby Institute, University of New South Wales, Sydney, Australia" - }, - { - "author_name": "Miles Philip Davenport", - "author_inst": "Kirby Institute, University of New South Wales, Sydney, Australia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.11.21261732", "rel_title": "COVID-19 in Connecticut institutions of higher education during the 2020-2021 academic year", @@ -624703,6 +626112,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.11.21261917", + "rel_title": "Epidemiological Study of COVID-19 Infections: Case of Ga East Municipal Hospital Treatment Centre - Kwabenya-Ghana.", + "rel_date": "2021-08-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.11.21261917", + "rel_abs": "BackgroundThe COVID-19 pandemic still poses a considerable threat to global health, resulting in an unprecedented demand for regular research to continuously identify and update its risk profiles to ensure relevant interventions.\n\nObjectivesThis study aimed to examine the epidemiological characteristics of the COVID-19 outbreak in Ghana and identify risk factors for severe COVID-19 disease.\n\nMethodThis was a cross-sectional study involving the data of patients with COVID-19 clinically managed at the Ga-East Municipal Hospital, the main COVID-19 treatment centre in Ghana, from 21st March to 21st June 2020. The data were retrieved from the electronic medical records and folders of the patients. It included sociodemographic characteristics, COVID-19 disease severity, and treatment outcomes. Binomial logistic regression was used to identify risk factors of severe COVID-19 illness.\n\nResultAmong the 360 COVID-19 cases in this study, 55.3% were males, and 44.7% were females. Their mean age was 39.9{+/-}16.7years. Most of them were Ghanaians (92.8%) and employed (72.5%). The majority (93%) presented with mild disease, and hypertension (19.2%) was the most common comorbidity. The average length of hospital admission was 10.6{+/-}6.4day. Many of the cases recovered (98.6%), resulting in a case fatality of 1.4%. Finally, the logistic regression showed that increasing age (OR=1.12, p= 0.002) and diabetes mellitus (OR=19.85, p=0.007) are risk factors for severe COVID-19 disease.\n\nConclusionFindings from the study confirmed that increasing age and diabetes mellitus are risk factors for severe COVID-19 disease. Thus, Ghana could prioritise these identified populations when implementing interventions to reduce the COVID-19 disease burden.\n\nStrength and limitations of this studyO_LIThis study is one of the few studies exploring the risk factors for severe COVID-19 disease in Ghana; thus, it presents novel context-specific findings that could inform COVID-19 case management in Ghana.\nC_LIO_LIThe study was limited in drawing a causal association between the explanatory and outcome variables due to the cross-sectional design.\nC_LIO_LIThe study included only one COVID-19 treatment centre. Consequently, the findings may not be generalizable to the entire COVID-19 population in Ghana, even though the included centre is the main COVID-19 treatment centre.\nC_LI", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Shirley Crankson", + "author_inst": "Brunel University London" + }, + { + "author_name": "Ebenezer Oduro-Mensah", + "author_inst": "Ga- East Municipal Hospital, Ghana Health Service, P. O. Box WY 1895, Kwabenya, Accra-Ghana." + }, + { + "author_name": "Delali Asubonteng", + "author_inst": "Ga- East Municipal Hospital, Ghana Health Service, P. O. Box WY 1895, Kwabenya, Accra-Ghana." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.11.21261845", "rel_title": "Changing Dynamics of COVID-19 in the U.S. with the Emergence of the Delta Variant: Projections of the COVID-19 Simulator", @@ -626354,77 +627790,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.12.21261951", - "rel_title": "Neutralization of VOCs including Delta one year post COVID-19 or vaccine", - "rel_date": "2021-08-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.12.21261951", - "rel_abs": "BackgroundSARS-CoV-2 variants, such as Alpha, Beta, Gamma and Delta, are raising concern about the efficiency of neutralizing antibodies (NAb) induced by wild-type infection or vaccines based on the wild-type spike.\n\nMethodsWe determined IgG and NAb against SARS-CoV-2 variants one year following mild wild-type infection (n=104) and two-dose regimens with BNT162b2 (BNT/BNT) (n=67), ChAdOx1 (ChAd/ChAd) (n=82), or heterologous ChAdOx1 followed by BNT162b2 (ChAd/BNT) (n=116).\n\nFindingsWild type spike IgG and NAb remained detectable in 80% (83/104) of unvaccinated participants one year post mild infection. The neutralizing capacity was similar against wild type (reference), Alpha (0.95 (0.92-0.98) and Delta 1.03 (0.95-1.11) but significantly reduced against Beta (0.54 (0.48-0.60)) and Gamma 0.51 (0.44-0.61). Similarly, BNT/BNT and ChAd/ChAd elicited sustained capacity against Alpha and Delta (1.01 (0.78-1.31) and 0.85 (0.64-1.14)) and (0.96 (0.84-1.09) and 0.82 (0.61-1.10) respectively), with reduced capacity against Beta (0.67 (0.50-0.88) and 0.53 (0.40-0.71)) and Gamma (0.12 (0.06-0.27) and 0.54 (0.37-0.80)). A similar trend was found following ChAd/BNT (0.74 (0.66-0.83) and 0.70 (0.50-0.97) against Alpha and Delta and 0.29 (0.20-0.42) and 0.13 (0.08-0.20) against Beta and Gamma).\n\nInterpretationPersistent neutralization of the wide-spread Alpha and Delta variants one year after wild-type infection may aid vaccine policy makers in low-resource settings when prioritizing vaccine supply. The reduced capacity of neutralizing Beta and Gamma strains, but not the Alpha and Delta strains following both infection and three different vaccine regimens argues for caution against Beta and Gamma-exclusive mutations in the efforts to optimize next generation SARS-CoV-2 vaccines.\n\nFundingA full list of funding bodies that contributed to this study can be found in the Acknowledgements section", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Sebastian Havervall", - "author_inst": "Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" - }, - { - "author_name": "Ulrika Marking", - "author_inst": "Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" - }, - { - "author_name": "Max Gordon", - "author_inst": "Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" - }, - { - "author_name": "Henry Ng", - "author_inst": "Department of Medical Cell Biology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden" - }, - { - "author_name": "Nina Greilert-Norin", - "author_inst": "Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" - }, - { - "author_name": "Sarah Lindbo", - "author_inst": "Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" - }, - { - "author_name": "Kim Blom", - "author_inst": "Public Health Agency of Sweden, Solna, Sweden" - }, - { - "author_name": "Peter Nilsson", - "author_inst": "Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" - }, - { - "author_name": "Mia Phillipson", - "author_inst": "Department of Medical Cell Biology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden" - }, - { - "author_name": "Jonas Klingstrom", - "author_inst": "Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden" - }, - { - "author_name": "Sara Mangsbo", - "author_inst": "Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden" - }, - { - "author_name": "Mikael Aberg", - "author_inst": "Department of Medical Sciences, Clinical Chemistry and Science for Life Laboratory, Uppsala University, Uppsala, Sweden" - }, - { - "author_name": "Sophia Hober", - "author_inst": "Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" - }, - { - "author_name": "Charlotte Thalin", - "author_inst": "Danderyd Hospital, Karolinska Institute, Stockholm, Sweden" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.12.21261970", "rel_title": "A highly efficient T-cell immunoassay provides assessment of B cell help function of SARS-CoV-2 specific memory CD4+ T cells", @@ -626713,6 +628078,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.11.21261930", + "rel_title": "Geospatial Variability in Excess Death Rates during the COVID-19 Pandemic in Mexico: Examining Socio Demographic and Population Health Characteristics", + "rel_date": "2021-08-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.11.21261930", + "rel_abs": "BackgroundMexico has suffered one of the highest COVID-19 mortality rates in the world. In this study we examined how socio demographic and population health characteristics shape the geospatial variability in excess mortality patterns during the COVID-19 pandemic in Mexico.\n\nMethodsWeekly all-cause mortality time series for all 32 Mexican states, from January 4, 2015 to April 10, 2021, were analyzed to estimate the excess mortality rates using Serfling regression models. The association between socio-demographic, health indicators and excess mortality rates were determined using multiple linear regression analyses. Finally, we used functional data analysis to characterize clusters of states with distinct mortality growth rate curves.\n\nResultsThe overall all-cause excess deaths rate during the COVID-19 pandemic in Mexico until April 10, 2021 was estimated at 39.66 per 10 000 population. The lowest excess death rates were observed in southeastern states including Chiapas (12.72), Oaxaca (13.42) and Quintana Roo (19.41) whereas Mexico City had the highest excess death rate (106.17), followed by Tlaxcala (51.99) and Morelos (45.90). We found a positive association of excess mortality rates with aging index (P value<.0001), marginalization index (P value<.0001), and average household size (P value=0.0003) in the final adjusted model (Model R2=76%). We identified four distinct clusters with qualitatively similar excess mortality curves.\n\nConclusionCentral states exhibited the highest excess mortality rates whereas the distribution of aging index, marginalization index, and average household size explained the variability in excess mortality rates across Mexico. Our findings can help tailor interventions to mitigate the mortality impact of the pandemic.\n\nKey messageO_LIThis study quantified and examined spatial patterns of excess mortality across states of Mexico, with lower rates of excess mortality in southeastern states and higher rates in central states.\nC_LIO_LIMexico City recorded 1 in 5 of all excess deaths in reported in Mexico, which accounted for 19% of total excess deaths across the country.\nC_LIO_LIFindinds indicate that aging index, marginalization index, and average household size played a significant role on excess death rates across Mexican states during the COVID-19 pandemic.\nC_LIO_LIFour distinct clusters characterized the excess mortality curves across Mexican states.\nC_LI", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Sushma Dahal", + "author_inst": "Georgia State University, School of Public Health" + }, + { + "author_name": "Ruiyan Luo", + "author_inst": "Georgia State University, School of Public Health" + }, + { + "author_name": "Monica H Swahn", + "author_inst": "Georgia State University, School of Public Health" + }, + { + "author_name": "Gerardo Chowell", + "author_inst": "Georgia State University, School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.12.21261966", "rel_title": "B and T cell responses after a third dose of SARS-CoV-2 vaccine in Kidney Transplant Recipients", @@ -628712,77 +630108,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.08.11.455959", - "rel_title": "Multiplexed detection of SARS-CoV-2 genomic and subgenomic RNA using in situ hybridization", - "rel_date": "2021-08-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.11.455959", - "rel_abs": "The widespread Coronavirus Disease 2019 (COVID-19) is caused by infection with the novel coronavirus SARS-CoV-2. Currently, we have a limited toolset available for visualizing SARS-CoV-2 in cells and tissues, particularly in tissues from patients who died from COVID-19. Generally, single-molecule RNA FISH techniques have shown mixed results in formalin fixed paraffin embedded tissues such as those preserved from human autopsies. Here, we present a platform for preparing autopsy tissue for visualizing SARS-CoV-2 RNA using RNA FISH with amplification by hybridization chain reaction (HCR). We developed probe sets that target different regions of SARS-CoV-2 (including ORF1a and N) as well as probe sets that specifically target SARS-CoV-2 subgenomic mRNAs. We validated these probe sets in cell culture and tissues (lung, lymph node, and placenta) from infected patients. Using this technology, we observe distinct subcellular localization patterns of the ORF1a and N regions, with the ORF1a concentrated around the nucleus and the N showing a diffuse distribution across the cytoplasm. In human lung tissue, we performed multiplexed RNA FISH HCR for SARS-CoV-2 and cell-type specific marker genes. We found viral RNA in cells containing the alveolar type 2 (AT2) cell marker gene (SFTPC) and the alveolar macrophage marker gene (MARCO), but did not identify viral RNA in cells containing the alveolar type 1 (AT1) cell marker gene (AGER). Moreover, we observed distinct subcellular localization patterns of viral RNA in AT2 cells and alveolar macrophages, consistent with phagocytosis of infected cells. In sum, we demonstrate the use of RNA FISH HCR for visualizing different RNA species from SARS-CoV-2 in cell lines and FFPE autopsy specimens. Furthermore, we multiplex this assay with probes for cellular genes to determine what cell-types are infected within the lung. We anticipate that this platform could be broadly useful for studying SARS-CoV-2 pathology in tissues as well as extended for other applications including investigating the viral life cycle, viral diagnostics, and drug screening.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Kofi K Acheampong", - "author_inst": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA" - }, - { - "author_name": "Dylan L Schaff", - "author_inst": "Department of Bioengineering, School of Engineering Arts and Sciences, University of Pennsylvania, Philadelphia PA" - }, - { - "author_name": "Benjamin L Emert", - "author_inst": "Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA" - }, - { - "author_name": "Jonathan Lake", - "author_inst": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA" - }, - { - "author_name": "Sam Reffsin", - "author_inst": "Department of Bioengineering, School of Engineering Arts and Sciences, University of Pennsylvania, Philadelphia PA" - }, - { - "author_name": "Emily K Shea", - "author_inst": "Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA" - }, - { - "author_name": "Courtney E Comar", - "author_inst": "Department of Microbiology, University of Pennsylvania, Philadelphia PA, Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Philadelphia PA" - }, - { - "author_name": "Leslie A Litzky", - "author_inst": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA" - }, - { - "author_name": "Nigar A Khurram", - "author_inst": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, Department of Pathology, Northwestern" - }, - { - "author_name": "Michael Feldman", - "author_inst": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA" - }, - { - "author_name": "Susan R Weiss", - "author_inst": "Department of Microbiology, University of Pennsylvania, Philadelphia PA Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Philadelphia PA" - }, - { - "author_name": "Kathleen T Montone", - "author_inst": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA" - }, - { - "author_name": "Sara Cherry", - "author_inst": "Department of Pathology and Laboratory Medicine, Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Department of Biochemistry and Biophysi" - }, - { - "author_name": "Sydney M Shaffer", - "author_inst": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, Department of Bioengineering, School " - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.08.10.455737", "rel_title": "Molecular mimicry between Spike and human thrombopoietin may induce thrombocytopenia in COVID-19", @@ -628922,6 +630247,29 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2021.08.11.455899", + "rel_title": "Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: a pan India study", + "rel_date": "2021-08-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.11.455899", + "rel_abs": "COVID-19 has posed unforeseen circumstances and throttled major economies worldwide. India has witnessed two waves affecting around 31 million people representing 16% of the cases globally. To date, the epidemic waves have not been comprehensively investigated to understand pandemic progress in India. In the present study, we aim for a cross-sectional analysis since its first incidence up to 26th July 2021. We have performed the pan Indian evolutionary study using 20,086 high-quality complete genomes of SARS-CoV-2. Based on the number of cases reported and mutation rates, we could divide the Indian epidemic into seven different phases. First, three phases constituting the pre-first wave had a very less average mutation rate (<11), which increased in the first wave to 17 and then doubled in the second wave (~34). In accordance with the mutation rate, variants of concern (alpha, beta, gamma and delta) and interest (eta and kappa) also started appearing in the first wave (1.5% of the genomes), which dominated the second (~96% of genomes) and post-second wave (100% of genomes) phases. Whole genome-based phylogeny could demarcate the post-first wave isolates from previous ones by the point of diversification leading to incidences of VOCs and VOIs in India. Nation-wide mutational analysis depicted more than 0.5 million events with four major mutations in ~97% of the total 20,086 genomes in the study. These included two mutations in coding (spike (D614G) and NSP 12b (P314L) of RNA dependent RNA polymerase), one silent mutation (NSP3 F106F) and one extragenic mutation (5 UTR 241). Large scale genome-wide mutational analysis is crucial in expanding knowledge on evolution of deadly variants of SARS-CoV-2 and timely management of the pandemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Sanjeet Kumar", + "author_inst": "Gangadhar Meher University" + }, + { + "author_name": "Kanika Bansal", + "author_inst": "CSIR-Institute of Microbial Technology, Chandigarh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "confirmatory results", + "category": "genomics" + }, { "rel_doi": "10.1101/2021.08.11.455984", "rel_title": "Durability of SARS-CoV-2-specific T cell responses at 12-months post-infection", @@ -630313,37 +631661,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.08.10.455799", - "rel_title": "Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences", - "rel_date": "2021-08-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.10.455799", - "rel_abs": "More than 2 million SARS-CoV-2 genome sequences have been generated and shared since the start of the COVID-19 pandemic and constitute a vital information source that informs outbreak control, disease surveillance, and public health policy. The Pango dynamic nomenclature is a popular system for classifying and naming genetically-distinct lineages of SARS-CoV-2, including variants of concern, and is based on the analysis of complete or near-complete virus genomes. However, for several reasons, nucleotide sequences may be generated that cover only the spike gene of SARS-CoV-2. It is therefore important to understand how much information about Pango lineage status is contained in spike-only nucleotide sequences. Here we explore how Pango lineages might be reliably designated and assigned to spike-only nucleotide sequences. We survey the genetic diversity of such sequences, and investigate the information they contain about Pango lineage status. Although many lineages, including the main variants of concern, can be identified clearly using spike-only sequences, some spike-only sequences are shared among tens or hundreds of Pango lineages. To facilitate the classification of SARS-CoV-2 lineages using subgenomic sequences we introduce the notion of designating such sequences to a \"lineage set\", which represents the range of Pango lineages that are consistent with the observed mutations in a given spike sequence. These data provide a foundation for the development of software tools that can assign newly-generated spike nucleotide sequences to Pango lineage sets.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Oliver Pybus", - "author_inst": "Department of Zoology, University of Oxford" - }, - { - "author_name": "Michael E Abram", - "author_inst": "Microbial Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA." - }, - { - "author_name": "Elizabeth J Kelly", - "author_inst": "Microbial Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA." - }, - { - "author_name": "Andrew Rambaut", - "author_inst": "Institute of Evolutionary Biology, University of Edinburgh" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.08.10.455627", "rel_title": "An ultrapotent neutralizing bispecific antibody with broad spectrum against SARS-CoV-2 variants", @@ -630672,6 +631989,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.08.21261763", + "rel_title": "Neuro-COVID long-haulers exhibit broad dysfunction in T cell memory generation and responses to vaccination", + "rel_date": "2021-08-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.08.21261763", + "rel_abs": "Many people experiencing long COVID syndrome, or post-acute sequelae of SARS-CoV-2 infection (PASC), suffer from debilitating neurologic symptoms (Neuro-PASC). However, whether virus-specific adaptive immunity is affected in Neuro-PASC patients remains poorly understood. We report that Neuro-PASC patients exhibit distinct immunological signatures composed of elevated humoral and cellular responses toward SARS-CoV-2 Nucleocapsid protein at an average of 6 months post-infection compared to healthy COVID convalescents. Neuro-PASC patients also had enhanced virus-specific production of IL-6 from and diminished activation of CD8+ T cells. Furthermore, the severity of cognitive deficits or quality of life disturbances in Neuro-PASC patients were associated with a reduced diversity of effector molecule expression in T cells but elevated IFN-{gamma} production to the C-terminal domain of Nucleocapsid protein. Proteomics analysis showed enhanced plasma immunoregulatory proteins and reduced pro-inflammatory and antiviral response proteins in Neuro-PASC patients compared with healthy COVID convalescents, which were also correlated with worse neurocognitive dysfunction. These data provide new insight into the pathogenesis of long COVID syndrome and a framework for the rational design of predictive biomarkers and therapeutic interventions.\n\nOne Sentence SummaryAdaptive immunity is altered in patients with neurologic manifestations of long COVID.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Lavanya Visvabharathy", + "author_inst": "Northwestern University" + }, + { + "author_name": "Barbara Alice Hanson", + "author_inst": "Northwestern University, Rush University Medical College" + }, + { + "author_name": "Zachary Orban", + "author_inst": "Northwestern University" + }, + { + "author_name": "Patrick H Lim", + "author_inst": "Northwestern University" + }, + { + "author_name": "Nicole M Palacio", + "author_inst": "Northwestern University" + }, + { + "author_name": "Jeffrey R Clark", + "author_inst": "Northwestern University" + }, + { + "author_name": "Edith L Graham", + "author_inst": "Northwestern University" + }, + { + "author_name": "Eric Michael Liotta", + "author_inst": "Northwestern University" + }, + { + "author_name": "George Tachas", + "author_inst": ",Antisense Therapeutics Ltd., Melbourne, Australia" + }, + { + "author_name": "Pablo Penaloza-MacMaster", + "author_inst": "Northwestern University" + }, + { + "author_name": "Igor J Koralnik", + "author_inst": "Northwestern University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.07.21261578", "rel_title": "SARS-CoV-2 vaccine effectiveness in immunosuppressed kidney transplant recipients", @@ -632399,61 +633775,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2021.08.06.455494", - "rel_title": "Broad-spectrum in vitro antiviral activity of ODBG-P-RVn: an orally-available, lipid-modified monophosphate prodrug of remdesivir parent nucleoside (GS-441524)", - "rel_date": "2021-08-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.06.455494", - "rel_abs": "The intravenous administration of remdesivir for COVID-19 confines its utility to hospitalized patients. We evaluated the broad-spectrum antiviral activity of ODBG-P-RVn, an orally available, lipid-modified monophosphate prodrug of the remdesivir parent nucleoside (GS-441524) against viruses that cause diseases of human public health concern, including SARS-CoV-2. ODBG-P-RVn showed 20-fold greater antiviral activity than GS-441524 and had near-equivalent activity to remdesivir in primary-like human small airway epithelial cells. Our results warrant investigation of ODBG-P-RVn efficacy in vivo.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Michael K Lo", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Punya Shrivastava-Ranjan", - "author_inst": "CDC" - }, - { - "author_name": "Payel Chatterjee", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Mike Flint", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "James R Beadle", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Nadejda Valiaeva", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Robert Schooley", - "author_inst": "UCSD" - }, - { - "author_name": "Karl Y. Hostetler", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Joel Montgomery", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Christina F Spiropoulou", - "author_inst": "U.S. Centers for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2021.08.06.455491", "rel_title": "High genetic barrier to escape from human polyclonal SARS-CoV-2 neutralizing antibodies", @@ -632930,6 +634251,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.07.21261740", + "rel_title": "'I can't cope with multiple inputs': Qualitative study of the lived experiences of 'brain fog' after Covid-19", + "rel_date": "2021-08-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.07.21261740", + "rel_abs": "ObjectiveTo explore the lived experience of brain fog--the wide variety of neurocognitive symptoms that can follow Covid-19.\n\nDesign and settingUK-wide longitudinal qualitative study comprising online interviews and focus groups with email follow-up.\n\nMethod50 participants were recruited from a previous qualitative study of the lived experience of long Covid (n = 23) and online support groups for people with persistent neurological problems following Covid-19 (n = 27). In remotely-held focus groups, participants were invited to describe their cognitive symptoms and comment on others accounts. Individuals were followed up by email 4-6 months later. Data were audiotaped, transcribed, anonymised and coded in NVIVO. They were analysed by an interdisciplinary team with expertise in general practice, clinical neuroscience, the sociology of chronic illness and service delivery, and checked by three people with lived experience of brain fog.\n\nResults84% of participants were female and 60% were White British ethnicity. Most had never been hospitalised for Covid-19. Qualitative analysis revealed the following themes: mixed views on the appropriateness of the term brain fog; rich descriptions of the experience of neurocognitive impairments (especially executive function, attention, memory and language), accounts of how the illness fluctuated--and in some but not all cases, resolved--over time; the profound psychosocial impact of the condition on relationships, personal and professional identity; self-perceptions of guilt, shame and stigma; strategies used for self-management; challenges accessing and navigating the healthcare system; and participants search for physical mechanisms to explain their symptoms.\n\nConclusionThese qualitative findings complement research into the epidemiology and underlying pathophysiological mechanisms for neurological symptoms after Covid-19. Services for such patients should include: an ongoing therapeutic relationship with a clinician who engages with the illness in its personal, social and occupational context as well as specialist services that are accessible, easily navigable, comprehensive, and interdisciplinary.\n\nSummaryO_ST_ABSStrengths and Limitations of StudyC_ST_ABSO_LITo our knowledge, this is the largest and most in-depth qualitative study of the lived experience of brain fog in survivors of Covid-19.\nC_LIO_LIThe research team was interdisciplinary and interprofessional, and included consultation with patient experts by experience, who helped with data interpretation and peer review.\nC_LIO_LIOversampling from men and non-white ethnic groups allowed partial correction of an initially skewed sample.\nC_LIO_LIThe sample was drawn entirely from the UK\nC_LIO_LIResidual skews in the samples, particularly regarding minority ethnic groups and occupational classes, limited our ability to capture the full range of experiences\nC_LI\n\nFunding statementThis research is funded from the following sources: National Institute for Health Research (BRC-1215-20008), ESRC (ES/V010069/1), and Wellcome Trust (WT104830MA). Funders had no say in the planning and execution of the study or writing up of the paper. KTSP is supported by the National Institute for Health Research Biomedical Research Centre based at Oxford University Hospitals NHS Foundation Trust and the University of Oxford.\n\nCompeting Interests StatementEL and TG provided evidence on long Covid for House of Lords Select Committee TG was on the oversight group for the long Covid guideline at the National Institute for Health and Clinical Excellence, and at the time of writing is on the UKs National Long Covid Task Force.\n\nKP and CC have no competing interests to declare.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Caitriona Callan", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford" + }, + { + "author_name": "Emma Ladds", + "author_inst": "University of Oxford" + }, + { + "author_name": "Laiba Hussain", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford" + }, + { + "author_name": "Kyle Pattinson", + "author_inst": "Nuffield Department of Neurosciences, University of Oxford" + }, + { + "author_name": "Trish Greenhalgh", + "author_inst": "University of Oxford, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.06.21261710", "rel_title": "Antibody Attributes that Predict the Neutralization and Effector Function of Polyclonal Responses to SARS-CoV-2", @@ -634261,45 +635617,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.05.21261660", - "rel_title": "Rapid antigen testing for SARS-CoV-2 infection in a university setting in Ireland: learning from a 6-week pilot study.", - "rel_date": "2021-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.05.21261660", - "rel_abs": "ObjectivesWith the ongoing circulation of SARS-CoV-2 in countries across the world it is essential to identify effective ways to reduce the risk of infection while allowing society to function as close to normal as possible. Serial testing using rapid lateral flow antigen tests is a possible way to do this by screening populations in a targeted way, identifying infectious (both symptomatic and asymptomatic) people and removing them from circulation while infectious. To make rapid antigen testing effective, high levels of participation are important. This study was designed to evaluate the establishment of a testing programme in a university setting and assess some of the factors that impact participation in such a study among both staff and students.\n\nStudy DesignObservational, survey\n\nMethodsA trial period of SARS-CoV-2 rapid testing using the Abbott Panbio rapid antigen test was set up and staff and students based in the University College Dublin Veterinary Hospital were asked to take part voluntarily for 6 weeks. Following the trial period, we used a questionnaire to evaluate satisfaction and to understand some reasons behind participation or lack thereof.\n\nResultsOverall, almost all respondents to the survey stated that they were happy with having a testing programme present in the workplace and it helped to reduce anxiety associated with COVID-19. Findings indicated that staff and students did not participate equally in the voluntary testing programme. The findings also highlighted that intrinsic motivations and extrinsic motivations for participation differ. For example, participation among staff was much higher than among students, motivational messaging focused on protecting others did not resonate with students as much as staff, convenience was a key factor driving participation in both cohorts and the pressure of being forced to miss class (if positive) close to exam time provided motivation to students to avoid testing.\n\nConclusionsIntroducing antigen testing into a workplace helped to reduce overall anxiety associated with the potential impact of COVID-19, but achieving good participation was challenging. Participation is key to a successful, campus wide antigen testing programme but reaching high levels of participation is not straightforward and can not be taken for granted. Different motivations drive participation in different cohorts and different messaging/incentivisation is needed to encourage participation in those different cohorts. The findings reported here should inform any SARS-CoV-2 testing programme that will run in these types of settings in the future.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Gerald Barry", - "author_inst": "University College Dublin" - }, - { - "author_name": "Catherine McCarney", - "author_inst": "University College Dublin" - }, - { - "author_name": "Marc Farrelly", - "author_inst": "University College Dublin" - }, - { - "author_name": "Carmel Mooney", - "author_inst": "University College Dublin" - }, - { - "author_name": "Rory Breathnach", - "author_inst": "University College Dublin" - }, - { - "author_name": "Simon More", - "author_inst": "University College Dublin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.05.21261642", "rel_title": "The unique evolutionary dynamics of the SARS-CoV-2 Delta variant", @@ -634536,6 +635853,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.05.21261677", + "rel_title": "Phenotyping of acute and persistent COVID-19 features in the outpatient setting: exploratory analysis of an international cross-sectional online survey", + "rel_date": "2021-08-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.05.21261677", + "rel_abs": "BACKGROUNDLong COVID, defined as presence of COVID-19 related symptoms 28 days or more after the onset of acute SARS-CoV-2 infection, is an emerging challenge to healthcare systems. The objective of this study was to phenotype recovery trajectories of non-hospitalized COVID-19 individuals.\n\nMETHODSWe performed an international, multi-center, exploratory online survey study on demographics, comorbidities, COVID-19 symptoms and recovery status of non-hospitalized SARS-CoV-2 infected adults (Austria: n=1157), and Italy: n= 893).\n\nRESULTSWorking age subjects (Austria median: 43 yrs (IQR: 31 - 53), Italy: 45 yrs (IQR: 35 - 55)) and females (65.1% and 68.3%) predominated the study cohorts. Course of acute COVID-19 was characterized by a high symptom burden (median 13 (IQR: 9 - 18) and 13 (7 - 18) out of 44 features queried), a 47.6 - 49.3% rate of symptom persistence beyond 28 days and 20.9 - 31.9% relapse rate. By cluster analysis, two acute symptom phenotypes could be discerned: the non-specific infection phenotype and the multi-organ phenotype (MOP), the latter encompassing multiple neurological, cardiopulmonary, gastrointestinal and dermatological features. Clustering of long COVID subjects yielded three distinct subgroups, with a subset of 48.7 - 55 % long COVID individuals particularly affected by post-acute MOP symptoms. The number and presence of specific acute MOP symptoms and pre-existing multi-morbidity was linked to elevated risk of long COVID.\n\nCONCLUSIONThe consistent findings of two independent cohorts further delineate patterns of acute and post-acute COVID-19 and emphasize the importance of symptom phenotyping of home-isolated COVID-19 patients to predict protracted convalescence and to allocate medical resources.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhich acute symptom patterns of acute COVID-19 are associated with prolonged symptom persistence, symptom relapse or physical performance impairment?\n\nFindingsIn this multicenter international comparative survey study on non-hospitalized SARS- CoV-2 infected adults (Austria: n = 1157, Italy: n = 893) we identified distinct and reproducible phenotypes of acute and persistent features. Acute multi-organ symptoms including neurological and cardiopulmonary manifestations are linked to elevated risk of long COVID.\n\nMeaningThese findings suggest to employ symptom phenotyping of home-isolated COVID-19 patients to predict protracted convalescence and to allocate medical resources.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Sabina Sahanic", + "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Piotr Tymoszuk", + "author_inst": "Data Analytics As a Service Tirol" + }, + { + "author_name": "Dietmar Ausserhofer", + "author_inst": "Institute of General Practice and Public Health, Claudiana Bolzano, Italy" + }, + { + "author_name": "Verena Rass", + "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Alex Pizzini", + "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Goetz Nordmeyer", + "author_inst": "Public Health Service Tyrol, Austria" + }, + { + "author_name": "Katharina H\u00fcfner", + "author_inst": "Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital for Psychiatry II, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Katharina Kurz", + "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Paulina Maria Weber", + "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Thomas Sonnweber", + "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Anna Boehm", + "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Magdalena Aichner", + "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Katharina Cima", + "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Barbara Boeckle", + "author_inst": "Department of Dermatology and Venereology, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Bernhard Holzner", + "author_inst": "Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital for Psychiatry II, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Gerhard Rumpold", + "author_inst": "Evaluation Software Development, Innsbruck, Austria" + }, + { + "author_name": "Christoph Puelacher", + "author_inst": "REHA-MED Tirol, Center for outpatient cardiac and pulmonary rehabilitation, Innsbruck, Austria" + }, + { + "author_name": "Stefan Kiechl", + "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Andreas Huber", + "author_inst": "Tyrolean Federal Institute for Integrated Care, Innsbruck, Austria" + }, + { + "author_name": "Christian J Wiedermann", + "author_inst": "Institute of General Practice and Public Health, Claudiana Bolzano, Italy" + }, + { + "author_name": "Barbara Sperner-Unterweger", + "author_inst": "Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital for Psychiatry II, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Ivan Tancevski", + "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Rosa Bellmann-Weiler", + "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Herbert Bachler", + "author_inst": "Institute of General Medicine, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Giuliano Piccoliori", + "author_inst": "Institute of General Practice and Public Health, Claudiana Bolzano, Italy" + }, + { + "author_name": "Raimund Helbok", + "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Guenter Weiss", + "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Judith Loeffler-Ragg", + "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.05.21259863", "rel_title": "Recording of 'COVID-19 vaccine declined' among vaccination priority groups: a cohort study on 57.9 million NHS patients' primary care records in situ using OpenSAFELY", @@ -636263,37 +637707,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.04.21261332", - "rel_title": "Temporal considerations in the 2021 COVID-19 lockdown of Ho Chi Minh City", - "rel_date": "2021-08-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.04.21261332", - "rel_abs": "The success of Vietnam in controlling the spread of COVID-19 hinges on a timely implementation of its coherent strategy of containment and rapid tracing and testing efforts. The Vietnamese living in Mekong Delta are currently being besieged by the SARS-Cov-2 Delta variant as they undergo several and extended levels of lockdown. In this work we examine the temporal aspects of the lockdown in Ho Chi Minh City and predict the progress of the outbreak in terms of the total number of confirmed cases.\n\nA compartmental model with containment is fit to data to estimate the rate of transmission in Ho Chi Minh City. The severity of the lockdown is estimated from publicly-available data on mobility and coupled to the rate of infection. Various scenarios on when to begin a lockdown and its duration are assessed. This report, dated 27 July 2021, supports a lockdown of at least 3 weeks and predicts that there could be half as many cases had the inevitable lockdown started a week earlier.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Emmanuel Lance Christopher VI M Plan", - "author_inst": "Duy Tan University" - }, - { - "author_name": "Huong Thi Le", - "author_inst": "Thang Long University" - }, - { - "author_name": "Manh Duy Le", - "author_inst": "Duy Tan University" - }, - { - "author_name": "Haidang Phan", - "author_inst": "Duy Tan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.03.21261365", "rel_title": "Population normalisation in wastewater-based epidemiology for improved understanding of SARS-CoV-2 prevalence: A multi-site study", @@ -636474,6 +637887,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.03.21260614", + "rel_title": "Survival of health workers infected by SARS-CoV-2 in the context of vaccination against COVID-19 in Peru", + "rel_date": "2021-08-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.03.21260614", + "rel_abs": "ObjectivesTo evaluate the survival of health workers infected by SARS-CoV-2 in the context of the vaccination process against COVID-19 in Peru.\n\nMethodsA survival analysis was performed using data from national health databases. Data from people between 18 and 59 years old infected with SARS-CoV-2 as evidenced by molecular or antigenic tests were included. Kaplan Meier graphs were produced to compare the survival of health workers and the rest of the population during 2021 and health workers during the first and second wave of mortality in Peru in 2020 and 2021, respectively.\n\nResultsData from 998,295 people were included. The average age was 41.2 years (SD 15.8) and 485,167 (48.6%) were women. A higher level of survival of health workers after vaccination was found compared to the general population and to the population of health workers before vaccination. It was evidenced that, at the beginning of the second wave, the risk of dying for health workers was twice that of the first wave (HR = 2). After vaccination (in the sixth month of the second wave), the risk of dying decreased to 87.5% less than in the first wave (HR = 0.125).\n\nConclusionsA positive change has been evidenced in the level of survival of health workers infected by SARS-CoV-2 during the context of vaccination against COVID-19 in Peru.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Stefan Escobar-Agreda", + "author_inst": "National Institute of Health / National University of San Marcos" + }, + { + "author_name": "Javier Silva-Valencia", + "author_inst": "National Institute of Health / National University of San Marcos" + }, + { + "author_name": "Leonardo Rojas-Mezarina", + "author_inst": "National Institute of Health / National University of San Marcos" + }, + { + "author_name": "Javier Vargas-Herrera", + "author_inst": "National Institute of Health / National University of San Marcos" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.02.21261480", "rel_title": "A qualitative exploration of the perspectives of international medical students residing in university hostels amid COVID-19 pandemic lockdown", @@ -638573,49 +640017,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.02.21261500", - "rel_title": "Temporal Geospatial Analysis of COVID-19 Pre-infection Determinants of Risk in South Carolina", - "rel_date": "2021-08-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.02.21261500", - "rel_abs": "IntroductionDisparities and their geospatial patterns exist in coronavirus disease 2019 (COVID-19) morbidity and mortality for people who are engaged with clinical care. However, studies centered on viral infection cases are scarce. It remains unclear with respect to the disparity structure, its geospatial characteristics, and the pre-infection determinants of risk (PIDRs) for people with the infection. This work aimed to assess the geospatial associations between PIDRs and COVID-19 infection at the county level in South Carolina by different timepoints during the pandemic.\n\nMethodWe used global models including spatial error model (SEM), spatial lag model (SLM), and conditional autoregressive model (CAR), as well as geographically weighted regression model (GWR) as a local model to examine the associations between COVID-19 infection rate and PIDRs. The data were retrieved from multiple sources including USAFacts, US Census Bureau, and Population Estimates Program.\n\nResultsThe percentage of males and the percentage of the unemployed population were statistically significant (p values < 0.05) with positive coefficients in the three global models (SEM, SLM, CAR) throughout the time. The percentage of white population and obesity rate showed divergent spatial correlations at different times of the pandemic. GWR models consistently have a better model fit than global models, suggesting non-stationary correlations between a region and its neighbors.\n\nConclusionCharacterized by temporal-geospatial patterns, disparities and their PIDRs exist in COVID-19 incidence at the county level in South Carolina. The temporal-geospatial structure of disparities and their PIDRs found in COVID-19 incidence are different from mortality and morbidity for patients who are connected with clinical care. Our findings provided important evidence for prioritizing different populations and developing tailored interventions at different times of the pandemic. These findings provided implications on containing early viral transmission and mitigating consequences of infectious disease outbreaks for possible future pandemics.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Tianchu Lyu", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Nicole Hair", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Nicholas Yell", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Zhenlong Li", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Shan Qiao", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Chen Liang", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Xiaoming Li", - "author_inst": "University of South Carolina" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.08.03.21261438", "rel_title": "COVID-19 impact on stroke admissions during France's first epidemic peak: an exhaustive, nationwide, observational study", @@ -638816,6 +640217,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.05.455212", + "rel_title": "Vaccination with B.1.1.7, B.1.351 and P.1 variants protects mice from challenge with wild type SARS-CoV-2", + "rel_date": "2021-08-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.05.455212", + "rel_abs": "Vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been highly efficient in protecting against coronavirus disease 2019 (COVID-19). However, the emergence of viral variants that are more transmissible and, in some cases, escape from neutralizing antibody responses has raised concerns. Here, we evaluated recombinant protein spike antigens derived from wild type SARS-CoV-2 and from variants B.1.1.7, B.1.351 and P.1 for their immunogenicity and protective effect in vivo against challenge with wild type SARS-CoV-2 in the mouse model. All proteins induced high neutralizing antibodies against the respective viruses but also induced high cross-neutralizing antibody responses. The decline in neutralizing titers between variants was moderate, with B.1.1.7 vaccinated animals having a maximum fold reduction of 4.8 against B.1.351 virus. P.1 induced the most cross-reactive antibody responses but was also the least immunogenic in terms of homologous neutralization titers. However, all antigens protected from challenge with wild type SARS-CoV-2 in a mouse model.\n\nAuthor SummaryThe emergence of variants of SARS-CoV-2 has led to an urgency to study whether vaccines will lead to cross-protection against these variants. Here, we demonstrate that vaccination with spike proteins of various variants leads to cross-neutralizing responses, as well as protection in a mouse model against wild type SARS-CoV-2.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Fatima Amanat", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Shirin Strohmeier", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Philip Meade", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Barbara M\u00fchlemann", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin: Charite Universitatsmedizin Berlin" + }, + { + "author_name": "Derek J. Smith", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Lynda Coughlan", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.08.04.455181", "rel_title": "Limited variation between SARS-CoV-2-infected individuals in domain specificity and relative potency of the antibody response against the spike glycoprotein", @@ -640391,65 +641835,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.02.21261479", - "rel_title": "Tear antibodies to SARS-CoV-2: implications for transmission", - "rel_date": "2021-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.02.21261479", - "rel_abs": "ObjectivesSARS-CoV-2 can be transmitted by aerosols and the ocular surface may be an important route of transmission. Little is known about protective antibody responses to SARS-CoV-2 in tears after infection or vaccination. We analysed SARS-CoV-2 specific IgG and IgA responses in human tears after either COVID-19 infection or vaccination.\n\nMethodsWe recruited 16 subjects with COVID-19 infection an average of 7 months previously and 15 subjects before and 2 weeks after Comirnaty (Pfizer-BioNtech) vaccination. Plasma, saliva and basal tears were collected. Pre-pandemic plasma, saliva and basal tears from 11 individuals were included as healthy controls. Antibody responses to 5 SARS-CoV-2 antigens were measured via multiplex.\n\nResultsIgG antibodies to Spike and Nucleoprotein were detected in tears, saliva and plasma from subjects with prior SARS-CoV-2 infection in comparison to uninfected controls. While RBD-specific antibodies were detected in plasma, minimal RBD-specific antibodies were detected in tears and saliva. In contrast, high levels of IgG antibodies to Spike and RBD, but not Nucleoprotein, were induced in tears, saliva and plasma of subjects receiving 2 doses of the Comirnaty vaccine. Increased levels of IgA1 and IgA2 antibodies to SARS-CoV-2 antigens were detected in plasma following infection or vaccination, but were unchanged in tears and saliva.\n\nConclusionBoth infection and vaccination induce SARS-CoV-2-specific IgG antibodies in tears. RBD-specific IgG antibodies in tears were induced by vaccination but were not present 7 months post-infection. This suggests neutralising antibodies may be low in the tears late following infection.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Kevin John Selva", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia" - }, - { - "author_name": "Samantha K Davis", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia" - }, - { - "author_name": "Ebene R Haycroft", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia" - }, - { - "author_name": "Wen Shi Lee", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia" - }, - { - "author_name": "Ester Lopez", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia" - }, - { - "author_name": "Arnold Reynaldi", - "author_inst": "Kirby Institute, University of New South Wales, Kensington, NSW, Australia" - }, - { - "author_name": "Miles Philip Davenport", - "author_inst": "Kirby Institute, University of New South Wales, Kensington, NSW, Australia" - }, - { - "author_name": "Helen E Kent", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia" - }, - { - "author_name": "Jennifer A Juno", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia" - }, - { - "author_name": "Amy W Chung", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia" - }, - { - "author_name": "Stephen J Kent", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.02.21260750", "rel_title": "Hydroxychloroquine Prophylaxis against Coronavirus Disease-19: Practice Outcomes among Health-Care Workers", @@ -640678,6 +642063,113 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.08.03.454858", + "rel_title": "Protective mucosal immunity against SARS-CoV-2 after heterologous systemic RNA-mucosal adenoviral vector immunization", + "rel_date": "2021-08-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.03.454858", + "rel_abs": "Several effective SARS-CoV-2 vaccines are currently in use, but in the light of waning immunity and the emergence of novel variants, effective boost modalities are needed in order to maintain or even increase immunity. Here we report that intranasal vaccinations with adenovirus 5 and 19a vectored vaccines following a systemic DNA or mRNA priming result in strong systemic and mucosal immunity in mice. In contrast to two intramuscular injections with an mRNA vaccine, the mucosal boost with adenoviral vectors induced high levels of IgA and tissue-resident memory T cells in the respiratory tract. Mucosal neutralization of virus variants of concern was also enhanced by the intranasal boosts. Importantly, priming with mRNA provoked a more comprehensive T cell response consisting of circulating and tissue-resident memory T cells after the boost, while a DNA priming induced mostly mucosal T cells. Concomitantly, the intranasal boost strategies provided protection against symptomatic disease. Therefore, a mucosal booster immunization after mRNA priming is a promising approach to establish mucosal immunity in addition to systemic responses.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Dennis Lapuente", + "author_inst": "University Hospital Erlangen" + }, + { + "author_name": "Jana Fuchs", + "author_inst": "Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuernberg, Erlangen, Germany" + }, + { + "author_name": "Jonas Willar", + "author_inst": "Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuernberg, Erlangen, Germany" + }, + { + "author_name": "Ana V Antao", + "author_inst": "Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuernberg, Erlangen, Germany" + }, + { + "author_name": "Valentina Everlein", + "author_inst": "Department of Immunology, Fraunhofer Institute for Cell Therapy and Immunology, IZI, Leipzig, Germany" + }, + { + "author_name": "Nadja Uhlig", + "author_inst": "Department of Immunology, Fraunhofer Institute for Cell Therapy and Immunology, IZI, Leipzig, Germany" + }, + { + "author_name": "Leila Issmail", + "author_inst": "Department of Immunology, Fraunhofer Institute for Cell Therapy and Immunology, IZI, Leipzig, Germany" + }, + { + "author_name": "Anna Schmidt", + "author_inst": "Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuernberg, Erlangen, Germany" + }, + { + "author_name": "Friederike Oltmanns", + "author_inst": "Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuernberg, Erlangen, Germany" + }, + { + "author_name": "Antonia Sophia Peter", + "author_inst": "Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuernberg, Erlangen, Germany" + }, + { + "author_name": "Sandra Mueller-Schmucker", + "author_inst": "Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuernberg, Erlangen, Germany" + }, + { + "author_name": "Pascal Irrgang", + "author_inst": "Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuernberg, Erlangen, Germany" + }, + { + "author_name": "Kirsten Fraedrich", + "author_inst": "Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuernberg, Erlangen, Germany" + }, + { + "author_name": "Andrea Cara", + "author_inst": "National Center for Global Health Istituto Superiore di Sanita" + }, + { + "author_name": "Markus Hoffmann", + "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" + }, + { + "author_name": "Stefan Poehlmann", + "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" + }, + { + "author_name": "Armin Ensser", + "author_inst": "Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuernberg, Erlangen, Germany" + }, + { + "author_name": "Cordula Pertl", + "author_inst": "Sirion Biotech, Martinsried, Germany" + }, + { + "author_name": "Torsten Willert", + "author_inst": "Sirion Biotech, Martinsried, Germany" + }, + { + "author_name": "Christian Thirion", + "author_inst": "Sirion Biotech, Martinsried, Germany" + }, + { + "author_name": "Thomas Grunwald", + "author_inst": "Department of Immunology, Fraunhofer Institute for Cell Therapy and Immunology, IZI, Leipzig, Germany" + }, + { + "author_name": "Klaus Ueberla", + "author_inst": "Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuernberg, Erlangen, Germany" + }, + { + "author_name": "Matthias Tenbusch", + "author_inst": "Uk Erlangen" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.08.02.454829", "rel_title": "Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit.", @@ -642349,89 +643841,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.29.21261006", - "rel_title": "Association of E484K and L452R spike protein mutations with SARS-CoV-2 infection in vaccinated persons---Maryland, January - May 2021", - "rel_date": "2021-08-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.29.21261006", - "rel_abs": "BackgroundThe E484K and L452R amino acid substitutions on the spike protein of SARS-CoV-2 are associated with reduced neutralization by antibodies from acquired immunity. This study examines the respective association of these mutations with infection in persons who had previously received a COVID-19 vaccine.\n\nMethodsGenetic sequences from SARS-CoV-2 specimens collected from Maryland residents and reported to Maryland Department of Health were linked to vaccination history. The prevalence of infections in fully vaccinated persons -- defined as being at least two weeks past receiving the final scheduled dose of a COVID-19 vaccine series -- was compared between infections caused by viruses carrying E484K to those not carrying E484K, and between infections caused by viruses carrying L452R to those not carrying L452R, using logistic regression to adjust for confounding.\n\nResultsOf 9,048 sequenced SARS-CoV-2 specimens examined, 265 (2.9%) were collected from fully vaccinated persons. In adjusted analysis, the E484K substitution was associated with an increase in the odds of the sequenced specimen being collected from a fully vaccinated person (OR 1.96, 95% CI, 1.36 to 2.83). The L452R mutation was not significantly associated with infections in vaccinated persons (OR 1.07, 95% CI, 0.69 to 1.68).\n\nConclusionThough more than 97% of SARS-CoV-2 infections were in persons who were not fully vaccinated, the E484K mutation was associated with increased odds of SARS-CoV-2 infection in vaccinated persons. Linking vaccination and sequencing data can help identify and estimate the impact SARS-CoV-2 mutations may have on vaccine effectiveness.\n\nSummaryIn viruses sequenced for Marylands routine SARS-CoV-2 genomic surveillance, the spike protein amino acid substitution E484K was more prevalent in viruses that infected vaccinated people than in viruses that infected people who were not vaccinated.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Kenneth Aaron Feder", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Ami Patel", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Venkata R Vepachedu", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Catherine Dominguez", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Eric N Keller", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Liore Klein", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Curi Kim", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Tim Blood", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Judie Hyun", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Theo Williams", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Katherine Anne Feldman", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Heba H Mostafa", - "author_inst": "Johns Hopkins University, School of Medicine, Department of Pathology, Division of Medical Microbiology" - }, - { - "author_name": "Christopher Paul Morris", - "author_inst": "Johns Hopkins University, School of Medicine, Department of Pathology, Division of Medical Microbiology" - }, - { - "author_name": "Jacques Ravel", - "author_inst": "University of Maryland School of Medicine, Institute for Genomic Sciences" - }, - { - "author_name": "Monique Duwell", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "David Blythe", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Robert Myers", - "author_inst": "Maryland Department of Health" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.29.21261314", "rel_title": "Rapid comparative evaluation of SARS-CoV-2 rapid point-of-care antigen tests", @@ -642724,6 +644133,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2021.07.29.21261325", + "rel_title": "Specialized interferon ligand action in COVID19", + "rel_date": "2021-08-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.29.21261325", + "rel_abs": "The impacts of IFN signaling on COVID19 pathology are multiple, with protective and harmful effects being documented. We report here a multi-omics investigation of IFN signaling in hospitalized COVID19 patients, defining the biosignatures associated with varying levels of 12 different IFN ligands. Previously we showed that seroconversion associates with decreased production of select IFN ligands (Galbraith et al, 2021). We show now that the antiviral transcriptional response in circulating immune cells is strongly associated with a specific subset of ligands, most prominently IFNA2 and IFNG. In contrast, proteomics signatures indicative of endothelial damage associate with levels of IFNB and IFNA6. Differential IFN ligand production is linked to distinct constellations of circulating immune cells. Lastly, IFN ligands associate differentially with activation of the kynurenine pathway, dysregulated fatty acid metabolism, and altered central carbon metabolism. Altogether, these results reveal specialized IFN ligand action in COVID19, with potential diagnostic and therapeutic implications.\n\nIMPACT STATEMENTAnalysis of multi-omics signatures associated with 12 different IFN ligands reveals their specialized action in COVID19.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Matthew D Galbraith", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Kohl T Kinning", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Kelly D Sullivan", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Paula Araya", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Keith P Smith", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Ross E Granrath", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Jessica R Shaw", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Ryan Baxter", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Kimberly R Jordan", + "author_inst": "University of Colorado School of Medicine" + }, + { + "author_name": "Seth Russell", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Monika Dzieciatkowska", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Julie A Reisz", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Tusharkanti Ghosh", + "author_inst": "Colorado School of Public Health" + }, + { + "author_name": "Andrew Monte", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Tellen D Benett", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Kirk Hansen", + "author_inst": "School of Medicine, University of Colorado at Anschutz Medical Center" + }, + { + "author_name": "Elena WY Hsieh", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Angelo D'Alessandro", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Joaqu\u00edn M Espinosa", + "author_inst": "University of Colorado Anschutz Medical Campus" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.07.30.454520", "rel_title": "Spike protein multiorgan tropism suppressed by antibodies targeting SARS-CoV-2", @@ -644519,57 +646019,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.29.21261317", - "rel_title": "Correlation of SARS-CoV-2 Breakthrough Infections to Time-from-vaccine; Preliminary Study", - "rel_date": "2021-07-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.29.21261317", - "rel_abs": "The short-term effectiveness of a two-dose regimen of the BioNTech/Pfizer mRNA BNT162b2 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine was widely demonstrated. However, long term effectiveness is still unknown. A nationwide vaccination campaign was initiated early in Israel, allowing for a real-world evaluation of the interaction between protection and time-from-vaccine. The Delta (B.1.617.2) variant became the dominant strain in Israel in June 2021, as Israel is currently experiencing a new surge of cases. Leveraging the centralized computerized database of Maccabi Healthcare Services (MHS), we assessed the correlation between time-from-vaccine and incidence of breakthrough infection. We found that the risk for infection was significantly higher for early vaccinees compared to those vaccinated later. This preliminary finding should prompt further investigagions into long-term protection against different strains, and prospective clinical trials to examine the effect of a booster vaccine against breakthrough infection.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Roni Lotan", - "author_inst": "Maccabi health care services" - }, - { - "author_name": "Sivan Gazit", - "author_inst": "Maccabi Healthcare Services" - }, - { - "author_name": "Gabriel Chodik", - "author_inst": "Maccabi Healthcare Services" - }, - { - "author_name": "Tal Patalon", - "author_inst": "Maccabi health care services" - }, - { - "author_name": "Galit Perez", - "author_inst": "Maccabi health care servises" - }, - { - "author_name": "Amir Ben Tov", - "author_inst": "Maccabi health care services" - }, - { - "author_name": "barak mizrahi", - "author_inst": "ki" - }, - { - "author_name": "Nir Kalkstein", - "author_inst": "KI" - }, - { - "author_name": "Asaf Peretz", - "author_inst": "Assuta medical center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.29.21261156", "rel_title": "Performance of Immunoglobulin G Serology on Finger Prick Capillary Dried Blood Spot Samples to Measure SARS-CoV-2 Humoral Immunogenicity", @@ -644830,6 +646279,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.07.29.21261260", + "rel_title": "Development of a Post-Acute Sequelae of COVID-19 (PASC) Symptom Lexicon Using Electronic Health Record Clinical Notes", + "rel_date": "2021-07-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.29.21261260", + "rel_abs": "ObjectiveTo develop a comprehensive post-acute sequelae of COVID-19 (PASC) symptom lexicon from clinical notes to support PASC symptom identification and research.\n\nMethodsWe identified 26,117 COVID-19 positive patients from the Mass General Brighams electronic health records (EHR) and extracted 328,879 clinical notes from their post-acute infection period (day 51-110 from first positive COVID-19 test). The PASC symptom lexicon incorporated Unified Medical Language System(R) (UMLS) Metathesaurus concepts and synonyms based on selected semantic types. The MTERMS natural language processing (NLP) tool was used to automatically extract symptoms from a development dataset. The lexicon was iteratively revised with manual chart review, keyword search, concept consolidation, and evaluation of NLP output. We assessed the comprehensiveness of the lexicon and the NLP performance using a validation dataset and reported the symptom prevalence across the entire corpus.\n\nResultsThe PASC symptom lexicon included 355 symptoms consolidated from 1,520 UMLS concepts. NLP achieved an averaged precision of 0.94 and an estimated recall of 0.84. Symptoms with the highest frequency included pain (43.1%), anxiety (25.8%), depression (24.0%), fatigue (23.4%), joint pain (21.0%), shortness of breath (20.8%), headache (20.0%), nausea and/or vomiting (19.9%), myalgia (19.0%), and gastroesophageal reflux (18.6%).\n\nDiscussion and ConclusionPASC symptoms are diverse. A comprehensive PASC symptom lexicon can be derived using a data-driven, ontology-driven and NLP-assisted approach. By using unstructured data, this approach may improve identification and analysis of patient symptoms in the EHR, and inform prospective study design, preventative care strategies, and therapeutic interventions for patient care.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Liqin Wang", + "author_inst": "Brigham and Women's Hospital; Harvard Medical School" + }, + { + "author_name": "Dinah Foer", + "author_inst": "Brigham and Women's Hospital; Harvard Medical School" + }, + { + "author_name": "Erin MacPhaul", + "author_inst": "Brigham and women's Hospital" + }, + { + "author_name": "Ying-Chih Lo", + "author_inst": "Brigham and women's Hospital; Harvard Medical School" + }, + { + "author_name": "David W. Bates", + "author_inst": "Brigham and women's Hospital; Harvard Medical School" + }, + { + "author_name": "Li Zhou", + "author_inst": "Brigham and women's Hospital; Harvard Medical School" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.07.30.21261361", "rel_title": "Increased Autotaxin levels in severe COVID-19, correlating with IL-6 levels, endothelial dysfunction biomarkers, and impaired functions of dendritic cells", @@ -646125,69 +647613,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.07.27.21261210", - "rel_title": "Can Vaccine Prioritization Reduce Disparities in Covid-19 Burden for Historically Marginalized Populations?", - "rel_date": "2021-07-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.27.21261210", - "rel_abs": "1.ImportanceNationally stated goals for distributing SARS-CoV-2 vaccines included to reduce COVID-19 mortality, morbidity, and inequity using prioritization groups. However, the impact of these prioritization strategies is not well understood, particularly their effect on health inequity in COVID-19 burden for historically marginalized racial and ethnic populations.\n\nObjectiveTo assess the impact of vaccination prioritization and operational strategies on disparities in COVID-19 burden among historically marginalized populations, and on mortality and morbidity by race and ethnicity.\n\nDesignWe use an agent-based simulation model of North Carolina to project SARS-CoV-2 infections and COVID-19-associated deaths (mortality), hospitalizations (morbidity), and cases over 18 months (7/1/2020-12/31/2021) with vaccine distribution beginning 12/13/2020 to frontline medical and people 75+, assuming initial uptake similar to influenza vaccine. We study two-stage subsequent prioritization including essential workers (\"essential\"), adults 65+ (\"age\"), adults with high-risk health conditions, HMPs, or people in low income tracts, with eligibility for the general population in the third stage. For age-essential and essential-age strategies, we also simulated maximal uptake (100% for HMP or 100% for everyone), and we allowed for distribution to susceptible-only people.\n\nResultsPrioritizing Age then Essential had the largest impact on mortality (2.5% reduction from no prioritization); Essential then Age had the lowest morbidity and reduced infections (4.2% further than Age-Essential) without significantly impacting mortality. Under each prioritization scenario, the age-adjusted mortality burden for HMPs is higher (e.g., 33.3-34.1% higher for the Black population, 13.3%-17.0% for the Hispanic population) compared to the White population, and the gap grew under some prioritizations. In the Age-Essential strategy, the burden on HMPs decreases only when uptake is increased to 100% in HMPs. However, the Black population still had the highest mortality rate even with the Susceptible-Only distribution.\n\nConclusions and RelevanceSimulation results show that prioritization strategies have differential impact on mortality, morbidity, and disparities overall and by race and ethnicity. If prioritization schemes were not paired with increased uptake in HMPs, disparities did not improve and could worsen. Although equity was one of the tenets of vaccine distribution, the vaccination strategies publicly outlined are insufficient to remove and may exacerbate disparities between racial and ethnic groups, thus targeted strategies are needed for the future.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Erik Rosenstrom", - "author_inst": "North Carolina State University" - }, - { - "author_name": "Jessica A. Mele", - "author_inst": "North Carolina State University" - }, - { - "author_name": "Julie Ivy", - "author_inst": "North Carolina State University" - }, - { - "author_name": "Maria Mayorga", - "author_inst": "North Carolina State University" - }, - { - "author_name": "Mehul Patel", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Kristen Hassmiller Lich", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Karl D Johnson", - "author_inst": "University of North Carolina Gillings School of Global Public Health" - }, - { - "author_name": "Paul Delamater", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Pinar Keskinocak", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Ross Boyce", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Raymond Smith", - "author_inst": "East Carolina University" - }, - { - "author_name": "Julie L Swann", - "author_inst": "North Carolina State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.07.26.21261162", "rel_title": "Diagnostic performance of a novel digital immunoassay (RapidTesta SARS-CoV-2): a prospective observational study with 1,127 nasopharyngeal samples", @@ -646376,6 +647801,133 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.07.29.454261", + "rel_title": "COVID-ONE-humoral immune: The One-stop Database for COVID-19-specific Antibody Responses and Clinical Parameters", + "rel_date": "2021-07-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.29.454261", + "rel_abs": "Coronavirus disease 2019 (COVID-19), which is caused by SARS-CoV-2, varies with regard to symptoms and mortality rates among populations. Humoral immunity plays critical roles in SARS-CoV-2 infection and recovery from COVID-19. However, differences in immune responses and clinical features among COVID-19 patients remain largely unknown. Here, we report a database for COVID-19-specific IgG/IgM immune responses and clinical parameters (COVID-ONE humoral immune). COVID-ONE humoral immunity is based on a dataset that contains the IgG/IgM responses to 21 of 28 known SARS-CoV-2 proteins and 197 spike protein peptides against 2,360 COVID-19 samples collected from 783 patients. In addition, 96 clinical parameters for the 2,360 samples and information for the 783 patients are integrated into the database. Furthermore, COVID-ONE humoral immune provides a dashboard for defining samples and a one-click analysis pipeline for a single group or paired groups. A set of samples of interest is easily defined by adjusting the scale bars of a variety of parameters. After the \"START\" button is clicked, one can readily obtain a comprehensive analysis report for further interpretation. COVID-ONE-humoral immune is freely available at www.COVID-ONE.cn.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Zhaowei Xu", + "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" + }, + { + "author_name": "Yang Li", + "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" + }, + { + "author_name": "Qing Lei", + "author_inst": "Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Likun Huang", + "author_inst": "Fujian Key Laboratory of Crop Breeding by Design, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agricult" + }, + { + "author_name": "Dan-yun Lai", + "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" + }, + { + "author_name": "Shu-juan Guo", + "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" + }, + { + "author_name": "He-wei Jiang", + "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" + }, + { + "author_name": "Hongyan Hou", + "author_inst": "Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Yun-xiao Zheng", + "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" + }, + { + "author_name": "Xue-ning Wang", + "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" + }, + { + "author_name": "Jiaoxiang Wu", + "author_inst": "Tongren Hospital, Shanghai Jiao Tong University School of Medicine" + }, + { + "author_name": "Ming-liang Ma", + "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" + }, + { + "author_name": "Bo Zhang", + "author_inst": "Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Hong Chen", + "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" + }, + { + "author_name": "Caizheng Yu", + "author_inst": "Department of Public Health, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Jun-biao Xue", + "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" + }, + { + "author_name": "Hai-nan Zhang", + "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" + }, + { + "author_name": "Huan Qi", + "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" + }, + { + "author_name": "Siqi Yu", + "author_inst": "Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University" + }, + { + "author_name": "Mingxi Lin", + "author_inst": "Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University" + }, + { + "author_name": "Yandi Zhang", + "author_inst": "Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Xiaosong Lin", + "author_inst": "Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Zongjie Yao", + "author_inst": "Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Huiming Sheng", + "author_inst": "Tongren Hospital, Shanghai Jiao Tong University School of Medicine" + }, + { + "author_name": "Ziyong Sun", + "author_inst": "Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Feng Wang", + "author_inst": "Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Xionglin Fan", + "author_inst": "Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Sheng-ce Tao", + "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.07.28.21260814", "rel_title": "Influence of social determinants of health and county vaccination rates on machine learning models to predict COVID-19 case growth in Tennessee", @@ -648127,153 +649679,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.07.28.21261159", - "rel_title": "Six Month Safety and Efficacy of the BNT162b2 mRNA COVID-19 Vaccine", - "rel_date": "2021-07-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.28.21261159", - "rel_abs": "BackgroundBNT162b2 is a lipid nanoparticle-formulated, nucleoside-modified RNA vaccine encoding a prefusion-stabilized, membrane-anchored SARS-CoV-2 full-length spike protein. BNT162b2 is highly efficacious against COVID-19 and is currently authorized for emergency use or conditional approval worldwide. At the time of authorization, data beyond 2 months post-vaccination were unavailable.\n\nMethodsIn an ongoing, placebo-controlled, observer-blinded, multinational, pivotal efficacy study, 44,165 [≥]16-year-old participants and 2,264 12-15-year-old participants were randomized to receive 2 doses, 21 days apart, of 30 {micro}g BNT162b2 or placebo. Study endpoints reported here are vaccine efficacy (VE) against laboratory-confirmed COVID-19 and safety data, both up to 6 months post-vaccination.\n\nResultsBNT162b2 continued to be safe and well tolerated. Few participants had adverse events leading to study withdrawal. VE against COVID-19 was 91% (95% CI 89.0-93.2) through up to 6 months of follow-up, among evaluable participants and irrespective of previous SARS-CoV-2 infection. VE of 86%-100% was seen across countries and in populations with diverse characteristics of age, sex, race/ethnicity, and COVID-19 risk factors in participants without evidence of previous SARS-CoV-2 infection. VE against severe disease was 97% (95% CI 80.3-99.9). In South Africa, where the SARS-CoV-2 variant of concern, B.1.351 (beta), was predominant, 100% (95% CI 53.5, 100.0) VE was observed.\n\nConclusionWith up to 6 months of follow-up and despite a gradually declining trend in vaccine efficacy, BNT162b2 had a favorable safety profile and was highly efficacious in preventing COVID-19. (ClinicalTrials.gov number, NCT04368728)", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Stephen J Thomas", - "author_inst": "State University of New York, Upstate Medical University, Syracuse , NY" - }, - { - "author_name": "Edson D Moreira Jr.", - "author_inst": "Associa\u00e7\u00e3o Obras Sociais Irm\u00e3 Dulce and Oswaldo Cruz Foundation, Bahia, Brazil" - }, - { - "author_name": "Nicholas Kitchin", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Hurley, UK" - }, - { - "author_name": "Judith Absalon", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "Alejandra Gurtman", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "Stephen Lockhart", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Hurley, UK" - }, - { - "author_name": "John L Perez", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Collegeville, PA" - }, - { - "author_name": "Gonzalo P\u00e9rez Marc", - "author_inst": "iTrials-Hospital Militar Central, Buenos Aires, Argentina" - }, - { - "author_name": "Fernando P Polack", - "author_inst": "Fundacion INFANT, Buenos Aires, Argentina" - }, - { - "author_name": "Cristiano Zerbini", - "author_inst": "Centro Paulista de Investiga\u00e7\u00e3o Clinica, S\u00e3o Paulo, Brazil" - }, - { - "author_name": "Ruth Bailey", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Hurley, UK" - }, - { - "author_name": "Kena A Swanson", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "Xia Xu", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Collegeville, PA" - }, - { - "author_name": "Satrajit Roychoudhury", - "author_inst": "Global Product Development, Pfizer Inc, Peapack, NJ" - }, - { - "author_name": "Kenneth Koury", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "Salim Bouguermouh", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "Warren V Kalina", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "David Cooper", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "Robert W Frenck Jr.", - "author_inst": "Cincinnati Children's Hospital, Cincinnati, OH" - }, - { - "author_name": "Laura L Hammitt", - "author_inst": "Johns Hopkins Bloomberg School of Public Health, Baltimore, MD" - }, - { - "author_name": "\u00d6zlem T\u00fcreci", - "author_inst": "BioNTech, Mainz, Germany" - }, - { - "author_name": "Haylene Nell", - "author_inst": "Tiervlei Trial Centre, Karl Bremer Hospital, Cape Town, South Africa" - }, - { - "author_name": "Axel Schaefer", - "author_inst": "Medizentrum Essen Borbeck, Essen, Germany" - }, - { - "author_name": "Serhat \u00dcnal", - "author_inst": "Hacettepe University, Ankara, Turkey" - }, - { - "author_name": "Qi Yang", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "Paul Liberator", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "Dina B Tresnan", - "author_inst": "Worldwide Safety, Safety Surveillance and Risk Management, Pfizer, Inc, Groton, CT" - }, - { - "author_name": "Susan Mather", - "author_inst": "Worldwide Safety, Safety Surveillance and Risk Management, Pfizer, Inc, Collegeville, PA" - }, - { - "author_name": "Philip R Dormitzer", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "U\u011fur \u015eahin", - "author_inst": "BioNTech, Mainz, Germany" - }, - { - "author_name": "William C Gruber", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "Kathrin U Jansen", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "- C4591001 Clinical Trial Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.26.21261130", "rel_title": "Vaccine effectiveness when combining the ChAdOx1 vaccine as the first dose with an mRNA COVID-19 vaccine as the second dose", @@ -648634,6 +650039,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.28.21260870", + "rel_title": "Monitoring and forecasting the SARS-Covid-19 pandemic in France", + "rel_date": "2021-07-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.28.21260870", + "rel_abs": "Before the availability of vaccines, many countries have resorted multiple times to drastic social restrictions to prevent saturation of their health care system, and to regain control over an otherwise exponentially increasing COVID-19 pandemic. With the advent of data-sharing, computational approaches are key to efficiently control a pandemic with non-pharmaceutical interventions (NPIs). Here we develop a data-driven computational framework based on a time discrete and age-stratified compartmental model to control a pandemic evolution inside and outside hospitals in a constantly changing environment with NPIs. Besides the calendrical time, we introduce a second time-scale for the infection history, which allows for non-exponential transition probabilities. We develop inference methods and feedback procedures to successively recalibrate model parameters as new data becomes available. As a showcase, we calibrate the framework to study the pandemic evolution inside and outside hospitals in France until February 2021. We combine national hospitalization statistics from governmental websites with clinical data from a single hospital to calibrate hospitalization parameters. We infer changes in social contact matrices as a function of NPIs from positive testing and new hospitalization data. We use simulations to infer hidden pandemic properties such as the fraction of infected population, the hospitalisation probability, or the infection fatality ratio. We show how reproduction numbers and herd immunity levels depend on the underlying social dynamics.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Juergen Reingruber", + "author_inst": "Ecole Normale Superieure, IBENS-PSL, INSERM U1024, Group of data modeling and computational biology, Paris, France." + }, + { + "author_name": "Andrea Papale", + "author_inst": "Group of data modeling and computational biology,IBENS-PSL, Ecole Normale Superieure, Paris, France." + }, + { + "author_name": "Stephane Ruckly", + "author_inst": "INSERM IAME, U1137, Team DesCID, Paris, France" + }, + { + "author_name": "Jean-Francois Timsit", + "author_inst": "AP-HP, Bichat Hospital, Medical and infectious diseases ICU (MI2), F-75018 Paris, France" + }, + { + "author_name": "David Holcman", + "author_inst": "Group of data modeling and computational biology,IBENS-PSL, Ecole Normale Superieure, Paris, France." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.28.453981", "rel_title": "Single-Cell Profiling of the Antigen-Specific Response to BNT162b2 SARS-CoV-2 RNA Vaccine", @@ -650081,77 +651521,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.24.21261046", - "rel_title": "High throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruses.", - "rel_date": "2021-07-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.24.21261046", - "rel_abs": "BackgroundIn the current phase of COVID-19 pandemic, we are facing two serious public health challenges that include deficits in SARS-CoV-2 variant monitoring, and neglect of other co-circulating respiratory viruses. Additionally, accurate assessment of the evolution, extent and dynamics of the outbreak are required to understand the transmission of the virus amongst seemingly unrelated cases and provide critical epidemiological information. To address these challenges, we evaluated a new high-throughput next-generation sequencing (NGS), respiratory viral panel (RVP) that includes 40 viral pathogens with the aim of analyzing viral subtypes, mutational variants of SARS-CoV-2, model to understand the spread of the virus in the state of Georgia, USA, and to assess other circulating viruses in the same population.\n\nMethodsThis study evaluated a total of 522 samples that included 483 patient samples and 42 synthetic positive control material. The performance metrics were calculated for both clinical and reference control samples by comparing detection results with the RT-PCR assay. The limit of detection (LoD) studies were conducted as per the FDA guidelines. Inference and visualization of the phylogeny of the SARS-CoV-2 sequences were performed through the Nextstrain Command-Line Interface (CLI) tool, utilizing the associated augur and auspice toolkits.\n\nResultsThe performance metrics calculated using both the clinical samples and the reference controls revealed a PPA, NPA and accuracy of 95.98%, 85.96% and 94.4%, respectively. The LoD was determined to be 10 copies/ml with all 25 replicates detected across two different runs. The clade for pangolin lineage B that contains certain distant variants, including P4715L in ORF1ab, Q57H in ORF 3a and, S84L in ORF8 covarying with the D614G spike protein mutation were the most prevalent, early in the pandemic, in Georgia, USA. In our analysis, isolates from the same county formed paraphyletic groups, which indicated virus transmission between counties.\n\nConclusionThe study demonstrates the clinical and public health utility of the NGS-RVP to identify novel variants that can provide actionable information to prevent or mitigate emerging viral threats, models that provide insights into viral transmission patterns and predict transmission/ resurgence of regional outbreaks and provide critical information on co-circulating respiratory viruses that might be independent factors contributing to the global disease burden.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Nikhil Shri Sahajpal", - "author_inst": "Augusta University" - }, - { - "author_name": "Ashis K Mondal", - "author_inst": "Augusta University" - }, - { - "author_name": "Allan Njau", - "author_inst": "Aga Khan University Hospital" - }, - { - "author_name": "Zachary Petty", - "author_inst": "University of Georgia" - }, - { - "author_name": "Jiani Chen", - "author_inst": "University of Georgia" - }, - { - "author_name": "Sudha Ananth", - "author_inst": "Augusta University" - }, - { - "author_name": "Pankaj Ahluwalia", - "author_inst": "Augusta University" - }, - { - "author_name": "Colin Williams", - "author_inst": "Augusta University" - }, - { - "author_name": "Ted M Ross", - "author_inst": "University System of Georgia" - }, - { - "author_name": "Alka Chaubey", - "author_inst": "Augusta University" - }, - { - "author_name": "Grace DeSantis", - "author_inst": "Illumina Inc." - }, - { - "author_name": "Gary P. Schroth", - "author_inst": "Illumina Inc." - }, - { - "author_name": "Justin Bahl", - "author_inst": "University of Georgia" - }, - { - "author_name": "Ravindra Kolhe", - "author_inst": "Augusta University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.24.21261065", "rel_title": "COVID-Q: validation of the first COVID-19 questionnaire based on patient-rated symptom gravity", @@ -650532,6 +651901,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.24.453631", + "rel_title": "SARS-CoV-2 Delta variant pathogenesis and host response in Syrian hamsters", + "rel_date": "2021-07-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.24.453631", + "rel_abs": "B.1.617 lineage is becoming a dominant SARS-CoV-2 lineage worldwide and was the dominant lineage reported in second COVID-19 wave in India, which necessitated studying the properties of the variant. We evaluated the pathogenicity and virus shedding of B.1.617.2 (Delta) and B.1.617.3 lineage of SARS-CoV-2 and compared with that of B.1, an early virus isolate with D614G mutation in Syrian hamster model. Viral load, antibody response and lung disease were studied. No significant difference in the virus shedding pattern was observed among these variants studied. A significantly high SARS-CoV-2 sub genomic RNA could be detected in the respiratory tract of hamsters infected with Delta variant for 14 days. Delta variant induced lung disease of moderate severity in 40% of infected animals. The neutralizing capability of the B.1, Delta and B.1.617.3 variant infected animals were found significantly lower with the B.1.351 (Beta variant). The findings of the study support the attributed disease severity and the increased transmission potential of the Delta variant.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Sreelekshmy Mohandas", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, Pin-411021" + }, + { + "author_name": "Pragya Dhruv Yadav", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, Pin-411021" + }, + { + "author_name": "Anita Aich Shete", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, Pin-411021" + }, + { + "author_name": "Dimpal Nyayanit", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, Pin-411021" + }, + { + "author_name": "Gajanan N Sapkal", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, Pin-411021" + }, + { + "author_name": "Kavita Lole", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, Pin-411021" + }, + { + "author_name": "Nivedita Gupta", + "author_inst": "Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi, India, Pin-110029" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.07.26.453787", "rel_title": "N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry", @@ -652323,37 +653735,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.24.21261047", - "rel_title": "Proxalutamide Improves Inflammatory, Immunologic, and Thrombogenic Markers in Mild-to-Moderate COVID-19 Males and Females: an Exploratory Analysis of a Randomized, Double-Blinded, Placebo-Controlled Trial Early Antiandrogen Therapy (EAT) with Proxalutamide (The EAT-Proxa Biochemical AndroCoV-Trial)", - "rel_date": "2021-07-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.24.21261047", - "rel_abs": "BackgroundThe androgen theory on COVID-19 is based on the fact that males, in particular when affected by androgenetic alopecia, and females with hyperandrogenic states are more severely affected by COVID-19, while chronic users of antiandrogens experiment lower rates of COVID-19 complications. The theory finds plausibility on the androgen-mediated transmembrane protease serine 2 (TMPRSS-2), a key protein for SARS-CoV-2 cell entry. We demonstrated reduction of hospitalization rate using a potent non-steroidal antiandrogen (NSAA), proxalutamide, in both females and males COVID-19 outpatients. In this joint exploratory analysis, we aimed to demonstrate whether the efficacy of proxalutamide on mild-to-moderate COVID-19 could be justified by improvements in inflammatory, immunologic, and thrombogenic responses.\n\nMethodsThis is a joint post-hoc analysis of two double-blind, placebo-controlled two-arm randomized clinical trials (RCTs) on proxalutamide 200mg/day for seven days for female and male COVID-19 outpatients, respectively, compared to standard of care (SOC), of hematocrit, neutrophils lymphocytes, eosinophils, platelets, neutrophil-to-lymphocyte (N/L) ratio, ferritin, fibrinogen, D-dimer, ultrasensitive C-reactive protein (usCRP) lactate 1-hour erythrocyte sedimentation rate (1hESR), total testosterone, estradiol, sex hormone binding globulin (SHBG), oxygen saturation and heart rate measured on days 0, 1 and 7.\n\nResultsA total of 445 subjects were enrolled (268 males and 177 females) between October 21th 2020 and February 28th 2021, with similar baseline characteristics. Neutrophils were lower in proxalutamide group in Day 1 (p = 0.005) and Day 7 (p < 0.0001). Lymphocytes were higher in the proxalutamide group in Day 7 (p = 0.0001). Eosinophils were higher in the proxalutamide arm in Day 1 (p = 0.04) and Day 7 (p < 0.00010. In Day 7, platelets were higher in proxalutamide arm (p = 0.03). Ferritin levels were lower in proxalutamide arm in Day 7 (p = 0.03) Fibrinogen levels were lower in proxalutamide group in Days 1 and 7 (p < 0.0001 for both days). D-dimer levels were lower in proxalutamide group in Days 1 and 7 (p < 0.0001 for both days). UsCRP levels were reduced in proxalutamide group in Day 7 (p < 0.0001). 1hESR) was reduced in proxalutamide arm in Day 1 (p = 0.0009) and Day 7 (p < 0.0001). In males, testosterone levels were higher in proxalutamide group in Day 1 (p = 0.048) and Day 7 (p = 0.0001). In females, testosterone levels were higher in proxalutamide group in Day 7 (p = 0.018), and estradiol levels were higher in proxalutamide arm in Day 1 (p = 0.044). Oxygen saturation was higher in proxalutamide in Day 1 (p = 0.0006) and Day 7 (p < 0.0001).\n\nConclusionsThe substantial improvements observed in immunologic, inflammatory, thrombotic and oxygen markers with proxalutamide may support the reduction of hospitalization rate observed in both females and males with COVID-19 using proxalutamide, compared to standard of care.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Flavio A Cadegiani", - "author_inst": "Applied Biology, Inc. Irvine, CA, USA, and Corpometria Institute, Brasilia, Brazil." - }, - { - "author_name": "Andy Goren", - "author_inst": "Applied Biology, Inc. Irvine, CA, USA." - }, - { - "author_name": "Carlos Gustavo Wambier", - "author_inst": "Warren Alpert Medical School of Brown University" - }, - { - "author_name": "Ricardo Zimerman", - "author_inst": "Hospital da Brigada Militar, Porto Alegre, Brazil" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.24.21261007", "rel_title": "Use of Indomethacin for mild and moderate Covid -19 patients. A Randomized Control Trial", @@ -652510,6 +653891,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.21.21260810", + "rel_title": "Off-season RSV epidemics in Australia after easing of COVID-19 restrictions", + "rel_date": "2021-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.21.21260810", + "rel_abs": "Human respiratory syncytial virus (RSV) is an important cause of acute respiratory infection (ARI) with the most severe disease in the young and elderly1,2. Non-pharmaceutical interventions (NPIs) and travel restrictions for controlling COVID-19 have impacted the circulation of most respiratory viruses including RSV globally, particularly in Australia, where during 2020 the normal winter epidemics were notably absent3-6. However, in late 2020, unprecedented widespread RSV outbreaks occurred, beginning in spring, and extending into summer across two widely separated states of Australia, Western Australia (WA) and New South Wales (NSW) including the Australian Capital Territory (ACT). Genome sequencing revealed a significant reduction in RSV genetic diversity following COVID-19 emergence except for two genetically distinct RSV-A clades. These clades circulated cryptically, likely localized for several months prior to an epidemic surge in cases upon relaxation of COVID-19 control measures. The NSW/ACT clade subsequently spread to the neighbouring state of Victoria (VIC) and caused extensive outbreaks and hospitalisations in early 2021. These findings highlight the need for continued surveillance and sequencing of RSV and other respiratory viruses during and after the COVID-19 pandemic as mitigation measures introduced may result in unusual seasonality, along with larger or more severe outbreaks in the future.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "John-Sebastian Eden", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Chisha Sikazwe", + "author_inst": "PathWest Laboratory Medicine WA" + }, + { + "author_name": "Ruopeng Xie", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Yi-Mo Deng", + "author_inst": "WHO Collaborating Centre for Reference and Research on Influenza" + }, + { + "author_name": "Sheena G Sullivan", + "author_inst": "WHO Collaborating Centre for Reference and Research on Influenza" + }, + { + "author_name": "Alice Michie", + "author_inst": "The University of Western Australia" + }, + { + "author_name": "Avram Levy", + "author_inst": "PathWest Laboratory Medicine WA" + }, + { + "author_name": "Elena Cutmore", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Christopher C Blyth", + "author_inst": "PathWest Laboratory Medicine WA" + }, + { + "author_name": "Philip N Britton", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Nigel Crawford", + "author_inst": "Murdoch Children's Research Institute" + }, + { + "author_name": "Xiaomin Dong", + "author_inst": "WHO Collaborating Centre for Reference and Research on Influenza" + }, + { + "author_name": "Dominic E Dwyer", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Kimberly M Edwards", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Bethany A Horsburgh", + "author_inst": "The University of Sydney" + }, + { + "author_name": "David Foley", + "author_inst": "PathWest Laboratory Medicine WA" + }, + { + "author_name": "Karina Kennedy", + "author_inst": "Canberra Hospital" + }, + { + "author_name": "Cara Minney-Smith", + "author_inst": "PathWest Laboratory Medicine WA" + }, + { + "author_name": "David Speers", + "author_inst": "PathWest Laboratory Medicine WA" + }, + { + "author_name": "Rachel L Tulloch", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Edward C Holmes", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Vijaykrishna Dhanasekaran", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "David W Smith", + "author_inst": "PathWest Laboratory Medicine WA" + }, + { + "author_name": "Jen Kok", + "author_inst": "NSW Health Pathology - ICPMR" + }, + { + "author_name": "Ian G Barr", + "author_inst": "WHO Collaborating Centre for Reference and Research on Influenza" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.07.21.21260956", "rel_title": "Ethnic disparities in incident SARS-CoV-2 infections became wider during the second wave of SARS-CoV-2 in Amsterdam, the Netherlands: a population-based longitudinal study", @@ -655217,89 +656713,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.22.21260854", - "rel_title": "Air travel-related outbreak of multiple SARS-CoV-2 variants", - "rel_date": "2021-07-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.22.21260854", - "rel_abs": "BackgroundA large cluster of 59 cases were linked to a single flight with 146 passengers from New Delhi to Hong Kong in April 2021. This outbreak coincided with early reports of exponential pandemic growth in New Delhi, which reached a peak of >400,000 newly confirmed cases on 7 May 2021.\n\nMethodsEpidemiological information including date of symptom onset, date of positive-sample detection, and travel and contact history for individual cases from this flight were collected. Whole genome sequencing was performed, and sequences were classified based on the dynamic Pango nomenclature system. Maximum-likelihood phylogenetic analysis compared sequences from this flight alongside other cases imported from India to Hong Kong on 26 flights between June 2020 and April 2021, as well as sequences from India or associated with India-related travel from February to April 2021, and 1,217 reference sequences.\n\nResultsSequence analysis identified six lineages of SARS-CoV-2 belonging to two variants of concern (Alpha and Delta) and one variant of public health interest (Kappa) involved in this outbreak. Phylogenetic analysis confirmed at least three independent sub-lineages of Alpha with limited onward transmission, a superspreading event comprising 37 cases of Kappa, and transmission of Delta to only one passenger. Additional analysis of another 26 flights from India to Hong Kong confirmed widespread circulation of all three variants in India since early March 2021.\n\nConclusionsThe broad spectrum of disease severity and long incubation period of SARS-CoV-2 pose a challenge for surveillance and control. As illustrated by this particular outbreak, opportunistic infections of SARS-CoV-2 can occur irrespective of variant lineage, and requiring a nucleic acid test within 72 hours of departure may be insufficient to prevent importation or in-flight transmission.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Vijaykrishna Dhanasekaran", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Kimberly M Edwards", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Ruopeng Xie", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Haogao Gu", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Dillon C Adam", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Lydia DJ Chang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Sammi SY Cheuk", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Shreya Gurung", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Pavithra Krishnan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Daisy YM Ng", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Gigi YZ Liu", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Carrie KC Wan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Samuel SM Cheng", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Dominic NC Tsang", - "author_inst": "Centre for Health Protection" - }, - { - "author_name": "Benjamin J Cowling", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Malik Peiris", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Leo LM Poon", - "author_inst": "The University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.21.21260964", "rel_title": "Phase 1 safety and pharmacokinetics studies of BRII-196 and BRII-198, SARS-CoV-2 spike-targeting monoclonal antibodies", @@ -655512,6 +656925,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.23.21261013", + "rel_title": "Herd immunity induced by COVID-19 vaccination programs to suppress epidemics caused by SARS-CoV-2 wild type and variants in China", + "rel_date": "2021-07-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.23.21261013", + "rel_abs": "BackgroundTo allow a return to a pre-COVID-19 lifestyle, virtually every country has initiated a vaccination program to mitigate severe disease burden and control transmission. However, it remains to be seen whether herd immunity will be within reach of these programs.\n\nMethodsWe developed a data-driven model of SARS-CoV-2 transmission for China, a population with low prior immunity from natural infection. The model is calibrated considering COVID-19 natural history and the estimated transmissibility of the Delta variant. Three vaccination programs are tested, including the one currently enacted in China and model-based estimates of the herd immunity level are provided.\n\nResultsWe found that it is unlike to reach herd immunity for the Delta variant given the relatively low efficacy of the vaccines used in China throughout 2021, the exclusion of underage individuals from the targeted population, and the lack of prior natural immunity. We estimate that, assuming a vaccine efficacy of 90% against the infection, vaccine-induced herd immunity would require a coverage of 93% or higher of the Chinese population. However, even when vaccine-induced herd immunity is not reached, we estimated that vaccination programs can reduce SARS-CoV-2 infections by 53-58% in case of an epidemic starts to unfold in the fall of 2021.\n\nConclusionsEfforts should be taken to increase populations confidence and willingness to be vaccinated and to guarantee highly efficacious vaccines for a wider age range.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Hengcong Liu", + "author_inst": "Fudan University" + }, + { + "author_name": "Juanjuan Zhang", + "author_inst": "Fudan University" + }, + { + "author_name": "Jun Cai", + "author_inst": "Fudan University" + }, + { + "author_name": "Xiaowei Deng", + "author_inst": "Fudan University" + }, + { + "author_name": "Cheng Peng", + "author_inst": "Fudan University" + }, + { + "author_name": "Xinghui Chen", + "author_inst": "Fudan University" + }, + { + "author_name": "Juan Yang", + "author_inst": "Fudan University" + }, + { + "author_name": "Qianhui Wu", + "author_inst": "Fudan University" + }, + { + "author_name": "Zhiyuan Chen", + "author_inst": "Fudan University" + }, + { + "author_name": "Wen Zheng", + "author_inst": "Fudan University" + }, + { + "author_name": "Cecile Viboud", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Wenhong Zhang", + "author_inst": "Fudan University" + }, + { + "author_name": "Marco Ajelli", + "author_inst": "Indiana University School of Public Health" + }, + { + "author_name": "Hongjie Yu", + "author_inst": "Fudan University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.22.21261008", "rel_title": "A collaborative maternity dashboard (CoMaND) for the COVID-19 pandemic: a protocol for timely, adaptive monitoring of perinatal outcomes in Melbourne, Australia", @@ -657119,69 +658603,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.20.21260754", - "rel_title": "Increase in ventilatory ratio indicates progressive alveolar damage and suggests poor prognosis in severe COVID-19: A single-center retrospective observational study.", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260754", - "rel_abs": "BackgroundThe symptoms of severe COVID-19 are complex and wide-ranging even in intensive care unit (ICU) patients, who may successfully discontinue respiratory support in a short period or conversely require prolonged respiratory support. Damage in the lungs of COVID-19 patients is characterized pathologically as diffuse alveolar damage, the degree of which correlates with the severity of the disease. We hypothesized that the ventilatory ratio (VR), a surrogate parameter for the dead space fraction, might stratify the severity of COVID-19 and predict the successful discontinuation of respiratory support.\n\nMethodsForty COVID-19 patients in our ICU were enrolled in this study. Respiratory variables were collected from 2 hours (day 0) after the initiation of respiratory support. We monitored the longitudinal values of VR and other respiratory parameters for 28 days. Patients successfully discontinued from respiratory support by day 28 of ICU stay were defined as the successfully discontinued group, while those who died or failed to discontinue were defined as the failed to discontinue group. VR and other respiratory parameters were compared between these groups.\n\nResultsExcept for advanced age, prolonged ventilation period, and higher mortality in the failed to discontinue group, there were no significant differences between the groups in terms of any other background or respiratory parameter at 2 hours (day 0) after initiation of respiratory support. Longitudinal VR monitoring revealed significantly higher VR values in the failed to discontinue group than the successfully discontinued group on day 4 of respiratory support. Upon predicting the failure to discontinue respiratory support, the area under the receiver operating characteristic curve of VR values on day 4 of respiratory support was 0.748. A threshold of 1.56 achieved the highest predictive performance with a sensitivity of 0.667 and a specificity of 0.762. This threshold enabled the prediction of the successfully discontinued outcome at 0.810 of the negative predictive value.\n\nConclusionsElevated VR values on day 4 of respiratory support were predictive of successful discontinuation of respiratory support in patients with severe COVID-19. Longitudinal VR values after initiation of respiratory support can be used as a practical index to stratify severe COVID-19.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Natsuko Kaku", - "author_inst": "Osaka City University" - }, - { - "author_name": "Yu Nakagama", - "author_inst": "Osaka City University" - }, - { - "author_name": "Michinori Shirano", - "author_inst": "Osaka City General Hospital, Osaka City Hospital Organization" - }, - { - "author_name": "Sari Shinomiya", - "author_inst": "Osaka City General Hospital, Osaka City Hospital Organization" - }, - { - "author_name": "Kazuhiro Shimazu", - "author_inst": "Osaka City General Hospital, Osaka City Hospital Organization" - }, - { - "author_name": "Katsuaki Yamazaki", - "author_inst": "National Cerebral and Cardiovascular Center Hospital" - }, - { - "author_name": "Yoshito Maehata", - "author_inst": "Osaka City General Hospital, Osaka City Hospital Organization" - }, - { - "author_name": "Ryo Morita", - "author_inst": "Osaka City General Hospital, Osaka City Hospital Organization" - }, - { - "author_name": "Yuko Nitahara", - "author_inst": "Osaka City University" - }, - { - "author_name": "Hiromasa Yamamoto", - "author_inst": "Osaka City University" - }, - { - "author_name": "Yasumitsu Mizobata", - "author_inst": "Osaka City University" - }, - { - "author_name": "Yasutoshi Kido", - "author_inst": "Osaka City University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2021.07.18.21260718", "rel_title": "Real-Time SARS-CoV-2 Genotyping by High-Throughput Multiplex PCR Reveals the Epidemiology of the Variants of Concern in Qatar", @@ -657402,6 +658823,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, + { + "rel_doi": "10.1101/2021.07.18.21260732", + "rel_title": "Immunogenicity of mRNA-1273, BNT162b2 and Ad26.COV2.S COVID-19 vaccines", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.18.21260732", + "rel_abs": "BackgroundUnderstanding immunogenicity and effectiveness of SARS-CoV-2 vaccines is critical to guide rational use.\n\nMethodsWe compared the immunogenicity of mRNA-1273, BNT-162b2 or Ad26.COV2.S in ambulatory adults in Massachusetts, USA. To correlate immunogenicity with effectiveness of the three vaccines, we performed an inverse-variance meta-analysis of population level effectiveness from public health reports in >40 million individuals.\n\nResultsA single dose of either mRNA vaccine yielded comparable antibody and neutralization titers to convalescent individuals. Ad26.COV2.S yielded lower antibody concentrations and frequently negative neutralization titers. Bulk and cytotoxic T-cell responses were higher in mRNA1273 and BNT162b2 than Ad26.COV2.S recipients, and <50% of vaccinees demonstrate CD8+ T-cell responses to spike peptides. Antibody concentrations and neutralization titers increased comparably after the first dose of either vaccine, and further in recipients of a second dose. Prior infection was associated with high antibody concentrations and neutralization even after a single dose and regardless of vaccine. Neutralization of beta, gamma and delta strains were poorer regardless of vaccine. Relative to mRNA1273, the effectiveness of BNT162b2 was lower against infection and hospitalization; and Ad26COV2.S was lower against infection, hospitalization and death.\n\nConclusionsVariation in the immunogenicity correlates with variable effectiveness of the three FDA EUA vaccines deployed in the USA.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Vivek Naranbhai", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Wilfredo F Garcia-Beltran", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Christina Catherine Chang", + "author_inst": "University of New South Wales, Sydney, Australia" + }, + { + "author_name": "Christhian Berrios Mairena", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Julia Cara Thierauf", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Grace Kirkpatrick", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Maristela L Onozato", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Ju Cheng", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Kerri St. Denis", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Evan C Lam", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Clarety Kaseke", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Rhoda Tano-Menka", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Diane Yang", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Maia Pavlovic", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Wendy Yang", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Alexander Kui", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Tyler E Miller", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Michael G Astudillo", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Jennifer E Cahill", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Anand Dighe", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "David J Gregory", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Mark C Poznansky", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Gaurav Gaiha", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Alejandro B Balazs", + "author_inst": "Massachusetts General Hospital, Boston USA" + }, + { + "author_name": "Anthony John Iafrate", + "author_inst": "Massachusetts General Hospital, Boston USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.07.16.21260509", "rel_title": "Access to COVID-19 Vaccines in High-, Middle-, and Low-Income Countries Hosting Clinical Trials", @@ -659293,53 +660829,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.19.21260792", - "rel_title": "Prevalence of SARS CoV-2 infection among Health Care Workers of a hybrid tertiary COVID 19 hospital in Kerala", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260792", - "rel_abs": "Back ground and objectivesThis study was undertaken to estimate the prevalence of SARS-CoV-2 infection among Health care workers [HCWs] of a hybrid COVID treatment hospital in Kerala.\n\nMethodsThe study was conducted during 3rd week of January 2021. Among 3550 HCWs, 979 subjects were selected by stratified random sampling and grouped into high risk and low risk category based on job setting. Demographic details and clinical information regarding previous history of COVID 19 were collected at the time of SARS-CoV-2 IgG testing.\n\nResultsFrom 979 subjects, the data with respect to 940 health care workers were analysed. SARS-CoV-2 IgG was detected in 19.1% of HCWs. Seroprevalence among high risk group was 20.3% and that in low risk group was 7.4% [p=0.005]. In high-risk group, seropositivity was noted in 30.54 % of nurses, 19% hospital attenders, 18.9% resident doctors and 6.4% consultant doctors. In those with past history of SARS-CoV-2 infection, seropositivity was 75.4%. In those who were COVID positive during July2020, 33.3% were still IgG reactive.\n\nInterpretation and conclusionThe study reported 19.1% SARS CoV-2 IgG reactivity among health care workers in our hospital. Seropositivity was significantly higher in high risk group compared to low risk group. Antibody decay kinetics in our study is comparable to that in published literature. Infection control challenges in hybrid hospitals account for higher seropositivity in this study compared to overall seroprevalence among HCWs in Kerala.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Jessy S J", - "author_inst": "Dept of Biochemistry, Government Medical College Hospital, Thiruvananthapuram, Kerala India" - }, - { - "author_name": "Shamha Beegum", - "author_inst": "Dept of Biochemistry, Goverment Medical College, Thiruvananthapuram, Kerala, India" - }, - { - "author_name": "Genga Gopakumar", - "author_inst": "Dept of Biochemistry, Government Medical College Thiruvananthapuram, Kerala, India" - }, - { - "author_name": "Bindu G", - "author_inst": "Dept of Biochemistry, Government Medical College Thiruvananthapuram, Kerala, India" - }, - { - "author_name": "Chntha S", - "author_inst": "Deot of Community Medicine, Government Medical College Thiruvananthapuram, Kerala, India" - }, - { - "author_name": "Sukshma Sasidharan", - "author_inst": "Dept of Biochemistry, Government Medical College Thiruvananthapuram, Kerala, India" - }, - { - "author_name": "Ansu Tonio", - "author_inst": "Dept of Biochemistry, Government Medical College Thiruvananthapuram, Kerala, India" - }, - { - "author_name": "ARAVIND REGHUKUMAR", - "author_inst": "Dept of Infectious Diseases, Government Medical College Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.20.21260855", "rel_title": "SARS-CoV-2 incidence, transmission and reinfection in a rural and an urban setting: results of the PHIRST-C cohort study, South Africa, 2020-2021", @@ -659528,6 +661017,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.07.20.21260278", + "rel_title": "Seroprevalence and Dynamics of anti-SARS-CoV-2 antibody among healthcare workers following ChAdOx1 nCoV-19 vaccination", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260278", + "rel_abs": "BackgroundThe serological evaluations of IgG, IgM, and IgA to the SARS-CoV-2 proteins are widely used for the epidemiological assessment of COVID-19. The Health Care Workers (HCWs) are presumably exposed to a higher risk of acquiring the disease owing to their regular contact with the patients.\n\nMethodsCOVID-19 prevalence was investigated by classifying 313 HCWs into four groups based on their degree of exposure and estimating the IgG and total antibody. The serological assessment of the anti-SARS-CoV-2 antibody was conducted 21 days post-vaccination of first or both doses of the ChAdOx1 nCoV-19 vaccine among 174 HCWs. The vaccinated HCWs were followed up for 3 months for SARS-CoV-2 infection.\n\nFindingsThe levels of anti-SARS-CoV-2 IgG were comparable among different groups, but the seroprevalence gradually decreased from the most exposed to the less exposed group. The neutralizing antibody was positively correlated with IgG as well as total antibody. IgG was marginally decreased after 2 months followed by a significant drop after 4-6 months post-infection. However, 80% of the HCWs developed a detectable amount of IgG after the first dose of vaccination, the median titer of which was comparable to the seropositive HCWs after natural infection. Almost 100% of the HCWs developed antibodies after the second dose of vaccine with boosting effect among the seropositive HCWs. Although [~]11.5% of the vaccinated HCWs were infected with the SARS-CoV-2, [~]94% of them showed mild symptoms and recovered in home isolation without any O2 support.\n\nInterpretationsThe varying level of seroprevalence among the four groups suggested stratified spread of the disease. One dose of SARS-CoV-2 vaccination was found to be effective in terms of the antibody titer, while the second dose was required to cover the larger population. The effectiveness of the ChAdOx1 nCoV-19 vaccine was noticeable due to the low rate of post-vaccination infection with moderate or severe symptoms.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Soma Sarkar", + "author_inst": "NRS Medical College & Hospital" + }, + { + "author_name": "Shantanab das", + "author_inst": "Indian Statistical Institute; NRS Medical College & Hispital" + }, + { + "author_name": "Kabita Choudhury", + "author_inst": "NRS Medical College & Hospital" + }, + { + "author_name": "Saibal Mukherjee", + "author_inst": "NRS Medical College & Hospital" + }, + { + "author_name": "Raghunath Chatterjee", + "author_inst": "Indian Statistical institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.20.21260577", "rel_title": "All-cause mortality during SARS-CoV-2 Pandemic in India: Nationally-representative estimates independent of official death registry", @@ -660955,33 +662479,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.18.21260733", - "rel_title": "Spanish Version of the Attitude Towards COVID-19 Vaccines Scale: Reliability and Validity Assessment", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.18.21260733", - "rel_abs": "Background and purpose: The negative attitude to vaccines for coronavirus disease (COVID-19) has motivated the adaptation of instruments for this specific purpose. However, details of the reliability and validity of these scales are unknown. The study aimed to evaluate some indicators of the reliability and validity of the Spanish version of the Attitude towards COVID-19 Vaccines Scale. Methods: A validation study was carried out with 1,136 students of emerging age (18 and 29 years) from a Colombian university; 65.5% were female. Cronbach's alpha and McDonald's omega were calculated for reliability, and exploratory and confirmatory factor analyzes for validity. Additionally, the gender differential item functioning (DIF) was estimated with Kendall's tau b. Results: The Spanish version of Attitude towards COVID-19 Vaccines Scale showed high internal consistency (Cronbach's alpha of 0.94 and McDonald's omega of 0.95), a one-dimensional structure with acceptable goodness-of-fit indicators (CFI=0.94, TLI=0.91, and SRMR=0.04), and non-gender DIF (Kendall's tau b between 0.02 and 0.06). Conclusions: The Spanish version of the Attitude towards COVID-19 Vaccines Scale presents some appropriate reliability and validity indicators among university emerging adults. These findings should be explored in samples with other characteristics.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Adalberto Campo-Arias", - "author_inst": "Universidad del Magdalena, Santa Marta, Colombia" - }, - { - "author_name": "Leynin Esther Caamano-Rocha", - "author_inst": "Universidad del Magdalena, Santa Marta, Colombia" - }, - { - "author_name": "John Carlos Pedrozo-Pupo", - "author_inst": "Universidad del Magdalena, Santa Marta, Colombia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.07.18.21260567", "rel_title": "Predicting Managers' Mental Health Across Countries Using Country-Level COVID-19 Statistics", @@ -661170,6 +662667,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.07.19.21260373", + "rel_title": "Sociodemographic differences in patient experience with virtual care during COVID-19", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260373", + "rel_abs": "PurposeWe sought to understand patients care-seeking behaviours during the pandemic, their use and views of different virtual care modalities, and whether these differed by sociodemographic factors.\n\nMethodsWe conducted a multi-site cross-sectional patient experience survey at thirteen academic primary care teaching practices between May and June of 2020. An anonymized link to an electronic survey was sent to a subset of patients with a valid email address on file; sampling was based on birth month. For each question, the proportion of respondents who selected each response was calculated, followed by a comparison by sociodemographic characteristics using chi-squared tests.\n\nResultsIn total, 7482 participants responded to the survey. Most received care from their primary care clinic during the pandemic (67.7%, 5068/7482), the majority via phone (82.5%, 4195/5086). Among those who received care, 30.53% (1509/4943) stated that they delayed seeking care because of the pandemic. Most participants reported a high degree of comfort with phone (92.4%, 3824/4139), video (95.2%, 238/250) and email or messaging (91.3%, 794/870). However, those reporting difficulty making ends meet, poor or fair health, and arriving in Canada in the last 10 years reported lower levels of comfort with virtual care and fewer wanted their practice to continue offering virtual options after the pandemic.\n\nConclusionsOur study suggest that newcomers, people living with a lower income, and those reporting poor or fair health have a stronger preference and comfort for in-person primary care. Further research should explore potential barriers to virtual care and how these could be addressed.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Payal Agarwal", + "author_inst": "Womens College Hospital" + }, + { + "author_name": "Rick Wang", + "author_inst": "MAP Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, St. Michael's Hospital" + }, + { + "author_name": "Christopher Meaney", + "author_inst": "Department of Family and Community Medicine, Temerty Faculty of Medicine, University of Toronto" + }, + { + "author_name": "Sakina Walji", + "author_inst": "Department of Family and Community Medicine, Temerty Faculty of Medicine, University of Toronto" + }, + { + "author_name": "Ali Damji", + "author_inst": "Department of Family and Community Medicine, Temerty Faculty of Medicine, University of Toronto" + }, + { + "author_name": "Navsheer Gill Toor", + "author_inst": "Department of Family and Community Medicine, Temerty Faculty of Medicine, University of Toronto" + }, + { + "author_name": "Gina Yip", + "author_inst": "Department of Family and Community Medicine, Temerty Faculty of Medicine, University of Toronto" + }, + { + "author_name": "Debbie Elman", + "author_inst": "Department of Family and Community Medicine, Temerty Faculty of Medicine, University of Toronto" + }, + { + "author_name": "Tiffany Florindo", + "author_inst": "Department of Family and Community Medicine, Temerty Faculty of Medicine, University of Toronto" + }, + { + "author_name": "Susanna Fung", + "author_inst": "Department of Family and Community Medicine, Temerty Faculty of Medicine, University of Toronto" + }, + { + "author_name": "Melissa Witty", + "author_inst": "Department of Family and Community Medicine, Temerty Faculty of Medicine, University of Toronto" + }, + { + "author_name": "Thuy Nga Pham", + "author_inst": "Department of Family and Community Medicine, Temerty Faculty of Medicine, University of Toronto" + }, + { + "author_name": "Noor Ramji", + "author_inst": "Department of Family and Community Medicine, Temerty Faculty of Medicine, University of Toronto" + }, + { + "author_name": "Tara Kiran", + "author_inst": "St. Michael's Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2021.07.16.21260675", "rel_title": "Estimation of COVID-19 recovery and decease periods in Canada using machine learning algorithms", @@ -662725,105 +664293,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2021.07.21.451321", - "rel_title": "Unlike Chloroquine, mefloquine inhibits SARS-CoV-2 infection in physiologically relevant cells and does not induce viral variants.", - "rel_date": "2021-07-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.21.451321", - "rel_abs": "Repositioning of clinical approved drugs could represent the fastest way to identify therapeutic options during public health emergencies, the majority of drugs explored for repurposing as antivirals for 2019 coronavirus disease (COVID-19) have failed to demonstrate clinical benefit. Without specific antivirals, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic continues to cause major global mortality. Antimalarial drugs, such as chloroquine (CQ)/hydroxychloroquine (HCQ) and mefloquine have emerged as potential anti-SARS-CoV-2 antivirals. CQ/HCQ entered the Solidarity and RECOVERY clinical trials against COVID-19 and showed lack of efficacy. Importantly, mefloquine is not a 4-aminoquinoline like CQ and HCQ and has been previously repurposed for other respiratory diseases. Unlike the 4-aminoquinolines that accumulate in the high pH of intracellular lysosomes of the lung, the high respiratory tract penetration of mefloquine is driven by its high lipophilicity. While CQ and HCQ exhibit activity in Vero E6 cells, their activity is obviated in TMPRSS2-expressing cells, such as Calu-3 cells, which more accurately recapitulate in vivo entry mechanisms for SARS-CoV-2. Accordingly, here we report the anti-SARS-CoV-2 activity of mefloquine in Calu-3 type II pneumocytes and primary human monocytes. Mefloquine inhibited SARS-CoV-2 replication in Calu-3 cells with low cytotoxicity and EC50 and EC90 values of 1.2 and 5.3 {micro}M, respectively. In addition, mefloquine reduced up to 68% the SARS-CoV-2 RNA levels in infected monocytes, reducing viral-induced inflammation. Mefloquine blocked early steps of the SARS-CoV-2 replicative cycle and was less prone than CQ to induce drug-associated viral mutations and synergized with RNA polymerase inhibitor. The pharmacological parameters of mefloquine are consistent with its plasma exposure in humans and its tissue-to-plasma predicted coefficient points that this drug may accumulate in the lungs. These data indicate that mefloquine could represent an orally available clinically approved drug option against COVID-19 and should not be neglected on the basis of the failure of CQ and HCQ.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Carolina Q. Sacramento", - "author_inst": "Fiocruz" - }, - { - "author_name": "Natalia Fintelman-Rodrigues", - "author_inst": "Fiocruz" - }, - { - "author_name": "Suelen S. G. Dias", - "author_inst": "Fiocruz" - }, - { - "author_name": "Jairo R Temerozo", - "author_inst": "Oswaldo Cruz Institute" - }, - { - "author_name": "Aline de Paula D. Da Silva", - "author_inst": "Fiocruz" - }, - { - "author_name": "Carine S. da Silva", - "author_inst": "Fiocruz" - }, - { - "author_name": "Andre C. Ferreira", - "author_inst": "FIOCRUZ" - }, - { - "author_name": "Mayara Mattos", - "author_inst": "Fiocruz" - }, - { - "author_name": "Vinicius C. Soares", - "author_inst": "Fiocruz" - }, - { - "author_name": "Filipe Pereira-Dutra", - "author_inst": "Fiocruz" - }, - { - "author_name": "Milene D. Miranda", - "author_inst": "Fiocruz" - }, - { - "author_name": "Debora F. Barreto-Vieira", - "author_inst": "Fiocruz" - }, - { - "author_name": "Marcos Alexandre N. da Silva", - "author_inst": "Fiocruz" - }, - { - "author_name": "Suzana de Siqueira Santos", - "author_inst": "Fundacao Getulio Vargas" - }, - { - "author_name": "Mateo Torres", - "author_inst": "Fundacao Getulio Vargas" - }, - { - "author_name": "Rajith K. R. Rajoli", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Alberto Paccanaro", - "author_inst": "Fundacao Getulio Vargas" - }, - { - "author_name": "Andrew Owen", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Dumith C. Bou-Habib", - "author_inst": "Fiocruz" - }, - { - "author_name": "Patricia T. Bozza", - "author_inst": "Fiocruz" - }, - { - "author_name": "Thiago Moreno L. Souza", - "author_inst": "Fiocruz" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.07.16.452756", "rel_title": "Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence", @@ -663180,6 +664649,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.17.21260655", + "rel_title": "Post-COVID Syndrome. A Case Series and Comprehensive Review", + "rel_date": "2021-07-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.17.21260655", + "rel_abs": "The existence of a variety of symptoms with a duration beyond the acute phase of COVID-19, is referred to as post-COVID syndrome (PCS). We aimed to report a series of patients with PCS attending a Post-COVID Unit and offer a comprehensive review on the topic. Adult patients with previously confirmed SARS-CoV-2 infection were systematically assessed through a semi-structured and validated survey. Total IgG, IgA and IgM serum antibodies to SARS-CoV-2 were evaluated by an electrochemiluminescence immunoassay. A systematic review of the literature and meta-analysis were conducted, following PRISMA guidelines. Univariate and multivariate methods were used to analyze data. Out of a total of 100 consecutive patients, 53 were women, the median of age was 49 years (IQR: 37.8 to 55.3), the median of post-COVID time after the first symptoms was 219 days (IQR: 143 to 258), and 65 patients were hospitalized during acute COVID-19. Musculoskeletal, digestive (i.e., diarrhea) and neurological symptoms including depression (by Zung scale) were the most frequent observed in PCS patients. A previous hospitalization was not associated with PCS manifestation. Arthralgia and diarrhea persisted in more than 40% of PCS patients. The median of anti-SARS-CoV-2 antibodies was 866.2 U/mL (IQR: 238.2 to 1681). Despite this variability, 98 patients were seropositive. Based on autonomic symptoms (by COMPASS 31) two clusters were obtained with different clinical characteristics. Levels of anti-SARS-CoV-2 antibodies were not different between clusters. A total of 40 articles (11,196 patients) were included in the meta-analysis. Fatigue/muscle weakness, dyspnea, pain and discomfort, anxiety/depression and impaired concentration were presented in more than 20% of patients reported. In conclusion, PCS is mainly characterized by musculoskeletal, pulmonary, digestive and neurological involvement including depression. PCS is independent of severity of acute illness and humoral response. Long-term antibody responses to SARS-CoV-2 infection and a high inter-individual variability were confirmed. Future studies should evaluate the mechanisms by which SARS-CoV-2 may cause PCS and the best therapeutic options.\n\nHighlightsO_LIPCS is mainly characterized by musculoskeletal, pulmonary, digestive and neurological involvement including depression.\nC_LIO_LIPCS is independent of severity of acute illness and humoral immune response.\nC_LIO_LIAutonomic symptoms may help to classify patients with PCS.\nC_LIO_LILong-term antibody responses to SARS-CoV-2 infection and a high inter-individual variability were confirmed.\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Juan-Manuel Anaya", + "author_inst": "Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia" + }, + { + "author_name": "Manuel Rojas", + "author_inst": "Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia" + }, + { + "author_name": "Martha L. Salinas", + "author_inst": "Clinica del Occidente, Bogota, Colombia" + }, + { + "author_name": "Yhojan Rodriguez", + "author_inst": "Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia" + }, + { + "author_name": "Geraldine Roa", + "author_inst": "Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia" + }, + { + "author_name": "Marcela Lozano", + "author_inst": "Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia" + }, + { + "author_name": "Monica Rodriguez-Jimenez", + "author_inst": "Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia" + }, + { + "author_name": "Norma Montoya", + "author_inst": "Clinica del Occidente, Bogota, Colombia" + }, + { + "author_name": "Elizabeth Zapata", + "author_inst": "Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia" + }, + { + "author_name": "- Post-COVID study group", + "author_inst": "" + }, + { + "author_name": "Diana M Monsalve", + "author_inst": "Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia" + }, + { + "author_name": "Yeny Acosta-Ampudia", + "author_inst": "Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia" + }, + { + "author_name": "Carolina Ramirez-Santana", + "author_inst": "Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.19.452809", "rel_title": "CRISPR screens for host factors critical for infection by SARS-CoV-2 variants of concern identify GATA6 as a central modulator of ACE2.", @@ -664519,129 +666055,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.15.21260213", - "rel_title": "Temporal Variations in Seroprevalence of SARS-CoV-2 Infections by Race and Ethnicity in Arkansas.", - "rel_date": "2021-07-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.15.21260213", - "rel_abs": "ObjectiveOur objective is to estimate CoV-2 infection rates in a rural state using seroprevalence of antibodies to CoV-2 as an indicator of infection.\n\nStudy Design and SettingThis is a single-site study within an academic center and regional programs within the state of Arkansas. We obtained residual serum samples from a convenience sample of adults who were outpatients and came to the hospital or regional clinic for non-COVID-related reasons. We collected remnant in three time periods (August 15 to September 5, September 12 to October 24, and November 7 to December 19).\n\nResultsIn 2020, the overall age, gender, and race standardized prevalence of CoV-2 antibodies was 2.6% (August to September), 4.1% (September to October), and 7.4% (November to December). There was no difference in seroprevalence between urban compared to rural areas. Positive tests were not uniformly distributed across racial and ethnic minorities. Higher seroprevalence rates were found in Hispanics and Blacks or African Americans compared to whites across all time periods.\n\nConclusionsIn a state with a large rural population, 2.6-7.4% of people experienced CoV-2 infection by December 2020. Blacks and Hispanics had disproportionately higher rates of CoV-2 infections than whites.\n\nWhat is new?O_ST_ABSKey findingsC_ST_ABSIn this prospective convenience sampling of remnant sera, we found increasing seroprevalence from 2.6% to 7.4% (August 2020 to December 2020). Higher seroprevalence rates were found in Hispanics and Blacks or African Americans compared to whites across all time periods, and no difference was determined between those individuals from rural or urban areas.\n\nWhat this adds to what is knownIn a largely rural population, Blacks and Hispanics had disproportionately higher rates of CoV-2 infections than whites, and these populations need to be studied further regarding outcomes.\n\nWhat is the implication?There are health disparities that exist regarding CoV-2 infections, and we should target vaccination information and education to these groups.\n\nHighlights- SARS-CoV-2 infections increased from 2.6% to 7.4% from August to December 2020.\n- Higher seroprevalence was found in Hispanics and Blacks as compared to whites.\n- There was no difference in the seroprevalence in rural compared to urban areas.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Joshua L Kennedy", - "author_inst": "University of Arkansas for Medical Sciences/ Arkansas Children's Research Institute" - }, - { - "author_name": "J Craig Forrest", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Sean G Young", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Benjamin Amick", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Mark Williams", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Laura James", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Jessica Snowden", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Victor Cardenas", - "author_inst": "UAMS Fay W. Boozman College of Public Health" - }, - { - "author_name": "Danielle Boothe", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Catherine Kirkpatrick", - "author_inst": "Arkansas Children's Research Institute" - }, - { - "author_name": "Zeel Modi", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Katherine Caid", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Shana Owens", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Marianne Kouassi", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Ryan Mann", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Claire Putt", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Katherine Irish-Clardy", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Michael Macechko", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Ronald K Brimberry", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Wendy N Nembhard", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Ruofei Du", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Jing Jin", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Namvar Zohoori", - "author_inst": "Arkansas Department of Health" - }, - { - "author_name": "Atul Kothari", - "author_inst": "Arkansas Department of Health" - }, - { - "author_name": "Hoda Hagrass", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Ericka Olgaard", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Karl W Boehme", - "author_inst": "University of Arkansas for Medical Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.15.21260561", "rel_title": "Viral Load of SARS-CoV-2 in Respiratory Aerosols Emitted by COVID-19 Patients while Breathing, Talking, and Singing", @@ -664954,6 +666367,145 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.15.21260621", + "rel_title": "Antibody and T cell responses to Sinopharm/BBIBP-CorV in naive and previously infected individuals in Sri Lanka", + "rel_date": "2021-07-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.15.21260621", + "rel_abs": "BackgroundAs there are limited data of the immunogenicity of the Sinopharm/BBIBP-CorV in different populations, antibody responses against different SARS-CoV-2 variants of concern and T cell responses, we investigated the immunogenicity of the vaccine, in individuals in Sri Lanka.\n\nMethodsSARS-CoV-2-specific antibodies were measured in 282 individuals who were seronegative at baseline, and ACE2 receptor blocking antibodies, antibodies to the receptor binding domain (RBD) of the wild type (WT), B.1.1.7, B.1.351 and B.1.617.2, ex vivo and cultured IFN{gamma} ELISpot assays, intracellular cytokine secretion assays and B cell ELISpot assays were carried out in a sub cohort of the vaccinees at 4 weeks and at 6 weeks (2 weeks after the second dose).\n\nResults95% of the vaccinees seroconverted, although the seroconversion rates were significantly lower (p<0.001) in individuals >60 years (93.3%) compared to those who were 20 to 39 years (98.9%). 81.25% had ACE2 receptor blocking antibodies at 6 weeks, and there was no difference in these antibody titres in vaccine sera compared to convalescent sera (p=0.44). Vaccinees had significantly less (p<0.0001) antibodies to the RBD of WT and B.1.1.7, although there was no difference in antibodies to the RBD of B.1.351 and B.1.617.2 compared to convalescent sera. 27.7% of 46.4% of vaccinees had ex vivo IFN{gamma} and cultured ELISpot responses respectively, and IFN{gamma} and CD107a responses were detected by flow cytometry.\n\nConclusionsSinopharm/BBIBP-CorV appeared to induce high seroconversion rates and induce a similar level of antibody responses against ACE2 receptor, B.1.617.2 and B.1.351 as seen following natural infection.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Chandima Jeewandara", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" + }, + { + "author_name": "Inoka Sepali Aberathna", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka" + }, + { + "author_name": "Pradeep Dharshana Pushpakumara", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka" + }, + { + "author_name": "Achala Kamaladasa", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka" + }, + { + "author_name": "Dinuka Guruge", + "author_inst": "Colombo Municipal Council, Colombo, Sri Lanka" + }, + { + "author_name": "Deshni Jayathilaka", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" + }, + { + "author_name": "Banuri Gunesekara", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" + }, + { + "author_name": "Shyrar Tanussiya", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" + }, + { + "author_name": "Heshan Kuruppu", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" + }, + { + "author_name": "Thushali Ranasinghe", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" + }, + { + "author_name": "Shashika Dayarathne", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" + }, + { + "author_name": "Osanda Dissanayaka", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka" + }, + { + "author_name": "Nayanathara Gamalath", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka" + }, + { + "author_name": "Dinithi Ekanayaka", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" + }, + { + "author_name": "M.P.D.J. Jayamali", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" + }, + { + "author_name": "Ayesha Wijesinghe", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" + }, + { + "author_name": "Madushika Dissanayaka", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" + }, + { + "author_name": "Deshan Madushanka", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" + }, + { + "author_name": "Tibutius Jayadas", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" + }, + { + "author_name": "Anushika Mudunkotuwa", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" + }, + { + "author_name": "Gayasha Somathilaka", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" + }, + { + "author_name": "Michael James Harvie", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" + }, + { + "author_name": "Thashmi Nimasha", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" + }, + { + "author_name": "Saubhagya Danasekara", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura," + }, + { + "author_name": "Ruwan Wijayamuni", + "author_inst": "Colombo Municipal Council, Colombo, Sri Lanka" + }, + { + "author_name": "Lisa Schimanski", + "author_inst": "Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford" + }, + { + "author_name": "Tiong Tan", + "author_inst": "Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford" + }, + { + "author_name": "Tao Dong", + "author_inst": "Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford" + }, + { + "author_name": "Alain Townsend", + "author_inst": "University of Oxford" + }, + { + "author_name": "Graham Ogg", + "author_inst": "MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford" + }, + { + "author_name": "Gathsaurie Neelika Malavige", + "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.07.15.21260234", "rel_title": "Post-COVID-19 symptoms are not uncommon among recovered patients-A cross-sectional online survey among the Indian population.", @@ -666513,37 +668065,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.07.19.452918", - "rel_title": "Rosin Soap Exhibits Virucidal Activity", - "rel_date": "2021-07-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.19.452918", - "rel_abs": "Chemical methods of virus inactivation are used routinely to prevent viral transmission in both a personal hygiene capacity but also in at-risk environments like hospitals. Several virucidal products exist, including hand soaps, gels and surface disinfectants. Resin acids, which can be derived from Tall oil produced from trees, have been shown to exhibit anti-bacterial activity. However, whether these products or their derivatives have virucidal activity is unknown. Here, we assessed the capacity of Rosin soap to inactivate a panel of pathogenic mammalian viruses in vitro. We show that Rosin soap can inactivate the human enveloped viruses: influenza A virus (IAV), respiratory syncytial virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For IAV, rosin soap could provide a 100,000-fold reduction in infectivity. However, Rosin soap failed to affect the non-enveloped encephalomyocarditis virus (EMCV). The inhibitory effect of Rosin soap against IAV infectivity was dependent on its concentration but not dependent on incubation time nor temperature. Together, we demonstrate a novel chemical inactivation method against enveloped viruses, which could be of use in preventing virus infections in certain settings.\n\nImportanceViruses remain a significant cause of human disease and death, most notably illustrated through the current Covid-19 pandemic. Control of virus infection continues to pose a significant global health challenge to the human population. Viruses can spread through multiple routes, including via environmental and surface contamination where viruses can remain infectious for days. Methods to inactivate viruses on such surfaces may help mitigate infection. Here we present evidence identifying a novel virucidal product in Rosin soap, which is produced from Tall oil from coniferous trees. Rosin soap was able to rapidly and potently inactivate influenza virus and other enveloped viruses.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Derek J Fairley", - "author_inst": "Belfast Health and Social Care Trust" - }, - { - "author_name": "Hannele Kettunen", - "author_inst": "Hankkija Oy" - }, - { - "author_name": "Juhani Vuorenmaa", - "author_inst": "Hankkija Oy" - }, - { - "author_name": "Juha Orte", - "author_inst": "Forchem Oy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.07.16.452748", "rel_title": "Key substitutions in the spike protein of SARS-CoV-2 variants can predict resistance to monoclonal antibodies, but other substitutions can modify the effects", @@ -666732,6 +668253,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.14.21260471", + "rel_title": "Validation of a Novel Molecular Assay to the Diagnostic of COVID-19 Based on Real Time PCR with High Resolution Melting", + "rel_date": "2021-07-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.14.21260471", + "rel_abs": "With the emergence of the Covid-19 pandemic, the world faced an unprecedented need for RT-qPCR-based molecular diagnostic tests, leading to a lack of kits and inputs, especially in developing countries. Hence, the costs for commercial kits and inputs were overrated, stimulating the development of alternative methods to detect SARS-CoV-2 in clinical specimens. The availability of the complete SARS-CoV-2 genome at the beginning of the pandemic facilitated the development of specific primers and standardized laboratory protocols for Covid-19 molecular diagnostic. High-sensitive and cost-effective molecular biology technique based on the Melting Temperature differences between purine and pyrimidine bases can be used to the detection and genotyping of pathogens in clinical specimens. Here, a RT-qPCR assays with High Resolution Melting (HRM-RTqPCR) was developed for different regions of the SARS-CoV-2 genome (RdRp, E and N) and an internal control (human RNAse P gene). The assays were validated using synthetic sequences from the viral genome and clinical specimens (nasopharyngeal swabs, serum and saliva) of sixty-five patients with severe or moderate COVID-19 from different states in Brazil, in comparison to a commercial TaqMan RT-qPCR assay, as gold standard. The sensitivity of the HRM-RTqPCR assays targeting N, RdRp and E were 94.12, 98.04 and 92.16%, with 100% specificity to the 3 targets, and diagnostic accuracy of 95.38, 98.46 and 93.85%, respectively. Thus, the HRM-RTqPCR emerges as an alternative and low-cost methodology to increase the molecular diagnostic of patients suspicious for Covid-19, especially in restricted-budget laboratories.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Beatriz Iandra da Silva Ferreira", + "author_inst": "Real Time PCR Platform RPT09A, Laboratory of Molecular Biology and Endemic Diseases, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil" + }, + { + "author_name": "Natalia Lins da Silva Gomes", + "author_inst": "Real Time PCR Platform RPT09A, Laboratory of Molecular Biology and Endemic Diseases, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil" + }, + { + "author_name": "Wagner Luis da Costa Nunes Pimentel Coelho", + "author_inst": "Laboratory of Technological Development in Virology, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil" + }, + { + "author_name": "Vanessa Duarte Costa", + "author_inst": "Laboratory of Viral Hepatitis, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil" + }, + { + "author_name": "Vanessa Cristine de Souza Carneiro", + "author_inst": "Laboratory of Molecular Virology, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil" + }, + { + "author_name": "Rafael Lopes Kader", + "author_inst": "University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro , Rio de Janeiro, Brazil" + }, + { + "author_name": "Marisa Pimentel Amaro", + "author_inst": "University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro , Rio de Janeiro, Brazil" + }, + { + "author_name": "Livia Melo Villar", + "author_inst": "Laboratory of Viral Hepatitis, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil" + }, + { + "author_name": "Fabio Miyajima", + "author_inst": "Oswaldo Cruz Foundation (Fiocruz), Branch Ceara, Eusebio, Brazil" + }, + { + "author_name": "Soniza Vieira Alves-Leon", + "author_inst": "University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro , Rio de Janeiro, Brazil" + }, + { + "author_name": "Vanessa Salete de Paula", + "author_inst": "Laboratory of Molecular Virology, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil" + }, + { + "author_name": "Luciane Almeida Amado Leon", + "author_inst": "Laboratory of Technological Development in Virology, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil" + }, + { + "author_name": "Otacilio C. Moreira", + "author_inst": "Real Time PCR Platform RPT09A, Laboratory of Molecular Biology and Endemic Diseases, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.14.21260291", "rel_title": "Sequencing SARS-CoV-2 from Antigen Tests", @@ -668439,77 +670027,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.07.13.21260417", - "rel_title": "Clinical outcomes in vaccinated individuals hospitalized with Delta variant of SARS-CoV-2", - "rel_date": "2021-07-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.13.21260417", - "rel_abs": "Emerging variants of SARS-CoV-2 with increased transmissibility or immune escape have been causing large outbreaks of COVID-19 infections across the world. As most of the vaccines currently in use have been derived from viral strains circulating in the early part of the pandemic, it becomes imperative to constantly assess the efficacy of these vaccines against emerging variants. In this hospital-based cohort study, we analysed clinical profiles and outcomes of 1161 COVID-19 hospitalized patients (vaccinated with COVISHIELD (ChAdOx1) or COVAXIN (BBV-152), n = 495 and unvaccinated n = 666) in Hyderabad, India between April 24th and May 31st 2021. Viral genome sequencing revealed that >90% of patients in both groups were harbouring the Delta variant (Pango lineage B.1.617.2) of SARS-CoV-2. Vaccinated individuals showed higher neutralizing antibodies (545{+/-}1256 AU/ml Vs 51.1{+/-}296 AU/ml; p<0.001) and significantly decreased Ferritin (392.26 {+/-} 448.4 ng/mL Vs 544.82 {+/-} 641.41 ng/mL; p<0.001) and LDH (559.45 {+/-} 324.05 U/L Vs 644.99 {+/-} 294.03 U/L; p<0.001), when compared to the unvaccinated group. Severity of the disease (3.2% Vs 7.2%; p=0.0039) and requirement of ventilatory support (2.8% Vs 5.9%; p=0.0154) were significantly low in the vaccinated group despite the fact that these individuals had significantly higher age and risk factors. The rate of mortality was about 50% lower (2/132=1.51%) in the completely vaccinated breakthrough infections although mortality in individuals who had received a single dose was similar to the unvaccinated group (9/269=3.35% vs 23/666= 3.45%). Our results demonstrate that both COVISHIELD and COVAXIN are effective in preventing disease severity and mortality against the Delta variant in completely vaccinated hospitalized patients.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Jagadeesh Kumar V", - "author_inst": "AIG Hospitals, Internal Medicine, Mindspace Rd, Gachibowli, Hyderabad, Telangana 500032" - }, - { - "author_name": "Divya Tej Sowpati", - "author_inst": "CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Habsiguda, Hyderabad 500007" - }, - { - "author_name": "Apoorva Munigela", - "author_inst": "AIG Hospitals, Internal Medicine, Mindspace Rd, Gachibowli, Hyderabad, Telangana 500032" - }, - { - "author_name": "Sofia Banu", - "author_inst": "CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Habsiguda, Hyderabad 500007" - }, - { - "author_name": "Archana Bharadwaj Siva", - "author_inst": "CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Habsiguda, Hyderabad 500007" - }, - { - "author_name": "Mitnala Sasikala", - "author_inst": "Asian Healthcare Foundation, Mindspace Rd, Gachibowli, Hyderabad, Telangana 500032" - }, - { - "author_name": "Chandrasekhar Nutalapati", - "author_inst": "AIG Hospitals, Internal Medicine, Mindspace Rd, Gachibowli, Hyderabad, Telangana 500032" - }, - { - "author_name": "Anand Kulkarni", - "author_inst": "AIG Hospitals, Internal Medicine, Mindspace Rd, Gachibowli, Hyderabad, Telangana 500032" - }, - { - "author_name": "Payel Mukherjee", - "author_inst": "CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Habsiguda, Hyderabad 500007" - }, - { - "author_name": "Lamuk Zaveri", - "author_inst": "CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Habsiguda, Hyderabad 500007" - }, - { - "author_name": "- CCMB COVID-19 Team", - "author_inst": "" - }, - { - "author_name": "- AIG Hospitals COVID-19 Vaccine study Team", - "author_inst": "" - }, - { - "author_name": "Karthik Bharadwaj Tallapaka", - "author_inst": "CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Habsiguda, Hyderabad 500007" - }, - { - "author_name": "Nageshwar Reddy D", - "author_inst": "AIG Hospitals, Internal Medicine, Mindspace Rd, Gachibowli, Hyderabad, Telangana 500032" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.13.21260442", "rel_title": "Rapid and Quantitative Detection of Human Antibodies Against the 2019 Novel Coronavirus SARS CoV2 and its Variants as a Result of Vaccination and Infection", @@ -668686,6 +670203,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.15.21260006", + "rel_title": "Social risk factors for SARS-CoV-2 acquisition in University students: cross sectional survey", + "rel_date": "2021-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.15.21260006", + "rel_abs": "ObjectivesTo define risk factors for SARS-CoV-2 infection in University of Cambridge students during a period of increased incidence in October and November 2020.\n\nStudy designSurvey\n\nMethodsRoutine public health surveillance identified a marked increase in the numbers of University of Cambridge students with respiratory illness and SARS-CoV-2 positivity in the 10 days after a national lockdown was announced in the UK on 5 November 2020. Cases were identified both through symptom-triggered testing and a universal asymptomatic testing program. An online questionnaire was sent to all University of Cambridge students on 25 November to investigate risk factors for testing positive in the period after 30th October 2020. This asked about symptoms, SARS-CoV-2 test results, in-person teaching settings, other aspects of University life, and attendance at social events in the period just prior to lockdown, from 30th October and 4th November 2020. Univariate and multivariable analyses were undertaken evaluating potential risk factors for SARS-CoV-2 positivity.\n\nResultsAmong 3,980 students responding to the questionnaire, 99 (2.5%) reported testing SARS-CoV-2 positive in the period studied; 28 (28%) were asymptomatic. We found strong independent associations with SARS-CoV-2 positivity were attendance at two social settings in the City of Cambridge (adjusted odds ratio favouring disease 13.0 (95% CI 6.2,26.9) and 14.2 (95% CI 2.9,70)), with weaker evidence of association with three further social settings. By contrast, we did not observe strong independent associations between disease risk and type of accommodation or attendance at, or participation in, a range of activities associated with the University curriculum.\n\nConclusionsAttendance at social settings can facilitate widespread SARS-CoV-2 transmission in University students. Constraint of transmission in higher education settings needs to emphasise risks outside University premises, as well as a COVID-safe environment within University premises.\n\nHighlightsO_LIIn a population of University students, a large increase in individuals testing positive for SARS-CoV-2 occurred in the days following a national lockdown.\nC_LIO_LIAttendance at particular social gatherings was strongly linked to the development of disease, independent of other risk factors.\nC_LIO_LIBy contrast, a range of risk factors including age, gender, ethnicity, accommodation type, shared kitchen facilities, attendance at supermarkets, and attending teaching sessions were not significantly associated with SARS-CoV-2 risk.\nC_LIO_LIThese data emphasise the increased risk associated with University students attending social settings with large numbers of others, even when other risks associated with university attendance are well controlled.\nC_LI", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Eleanor Blakey", + "author_inst": "Public Health England" + }, + { + "author_name": "Lucy Reeve", + "author_inst": "Public Health England" + }, + { + "author_name": "Neville Q Verlander", + "author_inst": "Public Health England" + }, + { + "author_name": "David Edwards Edwards", + "author_inst": "Public Health England" + }, + { + "author_name": "David Wyllie", + "author_inst": "Public Health England" + }, + { + "author_name": "Mark Reacher", + "author_inst": "Public Health England" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.13.21260482", "rel_title": "Acute phase clinical manifestation of COVID-19 is linked to long-COVID symptoms; A 9-month follow-up study", @@ -670017,29 +671573,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.07.14.452401", - "rel_title": "Improving comparability of studies using HCoV-OC43 as a surrogate for SARS-CoV-2", - "rel_date": "2021-07-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.14.452401", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has renewed interest in human coronaviruses that cause the common cold, particularly as research with them at biosafety level (BSL)-2 avoids the added costs and biosafety concerns that accompany work with SARS-COV-2, BSL-3 research. One of these, human coronavirus OC43 (HCoV-OC43), is a well-matched surrogate for SARS-CoV-2 because it is also a Betacoronavirus, targets the human respiratory system, is transmitted via respiratory aerosols and droplets and is relatively resistant to disinfectants. Unfortunately, growth of HCoV-OC43 in the recommended human colon cancer (HRT-18) cells does not produce obvious cytopathic effect (CPE) and its titration in these cells requires expensive antibody-based detection. Consequently, multiple quantification approaches for HCoV-OC43 using alternative cell lines exist, which complicates comparison of research results. Hence, we investigated the basic growth parameters of HCoV-OC43 infection in three of these cell lines (HRT-18, human lung fibroblasts (MRC-5) and African green monkey kidney (Vero E6) cells) including the differential development of cytopathic effect (CPE) and explored reducing the cost, time and complexity of antibody-based detection assay. Multi-step growth curves were conducted in each cell type in triplicate at a multiplicity of infection of 0.1 with daily sampling for seven days. Samples were quantified by tissue culture infectious dose50(TCID50)/ml or plaque assay (cell line dependent) and additionally analyzed on the Sartorius Virus Counter 3100 (VC), which uses flow virometry to count the total number of intact virus particles in a sample. We improved the reproducibility of a previously described antibody-based detection based TCID50 assay by identifying commercial sources for antibodies, decreasing antibody concentrations and simplifying the detection process. The growth curves demonstrated that HCoV-O43 grown in MRC-5 cells reached a peak titer of [~]107 plaque forming units/ml at two days post infection (dpi). In contrast, HCoV-OC43 grown on HRT-18 cells required six days to reach a peak titer of [~]106.5 TCID50/ml. HCoV-OC43 produced CPE in Vero E6 cells but these growth curve samples failed to produce CPE in a plaque assay after four days. Analysis of the VC data in combination with plaque and TCID50 assays together revealed that the defective:infectious virion ratio of MRC-5 propagated HCoV-OC43 was less than 3:1 for 1-6 dpi while HCoV-OC43 propagated in HRT-18 cells varied from 41:1 at 1 dpi, to 329:4 at 4 dpi to 94:1 at 7 dpi. These results should enable better comparison of extant HCoV-OC43 study results and prompt further standardization efforts.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Erin E. Schirtzinger", - "author_inst": "Kansas State University" - }, - { - "author_name": "A. Sally Davis", - "author_inst": "Kansas State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.07.12.21260360", "rel_title": "The impact of hypoxia on B cells in COVID-19", @@ -670384,6 +671917,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.13.21260459", + "rel_title": "The age-stratified analytical model for the spread of the COVID-19 epidemic", + "rel_date": "2021-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.13.21260459", + "rel_abs": "The previously developed ASILV model for calculating epidemic spread under conditions of lockdown and mass vaccination was modified to analyse the intensity of COVID-19 infection growth in the allocated age groups.\n\nComparison of the results of calculations of the epidemic spread, as well as the values of the seven-day incidence values with the corresponding observation data, shows their good correspondence for each of the selected age groups.\n\nThe greatest influence on the overall spread of the epidemic is in the 20-40 age groups. The relatively low level of vaccination and the high intensity of contact in these age groups contributes to the emergence of new waves of the epidemic, which is especially active when the virus mutates and the lockdown conditions are relaxed.\n\nThe intensity of the epidemic in the 90+ age group has some peculiarities compared to other groups, which may be explained by differences in contact patterns among individuals in this age group compared to others.\n\nApproximate ratios for estimating mortality as a function of the intensity of infection for individual age groups are provided.\n\nThe proposed stratified ASILV model by age group will allow more detailed and accurate prediction of the spread of the COVID-19 epidemic, including when new, more transmissible versions of the virus mutate and emerge.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Felix Mairanowski", + "author_inst": "Husmann Rus" + }, + { + "author_name": "Denis Below", + "author_inst": "Potsdam University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.14.21260494", "rel_title": "Variation in COVID-19 excess mortality by age, sex, and province within Italy", @@ -672058,33 +673614,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.14.21259081", - "rel_title": "Use of 1-MNA to Improve Exercise Tolerance and Fatigue in Patients After COVID-19", - "rel_date": "2021-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.14.21259081", - "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) is a serious respiratory disease that results from infection with a newly discovered coronavirus (SARS-COV-2). Unfortunately, COVID-19 is not only a short-term infection but that patients (pts) recovering from SARS-CoV2 infection complain of persisting symptoms including: fatigue, diffuse myalgia and weakness, which may lead to chronic fatigue syndrome. There is currently no evidence that nutritional supplements and/or physical exercise can assist in the recovery of pts with chronic fatigue syndrome. 1-Methylnicotinamide (1-MNA) is an endogenic substance that is produced in the liver when nicotinic acid is metabolized. 1-MNA demonstrates anti-inflammatory and anti-thrombotic properties. Therefore, we investigated whether 1-MNA supplements could improve exercise tolerance and decrease fatigue among patients recovering from SARS-CoV-2.\n\nMethodsThe study population was composed of pts after COVID-19, expressing subjective feelings of limited tolerance to exercise. The selected pts were randomized into two groups: GrM0 - without supplementation; GrM1 - with 1-MNA supplementation. At the beginning of the study (Phase 0), in both groups, a 6-minute walk test (6MWT) was carried out and fatigue assessment with Fatigue Severity Scale (FSS) was performed. After 1 month (Phase 1), a follow up FSS and 6MWT once more were performed in both groups.\n\nResultsA significant improvement in the mean distance covered in the 6MWT was noted among the pts in GrM1, compared to those in GrM0. We also noted that in GrM1 the 6MWT distance was significantly higher after 1 month of supplementation with 1-MNA, compared to the beginning of the study (515.18 m in Phase 0 vs 557.8m in Phase 1; p = 0.000034). In GrM1, significantly more pts improved their distance in the 6MWT (23 out of 25 pts, equal to 92%), by a mean of 47 meters, compared to GrM0 (15 of 25 pts, equal to 60%) (p = 0.0061). After one month, significantly more patients in the group without 1-MNA had severe fatigue (FSS [≥] 4) compared to the group with supplementation (GrM1 = 5 pts (20%) vs GrM0 = 14pts (56%); p = 0.008).\n\nConclusions1-MNA supplementation significantly improved physical performance in a 6-minute walk test and reduced the percentage of patients with severe fatigue after COVID-19. The comprehensive action of 1-MNA, including anti-inflammatory and anticoagulant effects, as well as activation of the SIRT1 enzyme, may be beneficial for the recovery of patients with persistent symptoms of fatigue and low tolerance to exercise after COVID-19.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Michal Chudzik", - "author_inst": "Cardiology Ambulatory Centre, Saint Family Hospital, Lodz, Poland" - }, - { - "author_name": "Joanna Kapusta", - "author_inst": "Department of Internal Medicine and Cardiac Rehabilitation, Medical University of Lodz, Poland" - }, - { - "author_name": "Monika Burzynska", - "author_inst": "Department of Epidemiology and Biostatistics, the Chair of Social and Preventive Medi-cine of the Medical University of Lodz, Poland." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2021.07.13.452256", "rel_title": "Tissue Specific Age Dependence of the Cell Receptors Involved in the SARS-CoV-2 Infection", @@ -672445,6 +673974,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.07.13.452259", + "rel_title": "Xeno-nucleic Acid (XNA) 2'-Fluoro-Arabino Nucleic Acid (FANA) Aptamers to the Receptor Binding Domain of SARS-CoV-2 S Protein Block ACE2 Binding", + "rel_date": "2021-07-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.13.452259", + "rel_abs": "The causative agent of COVID-19, SARS-CoV-2, gains access to cells through interactions of the receptor binding domain (RBD) on the viral S protein with angiotensin converting enzyme 2 (ACE2) on the surface of human host cells. Systematic Evolution of Ligands by Exponential Enrichment (SELEX) was used to generate aptamers (nucleic acids selected for high binding affinity to a target) to the RBD made from 2-fluoroarabinonucleic acid (FANA). The best selected ~ 79 nucleotide aptamers bound the RBD (Arg319-Phe541) and the larger S1 domain (Val16-Arg685) of the 1272 amino acid S protein with equilibrium dissociation constants (KD,app) of ~ 10-20 nM and a binding half-life for the RBD of 53 {+/-} 18 minutes. Aptamers inhibited the binding of the RBD to ACE2 in an ELISA assay. Inhibition, on a per weight basis, was similar to neutralizing antibodies that were specific for RBD. Aptamers demonstrated high specificity, binding with about 10-fold lower affinity to the related S1 domain from the original SARS virus, which also binds to ACE2. Overall, FANA aptamers show affinities comparable to previous DNA aptamers to RBD and S protein and directly block receptor interactions while using an alternative Xeno-nucleic acid (XNA) platform.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Irani Alves Ferreira-Bravo", + "author_inst": "University of Maryland" + }, + { + "author_name": "Jeffrey J. DeStefano", + "author_inst": "University of Maryland" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.07.14.452343", "rel_title": "Repurposing screen highlights broad-spectrum coronavirus antivirals and their host targets", @@ -673952,45 +675504,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.09.21260253", - "rel_title": "Transmission of SARS-CoV-2 into and within immigrant households. Nation-wide registry-study from Norway", - "rel_date": "2021-07-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.09.21260253", - "rel_abs": "BackgroundMinority ethnic groups and immigrants have been hit disproportionally hard by COVID-19 in many developed countries, including Norway. Most transmissions of SARS-CoV-2 occur in households.\n\nMethodsUsing individual-level registry data of all Norwegian residents we compared infections across all multi-person households. A household with at least one member born abroad was defined as an immigrant household. For the subset of households where at least one person tested positive for SARS-CoV-2 from August 1st 2020 to May 1st 2021, we calculated secondary attack rates (SARs) as the percent of other household members testing positive within 14 days after the first household member tested positive. Logistic regression model was used to adjust for sex, age, household composition and geography.\n\nResultsAmong all multi-person households in Norway (n=1 421 642), immigrant households (n=341 604) comprised more members on average (3.2) than households with only Norwegian-born members (2.8). The share of immigrant households where at least one member had been tested, was 56% (vs 49% in the households with only Norwegian-born members), and the share where at least one member was infected was 3.7% (vs 1.4% in households with only Norwegian-born members). Secondary attack rates were higher in immigrant (32%) than Norwegian-born households (20%). Results differed considerably by country of birth, with secondary attack rates particularly high in households from Syria, Iraq, Turkey, and Pakistan, also after adjustment for sex, age, household composition and geography.\n\nConclusionSARS-CoV-2 is more frequently introduced into multi-person immigrant households than into households with only Norwegian-born members, and transmission within the household occurs more frequently in immigrant households. The results are likely related to living conditions, family composition or differences in social interaction, emphasizing the need to prevent introduction of SARS-CoV-2 into these vulnerable households.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Fredrik Methi", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Rannveig Kaldager Hart", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Anna Aasen Godoy", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Silje Bakken Jorgensen", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Oliver Kacelnik", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Kjetil Elias Telle", - "author_inst": "Norwegian Institute of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.07.21260167", "rel_title": "Indications that Stockholm has reached herd immunity, given limited restrictions, against several variants of SARS-CoV-2", @@ -674207,6 +675720,109 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.07.13.452175", + "rel_title": "Development Of The Inactivated QazCovid-In Vaccine: Protective Efficacy Of The Vaccine In Syrian Hamsters", + "rel_date": "2021-07-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.13.452175", + "rel_abs": "In March 2020, the first cases of human coronavirus infection COVID-19 were registered in Kazakhstan. We isolated the SARS-CoV-2 virus from the clinical material from the patients. Subsequently, a whole virion inactivated candidate vaccine, QazCovid-in, was developed based on this virus. To obtain the vaccine, a virus grown in Vero cell culture was used, which was inactivated with formaldehyde, purified, concentrated, sterilized by filtration, and then sorbed on aluminum hydroxide gel particles. The formula virus and adjuvant in buffer saline solution was used as a vaccine. The safety and protective effectiveness of the developed vaccine was studied on Syrian hamsters. The results of the studies showed the absolute safety of the candidate vaccine on the Syrian hamsters. When studying the protective effectiveness, the developed vaccine with an immunizing dose of 5 mcg/dose of a specific antigen protected animals from wild virus at a dose of 104.5 TCID50/ml. The candidate vaccine formed virus-neutralizing antibodies in vaccinated hamsters in titers from 3.3 {+/-} 1.45 log2 to 7.25 {+/-} 0.78 log2, which were retained for 6 months (observation period) in the indicated titers. The candidate vaccine suppressed the replication of the wild virus in the body of vaccinated hamsters, protected against the development of acute pneumonia and ensured 100% survival of the animals. At the same time, no replicative virus was isolated from the lungs of vaccinated animals. At the same time, a virulent virus was isolated from the lungs of unvaccinated animals in relatively high titers, reaching 4.5 {+/-} 0.7 lg TCID50/ml. After challenge infection, 100% of unvaccinated hamsters became ill with clinical signs (stress state, passivity, tousled coat, decreased body temperature and body weight, and the development of acute pneumonia), of which 25 {+/-} 5% were fatal. The findings paved the way for testing the candidate vaccine in humans in clinical trials.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Kuandyk Zhugunissov", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Kunsulu Zakarya", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Berik Khairullin", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Mukhit Orynbayev", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Yergali Abduraimov", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Markhabat Kassenov", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Kulyaisan Sultankulova", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Aslan Kerimbayev", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Sergazy Nurabayev", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Balzhan Myrzhakhmetova", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Aziz Nakhanov", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Ainur Nurpeisova", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Olga Chervyakova", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Nurika Assanzhanova", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Yerbol Burashev", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Muratbay Mambetaliev", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Moldir Azanbekova", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Syrym Kopeyev", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Nurlan Kozhabergenov", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Aisha Issabek", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Moldir Tuyskanova", + "author_inst": "Research Institute for Biological Safety Problems" + }, + { + "author_name": "Lespek Kutumbetov", + "author_inst": "Research Institute for Biological Safety Problems" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.07.13.452194", "rel_title": "A drug candidate for treating adverse reactions caused by pathogenic antibodies inducible by COVID-19 virus and vaccines", @@ -675674,65 +677290,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.10.451880", - "rel_title": "A mouse-adapted SARS-CoV-2 strain replicating in standard laboratory mice.", - "rel_date": "2021-07-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.10.451880", - "rel_abs": "SARS-CoV-2 has infected almost 200 million humans and caused over 4 million deaths worldwide. Evaluating countermeasures and improving our understanding of COVID-19 pathophysiology require access to animal models that replicate the hallmarks of human disease. Mouse infection with SARS-CoV-2 is limited by poor affinity between the virus spike protein and its cellular receptor ACE2. We have developed by serial passages the MACo3 virus strain which efficiently replicates in the lungs of standard mouse strains and induces age-dependent lung lesions. Compared to other mouse-adapted strains and severe mouse models, infection with MACo3 results in mild to moderate disease and will be useful to investigate the role of host genetics and other factors modulating COVID-19 severity.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Xavier Montagutelli", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Matthieu Prot", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Gregory Jouvion", - "author_inst": "Ecole Nationale Veterinaire" - }, - { - "author_name": "Laurine Levillayer", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Laurine Conquet", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Eduard Reyes-Gomez", - "author_inst": "Ecole Nationale Veterinaire" - }, - { - "author_name": "Flora Donati", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Melanie Albert", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Sylvie van der Werf", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Jean Jaubert", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Etienne Simon-Loriere", - "author_inst": "Institut Pasteur" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.07.07.21260153", "rel_title": "Transient infection with SARS-CoV-2 without induction of systemic immunity", @@ -675933,6 +677490,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.08.21260162", + "rel_title": "Immunogenicity of Oxford-AstraZeneca COVID-19 vaccine in Vietnamese healthcare workers", + "rel_date": "2021-07-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.08.21260162", + "rel_abs": "We studied the immunogenicity of Oxford-AstraZeneca vaccine in Vietnamese healthcare workers. We collected blood samples before each dose, at 14 days after each dose, and month 1 and 3 after dose 1 from each participant alongside demographics data. We measured neutralizing antibodies using a surrogate virus neutralization assay. The 554 study participants (136 males and 418 females) were aged between 22-71 years (median: 36 years). 104 and 94 out of 144 selected participants were successfully followed up at 14 days after dose 2 and 3 months after dose 1, respectively. Neutralizing antibodies increased after each dose, with the sero-conversion rate reaching 98.1% (102/104) at 14 days after dose 2. At month 3 after dose 1, neutralizing antibody levels decreased, while 94.7% (89/94) of the study participants remained seropositive. Oxford-AstraZeneca COVID-19 vaccine is immunogenic in Vietnamese healthcare workers. The requirement for a third dose warrants further research.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Nguyen Van Vinh Chau", + "author_inst": "Hospital for Tropical Diseases" + }, + { + "author_name": "Lam Anh Nguyet", + "author_inst": "OUCRU" + }, + { + "author_name": "Nguyen Thanh Truong", + "author_inst": "HTD" + }, + { + "author_name": "Le Mau Toan", + "author_inst": "HTD" + }, + { + "author_name": "Nguyen Thanh Dung", + "author_inst": "HTD" + }, + { + "author_name": "Le Manh Hung", + "author_inst": "HTD" + }, + { + "author_name": "Mai Thanh Nhan", + "author_inst": "HTD" + }, + { + "author_name": "Dinh Nguyen Huy Man", + "author_inst": "HTD" + }, + { + "author_name": "Nghiem My Ngoc", + "author_inst": "HTD" + }, + { + "author_name": "Huynh Phuong Thao", + "author_inst": "HTD" + }, + { + "author_name": "Tran Nguyen Hoang Tu", + "author_inst": "HTD" + }, + { + "author_name": "Huynh Kim Mai", + "author_inst": "IP, Nha Trang" + }, + { + "author_name": "Do Thai Hung", + "author_inst": "IP, Nha Trang" + }, + { + "author_name": "Nguyen Thi Han Ny", + "author_inst": "OUCRU" + }, + { + "author_name": "Le Kim Thanh", + "author_inst": "OUCRU" + }, + { + "author_name": "Nguyen To Anh", + "author_inst": "OUCRU" + }, + { + "author_name": "Nguyen Thi Thu Hong", + "author_inst": "OUCRU" + }, + { + "author_name": "Le Nguyen Truc Nhu", + "author_inst": "OUCRU" + }, + { + "author_name": "Lam Minh Yen", + "author_inst": "OUCRU" + }, + { + "author_name": "Marc Choisy", + "author_inst": "OUCRU" + }, + { + "author_name": "Tran Tan Thanh", + "author_inst": "OUCRU" + }, + { + "author_name": "Guy Thwaites", + "author_inst": "OUCRU" + }, + { + "author_name": "Le Van Tan", + "author_inst": "OUCRU" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.09.21260249", "rel_title": "Pandemic trends in health care use: From the hospital bed to the general practitioner with COVID-19", @@ -677548,97 +679212,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.07.21260124", - "rel_title": "BNT162b2 vaccine-induced humoral and cellular responses against SARS-CoV-2 variants in Systemic Lupus Erythematosus", - "rel_date": "2021-07-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.07.21260124", - "rel_abs": "ObjectivesOur aims were to evaluate Systemic Lupus Erythematosus (SLE) disease activity and SARS-CoV-2 specific immune responses after BNT162b2 vaccination.\n\nMethodsIn this prospective study, disease activity and clinical assessments were recorded from the first dose of vaccine, until day 15 after the second dose in 126 SLE patients. SARS-CoV-2 antibody responses were measured against wild-type spike antigen while serum-neutralizing activity was assessed against the SARS-CoV-2 historical strain and variants of concerns (VOCs). Vaccine-specific T-cell responses were quantified by Interferon (IFN)-{gamma} release assay after the second dose.\n\nResultsBNT162b2 was well tolerated and no statistically significant variations of BILAG and SLEDAI scores were observed throughout the study in SLE patients with active and inactive disease at baseline. Mycophenolate Mofetil (MMF) and Methotrexate (MTX) treatments were associated with drastically reduced BNT162b2 antibody-response ({beta}=-78; p=0.007, {beta}=-122; p<0.001, respectively). Anti-spike antibody response was positively associated with baseline total IgG serum levels, naive B cell frequencies ({beta}=2; p=0.018, {beta}=2.5; p=0.003) and SARS-CoV-2-specific T cell response (r=0.462; p=0.003). In responders, serum neutralization activity decreased against VOCs bearing the E484K mutation but remained detectable in a majority of patients.\n\nConclusionMMF, MTX and poor baseline humoral immune status, particularly: low naive B cell frequencies, are independently associated with impaired BNT162b2 mRNA antibody response, delineating SLE patients who might need adapted vaccine regimens and follow-up.\n\nKEY MESSAGESO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIBNT162b2 efficacy and safety has been described in studies mixing different RMDs\nC_LI\n\nWhat does this study add?O_LINo serious adverse effects, nor SLE flares have been documented after BNT162b2 in SLE patients.\nC_LIO_LINot only MMF and MTX, but also a poor humoral immune status at baseline impair vaccine antibody response\nC_LIO_LIAlbeit decreased, serum neutralizing activity against VOCs is conferred to vaccine-responders.\nC_LI\n\nHow might this impact on clinical practice or future developments?O_LIThese parameters could be helpful for physicians to delineate which patients should have antibody measurement after full BNT162b2 vaccination and should be proposed a third injection of BNT162b2 vaccine.\nC_LI", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Quentin Moyon", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Delphine Sterlin", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Makoto Miyara", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Francois Anna", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Alexis Mathian", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Raphael Lhote", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Pascale Ghillani-Dalbin", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Paul Breillat", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Sasi Mudumba", - "author_inst": "Genalyte" - }, - { - "author_name": "Sophia de Alba", - "author_inst": "Genalyte" - }, - { - "author_name": "Fleur Cohen-Aubart", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Julien Haroche", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Micheline Pha", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Thi Huong Du Boutin", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Hedi Chaieb", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Pedro Flores", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Pierre Charneau", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Guy Gorochov", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Zahir Amoura", - "author_inst": "Sorbonne Universite" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.08.451640", "rel_title": "Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica", @@ -677827,6 +679400,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.07.07.451538", + "rel_title": "Atomistic Simulations and Deep Mutational Scanning of Protein Stability and Binding Interactions in the SARS-CoV-2 Spike Protein Complexes with Nanobodies: Molecular Determinants of Mutational Escape Mechanisms", + "rel_date": "2021-07-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.07.451538", + "rel_abs": "Structural and biochemical studies have recently revealed a range of rationally engineered nanobodies with efficient neutralizing capacity against SARS-CoV-2 virus and resilience against mutational escape. In this work, we combined atomistic simulations and conformational dynamics analysis with the ensemble-based mutational profiling of binding interactions for a diverse panel of SARS-CoV-2 spike complexes with nanobodies. Using this computational toolkit we identified dynamic signatures and binding affinity fingerprints for the SARS-CoV-2 spike protein complexes with nanobodies Nb6 and Nb20, VHH E, a pair combination VHH E+U, a biparatopic nanobody VHH VE, and a combination of CC12.3 antibody and VHH V/W nanobodies. Through ensemble-based deep mutational profiling of stability and binding affinities, we identify critical hotspots and characterize molecular mechanisms of SARS-CoV-2 spike protein binding with single ultra-potent nanobodies, nanobody cocktails and biparatopic nanobodies. By quantifying dynamic and energetic determinants of the SARS-CoV-2 S binding with nanobodies, we also examine the effects of circulating variants and escaping mutations. We found that mutational escape mechanisms may be controlled through structurally and energetically adaptable binding hotspots located in the host receptor-accessible binding epitope that are dynamically coupled to the stability centers in the distant epitope targeted by VHH U/V/W nanobodies. The results of this study suggested a mechanism in which through cooperative dynamic changes, nanobody combinations and biparatopic nanobody can modulate the global protein response and induce the increased resilience to common escape mutants.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Gennady Verkhivker", + "author_inst": "Chapman University School of Pharmacy" + }, + { + "author_name": "Steve Agajanian", + "author_inst": "Chapman University" + }, + { + "author_name": "Deniz Yasar Oztas", + "author_inst": "Chapman University" + }, + { + "author_name": "Grace Gupta", + "author_inst": "Chapman University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.07.08.451654", "rel_title": "Evaluation of intranasal nafamostat or camostat for SARS-CoV-2 chemoprophylaxis in Syrian golden hamsters", @@ -679406,37 +681010,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.07.06.451227", - "rel_title": "T-CoV: a comprehensive portal of HLA-peptide interactions affected by SARS-CoV-2 mutations", - "rel_date": "2021-07-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.06.451227", - "rel_abs": "Rapidly appearing SARS-CoV-2 mutations can affect T cell epitopes, which can help the virus to evade either CD8 or CD4 T-cell responses. We developed T-cell COVID-19 Atlas (T-CoV, https://t-cov.hse.ru) - the comprehensive web portal, which allows one to analyze how SARS-CoV-2 mutations alter the presentation of viral peptides by HLA molecules. The data are presented for common virus variants and the most frequent HLA class I and class II alleles. Binding affinities of HLA molecules and viral peptides were assessed with accurate in silico methods. The obtained results highlight the importance of taking HLA alleles diversity into account: mutation-mediated alterations in HLA-peptide interactions were highly dependent on HLA alleles. For example, we found that the essential number of peptides tightly bound to HLA-B*07:02 in the reference Wuhan variant ceased to be tight binders for the Indian (Delta) and the UK (Alpha) variants. In summary, we believe that T-CoV will help researchers and clinicians to predict the susceptibility of individuals with different HLA genotypes to infection with variants of SARS-CoV-2 and/or forecast its severity.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Stepan Nersisyan", - "author_inst": "HSE University" - }, - { - "author_name": "Anton Zhiyanov", - "author_inst": "HSE University" - }, - { - "author_name": "Maxim Shkurnikov", - "author_inst": "HSE University" - }, - { - "author_name": "Alexander Tonevitsky", - "author_inst": "HSE University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.07.06.451119", "rel_title": "Nonclinical Safety and Immunogenicity of an rVSV-\u0394G-SARS-CoV-2-S vaccine in mice, hamsters, rabbits and pigs", @@ -679817,6 +681390,37 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.07.06.451329", + "rel_title": "Investigating the conformational dynamics of SARS-CoV-2 NSP6 protein with emphasis on non-transmembrane 91-112 & 231-290 regions", + "rel_date": "2021-07-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.06.451329", + "rel_abs": "The NSP6 protein of SARS-CoV-2 is a transmembrane protein, with some regions lying outside the membrane. Besides, a brief role of NSP6 in autophagosome formation, this is not studied significantly. Also, there is no structural information available till date. Based on the prediction by TMHMM server for transmembrane prediction, it is found that the N-terminal residues (1-11), middle region residues (91-112) and C-terminal residues (231-290) lies outside the membrane. Molecular Dynamics (MD) simulations showed that NSP6 consisting of helical structures, whereas membrane outside lying region (91-112) showed partial helicity, which further used as model and obtain disordered type conformation after 1.5 microsecond. Whereas, the residues 231-290 has both helical and beta sheet conformations in its structure model. A 200ns simulations resulted in the loss of beta sheet structures, while helical regions remained intact. Further, we have characterized the residue 91-112 by using reductionist approaches. The NSP6 (91-112) was found disordered like in isolation, which gain helical conformation in different biological mimic environmental conditions. These studies can be helpful to study NSP6 (91-112) interactions with host proteins, where different protein conformation might play significant role. The present study adds up more information about NSP6 protein aspect, which could be exploited for its host protein interaction and pathogenesis.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=123 SRC=\"FIGDIR/small/451329v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (29K):\norg.highwire.dtl.DTLVardef@1b6e8aborg.highwire.dtl.DTLVardef@165564eorg.highwire.dtl.DTLVardef@551f7org.highwire.dtl.DTLVardef@1485518_HPS_FORMAT_FIGEXP M_FIG C_FIG The schematic representation of NSP6 membrane topology and conformational dynamics of residue 91-112. The N-terminal and C-terminal are shown in cytoplasmic side based on the experimental evidence on coronaviruses reported by Oostra et al., 2008. The membrane anchoring domain are shown based on the TMHMM server prediction.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Amit Kumar", + "author_inst": "Indian Institute of Technology Mandi" + }, + { + "author_name": "Prateek Kumar", + "author_inst": "Indian Institute of Technology Mandi" + }, + { + "author_name": "Kumar Udit Saumya", + "author_inst": "Indian Institute of Technology Mandi" + }, + { + "author_name": "Rajanish Giri", + "author_inst": "Indian Institute of Technology Mandi" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.07.05.451199", "rel_title": "An Autoantigen Profile from Jurkat T-Lymphoblasts Provides a Molecular Guide for Investigating Autoimmune Sequelae of COVID-19", @@ -681288,49 +682892,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.05.21250138", - "rel_title": "Peritraumatic Distress of COVID-19 on Physicians in Bangladesh: Implications and Policy Recommendations", - "rel_date": "2021-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.05.21250138", - "rel_abs": "COVID-19 pandemic has been an ultimate test of resource management for any governance, especially in the healthcare system. Bangladesh, being a developing country and with very limited resources, is fighting the COVID-19 pandemic. The frontline workers, especially the physicians and nurses are going through immense physical and psychological stress during the pandemic. Social unawareness, the absence of strict preventive policies, increasing workload, and the lack of resource management are making the frontline healthcare workers extremely vulnerable to COVID-19. In this paper, we present the outcome of our study on peritraumatic distress of COVID-19 among physicians in Bangladesh. Based on the user study, we have identified a number of key factors behind the peritraumatic distress and psychological stress caused by COVID-19. Our study shows, more than 78% respondents are suffering from peritraumatic psychological distress. We also recommended some very important and yet easy to implement policies to reduce the peritraumatic stress of the physicians of Bangladesh. These policy recommendations were a result of the survey analysis and the suggestions from the COVID-19 designated physicians.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Zafar Ahmad", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Abdullah al Kium", - "author_inst": "Sir Salimullah Medical College" - }, - { - "author_name": "Md Ripon Ahammed", - "author_inst": "National Institute of Cardiovascular Diseases" - }, - { - "author_name": "Md Montaser Hamid", - "author_inst": "Shahjalal University of Science and Technology" - }, - { - "author_name": "Sarmina Tarannum", - "author_inst": "Sir Salimullah Medical College" - }, - { - "author_name": "Mohammad Ruhul Amin", - "author_inst": "Fordham University" - }, - { - "author_name": "Md. Daharul Islam", - "author_inst": "Sir Salimullah Medical College" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.07.05.21259790", "rel_title": "What We Learned From COVID 19? Trying to find best approach from pathophysiology to treatment.", @@ -681515,6 +683076,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.06.21259792", + "rel_title": "Characteristics of children and antigen test performance at a SARS-CoV-2 community testing site", + "rel_date": "2021-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21259792", + "rel_abs": "BackgroundPerformance characteristics of SARS-CoV-2 antigen tests among children are limited despite the need for point-of-care testing in school and childcare settings. We describe children seeking SARS-CoV-2 testing at a community site and compare antigen test performance to real-time reverse transcription-polymerase chain reaction (RT-PCR) and viral culture.\n\nMethodsTwo anterior nasal specimens were self-collected for BinaxNOW antigen and RT-PCR testing, along with demographics, symptoms, and exposure information from individuals [≥]5 years at a community testing site. Viral culture was attempted on residual antigen or RT-PCR positive specimens. Demographic and clinical characteristics, and the performance of SARS-CoV-2 antigen tests, were compared among children (<18 years) and adults.\n\nResultsAbout one in ten included specimens were from children (225/2110); 16.4% (37/225) were RT-PCR positive. Cycle threshold values were similar among RT-PCR positive specimens from children and adults (22.5 vs 21.3, p=0.46) and among specimens from symptomatic and asymptomatic children (22.5 vs 23.2, p=0.39). Sensitivity of antigen test compared to RT-PCR was 73.0% (27/37) among specimens from children and 80.8% (240/297) among specimens from adults; among specimens from children, specificity was 100% (188/188), positive and negative predictive value were 100% (27/27) and 94.9% (188/198) respectively. Virus was isolated from 51.4% (19/37) of RT-PCR positive pediatric specimens; all 19 had positive antigen test results.\n\nConclusionsWith lower sensitivity relative to RT-PCR, antigen tests may not diagnose all positive COVID-19 cases; however, antigen testing identified children with live SARS-CoV-2 virus.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Laura Ford", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Melissa J. Whaley", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Melisa M. Shah", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Phillip P. Salvatore", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Hannah E. Segaloff", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Augustina Delaney", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Dustin W. Currie", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Lauren Boyle-Estheimer", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Michelle O'Hegarty", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Clint N. Morgan", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Jennifer Meece", + "author_inst": "Marshfield Clinic Research Institute" + }, + { + "author_name": "Lynn Ivacic", + "author_inst": "Marshfield Clinic Research Institute" + }, + { + "author_name": "Natalie J. Thornburg", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Azaibi Tamin", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Jennifer L. Harcourt", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Jennifer M. Folster", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Magdalena Medrzycki", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Shilpi Jain", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Phili Wong", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Kimberly Goffard", + "author_inst": "Health Department, Winnebago County" + }, + { + "author_name": "Douglas Gieryn", + "author_inst": "Health Department, Winnebago County" + }, + { + "author_name": "Juliana Kahrs", + "author_inst": "University of Wisconsin-Oshkosh" + }, + { + "author_name": "Kimberly Langolf", + "author_inst": "University of Wisconsin-Oshkosh" + }, + { + "author_name": "Tara Zochert", + "author_inst": "University of Wisconsin-Oshkosh" + }, + { + "author_name": "Jacqueline E. Tate", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Christopher H. Hsu", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Hannah L. Kirking", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.06.21259528", "rel_title": "Pre-vaccination and early B cell signatures predict antibody response to SARS-CoV-2 mRNA vaccine", @@ -683034,49 +684718,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.07.07.451505", - "rel_title": "Immunogenicity of low dose prime-boost vaccination of mRNA vaccine CV07050101 in non-human primates", - "rel_date": "2021-07-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.07.451505", - "rel_abs": "Many different vaccine candidates against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the etiological agent of COVID-19, are currently approved and under development. Vaccine platforms vary from mRNA vaccines to viral-vectored vaccines, and several candidates have been shown to produce humoral and cellular responses in small animal models, non-human primates and human volunteers. In this study, six non-human primates received a prime-boost intramuscular vaccination with 4 {micro}g of mRNA vaccine candidate CV07050101, which encodes a pre-fusion stabilized spike (S) protein of SARS-CoV-2. Boost vaccination was performed 28 days post prime vaccination. As a control, six animals were similarly injected with PBS. Humoral and cellular immune responses were investigated at time of vaccination, and two weeks afterwards. No antibodies could be detected two and four weeks after prime vaccination. Two weeks after boost vaccination, binding but no neutralizing antibodies were detected in 4 out of 6 non-human primates. SARS-CoV-2 S protein specific T cell responses were detected in these 4 animals. In conclusion, prime-boost vaccination with 4 {micro}g of vaccine candidate CV07050101 resulted in limited immune responses in 4 out of 6 non-human primates.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Neeltje van Doremalen", - "author_inst": "NIH" - }, - { - "author_name": "Robert Fischer", - "author_inst": "NIH" - }, - { - "author_name": "Jonathan Schulz", - "author_inst": "NIH" - }, - { - "author_name": "Myndi Holbrook", - "author_inst": "NIH" - }, - { - "author_name": "Jamie Lovaglio", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Benjamin Petsch", - "author_inst": "CureVac AG, Tuebingen, Germany" - }, - { - "author_name": "Vincent Munster", - "author_inst": "NIAID" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.07.06.451353", "rel_title": "Receptor-binding domain recombinant protein RBD219-N1C1 on alum-CpG induces broad protection against SARS-CoV-2 variants of concern", @@ -683465,6 +685106,57 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.06.30.21259816", + "rel_title": "Impacts of school closure due to COVID-19 on the mobility trend of Japanese citizens", + "rel_date": "2021-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.30.21259816", + "rel_abs": "School closure was the only main control measure that Japan took into action from late February to late March in 2020. Accurate evaluation of how Japanese citizens responded to the impact of school closure remains a challenge. Data from the Google COVID-19 Community Mobility Report was used to analyze the mobility trend of Japanese citizens regarding six categories, including retail and recreation, grocery and pharmacy, parks, transit stations, workplace, and residential. The median percentage of mobility in all 47 prefectures of Japan was calculated during five periods of time, including one week before school closure, one week, two weeks, three weeks, and four weeks after school closure. There was a significant decline in the mobility trend of transit stations, grocery and pharmacy, parks, retail and recreation, and workplace at the moment after school closure compared to the prior period. Inversely, the mobility trend in staying at home remarkably increased following the implementation of school closure. Our study determined a significant change in the mobility trend of Japanese citizens before and after school closure. These data reflected the responsibility and the consciousness of Japanese citizens in mitigating COVID-19.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Nguyen Hai Nam", + "author_inst": "Kyoto University" + }, + { + "author_name": "Anh PN Nguyen", + "author_inst": "Concordia College, Moorhead" + }, + { + "author_name": "Bao-Tran Do Le", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Abdelrahman Gamil Gad", + "author_inst": "Ain Shams University" + }, + { + "author_name": "Abdelrahman Sherif Mohamed Abdelnaeim Abdalla", + "author_inst": "Minia University" + }, + { + "author_name": "Adnan Safi", + "author_inst": "Nishtar Medical University and Hospital" + }, + { + "author_name": "Anh Gia Pham", + "author_inst": "University of Medicine and Pharmacy at Ho Chi Minh City" + }, + { + "author_name": "Vo Duc Khanh", + "author_inst": "University of Science, Vietnam National University" + }, + { + "author_name": "Nguyen Tien Huy", + "author_inst": "Institute of Tropical Medicine, Nagasaki University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.06.30.21259820", "rel_title": "SARS-CoV-2 B.1.1.7 lineage rapidly spreads and overwhelms R.1 lineage in Japan: serial and stationary observation in a community", @@ -684860,85 +686552,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.04.21259903", - "rel_title": "Relating SARS-CoV-2 shedding rate in wastewater to daily positive tests data: A consistent model based approach", - "rel_date": "2021-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.04.21259903", - "rel_abs": "During the COVID-19 pandemic, wastewater-based epidemiology (WBE) has been engaged to complement medical surveillance and in some cases to also act as an early diagnosis indicator of viral spreading in the community. Most efforts worldwide by the scientific community and commercial companies focus on the formulation of protocols for SARS CoV-2 analysis in wastewater and approaches addressing the quantitative relationship between WBE and medical surveillance are lacking. In the present study, a mathematical model is developed which uses as input the number of daily positive medical tests together with the highly non-linear shedding rate curve of individuals to estimate the evolution of virus shedding rate in wastewater along calendar days. A comprehensive parametric study by the model using as input actual medical surveillance and WBE data for the city of Thessaloniki ([~]700,000 inhabitants, North Greece) during the outbreak of November 2020 reveals the conditions under which WBE can be used as an early warning tool for predicting pandemic outbreaks. It is shown that early warning capacity is different along the days of an outbreak and depends strongly on the number of days apart between the day of maximum shedding rate of infected individuals in their disease cycle and the day of their medical testing. The present data indicate for Thessaloniki an average early warning capacity of around 2 days. Moreover, the data imply that there exists a proportion between unreported cases (asymptomatic persons with mild symptoms that do not seek medical advice) and reported cases. The proportion increases with the number of reported cases. The early detection capacity of WBE improves substantially in the presence of an increasing number of unreported cases. For Thessaloniki at the peak of the pandemic in mid-November 2020, the number of unreported cases reached a maximum around 4 times the number of reported cases.\n\nHIGHLIGHTSO_LIModel estimates viral load evolution in wastewater from infected people dynamics\nC_LIO_LIIdentifying actual conditions for which WBE can be used as an early warning tool\nC_LIO_LIEarly warning capacity increases with an increasing number of unreported cases\nC_LIO_LIIn Thessaloniki Nov20 outbreak, the early warning capacity of WBE was about 2 days\nC_LIO_LIIn Thessaloniki Nov20 outbreak, unreported cases were up to 4 times reported cases\nC_LI", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Maria Petala", - "author_inst": "Aristotle University of Thessaloniki" - }, - { - "author_name": "Margaritis Kostoglou", - "author_inst": "Aristotle University of Thessaloniki" - }, - { - "author_name": "Thodoris Karapantsios", - "author_inst": "Aristotle University of Thessaloniki" - }, - { - "author_name": "Chrysostomos Dovas", - "author_inst": "Aristotle University of Thessaloniki" - }, - { - "author_name": "Theodoros Lytras", - "author_inst": "National Public Health Organization, Athens, Greece & European University Cyprus, Nicosia, Cyprus" - }, - { - "author_name": "Dimitrios Paraskevis", - "author_inst": "National and Kapodistrian University of Athens, Athens, Greece" - }, - { - "author_name": "Emmanouel Roilides", - "author_inst": "Infectious Diseases Unit and 3rd Department of Pediatrics, Aristotle University School of Health Sciences, Hippokration Hospital" - }, - { - "author_name": "Anastasia Koutsolioutsou-Benaki", - "author_inst": "National Public Health Organization" - }, - { - "author_name": "Georgios Panagiotakopoulos", - "author_inst": "National Public Health Organization" - }, - { - "author_name": "Vana Sypsa", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Symeon Metallidis", - "author_inst": "Faculty of Medicine, AHEPA General Hospital, Aristotle University of Thessaloniki" - }, - { - "author_name": "Anna Papa", - "author_inst": "Medical School, Aristotle University of Thessaloniki, Thessaloniki" - }, - { - "author_name": "Efstratios Stylianidis", - "author_inst": "Aristotle University of Thessaloniki" - }, - { - "author_name": "Agis Papadopoulos", - "author_inst": "Thessaloniki Water Supply and Sewerage Company S.A." - }, - { - "author_name": "Sotirios Tsiodras", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Nikolaos Papaioannou", - "author_inst": "Aristotle University of Thessaloniki" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.04.21259992", "rel_title": "Late surges in COVID-19 cases and varying transmission potential partially due to public health policy changes in 5 Western states, March 10, 2020-January 10, 2021", @@ -685159,6 +686772,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.07.05.21260005", + "rel_title": "Mathematical modelling of SARS-CoV-2 variant outbreaks reveals their probability of extinction", + "rel_date": "2021-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.05.21260005", + "rel_abs": "When a virus spreads, it may mutate into, e.g., vaccine resistant or fast spreading lineages, as was the case for the Danish Cluster-5 mink variant (belonging to the B.1.1.298 lineage), the British B.1.1.7 lineage, and the South African B.1.351 lineage of the SARS-CoV-2 virus. A way to handle such spreads is through a containment strategy, where the population in the affected area is isolated until the spread has been stopped. Under such circumstances, it is important to monitor whether the mutated virus is extinct via massive testing for the virus sub-type. If successful, the strategy will lead to lower and lower numbers of the sub-type, and it will eventually die out. An important question is, for how long time one should wait to be sure the sub-type is extinct? We use a hidden Markov model for infection spread and an approximation of a two stage sampling scheme to infer the probability of extinction. The potential of the method is illustrated via a simulation study. Finally, the model is used to assess the Danish containment strategy when SARS-CoV-2 spread from mink to man during the summer of 2020, including the Cluster-5 sub-type. In order to avoid further spread and mink being a large animal virus reservoir, this situation led to the isolation of seven municipalities in the Northern part of the country, the culling of the entire Danish 17 million large mink population, and a bill to interim ban Danish mink production until the end of 2021.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Henrik Schi\u00f8ler", + "author_inst": "Department of Electronic Systems, Aalborg University" + }, + { + "author_name": "Torben Knudsen", + "author_inst": "Department of Electronic Systems, Aalborg University" + }, + { + "author_name": "Rasmus Froberg Br\u00f8ndum", + "author_inst": "Department of Clinical Medicine, Aalborg University; Department of Haematology, Aalborg University Hospital" + }, + { + "author_name": "Jakob Stoustrup", + "author_inst": "Department of Electronic Systems, Aalborg University" + }, + { + "author_name": "Martin B\u00f8gsted", + "author_inst": "Department of Clinical Medicine, Aalborg University; Department of Haematology, Aalborg University Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.04.21259490", "rel_title": "Generation of false positive SARS-CoV-2 antigen results with testing conditions outside manufacturer recommendations: A scientific approach to pandemic misinformation", @@ -686706,33 +688354,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.30.21259794", - "rel_title": "Examining the Relationship between COVID-19 Vaccinations and Reported Incidence", - "rel_date": "2021-07-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.30.21259794", - "rel_abs": "As COVID-19 has caused significant morbidity and mortality throughout the world, the development and distribution of an effective vaccine have been swift but not without challenges. Earlier demand and access barriers have seemingly been addressed with more free and accessible vaccines now available for a wide variety of ages. While rates of COVID-19 have decreased overall, some geographic areas continue to experience rapid outbreaks. The purpose of this study was to examine the relationship between vaccination uptake and weekly COVID-19 cases throughout locations in the state of Missouri.\n\nMethodsAmong all Missouri counties and two cities (n=117), weekly COVID-19 incidence and cumulative proportion of residents fully vaccinated were abstracted from the Missouri Department of Health and Senior Services during a 25-week period from January 4 to Jun 26, 2021. Additional ecological variables known to be associated with COVID-19 incidence and prevalence were collected from the U.S. Census Bureau and integrated into data: total population, proportion of nonwhite residents, annual median household income, proportion of residents working in public facing occupations. Descriptive and inferential statistics were completed which included the calculation of both linear and nonlinear models using repeated measure data to determine the quantitative association between vaccination uptake and reported COVID-19 cases in the presence of location characteristics.\n\nResultsThroughout the 25 weeks of observations, the average weekly number of COVID-19 cases reported was 66.1 (SD=260.8) while the average cumulative proportion vaccinated individuals at the end of the 25 weeks was 25.8% (SD=6.8%) among study locations. While graphing seemed to suggest a more nonlinear relationship between COVID-19 incidence and proportion vaccinated, comparison of crude linear and nonlinear models pointed to the relationship likely being linear during study period. The final adjusted linear model exhibited a significant relationship between COVID-19 cases and proportion vaccinated, specifically every percent increase in population vaccinated resulted in 3 less weekly COVID-19 cases being reported ({beta} -3.74, p<0.001. Additionally, when controlling for other factors, the adjusted model revealed locations with higher proportions of nonwhite residents were likely to experience less weekly COVID-19 cases ({beta} -1.48, p=0.037).\n\nDiscussionOverall, this study determined that increasing the proportion of residents vaccinated decreases COIVD-19 cases by a substantial amount over time. These findings provide insights into possible messaging strategies that can be leveraged to develop more effective implementation and uptake. As the COVID-19 pandemic persists and vaccination numbers begin to plateau, diverse communication strategies become a critical necessity to reach a wider population.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Enbal Shacham", - "author_inst": "Saint Louis University" - }, - { - "author_name": "Stephen Scroggins", - "author_inst": "Saint Louis University" - }, - { - "author_name": "Alexander Garza", - "author_inst": "SSM Health St. Louis" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.30.21259491", "rel_title": "Reduced COVID-19 Hospitalizations among New York City Residents Following Age-Based SARS-CoV-2 Vaccine Eligibility: Evidence from a Regression Discontinuity Design", @@ -687033,6 +688654,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2021.07.03.451025", + "rel_title": "A cGAMP-containing hydrogel for prolonged SARS-CoV-2 RBD subunit vaccine exposure induces a broad and potent humoral response", + "rel_date": "2021-07-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.03.451025", + "rel_abs": "The SARS-CoV-2 virus spike protein, specifically its receptor binding domain (RBD), has emerged as a promising target for generation of neutralizing antibodies. Although the RBD peptide subunit is easily manufactured and highly stable, RBD-based subunit vaccines have been hampered by its poor inherent immunogenicity. We hypothesize that this limitation can be overcome by sustained co-administration alongside a potent and optimized adjuvant. The innate immune second messenger, cGAMP, holds promise as it activates the potent anti-viral STING pathway, but has exhibited poor performance as a therapeutic due to its nonspecific pharmacodynamic profiles when administered systemically and its poor pharmacokinetics arising from rapid excretion and degradation by its hydrolase ENPP1. To overcome these limitations, we sought to mimic the natural scenario of viral infections by creating an artificial immunological niche that enables slow release of cGAMP and the RBD antigen. Specifically, we co-encapsulated cGAMP and RBD in an injectable polymer-nanoparticle (PNP) hydrogel system. This cGAMP-adjuvanted hydrogel vaccine elicited more potent, durable, and broad antibody responses and improved neutralization than both dose-matched bolus controls and a hydrogel-based vaccine lacking cGAMP. The cGAMP-adjuvanted hydrogel platform developed is suitable for delivery of other antigens and may provide enhanced immunity against a broad range of pathogens.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Emily C Gale", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Lauren J Lahey", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Volker B\u00f6hnert", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Abigail E Powell", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Ben S Ou", + "author_inst": "Stanford University" + }, + { + "author_name": "Jacqueline A Carozza", + "author_inst": "Stanford University" + }, + { + "author_name": "Lingyin Li", + "author_inst": "Stanford University" + }, + { + "author_name": "Eric Appel", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2021.07.03.450938", "rel_title": "A SARS-CoV-2 nucleocapsid protein TR-FRET assay amenable to high-throughput screening", @@ -688300,77 +689968,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.28.21258780", - "rel_title": "Transmission event of SARS-CoV-2 Delta variant reveals multiple vaccine breakthrough infections", - "rel_date": "2021-07-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21258780", - "rel_abs": "ImportanceVaccine breakthrough by an emergent SARS-CoV-2 variant poses a great risk to global public health.\n\nObjectiveTo determine the SARS-CoV-2 variant responsible for 6 cases of vaccine breakthrough.\n\nDesignNasopharyngeal swabs from suspected vaccine breakthrough cases were tested for SARS-CoV-2 by qPCR for Wuhan-Hu1 and Alpha variant. Positive samples were then sequenced by Swift Normalase Amplicon Panels to determine the causal variant.\n\nSettingTransmission event occurred at events surrounding a wedding outside of Houston, TX. Two patients from India, likely transmitted the Delta variant to other guests.\n\nParticipantsFollowing a positive SARS-CoV-2 qPCR test at a third-party site, six fully vaccinated patients were investigated. Three males and three females ranged from 53 to 69 years old. One patient suffered from diabetes while three others were classified as overweight. No significant other comorbidities were identified. None of the patients had a history of failed vaccination.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhich SARS-CoV-2 variant is responsible for 6 cases of vaccine breakthrough, one interventional monoclonal antibody treatment, and one death?\n\nFindingsViral sequencing revealed 6 vaccinated patients were infected with the Delta SARS-CoV-2 variant. With no histories of vaccine breakthrough, this suggests Delta variant may possess immune evasion in patients that received the Pfizer BNT162b2, Moderna mRNA-1273, and Covaxin BBV152.\n\nMeaningDelta variant may pose the highest risk out of any currently circulating SARS-CoV-2 variants, with increased transmissibility over Alpha variant and possible vaccine breakthrough.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Timothy Farinholt", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Harshavardhan Doddapaneni", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Xiang Qin", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Vipin Menon", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Qingchang Meng", - "author_inst": "Baylor College Medicine" - }, - { - "author_name": "Ginger Metcalf", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Hsu Chao", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Marie-Claude Gingras", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Paige Farinholt", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Charu Agrawal", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Donna Muzny", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Pedro A. Piedra", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Richard A. Gibbs", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Joseph Petrosino", - "author_inst": "Baylor College of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.02.450964", "rel_title": "SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome", @@ -688567,6 +690164,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, + { + "rel_doi": "10.1101/2021.06.29.21259494", + "rel_title": "The drop in reported invasive pneumococcal disease among adults during the first COVID-19 wave in the Netherlands explained.", + "rel_date": "2021-07-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.29.21259494", + "rel_abs": "Streptococcus pneumoniae is the main bacterial pathogen causing respiratory infections. Since the COVID-19 pandemic emerged, less pneumococcal disease was identified by surveillance systems around the world. Measures to prevent transmission of SARS-CoV-2 also reduce transmission of pneumococci, but this would gradually lead to lower disease rates. Here, we explore additional factors that have contributed to the instant drop in pneumococcal disease cases captured in surveillance. Our observations on referral practices and other impediments to diagnostic testing indicate that residual IPD has likely occurred but remained undetected by conventional hospital-based surveillance. Depending on setting, we discuss alternative monitoring strategies that could improve sight on pneumococcal disease dynamics.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Kirsten K. T. Dirkx", + "author_inst": "Radboudumc" + }, + { + "author_name": "Bert Mulder", + "author_inst": "Canisius Wilhelmina Ziekenhuis, Nijmegen" + }, + { + "author_name": "Annelies Post", + "author_inst": "Canisius-Wilhelmina Ziekenhuis" + }, + { + "author_name": "Martijn Rutten", + "author_inst": "Radboudumc" + }, + { + "author_name": "Caroline Swanink", + "author_inst": "Rijnstate Ziekenhuis, Arnhem" + }, + { + "author_name": "Heiman Wertheim", + "author_inst": "Radboudumc" + }, + { + "author_name": "Amelieke Cremers", + "author_inst": "Radboudumc" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.07.02.450959", "rel_title": "SARS-CoV-2 Lambda Variant Remains Susceptible to Neutralization by mRNA Vaccine-elicited Antibodies and Convalescent Serum", @@ -690214,49 +691854,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.06.23.21259415", - "rel_title": "Use of recently vaccinated individuals to detect bias in test-negative case-control studies of COVID-19 vaccine effectiveness", - "rel_date": "2021-07-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.23.21259415", - "rel_abs": "Post-authorization observational studies play a key role in understanding COVID-19 vaccine effectiveness following the demonstration of efficacy in clinical trials. While bias due to confounding, selection bias, and misclassification can be mitigated through careful study design, unmeasured confounding is likely to remain in these observational studies. Phase III trials of COVID-19 vaccines have shown that protection from vaccination does not occur immediately, meaning that COVID-19 risk should be similar in recently vaccinated and unvaccinated individuals, in the absence of confounding or other bias. Several studies have used the estimated effectiveness among recently vaccinated individuals as a negative control exposure to detect bias in vaccine effectiveness estimates. In this paper we introduce a theoretical framework to describe the interpretation of such a bias-indicator in test-negative studies, and outline assumptions that would allow the use of recently vaccinated individuals to correct bias due to unmeasured confounding.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Matt D.T. Hitchings", - "author_inst": "University of Florida" - }, - { - "author_name": "Joseph A. Lewnard", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Natalie E. Dean", - "author_inst": "University of Florida" - }, - { - "author_name": "Albert I. Ko", - "author_inst": "Yale University School of Public Health" - }, - { - "author_name": "Otavio T. Ranzani", - "author_inst": "Barcelona Institute for Global Health, ISGlobal, Barcelona, Spain" - }, - { - "author_name": "Jason R. Andrews", - "author_inst": "Stanford University" - }, - { - "author_name": "Derek A.T. Cummings", - "author_inst": "University of Florida" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.23.21259414", "rel_title": "The COVID-related mental health load of neonatal healthcare professionals: a multicentre study in Italy.", @@ -690525,6 +692122,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.06.28.21259672", + "rel_title": "The health impacts of a 4-month long community-wide COVID-19 lockdown: Findings from a prospective longitudinal study in the state of Victoria, Australia.", + "rel_date": "2021-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259672", + "rel_abs": "ObjectivesTo determine health impacts during, and following, an extended community lockdown and COVID-19 outbreak in the Australian state of Victoria, compared with the rest of Australia.\n\nMethodsA national cohort of 898 working-age Australians enrolled in a longitudinal cohort study, completing surveys before, during, and after a 112-day community lockdown in Victoria (8 July - 27 October 2020). Outcomes included psychological distress, mental and physical health, work, social interactions and finances. Regression models examined health changes during and following lockdown.\n\nResultsThe Victorian lockdown led to increased psychological distress. Health impacts coincided with greater social isolation and work loss. Following the extended lockdown, mental health, work and social interactions recovered to an extent whereby no significant long-lasting effects were identified in Victoria compared to the rest of Australia.\n\nConclusionThe Victorian community lockdown had adverse health consequences, which reversed upon release from lockdown. Governments should weigh all potential health impacts of lockdown. Services and programs to reduce the negative impacts of lockdown may include increases in mental health care, encouraging safe social interactions and supports to maintain employment relationships.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Daniel Griffiths", + "author_inst": "Monash University" + }, + { + "author_name": "Luke Sheehan", + "author_inst": "Monash University" + }, + { + "author_name": "Dennis Petrie", + "author_inst": "Monash University" + }, + { + "author_name": "Caryn van Vreden", + "author_inst": "Monash University" + }, + { + "author_name": "Peter Whiteford", + "author_inst": "Australian National University" + }, + { + "author_name": "Alex Collie", + "author_inst": "Monash University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.06.28.21259644", "rel_title": "The Role of CRP, Interleukin-6 and Their Derived Immune-Inflammatory Indices in Early Prediction of Severity and Mortality of COVID-19 Patients", @@ -692228,69 +693864,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.02.450920", - "rel_title": "Betacoronavirus-specific alternate splicing", - "rel_date": "2021-07-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.02.450920", - "rel_abs": "Viruses can subvert a number of cellular processes in order to block innate antiviral responses, and many viruses interact with cellular splicing machinery. SARS-CoV-2 infection was shown to suppress global mRNA splicing, and at least 10 SARS-CoV-2 proteins bind specifically to one or more human RNAs. Here, we investigate 17 published experimental and clinical datasets related to SARS-CoV-2 infection as well as datasets from the betacoronaviruses SARS-CoV and MERS as well as Streptococcus pneumonia, HCV, Zika virus, Dengue virus, influenza H3N2, and RSV. We show that genes showing differential alternative splicing in SARS-CoV-2 have a similar functional profile to those of SARS-CoV and MERS and affect a diverse set of genes and biological functions, including many closely related to virus biology. Additionally, the differentially spliced transcripts of cells infected by coronaviruses were more likely to undergo intron-retention, contain a pseudouridine modification and a smaller number of exons than differentially spliced transcripts in the control groups. Viral load in clinical COVID-19 samples was correlated with isoform distribution of differentially spliced genes. A significantly higher number of ribosomal genes are affected by DAS and DGE in betacoronavirus samples, and the betacoronavirus differentially spliced genes are depleted for binding sites of RNA-binding proteins. Our results demonstrate characteristic patterns of differential splicing in cells infected by SARS-CoV-2, SARS-CoV, and MERS, potentially modifying a broad range of cellular functions and affecting a diverse set of genes and biological functions.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Guy Karlebach", - "author_inst": "The Jackson Laboratory for Genomic Medicine" - }, - { - "author_name": "Stephen J Baylin", - "author_inst": "Johns Hopkins University, School of Medicine" - }, - { - "author_name": "Daniel Butler", - "author_inst": "Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY USA" - }, - { - "author_name": "Jonathan Foox", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Shawn Levy", - "author_inst": "HudsonAlpha Institute for Biotechnology" - }, - { - "author_name": "Cem Meydan", - "author_inst": "Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY USA" - }, - { - "author_name": "Christopher Mozsary", - "author_inst": "Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY USA" - }, - { - "author_name": "Amanda M Saravia-Butler", - "author_inst": "Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA" - }, - { - "author_name": "Eve Wurtele", - "author_inst": "Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, 50011, USA" - }, - { - "author_name": "Christopher Mason", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Afshin Beheshti", - "author_inst": "KBR, NASA Ames Research Center" - }, - { - "author_name": "Peter N. Robinson", - "author_inst": "The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.07.02.450896", "rel_title": "Implications of Spike-glycoprotein processing at S1/S2 by Furin, at S2' by Furin and/or TMPRSS2 and shedding of ACE2: cell-to-cell fusion, cell entry and infectivity of SARS-CoV-2", @@ -692499,6 +694072,105 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.06.23.21259321", + "rel_title": "The IDentif.AI 2.0 Pandemic Readiness Platform: Rapid Prioritization of Optimized COVID-19 Combination Therapy Regimens", + "rel_date": "2021-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.23.21259321", + "rel_abs": "ObjectivesWe aimed to harness IDentif.AI 2.0, a clinically actionable AI platform to rapidly pinpoint and prioritize optimal combination therapy regimens against COVID-19.\n\nMethodsA pool of starting candidate therapies was developed in collaboration with a community of infectious disease clinicians and included EIDD-1931 (metabolite of EIDD-2801), baricitinib, ebselen, selinexor, masitinib, nafamostat mesylate, telaprevir (VX-950), SN-38 (metabolite of irinotecan), imatinib mesylate, remdesivir, lopinavir, and ritonavir. Following the initial drug pool assessment, a focused, 6-drug pool was interrogated at 3 dosing levels per drug representing nearly 10,000 possible combination regimens. IDentif.AI 2.0 paired prospective, experimental validation of multi-drug efficacy on a SARS-CoV-2 live virus (propagated, original strain, B.1.351 and B.1.617.2 variants) and Vero E6 assay with a quadratic optimization workflow.\n\nResultsWithin 3 weeks, IDentif.AI 2.0 realized a list of combination regimens, ranked by efficacy, for clinical go/no-go regimen recommendations. IDentif.AI 2.0 revealed EIDD-1931 to be a strong candidate upon which multiple drug combinations can be derived.\n\nConclusionsIDentif.AI 2.0 rapidly revealed promising drug combinations for clinical translation. It pinpointed dose-dependent drug synergy behavior to play a role in trial design and realizing positive treatment outcomes. IDentif.AI 2.0 represents an actionable path towards rapidly optimizing combination therapy following pandemic emergence.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC=\"FIGDIR/small/21259321v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (32K):\norg.highwire.dtl.DTLVardef@f8a159org.highwire.dtl.DTLVardef@12908b7org.highwire.dtl.DTLVardef@fb6485org.highwire.dtl.DTLVardef@8493c3_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- When novel pathogens emerge, the immediate strategy is to repurpose drugs.\n- Good drugs delivered together in suboptimal combinations and doses can yield low or no efficacy, leading to misperception that the drugs are ineffective.\n- IDentif.AI 2.0 does not use in silico modeling or pre-existing data.\n- IDentif.AI 2.0 pairs optimization with prospectively acquired experimental data using a SARS-CoV-2/Vero E6 assay.\n- IDentif.AI 2.0 pinpoints EIDD-1931 as a foundation for optimized anti-SARS-CoV-2 combination therapies.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Agata Blasiak", + "author_inst": "The Institute for Digital Medicine (WisDM); The N.1 Institute for Health (N.1); Department of Biomedical Engineering, National University of Singapore" + }, + { + "author_name": "Anh TL Truong", + "author_inst": "The Institute for Digital Medicine (WisDM); The N.1 Institute for Health (N.1); Department of Biomedical Engineering, National University of Singapore" + }, + { + "author_name": "Alexandria Remus", + "author_inst": "The Institute for Digital Medicine (WisDM); The N.1 Institute for Health (N.1); Department of Biomedical Engineering, National University of Singapore" + }, + { + "author_name": "Lissa Hooi", + "author_inst": "Cancer Science Institute of Singapore, National University of Singapore" + }, + { + "author_name": "Shirley Gek Kheng Seah", + "author_inst": "Defence Medical & Environmental Research Institute, DSO National Laboratories" + }, + { + "author_name": "Peter Wang", + "author_inst": "The Institute for Digital Medicine (WisDM); The N.1 Institute for Health (N.1); Department of Biomedical Engineering, National University of Singapore" + }, + { + "author_name": "De Hoe Chye", + "author_inst": "Defence Medical & Environmental Research Institute, DSO National Laboratories" + }, + { + "author_name": "Angeline Pei Chiew Lim", + "author_inst": "Defence Medical & Environmental Research Institute, DSO National Laboratories" + }, + { + "author_name": "Kim Tien Ng", + "author_inst": "Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore" + }, + { + "author_name": "Swee Teng Teo", + "author_inst": "Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore" + }, + { + "author_name": "Yee-Joo Tan", + "author_inst": "Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore" + }, + { + "author_name": "David Michael Allen", + "author_inst": "Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore; Division of Infectious Diseases, National University Hospital, Singap" + }, + { + "author_name": "Louis Yi Ann Chai", + "author_inst": "Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore; Division of Infectious Diseases, National University Hospital, Singap" + }, + { + "author_name": "Wee Joo Chng", + "author_inst": "Cancer Science Institute of Singapore, National University of Singapore; Department of Haematology-Oncology, National University Cancer Institute, Singapore, Na" + }, + { + "author_name": "Raymond T.P. Lin", + "author_inst": "National Centre for Infectious Diseases (NCID), Singapore; Department of Laboratory Medicine, National University Hospital, Singapore" + }, + { + "author_name": "David C.B. Lye", + "author_inst": "National Centre for Infectious Diseases (NCID), Tan Tock Seng Hospital, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University " + }, + { + "author_name": "John Eu-Li Wong", + "author_inst": "Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore; Department of Haematology-Oncology, National University Cancer Instit" + }, + { + "author_name": "Gek-Yen Gladys Tan", + "author_inst": "Defence Medical & Environmental Research Institute, DSO National Laboratories" + }, + { + "author_name": "Conrad En Zuo Chan", + "author_inst": "Defence Medical & Environmental Research Institute, DSO National Laboratories" + }, + { + "author_name": "Edward Kai-Hua Chow", + "author_inst": "Cancer Science Institute of Singapore; Department of Pharmacology; National University of Singapore; NUS Centre for Cancer Research (N2CR), Yong Loo Lin School " + }, + { + "author_name": "Dean Ho", + "author_inst": "The Institute for Digital Medicine (WisDM); The N.1 Institute for Health (N.1); Department of Biomedical Engineering; Department of Pharmacology, National Unive" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.01.21259859", "rel_title": "Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages", @@ -694486,149 +696158,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2021.06.28.21259576", - "rel_title": "Immunogenicity of COVID-19 Vaccination in Immunocompromised Patients: An Observational, Prospective Cohort Study Interim Analysis", - "rel_date": "2021-06-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259576", - "rel_abs": "ObjectivesImmunocompromised patients were excluded from COVID-19 vaccine clinical trials. The objectives of the study were to measure antibody responses, levels, and neutralization capability after COVID-19 vaccination among immunocompromised patients and compare these variables to those of immunocompetent healthcare workers.\n\nMethodsThis is an interim analysis of an ongoing observational, prospective cohort study which launched on April 14, 2021 across Western Pennsylvania. Participants were healthy healthcare workers (HCW) and immunocompromised patients who had completed their COVID-19 vaccination series. Individuals with a history of COVID-19 were not eligible. Serum was collected to measure for the presence of IgG against the SARS-CoV-2 Spike protein using a semi-quantitative assay; antibody levels were available for comparisons. A quasi-random subset of patients was selected for pseudovirus neutralization assays. Seropositivity with 95% Clopper-Pearson exact confidence intervals and distribution of antibody levels were measured. To identify risk factors for seronegativity, clinical characteristics were univariately compared between antibody reactive and non-reactive individuals within the immunocompromised group.\n\nResults107 HCW and 489 immunocompromised patients were enrolled. Compared to HCWs, seropositivity was significantly lower (p<.001) among immunocompromised patients with Solid organ transplant (SOT), autoimmune, hematological malignancies, and solid tumors (HCW=98.1%; SOT=37.2%; autoimmune=83.8%; hematological malignancies=54.7%; and solid tumor=82.4%, p < 0.05). Over 94% of patients with Human Immunodeficiency Virus were seropositive. Among seropositive patients, antibody levels were much lower among SOT (4.5 [2.1,13.1], p=.020). Neutralization titers tightly correlated with antibody levels (Spearman r = 0.91, p < 0.0001).\n\nConclusionOur findings demonstrate the heterogeneity of the humoral immune response to COVID-19 vaccines based on underlying immunosuppressive condition and highlight an urgent need to optimize and individualize COVID-19 prevention in these patients. These findings also have implications on public health guidance, particularly given revised Centers for Disease Control and Prevention recommendations permitting vaccinated individuals to abandon masking and social distancing in most settings. Future studies are warranted to determine assessment of cellular immunity, longitudinal measurement of immune responses, and the safety and efficacy of revaccination.", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Ghady Haidar", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Mounzer Agha", - "author_inst": "UPMC Hillman Cancer Center" - }, - { - "author_name": "Amy Lukanski", - "author_inst": "UPMC Wolff Center" - }, - { - "author_name": "Kelsey Linstrum", - "author_inst": "UPMC Health Care Innovation" - }, - { - "author_name": "Rachel Troyan", - "author_inst": "UPMC Wolff Center" - }, - { - "author_name": "Andrew Bilderback", - "author_inst": "UPMC Wolff Center" - }, - { - "author_name": "Scott Rothenberger", - "author_inst": "Division of General Internal Medicine, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Deborah K McMahon", - "author_inst": "Division of Infectious Diseases, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Melissa Crandall", - "author_inst": "Clinical Laboratory, University of Pittsburgh Medical Center" - }, - { - "author_name": "P Nathan Enick", - "author_inst": "Division of Infectious Diseases, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Michelle Sobolewksi", - "author_inst": "Division of Infectious Diseases, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Kevin Collins", - "author_inst": "Clinical Analytics, University of Pittsburgh Medical Center" - }, - { - "author_name": "Marc B Schwartz", - "author_inst": "Department of Medicine, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Jeffrey M Dueker", - "author_inst": "Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Fernanda P Silveira", - "author_inst": "Division of Infectious Diseases, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Mary E Keebler", - "author_inst": "Department of Cardiology, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Abhinav Humar", - "author_inst": "Division of Transplantation, Department of Surgery, University of Pittsburgh School of Medicine" - }, - { - "author_name": "James D Luketich", - "author_inst": "Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Matthew R Morrell", - "author_inst": "Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Joseph M Pilewski", - "author_inst": "Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine" - }, - { - "author_name": "John F McDyer", - "author_inst": "Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Bhanu Pappu", - "author_inst": "Hillman Cancer Center, University of Pittsburgh Medical Center" - }, - { - "author_name": "Robert L Ferris", - "author_inst": "Hillman Cancer Center, University of Pittsburgh Medical Center" - }, - { - "author_name": "Stanley M Marks", - "author_inst": "Hillman Cancer Center, University of Pittsburgh Medical Center" - }, - { - "author_name": "Cynthia Klamar-Blain", - "author_inst": "Division of Infectious Diseases, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Urvi M Parikh", - "author_inst": "Division of Infectious Diseases, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Amy Heaps", - "author_inst": "Division of Infectious Diseases, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Paula L Kip", - "author_inst": "University of Pittsburgh Medical Center" - }, - { - "author_name": "Alan Wells", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Tami Minnier", - "author_inst": "UPMC Wolff Center" - }, - { - "author_name": "Derek Angus", - "author_inst": "UPMC Health Care Innovation" - }, - { - "author_name": "John W Mellors", - "author_inst": "Division of Infectious Diseases, University of Pittsburgh School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.21.21258023", "rel_title": "ASSESSMENT OF POTENTIAL SARS-CoV-2 VIRUS N GENE INTEGRATION INTO HUMAN GENOME REVEALS NO SIGNIFICANT IMPACT ON RT-qPCR COVID-19 DIAGNOSTIC TESTING", @@ -694789,6 +696318,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, + { + "rel_doi": "10.1101/2021.06.23.21259389", + "rel_title": "Altered cellular and humoral immune responses following SARS-CoV-2 mRNA vaccination in patients with multiple sclerosis on anti-CD20 therapy.", + "rel_date": "2021-06-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.23.21259389", + "rel_abs": "SARS-CoV-2 mRNA vaccination in healthy individuals generates effective immune protection against COVID-19. Little is known, however, about the SARS-CoV-2 mRNA vaccine-induced responses in immunosuppressed patients. We investigated induction of antigen-specific antibody, B cell and T cell responses in patients with multiple sclerosis on anti-CD20 (MS-aCD20) monotherapy following SARS-CoV-2 mRNA vaccination. Treatment with aCD20 significantly reduced Spike and RBD specific antibody and memory B cell responses in most patients, an effect that was ameliorated with longer duration from last aCD20 treatment and extent of B cell reconstitution. In contrast, all MS-aCD20 patients generated antigen-specific CD4 and CD8 T-cell responses following vaccination. However, treatment with aCD20 skewed these responses compromising circulating Tfh responses and augmenting CD8 T cell induction, while largely preserving Th1 priming. These data also revealed underlying features of coordinated immune responses following mRNA vaccination. Specifically, the MS-aCD20 patients who failed to generate anti-RBD IgG had the most severe defect in cTfh cell responses and more robust CD8 T cell responses compared to those who generated anti-RBD IgG, whose T cell responses were more similar to healthy controls. These data define the nature of SARS-CoV-2 vaccine-induced immune landscape in aCD20-treated patients, and provide insights into coordinated mRNA vaccine-induced immune responses in humans. Our findings have implications for clinical decision-making, patient education and public health policy for patients treated with aCD20 and other immunosuppressed patients.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Sokratis A. Apostolidis", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Mihir Kakara", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Mark M Painter", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Rishi Raj Goel", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Divij Mathew", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Kerry Lenzi", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ayman Rezk", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Kristina R. Patterson", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Diego Alexander Espinoza", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jessy C. Kadri", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Daniel M. Markowitz", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Clyde Markowitz", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ina Mexhitaj", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Dina Jacobs", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Allison Babb", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Michael R. Betts", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Eline T. Luning Prak", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Daniela Weiskopf", + "author_inst": "La Jolla Institute For Allergy & Immunology" + }, + { + "author_name": "Alba Grifoni", + "author_inst": "La Jolla Institute for Immunology" + }, + { + "author_name": "Kendall A. Lundgreen", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Sigrid Gouma", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Alessandro Sette", + "author_inst": "La Jolla Institute for Allergy & Immunology" + }, + { + "author_name": "Paul Bates", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Scott E. Hensley", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Allison R. Greenplate", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "E John Wherry", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Rui Li", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Amit Bar-Or", + "author_inst": "University of Pensylvania" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2021.06.26.21259568", "rel_title": "A Systematic Review: The Dimensions and Indicators utilized in the Performance Evaluation of Health Care Organizations- An Implication during COVID-19 Pandemic", @@ -696252,41 +697908,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.06.24.21259505", - "rel_title": "Assessment of COVID-19 vaccine hesitancy among Zimbabweans: A rapid national survey", - "rel_date": "2021-06-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.24.21259505", - "rel_abs": "BackgroundTo minimise the devastating effects of the coronavirus disease 2019 (COVID-19) pandemic, scientists hastily developed a vaccine. However, the scale-up of the vaccine is likely to be hindered by the widespread social media misinformation. We, therefore, conducted a study to assess the COVID-19 vaccine hesitancy among Zimbabweans.\n\nMethodsWe conducted a descriptive online cross-sectional survey using a self-administered questionnaire among adults. The questionnaire assessed willingness to be vaccinated; socio-demographic characteristics, individual attitudes and perceptions, effectiveness, and safety of the vaccine. Multivariable logistic regression analysis was utilized to examine the independent factors associated with vaccine uptake.\n\nResultsWe analysed data for 1168 participants, age range of 19-89 years with the majority being females (57.5%). Half (49.9%) of the participants reported that they would accept the COVID-19 vaccine. The majority were uncertain about the effectiveness of the vaccine (76.0%) and its safety (55.0%). About half lacked trust in the governments ability to ensure the availability of an effective vaccine and 61.0% mentioned that they would seek advice from a healthcare worker to vaccinate. Age 55 years and above [vs 18-25 years - Adjusted Odds Ratio (AOR): 2.04, 95% Confidence Interval (CI): 1.07-3.87], chronic disease [vs no chronic disease - AOR: 1.72, 95%CI: 1.32-2.25], males [vs females - AOR: 1.84, 95%CI: 1.44-2.36] and being a healthcare worker [vs not being a health worker - AOR: 1.73, 95%CI: 1.34-2.24] were associated with increased likelihood to vaccinate. History of COVID-19 infection [vs no history - AOR: 0.45, 95%CI: 0.25-0.81) and rural residence [vs urban - AOR: 0.64, 95%CI: 0.40-1.01] were associated with reduced likelihood to vaccinate.\n\nConclusionWe found half of the participants willing to vaccinate against COVID-19. The majority lacked trust in the government and were uncertain about vaccine effectiveness and safety. The policymakers should consider targeting geographical and demographic groups which were unlikely to vaccinate with vaccine information, education, and communication to improve uptake.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Paddington T Mundagowa", - "author_inst": "Africa University" - }, - { - "author_name": "Samantha N Tozivepi", - "author_inst": "Africa University" - }, - { - "author_name": "Edward T Chiyaka", - "author_inst": "Kent State University" - }, - { - "author_name": "Fadzai Mukora-Mutseyekwa", - "author_inst": "Africa University" - }, - { - "author_name": "Richard Makurumidze", - "author_inst": "University of Zimbabwe College of Health Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.28.450244", "rel_title": "Systematic genome-scale identification of host factors for SARS-CoV-2 infection across models yields a core single gene dependency; ACE2", @@ -696611,6 +698232,89 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.06.29.450133", + "rel_title": "Absolute quantitation of individual SARS-CoV-2 RNA molecules: a new paradigm for infection dynamics and variant differences", + "rel_date": "2021-06-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.29.450133", + "rel_abs": "Despite an unprecedented global research effort on SARS-CoV-2, early replication events remain poorly understood. Given the clinical importance of emergent viral variants with increased transmission, there is an urgent need to understand the early stages of viral replication and transcription. We used single molecule fluorescence in situ hybridisation (smFISH) to quantify positive sense RNA genomes with 95% detection efficiency, while simultaneously visualising negative sense genomes, sub-genomic RNAs and viral proteins. Our absolute quantification of viral RNAs and replication factories revealed that SARS-CoV-2 genomic RNA is long-lived after entry, suggesting that it avoids degradation by cellular nucleases. Moreover, we observed that SARS-CoV-2 replication is highly variable between cells, with only a small cell population displaying high burden of viral RNA. Unexpectedly, the B.1.1.7 variant, first identified in the UK, exhibits significantly slower replication kinetics than the Victoria strain, suggesting a novel mechanism contributing to its higher transmissibility with important clinical implications.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC=\"FIGDIR/small/450133v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (55K):\norg.highwire.dtl.DTLVardef@10f7bf1org.highwire.dtl.DTLVardef@192214dorg.highwire.dtl.DTLVardef@c84916org.highwire.dtl.DTLVardef@1366287_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefBy detecting nearly all individual SARS-CoV-2 RNA molecules, we quantified viral replication and defined cell susceptibility to infection. We discovered that a minority of cells show significantly elevated viral RNA levels and observed slower replication kinetics for the Alpha variant relative to the Victoria strain.\n\nHighlights O_LISingle molecule quantification of SARS-CoV-2 replication uncovers early infection kinetics\nC_LIO_LIThere is substantial heterogeneity between cells in rates of SARS-CoV-2 replication\nC_LIO_LIGenomic RNA is stable and persistent during the initial stages of infection\nC_LIO_LIB.1.1.7 variant replicates more slowly than the Victoria strain\nC_LI", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Jeffrey Y Lee", + "author_inst": "Department of Biochemistry, The University of Oxford, UK" + }, + { + "author_name": "Peter AC Wing", + "author_inst": "Nuffield Department of Medicine, The University of Oxford, Oxford, UK; Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), The University of Oxfo" + }, + { + "author_name": "Dalia S Gala", + "author_inst": "Department of Biochemistry, The University of Oxford, UK" + }, + { + "author_name": "Marko Noerenberg", + "author_inst": "Department of Biochemistry, The University of Oxford, UK; MRC-University of Glasgow Centre for Virus Research, The University of Glasgow, UK" + }, + { + "author_name": "Aino I Jarvelin", + "author_inst": "Department of Biochemistry, The University of Oxford, UK" + }, + { + "author_name": "Josh Titlow", + "author_inst": "Department of Biochemistry, The University of Oxford, UK" + }, + { + "author_name": "Xiaodong Zhuang", + "author_inst": "Nuffield Department of Medicine, The University of Oxford, Oxford, UK" + }, + { + "author_name": "Natasha Palmalux", + "author_inst": "MRC-University of Glasgow Centre for Virus Research, The University of Glasgow, UK" + }, + { + "author_name": "Louisa Iselin", + "author_inst": "Department of Biochemistry, The University of Oxford, UK" + }, + { + "author_name": "Mary Kay Thompson", + "author_inst": "Department of Biochemistry, The University of Oxford, UK" + }, + { + "author_name": "Richard M Parton", + "author_inst": "Department of Biochemistry, The University of Oxford, UK" + }, + { + "author_name": "Alan Wainman", + "author_inst": "Sir William Dunn School of Pathology, The University of Oxford, UK" + }, + { + "author_name": "Daniel Agranoff", + "author_inst": "Department of Infectious Diseases, University Hospitals Sussex NHS Foundation Trust, UK." + }, + { + "author_name": "William James", + "author_inst": "Sir William Dunn School of Pathology, The University of Oxford, UK" + }, + { + "author_name": "Alfredo Castello", + "author_inst": "Department of Biochemistry, The University of Oxford, UK; MRC-University of Glasgow Centre for Virus Research, The University of Glasgow, UK" + }, + { + "author_name": "Jane A McKeating", + "author_inst": "Nuffield Department of Medicine, The University of Oxford, Oxford, UK; Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), The University of Oxfo" + }, + { + "author_name": "Ilan Davis", + "author_inst": "Department of Biochemistry, The University of Oxford, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.06.29.450330", "rel_title": "Genetic diversity and evolution of SARS-CoV-2 in Belgium during the first wave outbreak", @@ -698766,69 +700470,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.06.28.449914", - "rel_title": "Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants", - "rel_date": "2021-06-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.28.449914", - "rel_abs": "The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has led to growing concerns over increased transmissibility and the ability of some variants to partially escape immunity. Sera from participants immunized on a prime-boost schedule with the mRNA-1273 COVID-19 vaccine were tested for neutralizing activity against several SARS-CoV-2 variants, including variants of concern (VOCs) and variants of interest (VOIs), compared to neutralization of the wild-type SARS-CoV-2 virus (designated as D614G). Results showed minimal effects on neutralization titers against the B.1.1.7 (Alpha) variant (1.2-fold reduction compared with D614G); other VOCs such as B.1.351 (Beta, including B.1.351-v1, B.1.351-v2, and B.1.351-v3), B.1.617.2 (Delta), and P.1 (Gamma) showed decreased neutralization titers ranging from 2.1-fold to 8.4-fold reductions compared with D614G, although all remained susceptible to mRNA-1273-elicited serum neutralization.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Angela Choi", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Matthew Koch", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Kai Wu", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Groves Dixon", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Judith Oestreicher", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Holly Legault", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Guillaume B.E. Stewart-Jones", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Tonya Colpitts", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Rolando Pajon", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Hamilton Bennett", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Andrea Carfi", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Darin K Edwards", - "author_inst": "Moderna Inc" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.06.25.449831", "rel_title": "Solar simulated ultraviolet radiation inactivates HCoV-NL63 and SARS-CoV-2 coronaviruses at environmentally relevant doses", @@ -699157,6 +700798,77 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.06.28.450214", + "rel_title": "A bifluorescent-based assay for the identification of neutralizing antibodies against SARS-CoV-2 variants of concern in vitro and in vivo", + "rel_date": "2021-06-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.28.450214", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged at the end of 2019 and has been responsible for the still ongoing coronavirus disease 2019 (COVID-19) pandemic. Prophylactic vaccines have been authorized by the United States (US) Food and Drug Administration (FDA) for the prevention of COVID-19. Identification of SARS-CoV-2 neutralizing antibodies (NAbs) is important to assess vaccine protection efficacy, including their ability to protect against emerging SARS- CoV-2 variants of concern (VoC). Here we report the generation and use of a recombinant (r)SARS-CoV-2 USA/WA1/2020 (WA-1) strain expressing Venus and a rSARS-CoV-2 expressing mCherry and containing mutations K417N, E484K, and N501Y found in the receptor binding domain (RBD) of the spike (S) glycoprotein of the South African (SA) B.1.351 (beta, {beta}) VoC, in bifluorescent-based assays to rapidly and accurately identify human monoclonal antibodies (hMAbs) able to neutralize both viral infections in vitro and in vivo. Importantly, our bifluorescent-based system accurately recapitulated findings observed using individual viruses. Moreover, fluorescent- expressing rSARS-CoV-2 and the parental wild-type (WT) rSARS-CoV-2 WA-1 had similar viral fitness in vitro, as well as similar virulence and pathogenicity in vivo in the K18 human angiotensin converting enzyme 2 (hACE2) transgenic mouse model of SARS-CoV-2 infection. We demonstrate that these new fluorescent-expressing rSARS- CoV-2 can be used in vitro and in vivo to easily identify hMAbs that simultaneously neutralize different SARS-CoV-2 strains, including VoC, for the rapid assessment of vaccine efficacy or the identification of prophylactic and/or therapeutic broadly NAbs for the treatment of SARS-CoV-2 infection.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Kevin Chiem", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Desarey Morales Vasquez", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Jesus Silvas", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Jun-Gyu Park", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Michael Piepenbrink", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Julien Sourimant", + "author_inst": "Georgia State University" + }, + { + "author_name": "Michelle J Lin", + "author_inst": "University of Washington" + }, + { + "author_name": "Alexander L. Greninger", + "author_inst": "University of Washington" + }, + { + "author_name": "Richard K. Plemper", + "author_inst": "Georgia State University" + }, + { + "author_name": "Jordi B Torrelles", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Mark R Walter", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Juan C de la Torre", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "James Kobie", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Luis Martinez-Sobrido", + "author_inst": "Texas Biomedical Research Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.06.24.21259453", "rel_title": "Conditionality of COVID-19 vaccine acceptance in European countries", @@ -700980,33 +702692,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.22.21258971", - "rel_title": "Temporal Analysis of Social Determinants Associated with COVID-19 Mortality", - "rel_date": "2021-06-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.22.21258971", - "rel_abs": "This study examines how social determinants associated with COVID-19 mortality change over time. Using US county-level data from July 5 and December 28, 2020, the effect of 19 high-risk factors on COVID-19 mortality rate was quantified at each time point with negative binomial mixed models. Then, these high-risk factors were used as controls in two association studies between 40 social determinants and COVID-19 mortality rates using data from the same time points. The results indicate that counties with certain ethnic minorities and age groups, immigrants, prevalence of diseases like pediatric asthma and diabetes and cardiovascular disease, socioeconomic inequalities, and higher social association are associated with increased COVID-19 mortality rates. Meanwhile, more mental health providers, access to exercise, higher income, chronic lung disease in adults, suicide, and excessive drinking are associated with decreased mortality. Our temporal analysis also reveals a possible decreasing impact of socioeconomic disadvantage and air quality, and an increasing effect of factors like age, which suggests that public health policies may have been effective in protecting disadvantaged populations over time or that analysis utilizing earlier data may have exaggerated certain effects. Overall, we continue to recognize that social inequality still places disadvantaged groups at risk, and we identify possible relationships between lung disease, mental health, and COVID-19 that need to be explored on a clinical level.\n\nCCS CONCEPTSO_LIApplied computing [->] Health informatics.\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Shayom Debopadhaya", - "author_inst": "Rensselaer Polytechnic Institute" - }, - { - "author_name": "John S Erickson", - "author_inst": "Rensselaer Polytechnic Institute" - }, - { - "author_name": "Kristin P Bennett", - "author_inst": "Rensselaer Polytechnic Institute" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.22.21259345", "rel_title": "Multi-centre post-implementation evaluation of SARS-CoV-2 antigen-based point of care tests used for asymptomatic screening of continuing care healthcare workers", @@ -701191,6 +702876,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.23.21258626", + "rel_title": "Report on Three Round COVID-19 Risk Blind Tests by Screening Eye-region Manifestations", + "rel_date": "2021-06-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.23.21258626", + "rel_abs": "The Coronavirus disease 2019 (COVID-19) has affected several million people since 2019. Despite various vaccines of COVID-19 protect million people in many countries, the worldwide situations of more the asymptomatic and mutated strain discovered are urging the more sensitive COVID-19 testing in this turnaround time. Unfortunately, it is still nontrivial to develop a new fast COVID-19 screening method with the easier access and lower cost, due to the technical and cost limitations of the current testing methods in the medical resource-poor districts. On the other hand, there are more and more ocular manifestations that have been reported in the COVID-19 patients as growing clinical evidence[1]. This inspired this project. We have conducted the joint clinical research since January 2021 at the ShiJiaZhuang City, Hebei province, China, which approved by the ethics committee of The fifth hospital of ShiJiaZhuang of Hebei Medical University. We undertake several blind tests of COVID-19 patients by Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. Meantime as an important part of the ongoing globally COVID-19 eye test program by AIMOMICS since February 2020, we propose a new fast screening method of analyzing the eye-region images, captured by common CCD and CMOS cameras. This could reliably make a rapid risk screening of COVID-19 with the sustainable stable high performance in different countries and races. For this clinical trial in ShiJiaZhuang, we compare and analyze 1194 eye-region images of 115 patients, including 66 COVID-19 positive patients, 44 rehabilitation patients (nucleic acid changed from positive to negative), 5 liver patients, as well as 117 healthy people. Remarkably, we consistently achieved very high testing results (> 0.94) in terms of both sensitivity and specificity in our blind test of COVID-19 patients. This confirms the viability of the COVID-19 fast screening by the eye-region manifestations. Particularly and impressively, the results have the similar conclusion as the other clinical trials of the globally COVID-19 eye test program[1]. Hopefully, this series of ongoing globally COVID-19 eye test study, and potential rapid solution of fully self-performed COVID risk screening method, can be inspiring and helpful to more researchers in the world soon. Our model for COVID-19 rapid prescreening have the merits of the lower cost, fully self-performed, non-invasive, importantly real-time, and thus enables the continuous health surveillance. We further implement it as the open accessible APIs, and provide public service to the world. Our pilot experiments show that our model is ready to be usable to all kinds of surveillance scenarios, such as infrared temperature measurement device at airports and stations, or directly pushing to the target people groups smartphones as a packaged application.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Yanwei Fu", + "author_inst": "Fudan University" + }, + { + "author_name": "Lei Zhao", + "author_inst": "Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022. China" + }, + { + "author_name": "Haojie Zheng", + "author_inst": "The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China" + }, + { + "author_name": "Qiang Sun", + "author_inst": "Academy for Engineering & Technology, Fudan University, Shanghai, 200433, China" + }, + { + "author_name": "Li Yang", + "author_inst": "The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China" + }, + { + "author_name": "Hong Li", + "author_inst": "Medical Examination Center,Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061, China" + }, + { + "author_name": "Jiao Xie", + "author_inst": "Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022. China" + }, + { + "author_name": "Xiangyang Sue", + "author_inst": "School of Data Science, Fudan University, Shanghai, 200433, China" + }, + { + "author_name": "Feng Li", + "author_inst": "department of respirology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China" + }, + { + "author_name": "Yuan Li", + "author_inst": "The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China" + }, + { + "author_name": "Wei Yang", + "author_inst": "The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China" + }, + { + "author_name": "Yantao Pei", + "author_inst": "The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China" + }, + { + "author_name": "Jianming Wang", + "author_inst": "The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China" + }, + { + "author_name": "Xiuqi Wu", + "author_inst": "The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China" + }, + { + "author_name": "Yanhua Zheng", + "author_inst": "The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China" + }, + { + "author_name": "Hongxia Tian", + "author_inst": "The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China" + }, + { + "author_name": "Mengwei Gu", + "author_inst": "Aimomics (Shanghai) Intelligent Technology Co., Ltd., Shanghai, 200433, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.22.21259346", "rel_title": "Can Auxiliary Indicators Improve COVID-19 Forecasting and Hotspot Prediction?", @@ -702666,37 +704434,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.24.449840", - "rel_title": "Phylogenetic network analysis revealed the recombinant origin of the SARS-CoV-2 VOC202012/01 (B.1.1.7) variant first discovered in U.K.", - "rel_date": "2021-06-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.24.449840", - "rel_abs": "The emergence of new variants of the SARS-CoV-2 virus poses serious problems to the control of the current COVID-19 pandemic. Understanding how the variants originate is critical for effective control of the spread of the virus and the global pandemic. The study of the virus evolution so far has been dominated by phylogenetic tree analysis, which however is inappropriate for a few important reasons. Here we used phylogenetic network approach to study the origin of the VOC202012/01 (Alpha) or so-called UK variant (PANGO Lineage B.1.1.7). The multiple network analyses using different methods consistently revealed that the VOC202012/01 variant was a result of recombination, in contrast to the common assumption that the variant evolved from step-wise mutations in a linear order. The study provides an example for the power and application of phylogenetic network analysis in studying virus evolution, which can be applied to study the evolutionary processes leading to the emergence of other variants of the SARS-CoV-2 virus as well as many other viruses.\n\nSignificanceThe emergence of new variants of the SARS-CoV-2 virus, including the Alpha variant first found in U.K., poses serious challenges to the control of the current COVID-19 pandemic. Understanding how new variant originated is paramount to end the pandemic as effectively and quickly as possible. The dominant phylogenetic tree approach to study virus evolution has been inadequate and even misleading. Here we used a phylogenetic network approach to study the origin of the VOC202012/01 (Alpha) variant which was first reported in U.K. last year but has soon spread into many other countries, leading to dramatic increase in infection and death. Multiple analyses consistently revealed that the variant originated through recombination of pre-existing virus strains, highlighting an important but largely ignored mechanism in the evolution of the SARS-CoV-2 virus so far.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Xianfa Xie", - "author_inst": "Virginia State University" - }, - { - "author_name": "Teash-Juan Lewis", - "author_inst": "Virginia State University" - }, - { - "author_name": "Nikoli Green", - "author_inst": "Virginia State University" - }, - { - "author_name": "Zhenping Wang", - "author_inst": "Virginia State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.06.25.449750", "rel_title": "A random priming amplification method for whole genome sequencing of SARS-CoV-2 and H1N1 influenza A virus.", @@ -702849,6 +704586,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.21.21258990", + "rel_title": "SARS-CoV-2 Breakthrough Infections in Fully Vaccinated Individuals", + "rel_date": "2021-06-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.21.21258990", + "rel_abs": "ImportanceWhile COVID-19 vaccines are highly effective against disease, breakthrough infections may occur in the context of rising variants of concern.\n\nObjectiveWe paired random and passive surveillance nucleic acid testing with analysis of viral whole genomic sequences to detect and describe breakthrough infections, focusing in a university community.\n\nDesignAnterior nasal swabs were collected from individuals for a nucleic acid amplification test (NAAT) for detection of SARS-CoV-2. A subset of NAAT positive samples was sequenced to determine variants associated with infections. Included in the testing and sequencing protocol were individuals that were fully vaccinated.\n\nSettingThis study was performed as part of a surveillance program for SARS-CoV-2 on a university campus with 49,700 students and employees.\n\nParticipantsSurveillance testing was random and included approximately 10% of the population each week. Additionally, individuals self-identified with COVID-19 related symptoms or those that had close contact with SARS-CoV-2 positive individuals were also tested.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Esteban Ramirez", + "author_inst": "Indiana University School of Medicine, One To One Health" + }, + { + "author_name": "Rebecca P. Wilkes", + "author_inst": "Purdue University Animal Disease Diagnostic Laboratory" + }, + { + "author_name": "Giovanna Carpi", + "author_inst": "Purdue University" + }, + { + "author_name": "Jack Dorman", + "author_inst": "Purdue University" + }, + { + "author_name": "Craig Bowen", + "author_inst": "Purdue University, Animal Disease Diagnostic Laboratory" + }, + { + "author_name": "Lisa Smith", + "author_inst": "University of Tennessee College of Medicine-Chattanooga, One to One Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.21.21259259", "rel_title": "Clinical profile and immediate outcome of Multisystem Inflammatory Syndrome in Children (MIS-C) associated with Covid-19: a multicentric study", @@ -704360,73 +706136,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.21.449211", - "rel_title": "Anti-prothrombin autoantibodies enriched after infection with SARS-CoV-2 and influenced by strength of antibody response against SARS-CoV-2 proteins", - "rel_date": "2021-06-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.21.449211", - "rel_abs": "Antiphospholipid antibodies (aPL), assumed to cause antiphospholipid syndrome (APS), are notorious for their heterogeneity and detect phospholipids and phospholipid-binding proteins. The persistent presence of Lupus anticoagulant and/or aPL against cardiolipin and/or {beta}2 glycoprotein I have been shown to be independent risk factors for vascular thrombosis and pregnancy morbidity in APS. aPL production is thought to be triggered by - among other factors - viral infections, though infection-associated aPL have mostly been considered non-pathogenic. Recently, the potential pathogenicity of infection-associated aPL has gained momentum since an increasing number of patients infected with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been described with coagulation abnormalities and hyperinflammation, together with the presence of aPL. Here, we present data from a multicentric, mixed-severity study including three cohorts of individuals who contracted SARS-CoV-2 as well as non-infected blood donors. We simultaneously measured 10 different criteria and non-criteria aPL (IgM and IgG) by using a line immunoassay. Further, IgG antibody response against three SARS-CoV-2 proteins was investigated using tripartite automated blood immunoassay technology. Our analyses revealed that selected non-criteria aPL were enriched concomitant to or after an infection with SARS-CoV-2. Linear mixed-effects models suggest an association of aPL to prothrombin (PT) with the strength of the antibody response against SARS-CoV-2 and that it is further influenced by SARS-CoV-2 disease severity and sex of the individuals. In conclusion, our study is the first to report an association between disease severity, anti-SARS-CoV-2 immunoreactivity and aPL against PT in patients with SARS-CoV-2.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Marc Emmenegger", - "author_inst": "University of Zurich" - }, - { - "author_name": "Sreedhar Saseendran Kumar", - "author_inst": "ETH Zurich, Basel" - }, - { - "author_name": "Vishalini Emmenegger", - "author_inst": "ETH Zurich, Basel" - }, - { - "author_name": "Tomas Malinauskas", - "author_inst": "Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK" - }, - { - "author_name": "Thomas Buettner", - "author_inst": "GA Generic Assays GmbH" - }, - { - "author_name": "Laura Rose", - "author_inst": "GA Generic Assays GmbH" - }, - { - "author_name": "Peter Schierack", - "author_inst": "Institute of Biotechnology, Faculty Environment and Natural Sciences and Faculty of Health Sciences Brandenburg, University of Technology Cottbus-Senftenberg" - }, - { - "author_name": "Martin F Sprinzl", - "author_inst": "Johannes Gutenberg University Medical Center Mainz" - }, - { - "author_name": "Clemens J Sommer", - "author_inst": "Johannes Gutenberg University Medical Center Mainz" - }, - { - "author_name": "Karl J Lackner", - "author_inst": "Johannes Gutenberg University Medical Center Mainz" - }, - { - "author_name": "Adriano Aguzzi", - "author_inst": "University Hospital Zurich" - }, - { - "author_name": "Dirk Roggenbuck", - "author_inst": "GA Generic Assays GmbH, Institute of Biotechnology, Faculty Environment and Natural Sciences and Faculty of Health Sciences Brandenburg, University of Technolog" - }, - { - "author_name": "Katrin B M Frauenknecht", - "author_inst": "Johannes Gutenberg University Medical Center Mainz and University Hospital Zurich" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.06.14.21258907", "rel_title": "Hybrid-Quantum approach for the optimal lockdown to stop the SARS-CoV-2 community spread subject to maximizing nation economy globally", @@ -704627,6 +706336,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.18.21259157", + "rel_title": "Clinical profiles at the time of diagnosis of COVID-19 in Costa Rica during the pre-vaccination period using a machine learning approach", + "rel_date": "2021-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.18.21259157", + "rel_abs": "BackgroundThe clinical manifestations of COVID-19 disease, caused by the SARS-CoV-2 virus, define a large spectrum of symptoms that are mainly dependent on the human host conditions. In Costa Rica, almost 319 000 cases have been reported during the first third of 2021, contrasting to the 590 000 fully vaccinated people. In the pre-vaccination period (the year 2020), this country accumulated 169 321 cases and 2185 deaths.\n\nMethodsTo describe the clinical presentations at the time of diagnosis of COVID-19 in Costa Rica during the pre-vaccination period, we implemented a symptom-based clustering using machine learning to identify clusters or clinical profiles among 18 974 records of positive cases. Profiles were compared based on symptoms, risk factors, viral load, and genomic features of the SARS-CoV-2 sequence.\n\nResultsA total of seven COVID-19 clinical profiles were identified, which were characterized by a specific composition of symptoms. In the comparison between clusters, a lower viral load was found for the asymptomatic group, while the risk factors and the SARS-CoV-2 genomic features were distributed among all the clusters. No other distribution patterns were found for age, sex, vital status, and hospitalization.\n\nConclusionDuring the pre-vaccination time in Costa Rica, the clinical manifestations at the time of diagnosis of COVID-19 were described in seven profiles. The host co-morbidities and the SARS-CoV-2 genotypes are not specific of a particular profile, rather they are present in all the groups, including asymptomatic cases. In further analyses, these results will be compared against the profiles of cases during the vaccination period.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC=\"FIGDIR/small/21259157v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (18K):\norg.highwire.dtl.DTLVardef@c39c0forg.highwire.dtl.DTLVardef@3abaedorg.highwire.dtl.DTLVardef@1c61db9org.highwire.dtl.DTLVardef@1c964c6_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jose Arturo Molina-Mora", + "author_inst": "Universidad de Costa Rica" + }, + { + "author_name": "Alejandra Gonzalez", + "author_inst": "INCIENSA" + }, + { + "author_name": "Sergio Jimenez-Morgan", + "author_inst": "Universidad de Costa Rica" + }, + { + "author_name": "Estela Cordero-Laurent", + "author_inst": "INCIENSA" + }, + { + "author_name": "Hebleen Brenes", + "author_inst": "INCIENSA" + }, + { + "author_name": "Claudio Soto-Gatira", + "author_inst": "INCIENSA" + }, + { + "author_name": "Jorge Sequeira-Soto", + "author_inst": "INCIENSA" + }, + { + "author_name": "Francisco Duarte-Martinez", + "author_inst": "INCIENSA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.18.21259150", "rel_title": "Small-molecule metabolome identifies potential therapeutic targets against COVID-19", @@ -706226,25 +707982,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.15.21258969", - "rel_title": "Modeling the waves of Covid-19", - "rel_date": "2021-06-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.15.21258969", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe challenges with modeling the spread of Covid-19 are its power-type growth during the middle stages with the exponents depending on time, and the saturations mainly due to the protective measures, though weakening and partial destruction of the virus due to mutations is a consideration too. The two-phase solution we propose for the total number of detected cases of Covid-19 describes the actual curves in many countries almost with the accuracy of physics laws. Bessel functions play the key role in our approach. The differential equations we obtain are of universal type; they describe momentum risk-management in behavioral psychology, transient processes in invasion ecology, etc. Due to a very small number of parameters, namely, the initial transmission rate and the intensity of the hard and soft measures, we obtain a convincing explanation of the surprising uniformity of the spread in many different areas. This theory can be used for forecasting the epidemic spread, evaluating the efficiency of the protective measures and the vaccinations. For instance, the early projection for the 3rd wave in the USA was very exact. The data until summer 2021 for India, South Africa and UK are discussed.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ivan Cherednik", - "author_inst": "UNC at Chapel Hill" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.18.21259156", "rel_title": "Factors affecting the transmission of SARS-CoV-2 in school settings", @@ -706353,6 +708090,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.19.21259173", + "rel_title": "Did social factors buffer against the effect of adversities on self-harm during the COVID-19 pandemic? A longitudinal analysis of 49,227 UK adults", + "rel_date": "2021-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.19.21259173", + "rel_abs": "BackgroundLittle is known about which factors exacerbate and buffer the impact of COVID-19 -related adversities on changes in thinking about and engaging in self-harm over time.\n\nAimsTo examine how changes in four social factors contribute to changes in self-harm thoughts and behaviours over time and how these factors in turn interact with adversities and worries about adversities to increase risk for these outcomes.\n\nMethodData from 49,227 UK adults in the UCL COVID-19 Social Study were analysed across the first 59 weeks of the pandemic. Fixed effects logistic regressions examined time-varying associations between social support quality, loneliness, number of days of face-to-face contact for [≥]15 minutes, and number of days phoning/video calling for [≥]15 minutes with self-harm thoughts and behaviours. We then examined how these four factors in turn interacted with the total number of adversities and worries about adversity on outcomes.\n\nResultsIncreases in the quality of social support decreased the likelihood of both outcomes, whilst greater loneliness increased their likelihood. Associations were inconsistent for telephone/video contact and face-to-face contact with outcomes. Social support buffered and loneliness exacerbated the impact of adversity experiences with self-harm behaviours. Other interactions were inconsistent, and some were in the unexpected direction.\n\nConclusionsThese findings suggest the importance of the quality of ones social support network, rather than the mere presence of contact, is important for reducing the likelihood of self-harm behaviours in the context of COVID-19 pandemic-related adversity and worry.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Elise Paul", + "author_inst": "University College London" + }, + { + "author_name": "Daisy Fancourt", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.06.17.21258837", "rel_title": "An Extended Susceptible-Exposed-Infected-Recovered (SEIR) Model with Vaccination for Forecasting the COVID-19 Pandemic in Sri Lanka", @@ -707320,117 +709080,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.16.21258673", - "rel_title": "Antibody neutralization to SARS-CoV-2 and variants after one year in Wuhan", - "rel_date": "2021-06-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.16.21258673", - "rel_abs": "Most COVID-19 patients can build effective humoral immunity against SARS-CoV-2 after recovery(1, 2). However, it remains unknown how long the protection can maintain and how efficiently it can protect people from the reinfection of the emerging SARS-CoV-2 variants. Here we evaluated the sera from 248 COVID-19 convalescents around one year post-infection in Wuhan, the earliest epicenter of SARS-CoV-2. We demonstrated that the SARS-CoV-2 immunoglobulin G (IgG) maintains at a high level and potently neutralizes the infection of the original strain (WT) and the B.1.1.7 variant in most patients. However, they showed varying degrees of efficacy reduction against the other variants of concern (P.1, B.1.525, and especially B.1.351) in a patient-specific manner. Mutations in RBD including K417N, E484K, and E484Q/L452R (B.1.617) remarkably impair the neutralizing activity of the convalescents sera. Encouragingly, we found that a small fraction of patients sera showed broad neutralization potency to multiple variants and mutants, suggesting the existence of broadly neutralizing antibodies recognizing the epitopes beyond the mutation sites. Our results suggest that the SARS-CoV-2 vaccination effectiveness relies more on the timely re-administration of the epitope-updated vaccine than the durability of the neutralizing antibodies.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Qianyun Liu", - "author_inst": "Wuhan University" - }, - { - "author_name": "Qing Xiong", - "author_inst": "Wuhan University" - }, - { - "author_name": "Fanghua Mei", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Chengbao Ma", - "author_inst": "Wuhan University" - }, - { - "author_name": "Zhen Zhang", - "author_inst": "Wuhan University" - }, - { - "author_name": "Bing Hu", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Junqiang Xu", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Yongzhong Jiang", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Faxian Zhan", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Xianying Chen", - "author_inst": "Wuhan University" - }, - { - "author_name": "Ming Guo", - "author_inst": "Wuhan University" - }, - { - "author_name": "Xin Wang", - "author_inst": "Wuhan University" - }, - { - "author_name": "Yaohui Fang", - "author_inst": "National Virus Resource Center, Wuhan Institute of Virology" - }, - { - "author_name": "Shu Shen", - "author_inst": "National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences" - }, - { - "author_name": "Yingle Liu", - "author_inst": "Wuhan University" - }, - { - "author_name": "Fang Liu", - "author_inst": "Wuhan University" - }, - { - "author_name": "Li Zhou", - "author_inst": "Wuhan University" - }, - { - "author_name": "Ke Xu", - "author_inst": "Wuhan University" - }, - { - "author_name": "Changwen Ke", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Fei Deng", - "author_inst": "National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences" - }, - { - "author_name": "Kun Cai", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Huan Yan", - "author_inst": "Wuhan University" - }, - { - "author_name": "Yu Chen", - "author_inst": "Wuhan University" - }, - { - "author_name": "Ke Lan", - "author_inst": "Wuhan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.18.21259072", "rel_title": "Evaluation of the effectiveness of remdesivir in treating severe COVID-19 using data from the ISARIC WHO Clinical Characterisation Protocol UK: a prospective, national cohort study.", @@ -707623,6 +709272,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.15.21251794", + "rel_title": "Neutrophil Lymphocyte Ratio as a Predictor of Glucocorticoid Effectiveness in Covid-19 Treatment", + "rel_date": "2021-06-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.15.21251794", + "rel_abs": "Glucocorticoids have been shown to improve outcomes of patients with severe cases of Covid-19. However, criteria for prescribing glucocorticoids are currently limited. To identify potential for targeting, we perform an observational analysis of mortality of hospitalized patients. Our results agree with current clinical understanding that glucocorticoids benefit patients with severe cases of Covid-19, and that elevated Neutrophil/Lymphocyte Ratio (NLR) is associated with mortality. Furthermore, our results suggest that glucocorticoids could be targeted to patients with elevated NLR (especially in the range 6-25) at time of admission. Finally, we note there are also high-risk patients with low NLR, suggesting varying presentations of severe Covid-19.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Benjamin J Lengerich", + "author_inst": "Carnegie Mellon University" + }, + { + "author_name": "Rich Caruana", + "author_inst": "Microsoft Research" + }, + { + "author_name": "Alex Peysakhovich", + "author_inst": "Facebook AI Research" + }, + { + "author_name": "Leora Horwitz", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Yin Aphinyanaphongs", + "author_inst": "NYU Langone Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.15.21258935", "rel_title": "The relative strength and timing of innate immune and CD8 T-cell responses underlie the heterogeneous outcomes of SARS-CoV-2 infection", @@ -709210,125 +710894,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.19.21259125", - "rel_title": "Plasma gradient of soluble urokinase-type plasminogen activator receptor is linked to pathogenic plasma proteome and immune transcriptome and stratifies outcomes in severe COVID-19", - "rel_date": "2021-06-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.19.21259125", - "rel_abs": "Disease caused by SARS-CoV-2 coronavirus (COVID-19) has resulted in significant morbidity and mortality world-wide. A systemic hyper-inflammation characterizes the severe COVID-19 disease often associated with acute respiratory distress syndrome (ARDS). Blood biomarkers capable of risk stratification are of great importance in effective triage and critical care of severe COVID-19 patients. In the present study we report higher plasma abundance of soluble urokinase-type plasminogen activator receptor (sUPAR), expressed by an abnormally expanded circulating myeloid cell population, in severe COVID-19 patients with ARDS. Plasma sUPAR level was found to be linked to a characteristic proteomic signature of plasma, linked to coagulation disorders and complement activation. Receiver operator characteristics curve analysis identified a cut-off value of sUPAR at 1996.809 pg/ml that could predict survival in our cohort (Odds ratio: 2.9286, 95% confidence interval 1.0427-8.2257). Lower sUPAR level than this threshold concentration was associated with a differential expression of the immune transcriptome as well as favourable clinical outcomes, both in terms of survival benefit (Hazard ratio: 0.3615, 95% confidence interval 0.1433-0.912) and faster disease remission in our patient cohort. Thus we identified sUPAR as a key pathogenic circulating molecule linking systemic hyperinflammation to the hypercoagulable state and stratifying clinical outcomes in severe COVID-19 patients with ARDS.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Jafar Sarif", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Deblina Raychaudhuri", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Ranit D'Rozario", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Purbita Bandopadhyay", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Praveen Singh", - "author_inst": "Cardiorespiratory Disease Biology, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India" - }, - { - "author_name": "Priyanka Mehta", - "author_inst": "INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India" - }, - { - "author_name": "Md. Asmaul Hoque", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Bishnu Prasad Sinha", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Manoj Kushwaha", - "author_inst": "Cardiorespiratory Disease Biology, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India" - }, - { - "author_name": "Shweta Sahni", - "author_inst": "INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India" - }, - { - "author_name": "Priti Devi", - "author_inst": "INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India" - }, - { - "author_name": "Partha Chattopadhyay", - "author_inst": "INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India" - }, - { - "author_name": "Shekhar Ranjan Paul", - "author_inst": "Department of Medicine, ID & BG Hospital, Kolkata, India" - }, - { - "author_name": "Yogiraj Ray", - "author_inst": "Department of Medicine, ID & BG Hospital, Kolkata, India" - }, - { - "author_name": "Kausik Chaudhuri", - "author_inst": "Department of Medicine, ID & BG Hospital, Kolkata, India" - }, - { - "author_name": "Sayantan Banerjee", - "author_inst": "Department of Medicine, ID & BG Hospital, Kolkata, India" - }, - { - "author_name": "Debajyoti Majumdar", - "author_inst": "Department of Medicine, ID & BG Hospital, Kolkata, India" - }, - { - "author_name": "Bibhuti Saha", - "author_inst": "School of Tropical Medicine, Kolkata, India" - }, - { - "author_name": "Biswanath Sharma Sarkar", - "author_inst": "Department of Medicine, ID & BG Hospital, Kolkata, India" - }, - { - "author_name": "Prasun Bhattacharya", - "author_inst": "Medical College, Kolkata, India" - }, - { - "author_name": "Shilpak Chatterjee", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Sandip Paul", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Pramit Ghosh", - "author_inst": "Deben Mahata Government Medical College & Hospital. Purulia, India" - }, - { - "author_name": "Rajesh Pandey", - "author_inst": "INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India" - }, - { - "author_name": "Shantanu Sengupta", - "author_inst": "Cardiorespiratory Disease Biology, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India" - }, - { - "author_name": "Dipyaman Ganguly", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.20.21258949", "rel_title": "Role of physiotherapy team in critically ill COVID-19 patients pronation: can a multidisciplinary management reduce the complications rate?", @@ -709540,6 +711105,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.06.21.449205", + "rel_title": "One viral sequence for each host? - The neglected within-host diversity as the main stage of SARS-CoV-2 evolution", + "rel_date": "2021-06-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.21.449205", + "rel_abs": "The standard practice of presenting one viral sequence for each infected individual implicitly assumes low within-host genetic diversity. It places the emphasis on the viral evolution between, rather than within, hosts. To determine this diversity, we collect SARS-CoV-2 samples from the same patient multiple times. Our own data in conjunction with previous reports show that two viral samples collected from the same individual are often very different due to the substantial within-host diversity. Each sample captures only a small part of the total diversity that is transiently and locally released from infected cells. Hence, the global SARS-CoV-2 population is a meta-population consisting of the viruses in all the infected hosts, each of which harboring a genetically diverse sub-population. Advantageous mutations must be present first as the within-host diversity before they are revealed as between-host polymorphism. The early detection of such diversity in multiple hosts could be an alarm for potentially dangerous mutations. In conclusion, the main forces of viral evolution, i.e., mutation, drift, recombination and selection, all operate within hosts and should be studied accordingly. Several significant implications are discussed.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yongsen Ruan", + "author_inst": "Sun Yat-sen University, Guangzhou" + }, + { + "author_name": "Mei Hou", + "author_inst": "Sun Yat-sen University, Guangzhou" + }, + { + "author_name": "Jiarui Li", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing" + }, + { + "author_name": "Yangzi Song", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing" + }, + { + "author_name": "Hurng-YI Wang", + "author_inst": "Graduate Institute of Clinical Medicine, National Taiwan University, Taipei." + }, + { + "author_name": "Hui Zeng", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing." + }, + { + "author_name": "Jian Lu", + "author_inst": "State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing." + }, + { + "author_name": "Haijun Wen", + "author_inst": "Sun Yat-sen University, Guangzhou" + }, + { + "author_name": "Chen Chen", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing" + }, + { + "author_name": "Chung-I Wu", + "author_inst": "Sun Yat-sen University, Guangzhou" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2021.06.21.449178", "rel_title": "Spatial transcriptomic characterization of COVID-19 pneumonitis identifies immune pathways related to tissue injury", @@ -711355,89 +712975,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.06.14.21258910", - "rel_title": "A Multi-center, Prospective, Observational-cohort controlled study of Clinical Outcomes following COVID-19 Convalescent plasma therapy in hospitalized COVID-19 patients", - "rel_date": "2021-06-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.14.21258910", - "rel_abs": "BackgroundThe SARS-CoV2 pandemic has caused high inpatient mortality and morbidity throughout the world. COVID19 convalescent plasma has been utilized as a potential therapy for patients hospitalized with COVID19 pneumonia. This study evaluated the outcomes of hospitalized COVID19 patients treated with COVID19 convalescent plasma in a prospective, observational multicenter trial.\n\nMethodsFrom April 2020 through August 2020, hospitalized COVID19 patients at 16 participating hospitals in Colorado were enrolled and treated with COVID19 convalescent plasma (CCP) and compared to hospitalized patients with COVID19 who were not treated with convalescent plasma. Plasma antibody levels were determined following the trial given that antibody tests were not approved at the initiation of the trial. CCP-treated and untreated COVID19 hospitalized patients were matched using propensity scores followed by analysis for length of hospitalization and inpatient mortality.\n\nResults542 total hospitalized COVID19 patients were enrolled at 16 hospitals across the region. A total of 468 hospitalized COVID19 patients were entered into propensity score matching with 188 patients matched for analysis in the CCP-treatment and control arms. Fine-Gray models revealed increased length of hospital stay in CCP-treated patients and no change in inpatient mortality compared to controls. In subgroup analysis of CCP-treated patients within 7 days of admission, there was no difference in length of hospitalization and inpatient mortality.\n\nConclusionsThese data show that treatment of hospitalized COVID19 patients with CCP did not significantly improve patient hospitalization length of stay or inpatient mortality.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Lakshmi Chauhan", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Jack Pattee", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Joshay Ford", - "author_inst": "University of Colorado School of Medicine" - }, - { - "author_name": "Chris Thomas", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Kelsey Lesteberg", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Eric Richards", - "author_inst": "University of Colorado Health System" - }, - { - "author_name": "Michele Loi", - "author_inst": "Children's Hospital Colorado" - }, - { - "author_name": "Larry J Dumont", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Kyle Annen", - "author_inst": "Children's Hospital Colorado" - }, - { - "author_name": "Mary Berg", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Mercedes Zirbes", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Amanda Miller", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Timothy C Jenkins", - "author_inst": "Denver Health Medical Center" - }, - { - "author_name": "Tellen D Bennett", - "author_inst": "University of Colorado School of Medicine" - }, - { - "author_name": "Daniel Monkowski", - "author_inst": "University of Colorado Health System" - }, - { - "author_name": "Rebecca S Boxer", - "author_inst": "Institute for Health Research, Kaiser Permanente of Colorado" - }, - { - "author_name": "J. David Beckham", - "author_inst": "University of Colorado Anschutz Medical Campus" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.14.21258855", "rel_title": "The Clinical Utility of Serial Procalcitonin and Procalcitonin Clearance in Predicting the Outcome of COVID-19 Patients", @@ -711658,6 +713195,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.17.448891", + "rel_title": "A Robust High-throughput Fluorescent Polarization Assay for the Evaluation and Screening of SARS-CoV-2 Fusion Inhibitors", + "rel_date": "2021-06-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.17.448891", + "rel_abs": "Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a serious threat to global health. One attractive antiviral target is the membrane fusion mechanism employed by the virus to gain access to the host cell. Here we report a robust protein-based fluorescent polarization assay, that mimicking the formation of the six-helix bundle (6-HB) process during the membrane fusion, for the evaluation and screening of SARS-CoV-2 fusion Inhibitors. The IC50 of known inhibitors, HR2P, EK1, and Salvianolic acid C (Sal C) were measured to be 6 nM, 2.5 nM, and 8.9 {micro}M respectively. In addition, we found Sal A has a slightly lower IC50 (3.9 {micro}M) than Sal C. Interesting, simple caffeic acid can also disrupt the formation of 6-HB with sub-mM concentration. A pilot high throughput screening (HTS) a small marine natural product library validates the assay with a Z factor close to 0.8. We envision the current assay provides a convenient way to screen SARS-CoV-2 fusion inhibitor and assess their binding affinity.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Xinjian Yin", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Litong Chen", + "author_inst": "Sun Yat-Sen University" + }, + { + "author_name": "Siwen Yuan", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Lan Liu", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Zhizeng Gao", + "author_inst": "Sun Yat-sen University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.06.18.448921", "rel_title": "Identification of SGLT2 inhibitor Ertugliflozin as a treatment for COVID-19 using computational and experimental paradigm", @@ -713129,25 +714701,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.06.17.448882", - "rel_title": "Post-Infection Entry Mechanism of Ricin A Chain-Pokeweed Antiviral Proteins (RTA-PAPs) Chimeras is Mediated by Viroporins", - "rel_date": "2021-06-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.17.448882", - "rel_abs": "The limitations of virus-specific antiviral drugs became apparent during the current COVID-19 pandemic. The search for broad range antiviral proteins of a new kind to answer current and future pandemics has become an even more pressing matter. Here, the author further describes the expected anti-SARS-CoV-2 mechanisms of a novel broad range antiviral chimeric protein constructed between ricin A chain and pokeweed antiviral proteins. The latest in protein-ligand docking software were used to determine binding affinity of RTA-PAPs to SARS-CoV-2 frameshift stimulation element and elucidate the preferential post-infection entry mechanisms of RTA-PAPs into virus infected cells over non-infected ones, by doing a comparative analysis between in vitro and in silico results on numerous viruses. The results obtained strongly suggest that the post-infection preferential entry of RTA-PAPs into infected cells is mediated by the presence of viroporins integrated into the host cell membrane. The discovery of this mechanism revealed RTA-PAPs, and proteins like them, to be a new class of broad range antivirals that target with high specificity viroporin producing viruses, and with gain of functions in antiviral activities, post-infection.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Yasser Hassan", - "author_inst": "Ophiuchus Medicine Inc." - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "synthetic biology" - }, { "rel_doi": "10.1101/2021.06.17.448459", "rel_title": "Memory B cells control SARS-CoV-2 variants upon mRNA vaccination of naive and COVID-19 recovered individuals.", @@ -713560,6 +715113,45 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.06.10.21258709", + "rel_title": "Effectiveness and Safety of Niclosamaide as Add-on Therapy to the Standard of Care Measures in COVID-19 Management: Randomized controlled clinical trial", + "rel_date": "2021-06-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.10.21258709", + "rel_abs": "BackgroundCOVID-19 pandemic has ignited the urge for repurposing old drugs as candidate antiviral medicines to treat novel challenges of viral infections. Niclosamide (NCS) is an anti-parasitic drug of known antiviral potential. Therefore, this study attempts to investigate the antiviral effect and safety of NCS on SARS-CoV-2 caused COVID-19 patients.\n\nMethodsRandomized controlled open label clinical trial encompassed 75 COVID-19 patients treated with standard of care plus NCS were included as experimental group and 75 COVID-19 patients treated with only standard of care therapy as control group. Each group was composed of 25 mild, 25 moderate and 25 severe patients. Survival rate, time to recovery, and side effects were the main endpoints for the assessment of the therapeutic effect and safety of NCS.\n\nResultsNCS did not enhance survival rate as three of severe COVID-19 patients in NCS and in control groups died (P>0.05). However, NCS, compared to control group, reduced the time to recovery in moderate and severe COVID-19 patients about 5 and 3 days, respectively but not in mild patients (P[≤]0.05). Most interestingly, NCS lowered time to recovery up to five days in patients with co-morbidities (P[≤]0.05) whereas only one day lowered in patients without co-morbidities (P>0.05).\n\nConclusionIt is concluded that NCS accelerates time to recovery about 3 to 5 days in moderate to severe COVID-19 patients especially those with co-morbidities; hence, NCS is of clinical benefit for freeing hospital beds for more patients in pandemic crisis.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ahmed S. Abdulamir", + "author_inst": "College of Medicine, Alnahrain University, Baghdad, Iraq" + }, + { + "author_name": "Faiq I. Gorial", + "author_inst": "College of Medicine-University of Baghdad, Baghdad, Iraq" + }, + { + "author_name": "Sattar J Saaedi", + "author_inst": "Authority of health and medical education. Kerbala, Iraq" + }, + { + "author_name": "Mohammed Fauzi Maulood", + "author_inst": "Alkarkh Hospital, Alatefiya, Baghdad, Iraq" + }, + { + "author_name": "Hashim Ali Hashim", + "author_inst": "Alforat Hospital, Airport road, Baghdad, Iraq" + }, + { + "author_name": "Manal K. abdulrrazaq", + "author_inst": "College of Medicine, University of Baghdad, Baghdad, Iraq" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.14.21258567", "rel_title": "Subcutaneous REGEN-COV Antibody Combination for Covid-19 Prevention", @@ -715863,69 +717455,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2021.06.14.447967", - "rel_title": "Interferon-stimulated and metallothionein-expressing macrophages are associated with acute and chronic allograft dysfunction after lung transplantation", - "rel_date": "2021-06-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.14.447967", - "rel_abs": "Lung transplant (LT) recipients experience episodes of immune-mediated acute lung allograft dysfunction (ALAD). ALAD episodes are a risk factor for chronic lung allograft dysfunction (CLAD), the major cause of death after LT. We have applied single-cell RNA sequencing (scRNAseq) to bronchoalveolar lavage (BAL) cells from stable and ALAD patients and to cells from explanted CLAD lung tissue to determine key cellular elements in dysfunctional lung allografts, with a focus on macrophages. We identified two alveolar macrophage (AM) subsets uniquely represented in ALAD. Using pathway analysis and differentially expressed genes, we annotated these as pro-inflammatory interferon-stimulated gene (ISG) and metallothionein-mediated inflammatory (MT) AMs. Functional analysis of an independent set of AMs in vitro revealed that ALAD AMs exhibited a higher expression of CXCL10, a marker of ISG AMs, and increased secretion of pro-inflammatory cytokines compared to AMs from stable patients. Using publicly available BAL scRNAseq datasets, we found that ISG and MT AMs are associated with more severe inflammation in COVID-19 patients. Analysis of cells from four explanted CLAD lungs revealed similar macrophage populations. Using a single nucleotide variation calling algorithm, we also demonstrated contributions of donor and recipient cells to all AM subsets early post-transplant, with loss of donor-derived cells over time. Our data reveals extensive heterogeneity among lung macrophages after LT and indicates that specific sub-populations may be associated with allograft dysfunction, raising the possibility that these cells may represent important therapeutic targets.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Sajad Moshkelgosha", - "author_inst": "UHN" - }, - { - "author_name": "Allen Duong", - "author_inst": "UHN" - }, - { - "author_name": "Gavin Wilson", - "author_inst": "UHN" - }, - { - "author_name": "Tallulah Andrews", - "author_inst": "UHN" - }, - { - "author_name": "Gregory Berra", - "author_inst": "UHN" - }, - { - "author_name": "Benjamin Renaud-Picard", - "author_inst": "UHN" - }, - { - "author_name": "Mingyao Liu", - "author_inst": "UHN" - }, - { - "author_name": "Shaf Keshavjee", - "author_inst": "UHN" - }, - { - "author_name": "Sonya MacParland", - "author_inst": "UHN" - }, - { - "author_name": "Jonathan Yeung", - "author_inst": "UHN" - }, - { - "author_name": "Tereza Martinu", - "author_inst": "UHN" - }, - { - "author_name": "Stephen C Juvet", - "author_inst": "University Health Network" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.06.14.448461", "rel_title": "Protective efficacy of rhesus adenovirus COVID-19 vaccines against mouse-adapted SARS-CoV-2", @@ -716121,6 +717650,37 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.06.14.448421", + "rel_title": "MMMVI: Detecting SARS-CoV-2 Variants of Concern in Metagenomic Samples", + "rel_date": "2021-06-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.14.448421", + "rel_abs": "MotivationSARS-CoV-2 is the causative agent of the COVID-19 pandemic. Variants of Concern (VOCs) and Variants of Interest (VOIs) are lineages that represent a greater risk to public health, and can be differentiated from the wildtype virus based on unique profiles of signature mutations. Metagenomic sequence analysis of wastewater represents an emerging form of surveillance that can capture early signal for these variants in a community prior to detection through public health testing or genomic surveillance activities. However, because multiple viral genomes are likely to be present in a metagenomic sample, additional analytical scrutiny of the sequencing reads beyond variant calling is needed to increase confidence in diagnostic determinations.\n\nResultsWhere multiple signature mutations are present on a given read, they can be used as enhanced biomarkers to confirm the presence of a VOC/VOI in the sample. We have developed MMMVI, a tool to aggregate and report on the likely presence of a VOC/VOI in a set of metagenomic reads based on the detection of reads bearing multiple signature mutations.\n\nAvailabilityMMMVI is implemented in Python, and is available under the MIT licence from https://github.com/dorbarker/voc-identify/\n\nContactdillon.barker@canada.ca", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Dillon O.R. Barker", + "author_inst": "Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, R3E 3R2, Winnipeg, Manitoba, Canada" + }, + { + "author_name": "Cody J. Buchanan", + "author_inst": "Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, R3E 3R2, Winnipeg, Manitoba, Canada" + }, + { + "author_name": "Chrystal Landgraff", + "author_inst": "Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, R3E 3R2, Winnipeg, Manitoba, Canada" + }, + { + "author_name": "Eduardo N Taboada", + "author_inst": "Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, R3E 3R2, Winnipeg, Manitoba, Canada" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.06.14.448358", "rel_title": "Multi-Dimensional Reduction Clustering of Complex Carbohydrates Reveal Tissue Metabolism, Heterogeneity and Histopathology", @@ -717348,29 +718908,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.11.21258661", - "rel_title": "Grouping theory of epidemiology", - "rel_date": "2021-06-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.11.21258661", - "rel_abs": "Background (traditional theory)there are general and principle models and calculation formulas for epidemics, mainly the basic reproduction number R0 of a certain epidemic disease such as COVID-19, the newly confirmed number Cn=Rn-1Cn-1, The threshold of herd immunity is (R0-1)/R0.\n\nInnovation theoryBased on the fact that there are groups of different tends (that is, different R0 or Rk), a grouping model of epidemiology is proposed, and a complete and detailed calculation formula is given. The basic relationship is that the overall infection numbers of is equal to the sum of the infection number of groups, namely: Rt={sum}(fkRk), where fk is the population proportion of each group, and Rk is the basic reproduction number of each groups. Its important application is the grouping strategy in which prevention and control measures are inclined to high-risk groups. The basic relationship is that the basic reproduction number of each group is equal to the product of the control coefficient of its measures and the original basic reproduction number, namely: Rk={zeta}kR0k. Compared with the traditional strategy of equal treatment, the grouping strategy has the characteristics of high efficiency, low consumption, and low threshold of herd immunity.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Chaohui Zhang", - "author_inst": "(Unaffiliated)" - }, - { - "author_name": "Wenyu Ling", - "author_inst": "(Unaffiliated)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.14.21258236", "rel_title": "Survey of COVID-19 associated symptoms and reported deaths in an urban community in Kano, Nigeria.", @@ -717511,6 +719048,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.06.13.21258654", + "rel_title": "Analysis of Social Combinations of Coronavirus Vaccination: Evidence from a Conjoint Analysis", + "rel_date": "2021-06-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.13.21258654", + "rel_abs": "Using a conjoint analysis based on cases in Japan, this study attempts to identify a preferable social strategic combination of \"Who is vaccinated, who is not, who waits.\" The analysis shows that the most desirable choice is a \"wait-and-see\" strategy, allowing for a risk assessment of side effects. We also find that subjects who recalled blood relatives as their familiar entities tend to prefer a \"wait-and-see\" strategy for themselves and their blood relatives.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Hanako Ohmura", + "author_inst": "Kwansei Gakuin University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2021.06.11.21258778", "rel_title": "Poor Readability of COVID-19 Vaccine Information for the General Public: A Lost Opportunity", @@ -718719,89 +720275,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.11.21258575", - "rel_title": "Support needs and barriers to accessing support: Baseline results of a mixed-methods national survey of people bereaved during the COVID-19 pandemic", - "rel_date": "2021-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.11.21258575", - "rel_abs": "BackgroundThe COVID-19 pandemic is a mass bereavement event which has profoundly disrupted grief experiences. Understanding support needs and access to support among people bereaved at this time is crucial to ensuring appropriate bereavement support infrastructure.\n\nAimTo investigate grief experiences, support needs and use of formal and informal bereavement support among people bereaved during the pandemic.\n\nDesignBaseline results from a longitudinal survey. Support needs and experiences of accessing support are reported using descriptive statistics and thematic analysis of free-text data.\n\nSetting/Participants711 adults bereaved in the UK between March-December 2020, recruited via media, social media, national associations and community/charitable organisations.\n\nResultsHigh-level needs for emotional support were identified. Most participants had not sought support from bereavement services (59%, n=422) or their GP (60%, n=428). Of participants who had sought such support, over half experienced difficulties accessing bereavement services (56%, n=149)/GP support (52%, n=135). 51% reported high/severe vulnerability in grief; among these, 74% were not accessing bereavement or mental-health services. Barriers included limited availability, lack of appropriate support, discomfort asking for help, and not knowing how to access services. 39% (n=279) experienced difficulties getting support from family/friends, including relational challenges, little face-to-face contact, and disrupted collective mourning. The perceived uniqueness of pandemic bereavement and wider societal strains exacerbated their isolation.\n\nConclusionsPeople bereaved during the pandemic have high levels of support needs alongside difficulties accessing support. We recommend increased provision and tailoring of bereavement services, improved information on support options, and social/educational initiatives to bolster informal support and ameliorate isolation.\n\nKey statementsO_ST_ABSWhat is already known about the topic?C_ST_ABS- Features of pandemic bereavement, such as traumatic death experiences, exacerbate family distress and add to the complexity of grief.\n- In pre-pandemic times most people mainly relied on the informal support of friends and family to cope with their bereavement, but an estimated 40% required more formal therapeutic support from bereavement or mental health services.\n- Bereaved people experience difficulties getting the support that they need from bereavement services and their social networks.\n\n\nWhat this paper adds- Participants had high level needs for emotional support, especially dealing with/expressing feelings, with 51% experiencing high or severe vulnerability in grief; however, 74% of this group were not accessing formal bereavement service or mental health support.\n- Most participants had not tried to access bereavement services, for reasons such as lack of appropriate support, discomfort in asking for help and uncertainty of how to access services; of the 41% who tried, 56% experienced difficulties such as long waiting lists or ineligibility.\n- A substantial proportion of people (39%) reported difficulties accessing support from friends and family; reduced in-person contact affected the perceived quality of support and disrupted collective mourning practices, whilst the wider social difficulties of the pandemic compounded feelings of isolation.\n\n\nImplications for policy and practice- Further investment in the provision of tailored bereavement support is needed to meet the diverse needs and backgrounds of bereaved people, including support that is culturally and crisis/context competent, and group-based support for those with shared experiences and characteristics.\n- To raise awareness of support options, information on grief and bereavement services should be provided proactively following a death and made available in online and community settings, with GPs and other primary care providers better resourced to signpost to appropriate support.\n- Following compassionate communities approaches, expanded provision of informal community-based support and activities could help with isolation, whilst longer-term educational and societal initiatives are needed to bolster community support for people experiencing death, dying and bereavement.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Emily J Harrop", - "author_inst": "Marie Curie Palliative Care Research Centre, Cardiff University" - }, - { - "author_name": "Silvia Goss", - "author_inst": "Marie Curie Palliative Care Research Centre, Cardiff University" - }, - { - "author_name": "Damian JJ Farnell", - "author_inst": "School of Dentistry, Cardiff University" - }, - { - "author_name": "Mirella Longo", - "author_inst": "Marie Curie Palliative Care Research Centre, Cardiff University" - }, - { - "author_name": "Anthony Byrne", - "author_inst": "Marie Curie Palliative Care Research Centre, Cardiff University" - }, - { - "author_name": "Kali Barawi", - "author_inst": "Marie Curie Palliative Care Research Centre, Cardiff University" - }, - { - "author_name": "Anna Torrens-Burton", - "author_inst": "PRIME Centre, Cardiff University" - }, - { - "author_name": "Annmarie Nelson", - "author_inst": "Marie Curie Palliative Care Research Centre, Cardiff University" - }, - { - "author_name": "Kathy Seddon", - "author_inst": "Marie Curie Palliative Care Research Centre, Cardiff University" - }, - { - "author_name": "Linda Machin", - "author_inst": "Keele University" - }, - { - "author_name": "Eileen Sutton", - "author_inst": "Palliative and End of Life Care Research Group, University of Bristol" - }, - { - "author_name": "Audrey Roulston", - "author_inst": "Queen's University Bristol" - }, - { - "author_name": "Anne Finucane", - "author_inst": "Clinical Psychology, School of Health in Social Science, University of Edinburgh" - }, - { - "author_name": "Alison Penny", - "author_inst": "National Bereavement Alliance" - }, - { - "author_name": "Kirsten V Smith", - "author_inst": "Centre for Anxiety Disorders and Trauma, Department of Experimental Psychology, University of Oxford" - }, - { - "author_name": "Stephanie Sivell", - "author_inst": "Marie Curie Palliative Care Research Centre, Cardiff University" - }, - { - "author_name": "Lucy E Selman", - "author_inst": "Palliative and End of Life Care Research Group, Population Health Sciences, Bristol Medical School, University of Bristol" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.14.448343", "rel_title": "COVID-eVax, an electroporated plasmid DNA vaccine candidate encoding the SARS-CoV-2 Receptor Binding Domain, elicits protective immune responses in animal models of COVID-19", @@ -719118,6 +720591,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.09.21258668", + "rel_title": "Modeling and reviewing analysis of the COVID-19 epidemic in Algeria with diagnostic shadow", + "rel_date": "2021-06-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.09.21258668", + "rel_abs": "In this paper, we formulate a special epidemic dynamic model to describe the transmission of COVID-19 in Algeria. We derive the threshold parameter control reproduction number [Formula], and present the effective control reproduction number (Rc(t)) as a real-time index for evaluating the epidemic under different control strategies. Due to the limitation of the reported data, we redefine the number of accumulative confirmed cases with diagnostic shadow and then use the processed data to do the optimal numerical simulations. According to the control measures, we divide the whole research period into six stages. And then the corresponding medical resource estimations and the average effective control reproduction numbers for each stage are given. Meanwhile, we use the parameter values which are obtained from the optimal numerical simulations to forecast the whole epidemic tendency under different control strategies.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jiwei Jia", + "author_inst": "Jilin University" + }, + { + "author_name": "Siyu Liu", + "author_inst": "Jilin University" + }, + { + "author_name": "Yawen Liu", + "author_inst": "Jilin University" + }, + { + "author_name": "Ruitong Shan", + "author_inst": "Jilin University" + }, + { + "author_name": "Khaled Zennir", + "author_inst": "Qassim University" + }, + { + "author_name": "Ran Zhang", + "author_inst": "Jilin University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.09.21258648", "rel_title": "SARS-CoV-2-antibody response in health care workers after vaccination or natural infection in a longitudinal observational study", @@ -720573,37 +722085,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.09.21258234", - "rel_title": "Personal space Increases during the COVID-19 Pandemic in Response to Real and Virtual Humans", - "rel_date": "2021-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.09.21258234", - "rel_abs": "Typically, people maintain a certain distance from others (\"personal space\") during daily life, in a largely automatic, unconscious manner. However during the COVID-19 pandemic, social distancing recommendations led to deliberate expansions of personal space outside of intimate social circles. In the laboratory, personal space preferences are quite stable over repeated measurements. Here, we collected such measurements both before and during the pandemic in the same individuals, using both conventional and virtual reality-based techniques. We found that the size of personal space, and discomfort ratings in response to personal space intrusions, increased significantly during the COVID-19 pandemic, in response to both real humans and virtual \"others\". Moreover, this increase in personal space requirements correlated with the perceived, not the actual, risk of being infected with COVID-19 - even in a virtual reality environment in which there was no possibility of infection. Thus, quantification of personal space may reveal some of the psychological effects of the pandemic, and subsequent progress towards recovery.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Daphne J Holt", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Sarah Zapetis", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Baktash Babadi", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Roger B.H. Tootell", - "author_inst": "Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.08.21258525", "rel_title": "COVID19, Consumption and Inequality: A Systematic Analysis of Rural Population of India", @@ -720740,6 +722221,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2021.06.05.21258311", + "rel_title": "Antibody Responses after SARS-CoV-2 Vaccination in Lymphoma", + "rel_date": "2021-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.05.21258311", + "rel_abs": "Individuals with lymphoid malignancies have an increased mortality risk from COVID-19. Paradoxically, this population is least likely to be protected by SARS-CoV-2 vaccination as a result of disease- or treatment-related immunosuppression. Current data on vaccine responses in persons with lymphoid malignancies is limited.\n\nPROSECO is a UK multi-centre prospective observational study evaluating COVID-19 vaccine immune responses in individuals with lymphoma. This early interim analysis details the antibody responses to first- and second-SARS-CoV-2 vaccination with either BNT162b2 (Pfizer-BioNTech) and ChAdOx1 (AstraZeneca), in 129 participants. Responses are compared to those obtained in healthy volunteers.\n\nThe key findings of this interim analysis are first, 61% of participants who are vaccinated during or within 6 months of receiving systemic anti-lymphoma treatment, do not have detectable antibodies despite two doses of vaccine. Second, individuals with curable disease such has Hodgkin (6/6) and aggressive B-cell non-Hodgkin lymphoma (13/16) develop robust antibody levels to either first or second doses, when vaccinated > 6 months after treatment completion. Third, participants incurable, indolent lymphomas have reduced antibody levels to first and second vaccine doses, irrespective of treatment history. Finally, whilst there was no difference in antibody responses between BNT162b2 and ChAdOx1 in lymphoma participants, BNT162b2 induces 11-fold higher antibody responses than ChAdOx1 after the second dose in healthy donors.\n\nThese findings serve to reassure the community that individuals with treated Hodgkin and aggressive B-NHL can develop antibody responses to SARS-CoV-2 vaccine. Simultaneously it also highlights the critical need to identify an alternative strategy against COVID-19 for those undergoing systemic anti-lymphoma treatment, and for individuals with indolent lymphomas.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Sean Hua Lim", + "author_inst": "Centre for Cancer Immunology, University of Southampton" + }, + { + "author_name": "Nicola Campbell", + "author_inst": "University Hospital Southampton" + }, + { + "author_name": "Marina Johnson", + "author_inst": "Great Ormond Street Institute of Child Healthy, University College London" + }, + { + "author_name": "Debora Joseph-Pietras", + "author_inst": "NIHR/CR UK Southampton Experimental Medicine Cancer Centre, University Hospital Southampton" + }, + { + "author_name": "Graham P Collins", + "author_inst": "NIHR Oxford Biomedical Research Centre, Churchill Hospital" + }, + { + "author_name": "Ann O'Callaghan", + "author_inst": "Portsmouth Hospitals NHS Trust" + }, + { + "author_name": "Christopher P Fox", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Matthew Ahearne", + "author_inst": "University Hospitals of Leicester NHS Trust" + }, + { + "author_name": "Peter WM Johnson", + "author_inst": "CRUK Research Centre, University of Southampton" + }, + { + "author_name": "David Goldblatt", + "author_inst": "Great Ormond Street Institute of Child Health, University College London" + }, + { + "author_name": "Andrew J Davies", + "author_inst": "NIHR/CRUK Southampton Experimental Medicine Cancer Centre, University Hospital Southampton" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2021.06.09.21258612", "rel_title": "Second wave of COVID-19 in India could be predicted with genomic surveillance of SARS-CoV-2 variants coupled with epidemiological data: A tool for future", @@ -722519,41 +724059,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.06.08.21258444", - "rel_title": "Does reactogenicity after a second injection of the BNT162b2 vaccine predict spike IgG antibody levels in healthy Japanese subjects?", - "rel_date": "2021-06-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258444", - "rel_abs": "Adverse reactions are more common after the second injection of messenger RNA vaccines such as Pfizer/BioNTechs BNT162b2. We hypothesized that the degree and severity of reactogenicity after the second injection reflects the magnitude of antibody production against the SARS CoV-2 virus spike protein (spike IgG). Blood samples were obtained from 67 healthy Japanese healthcare workers three weeks after the first injection and two weeks after the second injection of the BNT162b2 vaccine to measure spike IgG levels. Using questionnaires, we calculated an adverse event (AE) score (0-11) for each participant. The geometric mean of spike IgG titers increased from 1,047 antibody units (AU/mL) (95% CI: 855-1282 AU/mL) after the first injection to 17,378 AU/mL (14,622-20,663 AU/mL) after the second injection. The median AE score increased from 2 to 5. Spike IgG levels after the second injection were negatively correlated with age and positively correlated with spike IgG after the first injection. AE scores after the second injection were not significantly associated with log-transformed spike IgG after the second injection, when adjusted for age, sex, and log-transformed spike IgG after the first injection. Although the sample size was relatively small, reactogenicity after the second injection may not accurately reflect antibody production.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Masaaki Takeuchi", - "author_inst": "University of Occupational and Environmental Health" - }, - { - "author_name": "Yukie Higa", - "author_inst": "University of Occupational and Environmental Health" - }, - { - "author_name": "Akina Esaki", - "author_inst": "University of Occupational and Environmental Health" - }, - { - "author_name": "Yosuke Nabeshima", - "author_inst": "University of Occupational and Environmental Health" - }, - { - "author_name": "Akemi Nakazono", - "author_inst": "University of Occupational and Environmental Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.08.21258434", "rel_title": "The impact of COVID-19 pandemic on influenza transmission: molecular and epidemiological evidence", @@ -722754,6 +724259,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.06.10.21257749", + "rel_title": "Inferring global-scale temporal latent topics from news reports to predict public health interventions for COVID-19", + "rel_date": "2021-06-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.10.21257749", + "rel_abs": "The COVID-19 pandemic has highlighted the importance of non-pharmacological interventions (NPI) for controlling epidemics of emerging infectious diseases. Despite their importance, NPI have been monitored mainly through the manual efforts of volunteers. This approach hinders measurement of the NPI effectiveness and development of evidence to guide their use to control the global pandemic. We present EpiTopics, a machine learning approach to support automation of the NPI prediction and monitoring at both the document-level and country-level by mining the vast amount of unlabelled news reports on COVID-19. EpiTopics uses a 3-stage, transfer-learning algorithm to classify documents according to NPI categories, relying on topic modelling to support result interpretation. We identified 25 interpretable topics under 4 distinct and coherent COVID-related themes. Importantly, the use of these topics resulted in significant improvements over alternative automated methods in predicting the NPIs in labelled documents and in predicting country-level NPIs for 42 countries.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Zhi Wen", + "author_inst": "McGill University" + }, + { + "author_name": "Guido Powell", + "author_inst": "McGill University" + }, + { + "author_name": "Imane Chafi", + "author_inst": "McGill University" + }, + { + "author_name": "David Buckeridge", + "author_inst": "McGill University" + }, + { + "author_name": "Yue Li", + "author_inst": "McGill University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.06.07.21258484", "rel_title": "A functionally distinct neutrophil landscape in severe COVID-19 reveals opportunities for adjunctive therapies", @@ -724473,61 +726013,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.07.21258520", - "rel_title": "Post-Acute COVID Syndrome, the Aftermath of Mild to Severe COVID-19 in Brazilian Patients", - "rel_date": "2021-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.07.21258520", - "rel_abs": "ObjectiveTo describe persistent symptoms after acute COVID-19 in different spectrum of disease severity in a population from an upper/middle income country, and identify the main clinical features impacting the quality of life.\n\nDesignCross-sectional study.\n\nSettingOutpatient clinic from a public post-COVID-19 health center (CPC) at Bahia-Brazil, a state where 80% are black or mixed race.\n\nParticipantsPatients admitted between August 2020 and February 2021 with symptoms at least one month after the onset of COVID-19.\n\nMain outcome measuresPACS and related disorders such as hospitalization one month or later after disease onset, biochemical dysregulation and reduced quality of life (EQ-5D-5L questionnaire).\n\nResultsAmong 683 individuals assisted at CPC in this period, 602 were recruited. Patients had average of 52 ({+/-}14.6) years, 355 (59%) were female, 528 (88%) black/brown. Individuals were classified as mild (39.9%), moderate (27.9%) or severe (32.2%) during acute illness if outpatient, hospitalized non-UCI or UCI, respectively. Most patients reported a polysymptomatic profile, in median eight (IQR=6-9) acute symptoms. The most frequent residual symptoms were dyspnea (66%), fatigue (62%) and chest pain (43%). Women were more affected regardless disease severity at acute stage: presented more residual symptoms [4 (2-6) vs 3 (2-4)] and a higher impact in quality of life. Altered HbA1c [(184/275 (66.9%)], high CRP levels [195/484 (40.3%)] and anemia [143/545 (26.2%)] were the most common abnormalities in laboratory exams. 76 patients presented HbA1c above 6.4% although only 42 referred previous diagnosis of diabetes mellitus. After one month of disease onset, 30 patients required hospitalization, including seven cases with mild acute illness. Hospital admission after acute disease was required on 30 patients, seven (23%) were mild. Quality of life had been affected for 357/404 (88.4%) patients according to EuroQoL (EQ-5D-5L), mainly the domains of anxiety/depression [severe or extreme anxiety for 79/401 (19.7%)] and pain/discomfort [severe or extreme pain for 71/403 (17.6%)]. The median EuroQoL Global Score was 70 [IQR 50-80]. PACS symptoms such as dyspnea, chest pain, and fatigue, was associated with decreased quality of life.\n\nConclusionsPACS, such as dyspnea, chest pain and fatigue, occurred after variable degree of disease severity. Among this majority black/mixed-race patients, woman seemed to be more affected. Other consequences included post-acute hospitalization, and abnormal glucose metabolism and reduced quality of life.\n\nSummary BoxSection 1: What is already known on this topic:\n\n{checkmark}Post-Acute COVID Syndrome (PACS) comprises a set of persistent or new-onset symptoms after illness onset.\n{checkmark}As far as we know, there are no studies describing PACS in a population principally black and mixed-race. Additionally, few studies have addressed PACS among outpatients.\n\n\nSection 2: What this study adds:\n\n{checkmark}Similar PACS were reported after mild, moderate and severe illness. Dyspnea, fatigue and chest pain were the most prevalent symptoms in this population presenting majority of black/mixed-race patients.\n{checkmark}Women presented more residual symptoms, a higher frequency of myalgia and worse score for mobility, usual activities, anxiety/depression, and pain.\n{checkmark}Hospitalization may occur one month or later after mild or moderate/severe acute infection due to respiratory and vascular disorders. Abnormal glucose metabolism was detected in the absence of previous diagnosis of diabetes mellitus.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Ana Paula Andrade Barreto", - "author_inst": "Hospital Especializado Oct\u00e1vio Mangabeira (HEOM), Salvador, Brazil" - }, - { - "author_name": "Lucimeire Cardoso Duarte", - "author_inst": "Hospital Especializado Oct\u00e1vio Mangabeira (HEOM), Salvador, Brazil" - }, - { - "author_name": "Thiago Cerqueira-Silva", - "author_inst": "Instituto Gon\u00e7alo Moniz (Fiocruz-Bahia), Salvador, Brazil" - }, - { - "author_name": "Marcio Andrade Barreto Filho", - "author_inst": "Hospital Especializado Oct\u00e1vio Mangabeira (HEOM), Salvador, Brazil" - }, - { - "author_name": "Aquiles Camelier", - "author_inst": "Hospital Especializado Oct\u00e1vio Mangabeira (HEOM), Salvador, Brazil" - }, - { - "author_name": "Natalia Machado Tavares", - "author_inst": "Instituto Gon\u00e7alo Moniz (Fiocruz-Bahia), Salvador, Brazil" - }, - { - "author_name": "Manoel Barral-Netto", - "author_inst": "Instituto Gon\u00e7alo Moniz (Fiocruz-Bahia), Salvador, Brazil" - }, - { - "author_name": "Viviane Sampaio Boaventura", - "author_inst": "Instituto Gon\u00e7alo Moniz (Fiocruz-Bahia), Salvador, Brazil" - }, - { - "author_name": "Marcelo Chalhoub", - "author_inst": "Hospital Especializado Oct\u00e1vio Mangabeira (HEOM), Salvador, Brazil" - }, - { - "author_name": "- CPC Group Study", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.08.21258284", "rel_title": "Highly-specific memory B cells generation after the 2nd dose of BNT162b2 vaccine compensate for the decline of serum antibodies and absence of mucosal IgA", @@ -724752,6 +726237,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2021.06.06.21258430", + "rel_title": "WHAT ABOUT USING SNIFFIN STICKS 12 SCREENING TEST TO IDENTIFY POST-COVID-19 OLFACTORY DISORDERS?", + "rel_date": "2021-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.06.21258430", + "rel_abs": "BackgroundOlfactory impairment is a major sequela of SARS-CoV-2 infection and has a negative impact on daily life quality. Olfactory loss can be assessed in many ways but seems to be little realized in a daily clinical practice. The sniffin Sticks test - 12 items (SST-12) can be used in quick olfactory disorders screening. Its use in a post-covid19 situation was the main objective of this work.\n\nMethodologyConsecutive patients consulting to the ENT department with post-Covid-19 olfactory loss were included. The clinical examination included an analog scale for the self-assessment of olfactory recovery (VAS), self-reported salt and sugar intake, a nasofibroscopy, the complete Sniffin Stick Test (SST) and the SST-12.\n\nResultsAmong the 54 patients included, based on the SST-12, 14,8% (n=8) of the patients could be classified as normosmic (SST-12[≥]11), 48,1% (n=26) as hyposmic (6< SST-12<10) and 37% (n=20) as functional anosmic (SST-12[≤]6). We report excellent and significant correlations between SST-12 and SST or VAS assessments. Salt and Sugar increased intake seems significantly related to SST-12 results.\n\nConclusionsSST-12 is a reliable way to screen post-COVID-19 olfactory disorders could be used in a daily clinical practice and might be used to prevent bad diet habits and so cardiovascular risk.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Clair VANDERSTEEN", + "author_inst": "Institut universitaire de la face et du cou, CHU, UCA, NICE" + }, + { + "author_name": "Magali PAYNE", + "author_inst": "CobTeK laboratory, Institut Claude Pompidou, UCA, NICE" + }, + { + "author_name": "Louise Emilie DUMAS", + "author_inst": "Hopitaux pediatrique de Nice CHU LENVAL, UCA, NICE" + }, + { + "author_name": "Alexandra PLONKA", + "author_inst": "CobTeK laboratory, Institut Claude Pompidou, UCA, Nice" + }, + { + "author_name": "Gregoire D'ANDREA", + "author_inst": "Institut Universitaire de la Face et du Cou, CHU, UCA, NICE" + }, + { + "author_name": "David CHIRIO", + "author_inst": "Infectious Diseases department, CHU, UCA, NICE" + }, + { + "author_name": "Elisa DEMONCHY", + "author_inst": "Infectious diseases departement,CHU, UCA, Nice" + }, + { + "author_name": "Karine RISSO", + "author_inst": "Infectious diseases department, CHU, UCA, NICE" + }, + { + "author_name": "Florence GITTARD ASKENAZY", + "author_inst": "Hopitaux pediatrique de Nice CHU LENVAL, UCA, NICE" + }, + { + "author_name": "Nicolas GUEVARA", + "author_inst": "Institut Universitaire de la Face et du Cou, CHU, UCA, Nice" + }, + { + "author_name": "Laurent CASTILLO", + "author_inst": "Institut Universitaire de la Face et du Cou, CHU, UCA, NICE" + }, + { + "author_name": "Valeria MANERA", + "author_inst": "CoBTek Laboratory, Institut Universitaire de la Face et du Cou, UCA, NICE" + }, + { + "author_name": "Auriane GROS", + "author_inst": "CoBtek laboratory, Institut Universitaire de la Face et du COU, UCA, NICE" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "otolaryngology" + }, { "rel_doi": "10.1101/2021.06.06.21258442", "rel_title": "Financial Meltdown in Swing Hospitals during the COVID-19 Outbreak", @@ -726471,93 +728023,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.08.21258531", - "rel_title": "The UK Coronavirus Job Retention Scheme and changes in diet, physical activity and sleep during the COVID-19 pandemic: Evidence from eight longitudinal studies", - "rel_date": "2021-06-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258531", - "rel_abs": "BackgroundIn March 2020 the UK implemented the Coronavirus Job Retention Scheme (furlough) to minimize job losses. Our aim was to investigate associations between furlough and diet, physical activity, and sleep during the early stages of the COVID-19 pandemic.\n\nMethodsWe analysed data from 25,092 participants aged 16 to 66 years from eight UK longitudinal studies. Changes in employment (including being furloughed) were defined by comparing employment status pre- and during the first lockdown. Health behaviours included fruit and vegetable consumption, physical activity, and sleeping patterns. Study-specific estimates obtained using modified Poisson regression, adjusting for socio-demographic characteristics and pre-pandemic health and health behaviours, were statistically pooled using random effects meta-analysis. Associations were also stratified by sex, age, and education.\n\nResultsAcross studies, between 8 and 25% of participants were furloughed. Compared to those who remained working, furloughed workers were slightly less likely to be physically inactive (RR:0.85, [0.75-0.97], I2=59%) and did not differ in diet and sleep behaviours, although findings for sleep were heterogenous (I2=85%). In stratified analyses, furlough was associated with low fruit and vegetable consumption among males (RR=1.11; 95%CI: 1.01-1.22; I2: 0%) but not females (RR=0.84; 95%CI: 0.68-1.04; I2: 65%). Considering change in these health behaviours, furloughed workers were more likely than those who remained working to report increased fruit and vegetable consumption, exercise, and hours of sleep.\n\nConclusionsThose furloughed exhibited broadly similar levels of health behaviours to those who remained in employment during the initial stages of the pandemic. There was little evidence to suggest that such social protection policies if used in the post-pandemic recovery period and during future economic crises would have adverse impacts on population health behaviours.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Bozena Wielgoszewska", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - }, - { - "author_name": "Jane Maddock", - "author_inst": "MRC Unit for Lifelong Health and Ageing, University College London" - }, - { - "author_name": "Michael J Green", - "author_inst": "MRC/CSO Social & Public Health Sciences Unit, University of Glasgow" - }, - { - "author_name": "Giorgio Di Gessa", - "author_inst": "Institute of Epidemiology and Health Care, University College London" - }, - { - "author_name": "Sam Parsons", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - }, - { - "author_name": "Gareth J Griffith", - "author_inst": "MRC Integrative Epidemiology Unit, University of Bristol" - }, - { - "author_name": "Jazz Croft", - "author_inst": "MRC Integrative Epidemiology Unit, University of Bristol" - }, - { - "author_name": "Anna J Stevenson", - "author_inst": "Centre for Genomic and Experimental Medicine, University of Edinburgh" - }, - { - "author_name": "Charlotte Booth", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - }, - { - "author_name": "Richard J Silverwood", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - }, - { - "author_name": "David Bann", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - }, - { - "author_name": "Praveetha Patalay", - "author_inst": "UCL" - }, - { - "author_name": "Alun D Hughes", - "author_inst": "MRC Unit for Lifelong Health and Ageing, University College London" - }, - { - "author_name": "Nishi Chaturvedi", - "author_inst": "MRC Unit for Lifelong Health and Ageing, University College London" - }, - { - "author_name": "Laura D Howe", - "author_inst": "MRC Integrative Epidemiology Unit, University of Bristol" - }, - { - "author_name": "Emla Fitzsimons", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - }, - { - "author_name": "Srinivasa Vittal Katikireddi", - "author_inst": "MRC/CSO Social & Public Health Sciences Unit, University of Glasgow" - }, - { - "author_name": "George B Ploubidis", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.07.446560", "rel_title": "Mapping Potential Antigenic Drift Sites (PADS) on SARS-CoV-2 Spike in Continuous Epitope-Paratope Space", @@ -726786,6 +728251,57 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2021.06.08.447530", + "rel_title": "Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro", + "rel_date": "2021-06-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.08.447530", + "rel_abs": "Single domain shark VNAR antibodies can offer a viable alternative to conventional Ig-based monoclonal antibodies in treating COVID-19 disease during the current pandemic. Here we report the identification of neutralizing single domain VNAR antibodies selected against the SARS-CoV-2 spike protein derived from the Wuhan variant using phage display. We identified 56 unique binding clones that exhibited high affinity and specificity to the spike protein. Of those, 10 showed an ability to block both the spike protein receptor binding domain from the Wuhan variant and the N501Y mutant from interacting with recombinant ACE2 receptor in vitro. In addition, 3 antibody clones retained in vitro blocking activity when the E484K spike protein mutant was used. The inhibitory property of the VNAR antibodies was further confirmed for all 10 antibody clones using ACE2 expressing cells with spike protein from the Wuhan variant. The viral neutralizing potential of the VNAR clones was also confirmed for the 10 antibodies tested using live Wuhan variant virus in in vitro cell infectivity assays. Single domain VNAR antibodies due to their low complexity, small size, unique epitope recognition and formatting flexibility should be a useful adjunct to existing antibody approaches to treat COVID-19.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Aziz Gauhar", + "author_inst": "Ossianix Inc." + }, + { + "author_name": "Cyril V Privezentzev", + "author_inst": "Ossianix Inc." + }, + { + "author_name": "Mykhaylo Demydchuk", + "author_inst": "Ossianix Inc." + }, + { + "author_name": "Tanja Gerlza", + "author_inst": "Karl-Franzens-University Graz" + }, + { + "author_name": "Julia Rieger", + "author_inst": "Medical University Graz" + }, + { + "author_name": "Andreas J Kungl", + "author_inst": "Karl-Franzens-University Graz" + }, + { + "author_name": "Frank S Walsh", + "author_inst": "Ossianix Inc." + }, + { + "author_name": "J Lynn Rutkowski", + "author_inst": "Ossianix Inc." + }, + { + "author_name": "Pawel Stocki", + "author_inst": "Ossianix Inc." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2021.06.08.447224", "rel_title": "Predicted Coronavirus Nsp5 Protease Cleavage Sites in the Human Proteome: A Resource for SARS-CoV-2 Research", @@ -728357,37 +729873,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.03.21258312", - "rel_title": "Outcomes of SARS-CoV-2 Infection in Patients with Chronic Liver Disease and Cirrhosis: a N3C Study", - "rel_date": "2021-06-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258312", - "rel_abs": "Background and AimsIn patients with chronic liver diseases (CLD) with or without cirrhosis, existing data on the risk of adverse outcomes with SARS-CoV-2 infection have been mixed or have limited generalizability. We used the National COVID Cohort Collaborative (N3C) Data Enclave, a harmonized electronic health record (EHR) dataset of 5.9 million nationally-representative, diverse, and gender-balanced patients, to describe outcomes in patients with CLD and cirrhosis with SARS-CoV-2.\n\nMethodsWe identified all chronic liver diseases patients with and without cirrhosis who had SARS-CoV-2 testing documented in the N3C Data Enclave as of data release date 5/15/2021. The primary outcome was 30-day all-cause mortality. Survival analysis methods were used to estimate cumulative incidences of death, hospitalization, and mechanical ventilation, and to calculate the associations of SARS-CoV-2 infection, presence of cirrhosis, and demographic and clinical factors to 30-day mortality.\n\nResultsWe isolated 217,143 patients with CLD: 129,097 (59%) without cirrhosis and SARS-CoV-2 negative, 25,844 (12%) without cirrhosis and SARS-CoV-2 positive, 54,065 (25%) with cirrhosis and SARS-CoV-2 negative, and 8,137 (4%) with cirrhosis and SARS-CoV-2 positive. Among CLD patients without cirrhosis, 30-day all-cause mortality rates were 0.4% in SARS-CoV-2 negative patients and 1.8% in positive patients. Among CLD patients with cirrhosis, 30-day all-cause mortality rates were 4.0% in SARS-CoV-2 negative patients and 9.7% in positive patients.\n\nCompared to those who tested SARS-CoV-2 negative, SARS-CoV-2 positivity was associated with more than two-fold (aHR 2.43, 95% CI 2.23-2.64) hazard of death at 30 days among patients with cirrhosis. Compared to patients without cirrhosis, the presence of cirrhosis was associated with a three-fold (aHR 3.39, 95% CI 2.96-3.89) hazard of death at 30 days among patients who tested SARS-CoV-2 positive. Age (aHR 1.03 per year, 95% CI 1.03-1.04) was associated with death at 30 days among patients with cirrhosis who were SARS-CoV-2 positive.\n\nConclusionsIn this study of nearly 220,000 CLD patients, we found SARS-CoV-2 infection in patients with cirrhosis was associated with 2.43-times mortality hazard, and the presence of cirrhosis among CLD patients infected with SARS-CoV-2 were associated with 3.39-times mortality hazard. Compared to previous studies, our use of a nationally-representative, diverse, and gender-balanced dataset enables wide generalizability of these findings.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jin Ge", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Mark J. Pletcher", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jennifer C Lai", - "author_inst": "UCSF" - }, - { - "author_name": "- N3C Consortium", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2021.06.07.447287", "rel_title": "A Web Portal and Workbench for Biological Dissection of Single Cell COVID-19 Host Responses", @@ -728692,6 +730177,37 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.06.07.447334", + "rel_title": "Dynamics and self-assembly of the SARS-CoV-2 spike transmembrane domain", + "rel_date": "2021-06-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.07.447334", + "rel_abs": "The spike (S) protein is a trimeric, membrane-anchored fusion protein that enables coronaviruses, such as the SARS-CoV-2, to recognize and fuse with their hosts cells. While the prefusion and postfusion structures of the ectomembrane domain of the spike protein are available, the corresponding organization of its transmembrane domain is obscure. Since the transmembrane and ectomembrane domains of fusion proteins are conformationally linked, an understanding of trimerization and transmembrane conformations in the viral envelope is a prerequisite to completely understand viral fusion by the spike protein. To address this, we computationally explored the self-assembly of the SARS-CoV-2 spike transmembrane domain, starting first by determining the membrane boundaries of the spike transmembrane helix. Using atomistic molecular dynamics simulations, we found the spike protein transmembrane domain to be plastic, and the transmembrane helix to be very dynamic. The observed movements of the helix changed the membrane embedded sequence, and thereby affected the conformational ensemble of the transmembrane assembly in Martini coarse grained simulations, even flipping the super-helical handedness. Analysis of the transmembrane organization of the spike transmembrane helix provided rich insights into the interfaces utilized to self-associate. Moreover, we identified two distinct cholesterol binding regions on the transmembrane helix with different affinities for the sterol. The cholesterol binding pockets overlapped with regions involved in the initiation of transmembrane protein-protein interaction. Together, the results from our multiscale simulations not only provide insight into understudied trimeric helical interfaces in biomembranes, but also enhance our understanding of the elusive transmembrane conformational dynamics of SARS-CoV-2 spike and more generally of viral fusion proteins. These insights should enable the inclusion of the conformations of the spike protein transmembrane domain into the prevalent models of virus fusion.\n\nSignificanceEnveloped viruses rely on fusion proteins, called spike proteins in coronaviruses, to infect cells by fusing the virus envelope with the host cell membrane. The transmembrane domain (TMD) of the coronavirus spike protein is critically involved in successful viral fusion and other aspects of the virus lifecycle, but is poorly studied. Using multiscale molecular dynamics simulations of the SARS-CoV-2 spike TMD, we explore its conformational dynamics and self-assembly in different lipid environments. The results provided here improve our understanding of transmembrane stabilization of spike trimers, which are indispensable for viral infection. Exploiting this knowledge to destabilize spike trimers should facilitate design of transmembrane domain targeted viral fusion inhibitors.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Sahil Lall", + "author_inst": "National Centre for Biological Sciences. TIFR" + }, + { + "author_name": "Padmanabhan Balaram", + "author_inst": "National Centre for Biological Sciences, TIFR" + }, + { + "author_name": "Shachi Gosavi", + "author_inst": "National Centre for Biological Sciences, TIFR" + }, + { + "author_name": "M.K. Mathew", + "author_inst": "National Centre for Biological Sciences, TIFR" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.06.07.447321", "rel_title": "E156/G and Arg158, Phe-157/del mutation in NTD of spike protein in B.1.167.2 lineage of SARS-CoV-2 leads to immune evasion through antibody escape", @@ -730107,33 +731623,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.02.21258221", - "rel_title": "Classifying Texas counties using ARIMA Models on COVID-19 daily confirmed cases: the impact of political affiliation and face covering orders", - "rel_date": "2021-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.02.21258221", - "rel_abs": "The aim of this paper is to investigate whether the 254 Texas counties in the United States can be grouped in a meaningful way according to the characteristics of the ARIMA or seasonal ARIMA models fitting the logarithm of daily confirmed cases of the Coronavirus Disease 2019 (COVID-19) for 254 counties in Texas of the United States. We analyze clusters of the models non-seasonal parameters (p, d, q), distinguishing between county-level political affiliations and face covering orders, and also consider county-level population and poverty rate. Using data from March 4, 2020 to March 15, 2021, we find that 223 of the total 254 counties are clustered into 23 model parameters (p, d, q), while the number of cases in the remaining 31 counties could not be successfully fitted to ARIMA models. We also find the impact of the county-level infection rate and the county-level poverty rate on clusters of counties with different political affiliations and face covering orders. Further, we find that the infection rate and the poverty rate had a significant high positive correlation, and Democrat-leaning counties, which tend to have large populations, had a higher correlation coefficient between infection rate and poverty rate. We also observe a significant high positive correlation between the infection rate and the number of cumulative cases in Republican counties that had not imposed a face covering order.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Hao Jiang", - "author_inst": "Southern Methodist University" - }, - { - "author_name": "Brigitta Pulins", - "author_inst": "Southern Methodist University" - }, - { - "author_name": "Aurelie Thiele", - "author_inst": "Southern Methodist University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.02.21258257", "rel_title": "Efficacy of clarithromycin on COVID-19 pneumonia without oxygen administration; protocol for multicenter, open-label, randomized-controlled, 3-armed parallel group comparison, exploratory trial (CAME COVID study)", @@ -730286,6 +731775,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.03.21258258", + "rel_title": "Group Testing Large Populations for SARS-CoV-2", + "rel_date": "2021-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258258", + "rel_abs": "Group testing, the testing paradigm which combines multiple samples within a single test, was introduced in 1943 by Robert Dorfman. Since its original proposal for syphilis screening, group testing has been applied in domains such as fault identification in electrical and computer networks, machine learning, data mining, and cryptography. The SARS-CoV-2 pandemic has led to proposals for using group testing in its original context of identifying infected individuals in a population with few tests. Studies suggest that non-adaptive group testing - in which all the tests are determined in advance - for SARS-CoV-2 could help save 20% to 90% of tests depending on the prevalence. However, no systematic approach for comparing different non-adaptive group testing strategies currently exists.\n\nIn this paper we develop a software platform for evaluating non-adaptive group testing strategies in both a noiseless setting and in the presence of realistic noise sources, modelled on published experimental observations, which makes them applicable to polymerase chain reaction (PCR) tests, the dominant type of tests for SARS-CoV-2. This modular platform can be used with a variety of group testing designs and decoding algorithms. We use it to evaluate the performance of near-doubly-regular designs and a decoding algorithm based on an integer linear programming formulation, both of which are known to be optimal in some regimes. We find savings between 40% and 91% of tests for prevalences up to 10% when a small error (below 5%) is allowed. We also find that the performance degrades gracefully with noise. We expect our modular, user-friendly, publicly available platform to facilitate empirical research into non-adaptive group testing for SARS-CoV-2.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Hooman Zabeti", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Nick Dexter", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Ivan Lau", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Leonhardt Unruh", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ben Adcock", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Leonid Chindelevitch", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.02.21258229", "rel_title": "Vaccine nationalism and the dynamics and control of SARS-CoV-2", @@ -731597,89 +733125,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.04.21258316", - "rel_title": "A Prospective Observational Study to Investigate Performance of a Chest X-ray Artificial Intelligence Diagnostic Support Tool Across 12 U.S. Hospitals", - "rel_date": "2021-06-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.04.21258316", - "rel_abs": "ImportanceAn artificial intelligence (AI)-based model to predict COVID-19 likelihood from chest x-ray (CXR) findings can serve as an important adjunct to accelerate immediate clinical decision making and improve clinical decision making. Despite significant efforts, many limitations and biases exist in previously developed AI diagnostic models for COVID-19. Utilizing a large set of local and international CXR images, we developed an AI model with high performance on temporal and external validation.\n\nObjectiveInvestigate real-time performance of an AI-enabled COVID-19 diagnostic support system across a 12-hospital system.\n\nDesignProspective observational study.\n\nSettingLabeled frontal CXR images (samples of COVID-19 and non-COVID-19) from the M Health Fairview (Minnesota, USA), Valencian Region Medical ImageBank (Spain), MIMIC-CXR, Open-I 2013 Chest X-ray Collection, GitHub COVID-19 Image Data Collection (International), Indiana University (Indiana, USA), and Emory University (Georgia, USA)\n\nParticipantsInternal (training, temporal, and real-time validation): 51,592 CXRs; Public: 27,424 CXRs; External (Indiana University): 10,002 CXRs; External (Emory University): 2002 CXRs\n\nMain Outcome and MeasureModel performance assessed via receiver operating characteristic (ROC), Precision-Recall curves, and F1 score.\n\nResultsPatients that were COVID-19 positive had significantly higher COVID-19 Diagnostic Scores (median .1 [IQR: 0.0-0.8] vs median 0.0 [IQR: 0.0-0.1], p < 0.001) than patients that were COVID-19 negative. Pre-implementation the AI-model performed well on temporal validation (AUROC 0.8) and external validation (AUROC 0.76 at Indiana U, AUROC 0.72 at Emory U). The model was noted to have unrealistic performance (AUROC > 0.95) using publicly available databases. Real-time model performance was unchanged over 19 weeks of implementation (AUROC 0.70). On subgroup analysis, the model had improved discrimination for patients with \"severe\" as compared to \"mild or moderate\" disease, p < 0.001. Model performance was highest in Asians and lowest in whites and similar between males and females.\n\nConclusions and RelevanceAI-based diagnostic tools may serve as an adjunct, but not replacement, for clinical decision support of COVID-19 diagnosis, which largely hinges on exposure history, signs, and symptoms. While AI-based tools have not yet reached full diagnostic potential in COVID-19, they may still offer valuable information to clinicians taken into consideration along with clinical signs and symptoms.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Ju Sun", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Le Peng", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Taihui Li", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Dyah Adila", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Zach Zaiman", - "author_inst": "Emory University" - }, - { - "author_name": "Genevieve Melton", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Nicholas E Ingraham", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Eric Murray", - "author_inst": "M Health Fairview" - }, - { - "author_name": "Daniel Boley", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Sean Switzer", - "author_inst": "University of Minnesota" - }, - { - "author_name": "John L Burns", - "author_inst": "Indiana University" - }, - { - "author_name": "Kun Huang", - "author_inst": "Indiana University" - }, - { - "author_name": "Tadashi Allen", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Scott D Steenburg", - "author_inst": "Indiana University" - }, - { - "author_name": "Judy Wawira Gichoya", - "author_inst": "Emory University" - }, - { - "author_name": "Erich Kummerfeld", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Christopher J Tignanelli", - "author_inst": "University of Minnesota" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.06.03.21258240", "rel_title": "Aggregating probabilistic predictions of the safety, efficacy, and timing of a COVID-19 vaccine", @@ -731876,6 +733321,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.01.21258188", + "rel_title": "Antibody responses to BNT162b2 mRNA COVID-19 vaccine in 2,015 healthcare workers in a single tertiary referral hospital in Japan", + "rel_date": "2021-06-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.01.21258188", + "rel_abs": "We measured antibody responses in 2,015 healthcare workers who were receiving 2 doses of BNT162b2 mRNA vaccine against SARS-CoV-2. The vast majority (99.9%) had either seroconversion or a substantial increase in antibody titer. A multivariate linear regression model identified predictive factors for antibody responses which may have clinical implications.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Takahiro Kageyama", + "author_inst": "Chiba University" + }, + { + "author_name": "Kei Ikeda", + "author_inst": "Chiba University" + }, + { + "author_name": "Shigeru Tanaka", + "author_inst": "Chiba University" + }, + { + "author_name": "Toshibumi Taniguchi", + "author_inst": "Chiba University" + }, + { + "author_name": "Hidetoshi Igari", + "author_inst": "Chiba University" + }, + { + "author_name": "Yoshihiro Onouchi", + "author_inst": "Chiba University" + }, + { + "author_name": "Atsushi Kaneda", + "author_inst": "Chiba University" + }, + { + "author_name": "Kazuyuki Matsushita", + "author_inst": "Chiba University" + }, + { + "author_name": "Hideki Hanaoka", + "author_inst": "Chiba University" + }, + { + "author_name": "Taka-Aki Nakada", + "author_inst": "Chiba University" + }, + { + "author_name": "Seiji Ohtori", + "author_inst": "Chiba University" + }, + { + "author_name": "Ichiro Yoshino", + "author_inst": "Chiba University" + }, + { + "author_name": "Hisahiro Matsubara", + "author_inst": "Chiba University" + }, + { + "author_name": "Toshinori Nakayama", + "author_inst": "Chiba University" + }, + { + "author_name": "Koutaro Yokote", + "author_inst": "Chiba University" + }, + { + "author_name": "Hiroshi Nakajima", + "author_inst": "Chiba University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.02.21258184", "rel_title": "Passively Sensing SARS-CoV-2 RNA in Public Transit Buses", @@ -733615,69 +735139,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.05.31.21258129", - "rel_title": "Physical integrity of medical exam gloves with repeated applications of disinfecting agents: evidence for extended use", - "rel_date": "2021-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.31.21258129", - "rel_abs": "BackgroundThe COVID-19 pandemic has created global shortages of personal protective equipment (PPE) such as medical exam gloves, forcing healthcare workers to either forgo or reuse PPE to keep themselves and patients safe from infection. In severely resource-constrained situations, limited cycles of disinfection and extended use of gloves is recommended by the U.S. Centers for Disease Control and Prevention (CDC) to conserve supplies. However, these guidelines are based on limited evidence.\n\nMethodsSerial cycles of hand hygiene were performed on gloved hands using alcohol-based hand rub (ABHR) (six and ten cycles), 0.1% sodium hypochlorite (bleach) solution (ten cycles), or soap and water (ten cycles) on three types of latex and three types of nitrile medical exam gloves, purchased in the United States and India. A modified FDA-approved water-leak test was performed to evaluate glove integrity after repeated applications of these disinfecting agents. 80 gloves per disinfectant-glove type combination were tested. Within each glove type the proportion of gloves that failed the water-leak test for each disinfectant was compared to that of the control using a non-inferiority design with a non-inferiority margin of five percentage points. Results were also aggregated by glove material, and combined for overall results.\n\nFindingsWhen aggregated by glove material, the dilute bleach exposure demonstrated the lowest difference in proportion failed between treatment and control arms: -2.5 percentage points (95% CI: -5.3 to 0.3) for nitrile, 0.6 percentage points (95% CI: -2.6 to 3.8) for non-powdered latex. For US-purchased gloves tested with six and ten applications of ABHR, the mean difference in failure risk between treatment and control gloves was within the prespecified non-inferiority margin of five percentage points or less, though some findings were inconclusive because confidence intervals extended beyond the non-inferiority margin. The aggregated difference in failure risk between treatment and control gloves was 3.5 percentage points (0.6 to 6.4) for soap and water, and 2.3 percentage points (-0.5 to 5.0) and 5.0 percentage points (1.8 to 8.2) for 10 and 6 applications of ABHR, respectively. The majority of leaks occurred in the interdigital webs (35%) and on the fingers (34%).\n\nConclusionCurrent guidelines do not recommend extended use of a single-use PPE under normal supply conditions. However, our findings indicate that some combinations of glove types and disinfection methods may allow for extended use under crisis conditions. We found that ten applications of dilute bleach solution have the least impact on glove integrity, compared to repeated applications of ABHR and soap and water. However, the majority of glove and exposure combinations were inconclusive with respect to non-inferiority with a 5 percentage point non-inferiority margin. Testing specific glove and disinfectant combinations may be worthwhile for settings facing glove shortages during which extended use is necessary. The modified water-leak testing method used here is a low-resource method that could easily be reproduced in different contexts.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Jared S Shless", - "author_inst": "Department of Bioengineering, College of Engineering, University of California, Berkeley, 306 Stanley Hall, Berkeley, CA 94720" - }, - { - "author_name": "Yoshika S Crider", - "author_inst": "Energy and Resources Group, University of California, Berkeley, 345 Giannini Hall, Berkeley, CA 94720" - }, - { - "author_name": "Helen O Pitchik", - "author_inst": "Division of Epidemiology, School of Public Health, University of California, Berkeley, 2121 Berkeley Way, Berkeley, CA 4720" - }, - { - "author_name": "Alliya S Qazi", - "author_inst": "Department of Surgery, University of California, Irvine School of Medicine, 333 City West Blvd., Suite 1600, Orange, CA 92868" - }, - { - "author_name": "Ashley Styczynski", - "author_inst": "Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Lane 134, Palo Alto, CA 94305" - }, - { - "author_name": "Roger LeMesurier", - "author_inst": "Independent researcher, San Francisco, CA 94110" - }, - { - "author_name": "Daniel Haik", - "author_inst": "Department of Surgery, University of California, Irvine School of Medicine, 333 City West Blvd., Suite 1600, Orange, CA 92868" - }, - { - "author_name": "Laura H Kwong", - "author_inst": "Stanford University, Woods Institute for the Environment, 473 Via Ortega, Palo Alto, CA 94305" - }, - { - "author_name": "Christopher Leboa", - "author_inst": "Stanford University, Woods Institute for the Environment, 473 Via Ortega, Palo Alto, CA 94305" - }, - { - "author_name": "Arnab Bhattacharya", - "author_inst": "Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, India 400005" - }, - { - "author_name": "Youssef K Hamidi", - "author_inst": "Mechanical Engineering Program, College of Science and Engineering, University of Houston-Clear Lake, Houston, TX 77058" - }, - { - "author_name": "Robert N Phalen", - "author_inst": "Occupational Safety and Health Program, College of Science and Engineering, University of Houston-Clear Lake, Houston, TX 77058" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.01.21258147", "rel_title": "Minimum manufacturing costs, national prices and estimated global availability of new repurposed therapies for COVID-19.", @@ -733962,6 +735423,41 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2021.05.30.21258071", + "rel_title": "Implementing Mandatory Testing and a Public Health Commitment to Control COVID-19 on a College Campus", + "rel_date": "2021-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.30.21258071", + "rel_abs": "The COVID-19 pandemic has greatly impacted US colleges and universities. As The George Washington University (GWU), a large urban university, prepared to reopen for the Fall 2020 semester, GWU established protocols to protect the health and wellness of all members of campus community. Reopening efforts included a cadre of COVID-19 surveillance systems including development of a public health COVID-19 laboratory, weekly and symptomatic SARS-CoV-2 testing and daily risk screening and symptom monitoring. Other activities included completion of a mandatory COVID-19 training and influenza vaccination for the on-campus population, quarantining of students returning to campus, campus-focused case investigations and quarantining of suspected close contacts, clinical follow-up of infected persons, and regular communication and monitoring. A smaller on-campus population of 4,435 students, faculty and staff returned to campus with later expansion of testing to accommodate GWU students living in the surrounding area. Between August 17 and December 4, 2020, 38,288 tests were performed; 220 were positive. The surveillance program demonstrated a relatively low positivity rate, with temporal clustering of infected persons mirroring community spread, and little evidence for transmission among the GWU on-campus population. These efforts demonstrate the feasibility of safely partially reopening a large urban college campus by applying core principles of public health surveillance, infectious disease epidemiology, behavioral measures, and increased testing capacity, while continuing to promote educational and research opportunities. GWU will continue to monitor the program as the pandemic evolves and periodically reassess to determine if these strategies will be successful upon a full return to in-person learning.\n\nSummary BoxO_LIWhat is the current understanding of this subject? When the COVID-19 pandemic began, generally universities were not prepared and it was unclear how to safely reopen colleges and universities given the uncertain risks of transmission among students, faculty and staff.\nC_LIO_LIWhat does this report add to the literature? This case report highlights the successful approaches employed, including applying the core principles of public health surveillance and increasing testing capacity, to mitigate the spread of SARS-CoV-2 on a densely populated urban college campus resulting in a safe reopening.\nC_LIO_LIWhat are the implications for public health practice? This experience can provide a roadmap for other universities to consider as they plan for the safe reopening of their campuses.\nC_LI", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Cindy Liu", + "author_inst": "The George Washington University Milken Institute School of Public Health" + }, + { + "author_name": "Amita Vyas", + "author_inst": "The George Washington University Milken Institute School of Public Health" + }, + { + "author_name": "Amanda D Castel", + "author_inst": "The George Washington University Milken Institute School of Public Health" + }, + { + "author_name": "Karen A McDonnell", + "author_inst": "The George Washington University Milken Institute School of Public Health" + }, + { + "author_name": "Lynn R Goldman", + "author_inst": "The George Washington University Milken Institute School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.06.02.446468", "rel_title": "Pathogenic neutrophilia drives acute respiratory distress syndrome in severe COVID-19 patients", @@ -735621,129 +737117,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.26.21257063", - "rel_title": "Evaluation of the INDICAID COVID-19 Rapid Antigen Test in symptomatic populations and asymptomatic community testing", - "rel_date": "2021-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.26.21257063", - "rel_abs": "BackgroundAs the COVID-19 pandemic continues to cause substantial morbidity and mortality, there is an increased need for rapid, accessible assays for SARS-CoV-2 detection.\n\nMethodsHere we present a clinical evaluation and real-world implementation of the INDICAID COVID-19 Rapid Antigen Test (INDICAID Rapid Test). A multi-site clinical evaluation of the INDICAID Rapid Test using prospectively collected samples from symptomatic subjects was performed. The INDICAID Rapid Test was then implemented at COVID-19 outbreak screening centers in Hong Kong to screen individuals for COVID-19 to prioritize confirmatory RT-PCR testing among asymptomatic populations.\n\nResultsThe clinical evaluation in symptomatic patient populations demonstrated a positive percent agreement and negative percent agreement of 85.3% (95% confidence interval [95% CI]: 75.6% - 91.6%) and 94.9% (95% CI: 91.6% - 96.9%), respectively, when compared to laboratory-based RT-PCR testing. When used during outbreak testing of 22,994 asymptomatic patients, the INDICAID Rapid Test demonstrated a positive percent agreement of 84.2% (95% CI: 69.6% - 92.6%) and a negative percent agreement of 99.9% (95% CI: 99.9% - 100%) compared to laboratory-based RT-PCR testing. When incorporated in a testing algorithm, the INDICAID Rapid Test reduced time to confirmatory positive result from an average 10.85 hours (standard RT-PCR only) to 0.84 hours, depending on the algorithm.\n\nConclusionThe INDICAID Rapid Test has excellent performance when compared to laboratory-based RT-PCR testing, and when used in tandem with RT-PCR, reduces the time to confirmatory positive result.\n\nSummaryIn clinical evaluations, the INDICAID COVID-19 Rapid Antigen Test demonstrated high sensitivity and specificity in symptomatic and asymptomatic patient populations. When used in tandem with RT-PCR testing, the INDICAID Rapid Test expedited confirmatory results and may help reduce SARS-CoV-2 outbreaks.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Ricky Chiu", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Noah Kojima", - "author_inst": "UCLA" - }, - { - "author_name": "Garrett Mosley", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Kwok Kin Cheng", - "author_inst": "Phase Scientific" - }, - { - "author_name": "David Pereira", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Matthew Brobeck", - "author_inst": "Contractor" - }, - { - "author_name": "Tsun Leung Chan", - "author_inst": "Hong Kong Sanatorium and Hospital" - }, - { - "author_name": "Jonpaul Sze-Tsing Zee", - "author_inst": "Hong Kong Sanatorium and Hospital" - }, - { - "author_name": "Harsha Kittur", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Tenny Chung", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Eric Tsang", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Kajal Maran", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Raymond Wai-Hung Yung", - "author_inst": "Hong Kong Sanatorium and Hospital" - }, - { - "author_name": "Alex Chin-Pang Leung", - "author_inst": "Hong Kong Sanatorium and Hospital" - }, - { - "author_name": "Ryan Siu", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Jessica Ng", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Tsz Hei Choi", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Mei Wai Fung", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Sean Parkin", - "author_inst": "CityHealth Urgent Care" - }, - { - "author_name": "Wai Sing Chan", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Ho Yin Lam", - "author_inst": "Hong Kong Sanatorium and Hospital" - }, - { - "author_name": "Koon Kung Lee", - "author_inst": "Hong Kong Sanatorium and Hospital" - }, - { - "author_name": "Felix C Chao", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Stephen Ka-Kung Ho", - "author_inst": "Contractor" - }, - { - "author_name": "Dan MArshak", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Edmond Shiu-Kwan Ma", - "author_inst": "Hong Kong Sanatorium and Hospital" - }, - { - "author_name": "Jeffrey D Klausner", - "author_inst": "USC School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.01.21258124", "rel_title": "Regular testing of asymptomatic healthcare workers identifies cost-efficient SARS-CoV-2 preventive measures", @@ -735944,6 +737317,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.06.01.446639", + "rel_title": "Effects of the COVID-19 pandemic on publication landscape in chimeric antigen receptor-modified immune cell research", + "rel_date": "2021-06-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.01.446639", + "rel_abs": "Chimeric antigen receptors (CARs) are artificial receptors introduced mainly into T cells. CAR-induced immune cell (CARi) products have achieved impressive success rates in treating some difficult-to-treat hematological malignancies. Here, we describe effects of the global COVID-19 pandemic on CARi publication landscape. Due to the pandemic, the total number of publications decreased in 2020 compared to 2019 in all fields of cancer immunotherapy except CARi. Nearly exponential increases in the number of CARi publications slowed-down in 2020 for the first time in the past 11 years. There were more CARi than coronavirus publications until 2020 when coronavirus publications increased over 5,000% compared to 2019 (575 publications in 2019 vs. 30,390 in 2020). Unlike cancer immunotherapy where the majority of the publications consist of conference abstracts and review articles, majority of the coronavirus publications are original research articles. There are more coronavirus publications in Pubmed than Embase. The opposite is true for CARi publications. Our analysis of the data from the FDA Adverse Event Reporting System (FAERS) show significantly higher death rate in patients treated with Kymirah than Yescarta (28.14% vs. 16.02%). Kymirah and Yescarta are the two main CAR T cell products for treatment of DLBCL and/or B-ALL. However, despite being highly significant, this result is not easily interpretable due to multiple confounding variables in the FAERS data. Our analysis additionally suggest that the significant effects of co-stimulatory domains (4-1BB vs. CD28) consistently reported in preclinical studies do not translate into clinical results. Our manual curation of the CARi publications in PubMed shows that only 5.2% of the publications report results from CARi clinical trials, although we found 663 clinical trials listed on ClinicalTrials.gov database. In conclusion, publication landscape in CARi as well as other fields of cancer immunotherapy has changed due to the global COVID-19 pandemic. This trend will likely continue in the near future. CARi research is now in need of increased measures by publishers to reduce repetitive and/or duplicate publications and more stringent criteria for data entry into public databases including PubMed, Embase, ClinicalTrials.gov, and FAERS to advance this important field of medical research.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Jianhua Yu", + "author_inst": "City of Hope" + }, + { + "author_name": "Ahmet Yilmaz", + "author_inst": "The Ohio State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "cancer biology" + }, { "rel_doi": "10.1101/2021.05.27.21257908", "rel_title": "Policy and Effectiveness of Covid-19 Response", @@ -737367,81 +738763,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.29.21257760", - "rel_title": "Genomic epidemiology and associated clinical outcomes of a SARS-CoV-2 outbreak in a general adult hospital in Quebec", - "rel_date": "2021-06-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.29.21257760", - "rel_abs": "The first confirmed case of COVID-19 in Quebec, Canada, occurred at Verdun Hospital on February 25, 2020. A month later, a localized outbreak was observed at this hospital. We performed tiled amplicon whole genome nanopore sequencing on nasopharyngeal swabs from all SARS-CoV-2 positive samples from 31 March to 17 April 2020 in 2 local hospitals to assess the viral diversity of the outbreak. We report 264 viral genomes from 242 individuals (both staff and patients) with associated clinical features and outcomes, as well as longitudinal samples, technical replicates and the first publicly disseminated SARS-CoV-2 genomes in Quebec. Viral lineage assessment identified multiple subclades in both hospitals, with a predominant subclade in the Verdun outbreak, indicative of hospital-acquired transmission. Dimensionality reduction identified two subclades that evaded supervised lineage assignment methods, including Pangolin, and identified certain symptoms (headache, myalgia and sore throat) that are significantly associated with favorable patient outcomes. We also address certain limitations of standard SARS-CoV-2 bioinformatics procedures, notably when presented with multiple viral haplotypes.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Bastien Pare", - "author_inst": "Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal" - }, - { - "author_name": "Marieke Rozendaal", - "author_inst": "CHU Sainte-Justine Research Centre" - }, - { - "author_name": "Sacha Morin", - "author_inst": "Department of Computer Science and Operational Research, University of Montreal" - }, - { - "author_name": "Raphael Poujol", - "author_inst": "Montreal Heart Institute" - }, - { - "author_name": "Fatima Mostefai", - "author_inst": "Montreal Heart Institute" - }, - { - "author_name": "Jean-Christophe Grenier", - "author_inst": "Montreal Heart Institute" - }, - { - "author_name": "Lea Kaufmann", - "author_inst": "Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal" - }, - { - "author_name": "Henry Xing", - "author_inst": "CHU Sainte-Justine Research Centre" - }, - { - "author_name": "Miguelle Sanchez", - "author_inst": "Department of microbiology and infectious diseases, Hopital de Verdun" - }, - { - "author_name": "Ariane Yechouron", - "author_inst": "Department of microbiology and infectious diseases, Hopital de Verdun" - }, - { - "author_name": "Ronald Racette", - "author_inst": "Department of Emergency Medicine, Hopital de Verdun" - }, - { - "author_name": "Julie Hussin", - "author_inst": "Montreal Heart Institute" - }, - { - "author_name": "Guy Wolf", - "author_inst": "Mila - Quebec AI Institute, Montreal" - }, - { - "author_name": "Ivan Pavlov", - "author_inst": "Department of Emergency Medicine, Hopital de Verdun" - }, - { - "author_name": "Martin A Smith", - "author_inst": "University of Montreal" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.31.21255594", "rel_title": "Signatures of mast cell activation are associated with severe COVID-19", @@ -737638,6 +738959,41 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.06.01.446623", + "rel_title": "Synergistic inhibition of two host factors that facilitate entry of Severe Acute Respiratory Syndrome Coronavirus 2", + "rel_date": "2021-06-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.01.446623", + "rel_abs": "Repurposing FDA-approved inhibitors able to prevent infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could provide a rapid path to establish new therapeutic options to mitigate the effects of coronavirus disease 2019 (COVID-19). Proteolytic cleavages of the spike S protein of SARS-CoV-2, mediated by the host cell proteases cathepsin and TMPRSS2, alone or in combination, are key early activation steps required for efficient infection. The PIKfyve kinase inhibitor apilimod interferes with late endosomal viral traffic, and through an ill-defined mechanism prevents in vitro infection through late endosomes mediated by cathepsin. Similarly, inhibition of TMPRSS2 protease activity by camostat mesylate or nafamostat mesylate prevents infection mediated by the TMPRSS2-dependent and cathepsin-independent pathway. Here, we combined the use of apilimod with camostat mesylate or nafamostat mesylate and found an unexpected ~5-10-fold increase in their effectiveness to prevent SARS-CoV-2 infection in different cell types. Comparable synergism was observed using both, a chimeric vesicular stomatitis virus (VSV) containing S of SARS-CoV-2 (VSV-SARS-CoV-2) and SARS-CoV-2 virus. The substantial ~5-fold or more decrease of half maximal effective concentrations (EC50 values) suggests a plausible treatment strategy based on the combined use of these inhibitors.\n\nIMPORTANCEInfection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing the coronavirus disease 2019 (COVID-2019) global pandemic. There are ongoing efforts to uncover effective antiviral agents that could mitigate the severity of the disease by controlling the ensuing viral replication. Promising candidates include small molecules that inhibit the enzymatic activities of host proteins, thus preventing SARS-CoV-2 entry and infection. They include Apilimod, an inhibitor of PIKfyve kinase and camostat mesylate and nafamostat mesylate, inhibitors of TMPRSS2 protease. Our research is significant for having uncovered an unexpected synergism in the effective inhibitory activity of apilimod used together with camostat mesylate or with nafamostat mesylate.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ravi Ojha", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Jesse Pyle", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Olli Vapalahti", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Giuseppe Balistreri", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Tom Kirchhausen", + "author_inst": "Harvard Medical School" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.05.31.446420", "rel_title": "Virucidal activity of a proprietary blend of plant-based oils (Viruxal) against SARS-CoV-2 and influenza viruses - an in vitro study", @@ -738845,45 +740201,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.31.446476", - "rel_title": "COVID-19 Mortality is Associated with Impaired Innate Immunity in Pre-existing Health Conditions", - "rel_date": "2021-05-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.31.446476", - "rel_abs": "BackgroundCOVID-19 poses a life-threatening endangerment to individuals with chronic diseases. However, not all comorbidities affect COVID-19 prognosis equally. Some increase the risk of COVID-19 related death by more than six folds while others show little to no impact. To prevent severe outcomes, it is critical that we comprehend pre-existing molecular abnormalities in common health conditions that predispose patients to poor prognoses. In this study, we aim to discover some of these molecular risk factors by associating gene expression dysregulations in common health conditions with COVID-19 mortality rates in different cohorts.\n\nMethodsWe focused on fourteen pre-existing health conditions, for which age-and-sex-adjusted hazard ratios of COVID-19 mortality have been documented. For each health condition, we analyzed existing transcriptomics data to identify differentially expressed genes (DEGs) between affected individuals and unaffected individuals. We then tested if fold changes of any DEG in these pre-existing conditions were correlated with hazard ratios of COVID-19 mortality to discover molecular risk factors. We performed gene set enrichment analysis to identify functional groups overrepresented in these risk factor genes and examined their relationships with the COVID-19 disease pathway.\n\nResultsWe found that upregulated expression of 70 genes and downregulated expression of 181 genes in pre-existing health conditions were correlated with increased risk of COVID-19 related death. These genes were significantly enriched with endoplasmic reticulum (ER) function, proinflammatory reaction, and interferon production that participate in viral transcription and immune responses to viral infections.\n\nConclusionsImpaired innate immunity in pre-existing health conditions are associated with increased hazard of COVID-19 mortality. The discovered molecular risk factors are potential prognostic biomarkers and targets for therapeutic interventions.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Matthew E Lee", - "author_inst": "Arizona State University" - }, - { - "author_name": "Yung Chang", - "author_inst": "Arizona State University" - }, - { - "author_name": "Navid Ahmadinejad", - "author_inst": "Arizona State University" - }, - { - "author_name": "Crista E Johnson-Agbakwu", - "author_inst": "Valleywise Health Medical Center" - }, - { - "author_name": "Celeste Bailey", - "author_inst": "Valleywise Health Medical Center" - }, - { - "author_name": "Li Liu", - "author_inst": "Arizona State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.05.31.446421", "rel_title": "Accelerated Antibody Discovery Targeting the SARS-CoV-2 Spike Protein for COVID-19 Therapeutic Potential", @@ -739119,6 +740436,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.05.31.445667", + "rel_title": "Revealing the host antiviral protein ZAP-S as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting", + "rel_date": "2021-05-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.31.445667", + "rel_abs": "Programmed ribosomal frameshifting (PRF) is a fundamental gene expression event in many viruses including SARS-CoV-2, which allows production of essential structural and replicative enzymes from an alternative reading frame. Despite the importance of PRF for the viral life cycle, it is still largely unknown how and to what extent cellular factors alter mechanical properties of frameshifting RNA molecules and thereby impact virulence. This prompted us to comprehensively dissect the interplay between the host proteome and the SARS-CoV-2 frameshift element. Here, we reveal that zinc-finger antiviral protein (ZAP-S) is a direct and specific regulator of PRF in SARS-CoV-2 infected cells. ZAP-S overexpression strongly impairs frameshifting and viral replication. Using in vitro ensemble and single-molecule techniques, we further demonstrate that ZAP-S directly interacts with the SARS-CoV-2 RNA and ribosomes and interferes with the folding of the frameshift RNA. Together these data illuminate ZAP-S as de novo host-encoded specific inhibitor of SARS-CoV-2 frameshifting and expand our understanding of RNA-based gene regulation.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Matthias Michael Zimmer", + "author_inst": "Helmholtz Institute for RNA-based Infection Research" + }, + { + "author_name": "Anuja Nitin Kibe", + "author_inst": "Helmholtz Institute for RNA-based Infection Research" + }, + { + "author_name": "Ulfert Rand", + "author_inst": "Helmholtz-Zentrum fur Infektionsforschung GmbH" + }, + { + "author_name": "Lukas Pekarek", + "author_inst": "Helmholtz Institute for RNA-based Infection Research" + }, + { + "author_name": "Luca Cicin-Sain", + "author_inst": "Helmholtz Centre for Infection Research" + }, + { + "author_name": "Neva Caliskan", + "author_inst": "Helmholtz Institute for RNA-based Infection Research" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.05.27.21257952", "rel_title": "Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation", @@ -740498,33 +741854,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.05.28.21254613", - "rel_title": "Antibody Response to CoronaVac Vaccine in Indonesian COVID-19 Survivor", - "rel_date": "2021-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.28.21254613", - "rel_abs": "Several studies have shown that individuals with previous history of SARS-CoV-2 infection had boosted antibody response after single dose of mRNA or adenovirus-vectored vaccines. We wondered whether single dose CoronaVac, a whole-inactivated vaccine, could be considered for COVID-19 survivors in Indonesia. We measured IgG anti-RBD titre among 18 survivors and 37 non-survivors. Among survivors, there were 9 survivors with positive antibody titre (seropositive) before vaccination and 9 seronegative survivors. All respondents received two doses of CoronaVac vaccine at 14-days interval. We found no significant antibody titre difference between non-survivor at 14 or 28 days after second dose as well as seronegative survivor at at 14 days after second dose. Seropositive survivors were rapidly boosted after first dose with higher antibody titer than non-survivors and seronegative survivors after second dose. However, antibody titer did not differ between first and second dose among seropositive survivors. Seropositive COVID-19 survivors could receive single dose of CoronaVac vaccine which could potentially ease the vaccine supply constrain. A long-term follow-up must be conducted to observe difference in antibody response and persistence.\n\nArticle Summary LineSeropositive COVID-19 survivors had significantly higher antibody response after first dose of CoronaVac vaccine compared to non-survivors and seronegative survivors after second dose of vaccine.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Rahmat Azhari Kemal", - "author_inst": "Faculty of Medicine, Universitas Riau" - }, - { - "author_name": "Dita Kartika Sari", - "author_inst": "Department of Anatomy, Faculty of Medicine, Universitas Riau" - }, - { - "author_name": "Ariza Julia Paulina", - "author_inst": "Department of Clinical Pathology, Faculty of Medicine, Universitas Riau" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.26.21257834", "rel_title": "Development and external validation of a diagnostic multivariable prediction model for a prompt identification of cases at high risk for SARS-COV-2 infection among patients admitted to the emergency department", @@ -740753,6 +742082,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2021.05.27.21257916", + "rel_title": "Modeling of the COVID-19 Cases in Gulf Cooperation Council (GCC) countries using ARIMA and MA-ARIMA models.", + "rel_date": "2021-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.27.21257916", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is still a great pandemic presently spreading all around the world. In Gulf Cooperation Council (GCC) countries, there were 1015269 COVID-19 confirmed cases, 969424 recovery cases, and 9328 deaths as of 30th Nov. 2020. This paper, therefore, subjected the daily reported COVID-19 cases of these three variables to some statistical models including classical ARIMA, kth SMA-ARIMA, kth WMA-ARIMA, and kth EWMA-ARIMA to study the trend and to provide the long-term forecasting of the confirmed, recovery, and death cases of the novel COVID-19 pandemic in the GCC countries. The data analyzed in this study covered the period starting from the first case of coronavirus reported in each GCC country to Nov 30, 2020. To compute the best parameter estimates, each model was fitted for 90% of the available data in each country, which is called the in-sample forecast or training data, and the remaining 10% was used for the out-of-sample forecast or testing model. The AIC was applied to the training data as a criterion method to select the best model. Furthermore, the statistical measure RMSE was utilized for testing data, and the model with the minimum AIC and minimum RMSE was selected. The main finding, in general, is that the two models WMA-ARIMA and EWMA-ARIMA, besides the cubic linear regression model have given better results for in-sample and out-of-sample forecasts than the classical ARIMA models in fitting the confirmed and recovery cases while the death cases havent specific models.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Hussein Eledum", + "author_inst": "University of Tabuk" + }, + { + "author_name": "Rahamtalla Yagoub", + "author_inst": "University of Tabuk" + } + ], + "version": "1", + "license": "cc0_ng", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.27.21257932", "rel_title": "COVID-19 testing among children, parental preferences for testing venues and acceptability of school-based testing: a survey of US parents", @@ -742203,33 +743555,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.05.27.21257938", - "rel_title": "Non-pharmaceutical interventions and the emergence of pathogen variants", - "rel_date": "2021-05-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.27.21257938", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWNon-pharmaceutical interventions (NPIs), such as social distancing and contact tracing, are important public health measures that can reduce pathogen transmission. In addition to playing a crucial role in suppressing transmission, NPIs influence pathogen evolution by mediating mutation supply, restricting the availability of susceptible hosts, and altering the strength of selection for novel variants. Yet it is unclear how NPIs might affect the emergence of novel variants that are able to escape pre-existing immunity (partially or fully), are more transmissible, or cause greater mortality. We analyse a stochastic two-strain epidemiological model to determine how the strength and timing of NPIs affects the emergence of variants with similar or contrasting life-history characteristics to the wildtype. We show that, while stronger and timelier NPIs generally reduce the likelihood of variant emergence, it is possible for more transmissible variants with high cross immunity to have a greater probability of emerging at intermediate levels of NPIs. This is because intermediate levels of NPIs allow an epidemic of the wildtype that is neither too small (facilitating high mutation supply), nor too large (leaving a large pool of susceptible hosts), to prevent a novel variant becoming established in the host population. However, since one cannot predict the characteristics of a variant, the best strategy to prevent emergence is likely to be implementation of strong, timely NPIs.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ben Ashby", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Cameron A Smith", - "author_inst": "University of Bath" - }, - { - "author_name": "Robin N Thompson", - "author_inst": "University of Warwick" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.28.21258006", "rel_title": "Fear, Anxiety, Stress, and Depression of novel coronavirus (COVID-19) pandemic among patients and their healthcare workers", @@ -742394,6 +743719,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.25.21257501", + "rel_title": "Multiplexed Detection of COVID-19 with Single-Molecule Technology", + "rel_date": "2021-05-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.25.21257501", + "rel_abs": "The COVID-19 pandemic raises the need for diverse diagnostic approaches to rapidly detect different stages of viral infection. The flexible and quantitative nature of single-molecule imaging technology renders it optimal for development of new diagnostic tools. Here we present a proof-of-concept for a single-molecule based, enzyme-free assay for detection of SARS-CoV-2. The unified platform we developed allows direct detection of the viral genetic material from patients samples, as well as their immune response consisting of IgG and IgM antibodies. Thus, it establishes a platform for diagnostics of COVID-19, which could also be adjusted to diagnose additional pathogens.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Noa Furth", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Shay Shilo", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Niv Cohen", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Nir Erez", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Vadim Fedyuk", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Alexander M. Schrager", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Adina Weinberger", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Amiel A. Dror", + "author_inst": "Galilee Medical Center" + }, + { + "author_name": "Asaf Zigron", + "author_inst": "Galilee Medical Center" + }, + { + "author_name": "Mona Shehadeh", + "author_inst": "Galilee Medical Center" + }, + { + "author_name": "Eyal Sela", + "author_inst": "Galilee Medical Center" + }, + { + "author_name": "Samer Srouji", + "author_inst": "Galilee Medical Center" + }, + { + "author_name": "Sharon Amit", + "author_inst": "Sheba medical center" + }, + { + "author_name": "Itzchak Levy", + "author_inst": "Sheba medical center" + }, + { + "author_name": "Eran Segal", + "author_inst": "Weizmann Institute" + }, + { + "author_name": "Rony Dahan", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Dan Jones", + "author_inst": "SeqLL" + }, + { + "author_name": "Danny Doueck", + "author_inst": "NIH Vaccine Research Center" + }, + { + "author_name": "Efrat Shema", + "author_inst": "Weizmann Institute of Science" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.24.21257581", "rel_title": "Covid-19 and Mental Health of Individuals with Different Personalities", @@ -744093,45 +745509,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.24.21257707", - "rel_title": "Does immune recognition of SARS-CoV2 epitopes vary between different ethnic groups?", - "rel_date": "2021-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.24.21257707", - "rel_abs": "The SARS-CoV2 mediated Covid-19 pandemic has impacted humankind at an unprecedented scale. While substantial research efforts have focused towards understand the mechanisms of viral infection and developing vaccines/ therapeutics, factors affecting the susceptibility to SARS-CoV2 infection and manifestation of Covid-19 remain less explored. Given that the Human Leukocyte Antigen (HLA) system is known to vary among ethnic populations, it is likely to affect the recognition of the virus, and in turn, the susceptibility to Covid-19. To understand this, we used bioinformatic tools to probe all SARS-CoV2 peptides which could elicit T-cell response in humans. We also tried to answer the intriguing question of whether these potential epitopes were equally immunogenic across ethnicities, by studying the distribution of HLA alleles among different populations and their share of cognate epitopes. We provide evidence that the newer mutations in SARS-CoV2 are unlikely to alter the T-cell mediated immunogenic responses among the studied ethnic populations. The work presented herein is expected to bolster our understanding of the pandemic, by providing insights into differential immunological response of ethnic populations to the virus as well as by gauging the possible effects of mutations in SARS-CoV2 on efficacy of potential epitope-based vaccines through evaluating [~]40000 viral genomes.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Tungadri Bose", - "author_inst": "Tata Consultancy Services Ltd." - }, - { - "author_name": "Namrata Pant", - "author_inst": "TCS Research, Tata Consultancy Services Ltd" - }, - { - "author_name": "Nishal Kumar Pinna", - "author_inst": "TCS Research, Tata Consultancy Services Ltd" - }, - { - "author_name": "Subhrajit Bhar", - "author_inst": "TCS Research, Tata Consultancy Services Ltd" - }, - { - "author_name": "Anirban Dutta", - "author_inst": "Tata Consultancy Services" - }, - { - "author_name": "Sharmila S Mande", - "author_inst": "Tata Consultancy Services Limited" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.24.21257703", "rel_title": "COVID-19 mass testing: harnessing the power of wastewater epidemiology", @@ -744456,6 +745833,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.24.21257729", + "rel_title": "Standardised, quantitative neutralisation responses to SARS-CoV-2 Variants of Concern by convalescent anti-sera from first wave infections of UK Health Care Workers and Patients", + "rel_date": "2021-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.24.21257729", + "rel_abs": "BackgroundThe rise of SARS-CoV-2 variants has made the pursuit to define correlates of protection more troublesome, despite the availability of the World Health Organisation (WHO) International Standard for anti-SARS-CoV-2 Immunoglobulin sera, a key reagent used to standardise laboratory findings into an international unitage.\n\nMethodsUsing pseudotyped virus, we examine the capacity of convalescent sera, from a well-defined cohort of healthcare workers (HCW) and Patients infected during the first wave from a national critical care centre in the UK to neutralise B.1.1.298, variants of interest (VOI) B.1.617.1 (Kappa), and four VOCs, B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) and B.1.617.2 (Delta), including the B.1.617.2 K417N, informally known as Delta Plus. We utilised the WHO International Standard for anti-SARS-CoV-2 Immunoglobulin to report neutralisation antibody levels in International Units per mL.\n\nFindingsOur data demonstrate a significant reduction in the ability of first wave convalescent sera to neutralise the VOCs. Patients and HCWs with more severe COVID-19 were found to have higher antibody titres and to neutralise the VOCs more effectively than individuals with milder symptoms. Using an estimated threshold for 50% protection, 54 IU/mL, we found most asymptomatic and mild cases did not produce titres above this threshold.\n\nInterpretationExpressing our data in IU/ml, we provide a benchmark pre-vaccine standardised dataset that compares disease severity with neutralising antibody titres. Our data may now be compared across multiple laboratories. The continued use and aggregation of standardised data will eventually assist in defining correlates of protection.\n\nFundingUKRI and NIHR; grant number G107217\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSDuring the first wave outbreak, much focus was placed on the role of neutralising antibodies and titres generated upon infection to ancestral SARS-CoV-2. Due to the large amounts of different assays used to elucidate the antibody-mediated immunity and laboratory to laboratory, large amounts of invaluable data could not be directly compared in order to define a correlate of protection, due to variability in the results. The WHO International Standard for anti-SARS-CoV-2 Immunoglobulin sera was made in order to standardise future data so that comparisons may take place.\n\nAdded value of this studyOur study compares the neutralisation capacity of sera from patients and healthcare workers (HCWs) from the ancestral strain of SARS-CoV-2 against new variants, including the current variants of concern in circulation. We also provide data in International Units per mL, a standardised unitage, for infected individuals that have a clinical severity score, allowing us to assess levels of neutralising antibodies across different severities of COVID-19 disease. By providing a method to calibrate most of the variants of concern so that the WHO International Standard for anti-SARS-CoV-2 Immunoglobulin reagent could be used to standardise our results, therefore making them comparable to other laboratories who also standardised their data in an identical manner.\n\nImplications of all the available evidenceContinual use and accumulation of standardised data would eventually lead to defining the correlates of protection against SARS-CoV-2. This could help to inform medical staff to identify which individuals would be a greater risk of a potential reinfection to SARS-CoV-2.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Diego Cantoni", + "author_inst": "University of Kent" + }, + { + "author_name": "Martin Mayora-Neto", + "author_inst": "University of Kent" + }, + { + "author_name": "Angalee Nadesalingam", + "author_inst": "University of Cambridge" + }, + { + "author_name": "David A. Wells", + "author_inst": "University of Cambridge" + }, + { + "author_name": "George W. Carnell", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Luis Ohlendorf", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Matteo Ferrari", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Phil Palmer", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Andrew Chan", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Peter Smith", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Emma M. Bentley", + "author_inst": "National Institute for Biological Standards and Control" + }, + { + "author_name": "Sebastian Einhauser", + "author_inst": "Institute of medical Microbiology and Hygiene, University of Regensburg" + }, + { + "author_name": "Ralf Wagner", + "author_inst": "Institute of Medical Microbiology and Hygiene" + }, + { + "author_name": "Mark Page", + "author_inst": "National Institute for Biological Standards and Control" + }, + { + "author_name": "Gianmarco Raddi", + "author_inst": "Royal Papworth Hospital NHS Foundation Trust" + }, + { + "author_name": "Helen Baxendale", + "author_inst": "Royal Papworth Hospital NHS Foundation Trust" + }, + { + "author_name": "Jonathan Heeney", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Nigel James Temperton", + "author_inst": "University of Kent" + }, + { + "author_name": "- Humoral Immune Correlates for COVID19 Consortium", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.24.21257705", "rel_title": "Emergence of a new SARS-CoV-2 variant from GR clade with a novel S glycoprotein mutation V1230L in West Bengal, India", @@ -745815,85 +747283,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.21.21257624", - "rel_title": "Monoclonal Antibody Treatment, Prophylaxis and Vaccines Combined to Reduce SARS CoV-2 Spread", - "rel_date": "2021-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.21.21257624", - "rel_abs": "BackgroundAntiviral monoclonal antibodies (mAbs) developed for treatment of COVID-19 reduce the magnitude and duration of viral shedding and can thus potentially contribute to reducing transmission of the causative virus, severe acute respiratory coronavirus 2 (SARS-CoV-2). However, use of these mAbs in combination with a vaccine program has not been considered in public health strategic planning.\n\nMethodsWe developed an agent-based model to characterize SARS-CoV-2 transmission in the US population during an aggressive phase of the pandemic (October 2020 to April 2021), and simulated the effects on infections and mortality of combining mAbs as treatment and post-exposure prophylaxis (PEP) with a vaccine program plus non-pharmaceutical interventions. We also interrogated the impact of rapid diagnostic testing, increased mAb supply, and vaccine rollout.\n\nFindingsAllocation of mAbs as PEP or targeting those [≥]65 years provided the greatest incremental benefits relative to vaccine in averting infections and deaths, by up to 17% and 41%, respectively. Rapid testing, facilitating earlier diagnosis and mAb use, amplified these benefits. The model was sensitive to mAb supply; doubling supply further reduced infections and mortality, by up to two-fold, relative to vaccine. mAbs continued to provide incremental benefits even as proportion of the vaccinated population increased.\n\nInterpretationUse of anti-viral mAbs as treatment and PEP in combination with a vaccination program would substantially reduce SARS-CoV-2 transmission and pandemic burden. These results may help guide resource allocation and patient management decisions for COVID-19 and can also be used to inform public health policy for current and future pandemic preparedness.\n\nFundingRegeneron Pharmaceuticals.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Mohamed A. Kamal", - "author_inst": "Regeneron Pharmaceuticals; Tarrytown, NY, USA" - }, - { - "author_name": "Andreas Kuznik", - "author_inst": "Regeneron Pharmaceuticals; Tarrytown, NY, USA" - }, - { - "author_name": "Luyuan Qi", - "author_inst": "Certara; Paris, France" - }, - { - "author_name": "Witold Wi\u0119cek", - "author_inst": "Certara; London, United Kingdom" - }, - { - "author_name": "Mohamed Hussein", - "author_inst": "Regeneron Pharmaceuticals; Tarrytown, NY, USA" - }, - { - "author_name": "Hazem E. Hassan", - "author_inst": "Regeneron Pharmaceuticals; Tarrytown, NY, USA" - }, - { - "author_name": "Kashyap Patel", - "author_inst": "Certara; Princeton, New Jersey, USA" - }, - { - "author_name": "Thomas Obadia", - "author_inst": "Certara; Paris, France" - }, - { - "author_name": "Masood Khaksar Toroghi", - "author_inst": "Regeneron Pharmaceuticals; Tarrytown, NY, USA" - }, - { - "author_name": "Daniela J. Conrado", - "author_inst": "Regeneron Pharmaceuticals; Tarrytown, NY, USA" - }, - { - "author_name": "Nidal Al-Huniti", - "author_inst": "Regeneron Pharmaceuticals; Tarrytown, NY, USA" - }, - { - "author_name": "Roman Casciano", - "author_inst": "Certara; Princeton, New Jersey, USA" - }, - { - "author_name": "Meagan P. O'Brien", - "author_inst": "Regeneron Pharmaceuticals; Tarrytown, NY, USA" - }, - { - "author_name": "Ruanne V. Barnabas", - "author_inst": "Department of Global Health, University of Washington; Seattle, Washington, USA" - }, - { - "author_name": "Myron S. Cohen", - "author_inst": "Institute for Global Health and Infectious Diseases, University of North Carolina; Chapel Hill, North Carolina, USA" - }, - { - "author_name": "Patrick F. Smith", - "author_inst": "Certara; Princeton, New Jersey, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.21.21257631", "rel_title": "Detecting COVID-19 Related Pneumonia on CT Scans using Hyperdimensional Computing", @@ -746014,6 +747403,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.22.21257643", + "rel_title": "A statistical model of COVID-19 testing in populations: effects of sampling bias and testing errors", + "rel_date": "2021-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.22.21257643", + "rel_abs": "We develop a statistical model for the testing of disease prevalence in a population. The model assumes a binary test result, positive or negative, but allows for biases in sample selection and both type I (false positive) and type II (false negative) testing errors. Our model also incorporates multiple test types and is able to distinguish between retesting and exclusion after testing. Our quantitative framework allows us to directly interpret testing results as a function of errors and biases. By applying our testing model to COVID-19 testing data and actual case data from specific jurisdictions, we are able to estimate and provide uncertainty quantification of indices that are crucial in a pandemic, such as disease prevalence and fatality ratios.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Lucas B\u00f6ttcher", + "author_inst": "Computational Social Science, Frankfurt School of Finance and Management, 60322 Frankfurt am Main, Germany" + }, + { + "author_name": "Maria R. D'Orsogna", + "author_inst": "Dept. of Mathematics, California State University at Northridge, Los Angeles, 91330-8313, CA, United States" + }, + { + "author_name": "Tom Chou", + "author_inst": "Dept. of Computational Medicine, University of California, Los Angeles, 90095-1766, Los Angeles, CA, United States" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.23.21257672", "rel_title": "Racial disparities in prevalence, determinants, and impacts of COVID-19 in pregnancy: Protocol for a study using data from New Jersey hospitals", @@ -747685,93 +749101,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.22.21257658", - "rel_title": "Effectiveness of COVID-19 vaccines against the B.1.617.2 variant", - "rel_date": "2021-05-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.22.21257658", - "rel_abs": "BackgroundThe B.1.617.2 COVID-19 variant has contributed to the surge in cases in India and has now been detected across the globe, including a notable increase in cases in the UK. We estimate the effectiveness of the BNT162b2 and ChAdOx1 COVID-19 vaccines against this variant.\n\nMethodsA test negative case control design was used to estimate the effectiveness of vaccination against symptomatic disease with both variants over the period that B.1.617.2 began circulating with cases identified based on sequencing and S-gene target status. Data on all symptomatic sequenced cases of COVID-19 in England was used to estimate the proportion of cases with B.1.617.2 compared to the predominant strain (B.1.1.7) by vaccination status.\n\nResultsEffectiveness was notably lower after 1 dose of vaccine with B.1.617.2 cases 33.5% (95%CI: 20.6 to 44.3) compared to B.1.1.7 cases 51.1% (95%CI: 47.3 to 54.7) with similar results for both vaccines. With BNT162b2 2 dose effectiveness reduced from 93.4% (95%CI: 90.4 to 95.5) with B.1.1.7 to 87.9% (95%CI: 78.2 to 93.2) with B.1.617.2. With ChAdOx1 2 dose effectiveness reduced from 66.1% (95% CI: 54.0 to 75.0) with B.1.1.7 to 59.8% (95%CI: 28.9 to 77.3) with B.1.617.2. Sequenced cases detected after 1 or 2 doses of vaccination had a higher odds of infection with B.1.617.2 compared to unvaccinated cases (OR 1.40; 95%CI: 1.13-1.75).\n\nConclusionsAfter 2 doses of either vaccine there were only modest differences in vaccine effectiveness with the B.1.617.2 variant. Absolute differences in vaccine effectiveness were more marked with dose 1. This would support maximising vaccine uptake with two doses among vulnerable groups.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Jamie Lopez Bernal", - "author_inst": "Public Health England" - }, - { - "author_name": "Nick Andrews", - "author_inst": "Public Health England" - }, - { - "author_name": "Charlotte Gower", - "author_inst": "Public Health England" - }, - { - "author_name": "Eileen Gallagher", - "author_inst": "Public Health England" - }, - { - "author_name": "Ruth Simmons", - "author_inst": "Public Health England" - }, - { - "author_name": "Simon Thelwall", - "author_inst": "Public Health England" - }, - { - "author_name": "Elise Tessier", - "author_inst": "Public Health England" - }, - { - "author_name": "Natalie Groves", - "author_inst": "Public Health England" - }, - { - "author_name": "Gavin Dabrera", - "author_inst": "Public Health England" - }, - { - "author_name": "Richard Myers", - "author_inst": "Public Health England" - }, - { - "author_name": "Colin Campbell", - "author_inst": "Public Health England" - }, - { - "author_name": "Gayatri Amirthalingam", - "author_inst": "Public Health England" - }, - { - "author_name": "Matt Edmunds", - "author_inst": "Public Health England" - }, - { - "author_name": "Maria Zambon", - "author_inst": "Public Health England" - }, - { - "author_name": "Kevin Brown", - "author_inst": "Public Health England" - }, - { - "author_name": "Susan Hopkins", - "author_inst": "Public Health England" - }, - { - "author_name": "Meera Chand", - "author_inst": "Public Health England" - }, - { - "author_name": "Mary Ramsay", - "author_inst": "Public Health England" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.22.21257649", "rel_title": "The COVID in the Context of Pregnancy, Infancy and Parenting (CoCoPIP) Study: protocol for a longitudinal study of parental mental health, social interactions, physical growth, and cognitive development of infants during the pandemic.", @@ -748104,6 +749433,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.21.445201", + "rel_title": "Evidence for Deleterious Original Antigenic Sin in SARS-CoV-2 Immune Response", + "rel_date": "2021-05-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.21.445201", + "rel_abs": "A previous report demonstrated the strong association between the presence of antibodies binding to an epitope region from SARS-CoV-2 nucleocapsid, termed Ep9, and COVID-19 disease severity. Patients with anti-Ep9 antibodies (Abs) had hallmarks of antigenic imprinting (AIM), including early IgG upregulation and cytokine-associated injury. Thus, the immunological memory of a previous infection was hypothesized to drive formation of suboptimal anti-Ep9 Abs in severe COVID-19 infections. This study identifies a putative primary antigen capable of stimulating production of cross-reactive, anti-Ep9 Abs. Binding assays with patient blood samples directly show cross-reactivity between Abs binding to Ep9 and only one bioinformatics-derived, homologous potential antigen, a sequence derived from the neuraminidase protein of H3N2 Influenza A virus. This cross-reactive binding is highly influenza strain specific and sensitive to even single amino acid changes in epitope sequence. The neuraminidase protein is not present in the influenza vaccine, and the anti-Ep9 Abs likely resulted from the widespread influenza infection in 2014. Therefore, AIM from a previous infection could underlie some cases of COVID-19 disease severity.\n\nImportanceInfections with SARS-COV-2 result in diverse disease outcomes, ranging from asymptomatic to fatal. The mechanisms underlying different disease outcomes remain largely unexplained. Previously, our laboratory identified a strong association between the presence of an antibody and increased disease severity in a subset of COVID-19 patients. Here, we report that this severity-associated antibody cross-reacts with viral proteins from an influenza A viral strain from 2014. Therefore, we speculate that antibodies generated against previous infections, like the 2014 influenza A, play a significant role in directing some peoples immune responses against SARS-COV-2. Such understanding of the sources and drivers of COVID-19 disease severity can help early identification and pre-emptive treatment.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Sanjana R Sen", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Emily C Sanders", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Alicia M Santos", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Keertna Bhuvan", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Derek Y Tang", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Aidan A Gelston", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Brian M Miller", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Joni L Ricks-Oddie", + "author_inst": "Univerisity of California, Irvine" + }, + { + "author_name": "Gregory A Weiss", + "author_inst": "University of California, Irvine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.05.24.445443", "rel_title": "Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core", @@ -749575,165 +750955,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.05.18.21257396", - "rel_title": "A Phenome-Wide Association Study of genes associated with COVID-19 severity reveals shared genetics with complex diseases in the Million Veteran Program", - "rel_date": "2021-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.18.21257396", - "rel_abs": "The study aims to determine the shared genetic architecture between COVID-19 severity with existing medical conditions using electronic health record (EHR) data. We conducted a Phenome-Wide Association Study (PheWAS) of genetic variants associated with critical illness (n=35) or hospitalization (n=42) due to severe COVID-19 using genome-wide association summary from the Host Genetics Initiative. PheWAS analysis was performed using genotype-phenotype data from the Veterans Affairs Million Veteran Program (MVP). Phenotypes were defined by International Classification of Diseases (ICD) codes mapped to clinically relevant groups using published PheWAS methods. Among 658,582 Veterans, variants associated with severe COVID-19 were tested for association across 1,559 phenotypes. Variants at the ABO locus (rs495828, rs505922) associated with the largest number of phenotypes (nrs495828= 53 and nrs505922=59); strongest association with venous embolism, odds ratio (ORrs495828 1.33 (p=1.32 x 10-199), and thrombosis ORrs505922 1.33, p=2.2 x10-265. Among 67 respiratory conditions tested, 11 had significant associations including MUC5B locus (rs35705950) with increased risk of idiopathic fibrosing alveolitis OR 2.83, p=4.12 x 10-191; CRHR1 (rs61667602) associated with reduced risk of pulmonary fibrosis, OR 0.84, p=2.26x 10-12. The TYK2 locus (rs11085727) associated with reduced risk for autoimmune conditions, e.g., psoriasis OR 0.88, p=6.48 x10-23, lupus OR 0.84, p=3.97 x 10-06. PheWAS stratified by genetic ancestry demonstrated differences in genotype-phenotype associations across ancestry. LMNA (rs581342) associated with neutropenia OR 1.29 p=4.1 x 10-13 among Veterans of African ancestry but not European. Overall, we observed a shared genetic architecture between COVID-19 severity and conditions related to underlying risk factors for severe and poor COVID-19 outcomes. Differing associations between genotype-phenotype across ancestries may inform heterogenous outcomes observed with COVID-19. Divergent associations between risk for severe COVID-19 with autoimmune inflammatory conditions both respiratory and non-respiratory highlights the shared pathways and fine balance of immune host response and autoimmunity and caution required when considering treatment targets.", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Anurag Verma", - "author_inst": "Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Ph" - }, - { - "author_name": "Noah L. Tsao", - "author_inst": "Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Phi" - }, - { - "author_name": "Lauren O. Thomann", - "author_inst": "VA Boston Healthcare System, Boston, Massachusetts, USA" - }, - { - "author_name": "Yuk-Lam Ho", - "author_inst": "Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA" - }, - { - "author_name": "Sudha K. Iyengar", - "author_inst": "Departments of Population and Quantitative Health Sciences, Ophthalmology and Visual Sciences and Genetics and Genome Sciences, Case Western Reserve University," - }, - { - "author_name": "Shiuh-Wen Luoh", - "author_inst": "VA Portland Health Care System, Portland OR, USA" - }, - { - "author_name": "Rotonya Carr", - "author_inst": "Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Ph" - }, - { - "author_name": "Dana C. Crawford", - "author_inst": "Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA" - }, - { - "author_name": "Jimmy T. Efird", - "author_inst": "Cooperative Studies Program Epidemiology Center, Health Services Research and Development, DVAHCS (Duke University Affiliate), Durham, North Carolina, USA." - }, - { - "author_name": "Giulio Genovese", - "author_inst": "Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA." - }, - { - "author_name": "Adriana Hung", - "author_inst": "Tennessee Valley Healthcare System (Nashville VA) , Nashville, Tennessee, USA" - }, - { - "author_name": "Kerry L. Ivey", - "author_inst": "Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA" - }, - { - "author_name": "Michael G. Levin", - "author_inst": "Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Julie Lynch", - "author_inst": "VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, Utah, USA." - }, - { - "author_name": "Pradeep Natarajan", - "author_inst": "Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA." - }, - { - "author_name": "Saiju Pyarajan", - "author_inst": "VA Boston Healthcare System, Boston, Massachusetts, USA;Harvard Medical School, Boston, Massachusetts, USA" - }, - { - "author_name": "Alexander Bick", - "author_inst": "VA Boston Healthcare System, Boston, Massachusetts, USA;Vanderbilt University, Nashville, Tennessee, USA" - }, - { - "author_name": "Lauren Costa", - "author_inst": "Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA" - }, - { - "author_name": "Giulio Genovese", - "author_inst": "Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA." - }, - { - "author_name": "Richard Hauger", - "author_inst": "Department of Psychiatry, University of California, San Diego, La Jolla, CA; Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, " - }, - { - "author_name": "Ravi Madduri", - "author_inst": "University of Chicago Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois, USA;Data Science and Learning Division, Arg" - }, - { - "author_name": "Gita A. Pathak", - "author_inst": "Department of Psychiatry, Yale School of Medicine, Connecticut, USA" - }, - { - "author_name": "Renato Polimanti", - "author_inst": "Department of Psychiatry, Yale School of Medicine, Connecticut, USA" - }, - { - "author_name": "Benjamin F. Voight", - "author_inst": "Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Ph" - }, - { - "author_name": "Marijana Vujkovic", - "author_inst": "Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Ph" - }, - { - "author_name": "Maryam Zekavat", - "author_inst": "VA Boston Healthcare System, Boston, Massachusetts, USA" - }, - { - "author_name": "Hongyu Zhao", - "author_inst": "VA Connecticut Healthcare System, West Haven, CT, USA" - }, - { - "author_name": "Marylyn Ritchie", - "author_inst": "Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Kyong-Mi Chang", - "author_inst": "Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA" - }, - { - "author_name": "Kelly Cho", - "author_inst": "Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA" - }, - { - "author_name": "Juan P Casas", - "author_inst": "Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA" - }, - { - "author_name": "Philip S Tsao", - "author_inst": "VA Palo Alto Health Care System, Palo Alto, California, USA" - }, - { - "author_name": "J. Michael Gaziano", - "author_inst": "Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA" - }, - { - "author_name": "Christopher O?Donnell", - "author_inst": "VA Boston Healthcare System, Boston, Massachusetts, USA" - }, - { - "author_name": "Scott M. Damrauer", - "author_inst": "Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Phi" - }, - { - "author_name": "Katherine P. Liao", - "author_inst": "VA Boston Healthcare System, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA; Brigham and Women's Hospital, Boston, Massachusetts" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.05.17.21257134", "rel_title": "Heterologous vaccination strategy for containing COVID-19 pandemic", @@ -750094,6 +751315,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, + { + "rel_doi": "10.1101/2021.05.21.21257211", + "rel_title": "Clinical, immunological and genomic characterization of asymptomatic and symptomatic cases with SARS-CoV-2 infection, India", + "rel_date": "2021-05-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.21.21257211", + "rel_abs": "BackgroundThe current global pandemic of Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2 led to the investigation with clinical, biochemical, immunological and genomic characterization from the patients to understand the pathophysiology of viral infection.\n\nMethodsSamples were collected from six asymptomatic and six symptomatic SARS-CoV-2 confirmed hospitalized patients in Bhubaneswar, Odisha, India. Clinical details, biochemical parameters, treatment regime were collected from hospital, viral load was determined by RT-PCR, levels of cytokines and circulating antibodies in plasma were assessed by Bioplex and isotyping respectively. In addition, the whole genome sequencing of viral strains and mutational analysis were carried out.\n\nFindingsAnalysis of the biochemical parameters highlighted the increased levels of C-Reactive protein (CRP), lactate dehydrogenase (LDH), serum SGPT, serum SGOT and ferritin in symptomatic patients indicating that patients with higher levels of few biochemical parameters might experience severe pathophysiological complications after SARS-CoV-2 infection. This was also observed that symptomatic patients were mostly with one or more comorbidities, especially diabetes (66.6%). Surprisingly the virological estimation revealed that there was no significant difference in viral load of oropharyngeal (OP) samples between the two groups. This suggests that the viral load in OP sample does not correlate with the disease severity and both asymptomatic and symptomatic patients are equally capable of transmitting the virus. Whereas, viral load was higher in plasma and serum samples of symptomatic patients suggesting that the development of clinical complications is mostly associated to high viral load in plasma and serum. This also demonstrated that the patients with high viral load in plasma and serum samples were found to develop sufficient amounts of antibodies (IgG, IgM and IgA). Interestingly, the levels of 7 cytokines (IL-6, IL-.1, IP-10, IL-8, IL-10, IFN-2, IL-15) were found to be highly elevated in symptomatic patients, while three cytokines (soluble CD40L, GRO and MDC) were remarkably higher in asymptomatic patients. Therefore, this data suggest that cytokines and chemokines may serve as \"predictive indicator\" of SARS-CoV-2 infection and contribute to understand the pathogenesis of COVID-19. The whole genome sequence analysis revealed that the current isolates were clustered with 19B, 20A and 20B clades, however acquired 11 additional changes in Orf1ab, spike, Orf3a, Orf8 and nucleocapsid proteins. The data also confirmed that the D614G mutation in spike protein is mostly linked with higher virus replication efficiency and severe SARS-CoV-2 infection as three patients had higher viral load and among them two patients with this mutation passed away.\n\nInterpretationThis is the first comprehensive study of SARS CoV-2 patients from India. This will contribute to a better understanding of the pathophysiology of SARS-CoV-2 infection and advance in the implementation of effective disease control strategies.\n\nFundingThis study was supported by the core funding of Institute of Life Sciences, Bhubaneswar, Dept of Biotechnology, India.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSAsymptomatic patients are a source of concern as measures taken to control the spread of the virus are severely impacted by their undetectability. Presently, there is an inadequate information about the characteristics of the asymptomatic and symptomatic patients. The association between SARS-CoV-2 viral load, cytokines and risk of disease progression remains unclear in COVID-19 in Indian scenario. PubMed was searched for articles published up to May, 2021, using the keywords \"SARS CoV-2 patients in India\", or \"2019 novel coronavirus patients in India\". No published work about the patients data on SARS CoV-2 in Indian scenario could be identified.\n\nAdded value of this studyThis investigation highlights the ability of both asymptomatic and symptomatic patients to transmit the virus equally. This study also demonstrates that the D614G mutation in the spike protein is associated with severe SARS-CoV-2 infection and enhance levels of inflammatory markers such as CRP and ferritin which can be predictive biomarkers for critical condition of patients. This is the first comprehensive study of SARS CoV-2 patients from India and will contribute to a better understanding of the pathophysiology of SARS-CoV-2 infection by advancing the implementation of effective disease control strategies.\n\nImplications of all the available evidenceThe current global pandemic of Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2 led to the investigation with clinical, biochemical, immunological and viral genome sequencing to understand the pathophysiology of this virus infection. Samples were collected from six asymptomatic and six symptomatic SARS-CoV-2 confirmed hospitalized patients in Bhubaneswar, Odisha, India. This investigation highlights the ability of both asymptomatic and symptomatic patients to transmit the virus equally. This also demonstrated that the D614G mutation is mostly associated with higher virus replication capacity and severe SARS-CoV-2 infection and enhanced levels of inflammatory markers such as CRP and ferritin which are associated with critical conditions of patients. This is the first comprehensive study of SARS CoV-2 patients from India and will contribute to a better understanding of the pathophysiology of SARS-CoV-2 infection by advancing the implementation of competent disease control strategies.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Sanchari Chatterjee", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Ankita Datey", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Soumya Sengupta", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Arup Ghosh", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Atimukta Jha", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Safal Walia", + "author_inst": "Institute Of Life Sciences" + }, + { + "author_name": "Sharad Singh", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Sandhya Suranjika", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Gargee Bhattacharya", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Eshna Laha", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Supriya Suman Keshry", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Amrita Ray", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Sweta Smita Pani", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Amol Suryawanshi", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Rupesh Dash", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Shantibhusan Senapati", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Tushar K. Beuria", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Gulam Hussain Syed", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Punit Prasad", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Sunil Raghav", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Satish Devadas", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Rajeeb Swain", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Soma Chattopadhyay", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Ajay Parida", + "author_inst": "Institute of Life Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.21.21257575", "rel_title": "Measurement of multiple SARS-CoV-2 antibody titer after vaccination represents individual vaccine response and contributes to individually appropriate vaccination schedules", @@ -751733,45 +753065,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.20.21257523", - "rel_title": "Performance of the TaqMan COVID-19 Pooling Kit for detection of SARS-CoV-2 in Asymptomatic and Symptomatic populations at an Institution of Higher Education", - "rel_date": "2021-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21257523", - "rel_abs": "Clinical evidence for asymptomatic cases of coronavirus disease (COVID-19) has reinforced the significance of effective surveillance testing programs. Quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assays are considered the gold standard for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. However, the labor and resource requirements can be prohibitive with respect to large testing volumes associated with the pandemic. Pooled testing algorithms may serve to increase testing capacity with more efficient resource utilization. Due to the lack of carefully curated cohorts, there is limited evidence for the applicability of RT-PCR pooling in asymptomatic COVID-19 cases. In this study, we compared the analytical sensitivity of the TaqMan SARS-CoV-2 Pooling Assay to detect one positive sample in a pool of five anterior nare swabs in symptomatic and asymptomatic cohorts at an institute of higher education. Positive pools were deconvoluted and each individual sample was retested using the TaqPath COVID-19 Combo Kit. Both assays target the open reading frame (ORF) 1ab, nucleocapsid (N), and spike (S) gene of the strain that originated in Wuhan, Hubei, China. Qualitative results demonstrated absolute agreement between pooled and deconvoluted samples in both cohorts. Independent t-test performed on Ct shifts confirmed an insignificant difference between cohorts with p-values of 0.306 (Orf1ab), 0.147 (N), and 0.052 (S). All negative pools were correctly reported as negative. Thus, pooled PCR testing up to five samples is a valid method for surveillance testing of students and staff in a university setting, especially when the prevalence is expected to be low.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Troy Ganz", - "author_inst": "northeastern university" - }, - { - "author_name": "Sarah Sanderson", - "author_inst": "northeastern university" - }, - { - "author_name": "Connor Baush", - "author_inst": "northeastern university" - }, - { - "author_name": "Melanie Mejia", - "author_inst": "northeastern university" - }, - { - "author_name": "Manoj Gandhi", - "author_inst": "Thermo Fisher Scientific" - }, - { - "author_name": "Jared Auclair", - "author_inst": "Northeastern University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.19.21257470", "rel_title": "RT-qPCR half reaction optimization for the detection of SARS-CoV-2", @@ -751992,6 +753285,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.19.21257429", + "rel_title": "Efficacy of Sofosbuvir plus Ledipasvir in Egyptian patients with COVID-19 compared to standard treatment: Randomized controlled trial", + "rel_date": "2021-05-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.19.21257429", + "rel_abs": "BackgroundCOVID-19 is a pandemic disease caused by SARS-CoV-2, which is an RNA virus similar to HCV in the replication process. Sofosbuvir/ledipasvir is an approved drug by the FDA to treat HCV infection. This study investigates the efficacy of Sofosbuvir/ledipasvir as a treatment for patients with moderate COVID-19 infection..\n\nMethodsThis is a single-blinded parallel-randomized controlled trial. The participants were randomized equally into the intervention group received Sofosbuvir/ledipasvir (S.L. group), and the control group received Oseltamivir, Hydroxychloroquine, and Azithromycin (OCH group). The primary outcomes were the cure rate over time and the incidence of serious adverse events. The secondary outcomes included the laboratory findings.\n\nResultsTwo hundred and fifty patients were divided equally into each group. Both groups were similar regarding gender, but age was higher in the S.L. group (p=0.001). In the S.L. group, 89 (71.2%) patients were cured, while only 51 (40.8%) patients were cured in the OCH group. The cure rate was significantly higher in the S.L. group (RR=1.75, p<0.001). Kaplan-Meir plot showed a considerably higher cure over time in the S.L. group (Log-rank test, p=0.032). There were no deaths in the S.L. group, but there were six deaths (4.8%) in the OCH group (RR=0.08, p=0.013). Seven patients (5.6%) in the S.L. group and six patients (4.8%) in the OCH group were admitted to ICU (RR=1.17, P=0.776). There was no significant difference between treatment groups regarding Total Leukocyte Count, Neutrophils count, Lymph and Urea.\n\nConclusionSofosbuvir/ledipasvir is suggestive of being effective in treating patients with moderate COVID-19 infection. Further studies are needed to compare Sofosbuvir/ledipasvir with the new treatment protocols.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Mohamed Abdel-Salam Elgohary", + "author_inst": "Almaza Fever Hospital, Cairo, Egypt" + }, + { + "author_name": "Eman Medhat Hasan", + "author_inst": "Faculty of Medicine, Cairo University" + }, + { + "author_name": "Amany Ahmad Ibrahim", + "author_inst": "Faculty of Medicine, Ain Shams University" + }, + { + "author_name": "Mohamed Farouk Ahmed", + "author_inst": "4Al Galaa Military Medical Complex (GMMC), Cairo, Egypt" + }, + { + "author_name": "Raafat Zaher Abdel-Rahman", + "author_inst": "Central Military Laboratories, Cairo, Egypt" + }, + { + "author_name": "Ashraf Ibrahim Zaki", + "author_inst": "Almaza Fever Hospital, Cairo, Egypt" + }, + { + "author_name": "Mohamed Bakr Elaatar", + "author_inst": "Almaza Fever Hospital, Cairo, Egypt" + }, + { + "author_name": "Mohamed Thabet Elnagar", + "author_inst": "Almaza Fever Hospital, Cairo, Egypt" + }, + { + "author_name": "Mohamed Emam Emam", + "author_inst": "Almaza Fever Hospital, Cairo, Egypt" + }, + { + "author_name": "Mahmoud Moustafa Hamada", + "author_inst": "Almaza Fever Hospital, Cairo, Egypt" + }, + { + "author_name": "Taimour Mohamed Abdel-Hamid", + "author_inst": "Almaza Fever Hospital, Cairo, Egypt" + }, + { + "author_name": "Ahmad Samir Abdel-Hafez", + "author_inst": "Almaza Fever Hospital, Cairo, Egypt" + }, + { + "author_name": "Mohamed G. Seadawy", + "author_inst": "Main Chemical Laboratories, Egypt Army" + }, + { + "author_name": "Ahmad Rashad Fatoh", + "author_inst": "Almaza Fever Hospital, Cairo, Egypt" + }, + { + "author_name": "Mohamed Ali Elsaied", + "author_inst": "Almaza Fever Hospital, Cairo, Egypt" + }, + { + "author_name": "Marwa Abdel-Rahman Sakr", + "author_inst": "Almaza Fever Hospital, Cairo, Egypt" + }, + { + "author_name": "Ahmed Omar Elkady", + "author_inst": "Almaza Fever Hospital, Cairo, Egypt" + }, + { + "author_name": "Mohamed Muawad Shehata", + "author_inst": "Almaza Fever Hospital, Cairo, Egypt" + }, + { + "author_name": "Osama Mohamed Nawar", + "author_inst": "Almaza Fever Hospital, Cairo, Egypt" + }, + { + "author_name": "Mohamed Abu-elnaga Selem", + "author_inst": "Almaza Fever Hospital, Cairo, Egypt" + }, + { + "author_name": "Mohamed Saeed Abd-aal", + "author_inst": "Almaza Fever Hospital, Cairo, Egypt" + }, + { + "author_name": "Hany Hafez Lotfy", + "author_inst": "Military Medical Academy, Cairo, Egypt" + }, + { + "author_name": "Tarek Refaat Elnagdy", + "author_inst": "Egyptian Military Medical Services, Logistic support" + }, + { + "author_name": "Sherine Helmy", + "author_inst": "PHARCO Pharmaceuticals, Alexanderia,Egypt" + }, + { + "author_name": "Magdy Amin Mubark", + "author_inst": "Egyptian Military Medical Services, Logistic support" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.20.21257557", "rel_title": "Early Detection of COVID-19 Outbreaks Using Human Mobility Data", @@ -753307,29 +754715,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2021.05.18.21257416", - "rel_title": "Integrating health behavior theories to predict COVID-19 vaccine acceptance: differences between medical students and nursing students in Israel", - "rel_date": "2021-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.18.21257416", - "rel_abs": "BackgroundThis study aimed to explore behavioral-related factors predicting the intention of getting a COVID-19 vaccine among medical and nursing students using an integrative model combining the Health Belief Model (HBM) and the Theory of Planned Behavior (TPB).\n\nMethodsA cross-sectional online survey was conducted among medical and nursing students aged > 18 years in their clinical years in Israel between 27 August and 28 September 2020. Hierarchical logistic regression was used to predict acceptance of a COVID-19 vaccine.\n\nResultsA total number of 628 participants completed the survey. Medical students expressed higher intentions of getting vaccinated against COVID-19 than nursing students (88.1% vs. 76.2%, p < 0.01). The integrated model based on HBM and TPB was able to explain 66% of the variance (adjusted R2 = 0.66). Participants were more likely to be willing to get vaccinated if they reported higher levels of perceived susceptibility, benefits, barriers, cues to action, attitude, self-efficacy and anticipated regret. Two interaction effects revealed that male nurses had a higher intention of getting vaccinated than did female nurses and that susceptibility is a predictor of the intention of getting vaccinated only among nurses.\n\nConclusionsThis study demonstrates that both models considered (i.e., HBM and TPB) are important for predicting the intention of getting a COVID-19 vaccine among medical and nursing students, and can help better guide intervention programs, based on components from both models. Our findings also highlight the importance of paying attention to a targeted group of female nurses, who expressed low vaccine acceptance.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Hila Rosental", - "author_inst": "Bar-Ilan University" - }, - { - "author_name": "Liora Shmueli", - "author_inst": "Bar-Ilan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.05.18.21257426", "rel_title": "Modeling waning and boosting of COVID-19 in Canada with vaccination", @@ -753470,6 +754855,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.18.21257423", + "rel_title": "Telecommuting intensity among Japanese workers according to regional cumulative COVID-19 incidence: a cross-sectional study", + "rel_date": "2021-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.18.21257423", + "rel_abs": "This study aimed to examine the relationship between telecommuting and the regional cumulative COVID-19 incidence. This was a cross-sectional study analyzing 13,468 office workers. The participant groups, according to the level of cumulative COVID-19 incidence by prefecture, were used as the predictor variable, and telecommuting frequency and preference were used as outcomes. We employed an ordinal logistic regression analysis. In regions with a high cumulative COVID-19 incidence, the proportion of participants who telecommuted more than two days per week was 34.7%, which was approximately 20% higher than in other regions. Telecommuting preference was stronger in areas with higher COVID-19 influence. However, in other regions, the proportion of participants who did not want to telecommute was higher than that of those who wanted to telecommute. We found that telecommuting frequency and preference were higher in regions with high cumulative COVID-19 incidence.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Hiroka Baba", + "author_inst": "Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Kazunori Ikegami", + "author_inst": "Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Hajime Ando", + "author_inst": "Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health" + }, + { + "author_name": "Hisahi Eguchi", + "author_inst": "Institute of Industrial Ecological Sciences University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Mayumi Tsuji", + "author_inst": "School of Medicine, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Seiichiro Tateishi", + "author_inst": "School of Medicine, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Masako Nagata", + "author_inst": "Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Shinya Matsuda", + "author_inst": "School of Medicine, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Yoshihisa Fujino", + "author_inst": "Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.05.19.21257430", "rel_title": "CovidMulti-Net: A Parallel-Dilated Multi Scale Feature Fusion Architecture for the Identification of COVID-19 Cases from Chest X-ray Images", @@ -755353,33 +756789,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.18.444723", - "rel_title": "The effect of SARS-COV-2 Infections on Amyloid Formation of Serum Amyloid A", - "rel_date": "2021-05-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.18.444723", - "rel_abs": "A marker for the severeness and disease progress of COVID-19 is overexpression of serum amyloid A (SAA) to levels that in other diseases are associated with a risk for SAA amyloidosis. In order to understand whether SAA amyloidosis could also be a long-term risk of SARS-COV-2 infections we have used long all-atom molecular dynamic simulations to study the effect of a SARS-COV-2 protein segment on SAA amyloid formation. Sampling over 40 {micro}s we find that presence of the nine-residue segment SK9, located at the C-terminus of the Envelope protein, increases the propensity for SAA fibril formation by three mechanisms: it reduces the stability of the lipid-transporting hexamer shifting the equilibrium toward monomers, it increases the frequency of aggregation-prone configurations in the resulting chains, and it raises the stability of SAA fibrils. Our results therefore suggest that SAA amyloidosis and related pathologies may be a long-term risk of SARS-COV-2 infections.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Asis K Jana", - "author_inst": "Dept. of Chemistry and Biochemistry, University of Oklahoma" - }, - { - "author_name": "Augustus B. Greenwood", - "author_inst": "Departement of Chemistry and Biochemistry, University of Oklahoma" - }, - { - "author_name": "Ulrich H.E. Hansmann", - "author_inst": "University of Oklahoma" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.05.19.444569", "rel_title": "Spatially distributed infection increases viral load in a computational model of SARS-CoV-2 lung infection", @@ -755620,6 +757029,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nursing" }, + { + "rel_doi": "10.1101/2021.05.19.444774", + "rel_title": "Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution", + "rel_date": "2021-05-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.19.444774", + "rel_abs": "Background and objectivesTo understand how organisms evolve, it is fundamental to study how mutations emerge and establish. Here, we estimated the rate of mutation accumulation of SARS-CoV-2 in vitro and investigated the repeatability of its evolution when facing a new cell type but no immune or drug pressures.\n\nMethodologyWe performed experimental evolution with two strains of SARS-CoV-2, one carrying the originally described spike protein (CoV-2-D) and another carrying the D614G mutation that has spread worldwide (CoV-2-G). After 15 passages in Vero cells and whole genome sequencing, we characterized the spectrum and rate of the emerging mutations and looked for evidences of selection across the genomes of both strains.\n\nResultsFrom the mutations accumulated, and excluding the genes with signals of selection, we estimate a spontaneous mutation rate of 1.25x10-6 nt-1 per infection cycle for both lineages of SARS-CoV-2. We further show that mutation accumulation is heterogeneous along the genome, with the spike gene accumulating mutations at rate five-fold higher than the genomic average. We also observe the emergence of mutators in the CoV-2-G background, likely linked to mutations in the RNA-dependent RNA polymerase and/or in the error-correcting exonuclease protein.\n\nConclusions and implicationsThese results provide valuable information on how spontaneous mutations emerge in SARS-CoV-2 and on how selection can shape its genome towards adaptation to new environments.\n\nLay summaryMutation is the ultimate source of variation. We estimated how the SARS-COV-2 virus--cause of the COVID-19 pandemic--mutates. Upon infecting cells, its genome can change at a rate of 0.04 per replication. We also find that this rate can change and that its spike protein can adapt, even within few replications.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Massimo Amicone", + "author_inst": "Instituto Gulbenkian de Ciencia" + }, + { + "author_name": "Vitor Borges", + "author_inst": "National Institute of Health, Portugaal" + }, + { + "author_name": "Maria Joao Alves", + "author_inst": "Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Aguas de Moura, Portugal" + }, + { + "author_name": "Joana Isidro", + "author_inst": "Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal." + }, + { + "author_name": "Libia Ze-Ze", + "author_inst": "National Institute of Health Dr Ricardo Jorge, Centre for Vectors and Infectious Diseases Research" + }, + { + "author_name": "Silvia Duarte", + "author_inst": "Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal." + }, + { + "author_name": "Luis Vieira", + "author_inst": "Instituto Nacional de Saude" + }, + { + "author_name": "Raquel Guiomar", + "author_inst": "National Reference Laboratory for Influenza and other Respiratory Viruses, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge " + }, + { + "author_name": "Joao P Gomes", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Isabel Gordo", + "author_inst": "Instituto Gulbenkian de Ciencia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2021.05.18.21256801", "rel_title": "Evaluation of the Family Liaison Officer (FLO) role during the COVID-19 Pandemic", @@ -758631,57 +760095,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.13.21257152", - "rel_title": "Distinct Mucoinflammatory Phenotype and the Immunomodulatory Long Noncoding Transcripts Associated with SARS-CoV-2 Airway Infection", - "rel_date": "2021-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.13.21257152", - "rel_abs": "Respiratory epithelial cells are the primary target for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We investigated the 3D human airway tissue model to evaluate innate epithelial cell responses to SARS-CoV-2 infection. A SARS-CoV-2 clinical isolate productively infected the 3D-airway model with a time-dependent increase in viral load (VL) and concurrent upregulation of airway immunomodulatory factors (IL-6, ICAM-1, and SCGB1A1) and respiratory mucins (MUC5AC, MUC5B, MUC2, and MUC4), and differential modulation of select long noncoding RNAs (lncRNAs i.e., LASI, TOSL, NEAT1, and MALAT1). Next, we examined these immunomodulators in the COVID-19 patient nasopharyngeal swab samples collected from subjects with high- or low-VLs ([~]100-fold difference). As compared to low-VL, high-VL patients had prominent mucoinflammatory signature with elevated expression of IL-6, ICAM-1, SCGB1A1, SPDEF, MUC5AC, MUC5B, and MUC4. Interestingly, LASI, TOSL, and NEAT1 lncRNA expressions were also markedly elevated in high-VL patients with no change in MALAT1 expression. In addition, dual-staining of LASI and SARS-CoV-2 nucleocapsid N1 RNA showed predominantly nuclear/perinuclear localization at 24 hpi in 3D-airway model as well as in high-VL COVID-19 patient nasopharyngeal cells, which exhibited high MUC5AC immunopositivity. Collectively, these findings suggest SARS-CoV-2 induced lncRNAs may play a role in acute mucoinflammatory response observed in symptomatic COVID-19 patients.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Dinesh Devadoss", - "author_inst": "Florida International University" - }, - { - "author_name": "Arpan Acharya", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Marko Manevski", - "author_inst": "Florida International University" - }, - { - "author_name": "Kabita Pandey", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Glen M Borchert", - "author_inst": "University of South Alabama" - }, - { - "author_name": "Madhavan Nair", - "author_inst": "Florida International University" - }, - { - "author_name": "Mehdi S Mirsaeidi", - "author_inst": "University of Miami" - }, - { - "author_name": "Siddappa N Byrareddy", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Hitendra S Chand", - "author_inst": "Florida International University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.15.21257254", "rel_title": "Inhibitor screening of Spike variants reveals the heterogeneity of neutralizing antibodies to COVID-19 infection and vaccination", @@ -758946,6 +760359,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.14.21257218", + "rel_title": "Effectiveness of BNT162b2 mRNA vaccine and ChAdOx1 adenovirus vector vaccine on mortality following COVID-19", + "rel_date": "2021-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.14.21257218", + "rel_abs": "We estimated risk of death in vaccinated compared to unvaccinated COVID-19 cases. Cases vaccinated with 1 dose of BNT162b2 had 44% reduced risk of death, 55% with 1 dose of ChAdOx1, and 69% with 2 doses of BNT162b2. This is on top of the protection provided against becoming a case.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jamie Lopez Bernal", + "author_inst": "Public Health England" + }, + { + "author_name": "Nick Andrews", + "author_inst": "Public Health England" + }, + { + "author_name": "Charlotte Gower", + "author_inst": "Public Health England" + }, + { + "author_name": "Julia Stowe", + "author_inst": "Public Health England" + }, + { + "author_name": "Elise Tessier", + "author_inst": "Public Health England" + }, + { + "author_name": "Ruth Simmons", + "author_inst": "Public Health England" + }, + { + "author_name": "Mary Ramsay", + "author_inst": "Public Health England" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.14.21257247", "rel_title": "Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations", @@ -760469,85 +761925,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.05.18.21256128", - "rel_title": "Phylogenomics and population genomics of SARS-CoV-2 in Mexico reveals variants of interest (VOI) and a mutation in the Nucleocapsid protein associated with symptomatic versus asymptomatic carriers", - "rel_date": "2021-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.18.21256128", - "rel_abs": "Understanding the evolution of SARS-CoV-2 virus in various regions of the world during the Covid19 pandemic is essential to help mitigate the effects of this devastating disease. We describe the phylogenomic and population genetic patterns of the virus in Mexico during the pre-vaccination stage, including asymptomatic carriers. A RT-qPCR screening and phylogenomics reconstructions directed a sequence/structure analysis of the Spike glycoprotein, revealing mutation of concern E484K in genomes from central Mexico, in addition to the nationwide prevalence of the imported variant 20C/S:452R (B.1.427/9). Overall, the detected variants in Mexico show Spike protein mutations in the N-terminal domain (i.e., R190M), in the receptor-binding motif (i.e., T478K, E484K), within the S1-S2 subdomains (i.e., P681R/H, T732A), and at the basis of the protein, V1176F, raising concerns about the lack of phenotypic and clinical data available for the variants of interest (VOI) we postulate: 20B/478K.V1 (B.1.1.222 or B.1.1.519) and 20B/P.4 (B.1.1.28.4). Moreover, the population patterns of Single Nucleotide Variants (SNVs) from symptomatic and asymptomatic carriers obtained with a self-sampling scheme confirmed the presence of several fixed variants, and differences in allelic frequencies among localities. We identified the mutation N:S194L of the Nucleocapsid protein associated with symptomatic patients. Phylogenetically, this mutation is frequent in Mexican sub-clades, so we propose an additional VOI, 20A/N:194L.V2 (B.1.243). Our results highlight the dual and complementary role of Spike and Nucleocapsid proteins in adaptive evolution of SARS-CoV-2 to their hosts and provide a baseline for specific follow-up of mutations of concern during the vaccination stage.\n\nIMPACT STATEMENTFollowing self-sampling, screening of mutations of concern, and a combined phylogenomic and population genetics pipeline, we reveal the appearance of three VOI with mutations in the Spike protein, P.4 (B.1.1.28.4) and 20B/478K.V1 (B.1.1.222, leading to B.1.1.519), and in the Nucleocapsid protein, 20A/N:194L.V2 (B.1.243), in Mexico during the pre-vaccination stage. The mutation S194L in the Nucleocapsid was found to associate with symptomatic patients versus asymptomatic carriers in the population investigated. Our research can aid epidemiological genomics efforts during the vaccination stage in Mexico by contributing with a combined analytical platform and information about variants within different genetic lineages with the potential to evolve into variants of concern (VOC).", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Francisco Barona-Gomez", - "author_inst": "Unidad de Genomica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico." - }, - { - "author_name": "Luis Delaye", - "author_inst": "Departamento de Ingenieria Genetica, Unidad Irapuato, Cinvestav-IPN, Irapuato, Guanajuato, Mexico." - }, - { - "author_name": "Erik Diaz-Valenzuela", - "author_inst": "Unidad de Genomica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico." - }, - { - "author_name": "Fabien Plisson", - "author_inst": "Conacyt - Unidad de Genomica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico." - }, - { - "author_name": "Arely Cruz-Perez", - "author_inst": "Unidad de Genomica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico." - }, - { - "author_name": "Mauricio Diaz-Sanchez", - "author_inst": "Molecular Biology Research & Development Department, GrupoT4, Irapuato, Guanajuato, Mexico." - }, - { - "author_name": "Christian A Garcia-Sepulveda", - "author_inst": "Facultad de Medicina, Universidad Autonoma de San Luis Potosi, San Luis Potosi, Mexico." - }, - { - "author_name": "Alejandro Sanchez-Flores", - "author_inst": "Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico." - }, - { - "author_name": "Rafael Perez-Abreu", - "author_inst": "Centro de Investigacion en Matematicas AC (CIMAT), Sede Aguascalientes, Aguascalientes, Mexico." - }, - { - "author_name": "Francisco J Valencia-Valdespino", - "author_inst": "Prothesia, Monterrey, Nuevo Leon, Mexico." - }, - { - "author_name": "Alejandra Natali Vega-Magana", - "author_inst": "Laboratory for the Diagnosis of Emerging and Reemerging Diseases (LaDEER), University Center for Health Sciences, University of Guadalajara, Guadalajara, Jalisc" - }, - { - "author_name": "J. Francisco Munoz-Valle", - "author_inst": "Institute for Research in Biomedical Sciences, University Center for Health Sciences, University of Guadalajara, Guadalajara, Jalisco, Mexico." - }, - { - "author_name": "Octavio P Garcia-Gonzalez", - "author_inst": "Molecular Biology Research & Development Department, GrupoT4, Irapuato, Guanajuato, Mexico." - }, - { - "author_name": "Sofia Bernal-Silva", - "author_inst": "Centro de Investigacion en Ciencias de la Salud y Biomedicina, Universidad Autonoma de San Luis Potosi, San Luis Potosi, Mexico." - }, - { - "author_name": "Andreu Comas-Garcia", - "author_inst": "Centro de Investigacion en Ciencias de la Salud y Biomedicina, Universidad Autonoma de San Luis Potosi, San Luis Potosi, Mexico." - }, - { - "author_name": "Angelica Cibrian Jaramillo", - "author_inst": "Unidad de Genomica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.05.18.21257259", "rel_title": "SARS-CoV-2 Vaccine-Induced Antibody Response and Reinfection in Persons with Past Natural Infection", @@ -760732,6 +762109,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.17.21257092", + "rel_title": "Public attitudes to COVID-19 vaccines: A qualitative study", + "rel_date": "2021-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.17.21257092", + "rel_abs": "OBJECTIVETo explore public attitudes to COVID-19 vaccines in the UK, focused on intentions and decisions around taking vaccines, views on vaccine passports, and experiences and perspectives on post-vaccination behavior.\n\nDESIGNQualitative study consisting of 6 online focus groups conducted between 15th March - 22nd April 2021.\n\nSETTINGOnline video conferencing\n\nPARTICIPANTS29 adult UK-based participants\n\nRESULTSThree main groups regarding participants decision or intention to receive a COVID-19 vaccine were identified: (1) Accepters, (2) Delayers and (3) Refusers. Two reasons for vaccine delay were identified: delay due to a perceived need more information and delay until vaccine was \"required\" in the future. Three main facilitators (Vaccination as a social norm; Vaccination as a necessity; Trust in science) and six barriers (Preference for \"natural immunity\"; Concerns over possible side effects; Distrust in government; Perceived lack of information; Conspiracy theories; \"Covid echo chambers\") to vaccine uptake were identified. For some delayers, vaccine passports were perceived to be a reason why they would get vaccinated in the future. However, vaccine passports were controversial, and were framed in three main ways: as \"a necessary evil\"; as \"Orwellian\"; and as a \"human rights problem\". Participants generally felt that receiving a vaccine was not changing the extent to which people were adhering to COVID-19 measures.\n\nCONCLUSIONSOverall, positive sentiment toward vaccines was high. However, there remains a number of potential barriers which might be leading to vaccine delay in some. Vaccine delay might be a more useful and precise construct than vaccine hesitancy in explaining why some may initially ignore or be uncertain about vaccination invitations. Vaccine passports may increase or nudge uptake in some delayers but remain controversial. Earlier concerns that vaccination might reduce adherence to social distancing measures are not borne out in our data, with most people reporting ongoing adherence and caution.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Simon N Williams", + "author_inst": "Swansea University" + }, + { + "author_name": "Kimberly A Dienes", + "author_inst": "Swansea University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.05.17.21257337", "rel_title": "Pregnancy and birth outcomes after SARS-CoV-2 vaccination in pregnancy", @@ -762211,81 +763611,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.17.21257223", - "rel_title": "Serial interval of COVID-19 and the effect of Variant B.1.1.7: analyses from a prospective community cohort study (Virus Watch).", - "rel_date": "2021-05-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.17.21257223", - "rel_abs": "IntroductionIncreased transmissibility of B.1.17 variant of concern (VOC) in the UK may explain its rapid emergence and global spread. We analysed data from putative household infector - infectee pairs in the Virus Watch Community cohort study to assess the serial interval of COVID-19 and whether this was affected by emergence of the B.1.17 variant.\n\nMethodsThe Virus Watch study is an online, prospective, community cohort study following up entire households in England and Wales during the COVID-19 pandemic. Putative household infector-infectee pairs were identified where more than one person in the household had a positive swab matched to an illness episode. Data on whether individual infections were caused by the B.1.1.7 variant were not available. We therefore developed a classification system based on the percentage of cases estimated to be due to B.1.17 in national surveillance data for different English regions and study weeks.\n\nResultsOut of 24,887 illnesses reported, 915 tested positive for SARS-CoV-2 and 186 likely infector-infectee pairs in 186 households amongst 372 individuals were identified. The mean COVID-19 serial interval was 3.18 (95%CI: 2.55 - 3.81) days. There was no significant difference (p=0.267) between the mean serial interval for Variants of Concern (VOC) hotspots (mean = 3.64 days, (95%CI: 2.55 - 4.73)) days and non-VOC hotspots, (mean = 2.72 days, (95%CI: 1.48 - 3.96)).\n\nConclusionsOur estimates of the average serial interval of COVID-19 are broadly similar to estimates from previous studies and we find no evidence that B.1.1.7 is associated with a change in serial intervals. Alternative explanations such as increased viral load, longer period of viral shedding or improved receptor binding may instead explain the increased transmissibility and rapid spread and should undergo further investigation.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Cyril Roman Geismar", - "author_inst": "University College London" - }, - { - "author_name": "Ellen Fragaszy", - "author_inst": "University College London" - }, - { - "author_name": "Vincent Grigori Nguyen", - "author_inst": "University College London" - }, - { - "author_name": "Wing Lam Erica Fong", - "author_inst": "University College London" - }, - { - "author_name": "Madhumita Shrotri", - "author_inst": "University College London" - }, - { - "author_name": "Sarah Beale", - "author_inst": "University College London" - }, - { - "author_name": "Alison Rodger", - "author_inst": "University College London" - }, - { - "author_name": "Vasileios Lampos", - "author_inst": "University College London" - }, - { - "author_name": "Thomas Edward Byrne", - "author_inst": "University College London" - }, - { - "author_name": "Jana Kovar", - "author_inst": "University College London" - }, - { - "author_name": "Annalan Navaratnam", - "author_inst": "University College London" - }, - { - "author_name": "Parth Patel", - "author_inst": "University College London" - }, - { - "author_name": "Robert W Aldridge", - "author_inst": "University College London" - }, - { - "author_name": "Andrew Hayward", - "author_inst": "University College London" - }, - { - "author_name": "- Virus Watch Collaborative", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.13.21257146", "rel_title": "Sociodemographic inequality in COVID-19 vaccination coverage amongst elderly adults in England: a national linked data study", @@ -762558,6 +763883,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.17.444467", + "rel_title": "Moxidectin and ivermectin inhibit SARS-CoV-2 replication in Vero E6 cells but not in human primary airway epithelium cells", + "rel_date": "2021-05-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.17.444467", + "rel_abs": "Antiviral therapies are urgently needed to treat and limit the development of severe COVID-19 disease. Ivermectin, a broad-spectrum anti-parasitic agent, has been shown to have anti-SARS-CoV-2 activity in Vero cells at a concentration of 5 {micro}M. These in vitro results triggered the investigation of ivermectin as a treatment option to alleviate COVID-19 disease. In April 2021, the World Health Organization stated, however, the following: \"the current evidence on the use of ivermectin to treat COVID-19 patients is inconclusive\". It is speculated that the in vivo concentration of ivermectin is too low to exert a strong antiviral effect. Here, we performed a head-to head comparison of the antiviral activity of ivermectin and a structurally related, but metabolically more stable, moxidectin in multiple in vitro models of SARS-CoV-2 infection, including physiologically relevant human respiratory epithelial cells. Both moxidectin and ivermectin exhibited antiviral activity in Vero E6 cells. Subsequent experiments revealed that the compounds predominantly act on a step after virus cell entry. Surprisingly, however, in human airway-derived cell models, moxidectin and ivermectin failed to inhibit SARS-CoV-2 infection, even at a concentration of 10 {micro}M. These disappointing results calls for a word of caution in the interpretation of anti-SARS-CoV-2 activity of drugs solely based on Vero cells. Altogether, these findings suggest that, even by using a high-dose regimen of ivermectin or switching to another drug in the same class are unlikely to be useful for treatment against SARS-CoV-2 in humans.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Nilima Dinesh Kumar", + "author_inst": "University Medical Center Groningen, University of Groningen" + }, + { + "author_name": "Bram M ter Ellen", + "author_inst": "University Medical Center Groningen, University of Groningen" + }, + { + "author_name": "Ellen M Bouma", + "author_inst": "University Medical Center Groningen, University of Groningen" + }, + { + "author_name": "Berit Troost", + "author_inst": "University Medical Center Groningen, University of Groningen" + }, + { + "author_name": "Denise P. I van de Pol", + "author_inst": "University Medical Center Groningen, University of Groningen" + }, + { + "author_name": "Heidi H van der Ende-Metselaar", + "author_inst": "University Medical Center Groningen, University of Groningen" + }, + { + "author_name": "Djoke van Gosliga", + "author_inst": "University Medical Center Groningen, University of Groningen" + }, + { + "author_name": "Leonie Apperloo", + "author_inst": "University Medical Center Groningen, University of Groningen" + }, + { + "author_name": "Orestes A Carpaij", + "author_inst": "University Medical Center Groningen, University of Groningen" + }, + { + "author_name": "Maarten van den Berge", + "author_inst": "University Medical Center Groningen" + }, + { + "author_name": "Martijn C Nawijn", + "author_inst": "University Medical Center Groningen" + }, + { + "author_name": "Ymkje Stienstra", + "author_inst": "University Medical Center Groningen, University of Groningen" + }, + { + "author_name": "Izabela A Rodenhuis-Zybert", + "author_inst": "University Medical Center Groningen, University of Groningen" + }, + { + "author_name": "Jolanda Smit", + "author_inst": "University Medical Centre Groningen, University of Groningen" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.05.13.21257065", "rel_title": "HLA-B*15:01 is associated with asymptomatic SARS-CoV-2 infection", @@ -764512,33 +765908,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.12.21257079", - "rel_title": "Computational modelling of COVID-19: A study of compliance and superspreaders", - "rel_date": "2021-05-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.12.21257079", - "rel_abs": "BackgroundThe success of social distancing implementations of severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) depends heavily on population compliance. Mathematical modelling has been used extensively to assess the rate of viral transmission from behavioural responses. Previous epidemics of SARS-Cov-2 have been characterised by superspreaders, a small number of individuals who transmit a disease to a large group of individuals, who contribute to the stochasticity (or randomness) of transmission compared to other pathogens such as Influenza. This growing evidence proves an urgent matter to understand transmission routes in order to target and combat outbreaks.\n\nObjectiveTo investigate the role of superspreaders in the rate of viral transmission with various levels of compliance.\n\nMethodA SEIRS inspired social network model is adapted and calibrated to observe the infected links of a general population with and without superspreaders on four compliance levels. Local and global connection parameters are adjusted to simulate close contact networks and travel restrictions respectively and each performance assessed. The mean and standard deviation of infections with superspreaders and non-superspreaders were calculated for each compliance level.\n\nResultsIncreased levels of compliance of superspreaders proves a significant reduction in infections. Assuming long-lasting immunity, superspreaders could potentially slow down the spread due to their high connectivity.\n\nDiscussionThe main advantage of applying the network model is to capture the heterogeneity and locality of social networks, including the role of superspreaders in epidemic dynamics. The main challenge is the immediate attention on social settings with targeted interventions to tackle superspreaders in future empirical work.\n\nConclusionSuperspreaders play a central role in slowing down infection spread following compliance guidelines. It is crucial to adjust social distancing measures to prevent future outbreaks accompanied by population-wide testing and effective tracing.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Faith MY Lee", - "author_inst": "University College London" - }, - { - "author_name": "Maria Perez-Ortiz", - "author_inst": "University College London" - }, - { - "author_name": "John Shawe-Taylor", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.12.21257117", "rel_title": "Seven-day COVID-19 quarantine may be too short: assessing post-quarantine transmission risk in four university cohorts", @@ -764751,6 +766120,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.12.21257126", + "rel_title": "Bayesian Model Averaging to Account for Model Uncertainty in Estimates of a Vaccine's Effectiveness", + "rel_date": "2021-05-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.12.21257126", + "rel_abs": "Vaccine effectiveness (VE) studies are often conducted after the introduction of new vaccines to ensure they provide protection in real-world settings. Although susceptible to confounding, the test-negative case-control study design is the most efficient method to assess VE post-licensure. Control of confounding is often needed during the analyses, which is most efficiently done through multivariable modeling. When a large number of potential confounders are being considered, it can be challenging to know which variables need to be included in the final model. This paper highlights the importance of considering model uncertainty by re-analyzing a Lyme VE study using several confounder selection methods. We propose an intuitive Bayesian Model Averaging (BMA) framework for this task and compare the performance of BMA to that of traditional single-best-model-selection methods. We demonstrate how BMA can be advantageous in situations when there is uncertainty about model selection by systematically considering alternative models and increasing transparency.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Carlos R Oliveira", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Eugene D Shapiro", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Daniel M Weinberger", + "author_inst": "Yale University School of Public Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.12.21257125", "rel_title": "COVID-19 Serology in New York State Using a Multiplex Microsphere Immunoassay", @@ -766434,109 +767830,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.13.21257129", - "rel_title": "Immune Responses to COVID-19 mRNA Vaccines in Patients with Solid Tumors on Active, Immunosuppressive Cancer Therapy", - "rel_date": "2021-05-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.13.21257129", - "rel_abs": "Vaccines against SARS-CoV-2 have shown high efficacy, but immunocompromised participants were excluded from controlled clinical trials. We compared immune responses to the Pfizer/BioNTech mRNA vaccine in solid tumor patients (n=53) on active cytotoxic anti-cancer therapy to a control cohort (n=50) as an observational study. Using live SARS-CoV-2 assays, neutralizing antibodies were detected in 67% and 80% of cancer patients after the first and second immunizations, respectively, with a 3-fold increase in median titers after the booster. Similar trends were observed in serum antibodies against the receptor-binding domain (RBD) and S2 regions of Spike protein, and in IFN{gamma}+ Spike-specific T cells. Yet the magnitude of each of these responses was diminished relative to the control cohort. We therefore quantified RBD- and Spike S1-specific memory B cell subsets as predictors of anamnestic responses to additional immunizations. After the second vaccination, Spike-specific plasma cell-biased memory B cells were observed in most cancer patients at levels similar to those of the control cohort after the first immunization. We initiated an interventional phase 1 trial of a third booster shot (NCT04936997); primary outcomes were immune responses with a secondary outcome of safety. After a third immunization, the 20 participants demonstrated an increase in antibody responses, with a median 3-fold increase in virus-neutralizing titers. Yet no improvement was observed in T cell responses at 1 week after the booster immunization. There were mild adverse events, primarily injection site myalgia, with no serious adverse events after a month of follow-up. These results suggest that a third vaccination improves humoral immunity against COVID-19 in cancer patients on active chemotherapy with no severe adverse events.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Rachna T Shroff", - "author_inst": "University of Arizona" - }, - { - "author_name": "Pavani Chalasani", - "author_inst": "University of Arizona" - }, - { - "author_name": "Ran Wei", - "author_inst": "University of Arizona" - }, - { - "author_name": "Daniel Pennington", - "author_inst": "University of Arizona" - }, - { - "author_name": "Grace Quirk", - "author_inst": "University of Arizona" - }, - { - "author_name": "Marta V Schoenle", - "author_inst": "University of Arizona" - }, - { - "author_name": "Kameron L Peyton", - "author_inst": "University of Arizona" - }, - { - "author_name": "Jennifer L Uhrlaub", - "author_inst": "University of Arizona" - }, - { - "author_name": "Tyler J Ripperger", - "author_inst": "University of Arizona" - }, - { - "author_name": "Mladen Jergovic", - "author_inst": "University of Arizona" - }, - { - "author_name": "Shelby Dalgai", - "author_inst": "University of Arizona" - }, - { - "author_name": "Alexander Wolf", - "author_inst": "University of Arizona" - }, - { - "author_name": "Rebecca D Whitmer", - "author_inst": "University of Arizona" - }, - { - "author_name": "Hytham Hammad", - "author_inst": "University of Arizona" - }, - { - "author_name": "Amy Carrier", - "author_inst": "University of Arizona" - }, - { - "author_name": "Aaron J Scott", - "author_inst": "University of Arizona" - }, - { - "author_name": "Janko Nikolich-Zugich", - "author_inst": "University of Arizona" - }, - { - "author_name": "Michael Worobey", - "author_inst": "University of Arizona" - }, - { - "author_name": "Ryan Sprissler", - "author_inst": "University of Arizona" - }, - { - "author_name": "Michael D Dake", - "author_inst": "University of Arizona" - }, - { - "author_name": "Bonnie J LaFleur", - "author_inst": "University of Arizona" - }, - { - "author_name": "Deepta Bhattacharya", - "author_inst": "University of Arizona" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.07.21256823", "rel_title": "Evolution of human antibody responses up to one year after SARS-CoV-2 infection", @@ -766761,6 +768054,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.10.21256816", + "rel_title": "Cost-effectiveness of whole area testing of asymptomatic SARS-CoV-2 infections in Merthyr Tydfil, 2020: A Modelling and economic analysis", + "rel_date": "2021-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.10.21256816", + "rel_abs": "BackgroundMass community testing for SARS-CoV-2 by lateral flow devices (LFDs) aims to reduce prevalence in the community. However its effectiveness as a public heath intervention is disputed.\n\nMethodData from a mass testing pilot in the Borough of Merthyr Tydfil in late 2020 was used to model cases, hospitalisations, ICU admissions and deaths prevented. Further economic analysis with a healthcare perspective assessed cost-effectiveness in terms of healthcare costs avoided and QALYs gained.\n\nResultsAn initial conservative estimate of 360 (95% CI: 311-418) cases were prevented by the mass testing, representing a would-be reduction of 11% of all cases diagnosed in Merthyr Tydfil residents during the same period. Modelling healthcare burden estimates that 24 (16 - 36) hospitalizations, 5 (3-6) ICU admissions and 15 (11-20) deaths were prevented, representing 6.37%, 11.1% and 8.2%, respectively of the actual counts during the same period. A less conservative, best-case scenario predicts 2333 (1764-3115) cases prevented, representing 80% reduction in would-be cases. Cost effectiveness analysis indicates 108 (80-143) QALYs gained, an incremental cost ratio of {pound}2,143 ({pound}860-{pound}4,175) per QALY gained and net monetary benefit of {pound}6.2m ({pound}4.5m-{pound}8.4m). In the best-case scenario, this increases to {pound}15.9m ({pound}12.3m-{pound}20.5m).\n\nConclusionsA non-negligible number of cases, hospitalisations and deaths were prevented by the mass testing pilot. Considering QALYs gained and healthcare costs avoided, the pilot was cost-effective. These findings suggest mass testing with LFDs in areas of high prevalence (>2%) is likely to provide significant public health benefit. It is not yet clear whether similar benefits will be obtained in low prevalence settings or with vaccination rollout.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Mark Drakesmith", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Brendan Collins", + "author_inst": "Welsh Government" + }, + { + "author_name": "Kelechi Nnoaham", + "author_inst": "Cwm Taf Morgannwg University Health Board" + }, + { + "author_name": "Angela Jones", + "author_inst": "Cwm Taf Morgannwg University Health Board" + }, + { + "author_name": "Daniel Rhys Thomas", + "author_inst": "Public Health Wales" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.11.21257053", "rel_title": "Analysis of 472,688 severe cases of COVID-19 in Brazil showed lower mortality in those vaccinated against influenza", @@ -769204,57 +770532,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.05.12.443948", - "rel_title": "Plasmacytoid dendritic cells produce type I interferon and reduce viral replication in airway epithelial cells after SARS-CoV-2 infection", - "rel_date": "2021-05-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.12.443948", - "rel_abs": "Infection with SARS-CoV-2 has caused a pandemic of unprecedented dimensions. SARS-CoV-2 infects airway and lung cells causing viral pneumonia. The importance of type I interferon (IFN) production for the control of SARS-CoV-2 infection is highlighted by the increased severity of COVID-19 in patients with inborn errors of type I IFN response or auto-antibodies against IFN-. Plasmacytoid dendritic cells (pDCs) are a unique immune cell population specialized in recognizing and controlling viral infections through the production of high concentrations of type I IFN. In this study, we isolated pDCs from healthy donors and showed that pDCs are able to recognize SARS-CoV-2 and rapidly produce large amounts of type I IFN. Sensing of SARS-CoV-2 by pDCs was independent of viral replication since pDCs were also able to recognize UV-inactivated SARS-CoV-2 and produce type I IFN. Transcriptional profiling of SARS-CoV-2 and UV-SARS-CoV-2 stimulated pDCs also showed a rapid type I and III IFN response as well as induction of several chemokines, and the induction of apoptosis in pDCs. Moreover, we modeled SARS-CoV-2 infection in the lung using primary human airway epithelial cells (pHAEs) and showed that co-culture of pDCs with SARS-CoV-2 infected pHAEs induces an antiviral response and upregulation of antigen presentation in pHAE cells. Importantly, the presence of pDCs in the co-culture results in control of SARS-CoV-2 replication in pHAEs. Our study identifies pDCs as one of the key cells that can recognize SARS-CoV-2 infection, produce type I and III IFN and control viral replication in infected cells.\n\nImportanceType I interferons (IFNs) are a major part of the innate immune defense against viral infections. The importance of type I interferon (IFN) production for the control of SARS-CoV-2 infection is highlighted by the increased severity of COVID-19 in patients with defects in the type I IFN response. Interestingly, many cells are not able to produce type I IFN after being infected with SARS-CoV-2 and cannot control viral infection. In this study we show that plasmacytoid dendritic cells are able to recognize SARS-CoV-2 and produce type I IFN, and that pDCs are able to help control viral infection in SARS-CoV-2 infected airway epithelial cells.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Luisa Cervantes-Barragan", - "author_inst": "Emory University" - }, - { - "author_name": "Abigail Vanderheiden", - "author_inst": "Emory University" - }, - { - "author_name": "Charlotte J Royer", - "author_inst": "Emory University" - }, - { - "author_name": "Meredith E Davis-Gardner", - "author_inst": "Emory University" - }, - { - "author_name": "Philipp Ralfs", - "author_inst": "Emory University" - }, - { - "author_name": "Tatiana Chirkova", - "author_inst": "Emory University" - }, - { - "author_name": "Larry J Anderson", - "author_inst": "University of Emory School of Medicine" - }, - { - "author_name": "Arash Grakoui", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Mehul S Suthar", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.09.21250610", "rel_title": "Pooling of samples for SARS-CoV-2 detection using rapid antigen tests", @@ -769411,6 +770688,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.08.21256891", + "rel_title": "Homebrew reagents for low cost RT-LAMP", + "rel_date": "2021-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.08.21256891", + "rel_abs": "RT-LAMP (reverse transcription - Loop-mediated isothermal amplification) has gained popularity for the detection of SARS-CoV-2. The high specificity, sensitivity, simple protocols and potential to deliver results without the use of expensive equipment has made it an attractive alternative to RT-PCR. However, the high cost per reaction, the centralized manufacturing of required reagents and their distribution under cold chain shipping limits RT-LAMPs applicability in low-income settings. The preparation of assays using homebrew enzymes and buffers has emerged worldwide as a response to these limitations and potential shortages. Here, we describe the production of Moloney murine leukemia virus (M-MLV) Reverse Transcriptase and BstLF DNA polymerase for the local implementation of RT-LAMP reactions at low cost. These reagents compared favorably to commercial kits and optimum concentrations were defined in order to reduce time to threshold, increase ON/OFF range and minimize enzyme quantities per reaction. As a validation, we tested the performance of these reagents in the detection of SARS-CoV-2 from RNA extracted from clinical nasopharyngeal samples, obtaining high agreement between RT-LAMP and RT-PCR clinical results. The in-house preparation of these reactions results in an order of magnitude reduction in costs, and thus we provide protocols and DNA to enable the replication of these tests at other locations. These results contribute to the global effort of developing open and low cost diagnostics that enable technological autonomy and distributed capacities in viral surveillance.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Tamara Matute", + "author_inst": "Millennium Institute for Integrative Biology (iBio) - Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences" + }, + { + "author_name": "Isaac Nunez", + "author_inst": "Millennium Institute for Integrative Biology (iBio) - Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences" + }, + { + "author_name": "Maira Rivera", + "author_inst": "Millennium Institute for Integrative Biology (iBio) - Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences" + }, + { + "author_name": "Javiera Reyes", + "author_inst": "Millennium Institute for Integrative Biology (iBio) - Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences" + }, + { + "author_name": "Paula Blazquez-Sanchez", + "author_inst": "Millennium Institute for Integrative Biology (iBio) - Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences" + }, + { + "author_name": "Anibal Arce", + "author_inst": "Millennium Institute for Integrative Biology (iBio) - Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences" + }, + { + "author_name": "Alexander J. Brown", + "author_inst": "Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA Department of Immunology & Microbiology, University of Colorado Anschutz " + }, + { + "author_name": "Chiara Gandini", + "author_inst": "Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom" + }, + { + "author_name": "Jennifer Molloy", + "author_inst": "Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom" + }, + { + "author_name": "Cesar A. Ramirez-Sarmiento", + "author_inst": "Millennium Institute for Integrative Biology (iBio) - Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences" + }, + { + "author_name": "Fernan Federici", + "author_inst": "Millennium Institute for Integrative Biology (iBio) - Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.05.06.21256768", "rel_title": "Antibody Response to COVID-19 vaccination in Patients Receiving Dialysis", @@ -771030,61 +772366,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.05.11.443686", - "rel_title": "Impacts on the structure-function relationship of SARS-CoV-2 spike by B.1.1.7 mutations", - "rel_date": "2021-05-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.11.443686", - "rel_abs": "The UK variant of the severe acute respiratory syndrome coronavirus (SARS-CoV-2), known as B.1.1.7, harbors several point mutations and deletions on the spike (s) protein, which potentially alter its structural epitopes to evade host immunity while enhancing host receptor binding. Here we report the cryo-EM structures of the S protein of B.1.1.7 in its apo form and in the receptor ACE2-bound form. One or two of the three receptor binding domains (RBDs) were in the open conformation but no fully closed form was observed. In the ACE-bound form, all three RBDs were engaged in receptor binding. The B.1.1.7-specific A570D mutation introduced a salt bridge switch that could modulate the opening and closing of the RBD. Furthermore, the N501Y mutation in the RBD introduced a favorable {pi}-{pi} interaction manifested in enhanced ACE2 binding affinity. The N501Y mutation abolished the neutralization activity of one of the three potent neutralizing antibodies (nAbs). Cryo-EM showed that the cocktail of other two nAbs simultaneously bound to all three RBDs. Furthermore, the nAb cocktail synergistically neutralized different SARS-CoV-2 pseudovirus strains, including the B.1.1.7.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Tzu-Jing Yang", - "author_inst": "Academia Sinica" - }, - { - "author_name": "Pei-Yu Yu", - "author_inst": "Academia Sinica" - }, - { - "author_name": "Yuan-Chih Chang", - "author_inst": "Academia Sinica" - }, - { - "author_name": "Kang-Hao Liang", - "author_inst": "Academia Sinica" - }, - { - "author_name": "Hsian-Cheng Tso", - "author_inst": "Academia Sinica" - }, - { - "author_name": "Meng-Ru Ho", - "author_inst": "Academia Sinica" - }, - { - "author_name": "Wan-Yu Chen", - "author_inst": "Academia Sinica" - }, - { - "author_name": "Hsiu-Ting Lin", - "author_inst": "Academia Sinica" - }, - { - "author_name": "Han-Chung Wu", - "author_inst": "Academia Sinica" - }, - { - "author_name": "Shang-Te Danny Hsu", - "author_inst": "Academia Sinica" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.05.12.443228", "rel_title": "Interferon-armed RBD dimer enhances the immunogenicity of RBD for sterilizing immunity against SARS-CoV-2", @@ -771377,6 +772658,53 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.05.12.443888", + "rel_title": "mRNA vaccine-induced SARS-CoV-2-specific T cells recognize B.1.1.7 and B.1.351 variants but differ in longevity and homing properties depending on prior infection status", + "rel_date": "2021-05-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.12.443888", + "rel_abs": "While mRNA vaccines are proving highly efficacious against SARS-CoV-2, it is important to determine how booster doses and prior infection influence the immune defense they elicit, and whether they protect against variants. Focusing on the T cell response, we conducted a longitudinal study of infection-naive and COVID-19 convalescent donors before vaccination and after their first and second vaccine doses, using a high-parameter CyTOF analysis to phenotype their SARS-CoV-2-specific T cells. Vaccine-elicited spike-specific T cells responded similarly to stimulation by spike epitopes from the ancestral, B.1.1.7 and B.1.351 variant strains, both in terms of cell numbers and phenotypes. In infection-naive individuals, the second dose boosted the quantity and altered the phenotypic properties of SARS-CoV-2-specific T cells, while in convalescents the second dose changed neither. Spike-specific T cells from convalescent vaccinees differed strikingly from those of infection-naive vaccinees, with phenotypic features suggesting superior long-term persistence and ability to home to the respiratory tract including the nasopharynx. These results provide reassurance that vaccine-elicited T cells respond robustly to emerging viral variants, confirm that convalescents may not need a second vaccine dose, and suggest that vaccinated convalescents may have more persistent nasopharynx-homing SARS-CoV-2-specific T cells compared to their infection-naive counterparts.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jason Neidleman", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Xiaoyu Luo", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Matthew McGregor", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Guorui Xie", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Victoria Murray", + "author_inst": "UCSF" + }, + { + "author_name": "Warner C. Greene", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Sulggi A. Lee", + "author_inst": "UCSF" + }, + { + "author_name": "Nadia R. Roan", + "author_inst": "University of California, San Francisco; and Gladstone Institutes" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.05.10.443532", "rel_title": "Analysis of the Role of N-glycosylation in Cell-surface expression, Function and Binding Properties of SARS-CoV-2 receptor ACE2", @@ -773800,37 +775128,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2021.05.11.21256876", - "rel_title": "The Impact of Control and Mitigation Strategies during the Second Wave of COVID-19 Infections in Spain and Italy", - "rel_date": "2021-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21256876", - "rel_abs": "European countries struggled to fight against the second and the third waves of the COVID-19 pandemic, as the Test-Trace-Isolate (TTI) strategy widely adopted over the summer and early fall failed to effectively contain the spread of the disease. In this paper, we shed light on the effectiveness of such a strategy in two European countries (Spain and Italy) by analysing data from June to December 2020, collected via a large-scale online citizen survey with 95,251 answers in Spain and 43,393 answers in Italy. Through our analysis, we identify several weaknesses in each of the three pillars of the TTI strategy: testing, tracing and isolating. Moreover, we analyse the respondents self-reported behaviour before and after the mitigation strategies were deployed during the second wave of infections. We find that the changes in the participants behaviour were more pronounced in Italy than in Spain, whereas in both countries, respondents reported being very compliant with individual protection measures, such as wearing facial masks or frequently disinfecting their hands. Finally, we analyse the participants perceptions about their governments measures and the safety of everyday activities and places regarding the risk of getting an infection. We find that the perceived risk is often gender- and age-dependent and not aligned with the risk level identified by the literature. This finding emphasises the importance of deploying public-health communication campaigns to debunk misconceptions about SARS-CoV-2. Overall, our work shows the value of online citizen surveys to quickly and cheaply collect large-scale data to support and evaluate policy decisions to contrast the spread of the disease.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Marco De Nadai", - "author_inst": "Fondazione Bruno Kessler" - }, - { - "author_name": "Kristof Roomp", - "author_inst": "The European Laboratory for Learning and Intelligent Systems (ELLIS), Alicante Unit" - }, - { - "author_name": "Bruno Lepri", - "author_inst": "Fondazione Bruno Kessler" - }, - { - "author_name": "Nuria Oliver", - "author_inst": "The European Laboratory for Learning and Intelligent Systems (ELLIS), Alicante Unit" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.10.21256995", "rel_title": "Magnetofluidic platform for rapid multiplexed screening of SARS-CoV-2 variants and respiratory pathogens", @@ -774091,6 +775388,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.11.443659", + "rel_title": "SARS-CoV-2 Variant Identification Using a Genome Tiling Array and Genotyping Probes", + "rel_date": "2021-05-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.11.443659", + "rel_abs": "With over three million deaths worldwide attributed to the respiratory disease COVID-19 caused by the novel coronavirus SARS-CoV-2, it is essential that continued efforts be made to track the evolution and spread of the virus globally. We previously presented a rapid and cost-effective method to sequence the entire SARS-CoV-2 genome with 95% coverage and 99.9% accuracy. This method is advantageous for identifying and tracking variants in the SARS-CoV-2 genome when compared to traditional short read sequencing methods which can be time consuming and costly. Herein we present the addition of genotyping probes to our DNA chip which target known SARS-CoV-2 variants. The incorporation of the genotyping probe sets along with the advent of a moving average filter have improved our sequencing coverage and accuracy of the SARS-CoV-2 genome.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Ryota Shimada", + "author_inst": "University of New Mexico, Department of Chemistry and Chemical Biology" + }, + { + "author_name": "Emily N. Alden", + "author_inst": "University of New Mexico, Department of Chemistry and Chemical Biology" + }, + { + "author_name": "Kendall Hoff", + "author_inst": "Centrillion Technologies" + }, + { + "author_name": "Dun Ding", + "author_inst": "Centrillion Technologies" + }, + { + "author_name": "Jiayi Sun", + "author_inst": "Centrillion Technologies" + }, + { + "author_name": "Adam M Halasz", + "author_inst": "West Virginia University, Department of Mathematics" + }, + { + "author_name": "Wei Zhou", + "author_inst": "Centrillion Technologies" + }, + { + "author_name": "Jeremy S. Edwards", + "author_inst": "University of New Mexico, Department of Chemistry and Chemical Biology" + } + ], + "version": "1", + "license": "", + "type": "confirmatory results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.05.11.443384", "rel_title": "Structure and mechanism of SARS-CoV-2 Spike N679-V687 deletion variant elucidate cell-type specific evolution of viral fitness", @@ -775854,45 +777198,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.10.21256951", - "rel_title": "The impact of COVID-19 pandemic on the provision of ambulatory care for patients with chronic neurological diseases in Japan: evaluation of an administrative claims database", - "rel_date": "2021-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.10.21256951", - "rel_abs": "BackgroundThe COVID-19 pandemic has affected not only the emergency medical system, but also patients regular ambulatory care. The number of patients visiting outpatient internal medicine clinics decreased during March-April 2020 compared to 2019. Moreover, the ban on telephone re-examination for outpatient clinics in lieu of ambulatory care for chronic diseases has been lifted since March 2020. In this context, we investigate the impact of the COVID-19 pandemic on ambulatory care at Japanese outpatient clinics for patients with chronic neurological diseases during the first half of 2020.\n\nMethodsWe collected data from the administrative claims database by DeSC Healthcare. Serial changes in the frequency of subsequent outpatient visits to clinics or hospitals (excluding large hospitals with beds >200) for chronic ambulatory care of epilepsy, migraine, Parkinsons disease (PD), and Alzheimers disease were measured. We also evaluated the utilization rate of telephone re-examination at outpatient clinics.\n\nResultsSince April 2020, the monthly count of outpatient clinic visits for epilepsy or PD decreased slightly but significantly. The use of telephone re-examination was facility-dependent, and it was used in less than 5% of all outpatient clinic visits for the examined neurological diseases in May 2020. The utilization rate of telephone re-examination was not associated with age or the neurological diseases of interest.\n\nConclusionThe impact of the COVID-19 pandemic on ambulatory care for several chronic neurological diseases may have been relatively limited, in terms of the frequency or type of outpatient visit, during the first half of 2020 in Japan.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Kenichiro Sato", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Tatsuo Mano", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Yoshiki Niimi", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Atsushi Iwata", - "author_inst": "Tokyo Metropolitan Geriatric Institute" - }, - { - "author_name": "Tatsushi Toda", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Takeshi Iwatsubo", - "author_inst": "University of Tokyo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2021.05.08.21256775", "rel_title": "Intra-host evolution provides for continuous emergence of SARS-CoV-2 variants", @@ -776177,6 +777482,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.07.21256826", + "rel_title": "A quantitative risk-benefit analysis of ChAdOx1 nCoV-19 vaccine among people under 60 in Italy", + "rel_date": "2021-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.07.21256826", + "rel_abs": "ChAdOx1 nCoV-19 is a vaccine against the COVID-19 infection that was granted a conditional marketing authorization by the European Commission in January 2021. However, following a report from the Pharmacovigilance Risk Assessment Committee (PRAC) of European Medicines Agency, which reported an association with thrombo-embolic events (TEE), in particular Disseminated intravascular coagulation (DIC) and Cerebral venous sinus thrombosis (CVST), many European countries either limited to individuals older than 55-60 years or suspended its use. We used publicly available data to carry out a quantitative risk-benefit analysis of the vaccine among people under 60 in Italy. Specifically, we used data from PRAC, Eudravigilance and ECDC to estimate the excess number of deaths for TEE, DIC and CVST expected in vaccine users, stratified by age groups. We then used data from the National Institute of Health to calculate age-specific COVID-19 mortality rates in Italy. Preventable deaths were calculated assuming a 72% vaccine efficacy over an 8-month period. Finally, benefit-risk ratio of ChAdOx1 nCoV-19 vaccination was calculated as the ratio between preventable COVID-19 deaths and vaccine-related deaths, using Monte-Carlo simulations. We found that among subjects aged 20-29 years the benefit-risk [B-R] ratio was not clearly favorable (0.70; 95% Uncertainty Interval [UI]: 0.27-2.11). However, in the other age groups the benefits of vaccination largely exceeded the risks (for age 30-49, B-R ratio: 22.9: 95%UI: 10.1-186.4). For age 50-59, B-R ratio: 1577.1: 95%UI: 1176.9-2121.5). Although many countries have limited the use of the ChAdOx1 nCoV-19 vaccine, the benefits of using this vaccine clearly outweigh the risks in people older than 30 years. The use of this vaccine should be a strategic and fundamental part of the immunization campaign considering its safety and efficacy in preventing COVID-19 and its complications.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Raffaele Palladino", + "author_inst": "Department of Public Health, University Federico II of Naples, Italy" + }, + { + "author_name": "Daniele Ceriotti", + "author_inst": "Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy" + }, + { + "author_name": "Damiano De Ambrosi", + "author_inst": "Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy" + }, + { + "author_name": "Marta De Vito", + "author_inst": "Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy" + }, + { + "author_name": "Marco Farsoni", + "author_inst": "Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy" + }, + { + "author_name": "Giuseppina Seminara", + "author_inst": "Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy" + }, + { + "author_name": "Francesco Barone-Adesi", + "author_inst": "CRIMEDIM Research Center in Emergency and Disaster Medicine, University of Eastern Piedmont, Novara, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.05.10.21255146", "rel_title": "A population-level analysis of the protective effects of androgen deprivation therapy against COVID-19 disease incidence and severity", @@ -778272,133 +779620,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.05.07.443175", - "rel_title": "Vaccination boosts naturally enhanced neutralizing breadth to SARS-CoV-2 one year after infection", - "rel_date": "2021-05-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.07.443175", - "rel_abs": "Over one year after its inception, the coronavirus disease-2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) remains difficult to control despite the availability of several excellent vaccines. Progress in controlling the pandemic is slowed by the emergence of variants that appear to be more transmissible and more resistant to antibodies1,2. Here we report on a cohort of 63 COVID-19-convalescent individuals assessed at 1.3, 6.2 and 12 months after infection, 41% of whom also received mRNA vaccines3,4. In the absence of vaccination antibody reactivity to the receptor binding domain (RBD) of SARS-CoV-2, neutralizing activity and the number of RBD-specific memory B cells remain relatively stable from 6 to 12 months. Vaccination increases all components of the humoral response, and as expected, results in serum neutralizing activities against variants of concern that are comparable to or greater than neutralizing activity against the original Wuhan Hu-1 achieved by vaccination of naive individuals2,5-8. The mechanism underlying these broad-based responses involves ongoing antibody somatic mutation, memory B cell clonal turnover, and development of monoclonal antibodies that are exceptionally resistant to SARS-CoV-2 RBD mutations, including those found in variants of concern4,9. In addition, B cell clones expressing broad and potent antibodies are selectively retained in the repertoire over time and expand dramatically after vaccination. The data suggest that immunity in convalescent individuals will be very long lasting and that convalescent individuals who receive available mRNA vaccines will produce antibodies and memory B cells that should be protective against circulating SARS-CoV-2 variants.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Zijun Wang", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Frauke Muecksch", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Dennis Schaefer-Babajew", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Shlomo Finkin", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Charlotte Viant", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Christian Gaebler", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Hans- Heinrich Hoffmann", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Christopher O Barnes", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Melissa Cipolla", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Victor Ramos", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Thiago Y Oliveira", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Alice Cho", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Fabian Schmidt", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Justin Da Silva", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Eva Bednarski", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Lauren Aguado", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Jim Yee", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Mridushi Daga", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Martina Turroja", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Katrina G Millard", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Mila Jankovic", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Anna Gazumyan", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Zhen Zhao", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Charles M Rice", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Paul D Bieniasz", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Marina Caskey", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Theodora Hatziioannou", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Michel C Nussenzweig", - "author_inst": "The Rockefeller University" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.05.08.443275", "rel_title": "In-vivo Protection from SARS-CoV-2 infection by ATN-161 in k18-hACE2 transgenic mice", @@ -778679,6 +779900,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.05.08.443207", + "rel_title": "Suppression of Global Protein Translation in SARS-CoV-2 Infection", + "rel_date": "2021-05-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.08.443207", + "rel_abs": "The relationship of SARS-CoV-2 with the host translation remains largely unexplored. Using polysome profiling of SARS-CoV-2 infected Caco2 cells, we here demonstrate that the virus induces a strong suppression of global translation by 48 hours of infection. Heavy polysome fractions displayed substantial depletion in the infected cells, indicating the loss of major translational activities in them. Further assessment of the major pathways regulating translation in multiple permissive cell lines revealed strong eIF4E dephosphorylation accompanied by Mnk1 depletion and ERK1/2 dephosphorylations. p38MAPK showed consistent activation and its inhibition lowered viral titers, indicating its importance in viral survival. mTORC1 pathway showed the most profound inhibition, indicating its potential contribution to the suppression of global translation associated with the infection. Pharmacological activation of mTORC1 caused a drop in viral titers while inhibition resulted in higher viral RNA levels, confirming a critical role of mTORC1 in regulating viral replication. Surprisingly, the infection did not cause a general suppression of 5-TOP translation, as evident from the continued expression of ribosomal proteins. Our results collectively indicate that the differential suppression of mTORC1 might allow SARS-CoV-2 to hijack translational machinery in its favor and specifically target a set of host mRNAs.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Haripriya Parthasarathy", + "author_inst": "Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Divya Gupta", + "author_inst": "Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Abhirami P Suresh", + "author_inst": "Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Dixit Tandel", + "author_inst": "Centre for Cellular and Molecular Biology, Academy of Scientific and Innovative Research" + }, + { + "author_name": "Vishal Sah", + "author_inst": "Centre for Cellular and Molecular Biology, Academy of Scientific and Innovative Research" + }, + { + "author_name": "Krishnan Harinivas Harshan", + "author_inst": "Centre for Cellular and Molecular Biology" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.05.07.443177", "rel_title": "Mathematical Analysis and Topology of SARS-CoV-2, Bonding with Cells and Unbonding", @@ -780010,33 +781270,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.05.21256257", - "rel_title": "A Rapid and Reliable Liquid Chromatography/Mass Spectrometry Method for SARS-CoV-2 Diagnostics from Gargle Solutions and Saliva", - "rel_date": "2021-05-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256257", - "rel_abs": "We describe a rapid liquid chromatography/mass spectrometry (LC/MS) method for the direct detection and quantitation of SARS-CoV-2 nucleoprotein in gargle solutions and saliva. The method is based on a multiple-reaction monitoring (MRM) mass spectrometry approach with a total cycle time of 5 minutes per analysis and allows the detection and accurate quantitation of SARS-CoV-2 nucleoprotein as low as 500 amol/{micro}l. We improved the sample preparation protocol of our recent piloting SARS-CoV-2 LC/MS study regarding sensitivity, reproducibility, and compatibility with a complementary reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) analysis of the same sample. The aim of this work is to promote diagnostic tools that allow identifying and monitoring SARS-CoV-2 infections by LC/MS methods in a routine clinical environment.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Marc Kipping", - "author_inst": "Martin Luther University Halle-Wittenberg" - }, - { - "author_name": "Dirk Taenzler", - "author_inst": "Martin Luther University Halle-Wittenberg" - }, - { - "author_name": "Andrea Sinz", - "author_inst": "Martin Luther University Halle-Wittenberg" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.05.21256475", "rel_title": "Extracorporeal membrane oxygenation in COVID-19 patients and in-hospital mortality: results from the Brazilian Registry using a propensity score matched analysis", @@ -780273,6 +781506,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.04.21256472", + "rel_title": "Multicentric Evaluation of a Novel Point of Care Electrochemical ELISA Platform for SARS-CoV-2 Specific IgG and IgM Antibody Assay", + "rel_date": "2021-05-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256472", + "rel_abs": "New diagnostics technologies for the efficient detection and quantification of SARS-CoV-2 Antibodies is very crucial to manage the COVID-19 pandemic, especially in the context of emerging vaccination paradigms. Herein, we report on a novel point-of-care Electrochemical ELISA platform with disposable screen printed electrodes functionalized with SARS-CoV-2 Spike Glycoprotein S1, to enable fast and accurate quantitative estimation of total antibody concentration (IgG and IgM) in clinical samples. The quantification is performed with a comparison of electrochemical redox current against the current produced by the spiked monoclonal antibodies with known concentration. The assay is validated through multicentric evaluation against 3 different FDA authorized Laboratory standard techniques, using both EDTA whole blood and serum samples. We demonstrate that the proposed assay has excellent sensitivity and specificity, making it a suitable candidate for epidemiological surveys and quantification of antibodies in COVID-19 vaccination programs.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Vinay Kumar", + "author_inst": "PathShodh Healthcare Pvt. Ltd., Kamakshi Complex, 1st Floor, No 1 Sanjaynagar Main Road, Sanjaynagar, Bengaluru 560094" + }, + { + "author_name": "Kanad Ghosh", + "author_inst": "PathShodh Healthcare Pvt. Ltd., Kamakshi Complex, 1st Floor, No 1 Sanjaynagar Main Road, Sanjaynagar, Bengaluru 560094" + }, + { + "author_name": "Anagha Chandran", + "author_inst": "PathShodh Healthcare Pvt. Ltd., Kamakshi Complex, 1st Floor, No 1 Sanjaynagar Main Road, Sanjaynagar, Bengaluru 560094" + }, + { + "author_name": "Sachin Panwar", + "author_inst": "PathShodh Healthcare Pvt. Ltd., Kamakshi Complex, 1st Floor, No 1 Sanjaynagar Main Road, Sanjaynagar, Bengaluru 560094" + }, + { + "author_name": "Ananthram Bhat", + "author_inst": "PathShodh Healthcare Pvt. Ltd., Kamakshi Complex, 1st Floor, No 1 Sanjaynagar Main Road, Sanjaynagar, Bengaluru 560094" + }, + { + "author_name": "Shreenivas Konaje", + "author_inst": "PathShodh Healthcare Pvt. Ltd., Kamakshi Complex, 1st Floor, No 1 Sanjaynagar Main Road, Sanjaynagar, Bengaluru 560094" + }, + { + "author_name": "Saroj Das", + "author_inst": "Centre for Nano Science and Engineering, Indian Institute of Science, Bengaluru, India" + }, + { + "author_name": "Srikanta S", + "author_inst": "Samatvam Endocrinology Diabetes Center, 313, 17th Main, Jayanagar, Bengaluru, India" + }, + { + "author_name": "Latha Jaganathan", + "author_inst": "Bangalore Medical Services Trust, New Tippasandra, Bengaluru, India" + }, + { + "author_name": "Sujay Prasad", + "author_inst": "Neuberg Anand Diagnostics Laboratory, Bengaluru, India" + }, + { + "author_name": "Venkatesh D B", + "author_inst": "Neuberg Anand Diagnostics Laboratory, Bengaluru, India" + }, + { + "author_name": "Shivaram C", + "author_inst": "Manipal Hospitals, Bengaluru, India" + }, + { + "author_name": "Krishnaswamy P R", + "author_inst": "Centre for Nano Science and Engineering, Indian Institute of Science, Bengaluru, India" + }, + { + "author_name": "NAVAKANTA BHAT", + "author_inst": "Indian Institute of Science, Bangalore, INDIA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.04.21256571", "rel_title": "Fatal COVID-19 outcomes are associated with an antibody response targeting epitopes shared with endemic coronaviruses", @@ -782336,53 +783640,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.05.04.21256599", - "rel_title": "Derivation and external validation of a simple risk score to predict in-hospital mortality in patients hospitalized for COVID-19", - "rel_date": "2021-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256599", - "rel_abs": "BackgroundAs SARS-CoV-2 continues to spread, and hospitals are treating a large number of patients with COVID-19, easy-to-use risk models that predict hospital mortality can assist in clinical decision making and triage.\n\nObjectiveAs SARS-CoV-2 continues to spread, easy-to-use risk models that predict hospital mortality can assist in clinical decision making and triage. We aimed to develop a risk score model for in-hospital mortality in patients hospitalized with COVID-19 that was robust across hospitals and used clinical factors that are readily available and measured standardly across hospitals.\n\nMethodsIn this observational study we developed a risk score model using data collected by trained abstractors for patients in 20 diverse hospitals across the state of Michigan (Mi-COVID19) who were discharged between March 5, 2020 and August 14, 2020. Patients who tested positive for SARS-CoV-2 during hospitalization or were discharged with an ICD-10 code for COVID-19 (U07.1) were included. We employed an iterative forward selection approach to consider the inclusion of 145 potential risk factors available at hospital presentation. Model performance was externally validated with patients from 19 hospitals in the Mi-COVID19 registry not used in model development. We shared the model in an easy-to-use online application that allows the user to predict in-hospital mortality risk for a patient if they have any subset of the variables in the final model.\n\nResultsOur final model includes the patients age, first recorded respiratory rate, first recorded pulse oximetry, highest creatinine level on day of presentation, and hospitals COVID-19 mortality rate. No other factors showed sufficient incremental model improvement to warrant inclusion. The AUC for the derivation and validation sets were .796 and .829 respectively.\n\nConclusionsRisk of in-hospital mortality in COVID-19 patients can be reliably estimated using a few factors, which are standardly measured and available to physicians very early in a hospital encounter.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Charlotte Z Mann", - "author_inst": "University of Michigan" - }, - { - "author_name": "Chelsea Abshire", - "author_inst": "Michigan Value Collaborative" - }, - { - "author_name": "Monica Yost", - "author_inst": "Michigan Value Collaborative" - }, - { - "author_name": "Scott Kaatz", - "author_inst": "Henry Ford Hospital" - }, - { - "author_name": "Lakshmi Swaminathan", - "author_inst": "St. Joseph Mercy Hospital" - }, - { - "author_name": "Scott A Flanders", - "author_inst": "University of Michigan" - }, - { - "author_name": "Hallie C Prescott", - "author_inst": "University of Michigan" - }, - { - "author_name": "Johann A Gagnon-Bartsch", - "author_inst": "University of Michigan" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2021.05.04.21256609", "rel_title": "SARS-CoV-2 infection and reinfection in a seroepidemiological workplace cohort in the United States", @@ -782775,6 +784032,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.05.05.442875", + "rel_title": "The Effect of Minnelide against SARS-CoV-2 in a Murine Model", + "rel_date": "2021-05-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.05.442875", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, is the causative agent of coronavirus disease 2019, COVID-19, and the current COVID-19 pandemic. Even as more vaccine candidates are released, more treatment options are critically needed. Here, we investigated the use of Minnelide, a water soluble pro-drug with anti-inflammatory properties, for the treatment of COVID-19. To do this, k18-hACE2 mice were infected with SARS-CoV-2 or given PBS control intranasally. The next day mice were either treated daily with low dose (0.0025mg/day) or high dose Minnelide (0.005mg/day), or given vehicle control intraperitoneal. Mice were weighed daily, and sacrificed at day 6 and 10 post-infection to analyze viral burden, cytokine response, and pathology. We observed a reduction in viral load in the lungs of Minnelide-treated mice infected with SARS-CoV-2 at day 10 post-infection compared to day 6 post-infection. All SARS-CoV-2 infected non-treated mice were moribund six days post-infection while treatment with Minnelide extended survival for both low (60% survival) and high (100% survival) dose treated mice ten days post-infection. Interestingly, cytokine analysis demonstrated a significant reduction in IL-6 (lung and heart) and D-dimer (serum) in high dose treated SARS-CoV-2 infected mice compared to mice infected with SARS-CoV-2 alone at day 6 post-infection. Additionally, histology analysis revealed that Minnelide treatment significantly improved lung pathology ten days post-infection with SARS-CoV-2 with all the mice exhibiting normal lung tissue with thin alveolar septa and no inflammatory cells. Overall, our study exhibits potential for the use of Minnelide to improve survival in COVID-19 patients.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Marley C. Caballero Van Dyke", + "author_inst": "University of Texas at San Antonio" + }, + { + "author_name": "Heather L Mead", + "author_inst": "Northern Arizona University" + }, + { + "author_name": "Mitchell Bryant", + "author_inst": "Northern Arizona University" + }, + { + "author_name": "Klaire L Laux", + "author_inst": "Northern Arizona University" + }, + { + "author_name": "Daniel R Kollath", + "author_inst": "Northern Arizona University" + }, + { + "author_name": "Vanessa K Coyne", + "author_inst": "Northern Arizona University" + }, + { + "author_name": "Karis J Miller", + "author_inst": "Northern Arizona University" + }, + { + "author_name": "Nathan E Stone", + "author_inst": "Northern Arizona University" + }, + { + "author_name": "Sierra A Jaramillo", + "author_inst": "Northern Arizona University" + }, + { + "author_name": "Paul Keim", + "author_inst": "Northern Arizona University" + }, + { + "author_name": "Clara Milikowski", + "author_inst": "University of Miami" + }, + { + "author_name": "Vineet K Gupta", + "author_inst": "University of Miami" + }, + { + "author_name": "Selwyn M Vickers", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Ashok Saluja", + "author_inst": "University of Miami" + }, + { + "author_name": "Mohana R Velagapudi", + "author_inst": "Minneamrita Therapeutics LLC" + }, + { + "author_name": "Bridget M Barker", + "author_inst": "Northern Arizona University" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.05.05.442873", "rel_title": "Diversity and selection of SARS-CoV-2 minority variants in the early New York City outbreak", @@ -784097,61 +785433,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.05.01.21256090", - "rel_title": "Effect of commuting on the risk of COVID-19 and COVID-19-induced anxiety", - "rel_date": "2021-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.01.21256090", - "rel_abs": "BackgroundTo prevent the spread of coronavirus disease (COVID-19), it is important to avoid 3Cs (closed spaces, crowded places, and close-contact settings). However, the risk of contact with an unspecified number of people is inevitable while commuting to and from work. In this study, we investigated the relationship between commuting, and the risk of COVID-19 and COVID-19-induced anxiety.\n\nMethodsAn internet-based questionnaire survey was conducted to obtain a dataset from 27036 respondents. One-way commuting time was evaluated using a five-case method. The commuting distance was estimated using zip codes of the home and workplace. Logistic regression analysis was performed with the following outcomes: COVID-19 risk, close contact, infection anxiety, and infection anxiety due to commuting. Commuting distance and commuting time were analyzed separately in the model. We excluded participants with incalculable commuting distance, commuting distance exceeding 300 km, commuting distance of 0 km, or who telecommuted at least once a week.\n\nResultsThe total number of participants included in the analysis was 14038. The adjusted odds ratios (aORs) of using public transportation for severe acute respiratory syndrome coronavirus 2 infection were 4.17 (95% confidence interval [CI]: 2.51-6.93) (commuting time) and 5.18 (95% CI: 3.06-8.78) (commuting distance). The aOR of COVID-19 diagnosis decreased significantly with increasing commuting distance. The aORs of using public transportation to infection anxiety were 1.44 (95% CI: 1.31-1.59) (commuting time) and 1.45 (95% CI: 1.32-1.60) (commuting distance). The longer the commuting time, the more the aOR increased..\n\nConclusionsCOVID-19 risk, close contact, and infection anxiety were all associated with the use of public transportation during commuting. Both commuting distance and time were associated with infection anxiety due to commuting, and the strength of the association increased with increase in commuting time distance. Since transportation by commuting is associated with COVID-19 risk and anxiety, we recommend the use of telecommuting and other means of work.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Hajime Ando", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Kazunori Ikegami", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Tomohisa Nagata", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Seiichiro Tateishi", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Hisashi Eguchi", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Mayumi Tsuji", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Shinya Matsuda", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Yoshihisa Fujino", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Akira Ogami", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "- the CORoNaWork project", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.05.01.21256442", "rel_title": "Prevalence of anxiety, depression, and stress among teachers during the COVID-19 pandemic: Systematic review", @@ -784384,6 +785665,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.01.21256428", + "rel_title": "Prevalence use of nonsteroidal anti-inflammatory drugs in the general population with COVID-19 and associated COVID-19 risk, hospitalization, severity, death, and safety outcomes: A systematic review and meta-analysis", + "rel_date": "2021-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.01.21256428", + "rel_abs": "IntroductionRecent reports of potential harmful effects of nonsteroidal anti-inflammatory drugs (NSAIDs) in patients with Corona Virus Disease 2019 (COVID-19) have provoked great concern. Therefore, the safety of NSAIDs is still questioned.\n\nMethodsWe searched the PubMed, EMBASE, Cochrane Library and Web of Science databases from December 2019 to January 2021 to examine use prevalence for NSAIDs in general, as well as associated COVID-19 risk and outcomes. This study has been registered with PROSPERO (CRD42019132063)\n\nResultsWe included 25 studies with a total of 101,215 COVID-19 patients. The use of NSAIDs in COVID-19 patients reached 19%. Exposure to NSAIDs was not associated with significantly increased risk of developing COVID-19 (odds ratio [OR]=0.98, 95% confidence interval [CI]: 0.78-1.24; I2=82%), hospitalization (OR=1.06, 95%CI: 0.76-1.48; I2=81%), mechanical ventilation (OR=0.71, 95%CI: 0.47-1.06; I2=38%), and length of hospital stay. Moreover, use of NSAIDs was significantly associated with better outcomes, including severity of COVID-19 (OR=0.79, 95%CI: 71-0.89; I2=0%) and death (OR=0.68, 95%CI: 0.52-0.89; I2=85%) in patients with COVID-19. Regarding safety outcomes, exposure to NSAIDs was associated with increased risk of stroke (OR=2.32, 95%CI: 1.04-5.2; I2=0%), but not with myocardial infraction (OR=1.49; p=0.66; I2=0%), overt thrombosis (OR=0.76, p=0.50; I2=28%) and major bleeding (p=0.61).\n\nConclusionBased on current evidence, exposure to NSAIDs is not linked to increased odds or exacerbation of COVID-19 in the general COVID-19 population. Furthermore, administration of NSAIDs might have better outcomes and survival benefits in the general COVID-19 population, although potentially increasing the risk of stroke. Use of NSAIDs might be safe and beneficial in COVID-19. Future observational and randomized control trials are needed for further confirmation.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "huilei zhao", + "author_inst": "Department of Anesthesiology, the Third Hospital of Nanchang, Jiangxi, 330006, China" + }, + { + "author_name": "shanshan huang", + "author_inst": "Medical college of Nanchang University, Jiangxi, 330006, China" + }, + { + "author_name": "kaibo mei", + "author_inst": "Department of Anesthesiology, the Shangrao People Hospital, Jiangxi, 330006, China" + }, + { + "author_name": "wen shao", + "author_inst": "Medical college of Nanchang University, Jiangxi, 330006, China" + }, + { + "author_name": "yuan jiang", + "author_inst": "Department of Cardiology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, 510080 China" + }, + { + "author_name": "wengen zhu", + "author_inst": "Department of Cardiology, the first affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080 China" + }, + { + "author_name": "jianyong ma", + "author_inst": "Department of Pharmacology and Systems Physiology University of Cincinnati College of Medicine, Cincinnati, OH 45267" + }, + { + "author_name": "jing zhang", + "author_inst": "Department of Anesthesiology, the Second Affiliated Hospital of Nanchang University, Jiangxi, 330006, China" + }, + { + "author_name": "peng yu", + "author_inst": "Department of Endocrine, the Second Affiliated Hospital of Nanchang University, Jiangxi, 330006, China" + }, + { + "author_name": "xiao liu", + "author_inst": "Department of Cardiology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, 510080 China" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.03.21256468", "rel_title": "Lipid-Modulating Agents for Prevention or Treatment of COVID-19 in Randomized Trials", @@ -786111,25 +787447,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.05.01.21256389", - "rel_title": "Latin American Registry of renal involvement in COVID-19 disease. The relevance of assessing proteinuria throughout the clinical course.", - "rel_date": "2021-05-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.01.21256389", - "rel_abs": "The Latin American Society of Nephrology and Hypertension carried out a cohort prospective, multinational registry of patients with kidney impairment associated to COVID-19 in Latin America through open invitation in order to describe the characteristics of the disease in the region. A population of 870 patients from 12 countries were included. Median age was 63 years (54-74), most of patients were male (68.4%) and had comorbidities (87.2%). Acute kidney injury (AKI) was hospital-acquired in 64.7% and non-oliguric in 59.9%. Multiorgan dysfunction syndrome (MODS) due to COVID-19 and volume depletion were the main causes of AKI (59.2% and 35.7% respectively). Kidney replacement therapy was started in 46.2%. Non-recovery of renal function was observed in 65.3%. 71.5% of patients were admitted to ICU and 72.2% underwent mechanical ventilation. Proteinuria at admission was present in 62.4% of patients and proteinuria during hospital-stay occurred in 37.5%. Those patients with proteinuria at admission had higher burden of comorbidities, higher baseline sCr, higher mortality and MODS was severe. On the other hand, patients with de novo proteinuria had lower burden of comorbidities and near normal sCr at admission, but showed adverse course of disease and higher in-mortality. COVID-19 MODS was the main cause of AKI in both groups. All-cause mortality was 57.4%, and it was associated to age, chronic cardiac disease, fluid depletion, COVID-19 MODS, non-recovery of renal function, ICU admission, vasopressors, in-hospital complications and hospital stay. In conclusion, our study contributes to a better knowledge of this condition and highlights the relevance of the detection of proteinuria throughout the clinical course.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Raul Lombardi", - "author_inst": "Hospital de Clinicas" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2021.05.01.21256452", "rel_title": "A hemagglutination-based, semi-quantitative test for point-of-care determination of SARS-CoV-2 antibody levels", @@ -786342,6 +787659,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.01.21256458", + "rel_title": "COVID-19 monitoring in rural communities: First comparison of lagoon and pumping station samples for wastewater-based epidemiology", + "rel_date": "2021-05-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.01.21256458", + "rel_abs": "Wastewater-based epidemiology/wastewater surveillance has been a topic of significant interest over the last year due to its application in SARS-CoV-2 surveillance to track prevalence of COVID-19 in communities. Although SARS-CoV-2 surveillance has been applied in more than 50 countries to date, the application of this surveillance has been largely focused on relatively affluent urban and peri-urban communities. As such, there is a knowledge gap regarding the implementation of reliable wastewater surveillance in small and rural communities for the purpose of tracking rates of incidence of COVID-19 and other pathogens or biomarkers. This study examines the relationships existing between SARS-CoV-2 viral signal from wastewater samples harvested from an upstream pumping station and from an access port at a downstream wastewater treatment lagoon with the communitys COVID-19 rate of incidence (measured as percent test positivity) in a small, rural community in Canada. Real-time quantitative polymerase chain reaction (RT-qPCR) targeting the N1 and N2 genes of SARS-CoV-2 demonstrate that all 24-hr composite samples harvested from the pumping station over a period of 5.5 weeks had strong viral signal, while all samples 24-hr composite samples harvested from the lagoon over the same period were below the limit of quantification. RNA concentrations and integrity of samples harvested from the lagoon were both lower and more variable than from samples from the upstream pumping station collected on the same date, indicating a higher overall stability of SARS-CoV-2 RNA upstream of the lagoon. Additionally, measurements of PMMoV signal in wastewater allowed to normalize SARS-CoV-2 viral signal for fecal matter content, permitting the detection of actual changes in community prevalence with a high level of granularity. As a result, in sewered small and rural communities or low-income regions operating wastewater lagoons, samples for wastewater surveillance should be harvested from pumping stations or the sewershed as opposed to lagoons.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Patrick M. D'Aoust", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Syeda Tasneem Towhid", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Elisabeth Mercier", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Nada Hegazy", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Xin Tian", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Kamya Bhatnagar", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Zhihao Zhang", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Colleen C Naughton", + "author_inst": "University of California Merced" + }, + { + "author_name": "Alex E. MacKenzie", + "author_inst": "Children's Hospital of Eastern Ontario Research Institute" + }, + { + "author_name": "Tyson E Graber", + "author_inst": "Children's Hospital of Eastern Ontario Research Institute" + }, + { + "author_name": "Robert Delatolla", + "author_inst": "University of Ottawa" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.30.21256406", "rel_title": "Development of in-house, indirect ELISAs for the detection of SARS-CoV-2 spike protein-associated serology in COVID-19 patients in Panama.", @@ -787475,33 +788851,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.30.21256366", - "rel_title": "Age-dependent association between SARS-CoV-2 cases reported by passive surveillance and viral load in wastewater", - "rel_date": "2021-05-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.30.21256366", - "rel_abs": "The true number of individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is difficult to estimate using a case-reporting system (i.e., passive surveillance) alone because of asymptomatic infection. While wastewater-based epidemiology has been implemented as an alternative/additional monitoring tool to reduce reporting bias, the relationship between passive and wastewater surveillance data has yet to be explicitly examined. Since there is strong age dependency in the symptomatic ratio of SARS-CoV-2 infections, this study aimed to estimate i) an age-dependent association between the number of reported cases and the viral load in wastewater and ii) the time lag between those time series. The viral load in wastewater was modeled as a combination of contributions from different age groups virus shedding, incorporating the delay, and fitted with daily case count data collected from the Massachusetts Department of Public Health and SARS-CoV-2 RNA concentrations in wastewater collected by the Massachusetts Water Resources Authority. The estimated lag between the time series of viral loads in wastewater and of reported cases was 10.8 days (95% confidence interval =[10.2, 11.6]) for wastewater treatment plants northern area and 8.8 days [8.4, 9.1] for southern area. The estimated contribution rate of a reported case to the viral load in wastewater in the 0-19 yr age group was 0.38 [0.35, 0.41] for northern area and 0.40 [0.37, 0.43] for southern area, that in the 80+ yr age group was 0.67 [0.65, 0.69] for northern area and 0.51 [0.49, 0.52] for southern area. The estimated lag between those time series suggested the predictability of reported cases ten days later using viral loads in wastewater. The contribution of a reported case in passive surveillance to the viral load in wastewater differed by age, suggesting a large variation in viral shedding kinetics among age groups.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ryosuke Omori", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Fuminari Miura", - "author_inst": "Ehime University" - }, - { - "author_name": "Masaaki Kitajima", - "author_inst": "Hokkaido University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.30.21256385", "rel_title": "The immediate and longer-term impact of the COVID-19 pandemic on the mental health and wellbeing of older adults in England", @@ -787626,6 +788975,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2021.04.29.21251164", + "rel_title": "Uncovering the compounding effects of COVID-19 and racism on mental health disparities among biomedical PhD and MD students", + "rel_date": "2021-05-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.29.21251164", + "rel_abs": "The increasing visibility of mental health challenges for academic and graduate trainee populations has led to discussion of the role higher education institutions should play to address trainee mental health, particularly during the COVID-19 pandemic and ongoing racial injustice. To address the growing concern about training impacts on medical and biomedical doctoral trainee mental health, a cross-sectional study (n=957) was conducted using institutional annual survey data analyzed by type of training program, race/ethnicity, and survey year on measures of depression, anxiety, hazardous alcohol use, problems related to substance use, and suicidal ideation. Results indicated significant differences for rates of depression, anxiety, and suicidal ideation, with biomedical doctoral trainees showing greater incidence than medical doctoral trainees, and underrepresented minority trainees showing greater incidence than well-represented trainees. The concerningly high rates of depression, anxiety, and suicidal ideation among these trainee populations suggest that medical and biomedical doctoral training environments must be transformed in addition to expanding mental health support resources.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Allison Schad", + "author_inst": "University of North Carolina at Chapel Hill School of Medicine" + }, + { + "author_name": "Rebekah L. Layton", + "author_inst": "University of North Carolina at Chapel Hill School of Medicine" + }, + { + "author_name": "Debra Ragland", + "author_inst": "University of North Carolina at Chapel Hill School of Medicine" + }, + { + "author_name": "Jeanette Gowen Cook", + "author_inst": "University of North Carolina at Chapel Hill School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "medical education" + }, { "rel_doi": "10.1101/2021.05.01.21255871", "rel_title": "Passive and active immunity in infants born to mothers with SARS-CoV-2 infection during pregnancy: Prospective cohort study", @@ -789333,61 +790713,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2021.04.29.21256291", - "rel_title": "Evidence for the utility of cfDNA plasma concentrations to predict disease severity in COVID-19", - "rel_date": "2021-05-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.29.21256291", - "rel_abs": "COVID-19 is a pandemic caused by the highly infective SARS-CoV-2. There is a need for biomarkers not only for overall prognosis but also for predicting the response to treatments and thus for improvements in the clinical management of patients with COVID-19. Circulating cell-free DNA (cfDNA) has emerged as a promising biomarker in the assessment of various disease conditions. The aim of this retrospective and observational pilot study was to examine the potential value of cfDNA plasma concentrations as a correlative biomarker in hospitalized COVID-19 patients. Lithium-Heparin plasma samples were obtained from twenty-one COVID-19 patients during hospitalization in the University Medical Center of Mainz, Germany, and the cfDNA concentrations were determined by quantitative PCR yielding amplicons of long interspersed nuclear elements (LINE-1). cfDNA plasma concentrations of COVID-19 patients ranged between 247.5 and 6346.25 ng/ml and the mean concentrations were 1831 {+/-} 1388 ng/ml ({+/-} standard deviation). Correlations were found between cfDNA levels and the occurrence of acute respiratory distress symptom (ARDS), acute kidney injury (AKI), myositis, neurological complications, bacterial superinfection and disease severity as defined by sepsis-related organ failure assessment score (SOFA) score. D-Dimer and C-reactive-protein (CRP), determined by clinical laboratory analysis, showed the highest correlations with cfDNA levels. The results of this observational study suggest that cfDNA plasma concentrations may serve as a predictive biomarker of disease severity in COVID-19. Prospective studies enrolling larger patient cohorts are ongoing to test this hypothesis.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Katharina Hoeter", - "author_inst": "Department of Anesthesiology, University Medical Center of the Johannes Gutenberg-University Mainz, Germany" - }, - { - "author_name": "Elmo Neuberger", - "author_inst": "Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg University Mainz, Germany" - }, - { - "author_name": "Susanne Fischer", - "author_inst": "Department of Anesthesiology, University Medical Center of the Johannes Gutenberg-University Mainz, Germany" - }, - { - "author_name": "Manuel Herbst", - "author_inst": "Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center Mainz, Germany" - }, - { - "author_name": "Ema Juskeviciute", - "author_inst": "Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg University Mainz, Germany." - }, - { - "author_name": "Heidi Rossmann", - "author_inst": "Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University Mainz, Germany" - }, - { - "author_name": "Martin F Sprinzl", - "author_inst": "Department of Internal Medicine I, University Medical Center of the Johannes Gutenberg-University Mainz, Germany." - }, - { - "author_name": "Perikles Simon", - "author_inst": "Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg University Mainz, Germany" - }, - { - "author_name": "Marc Bodenstein", - "author_inst": "Department of Anesthesiology, University Medical Center of the Johannes Gutenberg-University Mainz, Germany" - }, - { - "author_name": "Michael K.E. Sch\u00e4fer", - "author_inst": "Department of Anesthesiology, University Medical Center of the Johannes Gutenberg-University of Mainz, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.27.21256207", "rel_title": "SARS-CoV-2 antibodies remain detectable 12 months after infection and antibody magnitude is associated with age and COVID-19 severity", @@ -789748,6 +791073,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.29.21256317", + "rel_title": "The comparison of vaccine hesitancy of COVID-19 vaccination in China and the United States", + "rel_date": "2021-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.29.21256317", + "rel_abs": "ObjectivesTo investigate the differences in vaccine hesitancy and preference of the currently available COVID-19 vaccines between two countries, viz. China and the United States (US).\n\nMethodA cross-national survey was conducted in both China and the US, and discrete choice experiments as well as Likert scales were utilized to assess vaccine preference and the underlying factors contributing to the vaccination acceptance. A propensity score matching (PSM) was performed to enable a direct comparison between the two countries.\n\nResultsA total of 9,077 (5,375 and 3,702, respectively, from China and the US) respondents have completed the survey. After propensity score matching, over 82.0% respondents from China positively accept the COVID-19 vaccination, while 72.2% respondents form the US positively accept it. Specifically, only 31.9% of Chinese respondents were recommended by a doctor to have COVID-19 vaccination, while more than half of the US respondents were recommended by a doctor (50.2%), local health board (59.4%), or friends and families (64.8%). The discrete choice experiments revealed that respondents from the US attached the greatest importance to the efficacy of COVID-19 vaccines (44.41%), followed by the cost of vaccination (29.57%), whereas those from China held a different viewpoint that the cost of vaccination covers the largest proportion in their trade-off (30.66%), and efficacy ranked as the second most important attribute (26.34%). Also, respondents from China tend to concerned much more about the adverse effect of vaccination (19.68% vs 6.12%) and have lower perceived severity of being infected with COVID-19.\n\nConclusionWhile the overall acceptance and hesitancy of COVID-19 vaccination in both countries are high, underpinned distinctions between countries are observed. Owing to the differences in COVID-19 incidence rates, cultural backgrounds, and the availability of specific COVID-19 vaccines in two countries, the vaccine rollout strategies should be nation-dependent.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Taoran Liu", + "author_inst": "Jinan University" + }, + { + "author_name": "Zonglin He", + "author_inst": "Jinan University" + }, + { + "author_name": "Jian Huang", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ni Yan", + "author_inst": "Jinan University" + }, + { + "author_name": "Qian Chen", + "author_inst": "Jinan University" + }, + { + "author_name": "Fengqiu Huang", + "author_inst": "Jinan University" + }, + { + "author_name": "Yuejia Zhang", + "author_inst": "Jinan University" + }, + { + "author_name": "Omoloma M Akinwunmi", + "author_inst": "University of Ibadan Nigeria" + }, + { + "author_name": "Babatunde O Akinwunmi", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Casper J. P. Zhang", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Yibo Wu", + "author_inst": "Peking University Health Science Center" + }, + { + "author_name": "Wai-kit Ming", + "author_inst": "Jinan University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.29.21256358", "rel_title": "Transition in Learning Approach for Undergraduate Medical Students of Bangladesh in Covid 19 Pandemic: A Situation Analysis", @@ -791035,85 +792423,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.27.21256193", - "rel_title": "Real-world effectiveness of Ad26.COV2.S adenoviral vector vaccine for COVID-19", - "rel_date": "2021-04-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.27.21256193", - "rel_abs": "In light of the massive and rapid vaccination campaign against COVID-19, continuous real-world effectiveness and safety assessment of the FDA-authorized vaccines is critical to amplify transparency, build public trust, and ultimately improve overall health outcomes. In this study, we leveraged large-scale longitudinal curation of electronic health records (EHRs) from the multi-state Mayo Clinic health system (MN, AZ, FL, WN, IA). We compared the infection rate of 2,195 individuals who received a single dose of the Ad26.COV2.S vaccine from Johnson & Johnson (J&J) to the infection rate of 21,950 unvaccinated, propensity-matched individuals between February 27th and April 14th 2021. Of the 1,779 vaccinated individuals with at least two weeks of follow-up, only 3 (0.17%) tested positive for SARS-CoV-2 15 days or more after vaccination compared to 128 of 17,744 (0.72%) unvaccinated individuals (4.34 fold reduction rate). This corresponds to a vaccine effectiveness of 76.7% (95% CI: 30.3-95.3%) in preventing SARS-CoV-2 infection with onset at least two weeks after vaccination. This data is consistent with the clinical trial-reported efficacy of Ad26.COV2.S in preventing moderate to severe COVID-19 with onset at least 14 days after vaccine administration (66.9%; 95% CI: 59.0-73.4%). Due to the recent authorization of the Ad26.COV2.S vaccine, there are not yet enough hospitalizations, ICU admissions, or deaths within this cohort to robustly assess the effect of vaccination on COVID-19 severity, but these outcomes will be continually assessed in near-real-time with our platform. Collectively, this study provides further evidence that a single dose of Ad26.COV2.S is highly effective in preventing SARS-CoV-2 infection and reaffirms the urgent need to continue mass vaccination efforts globally.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Juan Corchado-Garcia", - "author_inst": "nference" - }, - { - "author_name": "David Puyraimond-Zemmour", - "author_inst": "nference" - }, - { - "author_name": "Travis Hughes", - "author_inst": "nference" - }, - { - "author_name": "Tudor Cristea-Platon", - "author_inst": "nference" - }, - { - "author_name": "Patrick Lenehan", - "author_inst": "nference" - }, - { - "author_name": "Colin Pawlowski", - "author_inst": "nference" - }, - { - "author_name": "Sairam Bade", - "author_inst": "nference Labs" - }, - { - "author_name": "John C OHoro", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Gregory J Gores", - "author_inst": "nference" - }, - { - "author_name": "Amy W Williams", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Andrew D Badley", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "John Halamka", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Abinash Virk", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Melanie D Swift", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Tyler Wagner", - "author_inst": "nference" - }, - { - "author_name": "Venky Soundararajan", - "author_inst": "nference" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.29.21256255", "rel_title": "Objective and Subjective COVID-19 Vaccine Reactogenicity by Age and Vaccine Manufacturer", @@ -791250,6 +792559,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.29.21256260", + "rel_title": "COMPARISON OF PERFORMANCE CHARACTERISTICS BETWEEN LATERAL FLOW, ELISA AND ELECTROCHEMILUMINESCENCE IMMUNOASSAYS FOR THE DETECTION OF SARS-COV-2 ANTIBODIES AMONG HEALTHCARE WORKERS", + "rel_date": "2021-04-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.29.21256260", + "rel_abs": "BackgroundMedical professionals and researchers have been urging the need for wide and rapid testing of citizens in order to plan measures that can contain the spread of the virus. Antibody tests play an important role throughout the patient care pathway and are vital for the management and surveillance of the virus. Although RT-PCR is considered as the gold standard, serological tests based on antibodies are helpful for on-time detection. We performed one to one assessment of point-of-care lateral flow assay (POCTs), enzyme immunoassay (EIAs), electrochemiluminescence immunoassay (CLIA), to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) IgG antibody.\n\nMaterials and Methods611 healthcare workers were recruited between November and December 2020 at Central Research Laboratory, KIMS. Collected serum samples were analysed according to manufacturers protocol. The Standard Q IgG/IgM combo assay, Anti-SARS CoV-2 Human IgG ELISA, and the Elecsys(R) to measure the IgG titer of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).\n\nResultsThe kits displayed a sensitivity of 61.2%,79.5%, 91.8% and specificity of 61.7%,64.1%,80.2% for the Standard Q IgG/IgM combo assay, Anti-SARS CoV-2 Human IgG ELISA, and the Elecsys(R) in order.\n\nConclusionOur results indicate high sensitivity and specificity for the Elecsys(R) assay compared to Anti-SARS CoV-2 Human IgG ELISA, the Standard Q IgG/IgM combo assay.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "SHINCY M R", + "author_inst": "Central Research Laboratory , KIMS" + }, + { + "author_name": "Vandana Govindan", + "author_inst": "Central Research Laboratory, KIMS" + }, + { + "author_name": "Sudhakar H H", + "author_inst": "Kempegowda Institute of Medical Science" + }, + { + "author_name": "Venkatesha V T", + "author_inst": "Kempegowda Institute of Medical Science" + }, + { + "author_name": "Padmapriya K", + "author_inst": "Kempegowda Institute of Medical Science" + }, + { + "author_name": "Ravikumar K L", + "author_inst": "Central Research Laboratory , KIMS" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.29.21256002", "rel_title": "SARS-CoV-2 sculpts the immune system to induce sustained virus-specific nai\u0308ve-like and memory B cell responses", @@ -792739,73 +794087,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.28.441832", - "rel_title": "An enveloped virus-like particle vaccine expressing a stabilized prefusion form of the SARS-CoV-2 spike protein elicits potent immunity after a single dose.", - "rel_date": "2021-04-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.28.441832", - "rel_abs": "Development of efficacious single dose vaccines would substantially aid efforts to stop the uncontrolled spread of the COVID-19 pandemic. We evaluated enveloped virus-like particles (eVLPs) expressing various forms of the SARS-CoV-2 spike protein and several adjuvants in an effort to identify a COVID-19 vaccine candidate efficacious after a single dose. The eVLPs expressing a modified prefusion form of SARS-CoV-2 spike protein were selected as they induced the highest antibody binding titers and neutralizing activity after a single injection in mice. Formulation of SARS-CoV-2 S eVLPs with aluminum phosphate resulted in balanced induction of IgG2 and IgG1 isotypes and antibody binding and neutralization titers were undiminished for more than 3 months after a single immunization. A single dose of this candidate, VBI-2902a (prefusion S eVLPs formulated with aluminum phosphate), protected Syrian golden hamsters from challenge with SARS-CoV-2 and supports the on-going clinical evaluation of VBI-2902a as a potential single dose vaccine against COVID-19.\n\nHighlightsO_LIVBI-2902a is a VLP-based vaccine candidate against SARS-COV-2\nC_LIO_LIVBI-2902a contains VLPs pseudotyped with a modified prefusion SARS-COV-2 S in Alum.\nC_LIO_LIVBI-2902a induces robust neutralization antibody response against SARS-COV-2 S\nC_LIO_LIVBI-2902a protects hamsters from SARS-CoV-2 induced lung inflammation\nC_LIO_LIA single dose of VBI-2902a provides protective benefit in hamsters\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Anne-Catherine Fluckiger", - "author_inst": "VBIvaccines" - }, - { - "author_name": "Barthelemy Ontsouka", - "author_inst": "VBI Vaccines" - }, - { - "author_name": "Jasminka Bozic", - "author_inst": "VBI Vaccines" - }, - { - "author_name": "Abebaw Diress", - "author_inst": "VBI Vaccines" - }, - { - "author_name": "Tanvir Ahmed", - "author_inst": "VBI Vaccines" - }, - { - "author_name": "Tamara Berthoud", - "author_inst": "VBI Vaccines" - }, - { - "author_name": "Mingmin Liao", - "author_inst": "VIDO, University of Saskatchewan" - }, - { - "author_name": "Anh Tran", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Diana Duque", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Michael McCluskie", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Francisco Diaz-Mitoma", - "author_inst": "VBI Vaccines" - }, - { - "author_name": "David E Anderson", - "author_inst": "VBI Vaccines" - }, - { - "author_name": "Catalina Soare", - "author_inst": "VBI Vaccines" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.04.29.441258", "rel_title": "Allelic variation in Class I HLA determines pre-existing memory responses to SARS-CoV-2 that shape the CD8+ T cell repertoire upon viral exposure", @@ -793138,6 +794419,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.29.442018", + "rel_title": "Molecular interactions of the M and E integral membrane proteins of SARS-CoV-2", + "rel_date": "2021-04-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.29.442018", + "rel_abs": "Specific lipid-protein interactions are key for cellular processes, and even more so for the replication of pathogens. The COVID-19 pandemic has drastically changed our lives and cause the death of nearly three million people worldwide, as of this writing. SARS-CoV-2 is the virus that causes the disease and has been at the center of scientific research over the past year. Most of the research on the virus is focused on key players during its initial attack and entry into the cellular host; namely the S protein, its glycan shield, and its interactions with the ACE2 receptors of human cells. As cases continue to raise around the globe, and new mutants are identified, there is an urgent need to understand the mechanisms of this virus during different stages of its life cycle. Here, we consider two integral membrane proteins of SARS-CoV-2 known to be important for viral assembly and infectivity. We have used microsecond-long all-atom molecular dynamics to examine the lipid-protein and protein-protein interactions of the membrane (M) and envelope (E) structural proteins of SARS-CoV-2 in a complex membrane model. We contrast the two proposed protein complexes for each of these proteins, and quantify their effect on their local lipid environment. This ongoing work also aims to provide molecular-level understanding of the mechanisms of action of this virus to possibly aid in the design of novel treatments.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Viviana Monje-Galvan", + "author_inst": "University of Chicago" + }, + { + "author_name": "Gregory A Voth", + "author_inst": "University of Chicago" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.04.29.441933", "rel_title": "Possible link between higher transmissibility of B.1.617 and B.1.1.7 variants of SARS-CoV-2 and increased structural stability of its spike protein and hACE2 affinity", @@ -794645,73 +795949,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.26.21256152", - "rel_title": "Effectiveness of portable air filtration on reducing indoor aerosol counts: preclinical observational trials", - "rel_date": "2021-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.26.21256152", - "rel_abs": "ObjectiveTo assess the effectiveness of aerosol filtration by portable air cleaning devices with high efficiency particulate air (HEPA) filters used in addition to standard building heating ventilation and air-conditioning (HVAC).\n\nMethodsTest rooms, including a hospital single-patient room, were filled with test aerosol to simulate aerosol movement. Aerosol counts were measured over time with various portable air cleaning devices and room ventilation systems to quantify the aerosol concentration reduction rate and overall clearance rate.\n\nResultsPortable air cleaners were very effective in removing aerosols, especially for the devices with high flow rate. In a small control room, the aerosols were cleared 4 to 5 times faster with portable air cleaners than the room with HVAC alone. A single bed hospital room equipped with an excellent ventilation rate ([~] 14 air changes per hour) can clear the aerosols in 20 minutes. However, with the addition of two air cleaners, the clearance time became 3 times faster (in 6 minutes and 30 seconds).\n\nConclusionsPortable air cleaning devices with HEPA filtration were highly effective at removing aerosols. To clear aerosols (above 90% clearance) in under 10 minutes requires around 25 air changes per hour; readily feasible with air cleaners. Inexpensive portable air cleaning devices should be considered for small and enclosed spaces in health care settings such as inpatient rooms, personal protective equipment donning/doffing stations, and staff tea rooms. Portable air cleaners are particularly important where there is limited ability to reduce aerosol transmission with building HVAC ventilation.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Junghoon Lee", - "author_inst": "Department of Mechanical Engineering, University of Melbourne, Melbourne, Australia" - }, - { - "author_name": "Max Rounds", - "author_inst": "Department of Mechanical Engineering, University of Melbourne, Melbourne, Australia" - }, - { - "author_name": "Forbes McGain", - "author_inst": "Intensive Care, Western Health, Melbourne, Australia" - }, - { - "author_name": "Robyn Schofield", - "author_inst": "School of Earth Sciences, University of Melbourne, Melbourne, Australia" - }, - { - "author_name": "Grant Skidmore", - "author_inst": "Department of Mechanical Engineering, University of Melbourne, Melbourne, Australia" - }, - { - "author_name": "Imogen Wadlow", - "author_inst": "School of Earth Sciences, University of Melbourne, Melbourne, Australia" - }, - { - "author_name": "Kevin Kevin", - "author_inst": "Department of Mechanical Engineering, University of Melbourne, Melbourne, Australia" - }, - { - "author_name": "Ashley Stevens", - "author_inst": "5 Hospital Engineering, Royal Melbourne Hospital, Melbourne, Australia" - }, - { - "author_name": "Caroline Marshall", - "author_inst": "Infection Prevention and Surveillance Service, Royal Melbourne Hospital, Melbourne, Australia" - }, - { - "author_name": "Lou Irving", - "author_inst": "Respiratory Medicine, Royal Melbourne Hospital, Melbourne, Australia" - }, - { - "author_name": "Marion Kainer", - "author_inst": "Department of Infectious Diseases, Western Health, Melbourne, Australia" - }, - { - "author_name": "Kirsty Buising", - "author_inst": "Victorian Infectious Diseases service, Royal Melbourne Hospital, Melbourne, Australia" - }, - { - "author_name": "Jason Monty", - "author_inst": "Department of Mechanical Engineering, University of Melbourne, Melbourne, Australia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.26.21256154", "rel_title": "Optimal use of COVID19 Ag-RDT screening at border crossings to prevent community transmission: a modeling analysis", @@ -794980,6 +796217,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.27.441655", + "rel_title": "A broadly neutralizing antibody protects against SARS-CoV, pre-emergent bat CoVs, and SARS-CoV-2 variants in mice", + "rel_date": "2021-04-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.27.441655", + "rel_abs": "SARS-CoV in 2003, SARS-CoV-2 in 2019, and SARS-CoV-2 variants of concern (VOC) can cause deadly infections, underlining the importance of developing broadly effective countermeasures against Group 2B Sarbecoviruses, which could be key in the rapid prevention and mitigation of future zoonotic events. Here, we demonstrate the neutralization of SARS-CoV, bat CoVs WIV-1 and RsSHC014, and SARS-CoV-2 variants D614G, B.1.1.7, B.1.429, B1.351 by a receptor-binding domain (RBD)-specific antibody DH1047. Prophylactic and therapeutic treatment with DH1047 demonstrated protection against SARS-CoV, WIV-1, RsSHC014, and SARS-CoV-2 B1.351infection in mice. Binding and structural analysis showed high affinity binding of DH1047 to an epitope that is highly conserved among Sarbecoviruses. We conclude that DH1047 is a broadly neutralizing and protective antibody that can prevent infection and mitigate outbreaks caused by SARS-like strains and SARS-CoV-2 variants. Our results argue that the RBD conserved epitope bound by DH1047 is a rational target for pan Group 2B coronavirus vaccines.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "David Martinez", + "author_inst": "The University of North Carolina at Chapel Hill" + }, + { + "author_name": "Alexandra Schaefer", + "author_inst": "The University of North Carolina at Chapel Hill" + }, + { + "author_name": "Sophie Gobeil", + "author_inst": "Duke School of Medicine" + }, + { + "author_name": "Dapeng Li", + "author_inst": "Duke University" + }, + { + "author_name": "Gabriela De la Cruz", + "author_inst": "The University of North Carolina at Chapel Hill" + }, + { + "author_name": "Robert Parks", + "author_inst": "Duke University" + }, + { + "author_name": "Xiaozhi Lu", + "author_inst": "Duke University" + }, + { + "author_name": "Maggie Barr", + "author_inst": "Duke University" + }, + { + "author_name": "Kartik Manne", + "author_inst": "Duke University" + }, + { + "author_name": "Katayoun Mansouri", + "author_inst": "Duke University" + }, + { + "author_name": "Robert J Edwards", + "author_inst": "Duke University" + }, + { + "author_name": "Boyd Yount", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Kara Anasti", + "author_inst": "Duke University" + }, + { + "author_name": "Stephanie Montgomery", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Xiaoying Shen", + "author_inst": "Duke University" + }, + { + "author_name": "Tongqing Zhou", + "author_inst": "NIH" + }, + { + "author_name": "Peter Kwong", + "author_inst": "NIH" + }, + { + "author_name": "Barney Graham", + "author_inst": "NIH" + }, + { + "author_name": "John R. Mascola", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "David Montefiori", + "author_inst": "Duke University" + }, + { + "author_name": "Munir Alam", + "author_inst": "Duke University" + }, + { + "author_name": "Gregory Sempowski", + "author_inst": "Duke University School of Medicine" + }, + { + "author_name": "Kevin Wiehe", + "author_inst": "Duke University" + }, + { + "author_name": "Priyamvada Acharya", + "author_inst": "Duke University" + }, + { + "author_name": "Barton Haynes", + "author_inst": "Duke University" + }, + { + "author_name": "Ralph S. Baric", + "author_inst": "University of North Carolina at Chapel Hill" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.27.441707", "rel_title": "Therapeutic effect of CT-P59 against SARS-CoV-2 South African variant", @@ -796451,89 +797807,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.04.23.21255973", - "rel_title": "EVIDENCE FOR BIOLOGICAL AGE ACCELERATION AND TELOMERE2 SHORTENING IN COVID-19 SURVIVORS", - "rel_date": "2021-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.23.21255973", - "rel_abs": "Introduction & Backgroundthe SARS-CoV-2 infection determines the COVID-19 syndrome characterized, in the worst cases, by severe respiratory distress, pulmonary and cardiac fibrosis, inflammatory cytokines release, and immunodepression. This condition has led to the death of about 2.15% of the total infected world population so far. Among survivors, the presence of the so-called post-COVID19 syndrome (PPCS) is a common finding. In patients who survived the SARS-CoV-2 infection, overt PPCS presents one or more symptoms such as fatigue, dyspnea, memory loss, sleep disorders, and difficulty concentrating. The pathophysiology of PPCS is currently poorly understood, and whether epigenetic mechanisms are involved in this process is unexplored.\n\nMethods & ResultsIn this study, a cohort of 117 COVID19 survivors (post-COVID19) and 144 non-infected volunteers (COVID19-free) were analyzed using pyrosequencing of defined CpG islands previously identified as suitable for biological age determination. Besides, telomere length (TL) and ACE2 and DPP4 receptor expression were determined. The results show a consistent biological age increase in the post-covid population (58,44 {+/-} 14,66 ChronoAge Vs. 67,18 {+/-} 10,86 BioAge, P<0,0001), determining a DeltaAge acceleration of 10,45 {+/-} 7,29 years (+5.25 years above range of normality) compared to 3,68 {+/-} 8,17 years for the COVID19-free population (P<0,0001). A significant telomere shortening parallels this finding in the post-COVID19 cohort compared to COVID19-free subjects (post-COVID19 TL: 3,03 {+/-} 2,39 Kb vs. COVID19-free: 10,67 {+/-} 11,69 Kb; P<0,0001). Additionally, ACE2 expression was decreased in post-COVID19 patients compare to COVID19-free, while DPP-4 did not change.\n\nConclusionIn light of these observations, we hypothesize that some epigenetic alterations are associated with the post-COVID19 condition, particularly in the younger (<60 years). Although the consequences of such modifications on the long-term clinical outcome remain unclear, they might indicate a direction to investigate the pathophysiological basis of the post-COVID19 syndrome.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Alessia Mongelli", - "author_inst": "ICS MAUGERI S.P.A." - }, - { - "author_name": "veronica barbi", - "author_inst": "ICS Maugeri Pavia" - }, - { - "author_name": "michela gottardi zamperla", - "author_inst": "ICS Maugeri Pavia" - }, - { - "author_name": "sandra atlante", - "author_inst": "ICS Maugeri PAVIA" - }, - { - "author_name": "Luana Forleo", - "author_inst": "ICS Maugeri" - }, - { - "author_name": "Marialisa Nesta", - "author_inst": "policlinico Gemelli" - }, - { - "author_name": "massimo massetti", - "author_inst": "policlinico Gemelli" - }, - { - "author_name": "alfredo pontecorvi", - "author_inst": "policlinico Gemelli" - }, - { - "author_name": "simona nanni", - "author_inst": "Policlinico Gemelli" - }, - { - "author_name": "antonella farsetti", - "author_inst": "Institute for Systems Analysis and Computer Science \"A. Ruberti\"" - }, - { - "author_name": "oronzo catalano", - "author_inst": "ICS Maugeri Pavia" - }, - { - "author_name": "maurizio bussotti", - "author_inst": "ICS Maugeri Milano" - }, - { - "author_name": "laura dalla vecchia", - "author_inst": "ICS MAUGERI MILANO" - }, - { - "author_name": "tiziana bachetti", - "author_inst": "ICS Maugeri Pavia" - }, - { - "author_name": "fabio martelli", - "author_inst": "Policlinico San Donato" - }, - { - "author_name": "maria teresa la rovere", - "author_inst": "ICS Maugeri MONTESCANO" - }, - { - "author_name": "carlo gaetano", - "author_inst": "ICS Maugeri Pavia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.21.21255782", "rel_title": "Mathematical modeling suggests pre-existing immunity to SARS-CoV-2", @@ -796838,6 +798111,20 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.21.21255889", + "rel_title": "Evaluation of Different Types of Face Masks to Limit the Spread of SARS CoV 2, A Modeling Study", + "rel_date": "2021-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.21.21255889", + "rel_abs": "We updated a published mathematical model of SARS-CoV-2 transmission with laboratory-derived source and wearer protection efficacy estimates for a variety of face masks to estimate their impact on COVID-19 incidence and related mortality in the United States. When used at already-observed population rates of 80% for those [≥]65 years and 60% for those <65 years, face masks are associated with 69% (cloth) to 78% (medical procedure mask) reductions in cumulative COVID-19 infections and 82% (cloth) to 87% (medical procedure mask) reductions in related deaths over a 6-month timeline in the model, assuming a basic reproductive number of 2.5. If cloth or medical procedure masks source control and wearer protection efficacies are boosted about 30% each to 84% and 60% by cloth over medical procedure masking, fitters, or braces, the COVID-19 basic reproductive number of 2.5 could be reduced to an effective reproductive number [≤] 1.0, and from 6.0 to 2.3 for a variant of concern similar to delta (B.1.617.2).\n\nArticle Summary LineAdapting a published SARS-CoV-2 transmission model together with updated, laboratory-derived source control and wearer protection efficacy estimates for a variety of face coverings as well as N95 respirators, we demonstrate that community masking as currently practiced has likely reduced cases and deaths and that this benefit can be increased with wider adoption of better performing masks.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.27.21256140", "rel_title": "Predicting daily COVID-19 case rates from SARS-CoV-2 RNA concentrations across a diversity of wastewater catchments", @@ -798197,33 +799484,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.04.27.441661", - "rel_title": "Rapid structure-function insights via hairpin-centric analysis of big RNA structure probing datasets", - "rel_date": "2021-04-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.27.441661", - "rel_abs": "The functions of RNA are often tied to its structure, hence analyzing structure is of significant interest when studying cellular processes. Recently, large-scale structure probing (SP) studies have enabled assessment of global structure-function relationships via standard data summarizations or local folding. Here, we approach structure quantification from a hairpin-centric perspective where putative hairpins are identified in SP datasets and used as a means to capture local structural effects. This has the advantage of rapid processing of big (e.g., transcriptome-wide) data as RNA folding is circumvented, yet it captures more information than simple data summarizations. We reformulate a statistical learning algorithm we previously developed to significantly improve precision of hairpin detection, then introduce a novel nucleotide-wise measure, termed the hairpin-derived structure level (HDSL), which captures local structuredness by accounting for the presence of likely hairpin elements. Applying HDSL to data from recent studies recapitulates, strengthens, and expands on their findings which were obtained by more comprehensive folding algorithms, yet our analyses are orders of magnitude faster. These results demonstrate that hairpin detection is a promising avenue for global and rapid structure-function analysis, furthering our understanding of RNA biology and the principal features which drive biological insights from SP data.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Pierce Radecki", - "author_inst": "UC Davis" - }, - { - "author_name": "Rahul Uppuluri", - "author_inst": "UC Davis" - }, - { - "author_name": "Sharon Aviran", - "author_inst": "UC Davis" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.04.26.21256081", "rel_title": "Clinical validation of RCSMS: a rapid and sensitive CRISPR-Cas12a test for the molecular detection of SARS-CoV-2 from saliva", @@ -798404,6 +799664,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.18.21255682", + "rel_title": "Effective vaccine allocation strategies, balancing economy with infection control against COVID-19 in Japan", + "rel_date": "2021-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.18.21255682", + "rel_abs": "Due to COVID-19, many countries including Japan have implemented a suspension of economic activities for infection control. It has contributed to reduce the transmission of COVID-19 but caused severe economic losses. Today, several promising vaccines have been developed and are already being distributed in some countries. Therefore, we evaluated various vaccine and intensive countermeasure strategies with constraint of economic loss using SEIR model to obtain knowledge of how to balance economy with infection control in Japan. Our main result is that the vaccination strategy that prioritizes younger generation outperformed the other strategies in terms of deaths. On the other hand, when we focused on strategies that prioritize older generation, as Japan has decided to do, the optimal vaccination strategy was determined by the basic reproduction number and acceptable economic loss. The strategy vaccinating the young next to the old age group was the best when acceptable economic loss was high, or the basic reproduction number was low. Alternatively, the strategy vaccinating the middle next to the old age group was superior to the others with a moderate acceptable economic loss and the high basic reproduction number setting.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Satoshi Sunohara", + "author_inst": "School of medicine, Hokkaido University" + }, + { + "author_name": "Toshiaki Asakura", + "author_inst": "School of medicine, Hokkaido University" + }, + { + "author_name": "Takashi Kimura", + "author_inst": "Public health, Faculty of Medicine, Hokkaido University" + }, + { + "author_name": "Shun Ozawa", + "author_inst": "School of medicine, Hokkaido University" + }, + { + "author_name": "Satoshi Oshima", + "author_inst": "School of medicine, Hokkaido University" + }, + { + "author_name": "Daigo Yamauchi", + "author_inst": "School of medicine, Hokkaido University" + }, + { + "author_name": "Akiko Tamakoshi", + "author_inst": "Public health, Faculty of Medicine, Hokkaido University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.26.441280", "rel_title": "SARS-CoV-2 Entry Protein TMPRSS2 and Its Homologue, TMPRSS4 Adopts Structural Fold Similar to Blood Coagulation and Complement Pathway Related Proteins", @@ -799955,129 +801258,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.04.25.441271", - "rel_title": "Production of a Highly Immunogenic Antigen from SARS-CoV-2 by Covalent Coupling of the Receptor Binding Domain of Spike Protein to a Multimeric Carrier", - "rel_date": "2021-04-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.25.441271", - "rel_abs": "Since the discovery of SARS-CoV-2, several antigens have been proposed to be part of COVID-19 vaccines. The receptor binding domain (RBD) of Spike protein is one of the promising candidates to develop effective vaccines since it can induce potent neutralizing antibodies. We previously reported the production of RBD in Pichia pastoris and showed it is structurally identical to the protein produced in mammalian HEK-293T cells. In this work we designed an RBD multimer construct with the purpose of increasing RBD immunogenicity. We produced multimeric particles by a transpeptidation reaction between the RBD expressed in P. pastoris and Lumazine Synthase from Brucella abortus (BLS), which is a highly immunogenic and very stable decameric protein of 170 kDa. We vaccinated mice with two doses 30 days apart, and then we measured humoral immune response. When the number of RBD copies coupled to BLS was high (6-7 RBD molecules per BLS decamer, in average), the immune response was significantly better than that elicited by RBD alone or even by RBD-BLS comprising low number of RBD copies (1-2 RBD molecules per BLS decamer). Remarkably, the construct with high number of RBD copies induced high IgG titers with high neutralizing capacity. Furthermore, a superior immune response was observed when Al(OH)3 adjuvant was added to this formulation, exhibiting a higher titer of neutralizing antibodies. Altogether our results suggest that RBD covalent coupled to BLS forming a multimer-particle shows an advantageous architecture to the antigen-presentation to the immune system which enhances immune responses. This new antigen should be considered a potent candidate for a protein-based vaccine.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "- Argentinian AntiCovid Consortium", - "author_inst": "-" - }, - { - "author_name": "Paula M. Berguer", - "author_inst": "Fundaci\u00f3n Instituto Leloir, IIBBA, Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas (CONICET), Buenos Aires, Argentina." - }, - { - "author_name": "Matias Blaustein", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Luis Bredeston", - "author_inst": "Universidad de Buenos Aires. Facultad de Farmacia y Bioqu\u00edmica. Departamento de Qu\u00edmica Biol\u00f3gica. Junin 965 C1113AAD. Buenos Aires, Argentina. CONICET-Universi" - }, - { - "author_name": "Patricio O. Craig", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Qu\u00edmica Biol\u00f3gica. Buenos Aires, Argentina. CONICET-Universidad de Buenos" - }, - { - "author_name": "Fernanda Elias", - "author_inst": "Instituto de Ciencia y Tecnolog\u00eda Dr. C\u00e9sar Milstein (Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas-Fundaci\u00f3n Pablo Cassar\u00e1). Saladillo 2468 (C1440" - }, - { - "author_name": "Paola C. Farr\u00e9", - "author_inst": "Laboratorio Pablo Cassara S.R.L." - }, - { - "author_name": "Natalia B. Fern\u00e1ndez", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Hern\u00e1n G. Gentili", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Yamila G\u00e1ndola", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Javier Gasulla", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Gustavo E. Gudesblat", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Mar\u00eda G. Herrera", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Lorena I. Iba\u00f1ez", - "author_inst": "Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas (CONICET). Departamento de Qu\u00edmica Inorg\u00e1nica, Anal\u00edtica y Qu\u00edmica F\u00edsica, Facultad de Ciencias Exact" - }, - { - "author_name": "Tommy Idrovo-Hidalgo", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Alejnadro D Nadra", - "author_inst": "Universidad de Buenos Aires" - }, - { - "author_name": "Diego G. Noseda", - "author_inst": "Universidad Nacional de San Mart\u00edn - CONICET. Instituto de Investigaciones Biotecnol\u00f3gicas (IIBio). San Mart\u00edn, Buenos Aires, Argentina." - }, - { - "author_name": "Carlos H. Pav\u00e1n", - "author_inst": "Universidad de Buenos Aires, Facultad de Farmacia y Bioqu\u00edmica. Buenos Aires, Argentina. CONICET-Universidad de Buenos Aires. Facultad de Medicina. LANAIS-PROEM" - }, - { - "author_name": "Mar\u00eda F. Pavan", - "author_inst": "Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas (CONICET). Departamento de Qu\u00edmica Inorg\u00e1nica, Anal\u00edtica y Qu\u00edmica F\u00edsica, Facultad de Ciencias Exact" - }, - { - "author_name": "Mar\u00eda F. Pignataro", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Ernesto Roman", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Qu\u00edmica Biol\u00f3gica. Buenos Aires, Argentina. CONICET-Universidad de Buenos" - }, - { - "author_name": "Lucas A.M Ruberto", - "author_inst": "Universidad de Buenos Aires. Facultad de Farmacia y Bioqu\u00edmica. Departamento de Microbiolog\u00eda, Inmunolog\u00eda, Biotecnolog\u00eda y Gen\u00e9tica. Buenos Aires, Argentina. C" - }, - { - "author_name": "Natalia Rubinstein", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Mar\u00eda V. Sanchez", - "author_inst": "Instituto de Medicina y Biolog\u00eda Experimental de Cuyo (IMBECU).Centro Cient\u00edfico Tecnol\u00f3gico de Mendoza ( CCT-Mendoza), CONICET, Universidad Nacional de Cuyo, (" - }, - { - "author_name": "Javier Santos", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Diana E. Wetzler", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Qu\u00edmica Biol\u00f3gica. Buenos Aires, Argentina. CONICET-Universidad de Buenos" - }, - { - "author_name": "Alicia M. Zelada", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Laboratorio de Agrobiotecnolog" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.04.25.441372", "rel_title": "Control-theoretic immune tradeoffs explain SARS-CoV-2 virulence and transmission variation", @@ -800310,6 +801490,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.23.441209", + "rel_title": "Insertions in SARS-CoV-2 genome caused by template switch and duplications give rise to new variants of potential concern", + "rel_date": "2021-04-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.23.441209", + "rel_abs": "The appearance of multiple new SARS-CoV-2 variants during the winter of 2020-2021 is a matter of grave concern. Some of these new variants, such as B.1.617.2, B.1.1.7, and B.1.351, manifest higher infectivity and virulence than the earlier SARS-CoV-2 variants, with potential dramatic effects on the course of the COVID-19 pandemic. So far, analysis of new SARS-CoV-2 variants focused primarily on point nucleotide substitutions and short deletions that are readily identifiable by comparison to consensus genome sequences. In contrast, insertions have largely escaped the attention of researchers although the furin site insert in the spike protein is thought to be a determinant of SARS-CoV-2 virulence and other inserts might have contributed to coronavirus pathogenicity as well. Here, we investigate insertions in SARS-CoV-2 genomes and identify 347 unique inserts of different lengths. We present evidence that these inserts reflect actual virus variance rather than sequencing errors. Two principal mechanisms appear to account for the inserts in the SARS-CoV-2 genomes, polymerase slippage and template switch that might be associated with the synthesis of subgenomic RNAs. We show that inserts in the Spike glycoprotein can affect its antigenic properties and thus merit monitoring. At least, three inserts in the N-terminal domain of the Spike (ins245IME, ins246DSWG, and ins248SSLT) that were first detected in 2021 are predicted to lead to escape from neutralizing antibodies, whereas other inserts might result in escape from T-cell immunity.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Sofiya K Garushyants", + "author_inst": "NIH" + }, + { + "author_name": "Igor B Rogozin", + "author_inst": "NCBI/NLM/NIH" + }, + { + "author_name": "Eugene V. Koonin", + "author_inst": "NIH" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.24.21256042", "rel_title": "A Novel Evidence-Based Predictor Tool for Hospitalization and Length of Stay: Insights from COVID19 Patients in New York City", @@ -801601,41 +802808,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.23.21256007", - "rel_title": "Effects of the COVID-19 Pandemic on Park Use in U.S. Cities", - "rel_date": "2021-04-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.23.21256007", - "rel_abs": "IntroductionThe COVID-19 pandemic focused attention on city parks as important public resources. However, it is unknown how city park use in 2020 compared to prior years and whether COVID-19 may have exacerbated racial/ethnic inequities in access. Moreover, traditional methods of measuring park use present major drawbacks.\n\nMethodsWe analyzed monthly mobility data derived from a large panel of smartphone devices, cross-referenced with a database of parks locations sourced from local agencies. We assessed park use trends in 44 of the 50 most populous U.S. cities from January 2018 to November 2020 using interrupted time series regressions. We also compared parks to other city amenities (e.g., gyms and libraries).\n\nResultsBased on a sample of 5,559 city parks, park visits declined by 14.6% (95% CI [9.2, 19.7], p < 0.001) from March through November 2020, compared to prior levels and trends. When we segmented the COVID-19 period by time of widespread closures (March-April) and partial-to-full reopenings (May-November), we estimated a larger reduction during closures (35.7% reduction, 95% CI [33.5, 37.8], p < 0.001) compared to the reduction during reopenings (8.0% reduction, 95% CI [1.9, 13.7], p = 0.001). Reductions for other amenities were more prolonged. In park service areas where a greater proportion of residents were White, reopening was associated with more visits, suggesting that racial privilege influenced access.\n\nConclusionsSmartphone mobility data can address a data availability gap for monitoring park use. Park use only declined modestly in 2020. Opportunities exist to make access more racially equitable.\n\nSignificance statementParks are public resources that promote health. Little is known about how parks have been used during the COVID-19 pandemic, when parks have become particularly important public spaces. This study introduces an approach to monitor park use over time, using location data from smartphones. This approach enabled the authors to evaluate trends in park use during the pandemic, including major gaps in visits to parks according to whether they mostly served White residents or residents of color. This big data approach offers advantages over traditional methods for monitoring park use and can help city officials to identify and address inequities in park access.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jonathan Jay", - "author_inst": "Boston University School of Public Health" - }, - { - "author_name": "Felicia Heykoop", - "author_inst": "Boston University School of Public Health" - }, - { - "author_name": "Linda Hwang", - "author_inst": "Trust for Public Land" - }, - { - "author_name": "Jorrit de Jong", - "author_inst": "Harvard Kennedy School of Government" - }, - { - "author_name": "Michelle Kondo", - "author_inst": "United States Forest Service" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.21.21255880", "rel_title": "Efficacy of universal masking for source control and personal protection from simulated cough and exhaled aerosols in a room", @@ -801860,6 +803032,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, + { + "rel_doi": "10.1101/2021.04.22.440932", + "rel_title": "Convergent evolution of SARS-CoV-2 spike mutations, L452R, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India", + "rel_date": "2021-04-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.22.440932", + "rel_abs": "As the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic expands, genomic epidemiology and whole genome sequencing are being constantly used to investigate its transmissions and evolution. In the backdrop of the global emergence of \"variants of concern\" (VOCs) during December 2020 and an upsurge in a state in the western part of India since January 2021, whole genome sequencing and analysis of spike protein mutations using sequence and structural approaches was undertaken to identify possible new variants and gauge the fitness of current circulating strains.\n\nPhylogenetic analysis revealed that the predominant clade in circulation was a distinct newly identified lineage B.1.617 possessing common signature mutations D111D, G142D, L452R, E484Q, D614G and P681R, in the spike protein including within the receptor binding domain (RBD). Of these, the mutations at residue positions 452, 484 and 681 have been reported in other globally circulating lineages. The structural analysis of RBD mutations L452R and E484Q along with P681R in the furin cleavage site, revealed that these may possibly result in increased ACE2 binding and rate of S1-S2 cleavage resulting in better transmissibility. The same two RBD mutations indicated decreased binding to select monoclonal antibodies (mAbs) and may affect their neutralization potential. Experimental validation against a wider panel of mAbs, sera from vaccinees and those that recovered from natural infection needs to be studied.\n\nThe emergence of such local variants through the accumulation of convergent mutations during the COVID-19 second wave needs to be further investigated for their public health impact in the rest of the country and its possibility of becoming a VOC.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Sarah Cherian", + "author_inst": "ICMR-National Institute of Virology, Pune" + }, + { + "author_name": "Varsha Potdar", + "author_inst": "ICMR-National Institute of Virology, Pune" + }, + { + "author_name": "Santosh Jadhav", + "author_inst": "ICMR-National Institute of Virology, Pune" + }, + { + "author_name": "Pragya Yadav", + "author_inst": "ICMR-National Institute of Virology, Pune" + }, + { + "author_name": "Nivedita Gupta", + "author_inst": "Indian Council of Medical Research, New Delhi" + }, + { + "author_name": "Mousmi Das", + "author_inst": "ICMR-National Institute of Virology, Pune" + }, + { + "author_name": "Partha Rakshit", + "author_inst": "National Centre for Disease Control, New Delhi" + }, + { + "author_name": "Sujeet Singh", + "author_inst": "National Centre for Disease Control, New Delhi" + }, + { + "author_name": "Priya Abraham", + "author_inst": "ICMR-National Institute of Virology, Pune" + }, + { + "author_name": "Samiran Panda", + "author_inst": "Indian Council of Medical Research, New Delhi" + }, + { + "author_name": "- NIC team", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.04.20.21255670", "rel_title": "Protection of previous SARS-CoV-2 infection is similar to that of BNT162b2 vaccine protection: A three-month nationwide experience from Israel", @@ -803279,57 +804510,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2021.04.22.441041", - "rel_title": "Prefusion conformation of SARS-CoV-2 receptor-binding domain favors interactions with human receptor ACE2", - "rel_date": "2021-04-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.22.441041", - "rel_abs": "A new coronavirus pandemic COVID-19, caused by Severe Acute Respiratory Syndrome coronavirus (SARS-CoV-2), poses a serious threat across continents, leading the World Health Organization to declare a Public Health Emergency of International Concern. In order to block the entry of the virus into human host cells, major therapeutic and vaccine design efforts are now targeting the interactions between the SARS-CoV-2 spike (S) glycoprotein and the human cellular membrane receptor angiotensin-converting enzyme, hACE2. By analyzing cryo-EM structures of SARS-CoV-2 and SARS-CoV-1, we report here that the homotrimer SARS-CoV-2 S receptor-binding domain (RBD) that binds with hACE2 has expanded in size, undergoing a large conformational change relative to SARS-CoV-1 S protein. Protomer with the up-conformational form of RBD, which binds with hACE2, exhibits higher intermolecular interactions at the RBD-ACE2 interface, with differential distributions and the inclusion of specific H-bonds in the CoV-2 complex. Further interface analysis has shown that interfacial water promotes and stabilizes the formation of CoV-2/hACE2 complex. This interaction has caused a significant structural rigidification, favoring proteolytic processing of S protein for the fusion of the viral and cellular membrane. Moreover, conformational dynamics simulations of RBD motions in SARS-CoV-2 and SARS-CoV-1 point to the role in modification in the RBD dynamics and their likely impact on infectivity.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Nitesh Kumawat", - "author_inst": "School of Mathematics, Statistics and Computational Sciences, Central University of Rajasthan, Bandarsindri, Ajmer, India." - }, - { - "author_name": "Andrejs Tucs", - "author_inst": "Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan" - }, - { - "author_name": "Soumen Bera", - "author_inst": "Department of Microbiology, University of Tennessee, Knoxville, USA" - }, - { - "author_name": "Gennady N. Chuev", - "author_inst": "Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia." - }, - { - "author_name": "Marina V. Fedotova", - "author_inst": "G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russia." - }, - { - "author_name": "Koji Tsuda", - "author_inst": "Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan" - }, - { - "author_name": "Sergey E. Kruchinin", - "author_inst": "G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russia." - }, - { - "author_name": "Adnan Sljoka", - "author_inst": "RIKEN Center for Advanced Intelligence Project, Tokyo, Japan." - }, - { - "author_name": "AMIT CHAKRABORTY", - "author_inst": "Sikkim University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.04.20.440658", "rel_title": "Gut microbiota diversity and C-Reactive Protein are predictors of disease severity in COVID-19 patients", @@ -803730,6 +804910,125 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.20.21255810", + "rel_title": "A Multicenter Evaluation of Blood Purification with Seraph 100 Microbind Affinity Blood Filter for the Treatment of Severe COVID-19: A Preliminary Report", + "rel_date": "2021-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.20.21255810", + "rel_abs": "ObjectiveThe Seraph(R)100 Microbind Affinity Blood Filter(R) (Seraph 100) is an extracorporeal medical countermeasure that can remove many pathogens from blood, including the SARS-CoV-2 virus. The aim of this study was to evaluate safety and efficacy of Seraph 100 treatment for severe coronavirus disease 2019 (COVID-19).\n\nDesignMulticenter retrospective observational cohort study.\n\nSettingIntensive care units across four of thirteen participating sites who have completed data extraction.\n\nPatientsCritically ill COVID-19 patients treated with Seraph 100 under an Emergency Use Authorization (n=53) and historical control patients who met criteria for treatment (n=46).\n\nInterventionExtracorporeal treatment with the Seraph 100 filter.\n\nMeasurements and Main ResultsAt baseline, the median age was 61 years, 72.7% were male, and 59.6% required mechanical ventilation. The groups were matched in terms of sex, race/ethnicity, body mass index, APACHE II score, need for mechanical ventilation, and other COVID-19 treatments. However, patients in the Seraph 100 group were younger with a median age of 61 years (IQR 42-65) compared to controls who had a median age of 64 (IQR 56-68, p=0.036). The Seraph 100 group also had a lower median Charlson comorbidity index (2, IQR 0-3) compared to control patients (3, IQR 2-4, p=0.006). Mortality was lower in the Seraph 100 treated group compared to the historical controls (37.7% vs 67.4%, respectively, p=0.003). Multivariable logistic regression analysis yielded an odds ratio of 0.27 (95% confidence interval 0.09-0.79, p=0.016). Of the 53 patients treated with Seraph 100, only 1 patient experienced a serious adverse event (transient hypotension at the start of the treatment which required a brief period of vasopressor support).\n\nConclusionsThese data suggest that broad spectrum, pathogen agnostic, extracorporeal blood purification technologies can be safely and effectively deployed to meet new pathogen threats as an adjunct to standard treatments while awaiting the development of directed pharmacologic therapies and/or vaccines.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Stephen A Chitty", + "author_inst": "Southeast Georgia Health System, Brunswick, GA" + }, + { + "author_name": "Sarah Mobbs", + "author_inst": "Southeast Georgia Health System, Brunswick, GA" + }, + { + "author_name": "Brian S Rifkin", + "author_inst": "Hattiesburg Clinic, Hattiesburg, MS" + }, + { + "author_name": "Steven W Stogner", + "author_inst": "Hattiesburg Clinic, Hattiesburg, MS" + }, + { + "author_name": "Michael S Lewis", + "author_inst": "Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA" + }, + { + "author_name": "Jaime Betancourt", + "author_inst": "Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA" + }, + { + "author_name": "Jeffrey DellaVolpe", + "author_inst": "Methodist Hospital, San Antonio, TX" + }, + { + "author_name": "Fadi Abouzahr", + "author_inst": "Methodist Hospital, San Antonio, TX" + }, + { + "author_name": "Andrew M Wilhelm", + "author_inst": "University of Mississippi Medical Center, Jackson, MS" + }, + { + "author_name": "Harold M Szerlip", + "author_inst": "Baylor Scott & White Health, Dallas, TX" + }, + { + "author_name": "Robert M Gaeta", + "author_inst": "Dwight D. Eisenhower Army Medical Center, Fort Gordon, GA" + }, + { + "author_name": "Ian Rivera", + "author_inst": "Dwight D. Eisenhower Army Medical Center, Fort Gordon, GA" + }, + { + "author_name": "James D Oliver", + "author_inst": "Walter Reed National Military Medical Center, Bethesda, MD" + }, + { + "author_name": "Stephen W Olson", + "author_inst": "Walter Reed National Military Medical Center, Bethesda, MD" + }, + { + "author_name": "Subrata Debnath", + "author_inst": "University of Texas Health San Antonio, San Antonio, TX" + }, + { + "author_name": "Sean P Barnett", + "author_inst": "University of Texas Health San Antonio, San Antonio, TX" + }, + { + "author_name": "Amay Parikh", + "author_inst": "Advent Health, Orlando, FL" + }, + { + "author_name": "Robert J Walter", + "author_inst": "Brooke Army Medical Center, San Antonio, TX" + }, + { + "author_name": "Mai T Nguyen", + "author_inst": "Brooke Army Medical Center, San Antonio, TX" + }, + { + "author_name": "Breandan Sullivan", + "author_inst": "University of Colorado Anschutz, Aurora, CO" + }, + { + "author_name": "Karl C Alcover", + "author_inst": "Uniformed Services University of the Heath Sciences, Bethesda, MD" + }, + { + "author_name": "Ian J Stewart", + "author_inst": "Uniformed Services University of the Heath Sciences, Bethesda, MD" + }, + { + "author_name": "Kathleen P Pratt", + "author_inst": "Uniformed Services University of the Heath Sciences, Bethesda, MD" + }, + { + "author_name": "Kumar Sharma", + "author_inst": "University of Texas Health San Antonio, San Antonio, TX" + }, + { + "author_name": "Kevin K Chung", + "author_inst": "Uniformed Services University of the Heath Sciences, Bethesda, MD" + }, + { + "author_name": "- PURIFY INVESTIGATORS", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.04.20.21255792", "rel_title": "Retrospective Assessment of Treatments of Hospitalized Covid-19 Patients", @@ -805125,41 +806424,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.15.21252192", - "rel_title": "Previous COVID-19 infection but not Long-COVID is associated with increased adverse events following BNT162b2/Pfizer vaccination", - "rel_date": "2021-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.15.21252192", - "rel_abs": "ImportanceUnderstanding Adverse Events (AEs) associated with SARS-CoV-2 vaccination has public health implications, especially with regards to vaccine hesitancy.\n\nObjectiveTo establish whether individuals with prior history of COVID-19 were more likely to experience AEs after BNT162b2/Pfizer vaccination, than those without previous COVID-19, and whether COVID-19-vaccination interval influenced AE severity.\n\nDesignAn observational study explored AEs after vaccination. Participants were invited to complete an electronic survey, capturing self-reported COVID-19 symptoms, PCR/antibody results, and AEs following first dose of BNT162b2/Pfizer vaccine. In a subset where PCR/antibody results could be verified, a sensitivity analysis was conducted.\n\nSettingThree North-East England hospital Trusts in the United Kingdom.\n\nParticipantsHealthcare workers formed an opportunistic sample - 265 of 974 reported prior positive SARS-CoV-2 PCR and/or antibody.\n\nExposureAll participants had received their first dose of BNT162b2/Pfizer vaccine.\n\nMain Outcomes and MeasuresNature, severity, duration, and onset of self-reported AEs (reported via a modified version of the FDA Toxicity Grading Scale for vaccine-associated AEs), was compared between those with and without a prior history of COVID-19, using 2-way ANCOVA and logistic regression. Effects of age, gender, illness-vaccine interval, and ongoing symptoms ( Long-COVID) on AEs, were also explored.\n\nResultsOf 974 respondents (81% female, mean age 48), 265 (27%) reported previous COVID-19 infection. Within this group (symptoms median 8.9 months pre-vaccination), 30 (11%) complained of Long-COVID. The proportion reporting one moderate/severe symptom was higher in the previous COVID-19 group (56% v 47%, OR=1.5 [95%CI, 1.1-2.0], p=.009), with fever, fatigue, myalgia-arthralgia and lymphadenopathy significantly more common. There was no significant relationship between illness-vaccine interval and symptom composite score (rs=0.09, p=.44). Long-COVID was not associated with worse AEs in comparison to the group without previous COVID-19. In the smaller sensitivity analysis cohort (412 people) similar findings were obtained although only myalgia and arthralgia remained significant.\n\nConclusions and RelevancePrior COVID-19 infection but not ongoing Long-COVID symptoms were associated with an increase in the risk of self-reported adverse events following BNT162b2/Pfizer vaccination. COVID-19 illness-vaccination interval did not significantly influence AEs. This data can support education around vaccine-associated AEs and, through improved understanding, help to combat vaccine hesitancy.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSDoes previous COVID-19 infection or Long-COVID increase the frequency of Adverse Events (AEs) following first dose of BNT162b2/Pfizer vaccination?\n\nFindingsIn a survey-based observational study, healthcare workers in the United Kingdom reported AEs experienced after their first dose of BNT162b2/Pfizer vaccine. Prior COVID-19 infection, but not Long-COVID, were associated with increased risk of self-reported AEs including lymphadenopathy post-vaccination. Duration since COVID-19 infection did not affect severity of AEs.\n\nMeaningOur study can inform education and understanding of AEs associated with COVID-19 vaccination and help to combat vaccine hesitancy.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Rachael Kathleen Raw", - "author_inst": "Newcastle University" - }, - { - "author_name": "Clive Kelly", - "author_inst": "South Tees Hospitals NHS Foundation Trust" - }, - { - "author_name": "Jon Rees", - "author_inst": "Sunderland University" - }, - { - "author_name": "Caroline Wroe", - "author_inst": "South Tees Hospitals NHS Foundation Trust" - }, - { - "author_name": "David Robert Chadwick", - "author_inst": "South Tees Hospitals NHS Foundation Trust" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.14.21255443", "rel_title": "Association of in-hospital use of ACE-I/ARB and COVID-19 outcomes in African American population", @@ -805388,6 +806652,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.17.21255440", + "rel_title": "Understanding the barriers to pooled SARS-CoV-2 testing in the United States", + "rel_date": "2021-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.17.21255440", + "rel_abs": "Pooled testing for SARS-CoV-2 detection is instrumental for increasing test capacity while decreasing test cost, key factors for sustainable, long-term surveillance measures. While numerous pooled approaches have been described, uptake by labs has been limited. We surveyed 90 US labs to understand the barriers to implementing pooled testing.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Eli P Fenichel", + "author_inst": "Yale University" + }, + { + "author_name": "Anna Gilbert", + "author_inst": "Yale University" + }, + { + "author_name": "Gregg S. Gonsalves", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Anne L Wyllie", + "author_inst": "Yale School of Public Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.15.21255348", "rel_title": "Patient symptoms and experience following COVID-19: results from a UK wide survey", @@ -807058,53 +808353,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.20.440654", - "rel_title": "Rapid and Efficient Inactivation of SARS-CoV-2 from Surfaces using UVC Light Emitting Diode Device", - "rel_date": "2021-04-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.20.440654", - "rel_abs": "Efforts are underway to develop countermeasures to prevent the environmental spread of COVID-19 pandemic caused by SARS-CoV-2. Physical decontamination methods like Ultraviolet radiation has shown to be promising. Here, we describe a novel device emitting ultraviolet C radiation (UVC), called NuvaWave, to rapidly and efficiently inactivate SARS-CoV-2. SARS-CoV-2 was dried on a chambered glass slides and introduced in a NuvaWave robotic testing unit. The robot simulated waving NuvaWave over the virus at a pre-determined UVC radiation dose of 1, 2, 4 and 8 seconds. Post-UVC exposure, virus was recovered and titered by plaque assay in Vero E6 cells. We observed that relative control (no UVC exposure), exposure of the virus to UVC for one or two seconds resulted in a >2.9 and 3.8 log10 reduction in viral titers, respectively. Exposure of the virus to UVC for four or eight seconds resulted in a reduction of greater than 4.7-log10 reduction in viral titers. The NuvaWave device inactivates SARS-CoV-2 on surfaces to below the limit of detection within one to four seconds of UVC irradiation. This device can be deployed to rapidly disinfect surfaces from SARS-CoV-2, and to assist in mitigating its spread in a variety of settings.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Varun Dwivedi", - "author_inst": "Texas Biomedical Research Institute" - }, - { - "author_name": "Jun-Gyu Park", - "author_inst": "Texas Biomedical Research Institute" - }, - { - "author_name": "Stephen Grenon", - "author_inst": "UV Innovators, Inc" - }, - { - "author_name": "Nicholas Medendorp Jr.", - "author_inst": "UV Innovators, Inc" - }, - { - "author_name": "Cory Hallam", - "author_inst": "Texas Biomedical Research Institute" - }, - { - "author_name": "Jordi B Torrelles", - "author_inst": "Texas Biomedical Research Institute" - }, - { - "author_name": "Luis Martinez-Sobrido", - "author_inst": "Texas Biomedical Research Institute" - }, - { - "author_name": "Viraj Kulkarni", - "author_inst": "Texas Biomedical Research Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.04.20.440676", "rel_title": "Eicosanoid signaling as a therapeutic target in middle-aged mice with severe COVID-19", @@ -807333,6 +808581,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.13.21255447", + "rel_title": "Genetic risk prediction of COVID-19 susceptibility and severity in the Indian population", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255447", + "rel_abs": "Host genetic variants can determine the susceptibility to COVID-19 infection and severity as noted in a recent Genome-wide Association Study (GWAS) by Pairo-Castineira et al.1. Given the prominent genetic differences in Indian sub-populations as well as differential prevalence of COVID-19, here, we deploy the previous study and compute genetic risk scores in different Indian sub-populations that may predict the severity of COVID-19 outcomes in them. We computed polygenic risk scores (PRSs) in different Indian sub-populations with the top 100 single-nucleotide polymorphisms (SNPs) with a p-value cutoff of 10-6 derived from the previous GWAS summary statistics1. We selected SNPs overlapping with the Indian Genome Variation Consortium (IGVC) and with similar frequencies in the Indian population. For each population, median PRS was calculated, and a correlation analysis was performed to test the association of these genetic risk scores with COVID-19 mortality. We found a varying distribution of PRS in Indian sub-populations. Correlation analysis indicates a positive linear association between PRS and COVID-19 deaths. This was not observed with non-risk alleles in Indian sub-populations. Our analyses suggest that Indian sub-populations differ with respect to the genetic risk for developing COVID-19 mediated critical illness. Combining PRSs with other observed risk-factors in a Bayesian framework can provide a better prediction model for ascertaining high COVID-19 risk groups. This has a potential utility in the design of more effective vaccine disbursal schemes.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "P Prakrithi", + "author_inst": "CSIR-Institute Of Genomics And Integrative Biology" + }, + { + "author_name": "Priya Lakra", + "author_inst": "IIT-Delhi" + }, + { + "author_name": "- The Indian Genome Variation Consortium", + "author_inst": "" + }, + { + "author_name": "Durai Sundar", + "author_inst": "IIT-Delhi" + }, + { + "author_name": "Manav Kapoor", + "author_inst": "Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, 1425 Madison Ave, New York, NY, USA" + }, + { + "author_name": "Mitali Mukerji", + "author_inst": "CSIR- Institute of Genomics and Integrative Biology" + }, + { + "author_name": "Ishaan Gupta", + "author_inst": "IIT DELHI" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2021.04.14.21255507", "rel_title": "A seq2seq model to forecast the COVID-19 cases, deaths and reproductive R numbers in US counties", @@ -808792,89 +810083,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.13.21255345", - "rel_title": "Self-collected oral, nasal and saliva samples yield sensitivity comparable to professional-collected oro-nasopharyngeal swabs in SARS-CoV-2 diagnosis", - "rel_date": "2021-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255345", - "rel_abs": "Summary/AbstractO_ST_ABSIntroductionC_ST_ABSContainment of the COVID-19 pandemic requires broad-scale testing. Laboratory capacities for real-time-PCR were increased, and are complemented by Ag-tests. However, sample-collection still requires qualified personnel and protective equipement, may produce transmission to others during conduct and travel, and is perceived uncomfortable. We tested sensitivity of three simplified self-sampling techniques compared to professional-collected combined oro-nasopharyngeal samples (cOP/NP).\n\nMethodsFrom 62 symptomatic COVID-19 outpatients, we obtained simultaneously three self- and one professional-collected sample after initial confirmation in a testing centre: (i) combination swab (tongue, cheek, both nasal vestibula, MS, (ii) saliva sponge combined with both nasal vestibula, SN, and (iii) gargled tap water, GW, (iv) professionally-collected cOP/NP (standard). We compared the results of SARS-CoV-2 PCR-assays detecting E-gene and ORF1ab for the different sample types and performed bivariate statistical analysis to determine the variables reducing sensitivity of the self-collecting procedures.\n\nResultsSARS-CoV-2 RNA was detected in all 62 professionally-collected cOP/NP. MS and SN samples showed a sensitivity of 95.2% (95%CI 86.5-99.0) and GW samples of 88.7% (78.1-95.3). Compared to the median ct-values of cOP/NP samples for E-gene (20.7) and ORF1ab (20.2) these were higher for MS (22.6 and 21.8), SN (23.3 and 22.3), and for GW (30.3 and 29.8).\n\nFor MS and SN samples but not for GW specimens, false negativity in bivariate analysis was associated with non-German mother-tongue, number of sampling errors, and with symptom duration. For symptom duration of [≤]8 days, test sensitivity for SN samples was 98.2% (95%CI 90.4-100.0) and for MS 96.4% (95%CI 87.7-99.6) and drops after day 8 below 90%.\n\nDiscussionThe study is limited to sensitivity of self-collection in symptomatic patients. Still, in this group, self-collected oral/nasal/saliva samples are reliable alternatives to professional-collected cOP/NP samples, if symptom duration does not exceed eight days and operational errors are minimized. Self-sampling could contribute to up-scaling of safe and efficient testing.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Maximilian Gertler", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Tropical Medicine and Intern" - }, - { - "author_name": "Eva Krause", - "author_inst": "Robert Koch Institute - Centre for Biological Threats and Special Pathogens, Division Highly Pathogenic Viruses ZBS1, Berlin, Germany" - }, - { - "author_name": "Welmoed van Loon", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Tropical Medicine and Intern" - }, - { - "author_name": "Niklas Krug", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Tropical Medicine and Intern" - }, - { - "author_name": "Franka Kausch", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Tropical Medicine and Intern" - }, - { - "author_name": "Chiara Rohardt", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Tropical Medicine and Intern" - }, - { - "author_name": "Heike Roessig", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Medical D" - }, - { - "author_name": "Janine Michel", - "author_inst": "Robert Koch Institute - Centre for Biological Threats and Special Pathogens, Division Highly Pathogenic Viruses ZBS1, Berlin, Germany" - }, - { - "author_name": "Andreas Nitsche", - "author_inst": "Robert Koch Institute - Centre for Biological Threats and Special Pathogens, Division Highly Pathogenic Viruses ZBS1, Berlin, Germany" - }, - { - "author_name": "Marcus A. Mall", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Departmen" - }, - { - "author_name": "Olga Nikolai", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Tropical Medicine and Intern" - }, - { - "author_name": "Franziska Hommes", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Tropical Medicine and Intern" - }, - { - "author_name": "Susen Burock", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Charite C" - }, - { - "author_name": "Andreas K. Lindner", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Tropical Medicine and Intern" - }, - { - "author_name": "Frank P. Mockenhaupt", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Tropical Medicine and Intern" - }, - { - "author_name": "Ulrich Pison", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin; Department of Anaesthesiology and Inte" - }, - { - "author_name": "Joachim Seybold", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Medical D" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.15.21255533", "rel_title": "Evaluation of seven different rapid methods for nucleic acid detection of SARS-COV-2 virus", @@ -809159,6 +810367,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.15.21255577", + "rel_title": "Diagnostic accuracy of SARS-CoV-2 rapid antigen detection testing in symptomatic and asymptomatic children in the clinical setting", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.15.21255577", + "rel_abs": "ImportanceAntigen-based rapid diagnostic tests (RDTs) have shown good sensitivity for SARS-CoV-2 detection in adults and are used in children despite the lack data from children.\n\nObjectiveWe evaluated the diagnostic performance of the Panbio-COVID-19 Ag Rapid Test Device (P-RDT) in symptomatic and asymptomatic children against reverse-transcription polymerase chain reaction (RT-PCR) on nasopharyngeal swabs (NPS).\n\nDesignProspective diagnostic study from 11.2020 to 03.2021.\n\nSettingSingle-center.\n\nParticipantsConsecutive symptomatic and asymptomatic participants 0-16yo.\n\nInterventionTwo NPS for both RT-PCR and P-RDT.\n\nMain outcomeP-RDT sensitivity and specificity.\n\nResultsEight-hundred and twenty-two participants completed the study, of which 533 (64.9%) were symptomatic. Among the 119 (14.5%) RT-PCR positive patients, the overall P-RDT sensitivity was 0.66 (95%CI 0.57-0.74). Mean viral load (VL) was higher among P-RDT positive than negative ones (p<0.001). Sensitivity was 0.87 in specimens with VL>1.0E6 copies/mL (95%CI 0.87-1.00), which is the accepted cut-off for the presence of infectious virus, and decreased to 0.67 (95%CI 0.59-0.76) for specimens >1.0E3 copies/mL.\n\nAmong symptomatic participants, the P-RDT displayed a sensitivity of 0.73 (95%CI 0.64-0.82), which peaked at 1.00 at 2 days post onset of symptoms (DPOS; 95%CI 1.00-1.00), then decreased to 0.56 (95%CI 0.23-0.88) at 5 DPOS. There was a trend towards lower P-RDT sensitivity in symptomatic children <12 years (0.62 [95%CI 0.45-0.78]) versus [≥]12 years (0.80 [95%CI 0.69-0.91]; p=0.09). VL which was significantly lower in asymptomatic participants than in symptomatic ones (p<0.001). The P-RDT displayed a sensitivity of 0.43 (95%CI 0.26-0.61).\n\nSpecificity was 1.00 in symptomatic and asymptomatic children (95%CI 0.99-1.00).\n\nConclusion and relevanceThe overall respective 73% and 43% sensitivities of P-RDT in symptomatic and asymptomatic children was below the 80% cut-off recommended by the World Health Organization. These findings are likely explained by lower VLs in children at the time of diagnosis. As expected, we observed a direct correlation between VL and P-RDT sensitivity as well as variation of sensitivity according to DPOS, a major determinant of VL. These data highlight the limitations of RDTs both in symptomatic and asymptomatic children, with the potential exception in early symptomatic children [≥]12yrs where sensitivity reached 80%.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Arnaud L'Huillier", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Matthieu Lacour", + "author_inst": "University of Geneva" + }, + { + "author_name": "Debora Sadiku", + "author_inst": "University of Geneva" + }, + { + "author_name": "Mehdi A Gadiri", + "author_inst": "University of Geneva" + }, + { + "author_name": "Loraine De Siebenthal", + "author_inst": "University of Geneva" + }, + { + "author_name": "Manuel Schibler", + "author_inst": "University of Geneva Hospitals" + }, + { + "author_name": "Isabella Eckerle", + "author_inst": "University Hospitals of Geneva" + }, + { + "author_name": "Selina Pinosch", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Laurent Kaiser", + "author_inst": "University of Geneva Hospitals" + }, + { + "author_name": "Alain Gervaix", + "author_inst": "University Hospitals of Geneva" + }, + { + "author_name": "Alban Glangetas", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Annick Galetto-Lacour", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Laurence Lacroix", + "author_inst": "Geneva University Hospitals" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.19.21255657", "rel_title": "On whether therapeutic plasma exchange is an effective cure for severe/critical COVID-19 pneumonia", @@ -810662,69 +811937,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.04.20.439992", - "rel_title": "Drug repurposing to face Covid-19: Celastrol, a potential leading drug capable of inhibiting SARS-CoV-2 replication and induced inflammation", - "rel_date": "2021-04-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.20.439992", - "rel_abs": "The global emergence of Covid-19 has caused huge human casualties. Clinical manifestations of the disease vary from asymptomatic to lethal, and the symptomatic form can be associated with cytokine storm and non-homeostatic inflammatory response. In face of the urgent demand for effective drugs to treat Covid-19, we have searched for candidate compounds using a drug repurposing approach based on in silico analysis followed by biological validation. Here we identified celastrol, a pentacyclic triterpene isolated from Tripterygium wilfordii Hook F - a plant used in traditional Chinese medicine - as one of the best compounds out of 39 repurposed drug candidates. Celastrol reverted gene expression signature from SARS-CoV-2-infected cells; bound with high-affinity energy to viral molecular targets such as main protease (Mpro) and receptor-biding domain (RBD); inhibited SARS-CoV-2 replication in monkey (Vero and Vero-ACE2) and human (Caco-2 and Calu-3) cell lines; and decreased interleukin-6 (IL-6) secretion in SARS-CoV-2-infected human cell lines. Interestingly, celastrol acted in a concentration-dependent manner, with undetectable signs of cytotoxicity. Therefore, celastrol is a promising lead drug candidate to treat Covid-19 due to its ability to suppress SARS-CoV-2 replication and IL-6 production in infected cells, two critical events in the pathophysiology of this disease.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Carlos A. Fuzo", - "author_inst": "Departamento de An\u00e1lises Cl\u00ednicas, Toxicol\u00f3gicas e Bromatol\u00f3gicas. Faculdade de Ci\u00eancias Farmac\u00eauticas de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Pr" - }, - { - "author_name": "Ronaldo B. Martins", - "author_inst": "Departamento de Biologia Celular e Molecular e Bioagentes Patog\u00eanicos, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, SP, B" - }, - { - "author_name": "Thais F.C. Fraga-Silva", - "author_inst": "Departamento de Bioqu\u00edmica e Imunologia. Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, SP, Brazil." - }, - { - "author_name": "Martin K. Amstalden", - "author_inst": "Departamento de An\u00e1lises Cl\u00ednicas, Toxicol\u00f3gicas e Bromatol\u00f3gicas. Faculdade de Ci\u00eancias Farmac\u00eauticas de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Pr" - }, - { - "author_name": "Thais Canassa-DeLeo", - "author_inst": "Departamento de An\u00e1lises Cl\u00ednicas, Toxicol\u00f3gicas e Bromatol\u00f3gicas. Faculdade de Ci\u00eancias Farmac\u00eauticas de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Pr" - }, - { - "author_name": "Juliano P. Souza", - "author_inst": "Departamento de Biologia Celular e Molecular e Bioagentes Patog\u00eanicos, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, SP, B" - }, - { - "author_name": "Thais M. Lima", - "author_inst": "Departamento de Biologia Celular e Molecular e Bioagentes Patog\u00eanicos, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, SP, B" - }, - { - "author_name": "L\u00facia H. Faccioli", - "author_inst": "Departamento de An\u00e1lises Cl\u00ednicas, Toxicol\u00f3gicas e Bromatol\u00f3gicas. Faculdade de Ci\u00eancias Farmac\u00eauticas de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Pr" - }, - { - "author_name": "Suzelei C. Fran\u00e7a", - "author_inst": "Unidade de Biotecnologia, Universidade de Ribeir\u00e3o Preto, Ribeir\u00e3o Preto, SP, Brazil." - }, - { - "author_name": "V\u00e2nia L.D. Bonato", - "author_inst": "Departamento de Bioqu\u00edmica e Imunologia. Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, SP, Brazil." - }, - { - "author_name": "Eurico A. Neto", - "author_inst": "Departamento de Biologia Celular e Molecular e Bioagentes Patog\u00eanicos, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, SP, B" - }, - { - "author_name": "Marcelo Dias-Baruffi", - "author_inst": "Departamento de An\u00e1lises Cl\u00ednicas, Toxicol\u00f3gicas e Bromatol\u00f3gicas. Faculdade de Ci\u00eancias Farmac\u00eauticas de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Pr" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.04.20.440651", "rel_title": "Comparison of Mucosal and Intramuscular Immunization against SARS-CoV-2 with Replication-Defective and Replicating Single-cycle Adenovirus Vaccines", @@ -810949,6 +812161,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.04.18.21255700", + "rel_title": "Study Pre-protocol for 'BronchStart - The Impact of the COVID-19 Pandemic on the Timing, Age and Severity of Respiratory Syncytial Virus (RSV) Emergency Presentations; a Multi-Centre Prospective Observational Cohort Study'", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.18.21255700", + "rel_abs": "BackgroundBronchiolitis (most frequently caused by Respiratory Syncytial Virus; RSV) is a common winter disease predominantly affecting children under one year of age. It is a common reason for presentations to an Emergency Department (ED) and frequently results in hospital admission, contributing to paediatric units approaching or exceeding capacity each winter. During the SARS-CoV-2 pandemic, the circulation of RSV was dramatically reduced in the United Kingdom and Ireland. Evidence from the Southern Hemisphere and other European countries suggests that as social distancing restrictions for SARS-CoV-2 are relaxed, RSV infection returns, causing delayed or even summer epidemics, with different age distributions.\n\nStudy questionThe ability to track, anticipate and respond to a surge in RSV cases is critical for planning acute care delivery. There is an urgent need to understand the onset of RSV spread at the earliest opportunity. This will influence service planning, to inform clinicians whether the population at risk is a wider age range than normal, and whether there are changes in disease severity. This information is also needed to inform decision on the timing of passive immunisation of children at higher risk of hospitalisation, intensive care admission or death with RSV infection, which is a public health priority.\n\nMethods and likely impactThis multi-centre prospective observational cohort study will use a well-established research network (Paediatric Emergency Research in the UK and Ireland, PERUKI) to report in real time cases of RSV infection in children aged under two years, through the collection of essential, but non-identifying patient information. Forty centres will gather initial data on age, index of multiple deprivation quintile, clinical features on presentation, and co-morbidities. Each case will be followed up at 7 days to identify treatment, viral diagnosis and outcome. Information be released on a weekly basis and used to support clinical decision making.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Thomas C Williams", + "author_inst": "University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Mark D Lyttle", + "author_inst": "Faculty of Health and Applied Sciences, University of the West of England, Bristol, UK" + }, + { + "author_name": "Steve Cunningham", + "author_inst": "Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Ian Sinha", + "author_inst": "Alder Hey Children's Hospital, Liverpool, UK" + }, + { + "author_name": "Olivia Swann", + "author_inst": "Department of Child Life and Health, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Abigail Maxwell-Hodkinson", + "author_inst": "University of Liverpool Medical School, Liverpool, UK" + }, + { + "author_name": "Damian Roland", + "author_inst": "Paediatric Emergency Medicine Leicester Academic (PEMLA) Group, Leicester Royal Infirmary, Leicester, UK" + }, + { + "author_name": "- Paediatric Emergency Research in the UK and Ireland (PERUKI)", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.04.19.21255715", "rel_title": "Identification of clinical features associated with mortality in COVID-19 patients", @@ -812848,97 +814107,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.04.15.440089", - "rel_title": "Substantial Differences in SARS-CoV-2 Antibody Responses Elicited by Natural Infection and mRNA Vaccination", - "rel_date": "2021-04-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.15.440089", - "rel_abs": "We analyzed data from two ongoing COVID-19 longitudinal serological surveys in Orange County, CA., between April 2020 and March 2021. A total of 8,476 finger stick blood specimens were collected before and after an aggressive mRNA vaccination campaign. IgG levels were determined using a multiplex antigen microarray containing 10 SARS-CoV-2 antigens, 4 SARS, 3 MERS, 12 Common CoV, and 8 Influenza antigens. Twenty-six percent of 3,347 specimens from unvaccinated Orange County residents in December 2020 were SARS-CoV-2 seropositive. The Ab response was predominantly against nucleocapsid (NP), full length spike and the spike S2 domain. Anti-receptor binding domain (RBD) reactivity was low and there was no cross-reactivity against SARS S1 or SARS RBD. An aggressive mRNA vaccination campaign at the UCI Medical Center started on December 16, 2020 and 6,724 healthcare workers were vaccinated within 3 weeks. Seroprevalence increased from 13% in December to 79% in January, 93% in February and 99% in March. mRNA vaccination induced much higher Ab levels especially against the RBD domain and significant cross-reactivity against SARS RBD and S1 was also observed. Nucleocapsid protein Abs can be used to distinguish individuals in a population of vaccinees to classify those who have been previously infected and those who have not, because nucleocapsid is not in the vaccine. Previously infected individuals developed higher Ab titers to the vaccine than those who have not been previously exposed. These results indicate that mRNA vaccination rapidly induces a much stronger and broader Ab response than SARS-CoV-2 infection.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Rafael Ramiro de Assis", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Aarti Jain", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Rie Nakajima", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Algis Jasinskas", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Saahir Khan", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Anton Palma", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Daniel M. Parker", - "author_inst": "University of California Irvine School of Medicine" - }, - { - "author_name": "Anthony Chau", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Amanda Leung", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Christina Grabar", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Fjolla Muqolli", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Ghali Khalil", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Jessica Colin Escobar", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Jenny Ventura", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Huw Davies", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Bruce Albala", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Bernadette Boden-Albala", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Sebastian Schubl", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Philip L Felgner", - "author_inst": "University of California Irvine School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.04.18.440366", "rel_title": "An Immune Cell Atlas Reveals Dynamic COVID-19 Specific Neutrophil Programming Amendable to Dexamethasone Therapy", @@ -813235,6 +814403,81 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.19.440414", + "rel_title": "Low dose inocula of SARS-CoV-2 B.1.1.7 variant initiate more robust infections in the upper respiratory tract of hamsters than earlier D614G variants", + "rel_date": "2021-04-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.19.440414", + "rel_abs": "There is a lack of experimental evidence to explain how the B.1.1.7 variant spreads more quickly than pre-existing variants in humans. We found that B.1.1.7 displays increased competitive fitness over earlier D614G lineages in an in-vitro system. Furthermore,, we demonstrated that B.1.1.7 variant is able to replicate and shed more efficiently in the nasal cavity than other variants with lower dose and shorter duration of exposure.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Bobo Wing-Yee Mok", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Honglian Liu", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Siu-Ying Lau", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Shaofeng Deng Deng", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Siwen Liu", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Rachel Chun-Yee Tam", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Timothy Ting-Leung Ng", + "author_inst": "The Hong Kong Polytechnic University" + }, + { + "author_name": "Jake Siu-Lun Leung", + "author_inst": "The Hong Kong Polytechnic University" + }, + { + "author_name": "Pui Wang", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Kelvin Kai-Wang To", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Jasper Fuk-Woo Chan", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Kwok-Hung Chan", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Kwok-Yung Yuen", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Gilman Kit-Hang Siu", + "author_inst": "The Hong Kong Polytechnic University" + }, + { + "author_name": "Honglin Chen", + "author_inst": "University of Hong Kong" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.17.440288", "rel_title": "Emergence of a recurrent insertion in the N-terminal domain of the SARS-CoV-2 spike glycoprotein", @@ -814638,65 +815881,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.04.16.21255618", - "rel_title": "Adverse effects of COVID-19 vaccination: machine learning and statistical approach to identify and classify incidences of morbidity and post-vaccination reactogenicity", - "rel_date": "2021-04-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.16.21255618", - "rel_abs": "Good vaccine safety and reliability are essential to prevent infectious disease spread. A small but significant number of apparent adverse reactions to the new COVID-19 vaccines have been reported. Here, we aim to identify possible common causes for such adverse reactions with a view to enabling strategies that reduce patient risk by using patient data to classify and characterise patients those at risk of such reactions. We examined patient medical histories and data documenting post-vaccination effects and outcomes. The data analyses were conducted by different statistical approaches followed by a set of machine learning classification algorithms. In most cases, similar features were significantly associated with poor patient reactions. These included patient prior illnesses, admission to hospitals and SARS-CoV-2 reinfection. The analyses indicated that patient age, gender, allergic history, taking other medications, type-2 diabetes, hypertension and heart disease are the most significant pre-existing factors associated with risk of poor outcome and long duration of hospital treatments, pyrexia, headache, dyspnoea, chills, fatigue, various kind of pain and dizziness are the most significant clinical predictors. The machine learning classifiers using medical history were also able to predict patients most likely to have complication-free vaccination with an accuracy score above 85%. Our study identifies profiles of individuals that may need extra monitoring and care (e.g., vaccination at a location with access to comprehensive clinical support) to reduce negative outcomes through classification approaches. Important classifiers achieving these reactions notably included allergic susceptibility and incidence of heart disease or type-2 diabetes.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Md. Martuza Ahamad", - "author_inst": "Bangabandhu Sheikh Mujibur Rahman Science and Technology University" - }, - { - "author_name": "Sakifa Aktar", - "author_inst": "Bangabandhu Sheikh Mujibur Rahman Science and Technology University" - }, - { - "author_name": "Md. Jamal Uddin", - "author_inst": "Bangabandhu Sheikh Mujibur Rahman Science and Technology University" - }, - { - "author_name": "Md. Rashed-Al-Mahfuz", - "author_inst": "University of Rajshahi" - }, - { - "author_name": "AKM Azad", - "author_inst": "University of Technology Sydney" - }, - { - "author_name": "Shahadat Uddin", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Salem A. Alyami", - "author_inst": "Imam Mohammad Ibn Saud Islamic University (IMSIU)" - }, - { - "author_name": "Iqbal H. Sarker", - "author_inst": "Chittagong University of Engineering & Technology" - }, - { - "author_name": "Pietro Lio", - "author_inst": "The University of Cambridge" - }, - { - "author_name": "Julian M.W. Quinn", - "author_inst": "The Garvan Institute of Medical Research" - }, - { - "author_name": "Mohammad Ali Moni", - "author_inst": "University of New south Wales" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.04.16.21255616", "rel_title": "Prevalence and Transmission of SARS-CoV-2 in Childcare Facilities: A Longitudinal Study", @@ -815041,6 +816225,41 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.04.16.21255614", + "rel_title": "Evaluating Vaccine Efficacy Against SARS-CoV-2 Infection", + "rel_date": "2021-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.16.21255614", + "rel_abs": "Although interim results from several large placebo-controlled phase 3 trials demonstrated high vaccine efficacy (VE) against symptomatic COVID-19, it is unknown how effective the vaccines are in preventing people from becoming asymptomatically infected and potentially spreading the virus unwittingly. It is more difficult to evaluate VE against SARS-CoV-2 infection than against symptomatic COVID-19 because infection is not observed directly but rather is known to occur between two antibody or RT-PCR tests. Additional challenges arise as community transmission changes over time and as participants are vaccinated on different dates because of staggered enrollment or crossover before the end of the study. Here, we provide valid and efficient statistical methods for estimating potentially waning VE against SARS-CoV-2 infection with blood or nasal samples under time-varying community transmission, staggered enrollment, and blinded or unblinded crossover. We demonstrate the usefulness of the proposed methods through numerical studies mimicking the BNT162b2 phase 3 trial and the Prevent COVID U study. In addition, we assess how crossover and the frequency of diagnostic tests affect the precision of VE estimates.\n\nSummaryWe show how to estimate potentially waning efficacy of COVID-19 vaccines against SARS-CoV-2 infection using blood or nasal samples collected periodically from clinical trials with staggered enrollment of participants and crossover of placebo recipients.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Danyu Lin", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Yu Gu", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Donglin Zeng", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Holly Janes", + "author_inst": "Fred Hutch" + }, + { + "author_name": "Peter Gilbert", + "author_inst": "Fred Hutch" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.15.21255569", "rel_title": "Using rapid (point-of-care) tests for COVID-19: A decision analysis comparing the expected benefit of two screening strategies", @@ -816368,85 +817587,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.15.21253747", - "rel_title": "Multiplex Fragment Analysis Identifies SARS-CoV-2 Variants", - "rel_date": "2021-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.15.21253747", - "rel_abs": "The rapid spread of SARS-CoV-2 Variants of Concern (VOC) necessitates systematic efforts for epidemiological surveillance. The current method for identifying variants is viral whole genome sequencing (WGS). Broad clinical adoption of sequencing is limited by costly equipment, bioinformatics support, technical expertise, and time for implementation. Here we describe a scalable, multiplex, non-sequencing-based capillary electrophoresis assay to affordably screen for SARS-CoV-2 VOC.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Andrew E Clark", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Zhaohui Wang", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Brandi L Cantarel", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Mohammed Kanchwala", - "author_inst": "University of Texas Southwestern Medical" - }, - { - "author_name": "Chao Xing", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Li Chen", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Pei Irwin", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Yan Xu", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Dwight Oliver", - "author_inst": "University of Texas Southwestern Medical" - }, - { - "author_name": "Francesca Lee", - "author_inst": "University of Texas Southwestern Medical" - }, - { - "author_name": "Jeffrey R Gagan", - "author_inst": "University of Texas Southwestern Medical" - }, - { - "author_name": "Jason Y Park", - "author_inst": "University of Texas Southwestern Medical" - }, - { - "author_name": "Laura Filkins", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Alagarraju Muthukumar", - "author_inst": "UT Southwestern Medical Center, Dallas" - }, - { - "author_name": "Ravi Sarode", - "author_inst": "University of Texas Southwestern Medical" - }, - { - "author_name": "Jeffrey A SoRelle", - "author_inst": "University of Texas Southwestern Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.16.440173", "rel_title": "Viral neuroinvasion and neurotropism without neuronal damage in the hACE2 mouse model of COVID-19", @@ -816799,6 +817939,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.11.21255273", + "rel_title": "SARS-CoV-2 Immunogenicity in individuals infected before and after COVID-19 vaccination: Israel, January-March 2021: Implications for vaccination policy", + "rel_date": "2021-04-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.11.21255273", + "rel_abs": "Between December 2020-March 2021 we measured anti-SARS-CoV-2 IgG titers post-vaccination with the BNT162b2 vaccine among 725 Israeli hospital workers. Previously infected individuals who received one dose had higher IgG titres than fully vaccinated, never-infected workers. Post-vaccination infection did not increase IgG titres. Individuals infected post-dose one should receive the second.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Kamal Abu Jabal", + "author_inst": "Ziv Medical Centre, Bar-Ilan University" + }, + { + "author_name": "Hila Ben Amram", + "author_inst": "Ziv Medical Centre" + }, + { + "author_name": "Karine Beiruti", + "author_inst": "Ziv Medical Centre" + }, + { + "author_name": "Ira Brimat", + "author_inst": "Ziv Medical Centre" + }, + { + "author_name": "Ashraf Abu Saada", + "author_inst": "Ziv Medical Centre" + }, + { + "author_name": "Younes Bathish", + "author_inst": "Ziv Medical Centre" + }, + { + "author_name": "Christian Sussan", + "author_inst": "Ziv Medical Centre" + }, + { + "author_name": "Salman Zarka", + "author_inst": "Ziv Medical Centre, Bar-Ilan University" + }, + { + "author_name": "Michael Edelstein", + "author_inst": "Ziv Medical Centre, Bar Ilan University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.15.21255510", "rel_title": "More than a year after the onset of the CoVid-19 pandemic in the UK: lessons learned from a minimalistic model capturing essential features including social awareness and policy making", @@ -818078,37 +819269,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.13.21255328", - "rel_title": "Do people reduce compliance with COVID-19 guidelines following vaccination? A longitudinal analysis of matched UK adults", - "rel_date": "2021-04-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255328", - "rel_abs": "IntroductionCOVID-19 vaccines do not confer immediate immunity and vaccinated individuals may still be at risk of transmitting the virus. Governments have not exempted vaccinated individuals from behavioural measures to reduce the spread of COVID-19, such as practicing social distancing. However, vaccinated individuals may have reduced compliance with these measures, given lower perceived risks.\n\nMethodsWe used monthly panel data from October 2020 - March 2021 in the UK COVID-19 Social Study to assess changes in compliance following vaccination. Compliance was measured with two items on compliance with guidelines in general and compliance with social distancing. We used matching to create comparable groups of individuals by month of vaccination (January, February, or not vaccinated by February) and fixed effects regression to estimate changes in compliance over the study period.\n\nResultsCompliance increased between October 2020 - March 2021, regardless of vaccination status or month of vaccination. There was no clear evidence that vaccinated individuals decreased compliance relative to those who were not yet vaccinated.\n\nConclusionThere was little evidence that sample members vaccinated in January or February reduced compliance after receiving vaccination for COVID-19. Continued monitoring is required as younger individuals receive the vaccine, lockdown restrictions are lifted and individuals receive second doses of the vaccine.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Liam Wright", - "author_inst": "University College London" - }, - { - "author_name": "Andrew Steptoe", - "author_inst": "University College London" - }, - { - "author_name": "Hei Wan Mak", - "author_inst": "University College London" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.13.21255336", "rel_title": "Trajectories of compliance with COVID-19 related guidelines: longitudinal analyses of 50,000 UK adults", @@ -818349,6 +819509,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.13.21255342", + "rel_title": "Protocol for the COG-UK hospital onset COVID-19 infection (HOCI) multicentre interventional clinical study: evaluating the efficacy of rapid genome sequencing of SARS-CoV-2 in limiting the spread of COVID-19 in United Kingdom NHS hospitals", + "rel_date": "2021-04-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255342", + "rel_abs": "IntroductionNosocomial transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a significant cause of mortality in National Health Service (NHS) hospitals during the coronavirus disease 2019 (COVID-19) pandemic. The aim of this study is to evaluate the impact of rapid whole genome sequencing of SARS-CoV-2, supported by a novel probabilistic reporting methodology, to inform infection prevention and control (IPC) practice within NHS hospital settings.\n\nMethods and analysisCOG-UK HOCI (COG-UK Consortium Hospital-Onset COVID-19 Infections study) is a multicentre, prospective, interventional, superiority study. Eligible patients must be admitted to hospital with first confirmed SARS-CoV-2 PCR positive test result >48h from time of admission, where COVID-19 diagnosis was not suspected upon admission. The projected sample size for 14 participating sites covering all study phases over winter-spring 2020/2021 in the United Kingdom is 2,380 patients. The intervention is the return of a sequence report, within 48 hours in one phase (rapid local lab) and within 5-10 days in a second phase (mimicking central lab use), comparing the viral genome from an eligible study participant with others within and outside the hospital site. The primary outcomes are the incidence of Public Health England (PHE)/IPC-defined SARS-CoV-2 hospital-acquired infection during the baseline and two interventional phases, and proportion of hospital-onset cases with genomic evidence of transmission linkage following implementation of the intervention where such linkage was not suspected by initial IPC investigation. Secondary outcomes include incidence of hospital outbreaks, with and without sequencing data; actual and desirable changes to IPC actions; periods of healthcare worker (HCW) absence. A process evaluation using qualitative interviews with HCWs will be conducted alongside the study and analysis, underpinned by iterative programme theory of the sequence report. Health economic analysis will be conducted to determine cost-benefit of the intervention, and whether this leads to economic advantages within the NHS setting.\n\nEthics and disseminationThe protocol has been approved by the National Research Ethics Service Committee (Cambridge South 20/EE/0118). This manuscript is based on version 5.0 of the protocol. The study findings will be disseminated through peer-reviewed publications.\n\nStudy Registration numberISRCTN50212645\n\nStrengths and limitations of this studyO_LIThe COG-UK HOCI study harnesses the infrastructure of the UKs existing national COVID-19 genome sequencing platform to evaluate the specific benefit of sequencing to hospital infection control.\nC_LIO_LIThe evaluation is thought to be the first interventional study globally to assess effectiveness of genomic sequencing for infection control in an unbiased patient selection in secondary care settings.\nC_LIO_LIA range of institutional settings will participate, from specialist NHS-embedded or academic centres experienced in using pathogen genomics to district general hospitals.\nC_LIO_LIThe findings are likely to have wider applicability in future decisions to utilise genome sequencing for infection control of other pathogens (such as influenza, respiratory syncytial virus, norovirus, clostridium difficile and antimicrobial resistant pathogens) in secondary care settings.\nC_LIO_LIThe study has been awarded UK NIHR Urgent Public Health status, ensuring prioritised access to NIHR Clinical Research Network (CRN) research staff to recruit patients.\nC_LIO_LIThe study does not have a randomised controlled design due to the logistics of managing this against diverse standard practice.\nC_LI", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "James Blackstone", + "author_inst": "Comprehensive Clinical Trials Unit, University College London" + }, + { + "author_name": "Oliver Stirrup", + "author_inst": "Institute for Global Health, University College London" + }, + { + "author_name": "Fiona Mapp", + "author_inst": "Institute for Global Health, University College London" + }, + { + "author_name": "Monica Panca", + "author_inst": "Comprehensive Clinical Trials Unit, University College London" + }, + { + "author_name": "Andrew Copas", + "author_inst": "Institute for Global Health, University College London" + }, + { + "author_name": "Paul Flowers", + "author_inst": "School of Psychological Sciences and Health, University of Strathclyde" + }, + { + "author_name": "Leanne Hockey", + "author_inst": "Comprehensive Clinical Trials Unit, University College London" + }, + { + "author_name": "James Richard Price", + "author_inst": "Imperial College London" + }, + { + "author_name": "David G Partridge", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Christine Peters", + "author_inst": "Clinical Microbiology, NHS Greater Glasgow and Clyde, Glasgow" + }, + { + "author_name": "Thushan de Silva", + "author_inst": "Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, UK" + }, + { + "author_name": "Gaia Nebbia", + "author_inst": "Department of Infectious Diseases, Guys and St Thomas NHS Foundation Trust" + }, + { + "author_name": "Luke B Snell", + "author_inst": "Department of Infectious Diseases, Guys and St Thomas NHS Foundation Trust" + }, + { + "author_name": "Rachel McComish", + "author_inst": "Comprehensive Clinical Trials Unit, University College London" + }, + { + "author_name": "- COVID-19 Genomics UK (COG-UK) Consortium", + "author_inst": "" + }, + { + "author_name": "Judith Breuer", + "author_inst": "Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.13.21255117", "rel_title": "A distinct metabolic profile associated with a fatal outcome in COVID-19 patients during early epidemic in Italy", @@ -819996,57 +821235,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.04.12.21254876", - "rel_title": "Behavioral nudges increase COVID-19 vaccinations: Two randomized controlled trials", - "rel_date": "2021-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.12.21254876", - "rel_abs": "Fighting the COVID-19 pandemic requires quick and effective strategies to maximize vaccine uptake. We present two sequential randomized controlled trials (RCTs) that tackle this challenge with behavioral science insights. We deliver text-based nudges to UCLA Health patients one day (first RCT; N=113,229) and eight days (second RCT; N=90,662) after they receive notifications of vaccine eligibility. In the first RCT, text messages designed to make vaccination salient and easy to schedule boost appointment and vaccination rates by 86% and 26%, respectively. Nudges that make patients feel endowed with the vaccine heighten these effects, but addressing vaccine hesitancy via a video-based information intervention does not yield benefits beyond simple text. These results hold across ethnicity and age groups. By contrast, online experiments (N=2,003) soliciting hypothetical responses to the same messages reveal the opposite patterns, underscoring the importance of pilot-testing behavioral nudges in the real world before scaling them up. In the second RCT, we further find that receiving a second reminder boosts appointment and vaccination rates by 52% and 16%, respectively. Our findings suggest that text-based nudges can substantially increase and accelerate COVID-19 vaccinations at almost zero marginal cost, highlighting the promising role of behavioral science in addressing a critical component of the COVID-19 pandemic response.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Hengchen Dai", - "author_inst": "Anderson School of Management, University of California Los Angeles, Los Angeles, California, 90095. USA" - }, - { - "author_name": "Silvia Saccardo", - "author_inst": "Department of Social and Decision Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, 15213. USA" - }, - { - "author_name": "Maria A Han", - "author_inst": "Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, 90095. USA" - }, - { - "author_name": "Lily Roh", - "author_inst": "Office of Population Health and Accountable Care, University of California Los Angeles, 10960 Wilshire Blvd, Los Angeles, 90095. USA" - }, - { - "author_name": "Naveen Raja", - "author_inst": "Office of Population Health and Accountable Care, University of California Los Angeles, 10960 Wilshire Blvd, Los Angeles, 90095. USA" - }, - { - "author_name": "Sitaram Vangala", - "author_inst": "Department of Medicine Statistics Core, David Geffen School of Medicine, 1100 Glendon Avenue, Los Angeles, CA 90024, USA" - }, - { - "author_name": "Hardikkumar Modi", - "author_inst": "Office of Health Informatics and Analytics, University of California Los Angeles Health Sciences, Los Angeles, 90095. USA" - }, - { - "author_name": "Shital Pandya", - "author_inst": "Office of Health Informatics and Analytics, University of California Los Angeles Health Sciences, Los Angeles, 90095. USA" - }, - { - "author_name": "Daniel M Croymans", - "author_inst": "Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, 90095. USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2021.04.10.21255111", "rel_title": "Rapid spread and high impact of the Variant of Concern P.1 in the largest city of Brazil", @@ -820263,6 +821451,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.09.21255166", + "rel_title": "Two Distinct Dynamic Process Models of COVID-19 Spread with Divergent Vaccination Outcomes", + "rel_date": "2021-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.09.21255166", + "rel_abs": "Kinematic models of contagion-based viral transmission describe patterns of events over time (e.g., new infections), relying typically on systems of differential equations to reproduce those patterns. By contrast, agent-based models of viral transmission seek to relate those events or patterns of events to causes, expressed in terms of factors (parameters) that determine the dynamics that give rise to those events.\n\nThis paper is concerned with the dynamics of contagion-based spread of infection. Dynamics that reflect time homogeneous vs inhomogeneous transmission rates are generated via an agent-based infectious disease modeling tool (CovidSIMVL - github.com/ecsendmail/MultiverseContagion). These different dynamics are treated as causal factors and are related to differences in vaccine efficacy in an array of simulated vaccination trials. Visualizations of simulated trials and associated metrics illustrate graphically some cogent reasons for not effectively hard-coding assumptions of dynamic temporal homogeneity, which come pre-packaged with the mass action incidence assumption that underpins typical equation-based models of infection spread.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ernie Chang", + "author_inst": "Consultant" + }, + { + "author_name": "Kenneth Andrew Moselle", + "author_inst": "Island Health (Vancouver Island Health Authority)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.08.21254953", "rel_title": "Analysis on Action Tracking Reports of COVID-19 Informs Control Strategies and Vaccine Delivery in Post-Pandemic Era", @@ -821598,105 +822809,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.04.09.21255229", - "rel_title": "COVID-19 vaccine perceptions: An observational study on Reddit", - "rel_date": "2021-04-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.09.21255229", - "rel_abs": "ObjectivesAs COVID-19 vaccinations accelerate in many countries, narratives skeptical of vaccination have also spread through social media. Open online forums like Reddit provide an opportunity to quantitatively examine COVID-19 vaccine perceptions over time. We examine COVID-19 misinformation on Reddit following vaccine scientific announcements.\n\nMethodsWe collected all posts on Reddit from January 1 2020 - December 14 2020 (n=266,840) that contained both COVID-19 and vaccine-related keywords. We used topic modeling to understand changes in word prevalence within topics after the release of vaccine trial data. Social network analysis was also conducted to determine the relationship between Reddit communities (subreddits) that shared COVID-19 vaccine posts, and the movement of posts between subreddits.\n\nResultsThere was an association between a Pfizer press release reporting 90% efficacy and increased discussion on vaccine misinformation. We observed an association between Johnson and Johnson temporarily halting its vaccine trials and reduced misinformation. We found that information skeptical of vaccination was first posted in a subreddit (r/Coronavirus) which favored accurate information and then reposted in subreddits associated with antivaccine beliefs and conspiracy theories (e.g. conspiracy, LockdownSkepticism).\n\nConclusionsOur findings can inform the development of interventions where individuals determine the accuracy of vaccine information, and communications campaigns to improve COVID-19 vaccine perceptions. Such efforts can increase individual- and population-level awareness of accurate and scientifically sound information regarding vaccines and thereby improve attitudes about vaccines. Further research is needed to understand how social media can contribute to COVID-19 vaccination services.\n\nFundingStudy was funded by the Yale Institute for Global Health and the Whitney and Betty MacMillan Center for International and Area Studies at Yale University. The funding bodies had no role in the design, analysis or interpretation of the data in the study.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Navin Kumar", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Isabel Corpus", - "author_inst": "Yale University" - }, - { - "author_name": "Meher Hans", - "author_inst": "Yale University" - }, - { - "author_name": "Nikhil Harle", - "author_inst": "Yale University" - }, - { - "author_name": "Nan Yang", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Curtis McDonald", - "author_inst": "Yale University" - }, - { - "author_name": "Shinpei Nakamura Sakai", - "author_inst": "Yale University" - }, - { - "author_name": "Kamila A Janmohamed", - "author_inst": "Yale University" - }, - { - "author_name": "Weiming Tang", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Jason L Schwartz", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "S Mo Jones-Jang", - "author_inst": "Boston College" - }, - { - "author_name": "Koustuv Saha", - "author_inst": "Georgia Tech" - }, - { - "author_name": "Shahan Ali Memon", - "author_inst": "New York University" - }, - { - "author_name": "Chris Bauch", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Munmun De Chaudhury", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Orestis Papakyriakopoulos", - "author_inst": "Princeton University" - }, - { - "author_name": "Joseph D Tucker", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Abhay Goyal", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Aman Tyagi", - "author_inst": "carnegie mellon university" - }, - { - "author_name": "Kaveh Khoshnood", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Saad Omer", - "author_inst": "Yale School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.09.21255195", "rel_title": "Ovarian follicular function is not altered by SARS-Cov-2 infection or BNT162b2 mRNA Covid-19 vaccination.", @@ -822041,6 +823153,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.09.21255219", + "rel_title": "Early Experience With Neutralizing Monoclonal Antibody Therapy For COVID-19", + "rel_date": "2021-04-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.09.21255219", + "rel_abs": "ImportanceNeutralizing monoclonal antibody (MAB) therapies may benefit patients with mild to moderate COVID-19 at high risk for progressing to severe COVID-19 and/or hospitalization. Studies documenting approaches to deliver MAB infusions as well as demonstrating their efficacy are lacking.\n\nObjectiveWe describe our experience and patient outcomes of almost 3,000 patients who received MAB infusion therapy at Northwell Health, a large integrated health care system in New York.\n\nDesign, Setting, and ParticipantsThis is a descriptive study of adult patients who received MAB therapy between November 20, 2020, to January 31, 2021, and a retrospective cohort survival analysis comparing patients who received MAB therapy prior to admission versus those who did not. A multivariable Cox model with inverse probability weighting according to the propensity score including covariates (sociodemographic, comorbidities, and presenting vital signs) was used.\n\nMain outcomes and measuresThe primary outcome was in-hospital mortality; additional evaluations included ED utilization and hospitalization within 28 days of a positive COVID-19 test for patients who received MAB therapy.\n\nResultsDuring the study period, 2818 adult patients received MAB infusion. Following therapy and within 28 days of COVID-19 test, 123 patients (4.4%) presented to the ED and were released and 145 patients (5.1%) were hospitalized. These 145 patients were compared with 200 controls who were eligible for but did not receive MAB therapy, and were hospitalized. In the MAB group, 16 (11%) patients met the primary outcome of in-hospital mortality, versus 21 (10.5%) in the control group. In an unadjusted Cox model, the hazard ratio (HR) for time to in-hospital mortality for the MAB group was 1.38 (95% confidence interval [95% CI] 0.696-2.719). Models adjusting for demographics (HR 1.1, 95% CI 0.53-2.23), demographics and Charlson Comorbidity Index (CCI) (HR 1.22, 95% CI 0.573-2.59), and with inverse probability weighting according to propensity scores (HR 1.19, 95% CI 0.619-2.29) did not demonstrate significance. The hospitalization rate was 4.4% for patients who received MAB therapy within 0-4 days, 5% within 5-7 days, and 6.1% within [≥]8 days of symptom onset (p-value = 0.15).\n\nConclusions and relevanceEstablishing the capability to provide neutralizing MAB infusion therapy requires significant planning and coordination. While this therapy may be an important treatment option for early mild to moderate COVID-19 in high-risk patients, further investigations are needed to define the optimal timing of MAB treatment in order to reduce hospitalization and mortality.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Mark Paul Jarrett", + "author_inst": "Donald and Barbara Zucker School of Medicine at Hofstra/Northwell" + }, + { + "author_name": "Warren B. Licht", + "author_inst": "Donald and Barbara Zucker School of Medicine at Hofstra/Northwell" + }, + { + "author_name": "Kevin Bock", + "author_inst": "Donald and Barbara Zucker School of Medicine at Hofstra/Northwell" + }, + { + "author_name": "Zenobia Brown", + "author_inst": "Donald and Barbara Zucker School of Medicine at Hofstra/Northwell" + }, + { + "author_name": "Jamie S Hirsch", + "author_inst": "Donald and Barbara Zucker School of Medicine at Hofstra/Northwell" + }, + { + "author_name": "Kevin Coppa", + "author_inst": "Department of Information Services, Northwell Health" + }, + { + "author_name": "Rajdeep Brar", + "author_inst": "Department of Information Services, Northwell Health" + }, + { + "author_name": "Steve Bello", + "author_inst": "Northwell Health" + }, + { + "author_name": "Ira S Nash", + "author_inst": "Donald and Barbara Zucker School of Medicine at Hofstra/Northwell" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.12.21255343", "rel_title": "Long COVID In Adults at 12 Months After Mild-to-Moderate SARS-CoV-2 Infection", @@ -823668,49 +824831,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.04.10.439300", - "rel_title": "Combinatorial approach with mass spectrometry and lectin microarray dissected glycoproteomic features of virion-derived spike protein of SARS-CoV-2", - "rel_date": "2021-04-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.10.439300", - "rel_abs": "The COVID-19 pandemic caused by the novel coronavirus, SARS-CoV-2, has a global impact on public health. Since glycosylation of the viral envelope glycoproteins is known to be deeply associated with their immunogenicity, intensive studies on the glycans of its major glycoprotein, S protein, have been conducted. Nevertheless, the detailed site-specific glycan compositions of virion-associated S protein have not yet been clarified. Here, we conducted intensive glycoproteomic analyses of SARS-CoV-2 S protein using a combinatorial approach with two different technologies: mass spectrometry (MS) and lectin microarray. Using our unique MS1-based glycoproteomic technique, Glyco-RIDGE, in addition to MS2-based Byonic search, we identified 1,759 site-specific glycan compositions. The most frequent was HexNAc:Hex:Fuc:NeuAc:NeuGc = 6:6:1:0:0, suggesting a tri-antennary N-glycan terminating with LacNAc and having bisecting GlcNAc and a core fucose, which was found in 20 of 22 glycosylated sites. The subsequent lectin microarray analysis emphasized intensive outer arm fucosylation of glycans, which efficiently complemented the glycoproteomic features. The present results illustrate the high-resolution glycoproteomic features of SARS-CoV-2 S protein and significantly contribute to vaccine design, as well as the understanding of viral protein synthesis.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Takahiro Hiono", - "author_inst": "Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Scienc" - }, - { - "author_name": "Azusa Tomioka", - "author_inst": "Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Scienc" - }, - { - "author_name": "Hiroyuki Kaji", - "author_inst": "Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Scienc" - }, - { - "author_name": "Michihito Sasaki", - "author_inst": "Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan" - }, - { - "author_name": "Yasuko Orba", - "author_inst": "Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan" - }, - { - "author_name": "Hirofumi Sawa", - "author_inst": "Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan" - }, - { - "author_name": "Atsushi Kuno", - "author_inst": "Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Scienc" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2021.04.12.439473", "rel_title": "Revealing the threat of emerging SARS-CoV-2 mutations to antibody therapies", @@ -823855,6 +824975,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.04.12.439201", + "rel_title": "Impairment of SARS-CoV-2 spike glycoprotein maturation and fusion activity by the broad-spectrum anti-infective drug nitazoxanide", + "rel_date": "2021-04-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.12.439201", + "rel_abs": "SARS-CoV-2, the causative agent of COVID-19, has caused an unprecedented global health crisis. The SARS-CoV-2 spike, a surface-anchored trimeric class-I fusion-glycoprotein essential for viral entry, represents a key target for developing vaccines and therapeutics capable of blocking virus invasion. The emergence of SARS-CoV-2 spike-variants that facilitate virus spread and may affect vaccine efficacy highlights the need to identify novel antiviral strategies for COVID-19 therapy. Here we demonstrate that nitazoxanide, an antiprotozoal agent with recognized broad-spectrum antiviral activity, interferes with SARS-CoV-2 spike biogenesis, hampering its maturation at an endoglycosidase H-sensitive stage. Engineering multiple SARS-CoV-2 variant-pseudoviruses and utilizing quantitative cell-cell fusion assays, we show that nitazoxanide-induced spike modifications hinder progeny virion infectivity as well as spike-driven pulmonary cell-cell fusion, a critical feature of COVID-19 pathology. Nitazoxanide, being equally effective against the ancestral SARS-CoV-2 Wuhan-spike and different emerging variants, including the Delta variant of concern, may represent a useful tool in the fight against COVID-19 infections.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Anna Riccio", + "author_inst": "University of Rome Tor Vergata, Rome, Italy" + }, + { + "author_name": "Silvia Santopolo", + "author_inst": "University of Rome Tor Vergata" + }, + { + "author_name": "Antonio Rossi", + "author_inst": "Institute of Translational Pharmacology, CNR, Rome, Italy" + }, + { + "author_name": "Sara Piacentini", + "author_inst": "University of Rome Tor Vergata" + }, + { + "author_name": "Jean-Francois Rossignol", + "author_inst": "Romark Laboratories, L.C., Tampa, Florida, USA" + }, + { + "author_name": "Maria Gabriella Santoro", + "author_inst": "University of Rome Tor Vergata" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.12.439549", "rel_title": "Interactions between SARS-CoV-2 N-protein and \u03b1-synuclein accelerate amyloid formation", @@ -825402,49 +826561,6 @@ "type": "confirmatory results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.04.08.439088", - "rel_title": "The homology analysis of ACE2 gene and its distinct expression in laboratory and wild animals", - "rel_date": "2021-04-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.08.439088", - "rel_abs": "Angiotensin-converting enzyme-2 (ACE2) has been recognized as an entry receptor of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into the host cells while bats has been suspected as natural host of SARS-CoV-2. However, the detail of intermediate host or the route of transmission of SARS-CoV-2 is still unclear. In this study, we analyze the conservation of ACE2 gene in 11 laboratory and wild animals that live in close proximity either with Bats or human and further investigated its RNA and protein expression pattern in wild bats, mice and tree shrew. We verified that the wild-bats and mice were belonged to Hipposideros pomona and Rattus norvegicus, respectively. ACE2 gene is highly conserved among all 11 animals species at the DNA level. Phylogenetic analysis based on the ACE2 nucleotide sequences revealed that wild bat and Tree shrew were forming a cluster close to human. We further report that ACE2 RNA expression pattern is highly species-specific in different tissues of different animals. Most notably, we found that the expression pattern of ACE2 RNA and protein are very different in each animal species. In summary, our results suggested that ACE2 gene is highly conserved among all 11 animals species. However, different relative expression pattern of ACE2 RNA and protein in each animal species is interesting. Further research is needed to clarify the possible connection between different relative expression pattern of ACE2 RNA and protein in different laboratory and wild animal species and the susceptibility to SARS-CoV-2 infection.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Gang Wang", - "author_inst": "Kunming University of Science and Technology" - }, - { - "author_name": "Zhang A-Mei", - "author_inst": "Kunming University of Science and Technology" - }, - { - "author_name": "Wang Binghui", - "author_inst": "Kunming University of Science and Technology" - }, - { - "author_name": "Jianhua Yin", - "author_inst": "Kunming University of Science and technology" - }, - { - "author_name": "Feng Yue", - "author_inst": "Kunming University of Science and Technology" - }, - { - "author_name": "Zulqarnain Baloch", - "author_inst": "Kunming University of Science and technology" - }, - { - "author_name": "Xue-shan Xia", - "author_inst": "Kunming University of Science and Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.04.09.439203", "rel_title": "A trimeric hydrophobic zipper mediates the intramembrane assembly of SARS-CoV-2 spike", @@ -825633,6 +826749,249 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.04.09.439166", + "rel_title": "Efficacy and breadth of adjuvanted SARS-CoV-2 receptor-binding domain nanoparticle vaccine in macaques", + "rel_date": "2021-04-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.09.439166", + "rel_abs": "Emergence of novel variants of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) underscores the need for next-generation vaccines able to elicit broad and durable immunity. Here we report the evaluation of a ferritin nanoparticle vaccine displaying the receptor-binding domain of the SARS-CoV-2 spike protein (RFN) adjuvanted with Army Liposomal Formulation QS-21 (ALFQ). RFN vaccination of macaques using a two-dose regimen resulted in robust, predominantly Th1 CD4+ T cell responses and reciprocal peak mean neutralizing antibody titers of 14,000-21,000. Rapid control of viral replication was achieved in the upper and lower airways of animals after high-dose SARS-CoV-2 respiratory challenge, with undetectable replication within four days in 7 of 8 animals receiving 50 {micro}g RFN. Cross-neutralization activity against SARS-CoV-2 variant B.1.351 decreased only [~]2-fold relative to USA-WA1. In addition, neutralizing, effector antibody and cellular responses targeted the heterotypic SARS-CoV-1, highlighting the broad immunogenicity of RFN-ALFQ for SARS-like betacoronavirus vaccine development.\n\nSignificance StatementThe emergence of SARS-CoV-2 variants of concern (VOC) that reduce the efficacy of current COVID-19 vaccines is a major threat to pandemic control. We evaluate a SARS-CoV-2 Spike receptor-binding domain ferritin nanoparticle protein vaccine (RFN) in a nonhuman primate challenge model that addresses the need for a next-generation, efficacious vaccine with increased pan-SARS breadth of coverage. RFN, adjuvanted with a liposomal-QS21 formulation (ALFQ), elicits humoral and cellular immune responses exceeding those of current vaccines in terms of breadth and potency and protects against high-dose respiratory tract challenge. Neutralization activity against the B.1.351 VOC within two-fold of wild-type virus and against SARS-CoV-1 indicate exceptional breadth. Our results support consideration of RFN for SARS-like betacoronavirus vaccine development.", + "rel_num_authors": 57, + "rel_authors": [ + { + "author_name": "Hannah A. D. King", + "author_inst": "aUS Military HIV Research Program, Walter Reed Army Institute of Research (WRAIR), Silver Spring MD 20910, USA. bEmerging Infectious Diseases Branch, WRAIR, Sil" + }, + { + "author_name": "M. Gordon Joyce", + "author_inst": "bEmerging Infectious Diseases Branch, WRAIR, Silver Spring MD 20910, USA. cHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD 20" + }, + { + "author_name": "Ines Elakhal Naouar", + "author_inst": "cHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD 20817, USA. dDiagnostics and Countermeasures Branch, WRAIR, Silver Spring M" + }, + { + "author_name": "Aslaa Ahmed", + "author_inst": "eViral Diseases Branch, WRAIR, Silver Spring MD 20910, USA." + }, + { + "author_name": "Camila Macedo Cincotta", + "author_inst": "cHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD 20817, USA. dDiagnostics and Countermeasures Branch, WRAIR, Silver Spring MD " + }, + { + "author_name": "Caroline Subra", + "author_inst": "aUS Military HIV Research Program, Walter Reed Army Institute of Research (WRAIR), Silver Spring MD 20910, USA. bEmerging Infectious Diseases Branch, WRAIR, Sil" + }, + { + "author_name": "Kristina K. Peachman", + "author_inst": "dDiagnostics and Countermeasures Branch, WRAIR, Silver Spring MD 20910, USA." + }, + { + "author_name": "Holly H. Hack", + "author_inst": "cHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD 20817, USA. dDiagnostics and Countermeasures Branch, WRAIR, Silver Spring MD " + }, + { + "author_name": "Rita E. Chen", + "author_inst": "fDepartment of Medicine, Washington University, St. Louis, MO 63130, USA. gDepartment of Pathology & Immunology, Washington University, St. Louis, MO 63130, USA" + }, + { + "author_name": "Paul V. Thomas", + "author_inst": "bEmerging Infectious Diseases Branch, WRAIR, Silver Spring MD 20910, USA. cHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD 20" + }, + { + "author_name": "Wei-Hung Chen", + "author_inst": "bEmerging Infectious Diseases Branch, WRAIR, Silver Spring MD 20910, USA. cHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD 20" + }, + { + "author_name": "Rajeshwer S. Sankhala", + "author_inst": "bEmerging Infectious Diseases Branch, WRAIR, Silver Spring MD 20910, USA. cHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD 20" + }, + { + "author_name": "Agnes Hajduczki", + "author_inst": "bEmerging Infectious Diseases Branch, WRAIR, Silver Spring MD 20910, USA. cHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD 20" + }, + { + "author_name": "Elizabeth J. Martinez", + "author_inst": "bEmerging Infectious Diseases Branch, WRAIR, Silver Spring MD 20910, USA. cHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD 20" + }, + { + "author_name": "Caroline E. Peterson", + "author_inst": "bEmerging Infectious Diseases Branch, WRAIR, Silver Spring MD 20910, USA. cHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD 20" + }, + { + "author_name": "William C. Chang", + "author_inst": "bEmerging Infectious Diseases Branch, WRAIR, Silver Spring MD 20910, USA. cHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD 20" + }, + { + "author_name": "Misook Choe", + "author_inst": "bEmerging Infectious Diseases Branch, WRAIR, Silver Spring MD 20910, USA. cHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD 20" + }, + { + "author_name": "Clayton Smith", + "author_inst": "hCenter for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA." + }, + { + "author_name": "Jarrett A. Headley", + "author_inst": "bEmerging Infectious Diseases Branch, WRAIR, Silver Spring MD 20910, USA. cHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD 20" + }, + { + "author_name": "Hanne A. Elyard", + "author_inst": "iBIOQUAL, Inc., Rockville, MD 20850, USA." + }, + { + "author_name": "Anthony Cook", + "author_inst": "iBIOQUAL, Inc., Rockville, MD 20850, USA." + }, + { + "author_name": "Alexander Anderson", + "author_inst": "aUS Military HIV Research Program, Walter Reed Army Institute of Research (WRAIR), Silver Spring MD 20910, USA. bEmerging Infectious Diseases Branch, WRAIR, Si" + }, + { + "author_name": "Kathryn M. Wuertz", + "author_inst": "aUS Military HIV Research Program, Walter Reed Army Institute of Research (WRAIR), Silver Spring MD 20910, USA." + }, + { + "author_name": "Ming Dong", + "author_inst": "aUS Military HIV Research Program, Walter Reed Army Institute of Research (WRAIR), Silver Spring MD 20910, USA. bEmerging Infectious Diseases Branch, WRAIR, Si" + }, + { + "author_name": "Isabella Swafford", + "author_inst": "aUS Military HIV Research Program, Walter Reed Army Institute of Research (WRAIR), Silver Spring MD 20910, USA. bEmerging Infectious Diseases Branch, WRAIR, Si" + }, + { + "author_name": "James B. Case", + "author_inst": "fDepartment of Medicine, Washington University, St. Louis, MO 63130, USA." + }, + { + "author_name": "Jeffrey R. Currier", + "author_inst": "eViral Diseases Branch, WRAIR, Silver Spring MD 20910, USA." + }, + { + "author_name": "Kerri G. Lal", + "author_inst": "aUS Military HIV Research Program, Walter Reed Army Institute of Research (WRAIR), Silver Spring MD 20910, USA. bEmerging Infectious Diseases Branch, WRAIR, Si" + }, + { + "author_name": "Mihret F. Amare", + "author_inst": "bEmerging Infectious Diseases Branch, WRAIR, Silver Spring MD 20910, USA. cHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD 20" + }, + { + "author_name": "Vincent Dussupt", + "author_inst": "aUS Military HIV Research Program, Walter Reed Army Institute of Research (WRAIR), Silver Spring MD 20910, USA. bEmerging Infectious Diseases Branch, WRAIR, Si" + }, + { + "author_name": "Sebastian Molnar", + "author_inst": "aUS Military HIV Research Program, Walter Reed Army Institute of Research (WRAIR), Silver Spring MD 20910, USA. bEmerging Infectious Diseases Branch, WRAIR, Si" + }, + { + "author_name": "Sharon P. Daye", + "author_inst": "jCenter for Infectious Diseases Research, WRAIR, Silver Spring MD 20910, USA." + }, + { + "author_name": "Xiankun Zeng", + "author_inst": "kDivision of Pathology, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA." + }, + { + "author_name": "Erica K. Barkei", + "author_inst": "lVeterinary Pathology Branch, WRAIR, Silver Spring MD 20910, USA." + }, + { + "author_name": "Kendra Alfson", + "author_inst": "mDisease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio TX 78227, USA." + }, + { + "author_name": "Hilary M. Staples", + "author_inst": "mDisease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio TX 78227, USA." + }, + { + "author_name": "Ricardo Carrion", + "author_inst": "mDisease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio TX 78227, USA." + }, + { + "author_name": "Shelly J. Krebs", + "author_inst": "aUS Military HIV Research Program, Walter Reed Army Institute of Research (WRAIR), Silver Spring MD 20910, USA. bEmerging Infectious Diseases Branch, WRAIR, Si" + }, + { + "author_name": "Dominic Paquin-Proulx", + "author_inst": "aUS Military HIV Research Program, Walter Reed Army Institute of Research (WRAIR), Silver Spring MD 20910, USA. bEmerging Infectious Diseases Branch, WRAIR, Si" + }, + { + "author_name": "Nicos Karasavvas", + "author_inst": "cHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD 20817, USA. dDiagnostics and Countermeasures Branch, WRAIR, Silver Spring M" + }, + { + "author_name": "Victoria R. Polonis", + "author_inst": "aUS Military HIV Research Program, Walter Reed Army Institute of Research (WRAIR), Silver Spring MD 20910, USA." + }, + { + "author_name": "Linda L. Jagodzinski", + "author_inst": "dDiagnostics and Countermeasures Branch, WRAIR, Silver Spring MD 20910, USA." + }, + { + "author_name": "Sandhya Vasan", + "author_inst": "aUS Military HIV Research Program, Walter Reed Army Institute of Research (WRAIR), Silver Spring MD 20910, USA. bEmerging Infectious Diseases Branch, WRAIR, Si" + }, + { + "author_name": "Paul T. Scott", + "author_inst": "bEmerging Infectious Diseases Branch, WRAIR, Silver Spring MD 20910, USA." + }, + { + "author_name": "Yaoxing Huang", + "author_inst": "nAaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA." + }, + { + "author_name": "Manoj S. Nair", + "author_inst": "nAaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA." + }, + { + "author_name": "David D. Ho", + "author_inst": "nAaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA." + }, + { + "author_name": "Natalia de Val", + "author_inst": "hCenter for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA." + }, + { + "author_name": "Michael S. Diamond", + "author_inst": "fDepartment of Medicine, Washington University, St. Louis, MO 63130, USA. gDepartment of Pathology & Immunology, Washington University, St. Louis, MO 63130, USA" + }, + { + "author_name": "Mark G. Lewis", + "author_inst": "iBIOQUAL, Inc., Rockville, MD 20850, USA." + }, + { + "author_name": "Mangala Rao", + "author_inst": "aUS Military HIV Research Program, Walter Reed Army Institute of Research (WRAIR), Silver Spring MD 20910, USA." + }, + { + "author_name": "Gary R. Matyas", + "author_inst": "aUS Military HIV Research Program, Walter Reed Army Institute of Research (WRAIR), Silver Spring MD 20910, USA." + }, + { + "author_name": "Gregory D. Gromowski", + "author_inst": "eViral Diseases Branch, WRAIR, Silver Spring MD 20910, USA." + }, + { + "author_name": "Sheila A. Peel", + "author_inst": "dDiagnostics and Countermeasures Branch, WRAIR, Silver Spring MD 20910, USA." + }, + { + "author_name": "Nelson L. Michael", + "author_inst": "jCenter for Infectious Diseases Research, WRAIR, Silver Spring MD 20910, USA." + }, + { + "author_name": "Kayvon Modjarrad", + "author_inst": "bEmerging Infectious Diseases Branch, WRAIR, Silver Spring MD 20910, USA." + }, + { + "author_name": "Diane L. Bolton", + "author_inst": "aUS Military HIV Research Program, Walter Reed Army Institute of Research (WRAIR), Silver Spring MD 20910, USA. bEmerging Infectious Diseases Branch, WRAIR, Si" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.04.09.439154", "rel_title": "Atypical N-glycosylation of SARS-CoV-2 impairs the efficient binding of Spike-RBM to the human-host receptor hACE2", @@ -827000,45 +828359,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.06.21255013", - "rel_title": "Reduction in the 2020 Life Expectancy in Brazil after COVID-19", - "rel_date": "2021-04-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.06.21255013", - "rel_abs": "Brazil has the second-largest number of COVID-19 deaths worldwide. We use data on reported deaths to measure and compare the death toll across states from a demographic perspective. We estimate a decline in 2020 life expectancy at birth of 1.94 years, resulting in a mortality level not seen since 2013. The reduction in life expectancy at age 65 was 1.58 years, setting Brazil back to 2009 levels. The decline was larger for males, widening by 2.3% and 5.4% the female-male gap in life expectancy at birth and at age 65, respectively. Among states, Amazonas lost 59.6% of the improvements in life expectancy at birth since 2000. With 2021 COVID-19 deaths at about 43% of the total 2020 figures (as of mid-March) the demographic effect is likely to be even higher this year.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Marcia C. Castro", - "author_inst": "Department of Global Health and Population, Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Susie Gurzenda", - "author_inst": "Department of Global Health and Population, Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Cassio M. Turra", - "author_inst": "Demography Department, Cedeplar, Universidade Federal de Minas Gerais" - }, - { - "author_name": "Sun Kim", - "author_inst": "Department of Global Health and Population, Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Theresa Andrasfay", - "author_inst": "Leonard Davis School of Gerontology, University of Southern California" - }, - { - "author_name": "Noreen Goldman", - "author_inst": "Office of Population Research, Princeton University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.07.21255071", "rel_title": "Results Availability and Timeliness of Registered COVID-19 Clinical Trials: A Cross-Sectional Study", @@ -827231,6 +828551,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.07.21255024", + "rel_title": "Improved diagnosis of SARS-CoV-2 by using Nucleoprotein and Spike protein fragment 2 in quantitative dual ELISA tests", + "rel_date": "2021-04-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.07.21255024", + "rel_abs": "The novel Coronavirus, SARS-CoV-2, is the causative agent of the 2020 worldwide coronavirus pandemic. Antibody testing is useful for diagnosing historic infections of a disease in a population. These tests are also a helpful epidemiological tool for predicting how the virus spreads in a community, relating antibody levels to immunity and for assessing herd immunity. In the present study, SARS-CoV-2 viral proteins were recombinantly produced and used to analyse serum from individuals previously exposed, or not, to SARS-CoV-2. The nucleocapsid (Npro) and Spike subunit 2 (S2Frag) proteins were identified as highly immunogenic, although responses to the former were generally greater. These two proteins were used to develop two quantitative ELISA assays that when used in combination resulted in a highly reliable diagnostic test. Npro and S2Frag-ELISAs could detect at least 10% more true positive COVID-19 cases than the commercially available ARCHITECT test (Abbott). Moreover, our quantitative ELISAs also show that specific antibodies to SARS-CoV-2 proteins tend to wane rapidly even in patients that had developed severe disease. As antibody tests complement COVID-19 diagnosis and determine population-level surveillance during this pandemic, the alternative diagnostic we present in this study could play a role in controlling the spread of the virus.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Carolina De Marco Verissimo", + "author_inst": "Centre for One Health and Ryan Institute, School of Natural Science, National University of Ireland Galway, Galway, Republic of Ireland." + }, + { + "author_name": "Carol O'Brien", + "author_inst": "Department of Biology - National University of Ireland Maynooth, Maynooth, Ireland." + }, + { + "author_name": "Jesus Lopez Corrales", + "author_inst": "Centre for One Health and Ryan Institute, School of Natural Science, National University of Ireland Galway, Galway, Republic of Ireland." + }, + { + "author_name": "Amber Dorey", + "author_inst": "Centre for One Health and Ryan Institute, School of Natural Science, National University of Ireland Galway, Galway, Republic of Ireland." + }, + { + "author_name": "Krystyna Cwiklinski", + "author_inst": "Centre for One Health and Ryan Institute, School of Natural Science, National University of Ireland Galway, Galway, Republic of Ireland." + }, + { + "author_name": "Richard Lalor", + "author_inst": "Centre for One Health and Ryan Institute, School of Natural Science, National University of Ireland Galway, Galway, Republic of Ireland." + }, + { + "author_name": "Jack M Doyle", + "author_inst": "Department of Biology - National University of Ireland Maynooth, Maynooth, Ireland." + }, + { + "author_name": "Stephen Field", + "author_inst": "Clinical Associate Professor (TCD), Medical and Scientific Director, Irish Blood Transfusion Service, Dublin, Ireland." + }, + { + "author_name": "Claire Masterson", + "author_inst": "School of Medicine, and Regenerative Medicine Institute (REMEDI) at CURAM Centre for Research in Medical Devices, Biomedical Sciences Building, National Univers" + }, + { + "author_name": "Eduardo Ribes Martinez", + "author_inst": "School of Medicine, and Regenerative Medicine Institute (REMEDI) at CURAM Centre for Research in Medical Devices, Biomedical Sciences Building, National Univers" + }, + { + "author_name": "Gerry Hughes", + "author_inst": "School of Medicine, Trinity College Dublin, College Green, Dublin 2, Ireland; Department of Infectious Diseases, St James's Hospital, James's Street, Dublin 8, " + }, + { + "author_name": "Colm Bergin", + "author_inst": "School of Medicine, Trinity College Dublin, College Green, Dublin 2, Ireland; Department of Infectious Diseases, St James's Hospital, James's Street, Dublin 8, " + }, + { + "author_name": "Kieran Walshe", + "author_inst": "Department of Biology - National University of Ireland Maynooth, Maynooth, Ireland." + }, + { + "author_name": "Bairbre McNicholas", + "author_inst": "Department of Anaesthesia and Intensive Care Medicine, University Hospital Galway, Saolta University Hospital Group, Galway Ireland." + }, + { + "author_name": "John Laffey", + "author_inst": "School of Medicine, and Regenerative Medicine Institute (REMEDI) at CURAM Centre for Research in Medical Devices, Biomedical Sciences Building, National Univers" + }, + { + "author_name": "John P Dalton", + "author_inst": "Centre for One Health and Ryan Institute, School of Natural Science, National University of Ireland Galway, Galway, Republic of Ireland." + }, + { + "author_name": "Colm Kerr", + "author_inst": "School of Medicine, Trinity College Dublin, College Green, Dublin 2, Ireland; Department of Infectious Diseases, St James's Hospital, James's Street, Dublin 8, " + }, + { + "author_name": "Sean Doyle", + "author_inst": "Department of Biology - National University of Ireland Maynooth, Maynooth, Ireland." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.06.21255017", "rel_title": "Short-range exposure to airborne virus transmission and current guidelines", @@ -829042,45 +830449,6 @@ "type": "new results", "category": "synthetic biology" }, - { - "rel_doi": "10.1101/2021.04.06.438540", - "rel_title": "TMPRSS2 and RNA-dependent RNA polymerase are effective targets of therapeutic intervention for treatment of COVID-19 caused by SARS-CoV-2 variants (B.1.1.7 and B.1.351)", - "rel_date": "2021-04-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.06.438540", - "rel_abs": "SARS-CoV-2 is a causative agent of COVID-19 pandemic and the development of therapeutic interventions is urgently needed. So far, monoclonal antibodies and drug repositioning are the main methods for drug development and this effort was partially successful. Since the beginning of COVID-19 pandemic, the emergence of SARS-CoV-2 variants has been reported in many parts of the world and the main concern is whether the current vaccines and therapeutics are still effective against these variant viruses. The viral entry and viral RNA-dependent RNA polymerase (RdRp) are the main targets of current drug development, thus the inhibitory effects of TMPRSS2 and RdRp inhibitors were compared among the early SARS-CoV-2 isolate (lineage A) and the two recent variants (lineage B.1.1.7 and lineage B.1.351) identified in the UK and South Africa, respectively. Our in vitro analysis of viral replication showed that the drugs targeting TMPRSS2 and RdRp are equally effective against the two variants of concern.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Jihye Lee", - "author_inst": "Institut Pasteur Korea" - }, - { - "author_name": "JinAh Lee", - "author_inst": "Institut Pasteur Korea" - }, - { - "author_name": "Hyeon Ju Kim", - "author_inst": "Institut Pasteur Korea" - }, - { - "author_name": "Meehyun Ko", - "author_inst": "Institute Pasteur Korea" - }, - { - "author_name": "Youngmee Jee", - "author_inst": "Institut Pasteur Korea" - }, - { - "author_name": "Seungtaek Kim", - "author_inst": "Institut Pasteur Korea" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.04.07.438818", "rel_title": "Structural basis for broad sarbecovirus neutralization by a human monoclonal antibody", @@ -829473,6 +830841,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.06.21254973", + "rel_title": "COVID-19 vaccination acceptability in the UK at the start of the vaccination programme: a nationally representative cross-sectional survey (CoVAccS wave 2)", + "rel_date": "2021-04-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.06.21254973", + "rel_abs": "AimTo investigate factors associated with intention to have the COVID-19 vaccination following initiation of the UK national vaccination programme.\n\nMethods1,500 adults completed an online cross-sectional survey (13th-15th January 2021). Linear regression analyses were used to investigate associations between intention to be vaccinated for COVID-19 and sociodemographic factors, previous influenza vaccination, attitudes and beliefs about COVID-19, attitudes and beliefs about COVID-19 vaccination and vaccination in general. Participants main reasons for likely vaccination uptake/decline were also solicited.\n\nResults73.5% of participants (95% CI 71.2%, 75.7%) reported being likely to be vaccinated against COVID-19, 17.3% were unsure (95% CI 15.4%, 19.3%), and 9.3% (95% CI 7.9%, 10.8%) reported being unlikely to be vaccinated. The full regression model explained 69.8% of the variance in intention. Intention was associated with having been/intending to be vaccinated for influenza last winter/this winter, and with stronger beliefs about social acceptability of a COVID-19 vaccine; the need for vaccination; adequacy of information about the vaccine; and weaker beliefs that the vaccine is unsafe. Beliefs that only those at serious risk of illness should be vaccinated and that the vaccines are just a means for manufacturers to make money were negatively associated with vaccination intention.\n\nConclusionsMost participants reported being likely to get the COVID-19 vaccination. COVID-19 vaccination attitudes and beliefs are a crucial factor underpinning vaccine intention. Continued engagement with the public with a focus on the importance and safety of vaccination is recommended.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Susan Mary Sherman", + "author_inst": "Keele University" + }, + { + "author_name": "Julius Sim", + "author_inst": "Keele University" + }, + { + "author_name": "Megan Cutts", + "author_inst": "Keele University" + }, + { + "author_name": "Hannah Dasch", + "author_inst": "Kings College London" + }, + { + "author_name": "Richard Amlot", + "author_inst": "Public Health England" + }, + { + "author_name": "James Rubin", + "author_inst": "King's College London" + }, + { + "author_name": "Nick Sevdalis", + "author_inst": "Kings College London" + }, + { + "author_name": "Louise E. Smith", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.08.20205781", "rel_title": "Safe and effective pool testing for SARS-CoV-2 detection", @@ -831040,29 +832455,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.04.05.21254024", - "rel_title": "Strategies for antigen testing: An alternative approach to widespread PCR testing", - "rel_date": "2021-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.05.21254024", - "rel_abs": "Multiple applications of low cost and rapid antigen tests for individuals, in parallel (at the same time) or at times sufficiently close to each other, when appropriately interpreted can considerably increase sensitivity of these tests, improving on their performance greatly. Under reasonable assumptions, this occurs when considering a positive to arise in a composite test if at least one of two underlying repeated tests are positive. Parallel Rapid Testing can potentially provide a form of testing that is accessible (combining wide availability and lack of expense) and quick. Moreover, it can provide a level of sensitivity that is comparable to seemingly more sophisticated but more expensive alternatives. In combination with sequential testing, this strategy offers an alternative method of testing that can be applied immediately and on a widespread basis.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Sanjay G Reddy", - "author_inst": "The New School" - }, - { - "author_name": "Saumya Das", - "author_inst": "Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.05.21254722", "rel_title": "Outcomes of COVID-19 Vaccination Efforts in Florida from December 14, 2020 to March 15, 2021 on Older Individuals", @@ -831243,6 +832635,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.02.21254818", + "rel_title": "Covid-19 does not look like what you are looking for: clustering symptoms by nation and multi- morbidities reveal substantial differences to the classical symptom triad", + "rel_date": "2021-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.02.21254818", + "rel_abs": "COVID-19 is by convention characterised by a triad of symptoms: cough, fever and loss of taste/smell. The aim of this study was to examine clustering of COVID-19 symptoms based on underlying chronic disease and geographical location. Using a large global symptom survey of 78,299 responders in 190 different countries, we examined symptom profiles in relation to geolocation (grouped by country) and underlying chronic disease (single, co- or multi-morbidities) associated with a positive COVID-19 test result using statistical and machine learning methods to group populations by underlying disease, countries, and symptoms. Taking the responses of 7980 responders with a COVID-19 positive test in the top 5 contributing countries, we find that the most frequently reported symptoms differ across the globe: For example, fatigue 4108(51.5%), headache 3640(45.6%) and loss of smell and taste 3563(44.6%) are the most reported symptoms globally. However, symptom patterns differ by continent; India reported a significantly lower proportion of headache (22.8% vs 45.6%, p<0.05) and itchy eyes (7.0% vs. 15.3%, p<0.05) than other countries, as does Pakistan (33.6% vs 45.6%, p<0.05 and 8.6% vs 15.3%, p<0.05). Mexico and Brazil report significantly less of these symptoms. As with geographic location, we find people differed in their reported symptoms, if they suffered from specific underlying diseases. For example, COVID-19 positive responders with asthma or other lung disease were more likely to report shortness of breath as a symptom, compared with COVID-19 positive responders who had no underlying disease (25.3% vs. 13.7%, p<0.05, and 24.2 vs.13.7%, p<0.05). Responders with no underlying chronic diseases were more likely to report loss of smell and tastes as a symptom (46%), compared with the responders with type 1 diabetes (21.3%), Type 2 diabetes (33.5%) lung disease (29.3%), or hypertension (37.8%). Global symptom ranking differs markedly from the well-known and commonly described symptoms for COVID-19, which are based on a few localised studies. None of the five countries studied in depth recorded cough or temperature as the most common symptoms. The most common symptoms reported were fatigue and loss of smell and taste. Amongst responders from Brazil cough was the second most frequently reported symptom, after fatigue. Moreover, we find that across countries and based on underlying chronic diseases, there are significant differences in symptom profiles at presentation, that cannot be fully explained by the different chronic disease profiles of these countries, and may be caused by differences in climate, environment and ethnicities. These factors uncovered by our global comorbidity survey of COVID-19 positive tested people may contribute to the apparent large asymptotic COVID-19 spread and put patients with underlying disease systematically more at risk.\n\nExecutive SummaryO_ST_ABSEvidence before this workC_ST_ABSAn early meta-analysis of epidemiological variation in COVID-19 inside and outside China studied patient characteristics including, gender, age, fatality rate, and symptoms of fever, cough, shortness of breath and diarrhoea in COVID-19 patients. They found that important symptom differences existed in patients in China compared to other countries and recommended that clinical symptoms of COVID-19 should not be generalized to fever, shortness of breath and cough only, but other symptoms such as diarrhoea are also shown to be prevalent in patients with COVID-19.\n\nAdded value of this workWe find that across countries and based on underlying chronic diseases, there are significant differences in symptom profiles at presentation, that cannot be fully explained by the different chronic disease profiles of these countries, and may be caused by differences in climate, environment and ethnicities.\n\nImplications of the evidenceThese factors, uncovered by our global comorbidity survey of COVID-19 positive tested people may contribute to the apparent large asymptotic COVID-19 spread and put patients with underlying disease systematically more at risk.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Balasundaram Kadirvelu", + "author_inst": "Imperial College London" + }, + { + "author_name": "Gabriel Burcea", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jennifer Quint", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ceire E Costelloe", + "author_inst": "Imperial College London" + }, + { + "author_name": "Aldo A. Faisal", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.05.21251104", "rel_title": "Detection of two CAL.20C SARS-CoV-2 variants in Monterrey metropolitan area in Northeast Mexico", @@ -832914,57 +834341,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.04.06.21254840", - "rel_title": "Patient perspectives on healthcare at the time of COVID-19 and suggestions for care redesign after the pandemic: a qualitative study in all six WHO regions", - "rel_date": "2021-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.06.21254840", - "rel_abs": "ObjectiveThe COVID-19 pandemic has triggered significant changes in healthcare. As they were mainly driven by professionals and are likely to influence healthcare in the future, it is of utmost importance to consider patients perspectives equally. We, therefore, explored the lived experiences of patients and patient representatives in all six World Health Organisation (WHO) regions regarding healthcare at the time of COVID-19 and extracted suggestions for care redesign after the pandemic.\n\nMethodsWe conducted semi-structured interviews until saturation. Thematic analysis followed a modified form of meaning condensation. We established rigour by transcript checking, inter-coder agreement, quote variation and standardised reporting.\n\nResultsDisadvantaged people experienced an unprecedented inequity in healthcare due to the pandemic. The main reasons were the reduction in public care services and limited access to information, transportation, technology and income. Stigmatisation from COVID-19 differed between cultural contexts and ranged from none to feeling \"ashamed\" and \"totally bashed\". Participants experienced telehealth as indispensable but with limitations. These included giving \"bad news\", such as having an eye removed because of melanoma, and the difficulty of providing end-of-life care over the phone. Patient representatives redefined their role and became indispensable influencers throughout the pandemic and beyond.\n\nConclusionWe reached out to individuals with a diversity of perspectives, including minorities and marginalised populations. A systematic exclusion of people with limited technology access increases inequity in healthcare and biases research findings. Since preferences and personal meanings drive behaviour and could be foundations for targeted interventions, they must be considered in all groups of people to increase societys resilience as a whole.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Tanja Stamm", - "author_inst": "Medical University of Vienna, Austria" - }, - { - "author_name": "Yuki Seidler", - "author_inst": "Medical University of Vienna, Austria" - }, - { - "author_name": "Margaret R Andrews", - "author_inst": "Medical University of Vienna, Austria" - }, - { - "author_name": "Mohammad Eghbali", - "author_inst": "University of Social Welfare and Rehabilitation Sciences, Tehran, Iran" - }, - { - "author_name": "Juliet Kiguli", - "author_inst": "Makerere University, Kampala, Uganda" - }, - { - "author_name": "Valentin Ritschl", - "author_inst": "Medical University of Vienna, Austria" - }, - { - "author_name": "Maisa Omara", - "author_inst": "Medical University of Vienna, Austria" - }, - { - "author_name": "Gertraud Schaffer", - "author_inst": "Oesterreichische Rheumaliga, Maria Alm, Austria" - }, - { - "author_name": "Erika Mosor", - "author_inst": "Medical University of Vienna, Austria" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2021.04.05.21254952", "rel_title": "mRNA vaccination compared to infection elicits an IgG-predominant response with greater SARS-CoV-2 specificity and similar decrease in variant spike recognition", @@ -833261,6 +834637,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.06.21254800", + "rel_title": "Impacts of Morally Distressing Experiences on the Mental Health of Canadian Health Care Workers During the COVID-19 Pandemic", + "rel_date": "2021-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.06.21254800", + "rel_abs": "ObjectiveResearch is urgently needed to understand health care workers (HCWs) experiences of moral-ethical dilemmas encountered throughout the COVID-19 pandemic, and their associations with organizational perceptions and personal well-being. The purpose of this research is to evaluate associations between workplace experiences during COVID-19, moral distress, and the psychological well-being of Canadian HCWs.\n\nMethodA total of 1383 French- and English-speaking Canadian HCWs employed during the COVID-19 pandemic were recruited to participate in an online survey. Participants completed measures reflecting moral distress, perceptions of organizational response to the pandemic, burnout, and symptoms of psychological disorders, including depression, anxiety, and posttraumatic stress disorder.\n\nResultsStructural equation modeling showed that when organizational predictors were considered together, resource adequacy, positive work life impact, and ethical work environment negatively predicted severity of moral distress, whereas COVID-19 risk perception positively predicted severity of moral distress. Moral distress also significantly and positively predicted symptoms of depression, anxiety, PTSD, and burnout.\n\nConclusionsOur findings highlight an urgent need for HCW organizations to implement strategies designed to prevent long-term moral and psychological distress within the workplace. Ensuring availability of adequate resources, reducing HCW risk of contracting COVID-19, providing organizational support regarding individual priorities, and upholding ethical considerations are crucial to reducing severity of moral distress in HCWs.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Rachel Alexandra Plouffe", + "author_inst": "The MacDonald Franklin Operational Stress Injury Research Centre, Lawson Health Research Institute, London, Ontario" + }, + { + "author_name": "Anthony Nazarov", + "author_inst": "The MacDonald Franklin Operational Stress Injury Research Centre, Lawson Health Research Institute, London, Ontario" + }, + { + "author_name": "Callista A Forchuk", + "author_inst": "The MacDonald Franklin Operational Stress Injury Research Centre, Lawson Health Research Institute, London, Ontario" + }, + { + "author_name": "Dominic Gargala", + "author_inst": "The MacDonald Franklin Operational Stress Injury Research Centre, Lawson Health Research Institute, London, Ontario" + }, + { + "author_name": "Erisa Deda", + "author_inst": "St Josephs Operational Stress Injury Clinic, Parkwood Institute, St Josephs Health Care, London, Ontario, Canada" + }, + { + "author_name": "Tri Le", + "author_inst": "The MacDonald Franklin Operational Stress Injury Research Centre, Lawson Health Research Institute, London, Ontario" + }, + { + "author_name": "Jesse Bourret-Gheysen", + "author_inst": "The MacDonald Franklin Operational Stress Injury Research Centre, Lawson Health Research Institute, London, Ontario" + }, + { + "author_name": "Brittni Jackson", + "author_inst": "The MacDonald Franklin Operational Stress Injury Research Centre, Lawson Health Research Institute, London, Ontario" + }, + { + "author_name": "Vanessa Soares", + "author_inst": "The MacDonald Franklin Operational Stress Injury Research Centre, Lawson Health Research Institute, London, Ontario" + }, + { + "author_name": "Fardous Hosseiny", + "author_inst": "The Royals Institute for Mental Health Research, Ottawa, Ontario, Canada" + }, + { + "author_name": "Patrick Smith", + "author_inst": "The Royals Institute for Mental Health Research, Ottawa, Ontario, Canada" + }, + { + "author_name": "Maya Roth", + "author_inst": "St. Josephs Operational Stress Injury Clinic, Parkwood Institute, St. Josephs Health Care, London, Ontario, Canada" + }, + { + "author_name": "Arlene G MacDougall", + "author_inst": "Department of Psychiatry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada" + }, + { + "author_name": "Michelle Marlborough", + "author_inst": "St. Josephs Operational Stress Injury Clinic, Parkwood Institute, St. Josephs Health Care, London, Ontario, Canada" + }, + { + "author_name": "Rakesh Jetly", + "author_inst": "The Royals Institute for Mental Health Research, Ottawa, Ontario, Canada" + }, + { + "author_name": "Alexandra Heber", + "author_inst": "Veterans Affairs Canada, Ottawa, Ontario, Canada" + }, + { + "author_name": "Joy Albuquerque", + "author_inst": "Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada" + }, + { + "author_name": "Ruth Lanius", + "author_inst": "Department of Psychiatry, Department of Neuroscience, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada" + }, + { + "author_name": "Ken Balderson", + "author_inst": "St. Josephs Operational Stress Injury Clinic, Parkwood Institute, St. Josephs Health Care, London, Ontario, Canada" + }, + { + "author_name": "Gabrielle Dupuis", + "author_inst": "The Royals Institute for Mental Health Research, Ottawa, Ontario," + }, + { + "author_name": "Viraj Mehta", + "author_inst": "St. Josephs Health Care London and Parkwood Institute, Lawson Health Research Institute, London, Ontario, Canada" + }, + { + "author_name": "J Don Richardson", + "author_inst": "The MacDonald Franklin Operational Stress Injury Research Centre, Lawson Health Research Institute, London, Ontario" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.04.06.21254961", "rel_title": "It's possibly made us feel a little more alienated: How people from ethnic minority communities conceptualise COVID-19 and its influence on engagement with testing.", @@ -834676,53 +836155,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.02.21254493", - "rel_title": "Humoral response to Pfizer mRNA vaccine against SARS CoV2, in patients with autoimmune inflammatory rheumatic diseases and the impact on the rheumatic disease activity", - "rel_date": "2021-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.02.21254493", - "rel_abs": "BackgroundThe registration trials of mRNA vaccines against SARS CoV2 did not address patients with autoimmune inflammatory rheumatoid diseases (AIRD).\n\nAimsTo assess the humoral response to mRNA vaccine against SARS CoV2, in AIRD patients treated with immunomodulating drugs and the impact on AIRD activity.\n\nMethodsConsecutive patients treated at the rheumatology institute who received their first SARS-CoV-2 (Pfizer) vaccine were recruited to the study, at their routine visit. The patients were invited for serology test 4-6 weeks after receiving the second dose of vaccine. IgG Antibodies (Ab) against SARS COV2 virus were detected using the SARS-Cov-2 IgG II Quant (Abbott) assay\n\nResultsOne hundred fifty-six consecutive patients (76% females) treated at a single rheumatology center (mean age (range) 59.1 (21-83) years), mean (range) disease duration 10.8 (1-55) years), were recruited to the study. Thirty-five percents of patients received conventional synthetic (cs)DMARDs only, 64% biological/targeted synthetic (b/ts) DMARDs, 34% received combined treatment with csDMARDs and b/tsDMARDs and 32% corticosteroids (mean dose(range) 5.8mg(2.5-20mg) prednisone). One hundred thirty-seven patients (88%) were seropositive for IgG Ab against SARS CoV2 virus (median 2832.5 AU/ml, range 58-29499). Nineteen (12%) patients had negative tests, 11/19 were treated with B cell depleting agents. The reported side effects of the vaccine were minor (muscle sore, headache, low grade fever). The rheumatic disease remained stable in all patients.\n\nConclusionsThe vast majority of AIRD patients developed a significant humoral response following the administration of the second dose of the Pfeizer mRNA vaccine against SARS CoV2 virus. Only minor side effects were reported and no apparent impact on AIRD activity was noted.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Yolanda Braun-Moscovici", - "author_inst": "Rambam Health Care Campus" - }, - { - "author_name": "Marielle Kaplan", - "author_inst": "Biochemistry Laboratory, Rambam Health Care Campus, Rappaport Faculty of Medicine, Technion, Haifa" - }, - { - "author_name": "Doron Markovits", - "author_inst": "B Shine Rheumatology Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Technion, Haifa" - }, - { - "author_name": "Samy Giryes", - "author_inst": "B Shine Rheumatology Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Technion, Haifa" - }, - { - "author_name": "Kochava Toledano", - "author_inst": "B Shine Rheumatology Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Technion, Haifa" - }, - { - "author_name": "Yonit Tavor", - "author_inst": "B Shine Rheumatology Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Technion, Haifa" - }, - { - "author_name": "Katya Dolnikov", - "author_inst": "B Shine Rheumatology Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Technion, Haifa" - }, - { - "author_name": "Alexandra Balbir-Gurman", - "author_inst": "B Shine Rheumatology Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Technion, Haifa" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "rheumatology" - }, { "rel_doi": "10.1101/2021.03.31.21254674", "rel_title": "Efficient Maternal to Neonatal transfer of SARS-CoV-2 and BNT162b2 antibodies", @@ -835051,6 +836483,169 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2021.04.03.21254873", + "rel_title": "DRUL for School: Opening Pre-K with safe, simple, sensitive saliva testing for SARS-CoV-2", + "rel_date": "2021-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.03.21254873", + "rel_abs": "To address the need for simple, safe, sensitive, and scalable SARS-CoV-2 tests, we validated and implemented a PCR test that uses a saliva collection kit use at home. Individuals self-collected 300 {micro}l saliva in vials containing Darnell Rockefeller University Laboratory (DRUL) buffer and extracted RNA was assayed by RT-PCR (the DRUL saliva assay). The limit of detection was confirmed to be 1 viral copy/{micro}l in 20 of 20 replicate extractions. Viral RNA was stable in DRUL buffer at room temperature up to seven days after sample collection, and safety studies demonstrated that DRUL buffer immediately inactivated virus at concentrations up to 2.75x106 PFU/ml. Results from SARS-CoV-2 positive nasopharyngeal (NP) swab samples collected in viral transport media and assayed with a standard FDA Emergency Use Authorization (EUA) test were highly correlated with samples placed in DRUL buffer. Direct comparison of results from 162 individuals tested by FDA EUA oropharyngeal (OP) or NP swabs with co-collected saliva samples identified four otherwise unidentified positive cases in DRUL buffer. Over six months, we collected 3,724 samples from individuals ranging from 3 months to 92 years of age. This included collecting weekly samples over 10 weeks from teachers, children, and parents from a pre-school program, which allowed its safe reopening while at-risk pods were quarantined. In sum, we validated a simple, sensitive, stable, and safe PCR-based test using a self-collected saliva sample as a valuable tool for clinical diagnosis and screening at workplaces and schools.", + "rel_num_authors": 37, + "rel_authors": [ + { + "author_name": "Mayu Frank", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Nathalie E Blachere", + "author_inst": "Rockefeller University, Howard Hughes Medical Institute" + }, + { + "author_name": "Salina Parveen", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Ezgi Hacisuleyman", + "author_inst": "Rockefeller University" + }, + { + "author_name": "John Fak", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Joseph M Luna", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Eleftherios Michailidis", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Samara Wright", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Pamela Stark", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Ann H Campbell", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Ashley Foo", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Thomas P Sakmar", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Virginia Huffman", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Marissa Bergh", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Audrey Goldfarb", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Andrew Mansisidor", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Agata L Patriotis", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Karl H Palmquist", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Nicolas Poulton", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Rachel Leicher", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Cesar D Vargas", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Irene Duba", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Arlene Hurley", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Joseph P Colagreco", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Nicole Pagane", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Dana E Orange", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Kevin Mora", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Jennifer L Rakeman", + "author_inst": "Public Health Laboratory, NYC Department of Health and Mental Hygiene" + }, + { + "author_name": "Randal C Fowler", + "author_inst": "Public Health Laboratory, NYC Department of Health and Mental Hygiene" + }, + { + "author_name": "Helen Fernandes", + "author_inst": "Rockefeller University, Columbia University" + }, + { + "author_name": "Michelle F Lamendola-Essel", + "author_inst": "Rockefeller University, Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Nick Didkovsky", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Leopolda Silvera", + "author_inst": "Elmhurst Hospital Center, New York City Health and Hospitals" + }, + { + "author_name": "Joseph Masci", + "author_inst": "Elmhurst Hospital Center, New York City Health and Hospitals" + }, + { + "author_name": "Machelle Allen", + "author_inst": "Elmhurst Hospital Center, New York City Health and Hospitals" + }, + { + "author_name": "Charles M Rice", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Robert B Darnell", + "author_inst": "Rockefeller University, Howard Hughes Medical Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.31.21254739", "rel_title": "Global-scale analysis and longitudinal assessment of COVID-19 incidence in the first six months", @@ -836442,37 +838037,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.31.21254434", - "rel_title": "Impact of COVID-19 in Individuals with Autism Spectrum Disorders: Analysis of a National Private Claims Insurance Database", - "rel_date": "2021-04-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.31.21254434", - "rel_abs": "The COVID-19 pandemic continues to have a detrimental impact on individuals with disabilities. Data from FAIR Healths FH(R) NPIC (National Private Insurance Claims) database,1 one of the nations largest databases of private insurance claim records, were analyzed to understand the experiences of individuals with ASD in COVID-19 pandemic. Multivariate logistic regression models revealed that individuals with ASD + ID were nine times more likely to be hospitalized (OR = 9.3; 95% CI: 6.9 - 12.5) and were nearly six times more likely have an elevated length of hospital stay(OR = 5.9; 95% CI: 3.5 - 10.1) compared those without ASD + ID. These findings point to their need for prioritization in access to vaccines for preventing COVID-19 infection and morbidities.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Arun Karpur", - "author_inst": "Autism Speaks" - }, - { - "author_name": "Vijay Vasudevan", - "author_inst": "Autism Speaks" - }, - { - "author_name": "Andy J Shih", - "author_inst": "Autism Speaks" - }, - { - "author_name": "Thomas W Frazier", - "author_inst": "Autism Speaks, John Carroll University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.01.21254679", "rel_title": "Is convalescent plasma futile in COVID-19? A Bayesian re-analysis of the RECOVERY randomised controlled trial", @@ -836813,6 +838377,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.31.21254692", + "rel_title": "Autoantibodies stabilize neutrophil extracellular traps in COVID-19", + "rel_date": "2021-04-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.31.21254692", + "rel_abs": "The release of neutrophil extracellular traps (NETs) by hyperactive neutrophils is recognized to play an important role in the thromboinflammatory milieu inherent to severe presentations of COVID-19. At the same time, a variety of functional autoantibodies have been observed in individuals with severe COVID-19 where they likely contribute to immunopathology. Here, we aimed to determine the extent to which autoantibodies might target NETs in COVID-19 and, if detected, to elucidate their potential functions and clinical associations. We measured anti-NET antibodies in 328 individuals hospitalized with COVID-19 alongside 48 healthy controls. We found high anti-NET activity in the IgG and IgM fractions of 27% and 60% of patients, respectively. There was a strong correlation between anti-NET IgG and anti-NET IgM (r=0.4, p<0.0001). Both anti-NET IgG and IgM tracked with high levels of circulating NETs, impaired oxygenation efficiency, and high circulating D-dimer. Furthermore, patients who required mechanical ventilation had a greater burden of anti-NET antibodies than did those not requiring oxygen supplementation. Levels of anti-NET IgG (and to a lesser extent anti-NET IgM) demonstrated an inverse correlation with the efficiency of NET degradation by COVID sera. Furthermore, purified IgG from COVID sera with high levels of anti-NET antibodies impaired the ability of healthy control serum to degrade NETs. In summary, many individuals hospitalized with COVID-19 have anti-NET antibodies, which likely impair NET clearance and may potentiate SARS-CoV-2-mediated thromboinflammation.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Yu Zuo", + "author_inst": "University of Michigan" + }, + { + "author_name": "Srilakshmi Yalavarthi", + "author_inst": "University of Michigan" + }, + { + "author_name": "Sherwin Navaz", + "author_inst": "University of Michigan" + }, + { + "author_name": "Claire Hoy", + "author_inst": "University of Michigan" + }, + { + "author_name": "Alyssa Harbaugh", + "author_inst": "University of Michigan" + }, + { + "author_name": "Kelsey Gockman", + "author_inst": "University of Michigan" + }, + { + "author_name": "Melanie Zuo", + "author_inst": "University of Michigan" + }, + { + "author_name": "Jacqueline A. Madison", + "author_inst": "University of Michigan" + }, + { + "author_name": "Hui Shi", + "author_inst": "University of Michigan" + }, + { + "author_name": "Yogendra Kanthi", + "author_inst": "University of Michigan" + }, + { + "author_name": "Jason S. Knight", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.02.21253262", "rel_title": "Antibodies against type-I Interferon: detection and association with severe clinical outcome in COVID-19 patients", @@ -838364,61 +839987,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.02.21254856", - "rel_title": "Background rates of hospitalizations and emergency department visits for selected thromboembolic and coagulation disorders in Ontario, Canada, 2015 to 2020, to inform COVID-19 vaccine safety surveillance", - "rel_date": "2021-04-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.02.21254856", - "rel_abs": "ObjectiveThe objective of this study was to estimate background rates of selected thromboembolic and coagulation disorders in Ontario, Canada.\n\nDesignPopulation-based retrospective observational study using linked health administrative databases. Records of hospitalizations and emergency department visits were searched to identify cases using diagnostic codes from the International Statistical Classification of Diseases and Related Health Problems, Tenth Revision, Canada (ICD-10-CA).\n\nParticipantsAll Ontario residents.\n\nPrimary outcome measuresIncidence rates of stroke, deep vein thrombosis, pulmonary embolism, idiopathic thrombocytopenia, disseminated intravascular coagulation, and cerebral venous thrombosis during five pre-pandemic years (2015-2019, annually, averaged, and monthly average) and 2020.\n\nResultsThe average annual population was 14 million with 51% female. The mean annual rates during 2015-2019 were 127.1/100,000 population (95% confidence interval [CI], 126.2, 127.9) for ischemic stroke, 22.0/100,000 (95%CI, 21.6, 22.3) for intracerebral haemorrhage, 9.4 (95%CI, 9.2, 9.7) for subarachnoid haemorrhage, 86.8/100,000 (95%CI, 86.1, 87.5) for deep vein thrombosis, 63.7/100,000 (95%CI, 63.1, 64.3) for pulmonary embolism, 6.1/100,000 (95%CI, 5.9, 6.3) for idiopathic thrombocytopenia, 1.6/100,000 (95%CI, 1.5, 1.7) for disseminated intravascular coagulation, and 1.5/100,000 (95%CI, 1.4, 1.6) for cerebral venous thrombosis. Rates were lower in 2020 than during the pre-pandemic years for ischemic stroke, deep vein thrombosis, and idiopathic thrombocytopenia. Rates were generally consistent over time, except for pulmonary embolism, which increased from 57.1 to 68.5 per 100,000 between 2015 and 2019. Rates were higher for females than males for subarachnoid haemorrhage, pulmonary embolism, and cerebral venous thrombosis, and vice versa for ischemic stroke and intracerebral haemorrhage. Rates increased with age for most of these conditions, but idiopathic thrombocytopenia demonstrated a bimodal distribution with incidence peaks at 0-19 years and [≥]60 years.\n\nConclusionsOur estimated background rates help to contextualize observed events of these potential adverse events of special interest and to detect potential safety signals related to COVID-19 vaccines.\n\nStrengths and limitations of this study[tpltrtarr] Recent background rates of selected thromboembolic and coagulation disorders that are potential adverse events special interest related to COVID-19 vaccine are estimated.\n[tpltrtarr]Background rates during five pre-pandemic (2015-2019) years and 2020 will provide context for these events to identify vaccine safety signals.\n[tpltrtarr]We used recorded diagnostic codes in administrative data without information on clinical and/or diagnostic confirmation, and the validity of these data are imperfect, which may result in under or overestimation.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Sharifa Nasreen", - "author_inst": "University of Toronto" - }, - { - "author_name": "Andrew Calzavara", - "author_inst": "ICES" - }, - { - "author_name": "Maria Sundaram", - "author_inst": "University of Toronto" - }, - { - "author_name": "Shannon E MacDonald", - "author_inst": "University of Alberta" - }, - { - "author_name": "Christiaan Righolt", - "author_inst": "University of Manitoba" - }, - { - "author_name": "Menaka Pai", - "author_inst": "McMaster University" - }, - { - "author_name": "Thalia Field", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Lily W Zhou", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Sarah Wilson", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Jeff Kwong", - "author_inst": "ICES" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.02.438274", "rel_title": "Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN", @@ -838807,6 +840375,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.27.21254461", + "rel_title": "Determining the cutoff points of the 5C scale for assessment of COVID-19 vaccines psychological antecedents among the Arab population: A multinational study", + "rel_date": "2021-04-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.27.21254461", + "rel_abs": "BackgroundOne of the newly faced challenges during the COVID-19 is vaccine hesitancy (VH). The validated 5C scale, that assesses five psychological antecedents of vaccination, could be effective in exploring COVID-19 VH. This study aimed to determine a statistically valid cutoff points for the 5C sub-scales among the Arab population.\n\nMethodsA cross-sectional study was conducted among 446 subjects from three Arab countries (Egypt, United Arab Emirates UAE, and Jordan). Information regarding sociodemographics, clinical history, COVID-19 infection and vaccination history, and 5C scale were collected online. The 5C scores were analyzed to define the cutoff points using the receiver operating characteristic curve (ROC) and to verify the capability of the questionnaire to differentiate whether responders are hesitant or non-hesitant to accept vaccination. ROC curve analysis was conducted setting for previous vaccine administration as a response, with the predictors being the main five domains of the 5C questionnaire. The mean score of each sub-scale was compared with COVID-19 vaccine intake\n\nResultsThe mean age of the studied population was 37{+/-}11, 42.9% were males, 44.8% from Egypt, 21.1% from Jordan, and 33.6% from UAE. Statistically significant differences between vaccinated and unvaccinated participants, respectively, weredetetd in the median score of confidence [6.0(1.3) versus 4.7(2.0)], complacency [(2.7(2.0) versus 3.0(2.0), constraints [1.7(1.7) versus 3.7(2.3)], and collective responsibility [6.7(1.7) versus 5.7(1.7)]. The area under the curve of the five scales was 0.72, 0.60, 0.76, 0.66, 0.66 for confidence, complacency, constraints, calculation, and collective responsibility at cutoff values of 5.7, 4.7, 6.0, 6.3, and 6.2, respectively.\n\nConclusionthe Arabic validated version of the 5C scale has a good discriminatory power to predict COVID-19 vaccines antecedent.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ramy Ghazy", + "author_inst": "High Institute of Public Health" + }, + { + "author_name": "Samar Abd ElHafeez", + "author_inst": "High Institute of Public Health, Alexandria University, Egypt" + }, + { + "author_name": "Ramy Shaban", + "author_inst": "Department of Instructional Technology and Learning Sciences, Utah State University, USA" + }, + { + "author_name": "Iffat Elbarazi", + "author_inst": "Institute of Public Health, College of Medicine and Health Sciences, United Arab Emirates University, AlAin, UAE" + }, + { + "author_name": "Marwa Shawky Abdou", + "author_inst": "Epidemiology Department, High Institute of Public Health, Alexandria University, Egypt" + }, + { + "author_name": "Ahmed Mohamed Ramadan", + "author_inst": "National Research Centre" + }, + { + "author_name": "Khalid A. Kheirallah", + "author_inst": "(5)\tDepartment of Public Health, Medical School of Jordan University of Science and Technology, Irbid 22110, Jordan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.30.21254031", "rel_title": "Clinical efficacy of Early Administration of Convalescent Plasma among COVID-19 Cases in Egypt", @@ -840318,145 +841929,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.03.31.437925", - "rel_title": "SARS-CoV-2 immune evasion by variant B.1.427/B.1.429", - "rel_date": "2021-04-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.31.437925", - "rel_abs": "SARS-CoV-2 entry is mediated by the spike (S) glycoprotein which contains the receptor-binding domain (RBD) and the N-terminal domain (NTD) as the two main targets of neutralizing antibodies (Abs). A novel variant of concern (VOC) named CAL.20C (B.1.427/B.1.429) was originally detected in California and is currently spreading throughout the US and 29 additional countries. It is unclear whether antibody responses to SARS-CoV-2 infection or to the prototypic Wuhan-1 isolate-based vaccines will be impacted by the three B.1.427/B.1.429 S mutations: S13I, W152C and L452R. Here, we assessed neutralizing Ab responses following natural infection or mRNA vaccination using pseudoviruses expressing the wildtype or the B.1.427/B.1.429 S protein. Plasma from vaccinated or convalescent individuals exhibited neutralizing titers, which were reduced 3-6 fold against the B.1.427/B.1.429 variant relative to wildtype pseudoviruses. The RBD L452R mutation reduced or abolished neutralizing activity of 14 out of 35 RBD-specific monoclonal antibodies (mAbs), including three clinical-stage mAbs. Furthermore, we observed a complete loss of B.1.427/B.1.429 neutralization for a panel of mAbs targeting the N-terminal domain due to a large structural rearrangement of the NTD antigenic supersite involving an S13I-mediated shift of the signal peptide cleavage site. These data warrant closer monitoring of signal peptide variants and their involvement in immune evasion and show that Abs directed to the NTD impose a selection pressure driving SARS-CoV-2 viral evolution through conventional and unconventional escape mechanisms.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Matthew McCallum", - "author_inst": "University of Washington" - }, - { - "author_name": "Jessica Bassi", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Anna De Marco", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Alex Chen", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Alexandra C Walls", - "author_inst": "University of Washington" - }, - { - "author_name": "Julia Di Iulio", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "M. Alejandra Tortorici", - "author_inst": "University of Washington" - }, - { - "author_name": "Mary-Jane Navarro", - "author_inst": "University of Washington" - }, - { - "author_name": "Chiara Silacci-Fregni", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Christian Saliba", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Maria Agostini", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Dora Pinto", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Katja Culap", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Siro Bianchi", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Stefano Jaconi", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Elisabetta Cameroni", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "John E Bowen", - "author_inst": "University of Washington" - }, - { - "author_name": "Sasha W Tiles", - "author_inst": "University of Washington" - }, - { - "author_name": "Matteo Samuele Pizzuto", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Sonja Bernasconi Guastalla", - "author_inst": "Independent physician" - }, - { - "author_name": "Giovanni Bona", - "author_inst": "Independent physician" - }, - { - "author_name": "Alessandra Franzetti Pellanda", - "author_inst": "Clinica Luganese Moncucco" - }, - { - "author_name": "Christian Garzoni", - "author_inst": "Clinica Luganese Moncucco" - }, - { - "author_name": "Wesley C Van Voorhis", - "author_inst": "University of Washington" - }, - { - "author_name": "Laura E Rosen", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Gyorgy C Snell", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Amalio Telenti", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Herbert W Virgin", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Luca Piccoli", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Davide Corti", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "David Veesler", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.04.01.438035", "rel_title": "The neutralization potency of anti-SARS-CoV-2 therapeutic human monoclonal antibodies is retained against novel viral variants", @@ -840757,6 +842229,89 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.01.436305", + "rel_title": "An alphavirus replicon-based vaccine expressing a stabilized Spike antigen induces sterile immunity and prevents transmission of SARS-CoV-2 between cats", + "rel_date": "2021-04-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.01.436305", + "rel_abs": "Early in the global SARS-CoV-2 pandemic concerns were raised regarding infection of other animal hosts and whether these could play a significant role in the viral epidemiology. Infection of animals could be detrimental by causing clinical disease but also of concern if they become a viral reservoir allowing further mutations, plus having the potential to infect other animals or humans. The first reported animals to be infected both under experimental conditions and from anecdotal field evidence were cats described in China early in 2020. Given the concerns this finding raised and the close contacts between humans and cats, we aimed to determine whether a vaccine candidate could be developed that was suitable for use in multiple susceptible animal species and whether this vaccine could reduce infection of cats in addition to preventing spread to other cats.\n\nHere we report that a Replicon Particle (RP) vaccine based on Venezuelan equine encephalitis virus (VEEV), known to be safe and efficacious for use in a variety of animals, expressing a stabilised Spike antigen, could induce neutralising antibody titers in guinea pigs and cats. After two intramuscular vaccinations, virus neutralising antibodies were detected in the respiratory tract of the guinea pigs and a cell mediated immune response was induced. The design of the SARS-CoV-2 antigen was shown to be critical in developing a strong neutralising antibody response. Vaccination of cats was able to induce a serum neutralising antibody response which lasted for the course of the experiment. Interestingly, in contrast to control animals, infectious virus could not be detected in oropharyngeal or nasal swabs of vaccinated cats after challenge. Moreover, the challenged control cats spread the virus to in-contact cats whereas the vaccinated cats did not transmit virus. The results show that the RP vaccine induces sterile immunity preventing SARS-CoV-2 infection and transmission. This data suggests that this RP vaccine could be a multi-species vaccine useful for preventing spread to and between other animals should that approach be required.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Martijn Alexander Langereis", + "author_inst": "MSD Animal Health/Intervet International BV, Boxmeer, Netherlands" + }, + { + "author_name": "Ken Stachura", + "author_inst": "Merck Animal Health/Intervet inc., Elkhorn, NE, USA" + }, + { + "author_name": "Suzan Miller", + "author_inst": "Merck Animal Health/Intervet inc., Elkhorn, NE, USA" + }, + { + "author_name": "Angela M. Bosco-Lauth", + "author_inst": "College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA" + }, + { + "author_name": "Irina C. Albulescu", + "author_inst": "Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Net" + }, + { + "author_name": "Airn E. Hartwig", + "author_inst": "College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA" + }, + { + "author_name": "Stephanie M. Porter", + "author_inst": "College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA" + }, + { + "author_name": "Judith Stammen-Vogelzangs", + "author_inst": "MSD Animal Health/Intervet International BV, Boxmeer, Netherland" + }, + { + "author_name": "Mark Mogler", + "author_inst": "Merck Animal Health, Ames, IA, USA" + }, + { + "author_name": "Frank J.M. van Kuppeveld", + "author_inst": "Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Net" + }, + { + "author_name": "Berend Jan Bosch", + "author_inst": "Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Net" + }, + { + "author_name": "Paul Vermeij", + "author_inst": "MSD Animal Health/Intervet International BV, Boxmeer, Netherlands" + }, + { + "author_name": "Ad de Groof", + "author_inst": "MSD Animal Health/Intervet International BV, Boxmeer, Netherlands" + }, + { + "author_name": "Richard A. Bowen", + "author_inst": "College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA" + }, + { + "author_name": "Randy Davis", + "author_inst": "Merck Animal Health/Intervet inc., Elkhorn, NE, USA" + }, + { + "author_name": "Zach Xu", + "author_inst": "Merck Animal Health/Intervet inc., Elkhorn, NE, USA" + }, + { + "author_name": "Ian Tarpey", + "author_inst": "MSD Animal Health/Intervet UK Ltd., Milton Keynes, UK" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.03.31.437792", "rel_title": "Hydrogel-based slow release of a receptor-binding domain subunit vaccine elicits neutralizing antibody responses against SARS-CoV-2", @@ -842432,33 +843987,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.30.21254635", - "rel_title": "Validity of markers and indexes of systemic inflammation in predicting mortality in COVID 19 infection : A hospital based cross sectional study", - "rel_date": "2021-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.30.21254635", - "rel_abs": "BackgroundCOVID-19 is an ongoing global pandemic. It is a systemic infection with a significant impact on the hematopoietic and the immune system. In this study we aimed to evaluate the different inflammatory markers and indexes of systemic inflammatory response in predicting the mortality in patients with COVID 19.\n\nMethodsIn this cross sectional study, various inflammatory markers like D-dimer, CRP, serum ferritin, LDH and CBC derived indexes of inflammation were analyzed in predicting mortality in COVID 19 infection.\n\nResultsWe enrolled 302 COVID 19 patients who had a mean age of 54.51{+/-}15.39 yrs with 210 (69.5%) males. Among them 21% were asymptomatic and fever was the commonest among symptomatic patients. Majority of patients (66.7%) had no comorbidities and 20% had multiple comorbidities. On analyzing different hematological variables, survivors had statistically significant higher hemoglobin count, lymphocytes, monocytes, eosinophil and platelet count and lower leukocyte, neutrophil count. Inflammatory markers D-dimer, serum ferritin and LDH were significantly elevated among non survivors. Among the indexes of inflammation, only NLR showed significant higher values among non survivors.\n\nAll the inflammatory markers were able to predict mortality among the COVID 19 infected cases with a sensitivity and specificity of 85% and 65% for d dimer levels, 85% and 72% for serum ferritin, 85% and 72% for LDH, 85% and 51% for CRP levels respectively. Among the indexes of inflammation, validity of NLR was best in predicting mortality with 85% sensitivity and 51% specificity.\n\nConclusionAbnormalities in peripheral blood parameters and increase in inflammatory markers are common findings in COVID 19 infection. NLR was best at predicting mortality followed by D-dimer and serum ferritin levels\n\nContribution details\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@c4c8eaorg.highwire.dtl.DTLVardef@1627f25org.highwire.dtl.DTLVardef@1896e70org.highwire.dtl.DTLVardef@1b1b238org.highwire.dtl.DTLVardef@12b8087_HPS_FORMAT_FIGEXP M_TBL C_TBL", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Archana Baburao", - "author_inst": "Rajarajeswari Medical college and hospital" - }, - { - "author_name": "shylaja Shamsunder", - "author_inst": "Bhagawan mahaveer jain hospital" - }, - { - "author_name": "Rinki Das", - "author_inst": "Bhagawan Mahaveer Jain hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.29.21254334", "rel_title": "Estimating the asymptomatic proportion of SARS-CoV-2 infection in the general population: Analysis of a nationwide serosurvey in the Netherlands", @@ -842623,6 +844151,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, + { + "rel_doi": "10.1101/2021.03.29.21254526", + "rel_title": "Longitudinal experiences and impact of the COVID-19 pandemic among people with past or current eating disorders in Sweden", + "rel_date": "2021-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254526", + "rel_abs": "ObjectiveTo document the impact of the COVI-19 pandemic on the health and well-being of individuals with past and current eating disorders in Sweden.\n\nMethodWe re-contacted participants from two previous Swedish studies who had a known lifetime history of an eating disorder. Participants completed an online questionnaire about their health and functioning at baseline early in the pandemic (Wave 1; N=982) and six months later (Wave 2); N=646).\n\nResultsThree important patterns emerged: 1) higher current eating disorder symptom levels were associated with greater anxiety, worry, and pandemic-related eating disorder symptom increase; 2) patterns were fairly stable across time, although a concerning number who reported being symptom-free at Wave 1 reported re-emergence of symptoms at Wave 2; and only a minority of participants with current eating disorders were in treatment, and of those who were in treatment, many reported fewer treatment sessions than pre-pandemic and decreased quality of care.\n\nConclusionsThe COVID-19 pandemic is posing serious health challenges for individuals with eating disorders, whether currently symptomatic or in remission. We encourage health service providers and patient advocates to be alert to the needs of individuals with eating disorders and to take active measures to ensure access to appropriate evidence-based care both during and following the pandemic.\n\nSignificant Outcomes and LimitationsO_LIIndividuals with eating disorders symptoms or current active disorder report higher adverse impact of COVID-19 on their mental health\nC_LIO_LIEven individuals who were symptom-free early in the pandemic reported a resurgence of eating disorder symptoms\nC_LIO_LIA large proportion of symptomatic individuals were not in treatment for their eating disorder, services should be aware and access to evidence-based care should be ensured across Sweden\nC_LIO_LILimitations included the use of a convenience sample with atypical diagnostic distribution, and a low initial response rate, possibly introducing bias and limiting generalisability.\nC_LI\n\nData Availability StatementFully anonymized data are available from the corresponding author upon request.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Andreas Birgegard", + "author_inst": "Karolinska institutet" + }, + { + "author_name": "Afrouz Abbaspour", + "author_inst": "Karolinska institutet" + }, + { + "author_name": "Stina Borg", + "author_inst": "Karolinska institutet" + }, + { + "author_name": "David Clinton", + "author_inst": "Karolinska institutet" + }, + { + "author_name": "Emma Forsen Mantilla", + "author_inst": "Karolinska institutet" + }, + { + "author_name": "Jet D Termorshuizen", + "author_inst": "Karolinska institutet; Rivierduinen Eating Disorders Ursula" + }, + { + "author_name": "Cynthia M Bulik", + "author_inst": "University of North Carolina at Chapel Hill; Karolinska Institutet" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.03.30.21254614", "rel_title": "Prevalence and risk factors of internet gaming disorder and problematic internet use before and during the COVID-19 pandemic: A large online survey of Japanese adults", @@ -843914,29 +845485,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.29.21254583", - "rel_title": "Migration of households from New York City and the Second Peak in Covid-19 cases in New Jersey, Connecticut and New York Counties.", - "rel_date": "2021-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254583", - "rel_abs": "The five boroughs of New York City (NYC) were early epicenters of the Covid-19 pandemic in the United States, with over 380,000 cases by May 31. High caseloads were also seen in nearby counties in New Jersey (NJ), Connecticut (CT) and New York (NY). The pandemic started in the area in March with an exponential rise in the number of daily cases, peaked in early April, briefly declined, and then, showed clear signs of a second peak in several counties. We will show that despite control measures such as lockdown and restriction of movement during the exponential rise in daily cases, there was a significant net migration of households from NYC boroughs to the neighboring counties in NJ, CT and NY State. We propose that the second peak in daily cases in these counties around NYC was due, in part, to the movement of people from NYC boroughs to these counties. We estimate the movement of people using \"Change of Address\" (CoA) data from the US Postal Service, provided under the \"Freedom of Information Act\" of 1967. To identify the timing of the second peak and the number of cases in it, we use a previously proposed SIR model, which accurately describes the early stages of the coronavirus pandemic in European countries. Subtracting the model fits from the data identified, we establish the timing and the number of cases, NCS, in the second peak. We then related the number of cases in the second peak to the county population density, P, and the excess Change of Address, ECoA, into each county using the simple model [Formula] which fits the data very well with = 0.68, {beta} = 0.31 (R2 = 0.74, p = 1.3e-8). We also find that the time between the first and second peaks was proportional to the distance of the county seat from NY Penn Station, suggesting that this migration of households and disease was a directed flow and not a diffusion process. Our analysis provides a simple method to use change of address data to track the spread of an infectious agent, such as SARS-Cov-2, due to migrations away from epicenters during the initial stages of a pandemic.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Adam T Schulman", - "author_inst": "Rutgers Robert Wood Johnson" - }, - { - "author_name": "Gyan Bhanot", - "author_inst": "Rutgers University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.29.21254581", "rel_title": "A new Reproduction Index Ri and its Usefulness for Germany's Covid19-Data", @@ -844193,6 +845741,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.29.21254151", + "rel_title": "Six-month pulmonary impairment after severe COVID-19: a prospective, multicenter follow-up study", + "rel_date": "2021-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254151", + "rel_abs": "Background and objectiveLong-term pulmonary sequelae following SARS-CoV-2 pneumonia are not yet confirmed, however preliminary observations suggests a possible relevant clinical, functional and radiological impairment. The aim of this study was to identify and characterise pulmonary sequelae caused by SARS-CoV-2 pneumonia at 6-month follow-up.\n\nMethodsIn this multicenter, prospective, observational cohort study, patients hospitalised for SARS-CoV-2 pneumonia and without prior diagnosis of structural lung diseases were stratified by maximum ventilatory support (\"oxygen only\", \"continuous positive airway pressure (CPAP)\" and \"invasive mechanical ventilation (IMV)\") and followed up at 6 months from discharge. Pulmonary function tests and diffusion capacity for carbon monoxide (DLCO), 6 minutes walking test, chest X-ray, physical exam and modified Medical Research Council (mMRC) dyspnoea score were collected.\n\nResultsBetween March and June 2020, 312 patients were enrolled (83, 27% women; median [IQR] age 61.1 [53.4,69.3] years). The parameters that showed the highest rate of impairment were DLCO and chest-X-ray, in 46% and 25% of patients, respectively. However, only a minority of patients reported dyspnoea (31%), defined as mMRC [≥] 1, or showed a restrictive ventilatory defects (9%). In the logistic regression model, having asthma as comorbidity was associated with DLCO impairment at follow-up, while prophylactic heparin administration during hospitalisation appeared as a protective factor. Need for invasive ventilatory support during hospitalisation was associated with chest imaging abnormalities.\n\nConclusionDLCO and radiological assessment appear to be the most sensitive tools to monitor patients with COVID-19 during follow-up. Future studies with longer follow-up are warranted to better understand pulmonary sequelae.\n\nSummary at a glanceDLCO and radiological assessment are the most sensitive tools to monitor COVID-19 patients at 6-month follow-up. Invasive ventilatory support is a risk factor for detection of radiological abnormalities, but not for DLCO impairment, at follow-up. Whileuse of prophylactic heparin acts as a protective factor on the development of DLCOimpairment.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Paola Faverio", + "author_inst": "University of Milano Bicocca, Respiratory Unit, San Gerardo Hospital, ASST Monza, Monza, Italy" + }, + { + "author_name": "Fabrizio Luppi", + "author_inst": "University of Milano Bicocca, Respiratory Unit, San Gerardo Hospital, ASST Monza, Monza, Italy" + }, + { + "author_name": "Paola Rebora", + "author_inst": "Bicocca Bioinformatics Biostatistics and Bioimaging B4 Center, University of Milano Bicocca, Monza, Italy" + }, + { + "author_name": "Sara Busnelli", + "author_inst": "Respiratory Unit, San Gerardo Hospital, ASST Monza, Monza, Italy" + }, + { + "author_name": "Anna Stainer", + "author_inst": "University of Milano Bicocca, Monza; Respiratory Unit, San Gerardo Hospital, ASST Monza, Monza, Italy" + }, + { + "author_name": "Martina Catalano", + "author_inst": "University of Milano Bicocca, Monza; Respiratory Unit, San Gerardo Hospital, ASST Monza, Monza, Italy" + }, + { + "author_name": "Luca Parachini", + "author_inst": "University of Milano Bicocca, Monza; Respiratory Unit, San Gerardo Hospital, ASST Monza, Monza, Italy" + }, + { + "author_name": "Anna Monzani", + "author_inst": "University of Milano Bicocca, Monza; Respiratory Unit, San Gerardo Hospital, ASST Monza, Monza, Italy" + }, + { + "author_name": "Stefania Galimberti", + "author_inst": "Bicocca Bioinformatics Biostatistics and Bioimaging B4 Center, University of Milano Bicocca, Monza, Italy" + }, + { + "author_name": "Francesco Bini", + "author_inst": "UOC Pulmonology, Department of Internal Medicine, Ospedale G. Salvini, ASST-Rhodense, Garbagnate Milanese (MI), Italy" + }, + { + "author_name": "Bruno Dino Bodini", + "author_inst": "UOC Pulmonology, Department of Internal Medicine, Ospedale G. Salvini, ASST-Rhodense, Garbagnate Milanese (MI), Italy" + }, + { + "author_name": "Monia Betti", + "author_inst": "Division of Pulmonary Medicine, Cremona Hospital, ASST Cremona, Cremona, Italy" + }, + { + "author_name": "Federica De Giacomi", + "author_inst": "Division of Pulmonary Medicine, Cremona Hospital, ASST Cremona, Cremona, Italy" + }, + { + "author_name": "Paolo Scarpazza", + "author_inst": "Division of Pulmonary Medicine, Civile Hospital, Vimercate (MB), Italy" + }, + { + "author_name": "Elisa Oggionni", + "author_inst": "Division of Pulmonary Medicine, Civile Hospital, Vimercate (MB), Italy" + }, + { + "author_name": "Alessandro Scartabellati", + "author_inst": "Department of Pulmonology and Respiratory High-Dependency Unit, Ospedale Maggiore, Crema, Italy" + }, + { + "author_name": "Luca Bilucaglia", + "author_inst": "Department of Pulmonology and Respiratory High-Dependency Unit, Ospedale Maggiore, Crema, Italy" + }, + { + "author_name": "Paolo Ceruti", + "author_inst": "U.O. Pneumologia e Fisiopatologia Respiratoria - ASST Spedali Civili di Brescia, Brescia, Italy" + }, + { + "author_name": "Denise Modina", + "author_inst": "U.O. Pneumologia e Fisiopatologia Respiratoria - ASST Spedali Civili di Brescia, Brescia, Italy" + }, + { + "author_name": "Sergio Harari", + "author_inst": "Department of Medical Sciences, San Giuseppe Hospital, MultiMedica IRCCS and Department of Clinical Sciences and Community Health, University of Milan, Milan, I" + }, + { + "author_name": "Antonella Caminati", + "author_inst": "Division of Pulmonary Medicine San Giuseppe Hospital, MultiMedica IRCCS" + }, + { + "author_name": "Maria Grazia Valsecchi", + "author_inst": "Bicocca Bioinformatics Biostatistics and Bioimaging B4 Center, University of Milano Bicocca, Monza, Italy" + }, + { + "author_name": "Giacomo Bellani", + "author_inst": "School of Medicine and Surgery, University of Milano Bicocca, Monza; Department of Anesthesia and Intensive Care Medicine, ASST Monza, Monza, Italy" + }, + { + "author_name": "Giuseppe Foti", + "author_inst": "School of Medicine and Surgery, University of Milano Bicocca, Monza; Department of Anesthesia and Intensive Care Medicine, ASST Monza, Monza, Italy" + }, + { + "author_name": "Alberto Pesci", + "author_inst": "School of Medicine and Surgery, University of Milano Bicocca, Monza; Respiratory Unit, San Gerardo Hospital, ASST Monza, Monza, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.03.29.21254122", "rel_title": "Increased transmissibility of the B.1.1.7 SARS-CoV-2 variant: Evidence from contact tracing data in Oslo, January to February 2021", @@ -845760,101 +847423,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.27.21253966", - "rel_title": "Clinical performance evaluation of SARS-CoV-2 rapid antigen testing in point of care usage in comparison to RT-qPCR", - "rel_date": "2021-03-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.27.21253966", - "rel_abs": "BackgroundAntigen rapid diagnostic tests (RDT) for SARS-CoV-2 are fast, broadly available, and inexpensive. Despite this, reliable clinical performance data is sparse.\n\nMethodsIn a prospective performance evaluation study, RDT from three manufacturers (NADAL(R), Panbio, MEDsan(R)) were compared to quantitative reverse transcription polymerase chain reaction (RT-qPCR) in 5 068 oropharyngeal swabs for detection of SARS-CoV-2 in a hospital setting. Viral load was derived from standardized RT-qPCR Cycle threshold (Ct) values. The data collection period ranged from November 12, 2020 to February 28, 2021.\n\nFindingsOverall, sensitivity of RDT compared to RT-qPCR was 42{middle dot}57% (95% CI 33{middle dot}38%-52{middle dot}31%), and specificity 99{middle dot}68% (95% CI 99{middle dot}48%-99{middle dot}80%). Sensitivity declined with decreasing viral load from 100% in samples with a deduced viral load of [≥]108 SARS-CoV-2 RNA copies per ml to 8{middle dot}82% in samples with a viral load lower than 104 SARS-CoV-2 RNA copies per ml. No significant differences in sensitivity or specificity could be observed between the three manufacturers, or between samples with and without spike protein variant B.1.1.7. The NPV in the study cohort was 98{middle dot}84%; the PPV in persons with typical COVID-19 symptoms was 97{middle dot}37%, and 28{middle dot}57% in persons without or with atypical symptoms.\n\nInterpretationRDT are a reliable method to diagnose SARS-CoV-2 infection in persons with high viral load. RDT are a valuable addition to RT-qPCR testing, as they reliably detect infectious persons with high viral loads before RT-qPCR results are available.\n\nFundingGerman Federal Ministry for Education and Science (BMBF), Free State of Bavaria\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMED an MedRxiv for articles including \"COVID-19\", \"COVID\", \"SARS-CoV-2\", \"coronavirus\" as well as \"antigen detection\", \"rapid antigen test\", \"Point-of-Care test\" in title or abstract, published between January 1, 2020 and February 28, 2021. The more than 150 RDT on the market at the end of February 2021 represent a huge expansion of diagnostic possibilities.1 Performance of currently available RDT is evaluated in several international studies, with heterogeneous results. Sensitivity values of RDT range from 0{middle dot}0%2 to 98{middle dot}3%3, specificity from 19{middle dot}4%4 to 100{middle dot}0%.2,5-14. Some of this data differs greatly from manufacturers data. However, these previously published performance evaluation studies were conducted under laboratory conditions using frozen swabs, or in small cohorts with middle-aged participants. Comparable RDT performance data from large-scale clinical usage is missing.5-19\n\nAdded value of this studyBased on previous examinations the real life opportunities and limitations of SARS-CoV-2 RDT as an instrument of hospital infection detection and control are still unclear as well as further study results are limited in transferability to general public. Our findings show that RDT performance in daily clinical routine is reliable in persons with high viral for punctual detection and isolation of infectious persons before RT-qPCR become available. In persons with lower viral load, or in case of asymptomatic patients SARS-CoV2 detection by RDT was unsuccessful. The general sensitivity of 42{middle dot}57% is too low to accept the RDT in clinical use as an alternative to RT-qPCR in diagnosis of COVID-19. Calculated specificity was 99.68%. The results are based on a huge study cohort with more than 5 000 participants including a representative ages structure with pediatric patients up to geriatric individuals, which portrays approximately the demographic structure of the local society.\n\nImplications of all the available evidenceDue to the low general sensitivity RDT in clinical use cannot be accepted as an alternative but as an addition to RT-qPCR in SARS-CoV-2 diagnosis. The benefit of early detection of highly infectious persons has to be seen in context of the effort of testing and isolation of false positive tested persons.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Isabell Wagenhaeuser", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Kerstin Knies", - "author_inst": "Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Vera Rauschenberger", - "author_inst": "Infection Control Unit, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Michael Eisenmann", - "author_inst": "Infection Control Unit, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Miriam McDonogh", - "author_inst": "Department of Orthopaedic Trauma, Hand, Plastic and Reconstructive Surgery, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Nils Petri", - "author_inst": "Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Oliver Andres", - "author_inst": "Department of Pediatrics, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Sven Flemming", - "author_inst": "Department of General, Visceral, Transplantation, Vascular and Pediatric Surgery, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Micha Gawlik", - "author_inst": "Department of Psychiatry and Psychotherapy, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Michael Papsdorf", - "author_inst": "Department of Obstetrics and Gynecology, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Regina Taurines", - "author_inst": "Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Hartmut Boehm", - "author_inst": "Department of Oral and Maxillofacial Surgery, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Johannes Forster", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Dirk Weismann", - "author_inst": "Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Benedikt Weissbrich", - "author_inst": "Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Lars Doelken", - "author_inst": "Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Johannes Liese", - "author_inst": "Department of Pediatrics, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Oliver Kurzai", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Ulrich Vogel", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Manuel Krone", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.26.21254422", "rel_title": "Targeting the Microbiome With KB109 in Outpatients with Mild to Moderate COVID-19 Reduced Medically Attended Acute Care Visits and Improved Symptom Duration in Patients With Comorbidities", @@ -846087,6 +847655,121 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2021.03.29.437516", + "rel_title": "Sexually dimorphic placental responses to maternal SARS-CoV-2 infection", + "rel_date": "2021-03-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.29.437516", + "rel_abs": "There is a persistent male bias in the prevalence and severity of COVID-19 disease. Underlying mechanisms accounting for this sex difference remain incompletely understood. Interferon responses have been implicated as a modulator of disease in adults, and play a key role in the placental anti-viral response. Moreover, the interferon response has been shown to alter Fc-receptor expression, and therefore may impact placental antibody transfer. Here we examined the intersection of viral-induced placental interferon responses, maternal-fetal antibody transfer, and fetal sex. Placental interferon stimulated genes (ISGs), Fc-receptor expression, and SARS-CoV-2 antibody transfer were interrogated in 68 pregnancies. Sexually dimorphic placental expression of ISGs, interleukin-10, and Fc receptors was observed following maternal SARS-CoV-2 infection, with upregulation in males. Reduced maternal SARS-CoV-2-specific antibody titers and impaired placental antibody transfer were noted in pregnancies with a male fetus. These results demonstrate fetal sex-specific maternal and placental adaptive and innate immune responses to SARS-CoV-2.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Evan A Bordt", + "author_inst": "Department of Pediatrics, Lurie Center for Autism, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA" + }, + { + "author_name": "Lydia L Shook", + "author_inst": "Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Vincent Center for Reproductive Biology, Massa" + }, + { + "author_name": "Caroline Atyeo", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; PhD Program in Virology, Division of Medical Sciences, Harvard University, Boston, MA, USA" + }, + { + "author_name": "Krista M Pullen", + "author_inst": "Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA" + }, + { + "author_name": "Rose M De Guzman", + "author_inst": "Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Vincent Center for Reproductive Biology, Massa" + }, + { + "author_name": "Marie-Charlotte Meinsohn", + "author_inst": "Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA" + }, + { + "author_name": "Maeva Chauvin", + "author_inst": "Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA" + }, + { + "author_name": "Stephanie Fischinger", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA" + }, + { + "author_name": "Laura J Yockey", + "author_inst": "Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Vincent Center for Reproductive Biology, Massa" + }, + { + "author_name": "Kaitlyn James", + "author_inst": "Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA" + }, + { + "author_name": "Rosiane Lima", + "author_inst": "Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Lael M Yonker", + "author_inst": "Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Alessio Fasano", + "author_inst": "Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Sara Brigida", + "author_inst": "Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Vincent Center for Reproductive Biology, Massa" + }, + { + "author_name": "Lisa M Bebell", + "author_inst": "Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA" + }, + { + "author_name": "Drucilla J Roberts", + "author_inst": "Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA" + }, + { + "author_name": "David Pepin", + "author_inst": "Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA" + }, + { + "author_name": "Jun R Huh", + "author_inst": "Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and B" + }, + { + "author_name": "Staci D Bilbo", + "author_inst": "Department of Pediatrics, Lurie Center for Autism, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.; Duke University, Department of Psyc" + }, + { + "author_name": "Jonathan Z Li", + "author_inst": "Department of Medicine, Brigham and Womens Hospital, Boston, MA, USA" + }, + { + "author_name": "Anjali Kaimal", + "author_inst": "Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA" + }, + { + "author_name": "Kathryn J Gray", + "author_inst": "Department of Obstetrics and Gynecology, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA" + }, + { + "author_name": "Douglas Lauffenburger", + "author_inst": "Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA" + }, + { + "author_name": "Galit Alter", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA" + }, + { + "author_name": "Andrea G Edlow", + "author_inst": "Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Vincent Center for Reproductive Biology, Massa" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.03.28.437363", "rel_title": "SARS-CoV-2 variant B.1.1.7 caused HLA-A2+ CD8+ T cell epitope mutations for impaired cellular immune response", @@ -847326,69 +849009,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, - { - "rel_doi": "10.1101/2021.03.25.21253908", - "rel_title": "A unique SARS-CoV-2 spike protein P681H strain detected in Israel", - "rel_date": "2021-03-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.25.21253908", - "rel_abs": "Routine detection, surveillance and reporting of SARS-CoV-2 novel variants is important, as these threaten to hinder vaccination efforts. Herein we report a local novel strain that includes a non-synonymous mutation in the spike (S) protein - P681H and additional synonymous mutations. The P681H Israeli strain has not been associated with higher infection rates and was neutralized by sera from vaccinated individuals in comparable levels to the B.1.1.7 strain and a non-P681H strain from Israel.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Neta S Zuckerman", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "Shay Fleishon", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "Efrat Bucris", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "Dana Bar-Ilan", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "Michal Linial", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Itay Bar-Or", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "Victoria Indenbaum", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "Merav Weil", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "- Israel National Consortium for SARS-CoV-2 sequencing", - "author_inst": "" - }, - { - "author_name": "Ella Mendelson", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "Michal Mandelboim", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "Orna Mor", - "author_inst": "Israel Ministry of Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.25.21254335", "rel_title": "Infliximab is associated with attenuated immunogenicity to BNT162b2 and ChAdOx1 nCoV-19 SARS-CoV-2 vaccines", @@ -847669,6 +849289,69 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.03.27.437309", + "rel_title": "The nucleotide addition cycle of the SARS-CoV-2 polymerase", + "rel_date": "2021-03-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.27.437309", + "rel_abs": "Coronaviruses have evolved elaborate multisubunit machines to replicate and transcribe their genomes. Central to these machines are the RNA-dependent RNA polymerase subunit (nsp12) and its intimately associated cofactors (nsp7 and nsp8). We have used a high-throughput magnetic-tweezers approach to develop a mechanochemical description of this core polymerase. The core polymerase exists in at least three catalytically distinct conformations, one being kinetically consistent with incorporation of incorrect nucleotides. We provide the first evidence that an RdRp uses a thermal ratchet instead of a power stroke to transition from the pre- to post-translocated state. Ultra-stable magnetic tweezers enables the direct observation of coronavirus polymerase deep and long-lived backtrack that are strongly stimulated by secondary structure in the template. The framework presented here elucidates one of the most important structure-dynamics-function relationships in human health today, and will form the grounds for understanding the regulation of this complex.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Subhas Chandra Bera", + "author_inst": "FAU Erlangen-Nuremberg" + }, + { + "author_name": "Mona Seifert", + "author_inst": "FAU Erlangen-Nuremberg" + }, + { + "author_name": "Robert Kirchdoerfer", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Pauline van Nies", + "author_inst": "FAU Erlangen-Nuremberg" + }, + { + "author_name": "Yibulayin Wubulikasimu", + "author_inst": "FAU Erlangen-Nuremberg" + }, + { + "author_name": "Salina Quack", + "author_inst": "FAU Erlangen-Nuremberg" + }, + { + "author_name": "Flavia S. Papini", + "author_inst": "FAU Erlangen-Nuremberg" + }, + { + "author_name": "Jamie J. Arnold", + "author_inst": "University of North Carolina School of Medicine, Chapel Hill" + }, + { + "author_name": "Bruno Canard", + "author_inst": "CNRS" + }, + { + "author_name": "Craig E. Cameron", + "author_inst": "University of North Carolina School of Medicine, Chapel Hill" + }, + { + "author_name": "Martin Depken", + "author_inst": "TU Delft" + }, + { + "author_name": "David Dulin", + "author_inst": "VU Amsterdam and FAU Erlangen-Nuremberg" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.03.27.437323", "rel_title": "High Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Non-Covalent Inhibitor", @@ -849532,77 +851215,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.22.21254082", - "rel_title": "Epidemiology and transmission of COVID-19 in cases and close contacts in Georgia in the first four months of the epidemic", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.22.21254082", - "rel_abs": "BackgroundBetween February and June 2020, 917 COVID-19 cases and 14 COVID-19-related deaths were reported in Georgia. Early on, Georgia implemented non-pharmaceutical interventions (NPI) including extensive contact tracing and restrictions on movement.\n\nAimTo characterize the demographics of those tested and infected with COVID-19 in Georgia; to evaluate factors associated with transmission between cases and their contacts; and to determine how transmission varied due to NPI up to 24 June 2020.\n\nMethodsWe use data gathered by the Georgian National Center for Disease Control on all polymerase chain reaction tests conducted (among symptomatic patients, through routine testing and contact tracing); hospitalization data for confirmed cases, and contact tracing data. We calculated the number of contacts per index case, the secondary attack rate (% contacts infected), and effective R number (new cases per index case), and used logistic regression to estimate how age, gender, and contact type affected transmission.\n\nResultsMost contacts and transmission events were between family members. Contacts <40 years were less likely to be infected, while infected individuals >50 were more likely to die than younger patients. Contact tracing identified 917 index cases with mean 3.1 contacts tested per case, primarily family members. The overall secondary attack rate was 28% (95% confidence interval [CI]: 26-29%) and effective R number was 0.87 (95%CI 0.81-0.93), peaking at 1.1 (95%CI 0.98-1.2) during the period with strongest restrictions.\n\nConclusionGeorgia effectively controlled the COVID-19 epidemic in its early stages, although evidence does not suggest transmission was reduced during the strict lockdown period.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed and MedRxiv for papers reporting research using contact tracing data to evaluate the characteristics of the COVID-19 epidemic in any country. A number of analyses were identified from Asia, including China, Taiwan, Maldives, Thailand, South Korea, and India, but none from other regions other than one previous analysis conducted in Europe, focusing on the first two months of the COVID-19 epidemic in Cyprus. Studies evaluated number of contacts and different contact types, secondary attack rate, and effective R number. However, none of these studies compared characteristics between different time periods or under varied levels of non-pharmaceutical interventions or restrictions on social mixing.\n\nAdded value of this studyIn this study, we use contact tracing data from Georgia from all cases identified in the first four months of the epidemic, as well as testing and hospitalization data, to evaluate the number and type of contacts, effective R number (new cases per index case), and secondary attack rate (proportion of contacts infected) in this population, and whether these measures changed before, during, and after the lockdown period. We also evaluated how the chance of transmission varied by type of index case and contact. Our results indicate that number of contacts remained relatively low throughout the study period, so although the secondary attack rate was relatively high (28%) compared to that seen in studies in Asia (10-15%), the effective R number was less than one overall, peaking at 1.1 (0.98-1.2) during the strictest lockdown period, with easing of restrictions corresponding to a lower effective R of 0.87 (0.77-0.97). Most transmission occurred between family members with transmission very low between co-workers, friends, neighbours, and medical personnel, indicating that the restrictions on social mixing were effective at keeping the epidemic under control during this period.\n\nImplications of all the available evidenceOur study presents the first analysis of the successful control of a COVID-19 epidemic in a European country, indicating that despite a high secondary attack rate, reduction in contacts outside the home, and a well-timed lockdown, were able to keep transmission under control.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Josephine G Walker", - "author_inst": "University of Bristol" - }, - { - "author_name": "Irine Tskhomelidze", - "author_inst": "The Task Force for Global Health" - }, - { - "author_name": "Adam Trickey", - "author_inst": "University of Bristol" - }, - { - "author_name": "Vladimer Getia", - "author_inst": "National Center for Disease Control and Public Health" - }, - { - "author_name": "Lia Gvinjilia", - "author_inst": "The Task Force for Global Health" - }, - { - "author_name": "Paata Imnadze", - "author_inst": "National Center for Disease Control and Public Health" - }, - { - "author_name": "Tinatin Kuchuloria", - "author_inst": "The Task Force for Global Health" - }, - { - "author_name": "Aaron G Lim", - "author_inst": "University of Bristol" - }, - { - "author_name": "Jack Stone", - "author_inst": "University of Bristol" - }, - { - "author_name": "Sophia Surguladze", - "author_inst": "National Center for Disease Control and Public Health" - }, - { - "author_name": "Maia Tsereteli", - "author_inst": "National Center for Disease Control and Public Health" - }, - { - "author_name": "Khatuna Zakhashvili", - "author_inst": "National Center for Disease Control and Public Health" - }, - { - "author_name": "Peter Vickerman", - "author_inst": "University of Bristol" - }, - { - "author_name": "Amiran Gamkrelidze", - "author_inst": "National Center for Disease Control and Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.22.21254139", "rel_title": "Acute Brain Ischemia, Infarction and Hemorrhage in Subjects Dying with or Without Autopsy-Proven Acute Pneumonia", @@ -849791,6 +851403,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.23.21254150", + "rel_title": "Point-of-care lung ultrasonography for early identification of mild COVID-19: a prospective cohort of outpatients in a Swiss screening center", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21254150", + "rel_abs": "BackgroundEarly identification of SARS-CoV-2 infection is important to guide quarantine and reduce transmission. This study evaluates the diagnostic performance of lung ultrasound (LUS), an affordable, consumable-free point-of-care tool, for COVID-19 screening.\n\nMethodsThis prospective observational cohort included adults presenting with cough and/or dyspnea at a SARS-CoV-2 screening center of Lausanne University Hospital between March 31st and May 8th, 2020. Investigators recorded standardized LUS images and videos in 10 lung zones per subject. Two blinded independent experts reviewed LUS recording and classified abnormal findings according to pre-specified criteria to investigate their predictive value to diagnose SARS-CoV-2 infection according to PCR on nasopharyngeal swabs (COVIDpos vs COVIDneg). We finally combined LUS and clinical findings to derive a multivariate logistic regression diagnostic score.\n\nResultsOf 134 included patients, 23% (n=30/134) were COVIDpos and 77% (n=103/134) were COVIDneg; 85%, (n=114/134) cases were previously healthy healthcare workers presenting within 2 to 5 days of symptom onset (IQR). Abnormal LUS findings were significantly more frequent in COVIDpos compared to COVIDneg (45% versus 26%, p=0.045) and mostly consisted of focal pathologic B-lines. Combining LUS findings in a multivariate logistic regression score had an area under the receiver-operating curve of 63.9% to detect COVID-19, but improved to 84.5% with the addition of clinical features\n\nConclusionsCOVIDpos patients are significantly more likely to have lung pathology by LUS. Our findings have potential diagnostic value for COVID-19 at the point of care. Combination of clinical and LUS features showed promising results, which need confirmation in a larger study population.\n\nWhat is already known on the subjectO_LILung ultrasonography (LUS) is a consumable-free, easy-to-use, portable, non-radiating and non-invasive screening tool that can be performed at the bedside: its diagnostic performance for pneumonia has been established.\nC_LIO_LIRecent studies conducted in emergency department showed a correlation between LUS findings and COVID-19 diagnosis.\nC_LI\n\nWhat the study adsO_LIThis is the first study assessing the diagnostic performance of LUS for COVID-19 in outpatients with mild acute respiratory tract infection.\nC_LIO_LIMild COVID-19 patients are more likely to have lung pathology by LUS compared with COVID-19 negative.\nC_LIO_LICombination of clinical and LUS features showed promising results with a potential diagnostic value for COVID-19 at the point of care.\nC_LI", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Sim\u00e9on Schaad", + "author_inst": "Infectious Diseases Service, University Hospital of Lausanne, Switzerland" + }, + { + "author_name": "Thomas Brahier", + "author_inst": "Infectious Diseases Service, University Hospital of Lausanne, Switzerland" + }, + { + "author_name": "Mary-Anne Hartley", + "author_inst": "Digital global Health Department, Center for primary care and public health, University of Lausanne, Switzerland, Machine Learning and Optimization Laboratory, " + }, + { + "author_name": "Jean-Baptiste Cordonnier", + "author_inst": "Machine Learning and Optimization Laboratory, EPFL, Switzerland" + }, + { + "author_name": "Luca Bosso", + "author_inst": "Emergency Department, University Hospital of Lausanne, Switzerland" + }, + { + "author_name": "Tanguy Espejo", + "author_inst": "Emergency Department, University Hospital of Lausanne, Switzerland" + }, + { + "author_name": "Olivier Pantet", + "author_inst": "Intensive Care Unit, University Hospital of Lausanne, Switzerland" + }, + { + "author_name": "Olivier Hugli", + "author_inst": "Emergency Department, University Hospital of Lausanne, Switzerland" + }, + { + "author_name": "Pierre-Nicolas Carron", + "author_inst": "Emergency Department, University Hospital of Lausanne, Switzerland" + }, + { + "author_name": "Jean-Yves Meuwly", + "author_inst": "Department of Radiology, University Hospital of Lausanne, Switzerland" + }, + { + "author_name": "No\u00e9mie Boillat-Blanco", + "author_inst": "Infectious Diseases Service, University Hospital of Lausanne, Switzerland" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.22.21254120", "rel_title": "Multiplex Antibody Analysis of IgM, IgA and IgG to SARS-CoV-2 in Saliva and Serum from Infected Children and their Close Contacts", @@ -851374,41 +853045,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.03.23.21254209", - "rel_title": "Vascular Comorbidities Worsen Prognosis of Patients with Heart Failure Hospitalized with COVID-19", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21254209", - "rel_abs": "BackgroundPrior diagnosis of heart failure (HF) is associated with increased length of hospital stay (LOS) and mortality from Coronavirus disease-2019 (COVID-19). Associations between substance use, venous thromboembolism (VTE), or peripheral arterial disease (PAD) and its effects on LOS or mortality in patients with HF hospitalized with COVID-19 remains unknown.\n\nObjectiveThis study identified risk factors associated with poor in-hospital outcomes among patients with HF hospitalized with COVID-19.\n\nMethodsCase control study was conducted of patients with prior diagnosis of HF hospitalized with COVID-19 at an academic tertiary care center from January 1, 2020 to February 28, 2021. Patients with HF hospitalized with COVID-19 with risk factors were compared with those without risk factors for clinical characteristics, length of stay (LOS), and mortality. Multivariate regression was conducted to identify multiple predictors of increased LOS and in-hospital mortality in patients with HF hospitalized with COVID-19.\n\nResultsTotal of 211 HF patients were hospitalized with COVID-19. Females had longer LOS than males (9 days vs. 7 days; p < 0.001). Compared with patients without peripheral arterial disease (PAD) or ischemic stroke, patients with PAD or ischemic stroke had longer LOS (7 days vs. 9 days; p = 0.012 and 7 days vs. 11 days, p < 0.001; respectively). Older patients (aged 65 and above) had increased in-hospital mortality compared to younger patients (Adjusted OR: 1.04; 95% CI: 1.00 - 1.07; p = 0.036). VTE increased mortality more than three-fold in patients with HF hospitalized with COVID-19 (Adjusted OR: 3.33; 95% CI: 1.29 - 8.43; p = 0.011).\n\nConclusionVascular diseases increase LOS and mortality in patients with HF hospitalized with COVID-19.\n\nKEY QUESTIONSO_ST_ABSWhat is already known about this subject?C_ST_ABS- Prior diagnosis of heart failure (HF) increases LOS and mortality in patients admitted to the hospital for COVID-19\n- Antiplatelet, anticoagulation, and statin therapy decreased venous thromboembolism (VTE) in patients admitted for COVID-19\n\n\nWhat does this study add?- This study showed that patients with COVID-19, HF, and VTE had a higher mortality rate than patients with COVID-19 and either HF or VTE, or patients with HF and/or VTE who did not have COVID-19.\n- This study showed that patients with HF hospitalized with COVID-19 had greater length of stay with prior diagnosis of peripheral arterial disease (PAD) or ischemic stroke\n\n\nHow might this impact on clinical practice?- Our findings demonstrate clinical relevance by showing supportive evidence for antiplatelet, anticoagulation, and statin therapy in HF patients hospitalized with COVID-19", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jacob Mok", - "author_inst": "The University of Tennessee Health Science Center College of Medicine Chattanooga" - }, - { - "author_name": "Juan Carlos Malpartida", - "author_inst": "The University of Tennessee Health Science Center College of Medicine Chattanooga" - }, - { - "author_name": "Joshua Davis", - "author_inst": "The University of Tennessee Health Science Center College of Medicine Chattanooga" - }, - { - "author_name": "Cuilan Gao", - "author_inst": "The University of Tennessee at Chattanooga" - }, - { - "author_name": "Harish Manyam", - "author_inst": "Erlanger Health System, Heart and Lung Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2021.03.23.21254214", "rel_title": "Mouth-rinses and SARS-CoV-2 viral load in saliva: A living systematic review", @@ -851597,6 +853233,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.25.21254231", + "rel_title": "Monitoring occurrence of SARS-CoV-2 in school populations: a wastewater-based approach", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.25.21254231", + "rel_abs": "Clinical testing of children in schools is challenging, with economic implications limiting its frequent use as a monitoring tool of the risks assumed by children and staff during the COVID-19 pandemic. Here, a wastewater based epidemiology approach has been used to monitor 16 schools (10 primary, 5 secondary and 1 post-16 and further education for a total of 17 sites) in England. A total of 296 samples over 9 weeks have been analysed for N1 and E genes using qPCR methods. Of the samples returned, 47.3% were positive for one or both genes with a frequency of detection in line with the respective community. WBE offers a promising low cost, non-invasive approach for supplementing clinical testing and can offer longitudinal insights that are impractical with traditional clinical testing.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Victor Castro Gutierrez", + "author_inst": "Cranfield University, Bedfordshire, UK" + }, + { + "author_name": "Francis Hassard", + "author_inst": "Cranfield University, Bedfordshire, UK" + }, + { + "author_name": "Milan Vu", + "author_inst": "Department of Natural Science, School of Science and Technology, Middlesex University, London, UK" + }, + { + "author_name": "Rodrigo Leitao", + "author_inst": "Cranfield University, Bedfordshire, UK" + }, + { + "author_name": "Beata Burczynska", + "author_inst": "Department of Natural Science, School of Science and Technology, Middlesex University, London, UK" + }, + { + "author_name": "Dirk Wildeboer", + "author_inst": "Department of Natural Science, School of Science and Technology, Middlesex University, London, UK" + }, + { + "author_name": "Isobel Stanton", + "author_inst": "UK Centre for Ecology and Hydrology, Wallingford, UK" + }, + { + "author_name": "Shadi Rahimzadeh", + "author_inst": "Department of Natural Science, School of Science and Technology, Middlesex University, London, UK" + }, + { + "author_name": "Gianluca Baio", + "author_inst": "Department of Statistical Science, University College London, London, UK" + }, + { + "author_name": "Hemda Garelick", + "author_inst": "Department of Natural Science, School of Science and Technology, Middlesex University, London, UK" + }, + { + "author_name": "Jan Hofman", + "author_inst": "Water Innovation & Research Centre, Department of Chemical Engineering, University of Bath, UK" + }, + { + "author_name": "Barbara Kasprzyk-Hordern", + "author_inst": "Department of Chemistry, University of Bath, UK" + }, + { + "author_name": "Rachel Kwiatkowska", + "author_inst": "School of Population Health Sciences, University of Bristol- Field Services, National Infection Service, Public Health England" + }, + { + "author_name": "Azeem Majeed", + "author_inst": "Department of Primary Care & Social Medicine, Imperial College Faculty of Medicine, London, UK" + }, + { + "author_name": "Sally Priest", + "author_inst": "Department of Natural Science, School of Science and Technology, Middlesex University, London, UK" + }, + { + "author_name": "Jasmine Grimsley", + "author_inst": "Joint Biosecurity Centre, Department for Health and Social Care, London, UK" + }, + { + "author_name": "Lian Lundy", + "author_inst": "Department of Natural Science, School of Science and Technology, Middlesex University, London, UK" + }, + { + "author_name": "Andrew C Singer", + "author_inst": "UK Centre for Ecology and Hydrology, Wallingford, UK" + }, + { + "author_name": "Mariachiara Di Cesare", + "author_inst": "Middlesex University Faculty of Science and Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.25.21254360", "rel_title": "Disparities in Excess Deaths from the COVID-19 Pandemic Among Migrant Workers in Kuwait", @@ -852812,61 +854539,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.24.21252635", - "rel_title": "Tenofovir-DF versus Hydroxychloroquine in the Treatment of Hospitalized Patients with COVID-19: An Observational Study (THEDICOV)", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.24.21252635", - "rel_abs": "BackgroundAlthough several therapeutic agents have been suggested for the treatment of the disease caused by the Coronavirus of the year 2019 (COVID-19), no antiviral has yet demonstrated consistent efficacy.\n\nMethodsThe results of an observational study comparing Tenofovir-DF (TDF) with Hydroxychloroquine (HCQ) in the treatment of hospitalized patients with COVID-19 with evidence of pulmonary compromise and the vast majority with supplemental oxygen requirement are presented. Patients received HCQ consecutively at the dose of 400 mg. 12 hourly for 01 day and then 200 mg. every 8 to 12 hours PO for 5 to10 days; or TDF 300 mg. per day PO for 7 to 10 days. The primary outcomes of the study were the differences between the two groups regarding: hospital stay, the need for intensive care or mechanical ventilation (ICU / MV) and mortality.\n\nResults104 patients were included: 36 in the HCQ group and 68 in the TDF group. The unadjusted primary outcomes were: LOS (length of stay) 16.6 {+/-} 12.1 for HCQ versus 12.2 {+/-} 7.0 days for TDF (p = o.o102); need for admission to ICU / mechanical ventilation (MV): 61.1% for HCQ versus 11.8% for TDF (p = o.ooo); and mortality: 50.0% for HCQ and 8.8% for TDF (p = o.ooo). The patients in the HCQ group had significant differences at admission compared to those in the TDF group regarding: male sex, cardiovascular risk factor, greater respiratory involvement and higher glucose and creatinine levels, lower albumin levels and higher. Inflammatory markers. When the outcomes were adjusted for these baseline differences, in the multiple regression model for LOS, it was found that TDF decreased the hospital stay by 6.10 days (C.I.: -11.97 to -2.40, p = o.o42); In the logistic regression model for the need for ICU / MV, it was found that the use of TDF had an O.R. of 0.15 (C.I.: 0.03-0.76, p = o.o22); and for the Cox proportional hazards model for mortality, the H.R. was 0.16 for TDF (C.I.: 0.03-0.96, p = o.o41). In the estimation model of the treatment effects by regression adjustment, it was found that TDF decreased the stay by -6.38 days (C.I.: -12.34 to -0.42, p = o.o36); the need for ICU / MV at -41.74% (C.I.: -63.72 to -19.7, p = o.ooo); and mortality by -35.22% (C.I.: -56.47 to -13.96, p = o.oo1).\n\nConclusionTDF may be an effective antiviral in the treatment of COVID-19. Some of its advantages include: its wide availability, cost and oral presentation. Randomized clinical trials are imperatively required to confirm this possibility.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Mario Cornejo-Giraldo", - "author_inst": "Hospital Nacional CASE - EsSalud. Universidad Catolica Santa Maria" - }, - { - "author_name": "Nelson Rosado", - "author_inst": "Hospital Nacional CASE - EsSalud. Universidad Catolica Santa Maria." - }, - { - "author_name": "Jesus Salinas", - "author_inst": "Hospital Nacional CASE - EsSalud. Universidad Catolica Santa Maria" - }, - { - "author_name": "Nelson Aspilcueta", - "author_inst": "Hospital Nacional CASE - EsSalud" - }, - { - "author_name": "Eduardo Bernales", - "author_inst": "Hospital Nacional CASE - EsSalud" - }, - { - "author_name": "Jimmy Lipa", - "author_inst": "Hospital Nacional CASE - EsSalud" - }, - { - "author_name": "Johanna Coacalla", - "author_inst": "Hospital Nacional CASE - EsSalud" - }, - { - "author_name": "Yoisi Flores", - "author_inst": "Hospital Nacional CASE - EsSalud" - }, - { - "author_name": "Pamela Leon", - "author_inst": "Hospital Nacional CASE - EsSalud" - }, - { - "author_name": "Claudia Chamby", - "author_inst": "Hospital Nacional CASE - EsSalud" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.24.21253923", "rel_title": "Pattern of COVID-19 epidemics in Japan influenced by the control measures", @@ -853095,6 +854767,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.24.21254238", + "rel_title": "Dramatic drop of new SARS-CoV-2 infections among health care workers after the first dose of the BNT162b2 mRNA Covid-19 Vaccine", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.24.21254238", + "rel_abs": "ObjectivesTo evaluate the effect of mRNA SARS-Cov-2 vaccination on the incidence of new SARS-CoV-2 infections in health care workers (HCW).\n\nMethodsThe evolution of the incident rate of SARS-CoV-2 infection in a cohort of 2590 HCW after a mRNA SARS-CoV-2 vaccination was assessed, as compared to the rate in the community (n=170513). SARS-CoV-2 infections were microbiologically confirmed by an antigen, a CRP positive test, or both.\n\nResultsA total of 1820 HCW (70,3% of total) received the first dose of the vaccine between January 10-16, 2021), and 296 (11,4%) the following week. All of them completed vaccination 3 weeks later. New SARS-COV-2 infections in HCW declined by 62% at 2-4 weeks after the first dose of mRNA SARS-CoV-2 vaccination and virtually disappeared after the second dose of the vaccine. Vaccination rate was negligible for this time period in the community (<5%). The decline in the incident rate of SARS-COoV-2 new infection in HCW shortly after the administration of the first dose of the vaccine was strikingly higher than the reduction observed in the general population (p<0.001and became even more pronounced after the second dose of the vaccine (p<0.001).\n\nConclusionsmRNA SARS-CoV-2 vaccination is associated with a dramatic decline in new SARS-CoV-2 infection among HCW, even before the administration of the second dose of the vaccine.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Carlos Guijarro", + "author_inst": "Hospital Universitario Fundacion Alcorcon. Universidad Rey Juan Carlos" + }, + { + "author_name": "Isabel Maria Galan", + "author_inst": "Hospital Universitario Fundacion Alcorcon" + }, + { + "author_name": "Elia Perez-Fernandez", + "author_inst": "Hospital Universitario Fundacion Alcorcon" + }, + { + "author_name": "Diana Cecily Martinez-Ponce", + "author_inst": "Hospital Universitario Fundacion Alcorcon" + }, + { + "author_name": "Maria J Goyanes", + "author_inst": "Hospital Universitario Fundacion Alcorcon" + }, + { + "author_name": "Virgilio Castilla", + "author_inst": "Hospital Universitario Fundacion Alcorcon" + }, + { + "author_name": "Maria Velasco", + "author_inst": "Hospital Universitario Fundacion Alcorcon. Universidad Rey Juan Carlos" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.24.21252687", "rel_title": "Hospital mortality in COVID-19 patients in Belgium treated with statins, ACE inhibitors and/or ARBs", @@ -854566,41 +856281,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.03.24.21254270", - "rel_title": "Counties with lower insurance coverage are associated with both slower vaccine rollout and higher COVID-19 incidence across the United States", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.24.21254270", - "rel_abs": "Efficient and equitable vaccination distribution is a priority for effectively outcompeting the transmission of COVID-19 globally. A recent study from the Centers for Disease Control and Prevention (CDC) identified that US counties with high social vulnerability according to metrics such as poverty, unemployment, low income, and no high school diploma, have significantly lower rates of vaccination compared to the national average1. Here, we build upon this analysis to consider associations between county-level vaccination rates and 68 different demographic, socioeconomic, and environmental factors for 1,510 American counties with over 228 million individuals for which vaccination data was also available. Our analysis reveals that counties with high levels of uninsured individuals have significantly lower COVID-19 vaccination rates (Spearman correlation: -0.264), despite the fact that the CDC has mandated that all COVID-19 vaccines are free and cannot be denied to anyone based upon health insurance coverage or immigration status. Furthermore, we find that the counties with high levels of uninsured individuals tend to have the highest COVID-19 incidence rates in March 2021 relative to December 2020 (Spearman correlation: 0.388). Among the 68 factors analyzed, insurance coverage is the only factor which is highly correlated with both vaccination rate and change in COVID-19 incidence during the vaccination period (|Spearman correlation|> 0.25). We also find that counties with higher percentages of Black and Hispanic individuals have significantly lower vaccination rates (Spearman correlations: -0.128, -0.136) and lesser declines of COVID-incidence rates (Spearman correlations: 0.334, 0.330) during the vaccination period. Surprisingly however, after controlling for race, we find that the association between lack of insurance coverage and vaccination rate as well as COVID-19 incidence rates is largely driven by counties with a majority white population. Among the counties with high proportions of white residents (top 10% decile), the association between insurance coverage and vaccination rate is significant (Spearman correlation: -0.210, p-value: 0.002), but among counties with low proportions of white residents (bottom 10% decile) this association is not significant (Spearman correlation: 0.072, p-value: 0.088). Taken together, this study highlights the fact that intricate socioeconomic factors are correlated not just to COVID-19 vaccination rates, but also to COVID-19 incidence fluctuations, underscoring the need to improve COVID-19 vaccination campaigns in marginalized communities. The strong positive correlation between low levels of health insurance coverage and low vaccination rates is particularly concerning, and calls for improved public health messaging to emphasize the fact that health insurance is not required to be eligible for any of the FDA-authorized COVID-19 vaccines in the United States", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Emily Lindemer", - "author_inst": "nference" - }, - { - "author_name": "Mayank Choudhary", - "author_inst": "nference" - }, - { - "author_name": "Gregory Donadio", - "author_inst": "nference" - }, - { - "author_name": "Colin Pawlowski", - "author_inst": "nference" - }, - { - "author_name": "Venky Soundararajan", - "author_inst": "nference" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.26.437014", "rel_title": "Aberrant glycosylation of anti-SARS-CoV-2 IgG is a pro-thrombotic stimulus for platelets", @@ -854821,6 +856501,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.26.437153", + "rel_title": "Comparison of SARS-CoV-2 VOC 202012/01 (UK variant) and D614G variant transmission by different routes in Syrian hamsters", + "rel_date": "2021-03-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.26.437153", + "rel_abs": "Many SARS-CoV-2 variants of concern has been reported recently which were linked to increased transmission. In our earlier study on virus shedding using VOC 202012/01(UK variant) and D614G variant in hamster model, we observed significantly higher viral RNA shedding through nasal wash in case of UK variant. Hence, we compared the transmission of both the UK and D614G variant by various routes in Syrian hamsters to understand whether the high viral RNA shedding could enhance the transmission efficiency of the variant. The current study demonstrated comparable transmission efficiency of both UK and D614G variants of SARS-CoV-2 in Syrian hamsters.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sreelekshmy Mohandas", + "author_inst": "ICMR-National Institute of Virology" + }, + { + "author_name": "Pragya Yadav", + "author_inst": "ICMR-National Institute of Virology" + }, + { + "author_name": "Dimpal Nyayanit", + "author_inst": "ICMR-National Institute of Virology" + }, + { + "author_name": "Anita Shete-Aich", + "author_inst": "ICMR-National Institute of Virology" + }, + { + "author_name": "Prasad Sarkale", + "author_inst": "ICMR-National Institute of Virology" + }, + { + "author_name": "Supriya Hundekar", + "author_inst": "ICMR-National Institute of Virology" + }, + { + "author_name": "Sanjay Kumar", + "author_inst": "Department of Neurosurgery, Command Hospital (Southern Command), Armed Forces Medical College, Pune" + }, + { + "author_name": "Kavita Lole", + "author_inst": "ICMR-National Institute of Virology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.03.24.21254199", "rel_title": "Cryptic transmission of SARS-CoV-2 and the first COVID-19 wave in Europe and the United States", @@ -856567,57 +858294,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.19.21253429", - "rel_title": "SARS-CoV-2 Seroprevalence in 12 Cities of India from July-December 2020", - "rel_date": "2021-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253429", - "rel_abs": "ObjectivesWe sought to understand the spread of SARS-CoV-2 infection in urban India, which has surprisingly low COVID-19 deaths.\n\nDesignCross-sectional and trend analyses of seroprevalence in self-referred test populations, and of reported cases and COVID mortality data.\n\nParticipants448,518 self-referred individuals using a nationwide chain of private laboratories with central testing of SARS-CoV-2 antibodies and publicly available case and mortality data.\n\nSetting12 populous cities with nearly 92 million total population.\n\nMain outcome measuresSeropositivity trends and predictors (using a Bayesian geospatial model) and prevalence derived from mortality data and infection fatality rates (IFR).\n\nResultsFor the whole of India, 31% of the self-referred individuals undergoing antibody testing were seropositive for SARS-CoV-2 antibodies. Seropositivity was higher in females (35%) than in males (30%) overall and in nearly every age group. In these 12 cities, seroprevalence rose from about 18% in July to 41% by December, with steeper increases at ages <20 and 20-44 years than at older ages. The \"M-shaped\" age pattern is consistent with intergenerational transmission. Areas of higher childhood measles vaccination in earlier years had lower seropositivity. The patterns of increase in seropositivity and in peak cases and deaths varied substantially across cities. In Delhi, death rates and cases first peaked in June and again in November; Chennai had a single peak in July. Based local IFRs and COVID deaths (adjusted for undercounts), we estimate that 43%-65% of adults above age 20 had been infected (range of mid-estimates of 12%-77%) corresponding 26 to 36 million infected adults in these cities, or an average of 9-12 infected adults per confirmed case.\n\nConclusionEven with relatively low death rates, the large cities of India had remarkably high levels of SARS-CoV-2 infection. Vaccination strategies need to consider widespread intergenerational transmission.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Arokiaswamy Velumani", - "author_inst": "Thyrocare Laboratories" - }, - { - "author_name": "Chaitili Nikam", - "author_inst": "Thyrocare Laboratories" - }, - { - "author_name": "Wilson Suraweera", - "author_inst": "Centre for Global Health Research, University of Toronto" - }, - { - "author_name": "Sze Hang Fu", - "author_inst": "Centre for Global Health Research, University of Toronto" - }, - { - "author_name": "Hellen Gelband", - "author_inst": "Centre for Global Health Research, University of Toronto" - }, - { - "author_name": "Patrick E Brown", - "author_inst": "University of Toronto" - }, - { - "author_name": "Isaac Bogoch", - "author_inst": "University of Toronto" - }, - { - "author_name": "Nico Nagelkerke", - "author_inst": "Centre for Global Health Research, University of Toronto" - }, - { - "author_name": "Prabhat Jha", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.15.21253567", "rel_title": "Evaluation of pooling of samples for testing SARS-COV- 2 for mass screening of COVID-19", @@ -856794,6 +858470,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.17.21253821", + "rel_title": "Increased prevalence of AB group and FY*A red blood cell antigen in Caucasian SARS-CoV-2 convalescent plasma donors", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21253821", + "rel_abs": "IntroductionThe SARS-CoV-2 pandemic has put significant additional pressure on healthcare systems throughout the world. The identification of at-risk population beyond age, pre-existing medical conditions and socioeconomic status has been the subject of only a small part of the global COVID-19 research so far. To this day, more data is required regarding the association between HLA allele and red blood cell (RBC) antigens expression in regard to SARS-CoV-2 infection susceptibility and virus clearance capability, and COVID-19 susceptibility, severity, and duration.\n\nMethodsThe phenotypes for ABO and RhD, and the genotypes for 37 RBC antigens and HLA-A, B, C, DRB1, DQB1 and DPB1 were determined using high throughput platforms (Luminex and Next-generation Sequencing) in 90 Caucasian convalescent plasma donors. The results were compared to expected reference frequencies, local and international databases, and literature.\n\nResultsThe AB group was significantly increased (1.5x, p=0.018) and a non-significant (2.2x, p=0.030) increase was observed for the FY*A allele frequency in the convalescent cohort (N=90) compared to reference frequencies. Some HLA alleles were found significantly overrepresented (HLA-B*44:02, C*05:01, DPB1*04:01, DRB1*04:01 and DRB1*07:01) or underrepresented (A*01:01, B51:01 and DPB1*04:02) in convalescent individuals compared to the local bone marrow registry population.\n\nConclusionOur study of infection-susceptible but non-hospitalized Caucasian COVID-19 patients contributes to the global understanding of host genetic factors associated with SARS-CoV-2 infection susceptibility and severity of the associated disease.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "William Lemieux", + "author_inst": "Hema-Quebec" + }, + { + "author_name": "Josee Perreault", + "author_inst": "Hema-Quebec" + }, + { + "author_name": "Gabriel Andre Leiva", + "author_inst": "Hema-Quebec" + }, + { + "author_name": "Nadia Baillargeon", + "author_inst": "Hema-Quebec" + }, + { + "author_name": "Jessica Constanzo Yanez", + "author_inst": "Hema-Quebec" + }, + { + "author_name": "Marie-Claire Chevrier", + "author_inst": "Hema-Quebec" + }, + { + "author_name": "Lucie Richard", + "author_inst": "Hema-Quebec" + }, + { + "author_name": "Antoine Lewin", + "author_inst": "Hema-Quebec" + }, + { + "author_name": "Patrick Trepanier", + "author_inst": "Hema-Quebec" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.17.21253751", "rel_title": "Longitudinal determination of mRNA-vaccination induced strongly binding SARS-CoV-2 IgG antibodies in a cohort of healthcare workers with and without prior exposure to the novel coronavirus", @@ -858197,57 +859924,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.24.436850", - "rel_title": "Factors Associated with Emerging and Re-emerging of SARS-CoV-2 Variants", - "rel_date": "2021-03-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.24.436850", - "rel_abs": "Global spread of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has triggered unprecedented scientific efforts, as well as containment and treatment measures. Despite these efforts, SARS-CoV-2 infections remain unmanageable in some parts of the world. Due to inherent mutability of RNA viruses, it is not surprising that the SARS-CoV-2 genome has been continuously evolving since its emergence. Recently, four functionally distinct variants, B.1.1.7, B.1.351, P.1 and CAL.20C, have been identified, and they appear to more infectious and transmissible than the original (Wuhan-Hu-1) virus. Here we provide evidence based upon a combination of bioinformatics and structural approaches that can explain the higher infectivity of the new variants. Our results show that the greater infectivity of SARS-CoV-2 than SARS-CoV can be attributed to a combination of several factors, including alternate receptors. Additionally, we show that new SARS-CoV-2 variants emerged in the background of D614G in Spike protein and P323L in RNA polymerase. The correlation analyses showed that all mutations in specific variants did not evolve simultaneously. Instead, some mutations evolved most likely to compensate for the viral fitness.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Austin N Spratt", - "author_inst": "Christopher S. Bond Life Sciences Center, University of Missouri," - }, - { - "author_name": "Saathvik K Kannan", - "author_inst": "Christopher S. Bond Life Sciences Center, University of Missouri" - }, - { - "author_name": "Lucas T Woods", - "author_inst": "Department of Biochemistry, University of Missouri, Columbia" - }, - { - "author_name": "Gary A Weisman", - "author_inst": "Department of Biochemistry, University of Missouri, Columbia" - }, - { - "author_name": "Thomas D Quinn", - "author_inst": "Department of Biochemistry, University of Missouri, Columbia" - }, - { - "author_name": "Christian L Lorson", - "author_inst": "Department of Veterinary Pathobiology, University of Missouri, Columbia" - }, - { - "author_name": "Anders Sonnerborg", - "author_inst": "Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Huddinge 14186, Stockholm, Sweden" - }, - { - "author_name": "Siddappa N Byrareddy", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Kamal Singh", - "author_inst": "University of Missouri" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.03.24.436822", "rel_title": "Arginine Methylation Regulates SARS-CoV-2 Nucleocapsid Protein Function and Viral Replication", @@ -858452,6 +860128,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.23.21254175", + "rel_title": "The SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: analysis of high-throughput genetic, epigenetic, and gene expression studies", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21254175", + "rel_abs": "Patients affected by Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) show specific epigenetic and gene expression signatures of the disease. However, it is unknown whether these signatures include abnormal levels of the human angiotensin-converting enzymes, ACE and ACE2, the latter being the main receptor described for the host-cell invasion by SARS-CoV-2. To investigate that, we first re-analyzed available case-control epigenome-wide association studies based on DNA methylation data, and case-control gene expression studies based on microarray data. From these published studies, we found an association between ME/CFS and 4 potentially hypomethylated probes located in the ACE locus. We also found another disease association with one hypomethylated probe located in the transcription start site of ACE2. The same disease associations were obtained for women but not for men after performing sex-specific analyses. In contrast, a meta-analysis of gene expression levels could not provide evidence for a differentially expression of ACE and ACE2 in affected patients when compared to healthy controls. In line with this negative finding, the analysis of a new data set on the gene expression of ACE and ACE2 in peripheral blood mononuclear cells did not find any differences between a female cohort of 37 patients and 34 age-matched healthy controls. Future studies should be conducted to extend this investigation to other potential receptors used by SARS-CoV-2. These studies will help researchers and clinicians to improve the understanding of the health risk imposed by this virus when infecting patients affected by this debilitating disease.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Jo\u00e3o Malato", + "author_inst": "Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal" + }, + { + "author_name": "Franziska Sotzny", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt Universit\u00e4t zu Berlin and Berlin Institute of Health, Institute of Me" + }, + { + "author_name": "Sandra Bauer", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt Universit\u00e4t zu Berlin and Berlin Institute of Health, Institute of Me" + }, + { + "author_name": "Helma Freitag", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt Universit\u00e4t zu Berlin and Berlin Institute of Health, Institute of Me" + }, + { + "author_name": "Andr\u00e9 Fonseca", + "author_inst": "Faculdade de Ci\u00eancias e Tecnologia, Universidade do Algarve, Faro, Portugal" + }, + { + "author_name": "Anna D Grabowska", + "author_inst": "Department of Biophysics and Human Physiology, Medical University of Warsaw, Warsaw, Poland" + }, + { + "author_name": "Lu\u00eds Gra\u00e7a", + "author_inst": "Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal" + }, + { + "author_name": "Clara Cordeiro", + "author_inst": "Faculdade de Ci\u00eancias e Tecnologia, Universidade do Algarve, Faro, Portugal" + }, + { + "author_name": "Lu\u00eds Nacul", + "author_inst": "London School of Hygiene and Tropical Medicine, London, United Kingdom" + }, + { + "author_name": "Eliana M Lacerda", + "author_inst": "London School of Hygiene and Tropical Medicine, London, United Kingdom" + }, + { + "author_name": "Jesus Castro Marrero", + "author_inst": "Vall de Hebron Hospital Research Institute, Division of Rheumatology, ME/CFS Unit, Universitat Aut\u00f2noma de Barcelona, Barcelona, Spain" + }, + { + "author_name": "Carmen Scheibenbogen", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt Universit\u00e4t zu Berlin and Berlin Institute of Health, Institute of Me" + }, + { + "author_name": "Francisco Westermeier", + "author_inst": "Institute of Biomedical Science, FH Joanneum University of Applied Sciences, Graz, Austria" + }, + { + "author_name": "Nuno Sepulveda", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt Universit\u00e4t zu Berlin and Berlin Institute of Health, Institute of Me" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2021.03.23.21253503", "rel_title": "The role of classroom volume, natural ventilation and voice reduction in transmission risk of SARS-CoV2 in schools", @@ -859713,81 +861460,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.17.21253283", - "rel_title": "COVID-19 in Children with Brain-Based Developmental Disabilities: A Rapid Review Update", - "rel_date": "2021-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21253283", - "rel_abs": "ObjectiveInformation regarding the impact of COVID-19 in children with brain-based disabilities, or those at risk of developing such conditions, remains scarce. The objective was to evaluate if children with brain-based disabilities are more likely to (1) develop COVID-19, (2) develop complications from the disease, and (3) to have a poorer prognosis.\n\nStudy designWe conducted a rapid review using search strategies iteratively developed and tested by an experienced medical information specialist in consultation with the review team and a panel of knowledge users. Searches were initially performed on April 18th, 2021, and updated on October 31st, 2020. Four reviewers individually performed study selection using pilot-tested standardized forms. Single reviewers extracted the data using a standardized extraction form that included study characteristics, patients characteristics, and outcomes reported.\n\nResultsWe identified 1448 publications, of which 29 were included. Studies reported data on 2288 COVID-19 positive children, including 462 with a brain-based disability, and 72 at risk of developing such disability. Overall, the included studies showed a greater risk to develop severe COVID-19 disease in children with brain-based disabilities. Although mortality is very low, the case-fatality rate appeared to be higher in children with disabilities compared to children without disabilities.\n\nConclusionsOur review shows that children with brain-based disabilities are overrepresented in hospitalization numbers compared to children without disabilities. However, most studies included children that were hospitalized from COVID-19 in secondary and tertiary care centers. Results of this review should therefore be interpreted with caution.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Mich\u00e8le Dugas", - "author_inst": "VITAM Research Center, CIUSSS de la Capitale-Nationale" - }, - { - "author_name": "Th\u00e9o St\u00e9fan", - "author_inst": "VITAM Research Center, CIUSSS de la Capitale-Nationale" - }, - { - "author_name": "Johanie L\u00e9pine", - "author_inst": "VITAM Research Center, CIUSSS de la Capitale-Nationale" - }, - { - "author_name": "Patrick Blouin", - "author_inst": "VITAM Research Center, CIUSSS de la Capitale-Nationale" - }, - { - "author_name": "Andr\u00e9e-Anne Poirier", - "author_inst": "VITAM Research Center and INESSS" - }, - { - "author_name": "Val\u00e9rie Carnovale", - "author_inst": "VITAM Research Center, CIUSSS de la Capitale-Nationale" - }, - { - "author_name": "Benoit Mailhot", - "author_inst": "VITAM Research Center, CIUSSS de la Capitale-Nationale - Universit\u00e9 Laval" - }, - { - "author_name": "Becky Skidmore", - "author_inst": "Independent Information Specialist" - }, - { - "author_name": "Lena Faust", - "author_inst": "Patient partner, McGill University" - }, - { - "author_name": "Carrie Costello", - "author_inst": "Patient partner with the CHILD-BRIGHT Network" - }, - { - "author_name": "Donna Thomson", - "author_inst": "Patient partner with the CHILD-BRIGHT Network, and Kids Brain Health Network" - }, - { - "author_name": "Annette Majnemer", - "author_inst": "McGill University" - }, - { - "author_name": "Dan Goldowitz", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Steven P. Miller", - "author_inst": "University of Toronto" - }, - { - "author_name": "Annie LeBlanc", - "author_inst": "Universite Laval - VITAM Research Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.03.19.21253756", "rel_title": "Characterizing Post-Acute Sequelae of SARS-CoV-2 Infection across Claims and Electronic Health Record Databases", @@ -859964,6 +861636,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2021.03.17.21253138", + "rel_title": "Mortality during the COVID-19 pandemic: findings from the CLINIMEX exercise cohort in the year of 2020", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21253138", + "rel_abs": "Background and ObjectiveThe COVID-19 pandemic has heavily hit Brazil and, in particular, our Clinics current location in Copacabana - Rio de Janeiro city, where, as of mid-February 2021, it led to one death per 266 inhabitants. After having recently updated the vital status and mortality data in our exercise population (CLINIMEX exercise cohort), we hypothesized that the review of their evaluation reports would offer a unique opportunity to unearth some relevant information about the association between selected variables assessed in our comprehensive Exercise Medicine evaluation protocol, in particular, aerobic and musculoskeletal (MUSK) fitness, clinical variables, and death due to COVID-19.\n\nMethodsWe conducted a retrospective study using data from the CLINIMEX exercise cohort that included 6,101 non-athletic men and women aged >30 years who were alive as of March 12th, 2020, and whos vital status was followed up to December 14th, 2020. For data analysis, two approaches were used: 1) comparison of frequency of deaths and relative % of underlying causes of death between the last 18-months pre-pandemic and 9-month pandemic periods; and 2) data from 51 variables from the participants most recent evaluation, including sex, age and clinical profile plus other variables obtained from physical examination, spirometry, (MUSK) fitness (e.g., sitting-rising test) and maximal cycling leg cardiopulmonary exercise testing (e.g. maximal VO2 and cardiorespiratory optimal point) were selected for comparison between groups of non-COVID-19 and COVID-19 deaths. Results: Age at death varied from 51 to 102 years [mean = 80 years]. Only 4 participants that died - 3 COVID-19 and 1 non-COVID-19 - were healthy at the time of their evaluation [p=.52]. COVID-19 was the most frequent (n=35; 36.5%) cause of death among the 96 deaths during this 9-month period. Comparing pre-pandemic and pandemic periods, there was a 35% increase in deaths and proportionately fewer deaths due to neoplasia and other causes other than cardiovascular or endocrine diseases. Results of aerobic and MUSK fitness tests indicated that the majority of the study participants were relatively unfit when compared to available age and sex-reference values. Indeed, there were few differences in the 51 selected variables between the two groups, suggesting a somewhat healthier profile among COVID-19 death participants: lower body mass index [p=.04], higher % of predicted forced vital capacity [p=.04], lower number of previous percutaneous coronary interventions [p=.04] and lower resting supine diastolic blood pressure [p=.03], with no differences for aerobic/MUSK fitness variables or past history of exercise/sports [p>.05].\n\nConclusionOur data support that COVID-19 was a frequent and premature cause of death in a convenience sample of primarily white, unhealthy, middle-age and elderly individuals and that data from exercise/sport history and physical fitness testing obtained some years earlier were unable to distinguish non-COVID-19 and COVID-19 deaths.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Claudio Gil S Araujo", + "author_inst": "Exercise Medicine Clinic - CLINIMEX - Rio de Janeiro, Brazil" + }, + { + "author_name": "Christina G De Souza e Silva", + "author_inst": "Exercise Medicine Clinic - CLINIMEX - Rio de Janeiro, Brazil" + }, + { + "author_name": "Claudia Lucia B Castro", + "author_inst": "Exercise Medicine Clinic - CLINIMEX - Rio de Janeiro, Brazil" + }, + { + "author_name": "Jari A Laukkanen", + "author_inst": "Institute of Clinical Medicine, Department of Medicine, University of Eastern Finland, Kuopio, Finland and Central Finland Health Care District, Department of M" + }, + { + "author_name": "Jonathan Myers", + "author_inst": "VA Palo Alto Health Care System, Palo Alto, and Stanford University, Stanford, United States" + }, + { + "author_name": "Josef Niebauer", + "author_inst": "University Institute of Sports Medicine, Prevention and Rehabilitation, Paracelsus Medical University and Ludwig Boltzmann Institute for Digital Health and Prev" + }, + { + "author_name": "Aline Sardinha", + "author_inst": "Sexual Dysfunction Unit, Psychiatry and Mental Health Graduate Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil" + }, + { + "author_name": "Joao Felipe Franca", + "author_inst": "Exercise Medicine Clinic - CLINIMEX, Rio de Janeiro, Brazil" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "sports medicine" + }, { "rel_doi": "10.1101/2021.03.19.21253558", "rel_title": "Argentine Registry of neurological manifestations due to coronavirus-19 (COVID-19)", @@ -861919,53 +863638,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.11.21253231", - "rel_title": "Emergence of the E484K Mutation in SARS-CoV-2 Lineage B.1.1.220 in Upstate New York", - "rel_date": "2021-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253231", - "rel_abs": "Ongoing surveillance detected a SARS-CoV-2 B.1.1.220 variant carrying the E484K substitution in four patients from a hospital network in upstate New York. Patients reported no travel history and shared no obvious epidemiological linkage. A search of online databases identified 12 additional B.1.1.220 with E484K, all of which were detected in New York since December 2020. Detailed genomic analyses suggests that the mutation has emerged independently in at least two different B.1.1.220 strains in this region.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Emil Lesho", - "author_inst": "Rochester General Hospital" - }, - { - "author_name": "Brendan Corey", - "author_inst": "Walter Reed Army Institute of Research" - }, - { - "author_name": "Francois Lebreton", - "author_inst": "Walter Reed Army Institute of Research" - }, - { - "author_name": "Ana Ong", - "author_inst": "Walter Reed Army Institute of Research" - }, - { - "author_name": "Brett Swierczewski", - "author_inst": "Walter Reed Army Institute of Research" - }, - { - "author_name": "Jason Bennett", - "author_inst": "Walter Reed Army Institute of Research" - }, - { - "author_name": "Edward Walsh", - "author_inst": "University of Rochester School of Medicine" - }, - { - "author_name": "Patrick McGann", - "author_inst": "Walter Reed Army Institute of Research" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.23.436564", "rel_title": "Protein-primed RNA synthesis in SARS-CoVs and structural basis for inhibition by AT-527", @@ -862274,6 +863946,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.22.436481", + "rel_title": "Neutralization of European, South African, and United States SARS-CoV-2 mutants by a human antibody and antibody domains", + "rel_date": "2021-03-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.22.436481", + "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) transmission with several emerging variants remain uncontrolled in many countries, indicating the pandemic remains severe. Recent studies showed reduction of neutralization against these emerging SARS-CoV-2 variants by vaccine-elicited antibodies. Among those emerging SARS-CoV-2 variants, a panel of amino acid mutations was characterized including those in the receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) glycoprotein. In the present study, we evaluated our previously identified antibody and antibody domains for binding to these RBD variants with the emerging mutations, and neutralization of pseudo typed viruses carrying spike proteins with such mutations. Our results showed that one previously identified antibody domain, ab6, can bind 32 out of 35 RBD mutants tested in an ELISA assay. All three antibodies and antibody domains can neutralize pseudo typed B.1.1.7 (UK variant), but only the antibody domain ab6 can neutralize the pseudo typed virus with the triple mutation (K417N, E484K, N501Y). This domain and its improvements have potential for therapy of infections caused by SARS-CoV-2 mutants.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Zehua Sun", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Andrew Kim", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Michele D Sobolewski", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Nathan Enick", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Chuan Chen", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Cynthia Adams", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Jana L Jacobs", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Kevin D McCormick", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "John W. Mellors", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Dimiter S Dimitrov", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Wei Li", + "author_inst": "University of Pittsburgh" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.03.23.436613", "rel_title": "Application of an integrated computational antibody engineering platform to design SARS-CoV-2 neutralizers", @@ -863789,97 +865520,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2021.03.20.21254040", - "rel_title": "Symptoms of COVID-19 in a population-based cohort study", - "rel_date": "2021-03-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.20.21254040", - "rel_abs": "Accurate diagnosis of potential SARS-CoV-2 infections by symptoms is one strategy for continuing global surveillance, particularly in low-resource communities. We conducted a prospective, population-based cohort study, the Arizona CoVHORT, among Arizona residents to elucidate the symptom profile of laboratory-confirmed COVID-19 participants(16.2%) compared to laboratory-confirmed negative(22.4%) and untested general population participants(61.4%). Among the 1514 study participants, those who were COVID-19 positive were more likely to be Hispanic(33.5%) and more likely to report obesity > 30 kg/m2(34.7%) compared to COVID-19 negative participants(19.2%; 31.0%) and untested CoVHORT participants(13.8%; 23.8%). Of the 245 laboratory-confirmed COVID-19 cases, 15.0% reported having had no symptoms. Of those that did report symptoms, the most commonly-reported first symptoms were sore throat(19.0%), headache(15.5%), cough(12.7%), runny nose/cold-like symptoms(12.1%), and fatigue(12.0%). In adjusted logistic regression models, COVID-19 positive participants were more likely than negative participants to experience loss of taste and smell(OR:35.7; 95% CI 18.4-69.5); bone or nerve pain(OR:17.9; 95% CI 6.7-47.4), vomiting(OR:10.8; 95% CI 3.1-37.5), nausea(OR:10.5; 95% CI 5.5-19.9), and headache(OR:8.4; 95% CI 5.6-12.8). When comparing confirmed COVID-19 cases with confirmed negative or untested participants, the pattern of symptoms that discriminates SARS-CoV-2 infection from those arising from other potential circulating pathogens may differ from general reports of symptoms among cases alone.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Sana M Khan", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Leslie V Farland", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Erika Austhof", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Melanie L Bell", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Collin J Catalfamo", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Zhao Chen", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Felina Cordova-Marks", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Kacey C Ernst", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Pamela Garcia-Filion", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Kelly M Heslin", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Joshua Hoskinson", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Megan L Jehn", - "author_inst": "Arizona State University" - }, - { - "author_name": "Emily C.S. Joseph", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Connor P Kelley", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Yann Klimentidis", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Stephanie Carrol", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Lindsay N Kohler", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Kristen Pogreba-Brown", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Elizabeth T Jacobs", - "author_inst": "The University of Arizona" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.21.21253754", "rel_title": "Role of Combining Anticoagulant and Antiplatelet Agents in COVID-19 Treatment: A Rapid Review", @@ -864152,6 +865792,77 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.22.436375", + "rel_title": "An mRNA vaccine against SARS-CoV-2: Lyophilized, liposome-based vaccine candidate EG-COVID induces high levels of virus neutralizing antibodies", + "rel_date": "2021-03-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.22.436375", + "rel_abs": "In addition to the traditional method of vaccine development, the mRNA coronavirus vaccine, which is attractive as a challenging vaccination, recently opened a new era in vaccinology. Here we describe the EG-COVID which is a novel liposome-based mRNA candidate vaccine that encodes the spike (S) protein of SARS-CoV-2 with 2P-3Q substitution in European variant. We developed the mRNA vaccine platform that can be lyophilized using liposome-based technology. Intramuscular injection of the EG-COVID elicited robust humoral and cellular immune response to SARS-CoV-2. Furthermore, sera obtained from mice successfully inhibited SARS-CoV-2 viral infection into Vero cells. We developed EG-COVID and found it to be effective based on in vitro data, and we plan to initiate a clinical trial soon. Since EG-COVID is a lyophilized mRNA vaccine that is convenient for transportation and storage, accessibility to vaccines will be significantly improved.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "H. Christian Hong", + "author_inst": "EyeGene Inc." + }, + { + "author_name": "Kwang Sung Kim", + "author_inst": "EyeGene Inc." + }, + { + "author_name": "Shin Ae Park", + "author_inst": "EyeGene Inc." + }, + { + "author_name": "Min Jeong Chun", + "author_inst": "EyeGene Inc." + }, + { + "author_name": "Eun Young Hong", + "author_inst": "EyeGene Inc." + }, + { + "author_name": "Seung Won Chung", + "author_inst": "EyeGene Inc." + }, + { + "author_name": "Hyun Jong Kim", + "author_inst": "EyeGene Inc." + }, + { + "author_name": "Byeong Gyu Shin", + "author_inst": "EyeGene Inc." + }, + { + "author_name": "Yang Je Cho", + "author_inst": "EyeGene Inc." + }, + { + "author_name": "Abdennour Braka", + "author_inst": "PharmCadd" + }, + { + "author_name": "Jayaraman Thangappan", + "author_inst": "PharmCadd" + }, + { + "author_name": "Sunghoon Jang", + "author_inst": "PharmCadd" + }, + { + "author_name": "Sangwook Wu", + "author_inst": "PharmCadd and Pukyong National University" + }, + { + "author_name": "Seok-Hyun Kim", + "author_inst": "Eyegene Inc." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.03.21.436312", "rel_title": "Predicting hosts based on early SARS-CoV-2 samples and analyzing later world-wide pandemic in 2020", @@ -865919,41 +867630,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.19.21253945", - "rel_title": "Sarcopenic obesity and the risk of hospitalisation or death from COVID-19: findings from UK Biobank", - "rel_date": "2021-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253945", - "rel_abs": "BackgroundCoronavirus disease{square}2019 (COVID{square}19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS{square}CoV{square}2 virus). The role of skeletal muscle mass in modulating immune response is well documented. Whilst obesity is well-established as a key factor in COVID-19 infection and outcome, no study has examined the influence of both sarcopenia (low muscle mass) and obesity, termed sarcopenic obesity on COVID-19 risk.\n\nMethodsThis study uses data from UK Biobank. Probable sarcopenia was defined as low handgrip strength. Sarcopenic obesity was mutually exclusively defined as the presence of obesity and low muscle mass (based on two established criteria: appendicular lean mass (ALM) adjusted for either: 1) height and 2) body mass index (BMI)). Severe COVID-19 was defined by a positive test result in a hospital setting or death with a primary cause reported as COVID-19. Fully adjusted logistic regression models were used to analyse the associations between sarcopenic status and severe COVID-19. This work was conducted under UK Biobank application number 52553.\n\nResultsWe analysed data from 490,301 UK Biobank participants. 2203 (0.4%) had severe COVID-19 infection. Individuals with probable sarcopenia were 64% more likely to have had severe COVID-19 infection (odds ratio (OR) 1.638; P<.001). Obesity increased the likelihood of severe COVID-19 infection by 76% (P<.001). Using either ALM index and ALM/BMI index to define low muscle mass, those with sarcopenic obesity were 2.6 times more likely to have severe COVID-19 (OR: 2.619; P<.001). Sarcopenia alone did not increase the risk of COVID-19.\n\nConclusionsSarcopenic obesity may increase the risk of severe COVID-19 infection, over that of obesity alone. The mechanisms for this are complex but could be a result of a reduction in respiratory functioning, immune response, and ability to respond to metabolic stress.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Thomas Wilkinson", - "author_inst": "University of Leicester" - }, - { - "author_name": "Thomas Yates", - "author_inst": "Leicester NIHR Biomedical Research Centre" - }, - { - "author_name": "Luke A Baker", - "author_inst": "University of Leicester" - }, - { - "author_name": "Francesco Zaccardi", - "author_inst": "Leicester Diabetes Research Centre" - }, - { - "author_name": "Alice C Smith", - "author_inst": "University of Leicester" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.18.21253887", "rel_title": "Effect of Increased Alcohol Consumption During COVID-19 Pandemic on Alcohol-related Liver Disease: A Modelling Study", @@ -866150,6 +867826,173 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.19.21253946", + "rel_title": "The ongoing evolution of variants of concern and interest of SARS-CoV-2 in Brazil revealed by convergent indels in the amino (N)-terminal domain of the Spike protein", + "rel_date": "2021-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253946", + "rel_abs": "Mutations at both the receptor-binding domain (RBD) and the amino (N)-terminal domain (NTD) of the SARS-CoV-2 Spike (S) glycoprotein can alter its antigenicity and promote immune escape. We identified that SARS-CoV-2 lineages circulating in Brazil with mutations of concern in the RBD independently acquired convergent deletions and insertions in the NTD of the S protein, which altered the NTD antigenic-supersite and other predicted epitopes at this region. These findings support that the ongoing widespread transmission of SARS-CoV-2 in Brazil is generating new viral lineages that might be more resistant to neutralization than parental variants of concern.", + "rel_num_authors": 38, + "rel_authors": [ + { + "author_name": "Paola Cristina Resende", + "author_inst": "Oswaldo Cruz Institute" + }, + { + "author_name": "Felipe Gomes Naveca", + "author_inst": "Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia (EDTA), Instituto Leonidas e Maria Deane, FIOCRUZ-Amazonas" + }, + { + "author_name": "Roberto Dias Lins", + "author_inst": "Department of Virology, Instituto Aggeu Magalhaes, FIOCRUZ-Pernambuco" + }, + { + "author_name": "Filipe Zimmer Dezordi", + "author_inst": "Departamento de Entomologia e Nucleo de Bioinformatica, Instituto Aggeu Magalhaes, FIOCRUZ-Pernambuco, Brazil" + }, + { + "author_name": "Matheus V. F. Ferraz", + "author_inst": "Department of Virology, Instituto Aggeu Magalhaes, FIOCRUZ-Pernambuco" + }, + { + "author_name": "Emerson G. Moreira", + "author_inst": "Department of Virology, Instituto Aggeu Magalhaes, FIOCRUZ-Pernambuco" + }, + { + "author_name": "Danilo F. Coelho", + "author_inst": "Department of Fundamental Chemistry, Federal University of Pernambuco" + }, + { + "author_name": "Fernando Couto Motta", + "author_inst": "Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz" + }, + { + "author_name": "Anna Carolina Dias Paixao", + "author_inst": "Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz" + }, + { + "author_name": "Luciana Appolinario", + "author_inst": "Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz" + }, + { + "author_name": "Renata Serrano Lopes", + "author_inst": "Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz" + }, + { + "author_name": "Ana Carolina da Fonseca Mendonca", + "author_inst": "Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz" + }, + { + "author_name": "Alice Sampaio Barreto da Rocha", + "author_inst": "Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz" + }, + { + "author_name": "Valdinete Nascimento", + "author_inst": "Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia (EDTA), Instituto Leonidas e Maria Deane, FIOCRUZ-Amazonas" + }, + { + "author_name": "Victor Souza", + "author_inst": "Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia (EDTA), Instituto Leonidas e Maria Deane, FIOCRUZ-Amazonas" + }, + { + "author_name": "George Silva", + "author_inst": "Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia (EDTA), Instituto Leonidas e Maria Deane, FIOCRUZ-Amazonas" + }, + { + "author_name": "Fernanda Nascimento", + "author_inst": "Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia (EDTA), Instituto Leonidas e Maria Deane, FIOCRUZ-Amazonas" + }, + { + "author_name": "Lidio Goncalves Lima Neto", + "author_inst": "Laboratorio Central de Saude Publica do Estado do Maranhao (LACEN-MA)" + }, + { + "author_name": "Fabiano Vieira da Silva", + "author_inst": "Laboratorio Central de Saude Publica do Maranhao (LACEN-MA)" + }, + { + "author_name": "Irina Riediger", + "author_inst": "Laboratorio Central de Saude Publica do Estado do Parana (LACEN-PR)" + }, + { + "author_name": "Maria do Carmo Debur", + "author_inst": "Laboratorio Central de Saude Publica do Estado do Parana (LACEN-PR)" + }, + { + "author_name": "Anderson Brandao Leite", + "author_inst": "Laboratorio Central de Saude Publica do Estado do Alagoas (LACEN-AL)" + }, + { + "author_name": "Tirza Mattos", + "author_inst": "Laboratorio Central de Saude Publica do Amazonas (LACEN-AM)" + }, + { + "author_name": "Cristiano Fernandes da Costa", + "author_inst": "Fundacao de Vigilancia em Saude do Amazonas" + }, + { + "author_name": "Felicidade Mota Pereira", + "author_inst": "Laboratorio Central de Saude Publica do Estado da Bahia (LACEN-BA)" + }, + { + "author_name": "Cliomar Alves dos Santos", + "author_inst": "Laboratorio Central de Saude Publica do Estado de Sergipe (LACEN-SE)" + }, + { + "author_name": "Darcita Buerger Rovaris", + "author_inst": "Laboratorio Central de Saude Publica do Estado de Santa Catarina (LACEN-SC)" + }, + { + "author_name": "Sandra Bianchini Fernandes", + "author_inst": "Laboratorio Central de Saude Publica do Estado de Santa Catarina (LACEN-SC)" + }, + { + "author_name": "Adriano Abbud", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Claudio Sacchi", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Ricardo Khouri", + "author_inst": "Laboratorio de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Goncalo Moniz, FIOCRUZ-Bahia" + }, + { + "author_name": "Andre Felipe Leal Bernardes", + "author_inst": "Laboratorio Central de Saude Publica do Estado de Minas Gerais (LACEN-MG)" + }, + { + "author_name": "Edson Delatorre", + "author_inst": "Departamento de Biologia. Centro de Ciencias Exatas, Naturais e da Saude, Universidade Federal do Espirito Santo" + }, + { + "author_name": "Tiago Graf", + "author_inst": "Plataforma de Vigilancia Molecular, Instituto Goncalo Moniz, FIOCRUZ-Bahia" + }, + { + "author_name": "Marilda Mendonca Siqueira", + "author_inst": "Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz" + }, + { + "author_name": "Gonzalo Bello", + "author_inst": "Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz" + }, + { + "author_name": "Gabriel Luz Wallau", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "- Fiocruz COVID-19 Genomic Surveillance Network", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.18.21253874", "rel_title": "Diagnostic accuracy of rapid antigen tests in pre-/asymptomatic close contacts of individuals with a confirmed SARS-CoV-2 infection", @@ -868129,101 +869972,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.19.21253960", - "rel_title": "Within-country age-based prioritisation, global allocation, and public health impact of a vaccine against SARS-CoV-2: a mathematical modelling analysis", - "rel_date": "2021-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253960", - "rel_abs": "The worldwide endeavour to develop safe and effective COVID-19 vaccines has been extraordinary, and vaccination is now underway in many countries. However, the doses available in 2021 are likely to be limited. We extended a mathematical model of SARS-CoV-2 transmission across different country settings to evaluate the public health impact of potential vaccines using WHO-developed target product profiles. We identified optimal vaccine allocation strategies within- and between-countries to maximise averted deaths under constraints on dose supply. We found that the health impact of SARS-CoV-2 vaccination depends on the cumulative population-level infection incidence when vaccination begins, the duration of natural immunity, the trajectory of the epidemic prior to vaccination, and the level of healthcare available to effectively treat those with disease. Within a country we find that for a limited supply (doses for <20% of the population) the optimal strategy is to target the elderly. However, with a larger supply, if vaccination can occur while other interventions are maintained, the optimal strategy switches to targeting key transmitters to indirectly protect the vulnerable. As supply increases, vaccines that reduce or block infection have a greater impact than those that prevent disease alone due to the indirect protection provided to high-risk groups. Given a 2 billion global dose supply in 2021, we find that a strategy in which doses are allocated to countries proportional to population size is close to optimal in averting deaths and aligns with the ethical principles agreed in pandemic preparedness planning.\n\nHighlightsO_LIThe global dose supply of COVID-19 vaccines will be constrained in 2021\nC_LIO_LIWithin a country, prioritising doses to protect those at highest mortality risk is efficient\nC_LIO_LIFor a 2 billion dose supply in 2021, allocating to countries according to population size is efficient and equitable\nC_LI", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Alexandra B Hogan", - "author_inst": "Imperial College London" - }, - { - "author_name": "Peter Winskill", - "author_inst": "Imperial College London" - }, - { - "author_name": "Oliver J Watson", - "author_inst": "Imperial College London" - }, - { - "author_name": "Patrick G T Walker", - "author_inst": "Imperial College London" - }, - { - "author_name": "Charles Whittaker", - "author_inst": "Imperial College, London" - }, - { - "author_name": "Marc Baguelin", - "author_inst": "Imperial College London" - }, - { - "author_name": "Nicholas F Brazeau", - "author_inst": "Imperial College London" - }, - { - "author_name": "Giovanni D Charles", - "author_inst": "Imperial College London" - }, - { - "author_name": "Katy A M Gaythorpe", - "author_inst": "Imperial College London" - }, - { - "author_name": "Arran Hamlet", - "author_inst": "Imperial College London" - }, - { - "author_name": "Edward Knock", - "author_inst": "Imperial College London" - }, - { - "author_name": "Daniel J Laydon", - "author_inst": "Imperial College London" - }, - { - "author_name": "John A Lees", - "author_inst": "Imperial College London" - }, - { - "author_name": "Alessandra L\u00f8chen", - "author_inst": "Imperial College London" - }, - { - "author_name": "Robert Verity", - "author_inst": "Imperial College London" - }, - { - "author_name": "Lilith K Whittles", - "author_inst": "Imperial College London" - }, - { - "author_name": "Farzana Muhib", - "author_inst": "PATH" - }, - { - "author_name": "Katharina Hauck", - "author_inst": "Imperial College London" - }, - { - "author_name": "Neil M Ferguson", - "author_inst": "Imperial College London" - }, - { - "author_name": "Azra C Ghani", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.19.21253889", "rel_title": "Risk of reinfection after seroconversion to SARS-CoV-2: A population-based propensity-score matched cohort study", @@ -868424,6 +870172,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.16.21253736", + "rel_title": "Neurological manifestations of patients with mild-to-moderate COVID-19 attending a public hospital in Lima, Peru", + "rel_date": "2021-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253736", + "rel_abs": "ObjectiveTo determine the prevalence and characteristics of the most common neurological manifestations in Peruvian patients with mild-to-moderate COVID-19.\n\nMethodsWe conducted a single-center prospective, cross-sectional study at an isolation center functioning as a public acute-care hospital during the COVID-19 pandemic in Lima, the capital city of Peru. This was a convenience sample of patients with acute COVID-19 infection and mild-to-moderate respiratory symptoms who presented for hospital admission between September 25 and November 25, 2020. We interviewed participants and collected demographic, medical history and clinical presentation data; all participants underwent a complete physical and neurological examination. Descriptive statistics and prevalence ratios (PR) with corresponding 95% confidence intervals and p-values were calculated to explore between-groups differences.\n\nResultsOf 199 patients with mild-to-moderate COVID-19 enrolled in this study, 83% presented with at least one neurological symptom (mean symptom duration 8 +/-6 days). The most common neurological symptoms were headache (72%), hypogeusia or ageusia (41%), hyposmia or anosmia (40%) and dizziness (34%). Only 2.5% of the cohort had an abnormal neurological examination. The majority (42%) had no prior comorbidities. Presence of at least 1 neurological symptom was independently associated with fever, dyspnea, cough, poor appetite, sore throat, chest tightness or diarrhea, but not with comorbid conditions.\n\nConclusionsThis cross-sectional study found that headaches, and smell and taste dysfunction are common among patients presenting with mild-to-moderate acute COVID-19 in Lima, Peru. International longitudinal studies are needed to determine the long-term neurological sequelae of COVID-19 during the acute and post-infectious period.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Marco H. Carcamo Garcia", + "author_inst": "Epidemiology, STD, and HIV Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru; Care and Isolation Center for COV" + }, + { + "author_name": "Diego D Garcia Choza", + "author_inst": "Care and Isolation Center for COVID-19 Patients Villa Panamericana, EsSalud - Social Health Insurance Institute, Lima, Peru; Universidad de San Martin de Porres" + }, + { + "author_name": "Brenda J Salazar Linares", + "author_inst": "Care and Isolation Center for COVID-19 Patients Villa Panamericana, EsSalud - Social Health Insurance Institute, Lima, Peru; Universidad de San Martin de Porres" + }, + { + "author_name": "Monica M Diaz", + "author_inst": "Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2021.03.17.21253805", "rel_title": "The effect of Covid-19 isolation measures on the cognition and mental health of people living with dementia: a rapid systematic review of one year of evidence.", @@ -869775,65 +871554,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.03.19.435806", - "rel_title": "Combined computational and cellular screening identifies synergistic inhibition of SARS-CoV-2 by lenvatinib and remdesivir", - "rel_date": "2021-03-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.19.435806", - "rel_abs": "Rapid repurposing of existing drugs as new therapeutics for COVID-19 has been an important strategy in the management of disease severity during the ongoing SARS-CoV-2 pandemic. Here, we used high-throughput docking to screen 6000 compounds within the DrugBank library for their potential to bind and inhibit the SARS-CoV-2 3CL main protease, a chymotrypsin-like enzyme that is essential for viral replication. For 19 candidate hits, parallel in vitro fluorescence-based protease-inhibition assays and Vero-CCL81 cell-based SARS-CoV-2 replication-inhibition assays were performed. One hit, diclazuril (an investigational anti-protozoal compound), was validated as a SARS-CoV-2 3CL main protease inhibitor in vitro (IC50 value of 29 {micro}M) and modestly inhibited SARS-CoV-2 replication in Vero-CCL81 cells. Another hit, lenvatinib (approved for use in humans as an anti-cancer treatment), could not be validated as a SARS-CoV-2 3CL main protease inhibitor in vitro, but serendipitously exhibited a striking functional synergy with the approved nucleoside analogue remdesivir to inhibit SARS-CoV-2 replication, albeit this was specific to Vero-CCL81 cells. Lenvatinib is a broadly-acting host receptor tyrosine kinase (RTK) inhibitor, but the synergistic effect with remdesivir was not observed with other approved RTK inhibitors (such as pazopanib or sunitinib), suggesting that the mechanism-of-action is independent of host RTKs. Furthermore, time-of-addition studies revealed that lenvatinib/remdesivir synergy probably targets SARS-CoV-2 replication subsequent to host-cell entry. Our work shows that combining computational and cellular screening is a means to identify existing drugs with repurposing potential as antiviral compounds. Future studies could be aimed at understanding and optimizing the lenvatinib/remdesivir synergistic mechanism as a therapeutic option.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Marie O. Pohl", - "author_inst": "University of Zurich" - }, - { - "author_name": "Idoia Busnadiego", - "author_inst": "University of Zurich" - }, - { - "author_name": "Francesco Marrafino", - "author_inst": "University of Salerno" - }, - { - "author_name": "Lars Wiedmer", - "author_inst": "University of Zurich" - }, - { - "author_name": "Annika Hunziker", - "author_inst": "University of Zurich" - }, - { - "author_name": "Sonja Fernbach", - "author_inst": "University of Zurich" - }, - { - "author_name": "Irina Glas", - "author_inst": "University of Zurich" - }, - { - "author_name": "Elena V. Moroz-Omori", - "author_inst": "University of Zurich" - }, - { - "author_name": "Benjamin G Hale", - "author_inst": "University of Zurich" - }, - { - "author_name": "Amedeo Caflisch", - "author_inst": "University of Zurich" - }, - { - "author_name": "Silke Stertz", - "author_inst": "University of Zurich" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.03.19.435740", "rel_title": "The inhibitory effects of toothpaste and mouthwash ingredients on the interaction between the SARS-CoV-2 spike protein and ACE2, and the protease activity of TMPRSS2, in vitro", @@ -870162,6 +871882,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.18.435945", + "rel_title": "Myocarditis in naturally infected pets with the British variant of COVID-19", + "rel_date": "2021-03-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.18.435945", + "rel_abs": "Domestic pets can contract SARS-CoV-2 infection but, based on the limited information available to date, it is unknown whether the new British B.1.1.7 variant can more easily infect certain animal species or increase the possibility of human-to-animal transmission. In this study, we report the first cases of infection of domestic cats and dogs by the British B.1.1.7 variant of SARS-CoV-2 diagnosed at a specialist veterinary hospital in the South-East of England. Furthermore, we discovered that many owners and handlers of these pets had developed Covid-19 respiratory symptoms 3-6 weeks before their pets became ill and had also tested PCR positive for Covid-19. Interestingly, all these B.1.1.7 infected pets developed atypical clinical manifestations, including severe cardiac abnormalities secondary to myocarditis and a profound impairment of the general health status of the patient but without any primary respiratory signs. Together, our findings demonstrate for the first time the ability for companion animals to be infected by the B.1.1.7 variant of SARS-CoV-2 and raise questions regarding its pathogenicity in these animals. Moreover, given the enhanced infectivity and transmissibility of B.1.1.7 variant for humans, these findings also highlights more than ever the risk that companion animals may potentially play a significant role in SARS-CoV-2 outbreak dynamics than previously appreciated.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Luca Ferasin", + "author_inst": "The Ralph Veterinary Referral Centre" + }, + { + "author_name": "Matthieu Fritz", + "author_inst": "Institut de Recherche pour le Developpement" + }, + { + "author_name": "Heidi Ferasin", + "author_inst": "The Ralph Veterinary Referral Centre" + }, + { + "author_name": "Pierre Becquart", + "author_inst": "Institut de Recherche pour le Developpement" + }, + { + "author_name": "Vincent Legros", + "author_inst": "Centre International de Recherche en Infectiologie/VetAgro Sup" + }, + { + "author_name": "Eric M. Leroy", + "author_inst": "Institut de Recherche pour le Developpement" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.03.17.435863", "rel_title": "Mutational escape from the polyclonal antibody response to SARS-CoV-2 infection is largely shaped by a single class of antibodies", @@ -871625,37 +873384,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.03.15.21253566", - "rel_title": "Understanding Convergence Between Non-Hispanic Black and White COVID-19 Mortality: A County-Level Approach", - "rel_date": "2021-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.15.21253566", - "rel_abs": "BackgroundNon-Hispanic Black populations have suffered greater per capita COVID-19 mortality at more than 1.5 times that of White populations. Previous work has established that, over time, rates of Black and White mortality have converged; however, some studies suggest that regional shifts in COVID-19 prevalence may play a role in the relative change between racial groups. This studys objective was to investigate changes in Black and White COVID-19 mortality over time and uncover potential mechanisms driving these changes.\n\nMethods and FindingsUsing county-level COVID-19 mortality data stratified by race, we investigate the trajectory of non-Hispanic Black mortality, White mortality, and the Black/White per capita mortality ratio from June 2020-January 2021. Over this period, in the counties studied, cumulative mortality rose by 56.7% and 82.8% for Black and White populations respectively, resulting in a decrease in mortality ratio of 0.369 (23.8%). These trends persisted even when a county-level fixed-effects model was used to estimate changes over time within counties (controlling for all time-invariant county level characteristics and removing the effects of changes in regional distribution of COVID-19). Next, we leverage county-level variation over time in COVID-19 prevalence to show that the decline in the Black/White mortality ratio can be explained by changes in COVID-19 prevalence. Finally, we study heterogeneity in the time trend, finding that convergence occurs most significantly in younger populations, areas with less dense populations, and outside of the Northeast. Limitations include suppressed data in counties with fewer than 10 deaths in a racial category, and the use of provisional COVID-19 death data that may be incomplete.\n\nConclusionsThe results of this study suggest that convergence in Black/White mortality is not driven by county-level characteristics or changes in the regional dispersion of COVID-19, but instead by changes within counties. Further, declines in the Black/White mortality ratio appear strongly linked to changes in COVID-19 prevalence, rather than a time-specific effect. Further studies on changes in exposure by race over time, or on the vulnerability of individuals who died at different points in the pandemic, may provide crucial insight on mechanisms and strategies to further reduce COVID-19 mortality disparities.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ralph Ignacio Lawton", - "author_inst": "Duke University" - }, - { - "author_name": "Kevin Z Zheng", - "author_inst": "Duke University" - }, - { - "author_name": "Daniel Zheng", - "author_inst": "University of Maryland, Baltimore County" - }, - { - "author_name": "Erich S Huang", - "author_inst": "Duke University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.03.15.21253581", "rel_title": "Tocilizumab Effect in COVID-19 Hospitalized Patients: A Systematic Review and Meta-Analysis of Randomized Control Trials", @@ -871864,6 +873592,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.15.21253609", + "rel_title": "Seroreactivity to SARS-CoV-2 in individuals attending a university campus in Bogota Colombia", + "rel_date": "2021-03-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.15.21253609", + "rel_abs": "Most community-specific serological surveys for SARS-CoV-2 antibodies have been performed in healthcare workers and institutions. In this study, IgG antibodies specific to the virus were evaluated in individuals working at a university campus in Bogota, Colombia. The aim of this work was to determine previous exposure to SARS-CoV-2 in those attending the campus during city lockdown. A total of 237 individuals, including 93 women and 144 men were evaluated using chemiluminescent detection of IgG anti N-viral protein between November and December 2020. There were 32 positives individuals corresponding to a seroprevalence of 13.5% (10 women and 22 men) and mostly asymptomatic (68.75%) and three cluster of seropositive individuals were identified. Only 13 of the seropositive individuals had previous positive detection of SARS-CoV-2 RNA by RT-qPCR performed in average 91 days before serological test. Seropositive individuals did not come from boroughs having higher percentages of SARS-CoV-2 cases in the city. This survey was carried out after the first peak of SARS-CoV-2 transmission in the city, and before the preparedness to reopening the campus for students in 2021, demonstrating a low seroprevalence in high percentage of asymptomatic. These results will help to evaluate some of the strategies stablished to control virus spread in the campus or other similar communities.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "John M Gonzalez", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Juan Carlos Santos-Barbosa", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Catherine Jaller", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "German Otalora", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Luis J Hernandez", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Marcela Guevara-Suarez", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Silvia Restrepo", + "author_inst": "Universidad de los Andes" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.16.21253717", "rel_title": "Patterns of compliance with COVID-19 preventive behaviours: a latent class analysis of 20,000 UK adults", @@ -873511,185 +875282,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.03.17.21253131", - "rel_title": "Interim results of the safety and immune-efficacy of 1 versus 2 doses of COVID-19 vaccine BNT162b2 for cancer patients in the context of the UK vaccine priority guidelines", - "rel_date": "2021-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21253131", - "rel_abs": "BackgroundThe efficacy and safety profile of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have not been definitively established in immunocompromised patient populations. Patients with a known cancer diagnosis were hitherto excluded from trials of the vaccines currently in clinical use.\n\nMethodsThis study presents data on the safety and immune efficacy of the BNT162b2 (Pfizer-BioNTech) vaccine in 54 healthy controls and 151 mostly elderly patients with solid and haematological malignancies, respectively, and compares results for patients who were boosted with BNT162b2 at 3 weeks versus those who were not. Immune efficacy was measured as antibody seroconversion, T cell responses, and neutralisation of SARS-CoV-2 Wuhan strain and of a variant of concern (VOC) (B.1.1.7). We also collected safety data for the BNT162b2 vaccine up to 5 weeks following first dose.\n\nFindingsThe vaccine was largely well tolerated. However, in contrast to its very high performance in healthy controls (>90% efficacious), immune efficacy of a single inoculum in solid cancer patients was strikingly low (below 40%) and very low in haematological cancer patients (below 15%). Of note, efficacy in solid cancer patients was greatly and rapidly increased by boosting at 21-days (95% within 2 weeks of boost). Too few haematological cancer patients were boosted for clear conclusions to be drawn.\n\nConclusionsDelayed boosting potentially leaves most solid and haematological cancer patients wholly or partially unprotected, with implications for their own health; their environment and the evolution of VOC strains. Prompt boosting of solid cancer patients quickly overcomes the poor efficacy of the primary inoculum in solid cancer patients.\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSSome cancer patients have been shown to exhibit sustained immune dysregulation, inefficient seroconversion and prolonged viral shedding as a consequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Consequently, their exclusion and, in particular, the exclusion of patients receiving systemic anti-cancer therapies, from the registry trials of the 5 approved COVID-19 vaccines raises questions about the efficacy and safety of SARS-CoV-2 vaccination in this patient population. In addition, whilst the change in the UKs dosing interval to 12-weeks aimed to maximise population coverage, it is unclear whether this strategy is appropriate for cancer patients and those on systemic anti-cancer therapies.\n\nAdded value of this studyWe report that the RNA-based SARS-CoV-2 BNT162b2 vaccine administered in cancer patients was well tolerated, and we provide first insights into both antibody and T cell responses to the vaccine in an immunocompromised patient population.\n\nImplications of all the available evidenceIn cancer patients, one dose of 30ug of BNT162b2 yields poor vaccine efficacy, as measured by seroconversion rates, viral neutralisation capacity and T cell responses, at 3- and 5-weeks following the first inoculum. Patients with solid cancers exhibited a significantly greater response following a booster at 21-days. These data support prioritisation of cancer patients for an early (21-day) second dose of the BNT162b2 vaccine. Given the globally poor responses to vaccination in patients with haematological cancers, post-vaccination serological testing, creation of herd immunity around these patients using a strategy of ring vaccination, and careful follow-up should be prioritised.", - "rel_num_authors": 41, - "rel_authors": [ - { - "author_name": "Leticia Monin-Aldama", - "author_inst": "The Francis Crick Institute, London, UK." - }, - { - "author_name": "Adam G. Laing", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, Kings College London, London, UK." - }, - { - "author_name": "Miguel Munoz-Ruiz", - "author_inst": "The Francis Crick Institute, London, UK." - }, - { - "author_name": "Duncan R. McKenzie", - "author_inst": "The Francis Crick Institute, London, UK." - }, - { - "author_name": "Irene del Molino del Barrio", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, Kings College London, London, UK / UCL Cancer Institute, University College " - }, - { - "author_name": "Thanussuyah Alaguthurai", - "author_inst": "Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Kings College London, London, UK / Breast Cancer Now Research Unit, Kings College Londo" - }, - { - "author_name": "Clara Domingo Vila", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, Kings College London, London, UK." - }, - { - "author_name": "Thomas S. Hayday", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, Kings College London, London, UK." - }, - { - "author_name": "Carl Graham", - "author_inst": "Department of Infectious Diseases, School of Immunology & Microbial Sciences, Kings College London, London, UK" - }, - { - "author_name": "Jeffrey Seow", - "author_inst": "Department of Infectious Diseases, School of Immunology & Microbial Sciences, Kings College London, London, UK" - }, - { - "author_name": "Sultan Abdul-Jawad", - "author_inst": "Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Kings College London, London, UK." - }, - { - "author_name": "Shraddha Kamdar", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK / UCL Cancer Institute, University Colleg" - }, - { - "author_name": "Elizabeth Harvey-Jones", - "author_inst": "Breast Cancer Now Research Unit, Kings College London, London, UK" - }, - { - "author_name": "Rosalind Graham", - "author_inst": "Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Kings College London, London, UK." - }, - { - "author_name": "Jack Cooper", - "author_inst": "Guys and St Thomas NHS Foundation Trust, London, UK" - }, - { - "author_name": "Muhammad Khan", - "author_inst": "Guys and St Thomas NHS Foundation Trust, London, UK" - }, - { - "author_name": "Jennifer Vidler", - "author_inst": "Department of Haematological Medicine, Kings College Hospital, London, UK" - }, - { - "author_name": "Helen Kakkassery", - "author_inst": "Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Kings College London, London, UK." - }, - { - "author_name": "Shubhankar Sinha", - "author_inst": "Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Kings College London, London, UK." - }, - { - "author_name": "Richard Davis", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK / UCL Cancer Institute, University Colleg" - }, - { - "author_name": "Liane Dupont", - "author_inst": "Breast Cancer Now Research Unit, Kings College London, London, UK" - }, - { - "author_name": "Isaac Francos Quijorna", - "author_inst": "Regeneration Group, Wolfson Centre for Age-Related Diseases, IoPPN, Kings College London, London, UK." - }, - { - "author_name": "Puay Lee", - "author_inst": "The Francis Crick Institute, London, UK." - }, - { - "author_name": "Josephine Eum", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK." - }, - { - "author_name": "Maria Conde Poole", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK." - }, - { - "author_name": "Magdalene Joseph", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK." - }, - { - "author_name": "Daniel Davies", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK." - }, - { - "author_name": "Yin Wu", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK / Comprehensive Cancer Centre, School of" - }, - { - "author_name": "Ana Montes", - "author_inst": "Guys and St Thomas NHS Foundation Trust, London, UK" - }, - { - "author_name": "Mark Harries", - "author_inst": "Guys and St Thomas NHS Foundation Trust, London, UK" - }, - { - "author_name": "Anne Rigg", - "author_inst": "Guys and St Thomas NHS Foundation Trust, London, UK" - }, - { - "author_name": "James Spicer", - "author_inst": "Guys and St Thomas NHS Foundation Trust, London, UK" - }, - { - "author_name": "Michael H. Malim", - "author_inst": "Department of Infectious Diseases, School of Immunology & Microbial Sciences, Kings College London, London, UK" - }, - { - "author_name": "Paul Fields", - "author_inst": "Guys and St Thomas NHS Foundation Trust, London, UK / Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Kings College London, London, UK." - }, - { - "author_name": "Piers Patten", - "author_inst": "The Francis Crick Institute, London, UK / Department of Haematological Medicine, Kings College Hospital, London, UK" - }, - { - "author_name": "Francesca Di Rosa", - "author_inst": "Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy." - }, - { - "author_name": "Sophie Papa", - "author_inst": "Guys and St Thomas NHS Foundation Trust, London, UK / Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Kings College London, London, UK." - }, - { - "author_name": "Tim Tree", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK." - }, - { - "author_name": "Katie Doores", - "author_inst": "Department of Infectious Diseases, School of Immunology & Microbial Sciences, Kings College London, London, UK" - }, - { - "author_name": "Adrian C. Hayday", - "author_inst": "The Francis Crick Institute, London, UK / Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK" - }, - { - "author_name": "Sheeba Irshad", - "author_inst": "Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Kings College London, London, UK / Breast Cancer Now Research Unit, Kings College Londo" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2021.03.15.21253598", "rel_title": "U.S. adolescents' mental health and COVID-19-related changes in technology use, Fall 2020", @@ -873994,6 +875586,97 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.15.435496", + "rel_title": "Design and proof-of-concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain", + "rel_date": "2021-03-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.15.435496", + "rel_abs": "Development of effective vaccines against Coronavirus Disease 2019 (COVID-19) is a global imperative. Rapid immunization of the world human population against a widespread, continually evolving, and highly pathogenic virus is an unprecedented challenge, and many different vaccine approaches are being pursued to meet this task. Engineered filamentous bacteriophage (phage) have unique potential in vaccine development due to their inherent immunogenicity, genetic plasticity, stability, cost-effectiveness for large-scale production, and proven safety profile in humans. Herein we report the design, development, and initial evaluation of targeted phage-based vaccination approaches against Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) by using dual ligand peptide-targeted phage and adeno-associated virus/phage (AAVP) particles. Towards a unique phage- and AAVP-based dual-display candidate approach, we first performed structure-guided antigen design to select six solvent-exposed epitopes of the SARS-CoV-2 spike (S) protein for display on the recombinant major capsid coat protein pVIII. Targeted phage particles carrying one of these epitopes induced a strong and specific humoral response. In an initial experimental approach, when these targeted phage particles were further genetically engineered to simultaneously display a ligand peptide (CAKSMGDIVC) on the minor capsid protein pIII, which enables receptor-mediated transport of phage particles from the lung epithelium into the systemic circulation (termed \"dual-display\"), they enhanced a systemic and specific spike (S) protein-specific antibody response upon aerosolization into the lungs of mice. In a second line of investigation, we engineered targeted AAVP particles to deliver the entire S protein gene under the control of a constitutive cytomegalovirus (CMV) promoter, which induced tissue-specific transgene expression stimulating a systemic S protein-specific antibody response. As proof-of-concept preclinical experiments, we show that targeted phage- and AAVP-based particles serve as robust yet versatile enabling platforms for ligand-directed immunization and promptly yield COVID-19 vaccine prototypes for further translational development.\n\nSignificanceThe ongoing COVID-19 global pandemic has accounted for over 2.5 million deaths and an unprecedented impact on the health of mankind worldwide. Over the past several months, while a few COVID-19 vaccines have received Emergency Use Authorization and are currently being administered to the entire human population, the demand for prompt global immunization has created enormous logistical challenges--including but not limited to supply, access, and distribution--that justify and reinforce the research for additional strategic alternatives. Phage are viruses that only infect bacteria and have been safely administered to humans as antibiotics for decades. As experimental proof-of-concept, we demonstrated that aerosol pulmonary vaccination with lung-targeted phage particles that display short epitopes of the S protein on the capsid as well as preclinical vaccination with targeted AAVP particles carrying the S protein gene elicit a systemic and specific immune response against SARS-CoV-2 in immunocompetent mice. Given that targeted phage- and AAVP-based viral particles are sturdy yet simple to genetically engineer, cost-effective for rapid large-scale production in clinical grade, and relatively stable at room temperature, such unique attributes might perhaps become additional tools towards COVID-19 vaccine design and development for immediate and future unmet needs.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Daniela I. Staquicini", + "author_inst": "Rutgers Cancer Institute of New Jersey" + }, + { + "author_name": "Fenny H. F. Tang", + "author_inst": "Rutgers Cancer Institute of New Jersey" + }, + { + "author_name": "Christopher Markosian", + "author_inst": "Rutgers Cancer Institute of New Jersey" + }, + { + "author_name": "Virginia J. Yao", + "author_inst": "Rutgers Cancer Institute of New Jersey" + }, + { + "author_name": "Fernanda I. Staquicini", + "author_inst": "Rutgers Cancer Institute of New Jersey" + }, + { + "author_name": "Esteban Dodero Rojas", + "author_inst": "Rice University" + }, + { + "author_name": "Vinicius G. Contessoto", + "author_inst": "Rice University" + }, + { + "author_name": "Deodate Davis", + "author_inst": "Rutgers Cancer Institute of New Jersey" + }, + { + "author_name": "Nazia Habib", + "author_inst": "Rutgers Cancer Institute of New Jersey" + }, + { + "author_name": "Tracey L. Smith", + "author_inst": "Rutgers Cancer Institute of New Jersey" + }, + { + "author_name": "Natalie Bruiners", + "author_inst": "Rutgers University" + }, + { + "author_name": "Richard L. Sidman", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Maria L. Gennaro", + "author_inst": "Rutgers University" + }, + { + "author_name": "Steven K. Libutti", + "author_inst": "Rutgers Cancer Institute of New Jersey" + }, + { + "author_name": "Paul C. Whitford", + "author_inst": "Northeastern University" + }, + { + "author_name": "Stephen K. Burley", + "author_inst": "Rutgers Cancer Institute of New Jersey" + }, + { + "author_name": "Jos\u00e9 Nelson Onuchic", + "author_inst": "Rice University" + }, + { + "author_name": "Wadih Arap", + "author_inst": "Rutgers Cancer Institute of New Jersey" + }, + { + "author_name": "Renata Pasqualini", + "author_inst": "Rutgers Cancer Institute of New Jersey" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.03.16.435654", "rel_title": "DNA spike-ins enable confident interpretation of SARS-CoV-2 genomic data from amplicon-based sequencing", @@ -875781,65 +877464,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2021.03.15.435309", - "rel_title": "One-shot identification of SARS-CoV-2 S RBD escape mutants using yeast screening", - "rel_date": "2021-03-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.15.435309", - "rel_abs": "The potential emergence of SARS-CoV-2 Spike (S) escape mutants is a threat to reduce the efficacy of existing vaccines and neutralizing antibody (nAb) therapies. An understanding of the antibody/S escape mutations landscape is urgently needed to preemptively address this threat. Here we describe a rapid method to identify escape mutants for nAbs targeting the S receptor binding site. We identified escape mutants for five nAbs, including three from the public germline class VH3-53 elicited by natural COVID-19 infection. Escape mutations predominantly mapped to the periphery of the ACE2 recognition site on the RBD with K417, D420, Y421, F486, and Q493 as notable hotspots. We provide libraries, methods, and software as an openly available community resource to accelerate new therapeutic strategies against SARS-CoV-2.\n\nOne Sentence SummaryWe present a facile method to identify antibody escape mutants on SARS-CoV-2 S RBD.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Irene Francino Urdaniz", - "author_inst": "University of Colorado, Boulder" - }, - { - "author_name": "Paul J Steiner", - "author_inst": "University of Colorado, Boulder" - }, - { - "author_name": "Monica Kirby", - "author_inst": "University of Colorado, Boulder" - }, - { - "author_name": "Fangzhu Zhao", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Cyrus M Haas", - "author_inst": "University of Colorado, Boulder" - }, - { - "author_name": "Shawn Barman", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Emily R Rhodes", - "author_inst": "University of Colorado, Boulder" - }, - { - "author_name": "Linghang Peng", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Kayla Sprenger", - "author_inst": "University of Colorado, Boulder" - }, - { - "author_name": "Joseph Jardine", - "author_inst": "International AIDS Vaccine Initiative" - }, - { - "author_name": "Timothy A Whitehead", - "author_inst": "University of Colorado, Boulder" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.03.14.435322", "rel_title": "Effects of Mutations in the Receptor-Binding Domain of SARS-CoV-2 Spike on its Binding Affinity to ACE2 and Neutralizing Antibodies Revealed by Computational Analysis", @@ -876204,6 +877828,93 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.03.13.435221", + "rel_title": "Clomipramine suppresses ACE2-mediated SARS-CoV-2 entry", + "rel_date": "2021-03-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.13.435221", + "rel_abs": "Myocardial damage caused by the newly emerged coronavirus (SARS-CoV-2) infection is one of key determinants of COVID-19 severity and mortality. SARS-CoV-2 entry to host cells are initiated by binding with its receptor, angiotensin converting enzyme (ACE) 2, and the ACE2 abundance is thought to reflect the susceptibility to infection. Here, we found that clomipramine, a tricyclic antidepressant, potently inhibits SARS-CoV-2 infection and metabolic disorder in human iPS-derived cardiomyocytes. Among 13 approved drugs that we have previously identified as potential inhibitor of doxorubicin-induced cardiotoxicity, clomipramine showed the best potency to inhibit SARS-CoV-2 spike glycoprotein pseudovirus-stimulated ACE2 internalization. Indeed, SARS-CoV-2 infection to human iPS-derived cardiomyocytes (iPS-CMs) and TMPRSS2-expressing VeroE6 cells were dramatically suppressed even after treatment with clomipramine. Furthermore, the combined use of clomipramine and remdesivir was revealed to synergistically suppress SARS-CoV-2 infection. Our results will provide the potentiality of clomipramine for the breakthrough treatment of severe COVID-19.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Yuri Kato", + "author_inst": "Graduate School of Pharmaceutical Sciences, Kyushu University" + }, + { + "author_name": "Shigeru Yamada", + "author_inst": "Division of Pharmacology, National Institute of Health Sciences" + }, + { + "author_name": "Kazuhiro Nishiyama", + "author_inst": "Graduate School of Pharmaceutical Sciences, Kyushu University" + }, + { + "author_name": "Ayano Satsuka", + "author_inst": "Division of Pharmacology, National Institute of Health Sciences" + }, + { + "author_name": "Suyong Re", + "author_inst": "Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition" + }, + { + "author_name": "Daiki Tomokiyo", + "author_inst": "Graduate School of Pharmaceutical Sciences, Kyushu University" + }, + { + "author_name": "Jae Man Lee", + "author_inst": "Laboratory of Creative Science for Insect Industries, Faculty of Agriculture, Kyushu University" + }, + { + "author_name": "Tomohiro Tanaka", + "author_inst": "National Institute for Physiological Sciences & Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences" + }, + { + "author_name": "Akiyuki Nishimura", + "author_inst": "National Institute for Physiological Sciences & Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences" + }, + { + "author_name": "Kenzo Yonemitsu", + "author_inst": "Division of Biomedical Food Research, National Institute of Health Sciences" + }, + { + "author_name": "Hiroshi Asakura", + "author_inst": "Division of Biomedical Food Research, National Institute of Health Sciences" + }, + { + "author_name": "Yuko Ibuki", + "author_inst": "Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka" + }, + { + "author_name": "Yumiko Imai", + "author_inst": "National Institutes of Biomedical Innovation Health and Nutrition" + }, + { + "author_name": "Noriho Kamiya", + "author_inst": "Department of Applied Chemistry, Graduate School of Engineering & Division of Biotechnology, Center for Future Chemistry, Kyushu University" + }, + { + "author_name": "Kenji Mizuguchi", + "author_inst": "National Institutes of Biomedical Innovation, Health and Nutrition & Institute for Protein Research, Osaka University" + }, + { + "author_name": "Takahiro Kusakabe", + "author_inst": "Laboratory of Insect Genome Science, Faculty of Agriculture, Kyushu University" + }, + { + "author_name": "Yasunari Kanda", + "author_inst": "Division of Pharmacology, National Institute of Health Sciences" + }, + { + "author_name": "Motohiro Nishida", + "author_inst": "Graduate School of Pharmaceutical Sciences, Kyushu University & National Institute for Physiological Sciences & Exploratory Research Center on Life and Living S" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2021.03.12.21253373", "rel_title": "A randomized, double-blind, controlled trial of convalescent plasma in adults with severe COVID-19", @@ -878195,49 +879906,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.03.09.21253186", - "rel_title": "Forecasting the COVID-19 epidemic integrating symptom search behavior: an infodemiology study", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21253186", - "rel_abs": "BackgroundPrevious studies have suggested associations between trends of web searches and COVID-19 traditional metrics. It remains unclear whether models incorporating trends of digital searches lead to better predictions.\n\nMethodsAn open-access web application was developed to evaluate Google Trends and traditional COVID-19 metrics via an interactive framework based on principal components analysis (PCA) and time series modelling. The app facilitates the analysis of symptom search behavior associated with COVID-19 disease in 188 countries. In this study, we selected data of eight countries as case studies to represent all continents. PCA was used to perform data dimensionality reduction, and three different time series models (Error Trend Seasonality, Autoregressive integrated moving average, and feed-forward neural network autoregression) were used to predict COVID-19 metrics in the upcoming 14 days. The models were compared in terms of prediction ability using the root-mean-square error (RMSE) of the first principal component (PC1). Predictive ability of models generated with both Google Trends data and conventional COVID-19 metrics were compared with those fitted with conventional COVID-19 metrics only.\n\nFindingsThe degree of correlation and the best time-lag varied as a function of the selected country and topic searched; in general, the optimal time-lag was within 15 days. Overall, predictions of PC1 based on both searched termed and COVID-19 traditional metrics performed better than those not including Google searches (median [IQR]: 1.43 [0.74-2.36] vs. 1.78 [0.95-2.88], respectively), but the improvement in prediction varied as a function of the selected country and timeframe. The best model varied as a function of country, time range, and period of time selected. Models based on a 7-day moving average led to considerably smaller RMSE values as opposed to those calculated with raw data (median [IQR]: 0.74 [0.47-1.22] vs. 2.15 [1.55-3.89], respectively).\n\nInterpretationThe inclusion of digital online searches in statistical models may improve the prediction of the COVID-19 epidemic.\n\nFundingEOSCsecretariat.eu has received funding from the European Unions Horizon Programme call H2020-INFRAEOSC-05-2018-2019, grant Agreement number 831644.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Alessandro Rabiolo", - "author_inst": "Gloucestershire Hospitals NHS Foundation Trust, Cheltenham, United Kingdom" - }, - { - "author_name": "Eugenio Alladio", - "author_inst": "Department of Chemistry, University of Turin, Turin, Italy" - }, - { - "author_name": "Esteban Morales", - "author_inst": "Jules Stein Eye Institute, David Geffen School of Medicine, UCLA, Los Angeles, USA" - }, - { - "author_name": "Andrew Ian McNaught", - "author_inst": "Gloucestershire Hospitals NHS Foundation Trust, Cheltenham, United Kingdom" - }, - { - "author_name": "Francesco Bandello", - "author_inst": "(5)\tDepartment of Ophthalmology, Vita-Salute University, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy" - }, - { - "author_name": "Abdelmonem A Afifi", - "author_inst": "Department of Biostatistics, Fielding School of Public Health, UCLA, Los Angeles, USA" - }, - { - "author_name": "Alessandro Marchese", - "author_inst": "Department of Ophthalmology, Vita-Salute University, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.03.08.21252883", "rel_title": "Outcome of Different Therapeutic Interventions in Mild COVID-19 Patients in a Single OPD Clinic of West Bengal: A Retrospective study", @@ -878474,6 +880142,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.08.21253075", + "rel_title": "Evolutionary and phenotypic characterization of spike mutations in a new SARS-CoV-2 Lineage reveals two Variants of Interest", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21253075", + "rel_abs": "Molecular epidemiology of SARS-CoV-2 aims to monitor the appearance of new variants with the potential to change the virulence or transmissibility of the virus. During the first year of SARS-CoV-2 evolution, numerous variants with possible public health impact have emerged. We have detected two mutations in the Spike protein at amino acid positions 1163 and 1167 that have appeared independently multiple times in different genetic backgrounds, indicating they may increase viral fitness. Interestingly, the majority of these sequences appear in transmission clusters, with the genotype encoding mutations at both positions increasing in frequency more than single-site mutants. This genetic outcome that we denote as Lineage B.1.177.637, belongs to clade 20E and includes 12 additional single nucleotide polymorphisms but no deletions with respect to the reference genome (first sequence in Wuhan). B.1.177.637 appeared after the first wave of the epidemic in Spain, and subsequently spread to eight additional countries, increasing in frequency among sequences in public databases. Positions 1163 and 1167 of the Spike protein are situated in the HR2 domain, which is implicated in the fusion of the host and viral membranes. To better understand the effect of these mutations on the virus, we examined whether B.1.177.637 altered infectivity, thermal stability, or antibody sensitivity. Unexpectedly, we observed reduced infectivity of this variant relative to the ancestral 20E variant in vitro while the levels of viral RNA in nasopharyngeal swabs did not vary significantly. In addition, we found the mutations do not impact thermal stability or antibody susceptibility in vaccinated individuals but display a moderate reduction in sensitivity to neutralization by convalescent sera from early stages of the pandemic. Altogether, this lineage could be considered a Variant of Interest (VOI), we denote VOI1163.7. Finally, we detected a sub-cluster of sequences within VOI1163.7 that have acquired two additional changes previously associated with antibody escape and it could be identified as VOI1163.7.V2. Overall, we have detected the spread of a new Spike variant that may be advantageous to the virus and whose continuous transmission poses risks by the acquisition of additional mutations that could affect pre-existing immunity.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Paula Ruiz-Rodriguez", + "author_inst": "I2SysBio, University of Valencia-CSIC, FISABIO Joint Research Unit Infection and Public Health, Valencia" + }, + { + "author_name": "Clara Frances-Gomez", + "author_inst": "I2SysBio, University of Valencia-CSIC, FISABIO Joint Unit, Valencia, Spain" + }, + { + "author_name": "\u00c1lvaro Chiner-Oms", + "author_inst": "Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain" + }, + { + "author_name": "Mariana G. L\u00f3pez", + "author_inst": "Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain" + }, + { + "author_name": "Santiago Jim\u00e9nez-Serrano", + "author_inst": "Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain" + }, + { + "author_name": "Irving Cancino-Mu\u00f1oz", + "author_inst": "Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain" + }, + { + "author_name": "Paula Ruiz-Hueso", + "author_inst": "Sequencing and Bioinformatic Service of FISABIO (Valencian Region Foundation for the Promotion of Health and Biomedical Research), Valencia, Spain" + }, + { + "author_name": "Manuela Torres-Puente", + "author_inst": "Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain" + }, + { + "author_name": "Maria Alma Bracho", + "author_inst": "I2SysBio, University of Valencia-CSIC, FISABIO Joint Unit, Valencia, Spain" + }, + { + "author_name": "Giuseppe D'Auria", + "author_inst": "Sequencing and Bioinformatic Service of FISABIO (Valencian Region Foundation for the Promotion of Health and Biomedical Research), Valencia, Spain" + }, + { + "author_name": "Ll\u00facia Martinez-Priego", + "author_inst": "Sequencing and Bioinformatic Service of FISABIO (Valencian Region Foundation for the Promotion of Health and Biomedical Research), Valencia, Spain" + }, + { + "author_name": "Manuel Guerreiro", + "author_inst": "Hematology Department, Hospital Universitari i Politecnic la Fe, Valencia, Spain" + }, + { + "author_name": "Marta Montero-Alonso", + "author_inst": "Infectious Diseases Unit, Hospital Universitari i Politecnic la Fe, Valencia, Spain." + }, + { + "author_name": "Maria Dolores Gomez", + "author_inst": "Microbiology Department, Hospital Universitari i Politecnic La Fe, Valencia, Spain" + }, + { + "author_name": "Jose Luis Pi\u00f1ana", + "author_inst": "Hematology Service, Hospital Clinico Universitario, Institute for Research INCLIVA, Valencia, Spain." + }, + { + "author_name": "- SeqCOVID-SPAIN consortium", + "author_inst": "" + }, + { + "author_name": "Fernando Gonz\u00e1lez-Candelas", + "author_inst": "I2SysBio, University of Valencia-CSIC, FISABIO Joint Unit, Valencia, Spain" + }, + { + "author_name": "I\u00f1aki Comas", + "author_inst": "Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain" + }, + { + "author_name": "Alberto Marina", + "author_inst": "Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain" + }, + { + "author_name": "Ron Geller", + "author_inst": "I2SysBio, University of Valencia-CSIC, FISABIO Joint Unit, Valencia, Spain" + }, + { + "author_name": "Mireia Coscolla", + "author_inst": "I2SysBio, University of Valencia-CSIC, FISABIO Joint Unit, Valencia, Spain" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.08.21252788", "rel_title": "SARS-CoV-2 antibody prevalence and determinants of six ethnic groups living in Amsterdam, the Netherlands: a population-based cross-sectional study, June-October 2020", @@ -880001,53 +881768,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.09.21253242", - "rel_title": "Environmental drivers of SARS-CoV-2 lineage B.1.1.7 transmission in England, October to December 2020", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21253242", - "rel_abs": "Previous work has shown that environment affects SARS-CoV-2 transmission, but it is unclear whether emerging strains show similar responses. Here we show that, like other SARS-CoV-2 strains, lineage B.1.1.7 spread with greater transmission in colder and more densely populated parts of England. However, we also find evidence of B.1.1.7 having a transmission advantage at warmer temperatures compared to other strains. This implies that spring and summer conditions are unlikely to slow B.1.1.7s invasion in Europe and across the Northern hemisphere - an important consideration for public health interventions.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Thomas P Smith", - "author_inst": "Imperial College London" - }, - { - "author_name": "Ilaria Dorigatti", - "author_inst": "Imperial College London" - }, - { - "author_name": "Swapnil Mishra", - "author_inst": "Imperial College London" - }, - { - "author_name": "Erik Volz", - "author_inst": "Imperial College London" - }, - { - "author_name": "Patrick G T Walker", - "author_inst": "Imperial College London" - }, - { - "author_name": "Manon Ragonnet-Cronin", - "author_inst": "Imperial College London" - }, - { - "author_name": "Michael Tristem", - "author_inst": "Imperial College London" - }, - { - "author_name": "William D Pearse", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.09.21252822", "rel_title": "Genomic epidemiology of SARS-CoV-2 in the United Arab Emirates reveals novel virus mutation, patterns of co-infection and tissue specific host responses", @@ -880348,6 +882068,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.03.10.21253266", + "rel_title": "Acceptability of contact management and care of simple cases of COVID-19 at home: a mixed-method study in Senegal", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21253266", + "rel_abs": "IntroductionIn mid-2020, due to the health system challenges from increased COVID-19 cases, the Ministry of Health and Social Action in Senegal opted for contact management and care of simple cases at home. The studys objective was to determine the acceptability of contact management, home care of simple cases of COVID-19, and its associated factors.\n\nMethodThis was a sequential mixed-method study. We collected data from June 11, 2020, to July 10, 2020, for the quantitative survey (N=813) and from August 24 to September 16, 2020, for the qualitative survey (N=30). We carried out a sampling strategy using marginal quotas at the national level. We collected data using a structured questionnaire in a telephone interview for the quantitative survey and using an interview guide formulated from the quantitative surveys initial results for the qualitative data. We assessed acceptability using binomial logistic regression combined with content analysis.\n\nResultsThe care of simple cases of COVID-19 at home was well accepted (78.5%). This result was justified for some (saturation of the health system) but not for others (risk of contamination). The use of home contact management was less accepted (51.4%), with risk limitation as the main reason given. The acceptability of home-based care for simple cases was positively associated with knowledge of the modes of transmission of the virus (ORaj: 1.55 [95%CI: 1.04,2.28]), regular research into COVID-19 (ORaj: 2.12 [95%CI: 1.45,3.12]), belief in the existence of treatment (ORaj: 1.82 [95%CI: 1.19,2.83]), and confidence in institutional information (ORaj: 2.10 [95%CI: 1.43,3.10]). The acceptability of home-based contact management was positively associated with knowledge of the modes of transmission of the virus (ORaj: 1.77 [95%CI: 1.27,2.48]), regular research for information on COVID-19 (ORaj: 2.39 [95%CI: 1.76,3.26]), and confidence in the government in the fight against the epidemic (ORaj: 1.51 [95%CI: 1.10,2.08]).\n\nConclusionRegular information on the disease, knowledge of its mode of transmission and trust in institutions are factors in accepting COVID-19 management at the community level. Authorities should take these factors into account for better communication to improve the acceptability of home-based care.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Mouhamadou Faly Ba", + "author_inst": "Institut de sante et developpement, Universite Cheikh Anta Diop de Dakar" + }, + { + "author_name": "Valery Ridde", + "author_inst": "Institut de recherche pour le developpement" + }, + { + "author_name": "Amadou Ibra Diallo", + "author_inst": "Institut de sante et developpement, Universite Cheikh Anta Diop de Dakar" + }, + { + "author_name": "Jean Augustin Diegane Tine", + "author_inst": "Institut de sante et developpement, Universite Cheikh Anta Diop de Dakar" + }, + { + "author_name": "Babacar Kane", + "author_inst": "Institut de sante et developpement, Universite Cheikh Anta Diop de Dakar" + }, + { + "author_name": "Ibrahima Gaye", + "author_inst": "Institut de sante et developpement, Universite Cheikh Anta Diop de Dakar" + }, + { + "author_name": "Zoumana Traore", + "author_inst": "CloudlyYours" + }, + { + "author_name": "Emmanuel Bonnet", + "author_inst": "Institut de recherche pour le developpement" + }, + { + "author_name": "Adama Faye", + "author_inst": "Institut de sante et developpement, Universite Cheikh Anta Diop de Dakar" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.10.21252748", "rel_title": "An Extended COVID-19 Epidemiological Model with Vaccination and Multiple Interventions for Controlling COVID-19 Outbreaks in the UK", @@ -881635,41 +883406,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.11.21252969", - "rel_title": "Reducing the Cost of Rapid Antigen Tests through Swab Pooling and Extraction in a Device", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21252969", - "rel_abs": "The COVID-19 pandemic places a significant stress on the viral testing capabilities of many countries. The value of rapid point-of-care (PoC) antigen tests is becoming increasingly clear, but implementing frequent large scale testing is costly. We have developed an inexpensive device for pooling swabs, extracting specimens, and detecting viral antigens with a commercial lateral flow assay detecting the nucleocapsid protein of SARS-CoV-2 as antigen. The holder of the device can be produced locally through 3D printing. The extraction and the elution can be performed with the entire set-up encapsulated in a transparent bag, minimizing the risk of infection for the operator. With 6 swabs holding approx. 0.1 mL specimen each and 0.35 mL extraction buffer, 43{+/-}6 % (n= 8) of the signal for an individual extraction of a positive control standard was obtained. Image analysis still showed a signal-to-noise ratio of [≥] 7 upon further eight-fold dilution. Our current total cost of materials is below $ 2 per tested person or 20% of our cost for an individual PoC test. These findings suggest that pooling can make frequent testing more affordable for schools, universities and other institutions, without decreasing sensitivity to an unacceptable level. Further validation of the method is required.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Tim Berking", - "author_inst": "Institute of Organic Chemistry, University of Stuttgart" - }, - { - "author_name": "Sabrina G Lorenz", - "author_inst": "Institute of Organic Chemistry, University of Stuttgart" - }, - { - "author_name": "Alexander Ulrich", - "author_inst": "Institute of Organic Chemistry, University of Stuttgart" - }, - { - "author_name": "Joachim Greiner", - "author_inst": "Institute of Aircraft Design, University of Stuttgart" - }, - { - "author_name": "Clemens Richert", - "author_inst": "University of Stuttgart" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.11.21253226", "rel_title": "Analysis of Accumulated SARS-CoV-2 Seroconversion in North Carolina: The COVID-19 Community Research Partnership", @@ -881922,6 +883658,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.10.21253330", + "rel_title": "Characterizing the COVID-19 illness experience to inform the study of post-acute sequalae and recovery: a qualitative study", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21253330", + "rel_abs": "We aimed to characterize the variability in the illness experience and recovery process from COVID-19. We conducted in-depth individual interviews with participants enrolled in the Long-term Immunological Impact of Novel Coronavirus (LIINC) cohort study in San Francisco, California from June through October of 2020. Participants were adults who had a previously confirmed positive SARV-CoV-2 nucleic acid amplification test result, had recovered or were recovering from acute infection, and underwent serial evaluations at our clinical research center. We purposefully sampled 24 English- and Spanish-speaking adults with asymptomatic, mild and severe symptomatic infection, including those who were hospitalized, and those with HIV co-infection. Half of our sample (50.0%) identified as Latinx/Hispanic and most of the participants were men (62.5%). We used thematic analysis to characterize the illness experience, recovery process, and mental health impact of experiencing COVID-19 and present clinical data for each participant. Emergent themes were: (1) across symptom profiles and severity, experiencing COVID-19 was associated with psychological distress, (2) among participants with symptomatic infection, the illness experience was characterized by uncertainty in terms of managing symptoms and recovery, and (3) despite wide-ranging illness experiences, participants shared many common characteristics, including health information-seeking behavior facilitated by access to medical care, and uncertainty regarding the course of their illness and recovery. COVID-19 was associated with elevated levels of psychological distress, regardless of symptoms.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Edda I. Santiago-Rodriguez", + "author_inst": "University of Californina, San Francisco" + }, + { + "author_name": "Andres Maiorana", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Michael J Peluso", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Rebecca Hoh", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Viva Tai", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Emily A. Fehrman", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Yanel Hernandez", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Leonel Torres", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Matthew A. Spinelli", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Monica Gandhi", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "J. Daniel Kelly", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Jeffrey N. Martin", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Timothy J. Henrich", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Steven G Deeks", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "John A Sauceda", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.10.21253064", "rel_title": "Evaluation of anti-SARS-CoV-2 antibody testing in asymptomatic or mild COVID-19 patients in outbreak on a cruise ship", @@ -883385,37 +885196,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.10.21253324", - "rel_title": "Dynamic versus Continuous Interventions: Optimizing Lockdown Policies for COVID-19", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21253324", - "rel_abs": "In the context of the ongoing COVID-19 pandemic, while millions of people await the administration of a vaccine, social distancing remains the leading approach towards the effect commonly known as \"flattening the curve\" of infections. Over the last year, governmental administrations throughout the globe have implemented various lockdown policies in hopes of slowing down the transmission of the disease. However, the current lack of consensus on when and how these policies should be implemented reflects the need for further studies regarding these questions. In this paper, we tackle the issue of lockdown policy management, in particular in terms of lockdown placement (how often, when, and how long these periods should be), in order to minimize the peak of infections in a specific population. We introduce a novel combination of classic mathematical disease modelling using the equation-based SEIR model, and Evolutionary Strategies (ES) for optimizing the peak of infections. The method is evaluated using data collected in different countries, and a particular focus is placed on the study of the effect of specific model parameters on lockdown optimization, such as the transmission rate ({beta}), of which 4 alternative modelling functions have been proposed and analyzed. Our results indicate that this transmission rate parameter significantly influences the resulting optimal strategies. In particular, the presence of a gradual decay of the rate of transmission during lockdown leads to longer, more sparsely placed confinement periods while an abrupt, instantaneous drop in the amount of contacts per person favors shorter but more frequent lockdowns. Although these results are limited by the scope of action provided by the simplicity of the SEIR model, they suggest that the influence of the evolution of the rate of transmission along the disease should be assessed in further studies with alternative optimization strategies (agent-based) and models (SEIRSHUD).", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Kaan Akinci", - "author_inst": "Cross Labs" - }, - { - "author_name": "Javier Fdez", - "author_inst": "Cross Labs" - }, - { - "author_name": "Elena Pena-Tapia", - "author_inst": "Cross Labs" - }, - { - "author_name": "Olaf Witkowski", - "author_inst": "Cross Labs" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.11.21253364", "rel_title": "Analysis of severe outcomes associated with the SARS-CoV-2 Variant of Concern 202012/01 in England using ICNARC Case Mix Programme and QResearch databases.", @@ -883608,6 +885388,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.12.21253452", + "rel_title": "Google Trends as a method to predict new COVID-19 cases", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.12.21253452", + "rel_abs": "In this paper, we develop a method that can detect and predict the emergence of new cases of COVID-19 at an early stage. With this method, we try to lay the empirical basis for the development of the model of digital monitoring and prediction of the occurrence of new cases of COVID-19 in Croatia, relying on the analytical tool Google Trends (GT).\n\nResultsIn Croatia search activities using GT for terms such as PCR +Covid\", \"PCR + test\", and symptoms \"cough + corona\", \"pneumonia + corona\"; \"muscle pain + corona\" correlate strongly with officially reported cases of the disease. Google Trends tools are suitable for predicting the emergence of new COVID-19 cases in Croatia, and that the data collected by this method correlate with official data.\n\nThe benefit of this method is reliable estimates that can enable public health officials to prepare and better respond to the possible return of a pandemic in certain parts of the country. If a region experiences an early, sharp increase in Covid-19-like-illness Google searches, it may be possible to focus additional resources on that region to identify the etiology of the outbreak, providing extra medical capacity or raising local media awareness as necessary.\n\nBecause the relative frequency of certain queries is highly correlated with the percentage of physician visits in which a patient presents with Covid-19 symptoms, this method can serve as an early alarm to predict the emergence of new cases of COVID-19 in the specific area in Croatia.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Tado Juric", + "author_inst": "Catholic University of Croatia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.03.12.21253440", "rel_title": "Negative SARS-CoV-2 PCR or rapid antigen test result and the subsequent risk of being infectious: a mathematical simulation study", @@ -884974,45 +886773,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2021.03.09.21253212", - "rel_title": "Exploring the short-term role of particulate matter in the COVID-19 outbreak in USA cities", - "rel_date": "2021-03-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21253212", - "rel_abs": "The role of particulate matter (PM) in the COVID-19 pandemic is currently being discussed by the scientific community. Long-term (years) exposure to PM is known to affect human health by increasing susceptibility to viral infections as well as to the development of respiratory and cardiovascular symptoms. In the short-term (days to months), PM has been suggested to assist airborne viral transmission. However, confounding factors such as urban mobility prevent causal conclusions. In this study, we explore short-term relationships between PM concentrations and the evolution of COVID-19 cases in a number of cities in the United States of America. We focus on the role of PM in facilitating viral transmission in early stages of the pandemic. We analyzed PM concentrations in two particle size ranges, < 2.5 {micro}m, and between 10 and 2.5 {micro}m (PM2.5 and PM10 respectively) as well as carbon monoxide (CO) and nitrogen dioxide (NO2). Granger causality analysis was employed to identify instantaneous and lagged effects of pollution in peaks of COVID-19 new daily cases in each location. The effect of pollution in shaping the disease spread was evaluated by correlating the logistic growth rate of accumulated cases with pollutants concentrations for a range of time lags and accumulation windows. PM2.5 shows the most significant results in Granger causality tests in comparison with the other pollutants. We found a strong and significant association between PM2.5 concentrations and the growth rate of accumulated cases between the 1st and 18th days after the report of the infection, peaking at the 8th day. By comparing results of PM2.5 with PM10, CO and NO2 we rule out confounding effects associated with mobility. We conclude that PM2.5 is not a first order effect in the cities considered; however, it plays a significant role in facilitating the COVID-19 transmission. We estimate that the growth rate of COVID-19 cases would be risen by 12.5% if PM2.5 is increased from 25 to 35 {micro}g m-3.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Leonardo Yoshiaki Kamigauti", - "author_inst": "Department of Atmospheric Sciences, University of Sao Paulo, Brazil" - }, - { - "author_name": "Gabriel Martins Palma Perez", - "author_inst": "Department of Meteorology, University of Reading, United Kingdom" - }, - { - "author_name": "Carlos Eduardo Souto-Oliveira", - "author_inst": "Department of Atmospheric Sciences, Univeristy of Sao Paulo, Brazil" - }, - { - "author_name": "Elizabeth Cowdery", - "author_inst": "Department of Earth and Environment, University of Boston, United States of America" - }, - { - "author_name": "Paulo Hilario Nascimento Saldiva", - "author_inst": "Department of Pathology, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Maria de Fatima Andrade", - "author_inst": "Department of Atmospheric Sciences, University of Sao Paulo, Sao Paulo, Brazil" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.09.21253155", "rel_title": "High-resolution epigenome analysis in nasal samples derived from children with respiratory viral infections reveals striking changes upon SARS-CoV-2 infection", @@ -885185,6 +886945,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.10.432949", + "rel_title": "Bromodomain and Extraterminal Protein Inhibitor, Apabetalone (RVX-208), Reduces ACE2 Expression and Attenuates SARS-CoV-2 Infection in vitro", + "rel_date": "2021-03-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.10.432949", + "rel_abs": "Effective therapeutics are urgently needed to counter infection and improve outcomes for patients suffering from COVID-19 and to combat this pandemic. Manipulation of epigenetic machinery to influence viral infectivity of host cells is a relatively unexplored area. The bromodomain and extraterminal (BET) family of epigenetic readers have been reported to modulate SARS-CoV-2 infection. Herein, we demonstrate apabetalone, the most clinical advanced BET inhibitor, downregulates expression of cell surface receptors involved in SARS-CoV-2 entry, including angiotensin-converting enzyme 2 (ACE2) and dipeptidyl-peptidase 4 (DPP4 or CD26) in SARS-CoV-2 permissive cells. Moreover, we show that apabetalone inhibits SARS-CoV-2 infection in vitro to levels comparable to antiviral agents. Taken together, our study supports further evaluation of apabetalone to treat COVID-19, either alone or in combination with emerging therapeutics.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=192 SRC=\"FIGDIR/small/432949v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (54K):\norg.highwire.dtl.DTLVardef@127e6c4org.highwire.dtl.DTLVardef@9f6d3aorg.highwire.dtl.DTLVardef@bbfe3borg.highwire.dtl.DTLVardef@2ffad8_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Dean Gilham", + "author_inst": "Resverlogix Corp., Calgary, AB. Canada" + }, + { + "author_name": "Audrey L Smith", + "author_inst": "Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA" + }, + { + "author_name": "Li Fu", + "author_inst": "Resverlogix Corp., Calgar, AB, Canada" + }, + { + "author_name": "Dalia Y Moore", + "author_inst": "Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA" + }, + { + "author_name": "Abenaya Muralidharan", + "author_inst": "Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA" + }, + { + "author_name": "St. Patrick M Reid", + "author_inst": "Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA" + }, + { + "author_name": "Stephanie C Stotz", + "author_inst": "Resverlogix Corp., Calgary, AB, Canada" + }, + { + "author_name": "Jan O Johansson", + "author_inst": "Resverlogix Corp., Calgary, AB, Canada" + }, + { + "author_name": "Michael Sweeney", + "author_inst": "Resverlogix Corp., Calgary, AB, Canada" + }, + { + "author_name": "Norman CW Wong", + "author_inst": "Resverlogix Corp., Calgary, AB, Canada" + }, + { + "author_name": "Ewelina Kulikowski", + "author_inst": "Resverlogix Corp., Calgary, AB, Canada" + }, + { + "author_name": "Dalia El-Gamal", + "author_inst": "Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2021.03.11.434968", "rel_title": "Low ozone concentration and negative ions for rapid SARS-CoV-2 inactivation", @@ -887075,73 +888898,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.09.434592", - "rel_title": "Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes", - "rel_date": "2021-03-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.09.434592", - "rel_abs": "There is an urgent need to develop effective interventions resistant to the evolving variants of SARS-CoV-2. Nanobodies (Nbs) are stable and cost-effective agents that can be delivered by novel aerosolization route to treat SARS-CoV-2 infections efficiently. However, it remains unknown if they possess broadly neutralizing activities against the prevalent circulating strains. We found that potent neutralizing Nbs are highly resistant to the convergent variants of concern that evade a large panel of neutralizing antibodies (Abs) and significantly reduce the activities of convalescent or vaccine-elicited sera. Subsequent determination of 9 high-resolution structures involving 6 potent neutralizing Nbs by cryoelectron microscopy reveals conserved and novel epitopes on virus spike inaccessible to Abs. Systematic structural comparison of neutralizing Abs and Nbs provides critical insights into how Nbs uniquely target the spike to achieve high-affinity and broadly neutralizing activity against the evolving virus. Our study will inform the rational design of novel pan-coronavirus vaccines and therapeutics.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Dapeng Sun", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Zhe Sang", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Jeff Kim", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Yufei Xiang", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Tomer Cohen", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Anna K Belford", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Alexis Huet", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "James F Conway", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Ji Sun", - "author_inst": "St Jude Childrens Research Hospital" - }, - { - "author_name": "Derek Taylor", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Cheng Zhang", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Wei Huang", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Yi Shi", - "author_inst": "University of Pittsburgh" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.03.09.434030", "rel_title": "Development of Equine Immunoglobulin Fragment F(ab')2 with High Neutralizing Capability against SARS-CoV-2", @@ -887630,6 +889386,109 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.04.21252167", + "rel_title": "Tocilizumab efficacy in COVID-19 patients is associated with respiratory severity-based stages", + "rel_date": "2021-03-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252167", + "rel_abs": "BackgroundTocilizumab treatment is investigated, and effectiveness in ICU-admitted COVID-19 patients has been reported. Although controversy exists regarding the efficacy of tocilizumab treatment, it has been suggested that tocilizumab might show positive results depending on patient severity status. We examined an association between tocilizumab and distinct disease severity stages.\n\nMethods and FindingsFrom March 3 to March 23 2020, 494 consecutively admitted COVID-19 patients received tocilizumab or standard treatment alone. Data were obtained retrospectively. Clinical respiratory severity (CRS) stages were defined by patient oxygenation status and were also associated to scores of WHO clinical progression scale. We categorized patients in three stages, mild/moderate CRS1 (FiSpO2<0.35; WHO score 5), moderate/severe CRS2 (FiO2=0.5/high flow mask; WHO score 6) and severe/critical CRS3 (FiO2<80%/high flow/prone position or mechanical ventilation; score>6). The primary outcome was the composite of death or ICU admission in patients of stages CRS1, CRS2, and CRS3, as well as in total patients. We also addressed mortality alone in total patients. Kaplan-Maier curves, Cox proportional regression and inverse probability weighting marginal structural models were used. We conducted the study from March 3 to April 7 2020 with broad-ranged severity patients; 167 tocilizumab-treated and 327 untreated. CRS1 patients showed no apparent benefit after treatment, while the risk of the primary outcome was greatly reduced in CRS2 treated participants ((HR=0.22; 95% CI (0.16-0.44)). Moreover, tocilizumab treatment was associated with significantly decreased CRS2 patient proportion that reached the outcome compared to non-treated controls (27.8.0% vs. 65.4%; p<0.001). Severe/critical CRS3 patients, also showed benefit after treatment (HR=0.38; 95% CI (0.16-90)), although not as robust as was that of CRS2 treated individuals. Tocilizumab was associated with reduced outcome risk in total patients (HR=0.42; 95% CI (0.26-0.66)) after CRS adjustment, but not if CRS classification was not accounted as confounding factor (HR=1.19; 95% CI (0.84-1.69)). The outcome of mortality alone upon tocilizumab treatment was significant (HR=0.58; 95% CI (0.35-0.96)) after accounting for CRS classification.\n\nConclusionsTocilizumab treatment is associated with reduced COVID-19 escalation in CRS2 patients, suggesting efficacy in moderate/severe non-ICU-admitted patients. CRS classification could represent an essential confounding factor in evaluating tocilizumab in studies of broad-ranged severity patients.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Melchor Alvarez-Mon", + "author_inst": "Department of Medicine and Medical Specialties. Alcala University. Madrid" + }, + { + "author_name": "Angel Asunsolo", + "author_inst": "Department of Surgery and Medical Social Sciences. Alcala University. Madrid. Spain" + }, + { + "author_name": "Jose Sanz", + "author_inst": "Department of Medicine and Medical Specialties. Alcala University. Madrid. Spain" + }, + { + "author_name": "Benjamin Munoz", + "author_inst": "Department of Medicine and Medical Specialties. Alcala University. Madrid. Spain" + }, + { + "author_name": "Jose Alberto Arranz-Caso", + "author_inst": "Department of Medicine and Medical Specialties. Alcala University. Madrid. Spain" + }, + { + "author_name": "Maria Novella Mena", + "author_inst": "Internal Medicine Service, University Hospital Principe de Asturias, Alcala de Henares, Madrid" + }, + { + "author_name": "Cristina Hernandez-Gutierrez", + "author_inst": "InternalMedicine Service, University Hospital Principe de Asturias, Alcala de Henares, Madrid" + }, + { + "author_name": "Jorge Navarro", + "author_inst": "Internal Medicine Service, University Hospital Principe de Asturias, Alcala de Henares, Madrid. Spain" + }, + { + "author_name": "Maria Cristina Lozano Duran", + "author_inst": "Internal Medicine Service, University Hospital Principe de Asturias, Alcala de Henares, Madrid. Spain" + }, + { + "author_name": "Juan Arevalo Serrano", + "author_inst": "Internal Medicine Service, University Hospital Principe de Asturias, Alcala de Henares, Madrid. Spain" + }, + { + "author_name": "Rocio Heche Sanchez", + "author_inst": "Internal Medicine Service, University Hospital Principe de Asturias, Alcala de Henares, Madrid. Spain" + }, + { + "author_name": "Lara Bravo Quiroga", + "author_inst": "Respiratory Medicine Service, University Hospital Principe de Asturias, Alcala de Henares, Madrid. Spain" + }, + { + "author_name": "Julio Flores Segovia", + "author_inst": "Respiratory Medicine Service, University Hospital Principe de Asturias, Alcala de Henares, Madrid. Spain" + }, + { + "author_name": "Marta Garcia Sanchez", + "author_inst": "Internal Medicine Service, University Hospital Principe de Asturias, Alcala de Henares, Madrid. SpaIn" + }, + { + "author_name": "Aida Gutierrez Garcia", + "author_inst": "Internal Medicine Service, University Hospital Principe de Asturias, Alcala de Henares, Madrid. Spain" + }, + { + "author_name": "Ana Perez", + "author_inst": "Internal Medicine Service and Rheumatology-Autoimmunity Service. Principe de Asturias University Hospital. Alcala de Henares, Madrid. Spain" + }, + { + "author_name": "Marta Herrero", + "author_inst": "Pharmacy Service. Prncipe de Asturias University Hospital. Alcala de Henares, Madrid. Spain" + }, + { + "author_name": "Nieves Plana", + "author_inst": "Preventive Medicine Service. Principe de Asturias University Hospital. Alcala de Henares, Madrid. Spain" + }, + { + "author_name": "Daniel Troncoso", + "author_inst": "Preventive Medicine Service. Principe de Asturias University Hospital. Alcala de Henares, Madrid. Spain" + }, + { + "author_name": "Gorjana Rackov", + "author_inst": "Centro Nacional de Biotecnologia-CSIC" + }, + { + "author_name": "Carlos Martinez-A", + "author_inst": "Centro Nacional de Biotecnologia-CSIC, Madrid, Spain" + }, + { + "author_name": "Dimitrios Balomenos", + "author_inst": "Centro Nacional de Biotecnologia-CSIC, Madrid, Spain" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.05.21252520", "rel_title": "Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland", @@ -889533,33 +891392,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2021.03.05.433897", - "rel_title": "COVIDrugNet: a network-based web tool to investigate the drugs currently in clinical trial to contrast COVID-19", - "rel_date": "2021-03-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.05.433897", - "rel_abs": "The COVID-19 pandemic poses a huge problem of public health that requires the implementation of all available means to contrast it, and drugs are one of them. In this context, we observed an unmet need of depicting the continuously evolving scenario of the ongoing drug clinical trials through an easy-to-use, freely accessible online tool. Starting from this consideration, we developed COVIDrugNet (http://compmedchem.unibo.it/covidrugnet), a web application that allows users to capture a holistic view and keep up to date on how the clinical drug research is responding to the SARS-CoV-2 infection.\n\nHere, we describe the web app and show through some examples how one can explore the whole landscape of medicines in clinical trial for the treatment of COVID-19 and try to probe the consistency of the current approaches with the available biological and pharmacological evidence. We conclude that careful analyses of the COVID-19 drug-target system based on COVIDrugNet can help to understand the biological implications of the proposed drug options, and eventually improve the search for more effective therapies.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Luca Menestrina", - "author_inst": "Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna 40126 Bologna, Italy" - }, - { - "author_name": "Chiara Cabrelle", - "author_inst": "Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna 40126 Bologna, Italy" - }, - { - "author_name": "Maurizio Recanatini", - "author_inst": "Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna 40126 Bologna, Italy" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.03.09.434219", "rel_title": "The FDA-approved drug cobicistat synergizes with remdesivir to inhibit SARS-CoV-2 replication", @@ -889916,6 +891748,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2021.03.07.21253095", + "rel_title": "Exploration of interethnic variation and repurposed drug efficacy in the treatment of SARS-CoV-2 Infection (COVID-19)", + "rel_date": "2021-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.07.21253095", + "rel_abs": "The COVID-19 global pandemic has led to repurposing of drugs, with little underlying evidence for treatment safety and efficacy. This may increase complications for patients with acute viral respiratory infections. UGT1A1 and CYP2D6 enzymes are involved in the metabolism of atazanavir and fluvoxamine repurposed for COVID-19. This study aimed to elucidate the role of interethnic variation in these enzymes in the efficacy of repurposed drug therapies. A retrospective cohort of 101 Jordanian Arab samples were genotyped using Affymetrix DMET Plus Premier Package. Comprehensive global population genetic structure analyses were performed for CYP2D6 and UGT1A1 allele frequencies across multi-ethnic populations of over 131,000 global subjects from 417 published reports, revealing that Jordanian Arabs share the closest sequence homology to European and Near East populations. The East Asian populations have significantly over-representaiton of individuals with diplotype pairs for reduced atazanavir metabolism compared to the African populations and are more likely to show impaired UGT1A1 metabolism. East Asian populations are also 4.4x more likely to show impaired fluvoxamine metabolism than South Central Asian and Oceanian populations, and 8x more likely than other ancestry populations. The results here support previous findings that interethnic variation should be used for developing proper population-specific dosage guidelines.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ammar Ali Almarzooq", + "author_inst": "Galore Consultancy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2021.03.06.21252796", "rel_title": "SARS-CoV-2 infects blood monocytes to activate NLRP3 and AIM2 inflammasomes, pyroptosis and cytokine release", @@ -891655,65 +893506,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.04.21252913", - "rel_title": "Comparison of IgG and neutralizing antibody responses after one or two doses of COVID-19 mRNA vaccine in previously infected and uninfected persons", - "rel_date": "2021-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252913", - "rel_abs": "ObjectiveTo compare anti-SARS-CoV-2 spike receptor binding domain (RBD) IgG antibody concentrations and antibody-mediated neutralization of spike-ACE2 receptor binding in vitro following vaccination of non-hospitalized participants by sero-status and acute virus diagnosis history.\n\nMethodsParticipants were studied before and after mRNA vaccination in a community-based, home-collected, longitudinal serosurvey; none reported hospitalization for COVID-19. Prior to vaccination, some reported prior positive acute viral diagnostic testing and were seropositive (COVID-19+). Participants who did not report acute viral diagnostic testing were categorized as seropositive or seronegative based on anti-spike RBD IgG test results. Primary measures were anti-spike RBD IgG concentration and percent antibody-mediated neutralization of spike protein-ACE2 interaction prior to vaccination, and after one or two doses of vaccine.\n\nResultsOf 290 unique vaccine recipients, 42 reported a prior COVID-19 diagnosis and were seropositive (COVID-19+). Of the 248 with no history of acute viral diagnostic testing, 105 were seropositive and 143 seronegative before vaccination. The median age was 38yrs (range 21-83) with 65% female and 35% male; 40% were non-white. Responses were evaluated after one (n=140) or two (n=170) doses of BNT162b2/Pfizer or mRNA-1273/Moderna vaccine. After one dose, median post-vaccine IgG concentration and percent neutralization were each significantly higher among the COVID-19+ group (median 47.7 {micro}g/ml, IgG; >99.9% neutralization) compared to the seropositives (3.4 {micro}g /ml IgG; 62.8% neutralization) and seronegatives (2.2 {micro}g /ml IgG; 39.5% neutralization). The latter two groups reached >95% neutralization after the second vaccine dose.\n\nConclusionsA prior outpatient COVID-19 diagnosis was associated with strong anti-spike RBD IgG and in vitro neutralizing responses after one vaccine dose. Persons seropositive for anti-spike RBD IgG in the absence of acute viral diagnostic testing, and those who were seronegative, required two doses to achieve equivalently high levels of IgG and neutralization activity. One mRNA vaccine dose is not sufficient to generate in vitro evidence of strong protection against COVID-19 among most persons previously infected with SARS-CoV-2, nor among seronegative persons.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Alexis R. Demonbreun", - "author_inst": "Northwestern University" - }, - { - "author_name": "Amelia Sancilio", - "author_inst": "Northwestern University" - }, - { - "author_name": "Matt E. Velez", - "author_inst": "Northwestern University" - }, - { - "author_name": "Daniel T. Ryan", - "author_inst": "Northwestern University" - }, - { - "author_name": "Rana Saber", - "author_inst": "Northwestern University" - }, - { - "author_name": "Lauren A. Vaught", - "author_inst": "Northwestern University" - }, - { - "author_name": "Nina L. Reiser", - "author_inst": "Northwestern University" - }, - { - "author_name": "Richard T. D'Aquila", - "author_inst": "Northwestern University" - }, - { - "author_name": "Brian Mustanski", - "author_inst": "Northwestern University" - }, - { - "author_name": "Elizabeth M. McNally", - "author_inst": "Northwestern University" - }, - { - "author_name": "Thomas W. McDade", - "author_inst": "Northwestern University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.04.21252880", "rel_title": "Estimation and optimal control of the multi-scale dynamics of the Covid-19", @@ -891914,6 +893706,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.02.21252759", + "rel_title": "Trends in SARS-CoV-2 detection during social relaxation measures over ten months of COVID-19 pandemic in the metropolitan area of Rio de Janeiro, Brazil", + "rel_date": "2021-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.02.21252759", + "rel_abs": "We analyzed the effects of sequential reopening events during COVID-19 pandemic, based on 76,419 SARS-CoV-2 molecular tests performed from April 2020 to January 2021 in Rio de Janeiro metropolitan area, Brazil, third largest in South America. Post-opening events provoked different impacts on cases and deaths, but showing limited temporary effect.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Fabio de Oliveira Martinez Alonso", + "author_inst": "Contraprova Diagnosticos, RJ-Brazil" + }, + { + "author_name": "Bruno Duarte Sabino", + "author_inst": "Contraprova Diagnosticos, RJ- Brazil" + }, + { + "author_name": "Marcia Carreteiro de Oliveira", + "author_inst": "Universidade Federal Fluminense, RJ-Brazil" + }, + { + "author_name": "Fabiana Batalha Knackfuss", + "author_inst": "Universidade do Grande Rio, RJ-Brazil" + }, + { + "author_name": "Rafael Varella", + "author_inst": "Universidade Federal Fluminense, RJ-Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.04.21252921", "rel_title": "A systematic review and meta-analysis of longitudinal cohort studies comparing mental health before versus during the COVID-19 pandemic", @@ -893445,49 +895272,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.05.21253022", - "rel_title": "Non-uniform UV-C dose across N95 facepieces can cause 2.9-log variation in SARS-CoV-2 inactivation", - "rel_date": "2021-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.05.21253022", - "rel_abs": "During public health crises like the COVID-19 pandemic, ultraviolet-C (UV-C) decontamination of N95 respirators for emergency reuse has been implemented to mitigate shortages. However, decontamination efficacy across N95s is poorly understood, due to the dependence on received UV-C dose, which varies across the complex three-dimensional N95 shape. Robust quantification of UV-C dose across N95 facepieces presents challenges, as few UV-C measurement tools have sufficient 1) small, flexible form factor, and 2) angular response. To address this gap, we combine optical modeling and quantitative photochromic indicator (PCI) dosimetry with viral inactivation assays to generate high-resolution maps of \"on-N95\" UV-C dose and concomitant SARS-CoV-2 viral inactivation across N95 facepieces within a commercial decontamination chamber. Using modeling to rapidly identify on-N95 locations of interest, in-situ measurements report a 17.4 {+/-} 5.0-fold dose difference across N95 facepieces in the chamber, yielding 2.9 {+/-} 0.2-log variation in SARS-CoV-2 inactivation. UV-C dose at several on-N95 locations was lower than the lowest-dose locations on the chamber floor, highlighting the importance of on-N95 dose validation. Overall, we couple optical simulation with in-situ PCI dosimetry to relate UV-C dose and viral inactivation at specific on-N95 locations, informing the design of safe and effective decontamination protocols.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Alisha Geldert", - "author_inst": "UC Berkeley/UCSF Graduate Program in Bioengineering" - }, - { - "author_name": "Alison Su", - "author_inst": "UC Berkeley/UCSF Graduate Program in Bioengineering" - }, - { - "author_name": "Allison W. Roberts", - "author_inst": "Department of Molecular and Cell Biology, University of California, Berkeley" - }, - { - "author_name": "Guillaume Golovkine", - "author_inst": "Department of Molecular and Cell Biology, University of California, Berkeley" - }, - { - "author_name": "Samantha M. Grist", - "author_inst": "Department of Bioengineering, University of California, Berkeley" - }, - { - "author_name": "Sarah A. Stanley", - "author_inst": "Department of Molecular and Cell Biology & School of Public Health, University of California, Berkeley" - }, - { - "author_name": "Amy E. Herr", - "author_inst": "Department of Bioengineering, University of California, Berkeley" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.03.06.21251482", "rel_title": "A Rapid Method to Evaluate Pre-Travel Testing Programs for COVID-19: A Study in Hawaii", @@ -893628,6 +895412,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.05.21252590", + "rel_title": "First dose mRNA vaccination is sufficient to reactivate immunological memory to SARS-CoV-2 in ex COVID-19 subjects", + "rel_date": "2021-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.05.21252590", + "rel_abs": "Characterizing the adaptive immune response to COVID-19 vaccination in individuals who recovered from SARS-CoV-2 infection may define current and future clinical practice. To determine the effect of two doses BNT162b2 mRNA COVID-19 vaccination schedule in individuals who recovered from COVID-19 (ex COVID-19) compared to naive subjects we evaluated SARS-CoV-2 spike-specific T and B cell responses, as well as specific IgG, IgM and neutralizing antibodies titres in 22 individuals who received BNT162b2 mRNA COVID-19 vaccine, 11 of which had a previous history of SARS-CoV-2 infection. Evaluations were performed before vaccination and then weekly until 7 days post second injection. Data obtained clearly showed that one vaccine dose is sufficient to increase both cellular and humoral immune response in ex COVID-19 subjects without any additional improvement after the second dose. On the contrary, the second dose is mandatory in naive ones to further enhance the response. These results question whether a second vaccine jab in ex COVID-19 subjects is required and indicate that millions of vaccine doses may be redirected to naive individuals, thus shortening the time to reach herd immunity.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Alessio Mazzoni", + "author_inst": "University of Florence" + }, + { + "author_name": "Nicoletta Di Lauria", + "author_inst": "Azienda Ospedaliero-Universitaria Careggi" + }, + { + "author_name": "Laura Maggi", + "author_inst": "University of Florence" + }, + { + "author_name": "Lorenzo Salvati", + "author_inst": "University of Florence" + }, + { + "author_name": "Anna Vanni", + "author_inst": "University of Florence" + }, + { + "author_name": "Manuela Capone", + "author_inst": "University of Florence" + }, + { + "author_name": "Giulia Lamacchia", + "author_inst": "University of Florence" + }, + { + "author_name": "Elisabetta Mantengoli", + "author_inst": "Azienda Ospedaliero-Universitaria Careggi" + }, + { + "author_name": "Michele Spinicci", + "author_inst": "University of Florence, Azienda Ospedaliero-Universitaria Careggi" + }, + { + "author_name": "Lorenzo Zammarchi", + "author_inst": "University of Florence, Azienda Ospedaliero-Universitaria Careggi" + }, + { + "author_name": "Seble Tekle Kiros", + "author_inst": "University of Florence, Azienda Ospedaliero-Universitaria Careggi" + }, + { + "author_name": "Maria Grazia Colao", + "author_inst": "Azienda Ospedaliero-Universitaria Careggi" + }, + { + "author_name": "Paola Parronchi", + "author_inst": "University of Florence, Azienda Ospedaliero-Universitaria Careggi" + }, + { + "author_name": "Cristina Scaletti", + "author_inst": "University of Florence" + }, + { + "author_name": "Lucia Turco", + "author_inst": "Azienda Ospedaliero-Universitaria Careggi" + }, + { + "author_name": "Francesco Liotta", + "author_inst": "University of Florence, Azienda Ospedaliero-Universitaria Careggi" + }, + { + "author_name": "Gian Maria Rossolini", + "author_inst": "University of Florence, Azienda Ospedaliero-Universitaria Careggi" + }, + { + "author_name": "Lorenzo Cosmi", + "author_inst": "University of Florence, Azienda Ospedaliero-Universitaria Careggi" + }, + { + "author_name": "Alessandro Bartoloni", + "author_inst": "University of Florence, Azienda Ospedaliero-Universitaria Careggi" + }, + { + "author_name": "Francesco Annunziato", + "author_inst": "University of Florence, Azienda Ospedaliero-Universitaria Careggi" + }, + { + "author_name": "- COVID-19 Research Group", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.05.21252707", "rel_title": "Centenarians and extremely old people living with frailty can elicit durable SARS-CoV-2 spike specific IgG antibodies with virus neutralization functions following virus infection", @@ -895115,129 +896998,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.03.06.434193", - "rel_title": "SARS-CoV-2 501Y.V2 (B.1.351) elicits cross-reactive neutralizing antibodies", - "rel_date": "2021-03-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.06.434193", - "rel_abs": "Neutralization escape by SARS-CoV-2 variants, as has been observed in the 501Y.V2 (B.1.351) variant, has impacted the efficacy of first generation COVID-19 vaccines. Here, the antibody response to the 501Y.V2 variant was examined in a cohort of patients hospitalized with COVID-19 in early 2021 - when over 90% of infections in South Africa were attributed to 501Y.V2. Robust binding and neutralizing antibody titers to the 501Y.V2 variant were detected and these binding antibodies showed high levels of cross-reactivity for the original variant, from the first wave. In contrast to an earlier study where sera from individuals infected with the original variant showed dramatically reduced potency against 501Y.V2, sera from 501Y.V2-infected patients maintained good cross-reactivity against viruses from the first wave. Furthermore, sera from 501Y.V2-infected patients also neutralized the 501Y.V3 (P.1) variant first described in Brazil, and now circulating globally. Collectively these data suggest that the antibody response in patients infected with 501Y.V2 has a broad specificity and that vaccines designed with the 501Y.V2 sequence may elicit more cross-reactive responses.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Thandeka Moyo-Gwete", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Mashudu Madzivhandila", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Zanele Makhado", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Frances Ayres", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Donald Mhlanga", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Brent Oosthuysen", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Bronwen Lambson", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Prudence Kgagudi", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Houriiyah Tegally", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, So" - }, - { - "author_name": "Arash Iranzadeh", - "author_inst": "nstitute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Deelan Doolabh", - "author_inst": "nstitute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Lynn Tyers", - "author_inst": "Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Lionel Chinhoyi", - "author_inst": "Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Afric" - }, - { - "author_name": "Mathilda Mennen", - "author_inst": "Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Afric" - }, - { - "author_name": "Sango Skelem", - "author_inst": "Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Afric" - }, - { - "author_name": "Gert Marais", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Constantinos Kurt Wibmer", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Jinal Bhiman", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Veronica Ueckermann", - "author_inst": "Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria, Pretoria, South Africa" - }, - { - "author_name": "Theresa Rossouw", - "author_inst": "Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa." - }, - { - "author_name": "Michael Boswell", - "author_inst": "Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria, Pretoria, South Africa" - }, - { - "author_name": "Tulio de Oliveira", - "author_inst": "University of KwaZulu-Natal" - }, - { - "author_name": "Carolyn Williamson", - "author_inst": "Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Wendy Burgers", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Ntobeko Ntusi", - "author_inst": "Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Lynn Morris", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Penny Moore", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.03.03.21252838", "rel_title": "SARS-CoV-2 transmission in intercollegiate athletics not fully mitigated with daily antigen testing", @@ -895522,6 +897282,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.03.21252872", + "rel_title": "Longitudinal Analysis Reveals Distinct Antibody and Memory B Cell Responses in SARS-CoV2 Naive and Recovered Individuals Following mRNA Vaccination", + "rel_date": "2021-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.03.21252872", + "rel_abs": "Novel mRNA vaccines for SARS-CoV2 have been authorized for emergency use and are currently being administered to millions of individuals worldwide. Despite their efficacy in clinical trials, there is limited data on vaccine-induced immune responses in individuals with a prior SARS-CoV2 infection compared to SARS-CoV2 naive subjects. Moreover, how mRNA vaccines impact the development of antibodies as well as memory B cells in COVID-19 experienced versus COVID-19 naive subjects remains poorly understood. In this study, we evaluated antibody responses and antigen-specific memory B cell responses over time in 33 SARS-CoV2 naive and 11 SARS-CoV2 recovered subjects. mRNA vaccination induced significant antibody and memory B cell responses against full-length SARS-CoV2 spike protein and the spike receptor binding domain (RBD). SARS-CoV2 naive individuals benefitted from both doses of mRNA vaccine with additional increases in antibodies and memory B cells following booster immunization. In contrast, SARS-CoV2 recovered individuals had a significant immune response after the first dose with no increase in circulating antibodies or antigen-specific memory B cells after the second dose. Moreover, the magnitude of the memory B cell response induced by vaccination was lower in older individuals, revealing an age-dependence to mRNA vaccine-induced B cell memory. Side effects also tended to associate with post-boost antibody levels, but not with post-boost memory B cells, suggesting that side effect severity may be a surrogate of short-term antibody responses. The frequency of pre-vaccine antigen-specific memory B cells in SARS-CoV2 recovered individuals strongly correlated with post-vaccine antibody levels, supporting a key role for memory B cells in humoral recall responses to SARS-CoV2. This observation may have relevance for future booster vaccines and for responses to viral variants that partially escape pre-existing antibodies and require new humoral responses to be generated from memory B cells. Finally, post-boost antibody levels were not correlated with post-boost memory responses in SARS-CoV2 naive individuals, indicating that short-term antibody levels and memory B cells are complementary immunological endpoints that should be examined in tandem when evaluating vaccine response. Together, our data provide evidence of both serological response and immunological memory following mRNA vaccination that is distinct based on prior SARS-CoV2 exposure. These findings may inform vaccine distribution in a resource-limited setting.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC=\"FIGDIR/small/21252872v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (44K):\norg.highwire.dtl.DTLVardef@f9b82dorg.highwire.dtl.DTLVardef@aa9f2aorg.highwire.dtl.DTLVardef@1b79862org.highwire.dtl.DTLVardef@757b06_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Rishi R Goel", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Sokratis A Apostolidis", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Mark M Painter", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Divij Mathew", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ajinkya Pattekar", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Oliva Kuthuru", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Sigrid Gouma", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Leticia Kuri-Cervantes", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Wenzhao Meng", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Sharon Adamski", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Amy E Baxter", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Josephine R Giles", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Madison E Weirick", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Christopher M McAllister", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Amanda Hicks", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Scott Korte", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jeanette Dougherty", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Sherea Long", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Kurt D'Andrea", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jacob T Hamilton", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Eline T Luning Prak", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Michael R Betts", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Paul Bates", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Scott E Hensley", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Allison R Greenplate", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "E. John Wherry", + "author_inst": "University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.03.21252856", "rel_title": "REACT-1 round 9 final report: Continued but slowing decline of prevalence of SARS-CoV-2 during national lockdown in England in February 2021", @@ -897169,65 +899048,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.03.21252509", - "rel_title": "Efficacy of Nitazoxanide in reducing the viral load in COVID-19 patients. Randomized, placebo-controlled, single-blinded, parallel group, pilot study.", - "rel_date": "2021-03-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.03.21252509", - "rel_abs": "The fast spread of COVID-19 has overcrowded Public Health Systems facilities in major countries due to the large number of seriously ill patients, particularly those requiring admission to intensive care units. Reducing viral load, along with other recommended epidemiological measures, such as social distancing and home confinement, can in time significantly help to reduce the infection R0 (Basic Reproductive Rate) and then mitigate disease burden. Early negativization or otherwise reduction of the viral load can potentially diminish disease severity, resulting in a better-controlled public health response, avoiding collapse of healthcare systems. Nitazoxanide, a widely used thiazolide approved by the FDA as an antiparasitic drug, also approved in Brazil for Norovirus and Rotavirus treatments, has an excellent safety record for a variety of indications. Nitazoxanide exhibits activity in vitro against MERS-CoV and other coronaviruses; and a specific antiviral effect (in micro molar doses) against SARS-CoV-2. The objective of this study was to evaluate the efficacy and safety of Nitazoxanide in reducing the SARS-COV 2 viral load within 7 days of treatment in respiratory samples from COVID-19-infected patients with mild to moderate disease, compared to placebo. An interim analysis showed that the ratio of patients with a viral load reduction [≥] 35% from baseline up to day 7 of treatment was significantly greater for Nitazoxanide compared to placebo (47.8% vs. 15.4%; {Delta} 34.6%; 95% CI: 64.7; 4.6: p = 0.037).\n\nKEY POINTSO_ST_ABSState of the ArtC_ST_ABSO_LIDifferent studies conclude that viral load (VL) would correlate with morbidity, mortality and contagiousness of COVID-19.\nC_LIO_LIEarly negativization or reduction of the viral load can potentially reduce the severity of this disease.\nC_LIO_LIIn vitro data demonstrated a specific antiviral effect of Nitazoxanide for SARS-CoV-2.\nC_LI\n\nArticle contributionO_LINitazoxanide showed a statistically significant difference versus placebo in the number of patients who had their viral load reduced by at least 35% in mild to moderate COVID-19 disease.\nC_LIO_LIThe observed antiviral effect in vitro would seems to be verified in patients with mild to moderate COVID-19 infection, which should be confirmed by studies with a larger cohort of patients.\nC_LI", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Marcelo Silva", - "author_inst": "Unidad de Hepatologia y Trasplante Hepatico, Hospital Universitario Austral, Pilar, Argentina." - }, - { - "author_name": "Andres Espejo", - "author_inst": "Unidad de Hepatologia y Trasplante Hepatico, Hospital Universitario Austral, Pilar, Argentina." - }, - { - "author_name": "Maria Laura Pereyra", - "author_inst": "Unidad de Hepatologia y Trasplante Hepatico, Hospital Universitario Austral, Pilar, Argentina." - }, - { - "author_name": "Martin Lynch", - "author_inst": "Unidad de Hepatologia y Trasplante Hepatico, Hospital Universitario Austral, Pilar, Argentina." - }, - { - "author_name": "Marcos Thompson", - "author_inst": "Unidad de Hepatologia y Trasplante Hepatico, Hospital Universitario Austral, Pilar, Argentina." - }, - { - "author_name": "Hernan Taconelli", - "author_inst": "Sanatorio Nuestra Senora del Pilar, Ciudadela, Argentina." - }, - { - "author_name": "Patricia Bare", - "author_inst": "IIHEMA, IMEX-CONICET, Academia Nacional de Medicina" - }, - { - "author_name": "Matias Pereson", - "author_inst": "IIHEMA, IMEX-CONICET, Academia Nacional de Medicina." - }, - { - "author_name": "Marcelo Garbini", - "author_inst": "Roemmers" - }, - { - "author_name": "Pablo Crucci", - "author_inst": "Departamento de Investigacon Clinica, Laboratorios Roemmers" - }, - { - "author_name": "Diego Enriquez", - "author_inst": "Departamento de Investigacon Clinica, Laboratorios Roemmers" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.02.21252746", "rel_title": "Providing a safe, in-person, residential college experience during the COVID-19 pandemic", @@ -897496,6 +899316,149 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.03.21252812", + "rel_title": "Genome sequencing and analysis of an emergent SARS-CoV-2 variant characterized by multiple spike protein mutations detected from the Central Visayas Region of the Philippines", + "rel_date": "2021-03-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.03.21252812", + "rel_abs": "The emergence of SARS-CoV-2 variants of concern such as the B.1.1.7, B.1.35 and the P.1 have prompted calls for governments worldwide to increase their genomic biosurveillance efforts. Globally, quarantine and outbreak management measures have been implemented to stem the introduction of these variants and to monitor any emerging variants of potential clinical significance domestically. Here, we describe the emergence of a new SARS-CoV-2 lineage, mainly from the Central Visayas region of the Philippines. This emergent variant is characterized by 13 lineage-defining mutations, including the co-occurrence of the E484K, N501Y, and P681H mutations at the spike protein region, as well as three additional radical amino acid replacements towards the C-terminal end of the said protein. A three-amino acid deletion at positions 141 to 143 (LGV141_143del) in the spike protein was likewise seen in a region preceding the 144Y deletion found in the B.1.1.7 variant. A single amino acid replacement, K2Q, at the N-terminus of ORF8 was also shared by all 33 samples sequenced. The mutation profile of this new virus variant warrants closer investigation due to its potential public health implications. The current distribution of this emergent variant in the Philippines and its transmission are being monitored and addressed by relevant public health agencies to stem its spread in nearby islands and regions in the country.", + "rel_num_authors": 32, + "rel_authors": [ + { + "author_name": "Francis A. Tablizo", + "author_inst": "Core Facility for Bioinformatics, Philippine Genome Center, Univeristy of the Philippines System" + }, + { + "author_name": "Kenneth M. Kim", + "author_inst": "Core Facility for Bioinformatics, Philippine Genome Center, Univeristy of the Philippines System" + }, + { + "author_name": "Carlo M. Lapid", + "author_inst": "Core Facility for Bioinformatics, Philippine Genome Center, Univeristy of the Philippines System" + }, + { + "author_name": "Marc Jerrone R. Castro", + "author_inst": "Core Facility for Bioinformatics, Philippine Genome Center, Univeristy of the Philippines System" + }, + { + "author_name": "Maria Sofia L. Yangzon", + "author_inst": "Core Facility for Bioinformatics, Philippine Genome Center, Univeristy of the Philippines System" + }, + { + "author_name": "Benedict A. Maralit", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, Univeristy of the Philippines System" + }, + { + "author_name": "Marc Edsel C. Ayes", + "author_inst": "Clinical Genomics Laboratory, Philippine Genome Center, Univeristy of the Philippines System" + }, + { + "author_name": "Eva Maria Cutiongco-de la Paz", + "author_inst": "Philippine Genome Center, Univeristy of the Philippines System" + }, + { + "author_name": "Alethea R. de Guzman", + "author_inst": "Epidemiology Bureau, Department of Health , Philippines" + }, + { + "author_name": "Jan Michael C. Yap", + "author_inst": "Core Facility for Bioinformatics, Philippine Genome Center, Univeristy of the Philippines System" + }, + { + "author_name": "Jo-Hannah S. Llames", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, Univeristy of the Philippines System" + }, + { + "author_name": "Shiela Mae M. Araiza", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, Univeristy of the Philippines System" + }, + { + "author_name": "Kris P. Punayan", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, Univeristy of the Philippines System" + }, + { + "author_name": "Irish Coleen A. Asin", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, Univeristy of the Philippines System" + }, + { + "author_name": "Candice Francheska B. Tambaoan", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, Univeristy of the Philippines System" + }, + { + "author_name": "Asia Louisa U. Chong", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, Univeristy of the Philippines System" + }, + { + "author_name": "Karol Sophia Agape R. Padilla", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, Univeristy of the Philippines System" + }, + { + "author_name": "Rianna Patricia S. Cruz", + "author_inst": "Core Facility for Bioinformatics, Philippine Genome Center, Univeristy of the Philippines System" + }, + { + "author_name": "El King D. Morado", + "author_inst": "Core Facility for Bioinformatics, Philippine Genome Center, Univeristy of the Philippines System" + }, + { + "author_name": "Joshua Gregor A. Dizon", + "author_inst": "Core Facility for Bioinformatics, Philippine Genome Center, Univeristy of the Philippines System" + }, + { + "author_name": "Razel Nikka M. Hao", + "author_inst": "Disease Prevention and Control Bureau, Department of Health , Philippines" + }, + { + "author_name": "Arianne A. Zamora", + "author_inst": "Epidemiology Bureau, Department of Health , Philippines" + }, + { + "author_name": "Devon Ray Pacial", + "author_inst": "Epidemiology Bureau, Department of Health , Philippines" + }, + { + "author_name": "Juan Antonio R. Magalang", + "author_inst": "Epidemiology Bureau, Department of Health , Philippines" + }, + { + "author_name": "Marissa Alejandria", + "author_inst": "Inter-Agency Task Force on Emerging Infectious Diseases (IATF) Task Force on COVID-19 Variants, Department of Health, Philippines" + }, + { + "author_name": "Celia Carlos", + "author_inst": "Inter-Agency Task Force on Emerging Infectious Diseases (IATF) Task Force on COVID-19 Variants, Department of Health, Philippines" + }, + { + "author_name": "Anna Ong-Lim", + "author_inst": "Inter-Agency Task Force on Emerging Infectious Diseases (IATF) Task Force on COVID-19 Variants, Department of Health, Philippines" + }, + { + "author_name": "Edsel Maurice Salvana", + "author_inst": "Inter-Agency Task Force on Emerging Infectious Diseases (IATF) Task Force on COVID-19 Variants, Department of Health, Philippines" + }, + { + "author_name": "John Q. Wong", + "author_inst": "Inter-Agency Task Force on Emerging Infectious Diseases (IATF) Task Force on COVID-19 Variants, Department of Health, Philippines" + }, + { + "author_name": "Jaime C. Montoya", + "author_inst": "Inter-Agency Task Force on Emerging Infectious Diseases (IATF) Task Force on COVID-19 Variants, Department of Health, Philippines" + }, + { + "author_name": "Maria Rosario Singh-Vergeire", + "author_inst": "Inter-Agency Task Force on Emerging Infectious Diseases (IATF) Task Force on COVID-19 Variants, Department of Health, Philippines" + }, + { + "author_name": "Cynthia P. Saloma", + "author_inst": "Philippine Genome Center, Univeristy of the Philippines System" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.03.21252425", "rel_title": "Diagnostic Performance and Characteristics of Anterior Nasal Collection for the SARS-CoV-2 Antigen Test: A Prospective Study in Japan", @@ -898979,37 +900942,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.03.04.433846", - "rel_title": "SARS-CoV-2 viability in time on experimental surfaces", - "rel_date": "2021-03-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.04.433846", - "rel_abs": "We evaluated the SARS-CoV-2 viability preservation on different model surfaces over time. It was found that the SARS-CoV-2 RNA was detected on all studied surfaces for 360 minutes, while the viability of the virus was completely lost after 120 minutes. Type of experimental surface significantly affects viability preservation.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Maria Nikiforova", - "author_inst": "N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia" - }, - { - "author_name": "Andrei Siniavin", - "author_inst": "N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia" - }, - { - "author_name": "Elena Shidlovskaya", - "author_inst": "N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia" - }, - { - "author_name": "Nadezhda Kuznetsova", - "author_inst": "N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.03.04.433849", "rel_title": "Efficient Inhibition of SARS-CoV-2 Using Chimeric Antisense Oligonucleotides through RNase L Activation", @@ -899210,6 +901142,77 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.03.04.433919", + "rel_title": "UBXN3B Restricts Viral Pathogenesis by Maintaining Hematopoietic Homeostasis", + "rel_date": "2021-03-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.04.433919", + "rel_abs": "Hematopoiesis is finely regulated to enable timely production of the right numbers and types of mature immune cells to maintain tissue homeostasis. Dysregulated hematopoiesis may compromise antiviral immunity and/or exacerbate immunopathogenesis. Herein, we report an essential role of UBXN3B in maintenance of hematopoietic homeostasis and restriction of immunopathogenesis during respiratory viral infection. Ubxn3b deficient (Ubxn3b-/-) mice are highly vulnerable to SARS-CoV-2 and influenza A infection, characterized by more severe lung immunopathology, lower virus-specific IgG, significantly fewer B cells, but more myeloid cells than Ubxn3b+/+ littermates. This aberrant immune compartmentalization is recapitulated in uninfected Ubxn3b-/- mice. Mechanistically, UBXN3B controls precursor B-I (pre-BI) transition to pre-BII and subsequent proliferation in a cell-intrinsic manner, by maintaining BLNK protein stability and pre-BCR signaling. These results reveal an essential role of UBXN3B for the early stage of B cell development.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Tingting Geng", + "author_inst": "School of Medicine, UConn Health" + }, + { + "author_name": "Duomeng Yang", + "author_inst": "School of Medicine, UConn Health" + }, + { + "author_name": "Tao Lin", + "author_inst": "School of Medicine, UConn Health" + }, + { + "author_name": "Andrew G Harrison", + "author_inst": "School of Medicine, UConn Health" + }, + { + "author_name": "Binsheng Wang", + "author_inst": "University of Connecticut Health Center" + }, + { + "author_name": "Blake Torrance", + "author_inst": "University of Connecticut Health Center" + }, + { + "author_name": "Kepeng Wang", + "author_inst": "University of Connecticut Health Center" + }, + { + "author_name": "Yanlin Wang", + "author_inst": "University of Connecticut School of medicine" + }, + { + "author_name": "Long Yang", + "author_inst": "Tianjin University of Traditional Chinese Medicine" + }, + { + "author_name": "Laura Haynes", + "author_inst": "University of Connecticut Health Center" + }, + { + "author_name": "Gong Cheng", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Anthony T. Vella", + "author_inst": "University of Connecticut Health Center" + }, + { + "author_name": "Erol Fikrig", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "PENGHUA WANG", + "author_inst": "University of Connecticut Health Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.03.03.433579", "rel_title": "T-cell Repertoire Characteristics of Asymptomatic and Re-detectable Positive COVID-19 Patients", @@ -900917,125 +902920,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.09.21251168", - "rel_title": "A novel, multiplexed RT-qPCR assay to distinguish lineage B.1.1.7 from the remaining SARS-CoV-2 lineages", - "rel_date": "2021-03-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.09.21251168", - "rel_abs": "The emergence of a novel SARS-CoV-2 variant called lineage B.1.1.7 sparked global alarm due to evidence of increased transmissibility, mortality, and uncertainty about vaccine efficacy, thus accelerating efforts to detect and track the variant. Current approaches to detect lineage B.1.1.7 include sequencing and RT-qPCR tests containing a target assay that fails or results in reduced sensitivity towards the B.1.1.7 variant. Since many countries lack robust genomic surveillance programs and failed assays detect multiple unrelated variants containing similar mutations as B.1.1.7, we sought to develop an RT-qPCR test that can accurately and rapidly differentiate the B.1.1.7 variant from other SARS-CoV-2 variants. We used bioinformatics, allele-specific PCR, and judicious placement of LNA-modified nucleotides to develop a test that differentiates B.1.1.7 from other SARS-CoV-2 variants. We validated the test on 106 clinical samples with lineage status confirmed by sequencing. Our room temperature-stable, multiplexed RT-qPCR test consists of two assays that target either the common SARS-CoV-2 spike gene or spike gene deletions specific to lineage B.1.1.7. A simple relative comparison of the Ct values of the two assays permits not only identification of the B.1.1.7 variant but also its differentiation from other variants that harbor only the {Delta}H69/{Delta}V70 deletion.The test showed 97% clinical sensitivity at detecting lineage B.1.1.7. This test can easily be implemented in labs to rapidly scale B.1.1.7 surveillance efforts and is particularly useful in countries with high prevalence of variants possessing only the {Delta}H69/{Delta}V70 deletion because current strategies using target failure assays incorrectly identify these as putative B.1.1.7 variants.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Viera Kovacova", - "author_inst": "MultiplexDX, Inc., Comenius University Science Park, Bratislava, Slovakia" - }, - { - "author_name": "Krist\u00edna Bor\u0161ov\u00e1", - "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia; Department of Microbiology and Virology, Faculty of Natural" - }, - { - "author_name": "Evan D Paul", - "author_inst": "MultiplexDX, Inc., Comenius University Science Park, Bratislava, Slovakia" - }, - { - "author_name": "Monika Radvanszka", - "author_inst": "MultiplexDX, Inc., Comenius University Science Park, Bratislava, Slovakia" - }, - { - "author_name": "Roman Hajdu", - "author_inst": "MultiplexDX, Inc., Comenius University Science Park, Bratislava, Slovakia" - }, - { - "author_name": "Vikt\u00f3ria \u010cabanov\u00e1", - "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia" - }, - { - "author_name": "Monika Sl\u00e1vikov\u00e1", - "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia" - }, - { - "author_name": "Martina Li\u010dkov\u00e1", - "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia" - }, - { - "author_name": "\u013dubom\u00edra Luk\u00e1\u010dikov\u00e1", - "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia" - }, - { - "author_name": "Andrej Belak", - "author_inst": "Institute of Ethnology and Social Anthropology, Slovak Academy of Sciences, Bratislava, Slovakia; Intervention team, Ministry of Health, Slovakia" - }, - { - "author_name": "Lucia Roussier", - "author_inst": "Intervention team, Ministry of Health, Slovakia" - }, - { - "author_name": "Michaela Kosti\u010dov\u00e1", - "author_inst": "Intervention team, Ministry of Health, Slovakia; Institute of Social Medicine and Medical Ethics, Faculty of Medicine, Comenius University in Bratislava, Bratis" - }, - { - "author_name": "Anna L\u00ed\u0161kov\u00e1", - "author_inst": "Nitra Faculty Hospital, Department of Clinical Microbiology, Nitra, Slovakia" - }, - { - "author_name": "Lucia Ma\u010farov\u00e1", - "author_inst": "Regional Authority of Public Health, Banska Bystrica, Slovakia" - }, - { - "author_name": "M\u00e1ria \u0160tefkovi\u010dov\u00e1", - "author_inst": "Regional Authority of Public Health, Trencin, Slovakia; Faculty of Healthcare, Alexander Dubcek University of Trencin, Slovakia" - }, - { - "author_name": "Lenka Reizigov\u00e1", - "author_inst": "Regional Authority of Public Health, Trencin, Slovakia; Department of Laboratory Medicine, Faculty of Healthcare and Social Work, Trnava University, Trnava, Slo" - }, - { - "author_name": "Elena Nov\u00e1kov\u00e1", - "author_inst": "Department of Microbiology and Immunology, Comenius University in Bratislava, Jessenius Faculty of Medicine, Martin, Slovakia" - }, - { - "author_name": "Peter Sabaka", - "author_inst": "Department of Infectology and Geographical Medicine, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia" - }, - { - "author_name": "Alena Ko\u0161\u010d\u00e1lov\u00e1", - "author_inst": "Department of Infectology and Geographical Medicine, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia; Department of Infectious Dise" - }, - { - "author_name": "Bro\u0148a Brejov\u00e1", - "author_inst": "Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia" - }, - { - "author_name": "Edita Staro\u0148ov\u00e1", - "author_inst": "National Influenza Centre, National Public Health Authority of Slovak Republic in Bratislava, Bratislava, Slovakia" - }, - { - "author_name": "Matej Mi\u0161\u00edk", - "author_inst": "Institute for Healthcare Analyses, Ministry of Health, Slovakia" - }, - { - "author_name": "Tomas Vinar", - "author_inst": "Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia" - }, - { - "author_name": "Jozef Nosek", - "author_inst": "Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia" - }, - { - "author_name": "Pavol Cekan", - "author_inst": "MultiplexDX, Inc., Comenius University Science Park, Bratislava, Slovakia" - }, - { - "author_name": "Boris Klempa", - "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia" - } - ], - "version": "2", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.02.21250607", "rel_title": "Modeling University Reopening in Low Risk Countries During COVID-19", @@ -901168,6 +903052,113 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.03.02.432977", + "rel_title": "Neutralizing IFNL3 Autoantibodies in Severe COVID-19 Identified Using Molecular Indexing of Proteins by Self-Assembly", + "rel_date": "2021-03-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.02.432977", + "rel_abs": "Unbiased antibody profiling can identify the targets of an immune reaction. A number of likely pathogenic autoreactive antibodies have been associated with life-threatening SARS-CoV-2 infection; yet, many additional autoantibodies likely remain unknown. Here we present Molecular Indexing of Proteins by Self Assembly (MIPSA), a technique that produces ORFeome-scale libraries of proteins covalently coupled to uniquely identifying DNA barcodes for analysis by sequencing. We used MIPSA to profile circulating autoantibodies from 55 patients with severe COVID-19 against 11,076 DNA-barcoded proteins of the human ORFeome library. MIPSA identified previously known autoreactivities, and also detected undescribed neutralizing interferon lambda 3 (IFN-{lambda}3) autoantibodies. At-risk individuals with anti-IFN-{lambda}3 antibodies may benefit from interferon supplementation therapies, such as those currently undergoing clinical evaluation.\n\nOne-Sentence SummaryMolecular Indexing of Proteins by Self Assembly (MIPSA) identifies neutralizing IFNL3 autoantibodies in patients with severe COVID-19.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC=\"FIGDIR/small/432977v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (25K):\norg.highwire.dtl.DTLVardef@a3c55aorg.highwire.dtl.DTLVardef@1f1c840org.highwire.dtl.DTLVardef@920bc7org.highwire.dtl.DTLVardef@43633e_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Joel J. Credle", + "author_inst": "Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine" + }, + { + "author_name": "Jonathan Gunn", + "author_inst": "Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine" + }, + { + "author_name": "Puwanat Sangkhapreecha", + "author_inst": "Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine" + }, + { + "author_name": "Daniel R. Monaco", + "author_inst": "Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine" + }, + { + "author_name": "Xuwen Alice Zheng", + "author_inst": "Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine" + }, + { + "author_name": "Hung-Ji Tsai", + "author_inst": "Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston" + }, + { + "author_name": "Azaan Wilbon", + "author_inst": "Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine" + }, + { + "author_name": "William R. Morgenlander", + "author_inst": "Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine" + }, + { + "author_name": "Yi Dong", + "author_inst": "Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine" + }, + { + "author_name": "Sahana Jayaraman", + "author_inst": "Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine" + }, + { + "author_name": "Lorenzo Tosi", + "author_inst": "Department of Biomedical Engineering, Rutgers University" + }, + { + "author_name": "Biju Parekkadan", + "author_inst": "Department of Biomedical Engineering, Rutgers University" + }, + { + "author_name": "Alan N. Baer", + "author_inst": "Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine" + }, + { + "author_name": "Mario Roederer", + "author_inst": "ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Evan M. Bloch", + "author_inst": "Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University School of Medicine" + }, + { + "author_name": "Aaron A. R. Tobian", + "author_inst": "Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University School of Medicine" + }, + { + "author_name": "Israel Zyskind", + "author_inst": "Department of Pediatrics, NYU Langone Medical Center, New York, NY and Maimonides Medical Center" + }, + { + "author_name": "Jonathan I. Silverberg", + "author_inst": "Department of Dermatology, George Washington University School of Medicine and Health Sciences" + }, + { + "author_name": "Avi Z. Rosenberg", + "author_inst": "Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University" + }, + { + "author_name": "Andrea L. Cox", + "author_inst": "Division of Infectious Diseases, Department of Medicine, Johns Hopkins University" + }, + { + "author_name": "Tom Lloyd", + "author_inst": "Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine" + }, + { + "author_name": "Andrew L. Mammen", + "author_inst": "Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH and Departments of Neurology and Medicine, Johns Hopkins Univers" + }, + { + "author_name": "H. Benjamin Larman", + "author_inst": "Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.03.03.433704", "rel_title": "Low-dose lung radiotherapy for COVID-19 lung disease: a pre-clinical efficacy study in a bleomycin model of pneumonitis.", @@ -903059,61 +905050,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.28.21252633", - "rel_title": "A new accessible adaptable COVID-19 model", - "rel_date": "2021-03-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.28.21252633", - "rel_abs": "ObjectivesSophisticated epidemic models have been created to help governments and large healthcare organisations plan the necessary resources to manage the COVID-19 pandemic. Whilst helpful, current modelling systems are not widely accessible or easily adapted to different populations and circumstances. Our objective was to develop a widely applicable, easily accessible, adaptable model for projecting new COVID-19 infections and deaths that requires minimal expertise or resources to use. The model should be adaptable to different populations and able to accommodate social and pharmaceutical interventions as well as changes in the disease.\n\nDesignA Susceptible, Infected and Removed (SIR) infectious disease model was created using widely available Microsoft Excel(C) software. The model is deterministic, generating projections based on the available data and assumptions made. It uses a process of Monitored Forecasting through Visual Matching of predicated vs observed curves to improve accuracy and facilitate adaptability. A review of the COVID-19 literature was performed in order to produce an initial set of adjustable parameters on which to base the output of the model.\n\nSettingThis model can be adapted to different regions or countries for which the requisite input data (population size and number of deaths due to the disease) are available. This model has been successfully used with data from England, Sudan and Saudi Arabia. Data from NHS England were used for producing the illustrative results presented here. The model is a generic infectious disease forecast model which may be adapted to other epidemics.\n\nInterventionGovernments, public health organisations, pharmaceutical companies and other public institutions may introduce interventions that affect disease transmission or severity. Other unknown factors such as new variants of the infective agent may do the same. The effects of changes in disease transmission are identified by the model when predicted and observed curves deviate. By aligning the curves an evaluation of the effect of the changes can be made.\n\nOutcome MeasuresThe model graphically demonstrates projections for daily deaths, cumulative deaths, case mix (asymptomatic, symptomatic and severe infections requiring admission), hospital admissions and bed occupancy (ICU, general medical and total).\n\nResultsThe model successfully produced projections for the outcome measures using NHS England data. Users can adapt and continuously update the model correcting its projections as further local data becomes available. The Microsoft Excel platform allows the model to be used without expensive health information systems or computing infrastructure.\n\nConclusionWe present an SIR epidemic model that projects COVID-19 disease progression, is widely accessible, adaptable to different populations and environments as the disease progresses and is likely to be of benefit for identifying changing population healthcare needs.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Michael G Baker", - "author_inst": "epidemic projections.org, Surrey, England." - }, - { - "author_name": "Maximilian de Courten", - "author_inst": "Mitchell Institute, Victoria University, Melbourne, Australia." - }, - { - "author_name": "David A Sidloff", - "author_inst": "Nottingham University Hospitals, Nottingham, England." - }, - { - "author_name": "Alexander DL Baker", - "author_inst": "Lancashire Teaching Hospitals NHS Foundation Trust, Lancashire, England." - }, - { - "author_name": "Walid S El Sayes", - "author_inst": "King Saud Medical City, Riyadh, Saudi Arabia." - }, - { - "author_name": "Faisal A Alaklobi", - "author_inst": "King Saud Medical City, Riyadh, Saudi Arabia." - }, - { - "author_name": "Abdulrahman S Alqahtani", - "author_inst": "Ministry of Health, Riyadh, Saudi Arabia." - }, - { - "author_name": "Edward Fraser", - "author_inst": "First Riyadh Health Cluster, Saudi Arabia." - }, - { - "author_name": "Charles R Cohen", - "author_inst": "Projection Modeller, Riyadh, Saudi Arabia" - }, - { - "author_name": "Isam SM Osman", - "author_inst": "King Saud Medical City, Riyadh, Saudi Arabia." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.28.21252648", "rel_title": "Shifting research priorities in maternal and child health in the COVID-19 pandemic era in India: a renewed focus on systems strengthening", @@ -903326,6 +905262,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.28.21252610", + "rel_title": "Vaccine hesitancy and reasons for refusing the COVID-19 vaccination among the U.S. public: A cross-sectional survey", + "rel_date": "2021-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.28.21252610", + "rel_abs": "ImportanceAlthough widespread vaccination will be the most important cornerstone of the public health response to the COVID-19 pandemic, a critical question remains as to how much of the United States population will accept it.\n\nObjectiveDetermine: 1) rate of COVID-19 vaccine hesitancy in the United States public, 2) patient characteristics associated with hesitancy, 3) reasons for hesitancy, 4) healthcare sites where vaccine acceptors would prefer to be vaccinated.\n\nDesign43-question cross-sectional survey conducted November 17-18, 2020, distributed on Amazon Mechanical Turk, an online labor marketplace where individuals receive a nominal fee (here, $1.80) for anonymously completing tasks.\n\nEligible ParticipantsUnited States residents 18-88 years of age, excluding healthcare workers. A total 1,756 volunteer respondents completed the survey (median age 38 years, 53% female).\n\nMain Outcome MeasureMultivariable logistic regression modeled the primary outcome of COVID-19 vaccine hesitancy (defined as non-acceptance or being unsure about acceptance of the COVID-19 vaccine) with respondent characteristics.\n\nResultsA total 663 respondents (37.8%) were COVID-19 vaccine hesitant (374 [21.3%] non-acceptors and 289 [16.5%] unsure about accepting). Vaccine hesitancy was associated with not receiving influenza vaccination in the past 5 years (odds ratio [OR] 4.07, 95% confidence interval [CI] 3.26-5.07, p<0.01), female gender (OR 2.12, 95%CI 1.70-2.65, p<0.01), Black race (OR 1.54, 95%CI 1.05-2.26, p=0.03), having a high school education or less (OR 1.46, 95%CI 1.03-2.07, p=0.03), and Republican party affiliation (OR 2.41, 95%CI 1.88-3.10, p<0.01). Primary reasons for hesitancy were concerns about side effects, need for more information, and doubts about vaccine efficacy. Preferred sites for vaccination for acceptors were primary doctors offices/clinics, pharmacies, and dedicated vaccination locations.\n\nConclusionsIn this recent national survey, over one-third of respondents were COVID-19 vaccine hesitant. To increase vaccine acceptance, public health interventions should target vaccine hesitant populations with messaging that addresses their concerns about safety and efficacy.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ali S Raja", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Joshua D Niforatos", + "author_inst": "The Johns Hopkins Hospital" + }, + { + "author_name": "Nancy Anaya", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Joseph Graterol", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Robert M Rodriquez", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.28.21252644", "rel_title": "Optimal mobility restriction minimizing COVID-19 and excess suicide deaths in Japan", @@ -904969,61 +906940,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.26.21252504", - "rel_title": "Opening schools and trends in SARS-CoV-2 transmission in European countries", - "rel_date": "2021-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.26.21252504", - "rel_abs": "BackgroundIt is important to understand the role of schools in the community transmission of SARS-CoV-2, bearing in mind that children and adolescents can spread the infection within families, even when their own symptoms are mild. The aim of this study was to examine the trends of contagion before and after schools reopened across 27 countries in the European Union.\n\nMethodsAll data on the number of people testing positive for COVID-19 in each European country were collected from 20 days before schools reopened to 45 days afterwards. The Joinpoint regression method was used to detect single change points on the trend of contagion. The Bayesian Information Criterion (BIC) was used for model selection purposes.\n\nResultsWe calculated 27 linear regression models for the daily case numbers of SARS-CoV-2 infection in the 27 countries from 20 days before schools reopened to 45 days afterwards. A significant increase in the number of daily infections was seen for 21 countries after a change point in the linear regression lines. The change points in different countries varied, ranging from 10 to 42 days after schools reopened, with the majority occurring beyond the 21st day.\n\nConclusionThis study analysed the trend of SARS-CoV-2 transmission before and after schools reopened in Europe. We observed a significant increase in the number of new daily cases in most countries. This issue poses a public health problem that needs to be taken into account in deciding strategies to contain the spread of COVID-19.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Alessandra Buja", - "author_inst": "University of Padova" - }, - { - "author_name": "Matteo Paganini", - "author_inst": "University of Padova" - }, - { - "author_name": "Vittorio Cristofori", - "author_inst": "University of Padova" - }, - { - "author_name": "Tatjana Baldovin", - "author_inst": "University of Padova" - }, - { - "author_name": "Riccardo Fusinato", - "author_inst": "University of Padova" - }, - { - "author_name": "Giovanna Boccuzzo", - "author_inst": "University of Padova" - }, - { - "author_name": "Silvia Cocchio", - "author_inst": "University of Padova" - }, - { - "author_name": "Silvia Coretti", - "author_inst": "University of Padova" - }, - { - "author_name": "Vincenzo Rebba", - "author_inst": "University of Padova" - }, - { - "author_name": "Maria Parpinel", - "author_inst": "University of Udine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.27.21252593", "rel_title": "Surgical activity in England and Wales during the COVID-19 pandemic: a nationwide observational cohort study", @@ -905192,6 +907108,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.02.26.21252538", + "rel_title": "Prioritizing the first doses of SARS-CoV-2 vaccine to save the elderly: the case study of Italy", + "rel_date": "2021-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.26.21252538", + "rel_abs": "Many countries are currently facing high mortality caused by the circulation of SARS-CoV-2 among the elderly not yet vaccinated. Vaccine shortage poses relevant challenges to health authorities, called to act in a timely manner, and with scarcity of vaccine, and data. We have developed a model for estimating of the impact of vaccination on the mortality of the elderly following a schedule of mRNA SARS-CoV-2 vaccine that prioritize first dose administration, as alternative to the standard schedule of two doses administered 3 to 4 weeks apart. We studied the Italian scenario, considering it representative of other Countries facing similar conditions in terms of virus circulation, mortality, and vaccine shortage, in the period from February 10 to April 14 2021. Under different conditions of quantity of vaccine administration, the schedule prioritizing first doses showed always significant increase of protected individuals, and a decrease of deaths, up to 19.8% less than the standard schedule. These findings support the vaccination option of prioritizing first dose in the elderly until vaccine supplies are adequate.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Giuseppe Pontrelli", + "author_inst": "1Academic Department of Pediatrics (DPUO), Bambino Gesu Children Hospital IRCCS-University of Tor Vergata, Rome, Italy" + }, + { + "author_name": "Giulio Cimini", + "author_inst": "Physics Department and INFN, University of Tor Vergata, Rome, Italy; and Enrico Fermi Research Center, Rome, Italy" + }, + { + "author_name": "Marco Roversi", + "author_inst": "1Academic Department of Pediatrics (DPUO), Bambino Gesu Children Hospital IRCSS-University of Tor Vergata, Rome, Italy" + }, + { + "author_name": "Andrea Gabrielli", + "author_inst": "Engineering Department, Roma Tre University and Enrico Fermi Research Center, Rome, Italy" + }, + { + "author_name": "Gaetano Salina", + "author_inst": "Physics Department and INFN, University of Tor Vergata and Enrico Fermi Research Center, Rome, Italy" + }, + { + "author_name": "Stefania Bernardi", + "author_inst": "Academic Department of Pediatrics (DPUO), Bambino Gesu Children Hospital IRCSS-University of Tor Vergata, Rome, Italy" + }, + { + "author_name": "Francesca Rocchi", + "author_inst": "1Academic Department of Pediatrics (DPUO), Bambino Gesu Children Hospital IRCCS-University of Tor Vergata, Rome, Italy" + }, + { + "author_name": "Alessandra Simonetti", + "author_inst": "Academic Department of Pediatrics (DPUO), Bambino Gesu Children Hospital IRCSS-University of Tor Vergata, Rome, Italy" + }, + { + "author_name": "Carlo Giaquinto", + "author_inst": "University of Padua, Padua, Italy;" + }, + { + "author_name": "Paolo Rossi", + "author_inst": "Academic Department of Pediatrics (DPUO), Bambino Gesu Children Hospital IRCCS-University of Tor Vergata, Rome, Italy" + }, + { + "author_name": "Francesco Sylos Labini", + "author_inst": "Enrico Fermi Research Center, Rome, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.25.21252488", "rel_title": "Povidone iodine, hydrogen peroxide and chlorhexidine mouthwashes reduce SARS-CoV2 burden in whole mouth fluid and respiratory droplets", @@ -906827,33 +908802,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.03.01.433379", - "rel_title": "Meta-Research: Citation needed? Wikipedia and the COVID-19 pandemic", - "rel_date": "2021-03-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.01.433379", - "rel_abs": "BackgroundWith the COVID-19 pandemics outbreak, millions flocked to Wikipedia for updated information. Amid growing concerns regarding an \"infodemic\", ensuring the quality of information is a crucial vector of public health. Investigating if and how Wikipedia remained up to date and in line with science is key to formulating strategies to counter misinformation. Using citation analyses, we asked: which sources informed Wikipedias COVID-19-related articles before and during the pandemics first wave (January-May 2020).\n\nResultsWe found that coronavirus-related articles referenced trusted media sources and high-quality academic research. Moreover, despite a surge in COVID-19 preprints, Wikipedia had a clear preference for open-access studies published in respected journals and made little use of preprints. Building a timeline of English COVID-19 articles from 2001-2020 revealed a nuanced trade-off between quality and timeliness. It further showed how preexisting articles on key topics related to the virus created a framework for integrating new knowledge. Supported by a rigid sourcing policy, this \"scientific infrastructure\" facilitated contextualization and regulated the influx of new information. Lastly, we constructed a network of DOI-Wikipedia articles, which showed the shifting landscape of pandemic-related knowledge on Wikipedia and how academic citations create a web of shared knowledge supporting topics like COVID-19 vaccine development.\n\nConclusionsUnderstanding how scientific research interacts with the digital knowledge-sphere during the pandemic provides insight into how Wikipedia can facilitate access to science. It also reveals how, aided by what we term its \"citizen encyclopedists\", it successfully fended off COVID-19 disinformation and how this unique model may be deployed in other contexts.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Omer Benjakob", - "author_inst": "The Cohn Institute for the History and Philosophy of Science and Ideas, Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Rona Aviram", - "author_inst": "Weizmann Institute of Science, Rehovot, Israel" - }, - { - "author_name": "Jonathan Aryeh Sobel", - "author_inst": "Technion" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "scientific communication and education" - }, { "rel_doi": "10.1101/2021.02.27.21252577", "rel_title": "Nationwide rollout reveals efficacy of epidemic control through digital contact tracing", @@ -907042,6 +908990,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.25.21252441", + "rel_title": "Leveraging genetic data to elucidate the relationship between Covid-19 and ischemic stroke", + "rel_date": "2021-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.25.21252441", + "rel_abs": "BackgroundThe relationship between coronavirus disease 2019 (Covid-19) and ischemic stroke is poorly defined. We aimed to leverage genetic data to investigate reported associations.\n\nMethodsGenetic association estimates for liability to Covid-19 and cardiovascular traits were obtained from large-scale consortia. Analyses primarily focused on critical Covid-19, defined as hospitalization with Covid-19 requiring respiratory support or resulting in death. Cross-trait linkage disequilibrium score regression was used to estimate genetic correlations of critical Covid-19 with ischemic stroke, other related cardiovascular outcomes, and risk factors common to both Covid-19 and cardiovascular disease (body mass index, smoking and chronic inflammation, estimated using C-reactive protein). Mendelian randomization analysis was performed to investigate whether liability to critical Covid-19 was associated with increased risk of any of the cardiovascular outcomes for which genetic correlation was identified.\n\nResultsThere was evidence of genetic correlation between critical Covid-19 and ischemic stroke (rg=0.29, FDR p-value=4.65x10-3), body mass index (rg=0.21, FDR-p-value=6.26x10-6) and C-reactive protein (rg=0.20, FDR-p-value=1.35x10-4), but none of the other considered traits. In Mendelian randomization analysis, liability to critical Covid-19 was associated with increased risk of ischemic stroke (odds ratio [OR] per logOR increase in genetically predicted critical Covid-19 liability 1.03, 95% confidence interval 1.00-1.06, p-value=0.03). Similar estimates were obtained when considering ischemic stroke subtypes. Consistent estimates were also obtained when performing statistical sensitivity analyses more robust to the inclusion of pleiotropic variants, including multivariable Mendelian randomization analyses adjusting for potential genetic confounding through body mass index, smoking and chronic inflammation. There was no evidence to suggest that genetic liability to ischemic stroke increased the risk of critical Covid-19.\n\nConclusionsThese data support that liability to critical Covid-19 is associated with an increased risk of ischemic stroke. The host response predisposing to severe Covid-19 is likely to increase the risk of ischemic stroke, independent of other potentially mitigating risk factors.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Verena Zuber", + "author_inst": "Imperial College London" + }, + { + "author_name": "Alan Cameron", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Evangelos Pavlos Myserlis", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Leonardo Bottolo", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Israel Fernandez-Cadenas", + "author_inst": "Stroke Pharmacogenomics and Genetics Group" + }, + { + "author_name": "Stephen Burgess", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Christopher D Anderson", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Jesse Dawson", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Dipender Gill", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2021.02.24.21252390", "rel_title": "Graphical Models of Pandemic", @@ -908405,41 +910404,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.26.21252336", - "rel_title": "What is the effect of lockdown upon hospitalisation due to COVID-19 amongst patients from a heart failure registry?", - "rel_date": "2021-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.26.21252336", - "rel_abs": "IntroductionCoronavirus disease 2019 (COVID-19) is associated with a high risk of mortality especially in patients with cardiovascular conditions such as heart failure. The UK government announced a national lockdown last year to curb the spread of the virus. We conducted this study primarily to ascertain the impact of lockdown upon the incidence of COVID-19 hospitalisation amongst patients with a known diagnosis of heart failure (HF)\n\nMethodsThis was a retrospective cohort study of 1097 patients from our HF registry who had presented with acute decompensated HF in 2018 and 2019. Incidence and outcomes of hospitalisation due to COVID-19 were analysed in this cohort both during the 1st UK lockdown as well as after the lockdown period. Co-morbidities, frailty index, clinical features, blood results, and heart failure treatments were compared between the 2 groups (COVID versus no-COVID) and between the group of patients who died versus survivors.\n\nResults50 out of 801 surviving (6.2%) HF patients required hospitalisation due to COVID-19 from March to November 2020; 24 patients (3.1%) during the first lockdown and 26 (3.5%) in the post-lockdown period; p=0.7. In comparison to patients not hospitalised with COVID-19 (\"no-COVID group), there was a significantly higher prevalence of co-morbidities amongst HF patients who were hospitalised with COVID-19, such as hypertension (p<0.001), diabetes (p=0.005), ischaemic heart disease (p=0.01) and increased body mass index. 30 day mortality amongst HF patients hospitalised due to COVID-19 was 52%. Rockwood Frailty Score [≥]6 (OR 6.530695 % CI:1.8958 to 22.4961; p=0.003) and diabetes (OR 3.82;95% CI 1.13 to 12.95; p=0.03) were independent predictors of 30 day mortality.\n\nConclusionOur data suggests that the incidence of hospitalisation due to COVID-19 was similar both during as well as post lockdown amongst patients from our HF registry. HF patients with cardiovascular co-morbidities such as obesity, hypertension, diabetes and ischaemic heart disease have a higher risk of hospitalisation due to COVID-19. Diabetes and Rockwood Frailty score are independent predictors of short term mortality. Co-morbidity and frailty scores should be incorporated during initial assessment to help risk-prediction.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "hani abobakr essa", - "author_inst": "Aintree university hospital" - }, - { - "author_name": "Sophia brousas", - "author_inst": "Aintree university hospital" - }, - { - "author_name": "Isabel whybrow-huppatz", - "author_inst": "Aintree university hospital" - }, - { - "author_name": "thomas salmon", - "author_inst": "Aintree university hospital" - }, - { - "author_name": "rajiv sankaranarayanan", - "author_inst": "Aintree university hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2021.02.26.21252553", "rel_title": "Vaccination and herd immunity thresholds in heterogeneous populations", @@ -908596,6 +910560,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.26.21251868", + "rel_title": "The localized rise of a B.1.526 variant containing an E484K mutation in New York State", + "rel_date": "2021-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.26.21251868", + "rel_abs": "The E484K mutation in the spike protein of SARS CoV-2 contributes to immune escape from monoclonal antibodies as well as neutralizing antibodies in COVID-19 convalescent plasma. It appears in two variants of concern - B.1.351 and P.1 - but has evolved multiple times in different SARS-CoV-2 lineages, suggesting an adaptive advantage. Here we report on the emergence of a 484K variant in the B.1.526 lineage that has recently become prevalent in New York State, particularly in the New York City metropolitan area. In addition to the E484K mutation, these variants also harbor a D235G substitution in spike that might help to reduce the efficacy of neutralizing antibodies.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Erica Lasek-Nesselquist", + "author_inst": "Wadsworth Center" + }, + { + "author_name": "Pascal Lapierre", + "author_inst": "Wadsworth Center" + }, + { + "author_name": "Erasmus Schneider", + "author_inst": "Wadsworth Center" + }, + { + "author_name": "Kirsten St. George", + "author_inst": "Wadsworth Center, NYSDOH" + }, + { + "author_name": "Janice Pata", + "author_inst": "Wadsworth Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.25.21252481", "rel_title": "Excess deaths reveal the true spatial, temporal, and demographic impact of COVID-19 on mortality in Ecuador", @@ -910119,141 +912118,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.24.21252335", - "rel_title": "The neurology and neuropsychiatry of COVID-19: a systematic review and meta-analysis of the early literature reveals frequent CNS manifestations and key emerging narratives", - "rel_date": "2021-02-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.24.21252335", - "rel_abs": "ObjectivesThere is accumulating evidence of the neurological and neuropsychiatric features of infection with SARS-CoV-2. In this systematic review and meta-analysis, we aimed to describe the characteristics of the early literature and estimate point prevalences for neurological and neuropsychiatric manifestations.\n\nMethodsWe searched MEDLINE, Embase, PsycInfo and CINAHL up to 18 July 2020 for randomised controlled trials, cohort studies, case-control studies, cross-sectional studies and case series. Studies reporting prevalences of neurological or neuropsychiatric symptoms were synthesised into meta-analyses to estimate pooled prevalence.\n\nResults13,292 records were screened by at least two authors to identify 215 included studies, of which there were 37 cohort studies, 15 case-control studies, 80 cross-sectional studies and 83 case series from 30 countries. 147 studies were included in the meta-analysis. The symptoms with the highest prevalence were anosmia (43.1% [35.2--51.3], n=15,975, 63 studies), weakness (40.0% [27.9--53.5], n=221, 3 studies), fatigue (37.8% [31.6--44.4], n=21,101, 67 studies), dysgeusia (37.2% [30.0--45.3], n=13,686, 52 studies), myalgia (25.1% [19.8--31.3], n=66.268, 76 studies), depression (23.0 % [11.8--40.2], n=43,128, 10 studies), headache (20.7% [95% CI 16.1--26.1], n=64,613, 84 studies), anxiety (15.9% [5.6--37.7], n=42,566, 9 studies) and altered mental status (8.2% [4.4--14.8], n=49,326, 19 studies). Heterogeneity for most clinical manifestations was high.\n\nConclusionsNeurological and neuropsychiatric symptoms of COVID-19 in the pandemics early phase are varied and common. The neurological and psychiatric academic communities should develop systems to facilitate high-quality methodologies, including more rapid examination of the longitudinal course of neuropsychiatric complications of newly emerging diseases and their relationship to neuroimaging and inflammatory biomarkers.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Jonathan P Rogers", - "author_inst": "Division of Psychiatry, University College London, London, UK. South London and Maudsley NHS Foundation Trust, London, UK." - }, - { - "author_name": "Cameron Watson", - "author_inst": "Preventive Neurology Unit, Wolfson Institute of Preventive Medicine, Queen Mary University of Medicine. Barts Health NHS Trust." - }, - { - "author_name": "James Badenoch", - "author_inst": "Medical School, University of Birmingham" - }, - { - "author_name": "Benjamin Cross", - "author_inst": "East Lancashire Hospitals NHS Trust" - }, - { - "author_name": "Matthew Butler", - "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, King's College London" - }, - { - "author_name": "Jia Song", - "author_inst": "East London NHS Foundation Trust" - }, - { - "author_name": "Danish Hafeez", - "author_inst": "School of Medical Sciences, The University of Manchester, Manchester, UK" - }, - { - "author_name": "Hamilton Morrin", - "author_inst": "Maidstone & Tunbridge Wells NHS Trust, Kent, UK" - }, - { - "author_name": "Emma Rachel Rengasamy", - "author_inst": "Cwm Taf Morgannwg University Health Board" - }, - { - "author_name": "Lucretia Thomas", - "author_inst": "College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK." - }, - { - "author_name": "Silviya Ralovska", - "author_inst": "Department of Neurology, Psychiatry, Physiotherapy and Rehabilitation, Preventive Medicine, and Public Health, Sofia University \"St. Kliment Ohridski\"" - }, - { - "author_name": "Abigail Smakowski", - "author_inst": "Neuropsychiatry Outpatients & Persistent Physical Symptoms Research and Treatment Unit, Maudsley Hospital, South London and Maudsley Hospital NHS Trust, London," - }, - { - "author_name": "Ritika Dilip Sundaram", - "author_inst": "School of Medicine, University of Glasgow, UK" - }, - { - "author_name": "Camille Kaitlyn Hunt", - "author_inst": "MS & NMO Clinical Trials Group, Division of Neurology, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, B.C., Canada" - }, - { - "author_name": "Mao Fong Lim", - "author_inst": "Cambridge University Hospital NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK" - }, - { - "author_name": "Daruj Aniwattanapong", - "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK. Department of Psychiatry, Faculty of Medicine, Chulalongkorn University, Bangko" - }, - { - "author_name": "Vanshika Singh", - "author_inst": "Senior Sub-Editor and Staff Writer, The Wire Science" - }, - { - "author_name": "Zain Hussain", - "author_inst": "Edinburgh Medical School, College of Medicine and Veterinary Medicine, University of Edinburgh, UK" - }, - { - "author_name": "Stuti Chakraborty", - "author_inst": "Department of Physical Medicine and Rehabilitation, Christian Medical College and Hospital, Vellore, India" - }, - { - "author_name": "Ella Burchill", - "author_inst": "King's College London, Faculty of Medicine and Life Sciences, London SE1 1UL" - }, - { - "author_name": "Katrin Jansen", - "author_inst": "Department of Psychology, University of Munster, Germany" - }, - { - "author_name": "Heinz Holling", - "author_inst": "Department of Psychology, University of Munster, Germany" - }, - { - "author_name": "Dean Walton", - "author_inst": "Department of Neurology, The Walton Centre NHS Foundation Trust, Liverpool, UK" - }, - { - "author_name": "Thomas A Pollak", - "author_inst": "Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK" - }, - { - "author_name": "Mark Ellul", - "author_inst": "Department of Neurology, The Walton Centre NHS Foundation Trust, Liverpool, UK; National Institute for Health Research Health Protection Research Unit in Emergi" - }, - { - "author_name": "Ivan Koychev", - "author_inst": "Department of Psychiatry, University of Oxford, Oxford, UK; Department of Psychological Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK" - }, - { - "author_name": "Tom Solomon", - "author_inst": "National Institute for Health Research Health Protection Research Unit on Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sc" - }, - { - "author_name": "Benedict Daniel Michael", - "author_inst": "Department of Neurology, The Walton Centre NHS Foundation Trust, Liverpool, UK; National Institute for Health Research Health Protection Research Unit in Emergi" - }, - { - "author_name": "Timothy R Nicholson", - "author_inst": "Section of Cognitive Neuropsychiatry, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK" - }, - { - "author_name": "Alasdair G Rooney", - "author_inst": "Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.02.24.21252135", "rel_title": "Risk factors for increased COVID-19 case-fatality in the United States: A county-level analysis during the first wave", @@ -910490,6 +912354,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, + { + "rel_doi": "10.1101/2021.02.24.21252329", + "rel_title": "Long COVID neuropsychological deficits after severe, moderate or mild infection", + "rel_date": "2021-02-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.24.21252329", + "rel_abs": "BackgroundThere is growing awareness that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can include long-term neuropsychological deficits, even in its mild or moderate respiratory forms.\n\nMethodsStandardized neuropsychological, psychiatric, neurological and olfactory tests were administered to 45 patients (categorized according to the severity of their respiratory symptoms during the acute phase) 236.51 {+/-} 22.54 days post-discharge following SARS-CoV-2 infection.\n\nResultsDeficits were found in all the domains of cognition and the prevalence of psychiatric symptoms was also high in the three groups. The severe performed more poorly on long-term episodic memory and exhibited greater anosognosia. The moderate had poorer emotion recognition, which was positively correlated with persistent olfactory dysfunction. The mild were more stressed, anxious and depressed.\n\nConclusionThe data support the hypothesis that the virus targets the central nervous system (and notably the limbic system), and support the notion of different neuropsychological phenotypes.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Philippe Voruz", + "author_inst": "Clinical and Experimental Neuropsychology Laboratory, Faculty of Psychology, University of Geneva, Geneva, Switzerland" + }, + { + "author_name": "Gilles Allali", + "author_inst": "Neurology Department, Geneva University Hospitals, Switzerland" + }, + { + "author_name": "Lamyae Benzakour", + "author_inst": "Psychiatry Department, Geneva University Hospitals, Switzerland" + }, + { + "author_name": "Anthony Nuber-Champier", + "author_inst": "Clinical and Experimental Neuropsychology Laboratory, Faculty of Psychology, University" + }, + { + "author_name": "Marine Thomasson", + "author_inst": "Clinical and Experimental Neuropsychology Laboratory, Faculty of Psychology, University" + }, + { + "author_name": "Isabele Jacot", + "author_inst": "Clinical and Experimental Neuropsychology Laboratory, Faculty of Psychology, University" + }, + { + "author_name": "Jordan Pierce", + "author_inst": "Clinical and Experimental Neuropsychology Laboratory, Faculty of Psychology, University" + }, + { + "author_name": "Patrice Lalive", + "author_inst": "Neurology Department, Geneva University Hospitals, Switzerland" + }, + { + "author_name": "Karl-Olof Lovblad", + "author_inst": "Diagnostic and Interventional Neuroradiology Department, Geneva University Hospitals, Switzerland" + }, + { + "author_name": "Olivia Brallaird", + "author_inst": "Division and Department of Primary Care, Geneva University Hospitals, Switzerland" + }, + { + "author_name": "Matteo Coen", + "author_inst": "Internal Medicine Department, Geneva University Hospitals, Switzerland" + }, + { + "author_name": "Jacques Serratrice", + "author_inst": "Internal Medicine Department, Geneva University Hospitals, Switzerland" + }, + { + "author_name": "Jerome Pugin", + "author_inst": "Intensive Care Department, Geneva University Hospitals, Switzerland" + }, + { + "author_name": "Radek Ptak", + "author_inst": "Neurorehabilitation Department, Geneva University Hospital, Switzerland" + }, + { + "author_name": "Idriss Guessous", + "author_inst": "Division and Department of Primary Care, Geneva University Hospitals, Switzerland" + }, + { + "author_name": "Basile Landis", + "author_inst": "Rhinology-Olfactology Unit, Otorhinolaryngology Department, Geneva University Hospitals, Switzerland" + }, + { + "author_name": "Frederic Assal", + "author_inst": "Neurology Department, Geneva University Hospitals, Switzerland" + }, + { + "author_name": "Julie Anne Peron", + "author_inst": "Clinical and Experimental Neuropsychology Laboratory, Faculty of Psychology, University of Geneva, Geneva, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2021.02.23.21252323", "rel_title": "An empirical analysis of what people learned about COVID-19 through a web search and the impacts on misinformation and attitude towards public health safety guidelines.", @@ -912277,61 +914228,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.02.25.432853", - "rel_title": "Pyroptosis of syncytia formed by fusion of SARS-CoV-2 Spike and ACE2 expressing cells", - "rel_date": "2021-02-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.25.432853", - "rel_abs": "SARS-Cov-2 infected cells fused with the ACE2-positive neighboring cells forming syncytia. However, the effect of syncytia in disease development is largely unknown. We established an in vitro cell-cell fusion system and used it to mimic the fusion of SARS-CoV-2 infected cells with ACE2-expressing cells to form syncytia. We found that Caspase-9 was activated after syncytia formation, and Caspase-3/7 was activated downstream of Caspase-9, but it triggered GSDME-dependent pyroptosis rather than apoptosis. What is more, single cell RNA-sequencing data showed that both ACE2 and GSDME were expression in alveolar type 2 cells in human lung. We propose that pyroptosis is the fate of syncytia formed by SARS-CoV-2 infected host cells and ACE2-positive cells, which indicated that lytic death of syncytia may contribute to the excessive inflammatory responses in severe COVID-19 patients.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Huabin Ma", - "author_inst": "Institute of Drug Discovery Technology, Ningbo University" - }, - { - "author_name": "Zhoujie Zhu", - "author_inst": "Institute of Drug Discovery Technology, Ningbo University" - }, - { - "author_name": "Huaipeng Lin", - "author_inst": "Xiamen University" - }, - { - "author_name": "Shanshan Wang", - "author_inst": "Institute of Drug Discovery Technology, Ningbo University" - }, - { - "author_name": "Peipei Zhang", - "author_inst": "Xiamen University" - }, - { - "author_name": "Yanguo Li", - "author_inst": "Institute of Drug Discovery Technology, Ningbo University" - }, - { - "author_name": "Long Li", - "author_inst": "Institute of Drug Discovery Technology, Ningbo University" - }, - { - "author_name": "Jinling Wang", - "author_inst": "Department of Emergency, Zhongshan Hospital of Xiamen University" - }, - { - "author_name": "Yufen Zhao", - "author_inst": "Institute of Drug Discovery Technology, Ningbo University" - }, - { - "author_name": "Jiahuai Han", - "author_inst": "Xiamen University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2021.02.25.432762", "rel_title": "The type 2 asthma mediator IL-13 inhibits SARS-CoV-2 infection of bronchial epithelium", @@ -912576,6 +914472,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.24.21252337", + "rel_title": "A prospective evaluation of the analytical performance of GENECUBE(R) HQ SARS-CoV-2 and GENECUBE(R) FLU A/B", + "rel_date": "2021-02-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.24.21252337", + "rel_abs": "BackgroundMolecular tests are the mainstay for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, their accessibility can be limited by the long examination time and inability to evaluate multiple samples at once. This study evaluated the analytical performance of the newly developed rapid molecular assays GENECUBE(R) HQ SARS-CoV-2 and the GENECUBE(R) FLU A/B.\n\nMethodThis prospective study was conducted between December 14, 2020, and January 9, 2021, at a polymerase chain reaction (PCR) center. Samples were collected from the nasopharynx with flocked swabs. Molecular tests were performed with the GENECUBE(R) system and reference reverse transcription (RT)-PCR, and the results of the two assays were compared.\n\nResultAmong 1065 samples, 81 (7.6%) were positive for SARS-CoV-2 on the reference RT-PCR. Three showed discordance between GENECUBE(R) HQ SARS-CoV-2 and the reference RT-PCR; the total, positive and negative samples of concordance for the two assays were 99.7%, 100%, and 99.7%, respectively. All discordant cases were positive for GENECUBE(R) HQ SARS-CoV-2 and negative for the reference RT-PCR. SARS-CoV-2 was detected from all three samples by another molecular assay for SARS-CoV-2. For the GENECUBE(R) FLU A/B, the total, positive and negative samples of concordance for the two assays were 99.5%, 100%, and 99.1%.\n\nConclusionThe GENECUBE(R) HQ SARS-CoV-2 and GENECUBE(R) FLU A/B demonstrated sufficient analytical performance to detect SARS-CoV-2 and influenza virus A/B.\n\nKey pointsWe prospectively evaluated the analytical performance of the newly developed rapid molecular assays GENECUBE(R) HQ SARS-CoV-2 and the GENECUBE(R) FLU A/B. The two assays showed >99% concordance rate compared with a reference PCR, which indicated their sufficient analytical performance to detect SARS-CoV-2 and influenza virus A/B.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Yoshihiko Kiyasu Dr.", + "author_inst": "Department of Infectious Diseases, University of Tsukuba Hospital" + }, + { + "author_name": "Yusaku Akashi Dr.", + "author_inst": "Division of Infectious Diseases, Department of Medicine, Tsukuba Medical Center Hospital" + }, + { + "author_name": "Akio Sugiyama Mr.", + "author_inst": "Diagnostic System Department, TOYOBO Co., Ltd." + }, + { + "author_name": "Yuto Takeuchi Dr.", + "author_inst": "Department of Infectious Diseases, University of Tsukuba Hospital" + }, + { + "author_name": "Shigeyuki Notake Dr.", + "author_inst": "Department of Clinical Laboratory, Tsukuba Medical Center Hospital" + }, + { + "author_name": "Asami Naito Ms.", + "author_inst": "Tsukuba i-Laboratory LLP" + }, + { + "author_name": "Koji Nakamura Mr.", + "author_inst": "Department of Clinical Laboratory, Tsukuba Medical Center Hospital" + }, + { + "author_name": "Hiroichi Ishikawa Dr.", + "author_inst": "Department of Respiratory Medicine, Tsukuba Medical Center Hospital" + }, + { + "author_name": "Hiromichi Suzuki Prof.", + "author_inst": "Department of Infectious Diseases, Faculty of Medicine, University of Tsukuba" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.23.21251866", "rel_title": "Genetic predisposition to psychiatric disorders and risk of COVID-19", @@ -914015,41 +915962,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.02.24.432721", - "rel_title": "A missense variant effect prediction and annotation resource for SARS-CoV-2", - "rel_date": "2021-02-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.24.432721", - "rel_abs": "The COVID19 pandemic is a global crisis severely impacting many people across the world. An important part of the response is monitoring viral variants and determining the impact they have on viral properties, such as infectivity, disease severity and interactions with drugs and vaccines. In this work we generate and make available computational variant effect predictions for all possible single amino-acid substitutions to SARS-CoV-2 in order to complement and facilitate experiments and expert analysis. The resulting dataset contains predictions from evolutionary conservation and protein and complex structural models, combined with viral phosphosites, experimental results and variant frequencies. We demonstrate predictions effectiveness by comparing them with expectations from variant frequency and prior experiments. We then identify higher frequency variants with significant predicted effects as well as finding variants measured to impact antibody binding that are least likely to impact other viral functions. A web portal is available at sars.mutfunc.com, where the dataset can be searched and downloaded.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Alistair Dunham", - "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK" - }, - { - "author_name": "Gwendolyn M Jang", - "author_inst": "Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA" - }, - { - "author_name": "Monita Muralidharan", - "author_inst": "Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA" - }, - { - "author_name": "Danielle Swaney", - "author_inst": "Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA" - }, - { - "author_name": "Pedro Beltrao", - "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.02.24.432656", "rel_title": "SARS-CoV-2 ORF6 disturbs nucleocytoplasmic trafficking to advance the viral replication", @@ -914398,6 +916310,77 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.02.24.432694", + "rel_title": "Rapid adaptation and remote delivery of undergraduate research training during the COVID 19 Pandemic", + "rel_date": "2021-02-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.24.432694", + "rel_abs": "COVID-19 continues to alter daily life around the globe. Education is particularly affected by shifts to distance learning. This change has poignant effects on all aspects of academic life, including the consequence of increased mental stress reported specifically for students. COVID-19 cancellations of many summer fellowships and internships for undergraduates across the country increased students uncertainty about their educational opportunities and careers. When the pandemic necessitated elimination of on-campus programming at Mayo Clinic, a new program was developed for remote delivery. Summer Foundations in Research (SFIR) was drafted around 4 aims: 1) support the academic trajectory gap in research science created by COVID-19; 2) build sustainable scientific relationships with mentors, peers, and the community; 3) create opportunities for participants to share and address concerns with their own experiences in the pandemic; and 4) provide support for individual wellbeing. SFIR included research training, but also training in communication through generative Dialogue and resilience through Amit Soods SMART program. 170 participants were followed for outcomes in these spaces. Knowledge of and interest in careers involving biomedical research rose significantly following SFIR. Participants mean confidence levels in 12 Key areas of research rose between 0.08 to 1.32 points on a 7-point scale. The strongest gains in mean confidence levels were seen in designing a study and collaborating with others. SFIR participants demonstrated gains in perceived happiness, and measured resilience and a reduction in stress. Participants qualitative responses indicated exceptionally positive mentor relationships and specific benefit of both the SMART program and Dialogue.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Joanna Yang Yowler", + "author_inst": "Department of Research, Mayo Clinic, Jacksonville, FL, United States" + }, + { + "author_name": "Kit Knier", + "author_inst": "Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, United States; Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Roch" + }, + { + "author_name": "Zachary WareJoncas", + "author_inst": "Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States" + }, + { + "author_name": "Shawna L. Ehlers", + "author_inst": "Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, United States; Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, " + }, + { + "author_name": "Stephen C Ekker", + "author_inst": "Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States; Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Ro" + }, + { + "author_name": "Fabiola Guasp Reyes", + "author_inst": "University of Puerto Rico School of Medicine, San Juan, Puerto Rico, United States" + }, + { + "author_name": "Bruce F. Horazdovsky", + "author_inst": "Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States; Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Ro" + }, + { + "author_name": "Glenda Mueller", + "author_inst": "Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, United States" + }, + { + "author_name": "Adriana Morales Gomez", + "author_inst": "Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, United States" + }, + { + "author_name": "Amit Sood", + "author_inst": "Global Center for Resiliency and Wellbeing, Rochester, MN, United States" + }, + { + "author_name": "Caroline R. Sussman", + "author_inst": "Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, United States; Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic," + }, + { + "author_name": "Linda M. Scholl", + "author_inst": "Office of Applied Scholarship and Education Science, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States; Mayo Clinic Graduate School of " + }, + { + "author_name": "Karen M. Weavers", + "author_inst": "Office of Applied Scholarship and Education Science, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States; Mayo Clinic Graduate School of " + }, + { + "author_name": "Christopher Pierret", + "author_inst": "Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States; Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Ro" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2021.02.19.21252062", "rel_title": "International travel in times of the COVID-19 pandemic: Evidence from German school breaks", @@ -915941,93 +917924,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.22.21252237", - "rel_title": "Group IIA Secreted Phospholipase A2 Plays a Central Role in the Pathobiology of COVID-19", - "rel_date": "2021-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.22.21252237", - "rel_abs": "There is an urgent need to identify cellular and molecular mechanisms responsible for severe COVID-19 disease accompanied by multiple organ failure and high mortality rates. Here, we performed untargeted/targeted lipidomics and focused biochemistry on 127 patient plasma samples, and showed high levels of circulating, enzymatically active secreted phospholipase A2 Group IIA (sPLA2-IIA) in severe and fatal COVID-19 disease compared with uninfected patients or mild illness. Machine learning demonstrated that sPLA2-IIA effectively stratifies severe from fatal COVID-19 disease. We further introduce a PLA-BUN index that combines sPLA2-IIA and blood urea nitrogen (BUN) threshold levels as a critical risk factor for mitochondrial dysfunction, sustained inflammatory injury and lethal COVID-19. With the availability of clinically tested inhibitors of sPLA2-IIA, our study opens the door to a precision intervention using indices discovered here to reduce COVID-19 mortality.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Justin M Snider", - "author_inst": "University of Arizona" - }, - { - "author_name": "Jeehyun Karen You", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Xia Wang", - "author_inst": "University of Arizona" - }, - { - "author_name": "Ashley J Snider", - "author_inst": "University of Arizona" - }, - { - "author_name": "Brian Hallmark", - "author_inst": "University of Arizona" - }, - { - "author_name": "Michael C Seeds", - "author_inst": "Wake Forest School of Medicine" - }, - { - "author_name": "Susan Sergeant", - "author_inst": "Wake Forest School of Medicine" - }, - { - "author_name": "Laurel Johnstone", - "author_inst": "University of Arizona" - }, - { - "author_name": "Qiuming Wang", - "author_inst": "University of Arizona" - }, - { - "author_name": "Ryan Sprissler", - "author_inst": "University of Arizona" - }, - { - "author_name": "Hao Helen Zhang", - "author_inst": "University of Arizona" - }, - { - "author_name": "Chiara Luberto", - "author_inst": "Stony Brook University, Stony Brook Cancer Center" - }, - { - "author_name": "Richard R Kew", - "author_inst": "Stony Brook Cancer Center, Stony Brook University, Veteran Affairs Medical Center" - }, - { - "author_name": "Yusuf A Hannun", - "author_inst": "Stony Brook Cancer Center, Stony Brook University, Veteran Affairs Medical Center - Northport" - }, - { - "author_name": "Charles E McCall", - "author_inst": "Wake Forest Medical School" - }, - { - "author_name": "Guang Yao", - "author_inst": "University of Arizona, Arizona Cancer Center" - }, - { - "author_name": "Maurizio Del Poeta", - "author_inst": "Stony Brook University, Veteran Affairs Medical Center -Northport" - }, - { - "author_name": "Floyd H Chilton", - "author_inst": "University of Arizona" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.22.21251534", "rel_title": "The spatio-temporal distribution of COVID-19 infection in England between January and June 2020.", @@ -916232,6 +918128,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.21.21252132", + "rel_title": "Heterogeneity in COVID-19 severity patterns among age-gender groups: an analysis of 778 692 Mexican patients through a meta-clustering technique", + "rel_date": "2021-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.21.21252132", + "rel_abs": "We apply a meta-clustering technique to discover age-gender unbiased COVID-19 patient subphenotypes based on phenotypical before admission, including pre-existing comorbidities, habits and demographic features, to study the potential early severity stratification capabilities of the discovered subgroups through characterizing their severity patterns including prognostic, ICU and morbimortality outcomes. We used the Mexican Government COVID-19 open data including 778,692 SARS-CoV-2 population-based patient-level data as of September 2020. The meta-clustering technique consists of a two-stage clustering approach combining dimensionality reduction and hierarchical clustering: 56 clusters from independent age-gender clustering analyses supported 11 clinically distinguishable meta-clusters (MCs). MCs 1-3 showed high recovery rates (90.27-95.22%), including healthy patients of all ages; children with comorbidities alongside priority in medical resources; and young obese smokers. MCs 4-5 showed moderate recovery rates (81.3-82.81%): patients with hypertension or diabetes of all ages; and obese patients with pneumonia, hypertension and diabetes. MCs 6-11 showed low recovery rates (53.96-66.94%): immunosuppressed patients with high comorbidity rate; CKD patients with poor survival length and recovery; elderly smokers with COPD; severe diabetic elderly with hypertension; and oldest obese smokers with COPD and mild cardiovascular disease. Group outcomes conformed to the recent literature on dedicated age-gender groups. These results can potentially help in the clinical patient understanding and their stratification towards automated early triage, prior to further tests and laboratory results are available, or help decide priority in vaccination or resource allocation among vulnerable subgroups or locations where additional tests are not available.\n\nCode available at: https://github.com/bdslab-upv/covid19-metaclustering", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Lexin Zhou", + "author_inst": "Biomedical Data Science Laboratory (BDSLab), Instituto de Aplicaciones de las Tecnolog\u00edas de la Informaci\u00f3n y de las Comunicaciones Avanzadas (ITACA), Universit" + }, + { + "author_name": "Nekane Romero", + "author_inst": "Biomedical Data Science Laboratory (BDSLab), Instituto de Aplicaciones de las Tecnolog\u00edas de la Informaci\u00f3n y de las Comunicaciones Avanzadas (ITACA), Universit" + }, + { + "author_name": "Juan Mart\u00ednez Miranda", + "author_inst": "CONACyT - Centro de Investigaci\u00f3n Cient\u00edfica y de Educaci\u00f3n Superior de Ensenada - CICESE-UT3" + }, + { + "author_name": "J Alberto Conejero", + "author_inst": "Instituto Universitario de Matem\u00e1tica Pura y Aplicada (IUMPA), Universitat Polit\u00e8cnica de Val\u00e8ncia, Valencia, Spain" + }, + { + "author_name": "Juan M Garc\u00eda-G\u00f3mez", + "author_inst": "Biomedical Data Science Laboratory (BDSLab), Instituto de Aplicaciones de las Tecnolog\u00edas de la Informaci\u00f3n y de las Comunicaciones Avanzadas (ITACA), Universit" + }, + { + "author_name": "Carlos S\u00e1ez", + "author_inst": "Biomedical Data Science Laboratory (BDSLab), Instituto de Aplicaciones de las Tecnolog\u00edas de la Informaci\u00f3n y de las Comunicaciones Avanzadas (ITACA), Universit" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.18.21251422", "rel_title": "Smelling Household-Odorants Effectively Screens for COVID-19", @@ -918067,57 +920002,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.02.22.21252190", - "rel_title": "A cross-sectional study of socioeconomic status and treatment interruption among Japanese workers during the COVID-19 pandemic", - "rel_date": "2021-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.22.21252190", - "rel_abs": "BackgroundThe COVID-19 pandemic has caused interruptions to chronic disease and non-emergency treatment. The purpose of this study is to examine which socioeconomic status groups are most at risk of treatment interruption.\n\nMethodsThis cross-sectional internet monitor study was conducted on December 22-26, 2020, when Japan experienced its third wave of COVID-19 infection. Out of a total of 33,302 participants in the survey, 9510 (5392 males and 4118 females) who responded that they required regular treatment or hospital visits were included in the analysis. A multilevel logistic model nested in the prefecture of residence was used to estimate the odds ratio (OR) for treatment disruption. We examined separate multivariate models for socioeconomic factors, health factors, and lifestyle factors.\n\nResultsDuring a period of rapid COVID-19 infection, about 11% of Japanese workers who required regular treatment experienced interruptions to their treatment. The OR of treatment interruption associated with not being married compared to being married was 1.44; manual labor work compared to desk work was 1.30; loss of employment when the COVID-19 pandemic started and continued unemployment compared to being employed over the entire pandemic period was 1.62 and 2.57, respectively; and feeling financially unstable was 2.92.\n\nConclusionTreatment interruption is a new health inequality brought about by COVID-19 with possible medium- and long-term effects, including excess mortality, morbidity, and productivity loss due to increased presenteeism. Efforts are needed to reduce treatment interruptions among workers who require regular treatment.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Kenji Fujimoto", - "author_inst": "Occupational Health Data Science Center, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Tomohiro Ishimaru", - "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Seiichiro Tateishi", - "author_inst": "Department of Occupational Medicine, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Tomohisa Nagata", - "author_inst": "Department of Occupational Health Practice and Management, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Jap" - }, - { - "author_name": "Mayumi Tsuji", - "author_inst": "Department of Environmental Health, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Hisashi Eguchi", - "author_inst": "Department of Mental Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Akira Ogami", - "author_inst": "Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Shinya Matsuda", - "author_inst": "Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Yoshihisa Fujino", - "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.02.22.21252207", "rel_title": "Critical COVID-19 represents an endothelial disease with high similarity to kidney disease on the molecular level", @@ -918354,6 +920238,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.22.21252225", + "rel_title": "Neutralizing antibody responses 10 months after mild and moderately-severe SARS-CoV-2 infection", + "rel_date": "2021-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.22.21252225", + "rel_abs": "Improved understanding of immunity offered by the antibodies developed against SARS-CoV-2 is critical. Our study aimed at longitudinal analysis of presence and persistence of neutralizing antibodies over ten months in mild and moderately-severe COVID-19 recovered patients using two immunoassays.\n\nArticle Summary LineNeutralizing IgG antibody persistency was demonstrated in 63.3% of the subjects (19 out of 30) at ten months post-infection with zero re-infections.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Puya Dehgani-Mobaraki", + "author_inst": "Associazione Naso Sano, Italy" + }, + { + "author_name": "Asiya Kamber Zaidi", + "author_inst": "Associazione Naso Sano, Italy" + }, + { + "author_name": "Annamaria Porreca", + "author_inst": "Department of Economics, University \"G.d'Annunzio\", chieti-Pescara,Italy" + }, + { + "author_name": "Alessandro Floridi", + "author_inst": "Laboratory of Nuclear Lipid BioPathology, Centro Ricerche Analisi Biochimico Specialistiche, Perugia, Italy" + }, + { + "author_name": "Emanuela Floridi", + "author_inst": "Laboratory of Nuclear Lipid BioPathology, Centro Ricerche Analisi Biochimico Specialistiche, Perugia, Italy." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.23.432424", "rel_title": "Structural and functional characterization of SARS-CoV-2 RBD domains produced in mammalian cells", @@ -919781,37 +921700,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.18.21250271", - "rel_title": "Effectiveness of Non-Pharmaceutical Interventions on Child and Staff COVID-19 Cases in US Summer Camps", - "rel_date": "2021-02-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21250271", - "rel_abs": "BackgroundMost camps remained closed during Summer 2020, due to concerns regarding child transmission of SARS-CoV-2 and limited information about the effectiveness of non-pharmaceutical interventions (NPIs) within child congregate settings.\n\nMethodsWe surveyed US camps about on-site operations, camper and staff demographics, COVID-19 cases amongst campers and staff, and NPI usage as related to pre-camp quarantines, facial coverings, physical distancing, cleaning, and facility modifications. For all NPIs, save quarantines, responses were provided on a 5-point Likert scale format.\n\nResultsWithin 486 on-site camps, a range of NPIs were instituted, most often related to reduced camper interactions, staff face coverings, cleaning, and hand hygiene. Camper facial coverings were less common, with campers always wearing masks at [~]34% of the camps. Approximately 15% of camps reported 1+ confirmed COVID-19 case in either campers or staff, with three camps reporting a COVID outbreak. In both single and multi-NPI analyses, the risk of COVID-19 cases was lowest when campers always wore facial coverings. While less effective, constant use of staff facial coverings and targeted physical distancing measures, but not pre-camp quarantine, also reduced COVID-19 risks.\n\nConclusionsWe found constant facial coverings, especially for campers, and targeted physical distancing measures to reduce risks of SARS-CoV-2 transmission within summer camps. Our findings provide valuable guidance for future operations of camp and other child congregate settings with regard to efficient and effective NPI usage to mitigate SARS-CoV-2 infection.\n\nWhats Known on This SubjectApproximately 82% of US overnight camps did not open during Summer 2020 due to concerns regarding childrens ability to transmit SARS-CoV-2. Camps that did operate during this time instituted varied non-pharmaceutical interventions (NPIs) to reduce SARS-CoV-2 transmission, with little information available on the effectiveness of these NPIs within child congregate settings. Large population-based studies are needed to improve our understanding of the extent of SARS-CoV-2 infection amongst children and their caregivers and to determine whether and to what degree child congregate programs can safely open during the pandemic.\n\nWhat This Study AddsOur study, the largest survey of COVID-19 cases in child congregate settings at the national level, provides new information on the relative effectiveness of NPIs on mitigating COVID cases among children and staff within camp settings. We showed COVID-19 case rates in campers and staff to be low relative to corresponding case rates in the US and found constant camper facial coverings to be the most effective risk reduction method for SARS-CoV-2 transmission within camps. While less effective, constant use of staff facial coverings and targeted physical distancing measures, but not pre-camp quarantines, were also shown to reduce COVID-19 risks. Our findings has important implications for child congregate settings, helping to guide their successful opening and operation.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Helen H Suh", - "author_inst": "Tufts University" - }, - { - "author_name": "Laura Blaisdell", - "author_inst": "Department of Pediatrics, Maine Medical Center, Portland, ME & Camp Winnebago, Fayette, ME" - }, - { - "author_name": "Julianne Meehan", - "author_inst": "Environmental Health & Engineering, Inc." - }, - { - "author_name": "Laurie Browne", - "author_inst": "American Camp Association" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.20.432081", "rel_title": "Nanoceutical Fabric Prevents COVID-19 Spread through Expelled Respiratory Droplets: A Combined Computational, Spectroscopic and Anti-microbial Study", @@ -919968,6 +921856,121 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/341636", + "rel_title": "The interspecific fungal hybrid Verticillium longisporum displays sub-genome-specific gene expression", + "rel_date": "2021-02-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/341636", + "rel_abs": "Hybridization is an important evolutionary mechanism that can enable organisms to adapt to environmental challenges. It has previously been shown that the fungal allodiploid species Verticillium longisporum, causal agent of Verticillium stem striping in rape seed, has originated from at least three independent hybridization events between two haploid Verticillium species. To reveal the impact of genome duplication as a consequence of the hybridization, we studied the genome and transcriptome dynamics upon two independent V. longisporum hybridization events, represented by the hybrid lineages \"A1/D1\" and \"A1/D3\". We show that the V. longisporum genomes are characterized by extensive chromosomal rearrangements, including between parental chromosomal sets. V. longisporum hybrids display signs of evolutionary dynamics that are typically associated with the aftermath of allodiploidization, such as haploidization and a more relaxed gene evolution. Expression patterns of the two sub-genomes within the two hybrid lineages are more similar than those of the shared A1 parent between the two lineages, showing that expression patterns of the parental genomes homogenized within a lineage. However, as genes that display differential parental expression in planta do not typically display the same pattern in vitro, we conclude that sub-genome-specific responses occur in both lineages. Overall, our study uncovers the genomic and transcriptomic plasticity during evolution of the filamentous fungal hybrid V. longisporum and illustrate its adaptive potential.\n\nImportanceVerticillium is a genus of plant-associated fungi that include a handful of plant pathogens that collectively affect a wide range of hosts. On several occasions, haploid Verticillium species hybridized into the stable allodiploid species Verticillium longisporum, which is, in contrast to haploid Verticillium species, a Brassicaceae specialist. Here, we studied the evolutionary genome and transcriptome dynamics of V. longisporum and the impact of the hybridization. V. longisporum genomes display a mosaic structure due do genomic rearrangements between the parental chromosome sets. Similar to other allopolyploid hybrids, V. longisporum displays an ongoing loss of heterozygosity and a more relaxed gene evolution. Also, differential parental gene expression is observed, with an enrichment for genes that encode secreted proteins. Intriguingly, the majority of these genes displays sub-genome-specific responses under differential growth conditions. In conclusion, hybridization has incited the genomic and transcriptomic plasticity that enables adaptation to environmental changes in a parental allele-specific fashion.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Edurne Rujas", + "author_inst": "The Hospital for Sick Children Research Institute" + }, + { + "author_name": "Iga Kucharska", + "author_inst": "The Hospital for Sick Children Research Institute" + }, + { + "author_name": "Yong Zi Tan", + "author_inst": "The Hospital for Sick Children Research Institute" + }, + { + "author_name": "Samir Benlekbir", + "author_inst": "The Hospital for Sick Children Research Institute" + }, + { + "author_name": "Hong Cui", + "author_inst": "The Hospital for Sick Children Research Institute" + }, + { + "author_name": "Tiantian Zhao", + "author_inst": "University of Toronto" + }, + { + "author_name": "Gregory A Wasney", + "author_inst": "The Hospital for Sick Children Research Institute" + }, + { + "author_name": "Patrick Budylowski", + "author_inst": "University of Toronto" + }, + { + "author_name": "Furkan Guvenc", + "author_inst": "University of Toronto" + }, + { + "author_name": "Jocelyn C Newton", + "author_inst": "The Hospital for Sick Children Research Institute" + }, + { + "author_name": "Taylor Sicard", + "author_inst": "The Hospital for Sick Children Research Institute" + }, + { + "author_name": "Anthony Semesi", + "author_inst": "The Hospital for Sick Children Research Institute" + }, + { + "author_name": "Krithika Muthuraman", + "author_inst": "The Hospital for Sick Children Research Institute" + }, + { + "author_name": "Amy Nouanesengsy", + "author_inst": "The Hospital for Sick Children Research Institute" + }, + { + "author_name": "Katherine Prieto", + "author_inst": "The Hospital for Sick Children Research Institute" + }, + { + "author_name": "Stephanie A Bueler", + "author_inst": "The Hospital for Sick Children Research Institute" + }, + { + "author_name": "Sawsan Youssef", + "author_inst": "Distributed Bio" + }, + { + "author_name": "Sindy Liao-Chan", + "author_inst": "Distributed Bio" + }, + { + "author_name": "Jacob Glanville", + "author_inst": "Distributed Bio" + }, + { + "author_name": "Natasha Christie-Holmes", + "author_inst": "University of Toronto" + }, + { + "author_name": "Samira Mubareka", + "author_inst": "Sunnybrook Health Sciences Centre" + }, + { + "author_name": "Scott D Gray-Owen", + "author_inst": "University of Toronto" + }, + { + "author_name": "John L Rubinstein", + "author_inst": "The Hospital for Sick Children Research Institute" + }, + { + "author_name": "Bebhinn Treanor", + "author_inst": "University of Toronto" + }, + { + "author_name": "Jean-Philippe Julien", + "author_inst": "The Hospital for Sick Children Research Institute" + } + ], + "version": "2", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.02.21.432184", "rel_title": "High-Throughput, Single-Copy Sequencing Reveals SARS-CoV-2 Spike Variants Coincident with Mounting Humoral Immunity during Acute COVID-19", @@ -921295,37 +923298,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2021.02.18.21251776", - "rel_title": "Rapid increase of SARS-CoV-2 seroprevalence during the 2020 pandemic year in the population of the city of Tirana, Albania", - "rel_date": "2021-02-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21251776", - "rel_abs": "IntroductionWhile the identification of anti SARS-CoV-2 antibodies has been used to measure the hidden circulation of the COVID-19 in communities, there are few publications on the dynamics of SARS-CoV-2 seroprevalence during both waves of 2020. This study provides original data about the change in proportion of individuals showing immune response to COVID-19 between beginning of July and end of December 2020.\n\nMethodsThe study was conducted in two rounds, 27 June -3 July, and 21-28 December 2020, using two independently selected samples of individuals 20-70 years old. Study participants were randomly selected from lists of the inhabitants of the catchment communities of four primary health care centers in Tirana City. Serological testing was performed by an ELISA method which determines IgG class antibodies anti S1 protein of SARS-CoV-2 virus. The validity of the method was tested in a sample of blood donors sera of 2018.\n\nResultsThe proportion of individuals classified as seropositive during the first round, in early July was 7.5% (95% CI: 4.3% -10.7%). The proportion rose sharply in the second round, by late December 2020, reaching 48.2% (95% CI: 44.8% -51.7%). The same increasing pattern was observed in all studied categories. No statistical significance was found between men and women and between age categories. The prevalence of seropositive individuals was always significantly higher among those who reported symptoms and those who had done the molecular test.\n\nConclusionThe ratio of total infected cases over confirmed cases was estimated to be higher than 10 to 1 in Albania. The rapid increase in SARS-CoV-2 seroprevalence observed in Tirana City may have been facilitated by a number of factors, including the very low infection exposure during the period March -May 2020, and the consecutive high susceptibility in population. Despite the observed high seroprevalence, one month after the study, COVID-19 incidence continued to increase in Tirana.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Genc Sulcebe", - "author_inst": "1. Laboratory of Immunology, University of Medicine and University Hospital Center of Tirana; 2. Academy of Sciences of Albania" - }, - { - "author_name": "Alban Ylli", - "author_inst": "Institute of Public Health, Tirana, Albania; Tirana Univeresity of Medicine" - }, - { - "author_name": "Fabian Cenko", - "author_inst": "Catholic University \"Our Lady of Good Counsel\", Tirana, Albania" - }, - { - "author_name": "Margarita Kurti-Prifti", - "author_inst": "Laboratory of Immunology, University of Medicine and University Hospital Center of Tirana" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.18.21251793", "rel_title": "Accessible LAMP-Enabled Rapid Test (ALERT) for detecting SARS-CoV-2", @@ -921526,6 +923498,101 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.02.19.424337", + "rel_title": "Probing the SAM Binding Site of SARS-CoV-2 nsp14 in vitro Using SAM Competitive Inhibitors Guides Developing Selective bi-substrate Inhibitors", + "rel_date": "2021-02-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.19.424337", + "rel_abs": "The COVID-19 pandemic has clearly brought the healthcare systems world-wide to a breaking point along with devastating socioeconomic consequences. The SARS-CoV-2 virus which causes the disease uses RNA capping to evade the human immune system. Non-structural protein (nsp) 14 is one of the 16 nsps in SARS-CoV-2 and catalyzes the methylation of the viral RNA at N7-guanosine in the cap formation process. To discover small molecule inhibitors of nsp14 methyltransferase (MT) activity, we developed and employed a radiometric MT assay to screen a library of 161 in house synthesized S-adenosylmethionine (SAM) competitive methyltransferase inhibitors and SAM analogs. Among seven identified screening hits, SS148 inhibited nsp14 MT activity with an IC50 value of 70 {+/-} 6 nM and was selective against 20 human protein lysine methyltransferases indicating significant differences in SAM binding sites. Interestingly, DS0464 with IC50 value of 1.1 {+/-} 0.2 M showed a bi-substrate competitive inhibitor mechanism of action. Modeling the binding of this compound to nsp14 suggests that the terminal phenyl group extends into the RNA binding site. DS0464 was also selective against 28 out of 33 RNA, DNA, and protein methyltransferases. The structure-activity relationship provided by these compounds should guide the optimization of selective bi-substrate nsp14 inhibitors and may provide a path towards a novel class of antivirals against COVID-19, and possibly other coronaviruses.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Kanchan Devkota", + "author_inst": "University of Toronto" + }, + { + "author_name": "Matthieu Schapira", + "author_inst": "University of Toronto" + }, + { + "author_name": "Sumera Perveen", + "author_inst": "University of Toronto" + }, + { + "author_name": "Aliakbar Khalili Yazdi", + "author_inst": "University of Toronto" + }, + { + "author_name": "Fengling Li", + "author_inst": "University of Toronto" + }, + { + "author_name": "Irene Chau", + "author_inst": "University of Toronto" + }, + { + "author_name": "Pegah Ghiabi", + "author_inst": "University of Toronto" + }, + { + "author_name": "Taraneh Hajian", + "author_inst": "University of Toronto" + }, + { + "author_name": "Peter Loppnau", + "author_inst": "University of Toronto" + }, + { + "author_name": "Albina Bolotokova", + "author_inst": "University of Toronto" + }, + { + "author_name": "Karla J Satchell", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Ke Wang", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Deyao Li", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Jing Liu", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "David Smil", + "author_inst": "University of Toronto" + }, + { + "author_name": "Minkui Luo", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Jian Jin", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Paul V. Fish", + "author_inst": "University College London" + }, + { + "author_name": "Peter J. Brown", + "author_inst": "University of Toronto" + }, + { + "author_name": "Masoud Vedadi", + "author_inst": "University of Toronto" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.02.18.431919", "rel_title": "Adequate knowledge of COVID-19 impacts good practices amongst health profession students in the Philippines", @@ -922785,45 +924852,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.15.21251765", - "rel_title": "When efficacy and adherence conflict: preferences and patterns of response to public health advice during the COVID-19 pandemic", - "rel_date": "2021-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.15.21251765", - "rel_abs": "With recurring waves of the Covid-19 pandemic, a dilemma facing public health leadership is whether to provide public advice that is medically optimal (e.g., most protective against infection if followed), but unlikely to be adhered to, or advice that is less protective but is more likely to be followed. To provide insight about this dilemma, we examined and quantified public perceptions about the tradeoff between (a) the stand-alone value of health behavior advice, and (b) the advices adherence likelihood. In a series of studies about preference for public health leadership advice, we asked 1,061 participants to choose between (1) strict advice that is medically optimal if adhered to but which is less likely to be broadly followed, and (2) relaxed advice, which is less medically effective but more likely to gain adherence - given varying infection expectancies. Participants preference was consistent with risk aversion. Offering an informed choice alternative that shifts volition to advice recipients only strengthened risk aversion, but also demonstrated that informed choice was preferred as much or more than the risk-averse strict advice.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Oded Nov", - "author_inst": "New York University Tandon School of Engineering" - }, - { - "author_name": "Graham Dove", - "author_inst": "New York University Tandon School of Engineering" - }, - { - "author_name": "Martina Balestra", - "author_inst": "New York University Tandon School of Engineering" - }, - { - "author_name": "Katharine Lawrence", - "author_inst": "New York University Grossman School of Medicine" - }, - { - "author_name": "Devin Mann", - "author_inst": "New York University Grossman School of Medicine" - }, - { - "author_name": "Batia Wiesenfeld", - "author_inst": "New York University Stern School of Business" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.16.21251676", "rel_title": "Incidence and Outcomes of Pulmonary embolism among hospitalized COVID-19 patients", @@ -922992,6 +925020,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2021.02.11.20233593", + "rel_title": "'Trained immunity' from Mycobacterium spp. (environmental or BCG) exposure predicts protection from Coronavirus disease 2019 (COVID-19)", + "rel_date": "2021-02-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.11.20233593", + "rel_abs": "Endeavors to identify potentially protective variables for COVID-19 impact on certain populations have remained a priority. Multiple attempts have been made to attribute the reduced COVID-19 impact on populations to their bacillus Calmette-Guerin (BCG) vaccination coverage ignoring the fact that the effect of childhood BCG vaccination wanes within 5 years while most of the COVID-19 cases and deaths have occurred in aged with comorbidities. Since the supposed protection being investigated could come from heterologous trained immunity (TI) conferred by exposure to Mycobacterium spp. (i.e., environmental and BCG), it is argued that the estimates of the prevalence of TI of populations currently available as latent tuberculosis infection (LTBI) prevalence would be a better variable to evaluate such assertions. Indeed, when we analyze the European populations (twenty-four), and erstwhile East and West Germany populations completely disregarding their BCG vaccination coverage, the populations with higher TI prevalence consistently display reduced COVID-19 impact as compared to their lower TI prevalence neighbors. The TI estimates of the populations not the BCG coverage per se, negatively correlated with pandemic phase-matched COVID-19 incidences (r(24): - 0.79 to -0.57; p-value: <0.004), mortality (r(24): -0.63 to -0.45; p-value: <0.03), and interim case fatality rates(i-CFR) data. To decisively arrive at dependable conclusions about the potential protective benefit gained from BCG vaccination in COVID-19, the ongoing/planned randomized controlled trials should consciously consider including measures of TI as - a) all individuals immunized do not respond equally, b)small study groups from higher background TI could fail to indicate any protective effect.\n\nO_TEXTBOXSummary BoxO_ST_ABSWhat is already known?C_ST_ABSO_LIPreviously, COVID-19 incidence (SARS-CoV-2 infections) and mortality datasets of disparate populations with regard to phase of pandemic, demographics, medical infrastructure etc. have been modelled to negatively associate with highly transformed BCG vaccination coverage and policy of the countries.\nC_LIO_LIRecently BCG vaccination has been linked to risk of COVID-19 using vaccinated individuals from disparate populations (different underlying trained immunity) without any estimation of the underlying immune status or attempt to make the confounders for the groups being compared to be equal.\nC_LIO_LIAbout 8 out of 10 COVID-19 deaths have been in aged >65 years old.\nC_LIO_LIBCG vaccination is known to provide-cross protection from a number of unrelated diseases.\nC_LIO_LIBCG vaccination given in childhood protects children from milliary tuberculosis and the conferred protective trained-Immunity correlate or TIC (loosely equals tuberculin positivity) wanes away within 5 years from most in the absence of boosters or rechallenge from environmental Mycobacterium spp.\nC_LI\n\nNew FindingsO_LIDisregarding BCG vaccination coverage or policy, the prevailing TIC correlate of populations predict protection from COVID-19 in socially similar European countries, i.e., the countries which are more similar to each other than other parts of the world with regard to various supposed confounders (e.g., exposure, phase of pandemic, health services, social support, food, genetic relatedness etc.).\nC_LI\n\nRecommendations for Policy and PracticeO_LIThe planned and ongoing studies or clinical trials assessing the effectiveness of BCG vaccination in protecting populations against COVID-19 or making them vulnerable to COVID-19 should include TIC correlates information of the participants (both controls and vaccinated) to arrive at dependable conclusions about potential benefit of BCG vaccination in controlling COVID-19 infections and mortality.\nC_LI\n\nC_TEXTBOX", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Samer Singh", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Rakesh K Singh", + "author_inst": "Institute of Science, Banaras Hindu University" + }, + { + "author_name": "Dhiraj Kishore", + "author_inst": "Institute of Medical Sciences, Banaras Hindu University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.16.21251805", "rel_title": "The detection of SARS-CoV-2 in autolysed samples from an exhumed decomposed body: Implications to virus survival, genome stability, and spatial distribution in tissues", @@ -924575,33 +926630,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.02.18.21251981", - "rel_title": "Assessing Age-Specific Vaccination Strategies and Post-Vaccination Reopening Policies for COVID-19 Control Using SEIR Modeling Approach", - "rel_date": "2021-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21251981", - "rel_abs": "BackgroundAs the availability of COVID-19 vaccines, it is badly needed to develop vaccination guidelines to prioritize the vaccination delivery in order to effectively stop COVID-19 epidemic and minimize the loss.\n\nMethodsWe evaluated the effect of age-specific vaccination strategies on the number of infections and deaths using an SEIR model, considering the age structure and social contact patterns for different age groups for each of different countries.\n\nResultsIn general, the vaccination priority should be given to those younger people who are active in social contacts to minimize the number of infections; while the vaccination priority should be given to the elderly to minimize the number of deaths. But this principle may not always apply when the interaction of age structure and age-specific social contact patterns is complicated. Partially reopening schools, workplaces or households, the vaccination priority may need to be adjusted accordingly.\n\nConclusionsPrematurely reopening social contacts could initiate a new outbreak or even a new pandemic out of control if the vaccination rate and the detection rate are not high enough. Our result suggests that it requires at least nine months of vaccination before fully reopening social contacts in order to avoid a new pandemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Xia Wang", - "author_inst": "Shaanxi Normal University" - }, - { - "author_name": "Hulin Wu", - "author_inst": "University of Texas Health Science Center at Houston" - }, - { - "author_name": "Sanyi Tang Sr.", - "author_inst": "Shaanxi Normal University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.17.21251725", "rel_title": "Assessment of knowledge, attitude and practices among Accredited Social Health Activists (ASHAs) towards COVID-19: a descriptive cross-sectional study in Tripura, India", @@ -924742,6 +926770,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.17.21251961", + "rel_title": "Diagnostic Performance of Pooled RT-PCR Testing for SARS-CoV-2 Detection", + "rel_date": "2021-02-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.17.21251961", + "rel_abs": "BackgroundWith the high number of COVID-19 cases, a need to optimize testing strategy must be regarded to obtain timely diagnosis for early containment measures. With this, several studies have employed pooled RT-PCR testing for SARS-CoV-2 as this could potentially conserve laboratory resources while has the capacity to test several individuals. However, this was recommended to firstly validate the method as different laboratory reagents and equipment vary with its diagnostic performance.\n\nObjectiveThe aim of this study was to determine the diagnostic performance of pooled SARS-CoV-2 nasopharyngeal/oropharyngeal swabbed samples using RT-PCR technique.\n\nMethodsA records review of two-staged pooled RT-PCR testing data from August 10, 26, 30 and September 5, 2020 was utilized from Northern Mindanao Medical Center COVID-19 Satellite Laboratory (formerly CHDNM TB Regional Center). For the first stage, using known samples, a total of 30 pools were made for each of the pooling size, 5- and 10-pooled, on both pooling phase, pre- and post-RNA extraction. One positive individual was used to represent each of the Cycle threshold values given (<24, 25-28, 29-32, 33-36, and 37-40) while the rest of the samples were negative. For the second stage, 54 pools of five from 270 random unknown samples were used to validate the results. Target gene performance of N gene and RdRp was also determined.\n\nKey ResultsResults show that 5-pooled sample has higher sensitivity (SN), specificity (SP), positive predictive value (PPV), and negative predictive value (NPV) of 100% (95% confidence interval (CI) 88.97-100), 66.95% (95% CI, 60.75-72.6), 28.18% (95% CI, 20.62-37.22), and 100% (95% CI, 97.66-100) compared to 10-pooled sample that has 87.1% (95% CI, 71.15-94.87), 56.9% (50.57-63.02), 20.77% (95% CI, 14.68-28.53) and 97.14% (95% CI, 92.88-98.88). Further, these Ct values were only from the N gene, emphasizing its higher diagnostic performance as well to detect SARS-CoV-2 compared to RdRp as only a few samples were detected, thus, no analysis was made.\n\nConclusionThis study found out that 5-pooled sample has better diagnostic performance compared to 10-pooled samples. Specifically, all positive individual samples were detected in 5-pooled samples in pre-RNA extraction phase which these results are evident and consistent on both known and unknown samples. N gene was found out to detect more SARS-CoV-2 samples compared to RdRp.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Diadem Ricarte", + "author_inst": "Northern Mindanao Medical Center COVID-19 Satellite Laboratory, Department of Health Philippines - Center for Health Development Northern Mindanao" + }, + { + "author_name": "Aubrey Gador", + "author_inst": "Northern Mindanao Medical Center COVID-19 Satellite Laboratory, Department of Health Philippines - Center for Health Development Northern Mindanao" + }, + { + "author_name": "Leomill Mendiola", + "author_inst": "Northern Mindanao Medical Center COVID-19 Satellite Laboratory, Department of Health Philippines - Center for Health Development Northern Mindanao" + }, + { + "author_name": "Ian Christian Gonzales", + "author_inst": "Infectious Disease Cluster Department of Health Center for Health Development Northern Mindanao , Department of Health Philippines - Center for Health Developme" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.17.21251946", "rel_title": "Estimating the Failure Risk of Hotel-based Quarantine for Preventing COVID-19 Outbreaks in Australia and New Zealand", @@ -926337,113 +928396,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.15.21251753", - "rel_title": "Severe SARS-CoV-2 infection induces a distinct nasal cytokine profile", - "rel_date": "2021-02-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.15.21251753", - "rel_abs": "Although the COVID-19 pandemic has left no country untouched there has been limited research to understand clinical and immunological responses in African populations. Here we comprehensively characterise patients hospitalised with suspected or confirmed COVID-19, and healthy community controls. PCR-confirmed COVID-19 participants were more likely to receive dexamethasone and a beta-lactam antibiotic, and survive to hospital discharge than PCR-/IgG+ and PCR-/IgG-participants. PCR-/IgG+ participants exhibited a nasal and systemic cytokine signature analogous to PCR-confirmed COVID-19 participants, but increased propensity for Staphylococcus aureus and Streptococcus pneumoniae colonisation. We did not find evidence that HIV co-infection in COVID-19 participants was associated with mortality or altered cytokine responses. The nasal immune signature in PCR-/IgG+ and PCR-confirmed COVID-19 participants was distinct and predominated by chemokines and neutrophils. In addition, PCR-/IgG+ individuals with high COVID-19 clinical suspicion had inflammatory profiles analogous to PCR-confirmed disease and potentially represent a target population for COVID-19 treatment strategies.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Ben Morton", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Kayla Barnes", - "author_inst": "Broad Institute of MIT and Harvard, Cambridge, USA" - }, - { - "author_name": "Catherine Anscombe", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Khuzwayo Jere", - "author_inst": "University of Liverpool, Liverpool, United Kingdom" - }, - { - "author_name": "Comfort Brown", - "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi" - }, - { - "author_name": "James Nyirenda", - "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi" - }, - { - "author_name": "Tamara Phiri", - "author_inst": "Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi" - }, - { - "author_name": "Ndaziona Peter Banda", - "author_inst": "University of Malawi-College of Medicine, Blantyre, Malawi" - }, - { - "author_name": "Charlotte Van der veer", - "author_inst": "University of Liverpool, Liverpool, United Kingdom" - }, - { - "author_name": "Kwazizira Samson Mndolo", - "author_inst": "Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi" - }, - { - "author_name": "Kelvin Mponda", - "author_inst": "Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi" - }, - { - "author_name": "Jamie Rylance", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Chimota Phiri", - "author_inst": "Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi" - }, - { - "author_name": "Jane Mallewa", - "author_inst": "University of Malawi-College of Medicine, Blantyre, Malawi" - }, - { - "author_name": "Mulinda Nyirenda", - "author_inst": "University of Malawi-College of Medicine, Blantyre, Malawi" - }, - { - "author_name": "Grace Katha", - "author_inst": "Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi" - }, - { - "author_name": "Paul Kambiya", - "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi" - }, - { - "author_name": "James Jafali", - "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi" - }, - { - "author_name": "Henry Mwandumba", - "author_inst": "Liverpool School of Tropical Medicine, Liverpool, United Kingdom" - }, - { - "author_name": "Stephen Gordon", - "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi" - }, - { - "author_name": "Jenifer Cornick", - "author_inst": "University of Liverpool, Liverpool, United Kingdom" - }, - { - "author_name": "Kondwani Charles Jambo", - "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Programme" - }, - { - "author_name": "- Blantyre COVID-19 consortium", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.02.15.21251586", "rel_title": "Epidemiology of COVID-19 infection amongst workers in Primary Healthcare in Qatar", @@ -926604,6 +928556,81 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.02.17.431722", + "rel_title": "Homologous and heterologous serological response to the N-terminal domain of SARS-CoV-2", + "rel_date": "2021-02-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.17.431722", + "rel_abs": "The increasing numbers of infected cases of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses serious threats to public health and the global economy. Most SARS-CoV-2 neutralizing antibodies target the receptor binding domain (RBD) and some the N-terminal domain (NTD) of the spike protein, which is the major antigen of SARS-CoV-2. While the antibody response to RBD has been extensively characterized, the antigenicity and immunogenicity of the NTD protein are less well studied. Using 227 plasma samples from COVID-19 patients, we showed that SARS-CoV-2 NTD-specific antibodies could be induced during infection. As compared to the serological response to SARS-CoV-2 RBD, the SARS-CoV-2 NTD response is less cross-reactive with SARS-CoV. Furthermore, neutralizing antibodies are rarely elicited in a mice model when NTD is used as an immunogen. We subsequently demonstrate that NTD has an altered antigenicity when expressed alone. Overall, our results suggest that while NTD offers an alternative strategy for serology testing, it may not be suitable as an immunogen for vaccine development.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Huibin Lv", + "author_inst": "HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China" + }, + { + "author_name": "Owen Tak-Yin Tsang", + "author_inst": "Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong" + }, + { + "author_name": "Ray T. Y. So", + "author_inst": "HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China" + }, + { + "author_name": "Yiquan Wang", + "author_inst": "HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China" + }, + { + "author_name": "Hejun Liu", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA" + }, + { + "author_name": "Garrick K. Yip", + "author_inst": "HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China" + }, + { + "author_name": "Qi Wen Teo", + "author_inst": "HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China" + }, + { + "author_name": "Yihan Lin", + "author_inst": "HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China" + }, + { + "author_name": "Weiwen Liang", + "author_inst": "HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China" + }, + { + "author_name": "Jinlin Wang", + "author_inst": "HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China" + }, + { + "author_name": "Wilson W. Ng", + "author_inst": "HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China" + }, + { + "author_name": "Ian A. Wilson", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA" + }, + { + "author_name": "Malik Peiris", + "author_inst": "HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China" + }, + { + "author_name": "Nicholas C. Wu", + "author_inst": "Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA" + }, + { + "author_name": "Chris K. P. Mok", + "author_inst": "HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.02.18.431835", "rel_title": "Rotavirus as an Expression Platform of the SARS-CoV-2 Spike Protein", @@ -928035,193 +930062,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.02.17.431492", - "rel_title": "SARS-CoV-2 vaccination induces neutralizing antibodies against pandemic and pre-emergent SARS-related coronaviruses in monkeys", - "rel_date": "2021-02-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.17.431492", - "rel_abs": "Betacoronaviruses (betaCoVs) caused the severe acute respiratory syndrome (SARS) and Middle East Respiratory Syndrome (MERS) outbreaks, and now the SARS-CoV-2 pandemic. Vaccines that elicit protective immune responses against SARS-CoV-2 and betaCoVs circulating in animals have the potential to prevent future betaCoV pandemics. Here, we show that immunization of macaques with a multimeric SARS-CoV-2 receptor binding domain (RBD) nanoparticle adjuvanted with 3M-052-Alum elicited cross-neutralizing antibody responses against SARS-CoV-1, SARS-CoV-2, batCoVs and the UK B.1.1.7 SARS-CoV-2 mutant virus. Nanoparticle vaccination resulted in a SARS-CoV-2 reciprocal geometric mean neutralization titer of 47,216, and robust protection against SARS-CoV-2 in macaque upper and lower respiratory tracts. Importantly, nucleoside-modified mRNA encoding a stabilized transmembrane spike or monomeric RBD protein also induced SARS-CoV-1 and batCoV cross-neutralizing antibodies, albeit at lower titers. These results demonstrate current mRNA vaccines may provide some protection from future zoonotic betaCoV outbreaks, and provide a platform for further development of pan-betaCoV nanoparticle vaccines.", - "rel_num_authors": 43, - "rel_authors": [ - { - "author_name": "Kevin O Saunders", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA; Departme" - }, - { - "author_name": "Esther Lee", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Robert Parks", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "David R Martinez", - "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA" - }, - { - "author_name": "Dapeng Li", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Haiyan Chen", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Robert J Edwards", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Sophie M. C. Gobeil", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Maggie Barr", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Katayoun Mansouri", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "S Munir Alam", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Laura L Sutherland", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Fangping Cai", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Aja Sanzone", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Madison Berry", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Kartik Manne", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Anyway B Kapingidza", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Mihai Azoitei", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Longping V Tse", - "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA" - }, - { - "author_name": "Trevor D Scobey", - "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA" - }, - { - "author_name": "Rachel Spreng", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "R. Wes Rountree", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "C Todd DeMarco", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA" - }, - { - "author_name": "Thomas N Denny", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA" - }, - { - "author_name": "Christopher W Woods", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Elizabeth W Petzold", - "author_inst": "Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC 27710, USA" - }, - { - "author_name": "Thomas H Oguin III", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Gregory D Sempowski", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Matthew Gagne", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA" - }, - { - "author_name": "Daniel C Douek", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA" - }, - { - "author_name": "Mark A Tomai", - "author_inst": "Corporate Research Materials Lab, 3M Company, St. Paul, MN 55144, USA." - }, - { - "author_name": "Christopher B Fox", - "author_inst": "Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Beth" - }, - { - "author_name": "Robert Seder", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA" - }, - { - "author_name": "Kevin Wiehe", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Drew Weissman", - "author_inst": "Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA" - }, - { - "author_name": "Norbert Pardi", - "author_inst": "Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA" - }, - { - "author_name": "Priyamvada Acharya", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA" - }, - { - "author_name": "Hanne Andersen", - "author_inst": "BIOQUAL, Rockville, MD 20850, USA" - }, - { - "author_name": "Mark G Lewis", - "author_inst": "BIOQUAL, Rockville, MD 20850, USA" - }, - { - "author_name": "Ian N Moore", - "author_inst": "Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Beth" - }, - { - "author_name": "David C Montefiori", - "author_inst": "Department of Surgery, Duke University, Durham, NC 27710, USA" - }, - { - "author_name": "Ralph S Baric", - "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA" - }, - { - "author_name": "Barton F Haynes", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.16.430500", "rel_title": "Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants", @@ -928421,6 +930261,37 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.02.16.431437", + "rel_title": "Phase transitions may explain why SARS-CoV-2 spreads so fast and why new variants are spreading faster", + "rel_date": "2021-02-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.16.431437", + "rel_abs": "The novel coronavirus SARS CoV-2 responsible for the COVID-19 pandemic and SARS CoV-1 responsible for the SARS epidemic of 2002-2003 share an ancestor yet evolved to have much different transmissibility and global impact1. A previously developed thermodynamic model of protein conformations predicted that SARS CoV-2 is very close to a thermodynamic critical point, which makes it highly infectious but also easily displaced by a spike-based vaccine because there is a tradeoff between transmissibility and robustness2. The model identified a small cluster of four key mutations of SARS CoV-2 that promotes much stronger viral attachment and viral spreading. Here we apply the model to two new strains (B.1.1.7 and B.1.351)3 and predict, using no free parameters, how the new mutations can further enhance infectiousness.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "James C Phillips", + "author_inst": "Rutgers University" + }, + { + "author_name": "Marcelo Moret", + "author_inst": "SENAI CIMATEC" + }, + { + "author_name": "Gilney F Zebende", + "author_inst": "State University of Feira de Santana" + }, + { + "author_name": "Carson C Chow", + "author_inst": "National Institutes of Health" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.02.17.431579", "rel_title": "Traditional use of Cissampelos pareira L. for hormone disorder and fever provides molecular links of ESR1 modulation to viral inhibition", @@ -929855,49 +931726,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.13.21251682", - "rel_title": "Mortality from injury, overdose and suicide during the 2020 COVID-19 pandemic, March-July, 2020", - "rel_date": "2021-02-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.13.21251682", - "rel_abs": "Introduction\n\nThe COVID-19 pandemic has been associated with substantial rates of all-cause excess mortality. The contribution of external causes of death to excess mortality including drug overdose, homicide, suicide, and unintentional injuries during the initial outbreak in the United States is less well documented.\n\nMethodsUsing public data published by the National Center for Health Statistics on February 10, 2021, we measured monthly excess mortality (the gap between observed and expected deaths) from five external causes using national-level data published by National Center for Health Statistics; assault (homicide); intentional self-harm (suicide); accidents (unintentional injuries); and motor vehicle accidents. We used seasonal autoregressive integrated moving average (sARIMA) models developed with cause-specific monthly mortality counts and US population data from 2015-2019 and estimated the contribution of individual cause-specific mortality to all-cause excess mortality from March-July 2020.\n\nResultsFrom March-July, 2020, 212,825 (95% CI 136,236-290,776) all-cause excess deaths occurred in the US). There were 8,540 excess drug overdoses (all intents) (95% CI 5,106 to 11,975), accounting for 4% of all excess mortality; 1,455 excess homicide deaths (95% CI 708 to 2202, accounting for 0.7% of excess mortality; 5,492 excess deaths due to unintentional accidents occurred (95% CI 85 to 10,899, accounting for 2.6% of excess mortality. Though a non-significantly 135 (95% CI -1361 to 1,630) more MVA deaths were recorded during the study period, a significant decrease in April (525; 95% CI -817 to -233) and significant increases in June-July (965; 95% CI 348 to 1,587) were observed. Suicide deaths were statistically lower than projected by 2,067 (95% CI 941-3,193 fewer deaths).\n\nMeaningExcess deaths from drug overdoses, homicide, and addicents occurred during the pandemic but represented a small fraction of all-cause excess mortality. The excess external causes of death, however, still represent thousands of lives lost. Notably, deaths from suicide were lower than expected and therefore did not contribute to excess mortality.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jeremy Faust", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Chengan Du", - "author_inst": "Yale University School of Medicine, Yale New Haven Hospital, Center for Outcomes Research and Evaluation New Haven, CT" - }, - { - "author_name": "Katherine Mayes", - "author_inst": "Harvard Affiliated Emergency Medicine Residency, Boston, Massachusetts" - }, - { - "author_name": "Shu-Xia Li", - "author_inst": "Yale New Haven Hospital, Center for Outcomes Research and Evaluation, New Haven, CT" - }, - { - "author_name": "Zhenqiu Lin", - "author_inst": "Yale New Haven Hospital, Center for Outcomes Research and Evaluation, New Haven, CT" - }, - { - "author_name": "Michael L Barnett", - "author_inst": "Department of Health Policy and Management, Harvard T. H. Chan School of Public Health, Boston, MA" - }, - { - "author_name": "Harlan M Krumholz", - "author_inst": "Yale University School of Medicine, Yale New Haven Hospital, Center for Outcomes Research and Evaluation, New Haven, CT" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.12.21251479", "rel_title": "Severe COVID-19 pneumonia and barotrauma: From the frying pan into the fire.", @@ -930154,6 +931982,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.07.21251322", + "rel_title": "Confirmation of an Inverse Relationship between Bioaerosol Count and Influenza-like Illnesses, Including COVID-19. On the Contribution of Mold Spores", + "rel_date": "2021-02-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.07.21251322", + "rel_abs": "Data from Chicago confirm the end of flu season coincides with the beginning of pollen season. The end of flu season also coincides with onset of seasonal aerosolization of mold spores. Overall, the data suggest bioaerosols, especially mold spores, compete with viruses for a shared receptor, with the periodicity of influenza-like illnesses, including COVID-19, a consequence of seasonal factors that influence aerosolization of competing species.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Richa B. Shah", + "author_inst": "Northwestern University" + }, + { + "author_name": "Rachna D. Shah", + "author_inst": "Department of Medicine, Stritch School of Medicine, Loyola University" + }, + { + "author_name": "Damien G. Retzinger", + "author_inst": "Graycore" + }, + { + "author_name": "Andrew C. Retzinger", + "author_inst": "Department of Emergency Medicine, West Virginia University, Camden Clark Medical Center" + }, + { + "author_name": "Deborah A. Retzinger", + "author_inst": "No affiliation" + }, + { + "author_name": "Gregory S. Retzinger", + "author_inst": "Department of Pathology, Feinberg School of Medicine, Northwestern University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.12.21251419", "rel_title": "Treatment of irritant contact dermatitis in healthcare settings during the COVID19 pandemic: The emollient Dermol 500 exhibits virucidal activity against influenza A virus and SARS-CoV-2.", @@ -931673,65 +933540,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.11.21251548", - "rel_title": "Association of demographic and occupational factors with SARS-CoV-2 vaccine uptake in a multi-ethnic UK healthcare workforce: a rapid real-world analysis", - "rel_date": "2021-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.11.21251548", - "rel_abs": "BackgroundHealthcare workers (HCWs) and ethnic minority groups are at increased risk of COVID-19 infection and adverse outcome. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) vaccination is now available for frontline UK HCWs; however, demographic/occupational associations with vaccine uptake in this cohort are unknown. We sought to establish these associations in a large UK hospital workforce.\n\nMethodsWe conducted cross-sectional surveillance examining vaccine uptake amongst all staff at University Hospitals of Leicester NHS Trust. We examined proportions of vaccinated staff stratified by demographic factors, occupation and previous COVID-19 test results (serology/PCR) and used logistic regression to identify predictors of vaccination status after adjustment for confounders.\n\nFindingsWe included 19,044 HCWs; 12,278 (64.5%) had received SARS-CoV-2 vaccination. Compared to White HCWs (70.9% vaccinated), a significantly smaller proportion of ethnic minority HCWs were vaccinated (South Asian 58.5%, Black 36.8% p<0.001 for both). After adjustment, factors found to be negatively associated with vaccine uptake were; younger age, female sex, increasing deprivation and belonging to any non-White ethnic group (Black: aOR0.30, 95%CI 0.26-0.34, South Asian:0.67, 0.62-0.72). Those that had previously had confirmed COVID-19 (by PCR) were less likely to be vaccinated than those who had tested negative.\n\nInterpretationEthnic minority HCWs and those from more deprived areas as well as younger, female staff are less likely to take up SARS-CoV-2 vaccination. These findings have major implications for the delivery of SARS-CoV-2 vaccination programmes in HCWs and the wider population and should inform the national vaccination programme to prevent the disparities of the pandemic from widening.\n\nFundingNIHR, UKRI/MRC", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Christopher A Martin", - "author_inst": "University of Leicester" - }, - { - "author_name": "Collette Marshall", - "author_inst": "University Hospitals of Leicester NHS Trust" - }, - { - "author_name": "Prashanth Patel", - "author_inst": "University of Leicester" - }, - { - "author_name": "Charles Goss", - "author_inst": "University Hospitals of Leicester NHS Trust" - }, - { - "author_name": "David R Jenkins", - "author_inst": "University Hospitals of Leicester NHS Trust" - }, - { - "author_name": "Claire Ellwood", - "author_inst": "University Hospitals of Leicester NHS Trust" - }, - { - "author_name": "Linda Barton", - "author_inst": "University Hospitals of Leicester NHS Trust" - }, - { - "author_name": "Arthur Price", - "author_inst": "University Hospitals of Leicester NHS Trust" - }, - { - "author_name": "Nigel J Brunskill", - "author_inst": "University of Leicester" - }, - { - "author_name": "Kamlesh Khunti", - "author_inst": "University of Leicester" - }, - { - "author_name": "Manish Pareek", - "author_inst": "University of Leicester" - } - ], - "version": "2", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.11.21251562", "rel_title": "Population Age-Ineligible for COVID-19 Vaccine in the United States: Implications for State, County, and Race/Ethnicity Vaccination Targets", @@ -931884,6 +933692,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.11.21251590", + "rel_title": "Evaluating COVID-19 reporting data in the context of testing strategies across 31 LMICs", + "rel_date": "2021-02-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.11.21251590", + "rel_abs": "0.1 BackgroundCOVID-19 case counts are the predominant measure used to track epidemiological dynamics and inform policy decision-making. Case counts, however, are influenced by testing rates and strategies, which have varied over time and space. A method to consistently interpret COVID-19 case counts in the context of other surveillance data is needed, especially for data-limited settings in low- and middle-income countries (LMICs).\n\n0.2 MethodsWe leverage statistical analyses to detect changes in COVID-19 surveillance data. We apply the pruned exact linear time change detection method for COVID-19 case counts, number of tests, and test positivity rate over time. With this information, we categorize change points as likely driven by epidemiological dynamics or non-epidemiological influences such as noise.\n\n0.3 FindingsHigher rates of epidemiological change detection are more associated with open testing policies than with higher testing rates. We quantify alignment of non-pharmaceutical interventions with epidemiological changes. LMICs have the testing capacity to measure prevalence with precision if they use randomized testing. Rwanda stands out as a country with an efficient COVID-19 surveillance system. Sub-national data reveal heterogeneity in epidemiological dynamics and surveillance.\n\n0.4 InterpretationRelying solely on case counts to interpret pandemic dynamics has important limitations. Normalizing counts by testing rate mitigates some of these limitations, and open testing policy is key to efficient surveillance. Our findings can be leveraged by public health officials to strengthen COVID-19 surveillance and support programmatic decision-making.\n\n0.5 FundingThis publication is based on models and data analysis performed by the Institute for Disease Modeling at the Bill & Melinda Gates Foundation.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe searched for articles on the current practices, challenges, and proposals for COVID-19 surveillance in LMICs. We used Google Scholar with search terms including \"COVID surveillance.\" Existing studies were found to be qualitative, anecdotal, or highly location-specific.\n\nAdded value of this studyWe developed a quantitative method that makes use of limited information available from LMICs. Our approach improves interpretation of epidemiological data and enables evaluation of COVID-19 surveillance dynamics across countries.\n\nImplications of all the available evidenceOur results demonstrate the importance of open testing for strong surveillance systems, bolstering existing anecdotal evidence. We show strong alignment across LMICs between non-pharmaceutical interventions and epidemiological changes. We demonstrate the importance of considering sub-national heterogeneity of epidemiological dynamics and surveillance.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Mollie M. Van Gordon", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "Kevin A. McCarthy", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "Joshua L. Proctor", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "Brittany L. Hagedorn", + "author_inst": "Institute for Disease Modeling" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.10.21251510", "rel_title": "Identification of high-risk COVID-19 patients using machine learning", @@ -933283,69 +935122,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.02.12.430907", - "rel_title": "A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients", - "rel_date": "2021-02-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.12.430907", - "rel_abs": "COVID-19 disease outcome is highly dependent on adaptive immunity from T and B lymphocytes, which play a critical role in the control, clearance and long-term protection against SARS-CoV-2. To date, there is limited knowledge on the composition of the T and B cell immune receptor repertoires [T cell receptors (TCRs) and B cell receptors (BCRs)] and transcriptomes in convalescent COVID-19 patients of different age groups. Here, we utilize single-cell sequencing (scSeq) of lymphocyte immune repertoires and transcriptomes to quantitatively profile the adaptive immune response in COVID-19 patients of varying age. We discovered highly expanded T and B cells in multiple patients, with the most expanded clonotypes coming from the effector CD8+ T cell population. Highly expanded CD8+ and CD4+ T cell clones show elevated markers of cytotoxicity (CD8: PRF1, GZMH, GNLY; CD4: GZMA), whereas clonally expanded B cells show markers of transition into the plasma cell state and activation across patients. By comparing young and old convalescent COVID-19 patients (mean ages = 31 and 66.8 years, respectively), we found that clonally expanded B cells in young patients were predominantly of the IgA isotype and their BCRs had incurred higher levels of somatic hypermutation than elderly patients. In conclusion, our scSeq analysis defines the adaptive immune repertoire and transcriptome in convalescent COVID-19 patients and shows important age-related differences implicated in immunity against SARS-CoV-2.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Florian Bieberich", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Rodrigo Vazquez-Lombardi", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Alexander Yermanos", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Roy A Ehling", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Derek M Mason", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Bastian Wagner", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Edo Kapetanovic", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Raphael Brisset Di Roberto", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Cedric R Weber", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Miodrag Savic", - "author_inst": "University of Basel" - }, - { - "author_name": "Fabian Rudolf", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Sai T Reddy", - "author_inst": "ETH Zurich" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.12.430933", "rel_title": "Rapidly Increasing SARS-CoV-2 Neutralization by Intravenous Immunoglobulins Produced from Plasma Collected During the 2020 Pandemic", @@ -933614,6 +935390,121 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.02.12.430472", + "rel_title": "Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies", + "rel_date": "2021-02-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.12.430472", + "rel_abs": "SARS-CoV-2 B.1.1.7 and B.1.351 variants emerged respectively in United Kingdom and South Africa and spread in many countries. Here, we isolated infectious B.1.1.7 and B.1.351 strains and examined their sensitivity to anti-SARS-CoV-2 antibodies present in sera and nasal swabs, in comparison with a D614G reference virus. We established a novel rapid neutralization assay, based on reporter cells that become GFP+ after overnight infection. B.1.1.7 was neutralized by 79/83 sera from convalescent patients collected up to 9 months post symptoms, almost similar to D614G. There was a mean 6-fold reduction in titers and even loss of activity against B.1.351 in 40% of convalescent sera after 9 months. Early sera from 19 vaccinated individuals were almost as potent against B.1.1.7 but less efficacious against B.1.351, when compared to D614G. Nasal swabs from vaccine recipients were not neutralizing, except in individuals who were diagnosed COVID-19+ before vaccination. Thus, faster-spreading variants acquired a partial resistance to humoral immunity generated by natural infection or vaccination, mostly visible in individuals with low antibody levels.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Delphine Planas", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Timothee Bruel", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Ludivine Grzelak", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Florence Guivel-Benhassine", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Isabelle Staropoli", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Francoise Porrot", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Cyril Planchais", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Julian Buchrieser", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Maaran Michael Rajah", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Elodie Bishop", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Melanie Albert", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Flora Donati", + "author_inst": "INSERM U955" + }, + { + "author_name": "Sylvie Behillil", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Vincent Enouf", + "author_inst": "Insitut Pasteur" + }, + { + "author_name": "Maquart Marianne", + "author_inst": "Universite de Tours" + }, + { + "author_name": "Maria Gonzalez", + "author_inst": "Hopitaux Universitaire de Strasbourg" + }, + { + "author_name": "Jerome De Seze", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Helene Pere", + "author_inst": "AP-HP" + }, + { + "author_name": "David Veyer", + "author_inst": "AP-HP" + }, + { + "author_name": "Etienne Simon-Loriere", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Samira Fafi-Kremer", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Karl Stefic", + "author_inst": "Hopital de Tours" + }, + { + "author_name": "Hugo Mouquet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Sylvie van der Werf", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Olivier Schwartz", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.02.12.430940", "rel_title": "Single-cell sequencing of plasma cells from COVID-19 patients reveals highly expanded clonal lineages produce specific and neutralizing antibodies to SARS-CoV-2", @@ -934968,24 +936859,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.10.21251523", - "rel_title": "Decline in mitigation readiness facilitated second waves of SARS-CoV-2", - "rel_date": "2021-02-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251523", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Kai W Wirtz", - "author_inst": "Helmholtz Centre Geesthacht" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.10.21251533", "rel_title": "County-Specific, Real-Time Projection of the Effect of Business Closures on the COVID-19 Pandemic", @@ -935238,6 +937111,56 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.11.21251563", + "rel_title": "Long stability of SARS-CoV-2 RNA in dry and saliva swab samples stored for diagnostics, Denmark", + "rel_date": "2021-02-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.11.21251563", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Alonzo Alfaro-Nunez", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Stephanie Crone", + "author_inst": "SSI Diagnostica" + }, + { + "author_name": "Shila Mortensen", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Maiken Worsoe Rosenstierne", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Anders Fomsgaard", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Ellinor Marving", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Sofie Holdflod Nielsen", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Michelle Grace Pinto Jorgensen", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Claus Nielsen", + "author_inst": "Statens Serum Institut" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.11.21251587", "rel_title": "Assessing the impact of secondary school reopening strategies on within-school COVID-19 transmission and absences: a modelling study", @@ -937255,25 +939178,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.08.21251290", - "rel_title": "Confirmed forecasts for the expansion of the COVID-19 epidemic in the S. Paulo city, Brazil", - "rel_date": "2021-02-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21251290", - "rel_abs": "ObjectiveA SEIR compartmental model was previously selected to estimate future outcomes to the dynamics of the Covid-19 epidemic breakout in Brazil.\n\nMethodCompartments for individuals vaccinated, and prevalent SARS-Cov-2 variants were not included. A time-dependent incidence weight on the reproductive basic number accounted for Non Pharmaceutical Interventions (NPI). A first series of published data from March 1st to May 8, 2020 was used to adjust all model parameters aiming to forecast one year of evolutionary outbreak. The cohort study was set as a city population-based analysis.\n\nAnalysisThe population-based sample, 25,366 during the study period, was the number of confirmed cases on exposed individuals. The analysis was applied to predict the consequences of holding for posterior NPI releases, and indicates the appearance of a second wave starting last quarter of 2020.\n\nFindingsBy March 1st2021, the number of confirmed cases was predicted to reach 0.47Million (0.24-0.78), and fatalities would account for 21 thousand (12-33), 5 to 95% CRI. A second series of data published from May 9, 2020 to March 1st, 2021 confirms the forecasts previously reported for the evolution of infected people and fatalities.\n\nNoveltyBy March 1st 2021, the number of confirmed cases reached 527,710 (12% bellow predicted average of accumulated cases), and fatalities accounted for 18,769 (10% above the accumulated average of estimated fatalities). After March 1st, new peaks on reported numbers of daily new infected and new fatalities appeared as a combined result to the appearance of the prevalent SARS-CoV-2 P1 variant, and the increased number of vaccinated individuals.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Sergio Celaschi", - "author_inst": "CTI Renato Archer" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.08.21251352", "rel_title": "Assessment of Post SARS CoV 2 Fatigue among Physicians Working in COVID Designated Hospitals in Dhaka, Bangladesh", @@ -937510,6 +939414,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.08.21251343", + "rel_title": "Machine learning approach to dynamic risk modeling of mortality in COVID-19: a UK Biobank cohort study", + "rel_date": "2021-02-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21251343", + "rel_abs": "The COVID-19 pandemic has created an urgent need for robust, scalable monitoring tools supporting stratification of high-risk patients. This research aims to develop and validate prediction models, using the UK Biobank, to estimate COVID-19 mortality risk in confirmed cases. From the 11,245 participants testing positive for COVID-19, we develop a data-driven random forest classification model with excellent performance (AUC: 0.91), using baseline characteristics, pre-existing conditions, symptoms, and vital signs, such that the score could dynamically assess mortality risk with disease deterioration. We also identify several significant novel predictors of COVID-19 mortality with equivalent or greater predictive value than established high-risk comorbidities, such as detailed anthropometrics and prior acute kidney failure, urinary tract infection, and pneumonias. The model design and feature selection enables utility in outpatient settings. Possible applications include supporting individual-level risk profiling and monitoring disease progression across patients with COVID-19 at-scale, especially in hospital-at-home settings.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Mohammad A. Dabbah", + "author_inst": "Huma Therapeutics Limited" + }, + { + "author_name": "Angus B. Reed", + "author_inst": "Huma Therapeutics Limited" + }, + { + "author_name": "Adam T.C. Booth", + "author_inst": "Huma Therapeutics Limited" + }, + { + "author_name": "Arrash Yassaee", + "author_inst": "Huma Therapeutics Limited" + }, + { + "author_name": "Alex Despotovic", + "author_inst": "Huma Therapeutics Limited" + }, + { + "author_name": "Benjamin Klasner", + "author_inst": "Huma Therapeutics Limited" + }, + { + "author_name": "Emily Binning", + "author_inst": "Huma Therapeutics Limited" + }, + { + "author_name": "Mert Aral", + "author_inst": "Huma Therapeutics Limited" + }, + { + "author_name": "David Plans", + "author_inst": "Huma Therapeutics Limited" + }, + { + "author_name": "Alain B. Labrique", + "author_inst": "Johns Hopkins Bloomberg School Public Health" + }, + { + "author_name": "Diwakar Mohan", + "author_inst": "Johns Hopkins Bloomberg School Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.02.08.21251358", "rel_title": "Large-scale silane bead-based SARS-CoV-2 testing of a nursing home in Spain identifies a viral reservoir during lockdown period", @@ -939021,93 +940984,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.07.21251281", - "rel_title": "Galectin-3 as a potential prognostic biomarker of severe COVID-19 in SARS-CoV-2 infected patients", - "rel_date": "2021-02-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.07.21251281", - "rel_abs": "BACKGROUNDPrognostic biomarkers are needed to identify patients at high-risk for severe COVID-19. Galectin-3 is known to drive neutrophil infiltration and release of pro-inflammatory cytokines contributing to airway inflammation.\n\nMETHODSIn this prospective cohort, we assessed galectin-3 levels in 156 hospitalized patients with confirmed COVID-19. COVID-19 patients were diagnosed as either critical (>50% lung damage) or moderate (<50% of lung damage) based on computerized tomography. Patients who required invasive mechanical ventilation (IMV) and/or died during hospitalization were categorized as having a severe outcome, and a non-severe outcome if they were discharged and none of the former occurred.\n\nRESULTSElevated serum galectin-3 was significantly higher in critical patients compared to moderate ones (35.91 {+/-} 19.37 ng/mL vs. 25 {+/-} 14.85 ng/mL, p<0.0001). Patients who progressed to a severe outcome including IMV and/or in-hospital death, presented higher galectin-3 levels (41.17 ng/mL [IQR 29.71 - 52.25] vs. 23.76 ng/mL [IQR 15.78 - 33.97] compared to those of a non-severe outcome, p<0.0001). Galectin-3 discriminated well between those with severe and non-severe outcome, with an AUC of 0.75 (95% CI 0.67 - 0.84, p<0.0001) and was found to be an independent predictor of severe outcome regardless of the percentage of lung involvement. Additionally, the combination of galectin-3, CRP and albumin, significantly improved its individual predicting ability with an AUC 0.84 (95% CI 0.77 - 0.91, p<0.0001).\n\nCONCLUSIONCirculating galectin-3 levels can be used to predict severe outcomes in COVID-19 patients, including the requirement of mechanical ventilation and/or death, regardless of the initial severity of the disease.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Eduardo Cervantes-Alvarez", - "author_inst": "PECEM, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico" - }, - { - "author_name": "Nathaly Limon-de la Rosa", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Gastroenterology, Mexico City, Mexico" - }, - { - "author_name": "Moises Salgado-de la Mora", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Internal Medicine, Mexico City, Mexico" - }, - { - "author_name": "Paola Valdez-Sandoval", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Internal Medicine, Mexico City, Mexico" - }, - { - "author_name": "Mildred Palacios-Jimenez", - "author_inst": "Universidad Veracruzana, Veracruz, Mexico" - }, - { - "author_name": "Fatima Rodriguez-Alvarez", - "author_inst": "Universidad Veracruzana, Veracruz, Mexico" - }, - { - "author_name": "Brenda I. Vera-Maldonado", - "author_inst": "Universidad Veracruzana, Veracruz, Mexico" - }, - { - "author_name": "Eduardo Aguirre-Aguilar", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Internal Medicine, Mexico City, Mexico" - }, - { - "author_name": "Juan Manuel Escobar-Valderrama", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Internal Medicine, Mexico City, Mexico" - }, - { - "author_name": "Jorge Alanis-Mendizabal", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Internal Medicine, Mexico City, Mexico" - }, - { - "author_name": "Osvely Mendez-Guerrero", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Gastroenterology, Mexico City, Mexico" - }, - { - "author_name": "Farid Tejeda-Dominguez", - "author_inst": "Universidad Panamericana School of Medicine, Campus Mexico, Mexico City" - }, - { - "author_name": "Jiram Torres-Ruiz", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Immunology and Rheumatology, Mexico City, Mexico" - }, - { - "author_name": "Diana Gomez-Martin", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Immunology and Rheumatology, Mexico City, Mexico" - }, - { - "author_name": "Kathryn L. Colborn", - "author_inst": "Department of Surgery, University of Colorado Anschutz Medical Campus, Denver, CO" - }, - { - "author_name": "David Kershenobich", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico" - }, - { - "author_name": "Christene A. Huang", - "author_inst": "Department of Surgery, University of Colorado Anschutz Medical Campus, Denver, CO" - }, - { - "author_name": "Nalu Navarro-Alvarez", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Gastroenterology, Mexico City, Mexico" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.08.21251070", "rel_title": "The protective association between statins use and adverse outcomes among COVID-19 patients: a systematic review and meta-analysis", @@ -939324,6 +941200,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.07.21251287", + "rel_title": "Modelling the impact of reopening schools in early 2021 in the presence of the new SARS-CoV-2 variant and with roll-out of vaccination against COVID-19", + "rel_date": "2021-02-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.07.21251287", + "rel_abs": "BackgroundFollowing the resurgence of the COVID-19 epidemic in the UK in late 2020 and the emergence of the alpha (also known as B117) variant of the SARS-CoV-2 virus, a third national lockdown was imposed from January 4, 2021. Following the decline of COVID-19 cases over the remainder of January 2021, the question of when and how to reopen schools became an increasingly pressing one in early 2021. This study models the impact of a partial national lockdown with social distancing measures enacted in communities and workplaces under different strategies of reopening schools from March 8, 2021 and compares it to the impact of continual full national lockdown remaining until April 19, 2021.\n\nMethodsWe used our previously published agent-based model, Covasim, to model the emergence of the alpha variant over September 1, 2020 to January 31, 2021 in presence of Test, Trace and Isolate (TTI) strategies. We extended the model to incorporate the impacts of the roll-out of a two-dose vaccine against COVID-19, with 200,000 daily vaccine doses prioritised by age starting with people 75 years or older, assuming vaccination offers a 95% reduction in disease acquisition risk and a 30% reduction in transmission risk. We used the model, calibrated until January 25, 2021, to simulate the impact of a full national lockdown (FNL) with schools closed until April 19, 2021 versus four different partial national lockdown (PNL) scenarios with different elements of schooling open: 1) staggered PNL with primary schools and exam-entry years (years 11 and 13) returning on March 8, 2021 and the rest of the schools years on March 15, 2020; 2) full-return PNL with both primary and secondary schools returning on March 8, 2021; 3) primary-only PNL with primary schools and exam critical years (years 11 and 13) going back only on March 8, 2021 with the rest of the secondary schools back on April 19, 2021 and 4) part-rota PNL with both primary and secondary schools returning on March 8, 2021 with primary schools remaining open continuously but secondary schools on a two-weekly rota-system with years alternating between a fortnight of face-to-face and remote learning until April 19, 2021. Across all scenarios, we projected the number of new daily cases, cumulative deaths and effective reproduction number R until April 30, 2021.\n\nResultsOur calibration across different scenarios is consistent with alpha variant being around 60% more transmissible than the wild type. We find that strict social distancing measures, i.e. national lockdowns, were essential in containing the spread of the virus and controlling hospitalisations and deaths during January and February 2021. We estimated that a national lockdown over January and February 2021 would reduce the number of cases by early March to levels similar to those seen in October 2020, with R also falling and remaining below 1 over this period. We estimated that infections would start to increase when schools reopened, but found that if other parts of society remain closed, this resurgence would not be sufficient to bring R above 1. Reopening primary schools and exam critical years only or having primary schools open continuously with secondary schools on rotas was estimated to lead to lower increases in cases and R than if all schools opened. Without an increase in vaccination above the levels seen in January and February, we estimate that R could have increased above 1 following the reopening of society, simulated here from April 19, 2021.\n\nFindingsOur findings suggest that stringent measures were integral in mitigating the increase in cases and bringing R below 1 over January and February 2021. We found that it was plausible that a PNL with schools partially open from March 8, 2021 and the rest of the society remaining closed until April 19, 2021 would keep R below 1, with some increase evident in infections compared to continual FNL until April 19, 2021. Reopening society in mid-April, without an increase in vaccination levels, could push R above 1 and induce a surge in infections, but the effect of vaccination may be able to control this in future depending on the transmission blocking properties of the vaccines.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Jasmina Panovska-Griffiths", + "author_inst": "UCL" + }, + { + "author_name": "Robyn Margaret Stuart", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Cliff Kerr", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "Katherine Rosenfeld", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "Dina Mistry", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "William Waites", + "author_inst": "LSHTM" + }, + { + "author_name": "Daniel J Klein", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "Chris Bonell", + "author_inst": "LSHTM" + }, + { + "author_name": "Russell M Viner", + "author_inst": "UCL Great Ormond St. Institute of Child Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.07.21251314", "rel_title": "High School Sports During the CoVID-19 Pandemic: The Impact of Sport Participation on the Health of Adolescents", @@ -940771,45 +942698,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.02.04.21251167", - "rel_title": "A mechanistic and data-driven reconstruction of the time-varying reproduction number: Application to the COVID-19 epidemic", - "rel_date": "2021-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.04.21251167", - "rel_abs": "The effective reproduction number Reff is a critical epidemiological parameter that characterizes the transmissibility of a pathogen. However, this parameter is difficult to estimate in the presence of silent transmission and/or significant temporal variation in case reporting. This variation can occur due to the lack of timely or appropriate testing, public health interventions and/or changes in human behavior during an epidemic. This is exactly the situation we are confronted with during this COVID-19 pandemic.\n\nIn this work, we propose to estimate Reff for the SARS-CoV-2 (the etiological agent of the COVID-19), based on a model of its propagation considering a time-varying transmission rate. This rate is modeled by a Brownian diffusion process embedded in a stochastic model. The model is then fitted by Bayesian inference (particle Markov Chain Monte Carlo method) using multiple well-documented hospital datasets from several regions in France and in Ireland. This mechanistic modeling framework enables us to reconstruct the temporal evolution of the transmission rate of the COVID-19 based only on the available data. Except for the specific model structure, it is non-specifically assumed that the transmission rate follows a basic stochastic process constrained by the observations. This approach allows us to follow both the course of the COVID-19 epidemic and the temporal evolution of its Reff(t). Besides, it allows to assess and to interpret the evolution of transmission with respect to the mitigation strategies implemented to control the epidemic waves in France and in Ireland. We thus can estimate a reduction of more than 80% for the first wave in all the studied regions but a smaller reduction for the second wave when the epidemic was less active. For the third wave in Ireland the reduction was again significant (>70%).\n\nAuthor SummaryIn the early stages of any new epidemic, one of the first steps to design a control strategy is to estimate pathogen transmissibility in order to provide information on its potential to spread in the population. Among the different epidemiological indicators that characterize the transmissibility of a pathogen, the effective reproduction number Reff is commonly used for measuring time-varying transmissibility. It measures how many additional people can be infected by an infected individual during the course of an epidemic. However, Reff is difficult to estimate in the presence of silent transmission and/or significant temporal variation in case reporting. This is exactly the situation we are confronted with during this COVID-19 pandemic.\n\nThe statistical methods classically used for the estimation of Reff have some shortcomings in the rigorous consideration of the transmission characteristics of SARS-CoV-2. We propose here to use an original approach based on a stochastic model whose parameters vary in time and are inferred in a Bayesian framework from reliable hospital data. This enables us to reconstruct both the COVID-19 epidemic and its Reff. The Reff time evolution allows us to get information regarding the potential effects of mitigation measures taken during and between epidemics waves.\n\nThis approach, based on a stochastic model that realistically describes the hospital multiple datasets and which overcomes many of the biases associated with Reff estimates, appears to have some advantage over previously developed methods.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Bernard Cazelles", - "author_inst": "Sorbonne University" - }, - { - "author_name": "Clara Champagne", - "author_inst": "Universty of Basel" - }, - { - "author_name": "Benjamin Nguyen Van Yen", - "author_inst": "Ecole Normale Superieure" - }, - { - "author_name": "Catherine Comiskey", - "author_inst": "Trinity College Dublin, The University of Dublin" - }, - { - "author_name": "Elisabeta Vergu", - "author_inst": "INRAE" - }, - { - "author_name": "Benjamin Roche", - "author_inst": "IRD" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.04.21251171", "rel_title": "Mapping internet activity in Australian cities during COVID-19 lockdown: how occupational factors drive inequality", @@ -941042,6 +942930,61 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.02.05.21251173", + "rel_title": "Longitudinal Metabolomics of Human Plasma Reveals Robust Prognostic Markers of COVID-19 Disease Severity", + "rel_date": "2021-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.05.21251173", + "rel_abs": "There is an urgent need to identify which COVID-19 patients will develop life-threatening illness so that scarce medical resources can be optimally allocated and rapid treatment can be administered early in the disease course, when clinical management is most effective. To aid in the prognostic classification of disease severity, we performed untargeted metabolomics profiling of 341 patients with plasma samples collected at six longitudinal time points. Using the temporal metabolic profiles and machine learning, we then built a predictive model of disease severity. We determined that the levels of 25 metabolites measured at the time of hospital admission successfully predict future disease severity. Through analysis of longitudinal samples, we confirmed that these prognostic markers are directly related to disease progression and that their levels are restored to baseline upon disease recovery. Finally, we validated that these metabolites are also altered in a hamster model of COVID-19. Our results indicate that metabolic changes associated with COVID-19 severity can be effectively used to stratify patients and inform resource allocation during the pandemic.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Miriam Sindelar", + "author_inst": "Washington University" + }, + { + "author_name": "Ethan Stancliffe", + "author_inst": "Washington University" + }, + { + "author_name": "Michaela Schwaiger-Haber", + "author_inst": "Washington University" + }, + { + "author_name": "Dhanalakshmi S Anbukumar", + "author_inst": "Washington University" + }, + { + "author_name": "Randy A Albrecht", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "wen-chun Liu", + "author_inst": "Ichan School of Medicine at Mount Sinai" + }, + { + "author_name": "Kayla Adkins-Travis", + "author_inst": "University of Akron" + }, + { + "author_name": "Adolfo Garcia-Sastre", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Leah P Shriver", + "author_inst": "Washington University" + }, + { + "author_name": "Gary J Patti", + "author_inst": "Washington University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.05.21251208", "rel_title": "The kinetic variations of anti-nucleocapsid antibody in SARS-CoV-2 infection", @@ -942713,85 +944656,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.06.21251246", - "rel_title": "Dynamics of neutralizing antibody responses in acute-phase COVID-19: A potential relationship between disease progression and rapid neutralizing antibody response", - "rel_date": "2021-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.06.21251246", - "rel_abs": "IntroductionAdaptive immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) dynamics remain largely unknown. The neutralizing antibody (NAb) levels in patients with coronavirus disease 2019 (COVID-19) are helpful for understanding the pathology.\n\nPatients and MethodsUsing SARS-CoV-2 pseudotyped virus, serum sample neutralization values in symptomatic COVID-19 patients were measured using the chemiluminescence reduction neutralization test (CRNT). At least two sequential serum samples collected during hospitalization were analyzed to assess NAbs neutralizing activity dynamics at different time points.\n\nResultsOf the 11 patients, four (36.4%), six (54.5%), and one (9.1%) had moderate, severe, and critical disease, respectively. Fifty percent neutralization (N50%-CRNT) was observed upon admission in 90.9% (10/11); all patients acquired neutralizing activity 2-12 days after onset. In patients with moderate disease, neutralization was observed at earliest within two days after symptom onset. In patients with severe-to-critical disease, neutralization activity increased, plateauing 9-16 days after onset. Neutralization activity on admission was significantly higher in patients with moderate disease than in patients with severe-to-critical disease (relative % of infectivity, 6.4% vs. 41.1%; P=.0011).\n\nConclusionsNeutralization activity on admission inversely correlated with disease severity. The rapid NAb response may play a crucial role in preventing the progression of COVID-19.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Hitoshi Kawasuji", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Yoshitomo Morinaga", - "author_inst": "Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Hideki Tani", - "author_inst": "Department of Virology, Toyama Institute of Health" - }, - { - "author_name": "Miyuki Kimura", - "author_inst": "Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Hiroshi Yamada", - "author_inst": "Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Yoshihiro Yoshida", - "author_inst": "Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Yusuke Takegoshi", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Makito Kaneda", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Yushi Murai", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Kou Kimoto", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Akitoshi Ueno", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Yuki Miyajima", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Koyomi Kawago", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Yasutaka Fukui", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Ippei Sakamaki", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Yoshihiro Yamamoto", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.07.21250586", "rel_title": "The impact of mobility network properties on predicted epidemic dynamics in Dhaka and Bangkok", @@ -942936,6 +944800,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.06.21251221", + "rel_title": "Social predictors of food insecurity during the stay-at-home order due to the COVID-19 pandemic in Peru. Results from a cross-sectional web-based survey", + "rel_date": "2021-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.06.21251221", + "rel_abs": "BackgroundStay-at-home orders and social distancing have been implemented as the primary tools to reduce the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, this approach has indirectly lead to the unemployment of 2{middle dot}3 million Peruvians, in Lima, Peru alone. As a result, the risk of food insecurity may have increased, especially in low-income families who rely on a daily wage. This study estimates the prevalence of moderate or severe food insecurity (MSFI) and identifies the associated factors that explain this outcome during the stay-at-home order.\n\nMethodsA cross-sectional web-based survey, with non-probabilistic sampling, was conducted between May 18 and June 30, 2020, during the stay-at-home order in Peru. We used social media advertisements on Facebook to reach 18-59-year-olds living in Peru. MSFI was assessed using the Food Insecurity Experience Scale (FIES). Rasch model methodology requirements were considered, and factors associated with MSFI were selected using stepwise forward selection. A Poisson generalized linear model (Poisson GLM), with log link function, was employed to estimate adjusted prevalence ratios (aPR).\n\nFindingsThis analysis is based on 1846 replies. The prevalence of MSFI was 23{middle dot}2%, and FIES proved to be an acceptable instrument with reliability 0{middle dot}72 and infit 0{middle dot}8-1{middle dot}3. People more likely to experience MSFI were those with low income (less than 255 US$/month) in the pre-pandemic period (aPR 3{middle dot}77; 95%CI, 1{middle dot}98-7{middle dot}16), those whose income was significantly reduced during the pandemic period (aPR 2{middle dot}27; 95%CI, 1{middle dot}55-3{middle dot}31), and those whose savings ran out in less than 21 days (aPR 1{middle dot}86; 95%CI, 1{middle dot}43-2{middle dot}42). Likewise, heads of households (aPR 1{middle dot}20; 95%CI, 1{middle dot}00-1{middle dot}44) and those with probable SARS-CoV2 cases as relatives (aPR 1{middle dot}29; 95%CI, 1{middle dot}05-1{middle dot}58) were at an increased risk of MSFI. Additionally, those who perceived losing weight during the pandemic (aPR 1{middle dot}21; 95%CI, 1{middle dot}01-1{middle dot}45), and increases in processed foods prices (aPR 1{middle dot}31; 95%CI, 1{middle dot}08-1{middle dot}59), and eating less minimally processed food (aPR 1{middle dot}82; 95%CI, 1{middle dot}48-2{middle dot}24) were more likely to experience MSFI.\n\nInterpretationPeople most at risk of MSFI were those in a critical economic situation before and during the pandemic. Social protection policies should be reinforced to prevent or mitigate these adverse effects.\n\nFundingNone.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Jorge L. Canari-Casano", + "author_inst": "Clima, Latin American Center of Excellence for Climate Change and Health, Universidad Peruana Cayetano Heredia. Emerge, Emerging Diseases and Climate Change Res" + }, + { + "author_name": "Omaira Cochachin-Henostroza", + "author_inst": "Grupo de Investigacion Nutobes, Universidad Nacional Mayor de San Marcos, Lima, Peru" + }, + { + "author_name": "Oliver A. Elorreaga", + "author_inst": "GMINIS Research Group, Pontificia Universidad Catolica del Peru" + }, + { + "author_name": "Gandy Dolores-Maldonado", + "author_inst": "Escuela Profesional de Nutricion, Facultad de Medicina, Universidad Nacional Mayor de San Marcos, Lima, Peru" + }, + { + "author_name": "Anthony Aquino-Ramirez", + "author_inst": "Grupo de Investigacion Nutobes, Universidad Nacional Mayor de San Marcos, Lima, Peru" + }, + { + "author_name": "Sindy Huaman-Gil", + "author_inst": "Sociedad Cientifica de Estudiantes de Nutricion, Universidad Nacional Mayor de San Marcos, Lima, Peru" + }, + { + "author_name": "Juan P. Giribaldi-Sierralta", + "author_inst": "Sociedad Cientifica de Estudiantes de Nutricion, Universidad Nacional Mayor de San Marcos, Lima, Peru" + }, + { + "author_name": "Juan Pablo Aparco", + "author_inst": "Centro Nacional de Alimentacion y Nutricion, Instituto Nacional de Salud, Lima, Peru" + }, + { + "author_name": "Daniel A. Antiporta", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA." + }, + { + "author_name": "Mary Penny", + "author_inst": "Nutrition Research Institute, Lima, Peru." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.05.21250735", "rel_title": "Sero-surveillance for IgG to SARS-CoV-2 at antenatal care clinics in two Kenyan referral hospitals", @@ -944679,61 +946598,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.01.21249903", - "rel_title": "Quantifying transmissibility of COVID-19 and impact of intervention within long-term health care facilities", - "rel_date": "2021-02-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.01.21249903", - "rel_abs": "Estimates of the basic reproduction number (R0) for Coronavirus disease 2019 (COVID-19) are particularly variable in the context of transmission within locations such as long-term health care (LTHC) facilities. We sought to characterise the heterogeneity of R0 across known outbreaks within these facilities. We used a unique comprehensive dataset of all outbreaks that have occurred within LTHC facilities in British Columbia, Canada. We estimated R0 with a Bayesian hierarchical dynamic model of susceptible, exposed, infected, and recovered individuals, that incorporates heterogeneity of R0 between facilities. We further compared these estimates to those obtained with standard methods that utilize the exponential growth rate and maximum likelihood. The total size of an outbreak varied dramatically, with a range of attack rates of 2%-86%. The Bayesian analysis provides more constrained overall estimates of R0 = 2.19 (90% CrI [credible interval] 0.19-6.69) than standard methods, with a range within facilities of 0.48-10.08. We further estimated that intervention led to 57% (47%-66%) of all cases being averted within the LTHC facilities, or 73% (63%-78%) when using a model with multi-level intervention effect. Understanding the risks and impact of intervention are essential in planning during the ongoing global pandemic, particularly in high-risk environments such as LTHC facilities.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Jessica E Stockdale", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Sean C Anderson", - "author_inst": "Simon Fraser University; Pacific Biological Station, Fisheries and Oceans Canada" - }, - { - "author_name": "Andrew M Edwards", - "author_inst": "Pacific Biological Station, Fisheries and Oceans Canada; University of Victoria" - }, - { - "author_name": "Sarafa I Iyaniwura", - "author_inst": "University of British Columbia; British Columbia Centre for Disease Control" - }, - { - "author_name": "Nicola Mulberry", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Michael C Otterstatter", - "author_inst": "British Columbia Centre for Disease Control; University of British Columbia" - }, - { - "author_name": "Naveed Z Janjua", - "author_inst": "British Columbia Centre for Disease Control; University of British Columbia" - }, - { - "author_name": "Daniel Coombs", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Caroline Colijn", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Michael A Irvine", - "author_inst": "British Columbia Centre for Disease Control; British Columbia Children's Hospital Research Institute; Simon Fraser University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.02.21251042", "rel_title": "Mental Health, Substance Use, and Suicidal Ideation Among Unpaid Caregivers in the United States During the COVID-19 Pandemic: Relationships to Age, Race/Ethnicity, Employment, and Caregiver Intensity", @@ -944894,6 +946758,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.02.03.21251056", + "rel_title": "Impact of personal protective equipment use on health care workers physical health during the COVID-19 pandemic: a systematic review and meta-analysis", + "rel_date": "2021-02-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.03.21251056", + "rel_abs": "BackgroundDuring the COVID-19 pandemic, health care workers (HCWs) caring for patients with coronavirus disease 2019 (COVID-19) in high-risk clinical settings have been obliged to wear personal protective equipment (PPE).\n\nAimTo assess the impact of PPE use on HCWs physical health during the COVID-19 pandemic. Also, we examined factors related with a greater risk of adverse events among HCWs due to PPE use.\n\nMethodsWe applied the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines and the Cochrane criteria for this systematic review and meta-analysis. We searched PubMed, Medline, Scopus, ProQuest, CINAHL and pre-print services (medRxiv) from January 1, 2020 to December 27, 2020.\n\nFindingsOur review included 14 studies with 11,746 HCWs from 16 countries. The estimated overall prevalence of adverse events among HCWs was 78% (95% CI: 66.7-87.5%) with a range from 42.8% to 95.1% among studies. The prevalence of adverse events was higher for the studies with poor quality compared to those with moderate quality (83.5% vs. 67.1%), while increased sample size was related with decreased prevalence (p<0.001). The most frequent adverse events were headache (55.9%), dry skin (54.4%), dyspnoea (53.4%), pressure injuries (40.4%), itching (39.8%), hyperhidrosis (38.5%), and dermatitis (31.0%). Among others, the following factors were related with the risk of adverse events among HCWs due to PPE use: female gender, younger age, obesity, diabetes mellitus, smoking pre-existing headache, longer duration of shifts wearing PPE, increased consecutive days with PPE, and increased exposure to confirmed or suspected COVID-19 patients.\n\nConclusionThe frequency of adverse events amongst HCWs due to PPE use is very high. Further studies should be conducted since the limitations of this review do not allow us to infer conclusive results especially in case of risk factors for the occurrence of adverse events. Healthcare facilities should take the necessary precautions and change the working conditions during the COVID-19 pandemic to prevent adverse events associated with PPE use and minimize harm to HCWs.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Petros A Galanis", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Irene Vraka", + "author_inst": "Department of Radiology, P & A Kyriakou Children's Hospital" + }, + { + "author_name": "Despoina Fragkou", + "author_inst": "Faculty of Nursing, Center for Health Services Management and Evaluation, National and Kapodistrian University of Athens" + }, + { + "author_name": "Angeliki Bilali", + "author_inst": "Hospital Waste Management Unit, P & A Kyriakou Children's Hospital" + }, + { + "author_name": "Daphne Kaitelidou", + "author_inst": "Faculty of Nursing, Center for Health Services Management and Evaluation, National and Kapodistrian University of Athens" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.02.02.21250639", "rel_title": "HEALTHCARE WORKERS PSYCHOLOGICAL DISTRESS At EARLY PHASE OF THE COVID-19 PANDEMIC IN MOROCCO", @@ -946357,65 +948256,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.03.429628", - "rel_title": "Development of a highly sensitive bioanalytical assay for the quantification of favipiravir.", - "rel_date": "2021-02-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.03.429628", - "rel_abs": "Favipiravir (FAV; T-705) has been approved for use as an anti-influenza therapeutic and has reports against a wide range of viruses (e.g., Ebola virus, rabies and norovirus). Most recently FAV has been reported to demonstrate activity against SARS-CoV-2. Repurposing opportunities have been intensively studied with only limited success to date. If successful, repurposing will allow interventions to become more rapidly available than development of new chemical entities. Pre-clinical and clinical investigations of FAV require robust, reproducible and sensitive bioanalytical assay. Here, a liquid chromatography tandem mass spectrometry assay is presented which was linear from 0.78-200 ng/mL Accuracy and precision ranged between 89% and 110%, 101% and 106%, respectively. The presented assay here has applications in both pre-clinical and clinical research and may be used to facilitate further investigations into the application of FAV against SARS-CoV-2.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Paul Curley", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Megan Neary", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Usman Arshad", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Lee Tatham", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Henry Pertinez", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Helen Box", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Rajith K R Rajoli", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Anthony Valentijn", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Joanne Sharp", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Steve Rannard", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Andrew Owen", - "author_inst": "University of Liverpool" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2021.02.03.21250974", "rel_title": "Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the US", @@ -947848,6 +949688,73 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.02.05.429937", + "rel_title": "Post-infection treatment with a protease inhibitor increases survival of mice with a fatal SARS-CoV-2 infection", + "rel_date": "2021-02-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.05.429937", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection continues to be a serious global public health threat. The 3C-like protease (3CLpro) is a virus protease encoded by SARS-CoV-2, which is essential for virus replication. We have previously reported a series of small molecule 3CLpro inhibitors effective for inhibiting replication of human coronaviruses including SARS-CoV-2 in cell culture and in animal models. Here we generated a series of deuterated variants of a 3CLpro inhibitor, GC376, and evaluated the antiviral effect against SARS-CoV-2. The deuterated GC376 displayed potent inhibitory activity against SARS-CoV-2 in the enzyme and the cell-based assays. The K18-hACE2 mice develop mild to lethal infection commensurate with SARS-CoV-2 challenge doses and was proposed as a model for efficacy testing of antiviral agents. We treated lethally infected mice with a deuterated derivative of GC376. Treatment of K18-hACE2 mice at 24 hr post infection with a derivative (compound 2) resulted in increased survival of mice compared to vehicle-treated mice. Lung virus titers were decreased, and histopathological changes were ameliorated in compound 2-treated mice compared to vehicle-treated mice. Structural investigation using high-resolution crystallography illuminated binding interactions of 3CLpro of SARS-CoV-2 and SARS-CoV with deuterated variants of GC376. Taken together, deuterated GC376 variants have excellent potential as antiviral agents against SARS-CoV-2.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Chamandi Dampalla", + "author_inst": "Wichita State University" + }, + { + "author_name": "Jian Zheng", + "author_inst": "University of Iowa" + }, + { + "author_name": "Krishani Perera", + "author_inst": "Kansas State University" + }, + { + "author_name": "Lok Yin Roy Wong", + "author_inst": "University of Iowa" + }, + { + "author_name": "David Meyerholz", + "author_inst": "University of Iowa" + }, + { + "author_name": "Harry Nguyen", + "author_inst": "Wichita State University" + }, + { + "author_name": "Maithri Kashipathy", + "author_inst": "Kansas University" + }, + { + "author_name": "Kevin Battaile", + "author_inst": "NYSBC" + }, + { + "author_name": "Scott Lovell", + "author_inst": "Kansas University" + }, + { + "author_name": "Yunjeong Kim", + "author_inst": "Kansas State University" + }, + { + "author_name": "Stanley Perlman", + "author_inst": "University of Iowa" + }, + { + "author_name": "William Groutas", + "author_inst": "Wichita State University" + }, + { + "author_name": "Kyeong-Ok Chang", + "author_inst": "Kansas State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.02.05.429940", "rel_title": "Protein glycosylation is essential for SARS-CoV-2 infection", @@ -949063,57 +950970,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.01.21250537", - "rel_title": "Towards a COVID-19 symptom triad: The importance of symptom constellations in the SARS-CoV-2 pandemic", - "rel_date": "2021-02-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.01.21250537", - "rel_abs": "Pandemic scenarios like SARS-Cov-2 require rapid information aggregation. In the age of eHealth and data-driven medicine, publicly available symptom tracking tools offer efficient and scalable means of collecting and analyzing large amounts of data. As a result, information gains can be communicated to front-line providers. We have developed such an application in less than a month and reached more than 500 thousand users within 48 hours. The dataset contains information on basic epidemiological parameters, symptoms, risk factors and details on previous exposure to a COVID-19 patient. Exploratory Data Analysis revealed different symptoms reported by users with confirmed contacts vs. no confirmed contacts. The symptom combination of anosmia, cough and fatigue was the most important feature to differentiate the groups, while single symptoms such as anosmia, cough or fatigue alone were not sufficient. A linear regression model from the literature using the same symptom combination as features was applied on all data. Predictions matched the regional distribution of confirmed cases closely across Germany, while also indicating that the number of cases in northern federal states might be higher than officially reported. In conclusion, we report that symptom combinations anosmia, fatigue and cough are most likely to indicate an acute SARS-CoV-2 infection.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Leander Edwin Melms", - "author_inst": "Institute of Artificial Intelligence, Philipps-University Marburg" - }, - { - "author_name": "Evelyn Falk", - "author_inst": "Institute of Artificial Intelligence, Philipps-University Marburg" - }, - { - "author_name": "Bernhard Schieffer", - "author_inst": "Cardiology Department, University Hospital Giessen and Marburg" - }, - { - "author_name": "Andreas Jerrentrup", - "author_inst": "Emergency Department, University Hospital Giessen and Marburg" - }, - { - "author_name": "Uwe Wagner", - "author_inst": "Department of Gynaecology, University Hospital Giessen and Marburg" - }, - { - "author_name": "Sami Matrood", - "author_inst": "Department of Gastroenterology, Endocrinology, Metabolism and Infectiology, Philipps-University, Marburg" - }, - { - "author_name": "J\u00fcrgen R Schaefer", - "author_inst": "Centre for undiagnosed and rare diseases, University Hospital Giessen and Marburg" - }, - { - "author_name": "Tobias M\u00fcller", - "author_inst": "Centre for undiagnosed and rare diseases, University Hospital Giessen and Marburg" - }, - { - "author_name": "Martin Hirsch", - "author_inst": "Institute of Artificial Intelligence, Philipps-University Marburg" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.01.21250877", "rel_title": "Optimal time to return to normality: parallel use of COVID-19 vaccines and circuit breakers", @@ -949354,6 +951210,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.02.01.21250919", + "rel_title": "How lifestyle changes within the COVID-19 global pandemic have affected the pattern and symptoms of the menstrual cycle.", + "rel_date": "2021-02-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.01.21250919", + "rel_abs": "BackgroundThe coronavirus 2019 (COVID-19) pandemic has caused significant changes to homes, working life and stress. The purpose of this research was to investigate the implications that the COVID-19 pandemic has had on the menstrual cycle and any contributing factors to these changes.\n\nMethodsA questionnaire was completed by 749 participants, whom ranged from physically active to elite, in their training status. The questionnaire captured detail on menstrual cycle symptoms and characteristics prior to and during the COVID-19 pandemic lockdown period, as well as lifestyle, stress, exercise and nutrition. Descriptive statistics and frequency distribution were reported and decision tree analysis performed. Statistical significance was assumed at p<0.05.\n\nResultsFifty-two point six percent of females experienced a change in their menstrual cycle during the lockdown period. Psychosocial symptoms had changed in over half of all participants. Participants who reported increased stress/worry in family and personal health were significantly associated with changes in menstrual symptoms. Similarly, job security stress was associated with increases in bleeding time (p<0.05).\n\nConclusionsIt is important that females and practitioners become aware of the implications of stressful environments and the possible long-term implications on fertility, particularly given the uncertainty around a second wave of the global pandemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Georgie Bruinvels", + "author_inst": "St Mary's University" + }, + { + "author_name": "Esther Goldsmith", + "author_inst": "Orreco Ltd" + }, + { + "author_name": "Richard Blagrove", + "author_inst": "Loughborough University" + }, + { + "author_name": "Dan Martin", + "author_inst": "University of Lincoln" + }, + { + "author_name": "Laurence Shaw", + "author_inst": "Nottingham Trent University" + }, + { + "author_name": "Jessica Piasecki", + "author_inst": "Nottingham Trent University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "sports medicine" + }, { "rel_doi": "10.1101/2021.02.01.21250935", "rel_title": "The effect of mobility restrictions on the SARS-CoV-2 diffusion during the first wave: what are the impacts in Sweden, USA, France and Colombia.", @@ -951269,93 +953164,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.02.21250910", - "rel_title": "Elevated mucosal antibody responses against SARS-CoV-2 are correlated with lower viral load and faster decrease in systemic COVID-19 symptoms", - "rel_date": "2021-02-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21250910", - "rel_abs": "Mucosal antibodies play a key role in protection against SARS-CoV-2 exposure, but their role during primary infection is not well understood. We assessed mucosal antibody responses during primary infection with SARS-CoV-2 and examined their relationship with viral load and clinical symptoms. Elevated mucosal IgM was associated with lower viral load. RBD and viral spike protein-specific mucosal antibodies were correlated with decreases in systemic symptoms, while older age was associated with an increase in respiratory symptoms. Up to 42% of household contacts developed SARS-CoV-2-specific mucosal antibodies, including children, indicating high transmission rates within households in which children might play an important role.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Janeri Fr\u00f6berg", - "author_inst": "Radboud university medical center, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, Nijm" - }, - { - "author_name": "Joshua Gillard", - "author_inst": "Centre for molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre Nijmegen, 6525 GA Nijmegen, " - }, - { - "author_name": "Ria Philipsen", - "author_inst": "RTC CS Radboud Technology Center Clinical Studies, Radboudumc, Nijmegen" - }, - { - "author_name": "Kjerstin Lanke", - "author_inst": "Radboud Center for Infectious Diseases, Radboudumc, Nijmegen" - }, - { - "author_name": "Joyce Rust", - "author_inst": "RTC CS Radboud Technology Center Clinical Studies, Radboudumc, Nijmegen" - }, - { - "author_name": "Diana van Tuijl", - "author_inst": "RTC CS Radboud Technology Center Clinical Studies, Radboudumc, Nijmegen" - }, - { - "author_name": "Teun Bousema", - "author_inst": "Radboud Center for Infectious Diseases, Radboudumc, Nijmegen" - }, - { - "author_name": "Elles Simonetti", - "author_inst": "Radboud university medical center, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, Nijm" - }, - { - "author_name": "Christa van der Gaast-de Jongh", - "author_inst": "Radboud university medical center, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, Nijm" - }, - { - "author_name": "Mariska Bos", - "author_inst": "Radboud university medical center, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, Nijm" - }, - { - "author_name": "Frank J.M. van Kuppeveld", - "author_inst": "Utrecht University, Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Utrecht, the Nether" - }, - { - "author_name": "Berend Jan Bosch", - "author_inst": "Utrecht University" - }, - { - "author_name": "Marrigje Nabuurs-Franssen", - "author_inst": "Department of medical microbiology and infectious diseases, Canisius Wilhelmina hospital, Nijmegen" - }, - { - "author_name": "Nannet van der Geest-Blankert", - "author_inst": "Department of Occupational Health, Radboud university medical centre" - }, - { - "author_name": "Charlotte van Daal", - "author_inst": "Department of Occupational Health, Radboud university medical centre" - }, - { - "author_name": "Martijn A. Huynen", - "author_inst": "Centre for molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre Nijmegen" - }, - { - "author_name": "Marien I. de Jonge", - "author_inst": "Radboud university medical center, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, Nijm" - }, - { - "author_name": "Dimitri A Diavatopoulos", - "author_inst": "Radboud university medical center, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, Nijm" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.02.21250985", "rel_title": "Rapid vaccination and early reactive partial lockdown will minimize deaths from emerging highly contagious SARS-CoV-2 variants", @@ -951560,6 +953368,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.01.21250923", + "rel_title": "A cautionary note on recall vaccination in ex-COVID-19 subjects", + "rel_date": "2021-02-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.01.21250923", + "rel_abs": "Currently approved COVID-19 vaccines based on mRNA or adenovirus require a first jab followed by recall immunization. There is no indication as to whether individuals who have recovered from COVID-19 should be vaccinated, and if so, if they should receive one or two vaccine doses. Here, we tested the antibody response developed after the first dose of the mRNA based vaccine encoding the SARS-CoV-2 full-length spike protein (BNT162b2) in 124 healthcare professionals of which 57 had a previous history of COVID-19 (ExCOVID). Post-vaccine antibodies in ExCOVID individuals increase exponentially within 7-15 days after the first dose compared to naive subjects (p<0.0001). We developed a multivariate Linear Regression (LR) model with l2 regularization to predict the IgG response for SARS-COV-2 vaccine. We found that the antibody response of ExCOVID patients depends on the IgG pre-vaccine titer and on the symptoms that they developed during the disorder, with anosmia/dysgeusia and gastrointestinal disorders being the most significantly positively correlated in the LR. Thus, one vaccine dose is sufficient to induce a good antibody response in ExCOVID subjects. This poses caution for ExCOVID subjects to receive a second jab both because they may have a overreaction of the inflammatory response and also in light of the current vaccine shortage.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Riccardo Levi", + "author_inst": "Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Milan, Italy." + }, + { + "author_name": "Elena Azzolini", + "author_inst": "IRCSS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy." + }, + { + "author_name": "Chiara Pozzi", + "author_inst": "IRCSS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy." + }, + { + "author_name": "Leonardo Ubaldi", + "author_inst": "Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Milan, Italy." + }, + { + "author_name": "Michele Lagioia", + "author_inst": "IRCSS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy" + }, + { + "author_name": "Alberto Mantovani", + "author_inst": "IRCSS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy" + }, + { + "author_name": "Maria Rescigno", + "author_inst": "Humanitas University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.02.02.21250630", "rel_title": "First indication of the effect of COVID-19 vaccinations on the course of the COVID-19 outbreak in Israel", @@ -953391,45 +955242,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.03.429522", - "rel_title": "Knowledge and Awareness of coronavirus disease 2019 (COVID-19) among Chinese dental students----a comparison study.", - "rel_date": "2021-02-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.03.429522", - "rel_abs": "BackgroudThis study aimed to measure the knowledge and awareness of COVID-19 among Chinese dental students during the global outbreak recently.\n\nMethodA descriptive cross-sectional study was performed among dental students and nonmedical college students in China. All the participants were required to anonymously answer a reliable online questionnaire, which covered 3 different fields of COVID-19. Average scores of dental students (D group), including junior (JD group) and senior dental students (SD group), and nonmedical college students (N group) were compared respectively. Chi-square test and independent sample T test were taken for statistical analysis with SPSS.12.\n\nResultsTotally 497 questionnaires were collected, including 224 from dental students and 273 from non-medical students. The overall average score was 57{+/-}19.2. The average scores of dental students were 64.5{+/-}18. The D group had significantly higher scores on the total score, section scores, and 20 questions respectively than with the N group. No significant differences were found on 5 questions. Compared with the N group, the SD group won on all three sections while JD group failed to win on the diagnose section.\n\nConclusionAlthough the dental student showed good awareness regarding the clinical aspects of COVID-19 than non-medical students, there are still some weakness in the part of treatment and prevention, which need to be strengthened for better prepare during work. Besides, the low accuracy rate of lower grade dental students is also worth noting.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "bing Shi", - "author_inst": "Sichuan University West China College of Stomatology" - }, - { - "author_name": "Chengdan Deng", - "author_inst": "Sichuan University West China Hospital of Stomatology: Sichuan University West China College of Stomatology" - }, - { - "author_name": "HuangShui Ma", - "author_inst": "Sichuan University West China Hospital of Stomatology: Sichuan University West China College of Stomatology" - }, - { - "author_name": "Yuke Shou", - "author_inst": "Sichuan University West China Hospital of Stomatology: Sichuan University West China College of Stomatology" - }, - { - "author_name": "Yuke Zhao", - "author_inst": "Sichuan University West China Hospital of Stomatology: Sichuan University West China College of Stomatology" - }, - { - "author_name": "Yang Li", - "author_inst": "Sichuan University West China Hospital of Stomatology: Sichuan University West China College of Stomatology" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "scientific communication and education" - }, { "rel_doi": "10.1101/2021.02.03.429201", "rel_title": "'Phytopathological strolls' in the dual context of COVID-19 lockdown and IYPH2020: transforming constraints into an opportunity for public education about plant pathogens", @@ -953562,6 +955374,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.29.21250784", + "rel_title": "COVID-19 vaccine acceptability and inequity in the United States: Results from a nationally representative survey", + "rel_date": "2021-02-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250784", + "rel_abs": "BackgroundAt the time of this survey, September 1st, there were roughly 6 million COVID-19 cases and 176,771 deaths in the United States and no federally approved vaccine. The objective of this study was to explore the willingness to accept a COVID-19 vaccine in the United States and describe variability in this acceptability by key racial, ethnic and socio-demographic characteristics.\n\nMethodsThis was a cross-sectional digital survey that sampled participants from a nationally-representative panel maintained by a third party, Dynata. Dynata randomly sampled their database and emailed web-based surveys to United States residents ensuring the sample was matched to US Census estimates for age, race, gender, income, and Census region. Participants were asked how willing or unwilling they would be to: 1) receive a COVID-19 vaccine as soon as it was made publicly available, and 2) receive the influenza vaccine for the upcoming influenza season. Participants could respond with extremely willing, willing, unwilling, or extremely unwilling. For those who reported being unwilling to receive a COVID-19 vaccine, reasons for this hesitancy were captured. All participants were asked about where they obtain vaccine-related information, and which sources they trust most. Univariable and multivariable logistic regressions were conducted to examine the association of all demographic characteristics with willingness to receive COVID-19 vaccine.\n\nFindingsFrom September 1st to September 7, 2020, 1592 respondents completed the online survey. Overall, weighted analyses found that only 58.9% of the sample population were either willing or extremely willing to receive a COVID-19 vaccine as soon as it was made publicly available. In comparison, 67.7% of the respondents were willing or extremely willing to take the influenza vaccine. By gender, 66.1% of males and 51.5% of females were willing to receive a COVID-19 vaccine. Males were significantly more willing to receive a COVID-19 vaccine (adjusted odds ratio (OR)=1.98, 95% CI: 1.56, 2.53; p<0.001) than females. Blacks were the least willing racial/ethnic group (48.8%) Blacks, (aOR=0.59, 95%CI: 0.43, 0.80; p<0.001) were significantly less willing, than whites, to receive a COVID-19 vaccine. There were numerous reasons provided for being unwilling to receive a COVID-19 vaccine. The most common reason was concern about the vaccines safety (36.9%), followed by concerns over its efficacy (19.1%).\n\nInterpretationIn conclusion, we found that a substantial proportion (41%) of United States residents are unwilling to receive a COVID-19 vaccine as soon as one is made publicly available. We found that vaccine acceptance differs by sub-populations. In addition to sub-group differences in willingness to receive the vaccine, respondents provided a variety of reasons for being unwilling to receive the vaccine, driven by various sources of vaccine information (and misinformation). This compounds the challenge of delivering a safe and efficacious COVID-19 vaccine at a population level to achieve herd immunity. A multi-pronged and targeted communications and outreach effort is likely needed to achieve a high level of immunization coverage.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Dustin G Gibson", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Smisha Agarwal", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Ankita Meghani", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Rupali Limaye", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Alain Bernard Labrique", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.29.21250786", "rel_title": "Sustainable targeted interventions to mitigate the COVID-19 pandemic: A big data-driven modeling study in Hong Kong", @@ -955065,57 +956912,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.02.01.429176", - "rel_title": "Host PDZ-containing proteins targeted by SARS-Cov-2", - "rel_date": "2021-02-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.01.429176", - "rel_abs": "Small linear motif targeting protein interacting domains called PDZ have been identified at the C-terminus of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins E, 3a, and N. Using a high-throughput approach of affinity-profiling against the full human PDZome, we identified sixteen human PDZ binders of SARS-CoV-2 proteins E, 3A and N showing significant interactions with dissociation constants values ranging from 3 M to 82 M. Six of them (TJP1, PTPN13, HTRA1, PARD3, MLLT4, LNX2) are also recognized by SARS-CoV while three (NHERF1, MAST2, RADIL) are specific to SARS-CoV-2 E protein. Most of these SARS-CoV-2 protein partners are involved in cellular junctions/polarity and could be also linked to evasion mechanisms of the immune responses during viral infection. Seven of the PDZ-containing proteins among binders of the SARS-CoV-2 proteins E, 3a or N affect significantly viral replication under knock-down gene expression in infected cells. This PDZ profiling identifying human proteins potentially targeted by SARS-CoV-2 can help to understand the multifactorial severity of COVID19 and to conceive effective anti-coronaviral agents for therapeutic purposes.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Celia Caillet-Saguy", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Fabien Durbesson", - "author_inst": "AFMB" - }, - { - "author_name": "Veronica V. REZELJ", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Gergo Gogl", - "author_inst": "IGBMC" - }, - { - "author_name": "Quang Dinh Tran", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Jean-Claude Twizere", - "author_inst": "University of Liege" - }, - { - "author_name": "Marco Vignuzzi", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Renaud Vincentelli", - "author_inst": "AFMB" - }, - { - "author_name": "Nicolas Wolff", - "author_inst": "Institut Pasteur" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.01.30.428979", "rel_title": "Production of SARS-CoV-2 virus-like particles in insect cells", @@ -955304,6 +957100,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.01.29.21250592", + "rel_title": "Hot days and Covid19 - unusual heat stress for nursing professions in Germany", + "rel_date": "2021-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250592", + "rel_abs": "ObjectivesOur aim was to identify whether working during hot days alongside with Covid-19 related personal protective equipment causes heat stress for nursing professionals in Germany.\n\nMethodsUsing an online survey, we assessed the impact of hot weather on nursing staff performing in personal protective equipment. A random selection of nursing staff from hospitals, nursing homes and outpatient care participated in the survey.\n\nResultsOut of 428 participants, 6.3% were between 16 and 25 years old, 22.8% between 26 and 35 years, 21.9% between 36 and 45 years, 30.5% between 45 and 55 years, 18.2% between 56 and 65 years, and 0.3% were older than 65 years. Out of all participants, 18.2% were male and 82.5% female. The results of the survey showed that 48.3% had more than 20 years of experience in nursing and 46.2% cardiac, pulmonary, or other pre-existing conditions. Work was found exhaustive while working in PPE by 96.5% of the participants, and 93% complained of worse breathing. We found out that 85.8% reported difficulties to focus. Many workplaces turned out to lack adequate heat protection, with distinct differences concerning the amount of prophylactic and heat mitigating measures across institutions.\n\nConclusionsOur results clearly show that employers must make more of an effort to provide adequate heat protection for their nursing staff. In order to secure the public health care, there is a need for action, especially in the case of previous conditions of caregivers.\n\nWhat is already known about this subject?{blacktriangleright} Working in personal protective equipment is often needed during pandemics, to protect nurses, doctors and staff from an infection.\n{blacktriangleright}However, the equipment can also hamper efficiency and productivity of healthcare workers and lead to personal discomfort, for example, during heat waves.\n\n\nWhat are the new findings?{blacktriangleright} According to our study, nurses and nursing assistants in Germany are often older than 45 years and, in many cases, suffer from pre-existing conditions, which exacerbate the problems with personal protective equipment during periods of hot temperatures.\n{blacktriangleright}Many healthcare institutions do not offer adequate ways to mitigate heat stress for their staff.\n\n\nHow might this impact on policy or clinical practice in the foreseeable future?{blacktriangleright} The results from this study can inform policy makers and clinical practitioners to modify their protocols to include better protective measures during extreme heat or other adverse environmental conditions.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Yvette Jegodka", + "author_inst": "FOM University of Applied Sciences" + }, + { + "author_name": "Lena Lagally", + "author_inst": "LMU University Hospital Munich" + }, + { + "author_name": "Hanna Mertes", + "author_inst": "LMU University Hospital Munich" + }, + { + "author_name": "Katharina Deering", + "author_inst": "LMU University Hospital Munich" + }, + { + "author_name": "Julia Schoierer", + "author_inst": "LMU University Hospital Munich" + }, + { + "author_name": "Barbara Buchberger", + "author_inst": "FOM University of Applied Sciences" + }, + { + "author_name": "Stephan Bose-O'Reilly", + "author_inst": "LMU University Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.01.28.21250714", "rel_title": "Discrimination of SARS-Cov 2 and arboviruses (DENV, ZIKV and CHIKV) clinical features using machine learning techniques: a fast and inexpensive clinical screening for countries simultaneously affected by both diseases", @@ -956771,57 +958610,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.28.21250163", - "rel_title": "Ultra-short-wave diathermy shortens the course of moderate and severe COVID-19: a randomized controlled trial", - "rel_date": "2021-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.28.21250163", - "rel_abs": "QuestionIs ultra-short-wave diathermy (USWD) safe and effective in coronavirus disease 2019 (COVID-19) ?\n\nDesignSingle-centre, evaluator-blinded, two-arm, parallel design, randomized controlled clinical trial.\n\nParticipantsModerate and severe COVID-19 patients with acute respiratory syndrome.\n\nInterventionUSWD for 10 minutes twice daily for 12 consecutive days along with standard medical treatment (USWD group, n = 25), versus standard medical treatment alone (control group, n = 25).\n\nOutcome measuresThe primary outcomes were the duration of recovery and negative conversion rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on days 7, 14, 21, and 28. Secondary outcomes included clinical status (seven-category ordinal and systemic inflammatory response syndrome (SIRS) scores), computed tomography (CT), routine blood tests, and adverse events.\n\nResultsTime to clinical recovery (USWD 36.84{+/-}9.93 vs. control 43.56{+/-}12.15, P = 0.037) was significantly shortened with a between-group difference of 6.72 days. Clinical status was improved with significant between-group differences on day 28 (SIRS, P = 0.011; seven-category scale, P = 0.003). The rate of RNA negative conversion at days 7 (P = 0.066), 14 (P = 0.239), 21 (P = 0.269), and 28 (P = 0.490) was statistically insignificant. Moreover, insignificant differences were observed in the artificial intelligence-assisted CT analysis. No treatment-associated adverse events or worsening of pulmonary fibrosis were observed.\n\nConclusionUSWD, as adjunctive therapy, shortened the recovery course and improved clinical status of patients with COVID-19 without aggravating pulmonary fibrosis. the findings are limited due to the small sample size and early termination.\n\nRegistrationChiCTR2000029972", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "liangjiang huang", - "author_inst": "Department of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic o" - }, - { - "author_name": "qian li", - "author_inst": "Department of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic o" - }, - { - "author_name": "Shah Zulfiqar Ali Sayed", - "author_inst": "Department of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic o" - }, - { - "author_name": "Nasb Mohammad", - "author_inst": "Department of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic o" - }, - { - "author_name": "bin chen", - "author_inst": "Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China." - }, - { - "author_name": "MPhil Ali Iftikhar", - "author_inst": "Paraplegic Center, Hayatabad, Peshawar, Pakistan" - }, - { - "author_name": "Lingfeng Xie", - "author_inst": "Department of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic o" - }, - { - "author_name": "Jifa Hu", - "author_inst": "Office of Academic Research, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "hong chen", - "author_inst": "Department of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic o" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "rehabilitation medicine and physical therapy" - }, { "rel_doi": "10.1101/2021.01.29.21250757", "rel_title": "Updated SARS-CoV-2 Single Nucleotide Variants and Mortality Association", @@ -957038,6 +958826,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.29.21250712", + "rel_title": "MOATAI-VIR - an AI algorithm that predicts severe adverse events and molecular features for COVID-19's complications", + "rel_date": "2021-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250712", + "rel_abs": "Following SARS-CoV-2 infection, some COVID-19 patients experience severe adverse events caused by pathogenic host responses. To treat these complications, their underlying etiology must be identified. Thus, a novel AI-based methodology, MOATAI-VIR, which predicts disease-protein-pathway relationships for 22 clinical manifestations attributed to COVID-19 was developed. SARS-CoV-2 interacting human proteins and GWAS identified respiratory failure associated risk genes provide the input from which the mode-of-action (MOA) proteins/pathways of the resulting disease comorbidities are predicted. These comorbidities are then mapped to their clinical manifestations. Three uncharacterized manifestation categories are found: neoplasms, mental and behavioral disorders, and congenital malformations, deformations, and chromosomal abnormalities. The prevalence of neoplasms suggests a possible association between COVID-19 and cancer, whether by shared molecular mechanisms between oncogenesis and viral replication, or perhaps, SARS-CoV-2 is an oncovirus. To assess the molecular basis of each manifestation, the proteins shared across each group of comorbidities were prioritized and subject to global pathway analysis. From these most frequent pathways, the molecular features associated with hallmark COVID-19 phenotypes, such as loss of sense of smell/taste, unusual neurological symptoms, cytokine storm, and blood clots were explored. Results of MOATAI-VIR are available for academic users at: http://pwp.gatech.edu/cssb/MOATAI-VIR/.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Courtney Alexandra Astore", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Hongyi Zhou", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Joshy Jacob", + "author_inst": "Emory University" + }, + { + "author_name": "Jeffrey Skolnick", + "author_inst": "Georgia Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.30.21250844", "rel_title": "Retinol Depletion in Severe COVID-19", @@ -958289,41 +960108,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.29.21250643", - "rel_title": "Emergence of first strains of Sars-CoV-2 lineage B.1.1.7 in Romania", - "rel_date": "2021-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250643", - "rel_abs": "United Kingdom reported the emergence of a new and highly transmissible SARS-CoV-2 variant B.1.1.7. that rapidly spread to other contries. The impact of this new mutation that occurs in the S protein, on infectivity, virulence and current vaccine effectiveness is still under evaluation. We have identified the first cases of the B.1.1.7 variant in samples collected from Romanian patients, of which one was traced to the UK region where the new variant was originally sequenced. Mutations in the Nsp3 protein, N844S and D455N and L15F in Orf3a were also detected, indicating common ancestry with UK strains as well as remote connections with strains from Nagasaki, Japan. These results indicate, for the first time, the presence and characteristics of the new variant B.1.1.7 in Romania and underscore the need for increased genomic sequencing in confirmed COVID-19 patients.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Andrei Lobiuc", - "author_inst": "University Stefan cel Mare Suceava, Romania" - }, - { - "author_name": "Mihai Dimian", - "author_inst": "University Stefan cel Mare Suceava, Romania" - }, - { - "author_name": "Olga Sturdza", - "author_inst": "University Stefan cel Mare, Suceava, Romania" - }, - { - "author_name": "Roxana Filip", - "author_inst": "University Stefan cel Mare, Suceava, Romania" - }, - { - "author_name": "Mihai Covasa", - "author_inst": "Universitatea Stefan cel Mare Suceava, Romania" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.29.21250653", "rel_title": "Robust spike antibody responses and increased reactogenicity in seropositive individuals after a single dose of SARS-CoV-2 mRNA vaccine", @@ -958572,6 +960356,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.01.27.21250597", + "rel_title": "Modeling the asymptomatic prevalence of SARS-CoV-2 epidemic in Italy and the ISTAT survey", + "rel_date": "2021-01-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.27.21250597", + "rel_abs": "objectivesAugust 3rd, 2020, the Italian National Institute of Statistics (ISTAT) presented preliminary results of seroprevalence survey on the percentage of individuals affected by Covid-19. The survey aims to define (within the entire population of Italy) the portion of individuals that developed an antibody response against SARS-CoV-2. For the first time one has an estimate of the asymptomatic infected population and the possibility to acknowledge its potential role in the infection spread in Italy, one of the most affected areas in Europe. The information obtained allow a particularly sensitive validation of epidemiological models which include the asymptomatic class.\n\nmethodsThe present study is devoted to the construction of a model able to simulate, in a systematic way, the asymptomatic group whose relevance in the, SARS-CoV-2 epidemic, has been recently investigated and discussed. The investigation involves the description of the first epidemic outbreak in Italy as well as the predictive analysis of the ongoing second wave. In particular the possible correction to the data of the serological tests because of their sensitivity and specificity.\n\nresultsThe model: taken as an example of the models presently used, satisfactory reproduces the data of the ISTAT survey showing a relevant predictive power and relegating in a secondary position models which do not include, in the simulation, the presence of asymptomatic groups. The corrections due to the serological test sensitivity (in particular those ones depending on the symptoms onset) make the comparison between data and models less accurate.\n\nconclusionsThe predictions of the model confirm a relevant presence of asymptomatic individuals also during the second pandemic wave in Italy. The ratio of reported to unreported cases is predicted to be roughly 1:4. A more detailed knowledge of the results of the survey could allow to correct, in a relevant way, the data by means of the experimental evidences on the antibodies sensibility. The model analyses of the vaccination strategies, confirms the relevance of a massive administration with the beginning of the year to arrive at the end of the infection within August 2021.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Marco Claudio Traini", + "author_inst": "Trento University" + }, + { + "author_name": "Carla Caponi", + "author_inst": "Clinica Geriatrica, Azienda Ospedaliero-Universitaria, Piazzale Gambuli 1, 06132, Perugia, Italy" + }, + { + "author_name": "Riccardo Ferrari", + "author_inst": "Bilubah LLC, 30 N. Gould St, Suite 6739, Sheridan, WY 82801, U.S.A." + }, + { + "author_name": "Giuseppe Vittorio De Socio", + "author_inst": "Clinica Malattie Infettive, Azienda Ospedaliero-Universitaria, Piazzale Gambuli 1, 06132, Perugia, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.27.21250618", "rel_title": "Neighbourhood-level risk factors of COVID-19 incidence and mortality", @@ -960487,37 +962302,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.01.27.21250238", - "rel_title": "Disentangling the association of hydroxychloroquine treatment with mortality in Covid-19 hospitalized patients through Hierarchical Clustering", - "rel_date": "2021-01-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.27.21250238", - "rel_abs": "The efficacy of hydroxychloroquine (HCQ) in treating SARS-CoV-2 infection is harshly debated, with observational and intervention studies reporting contrasting results.\n\nTo clarify the role of HCQ in Covid-19 patients, we carried out a retrospective observational study of 4,396 unselected patients hospitalized for Covid-19 in Italy (February-May 2020). Patients characteristics were collected at entry, including age, sex, obesity, smoking status, blood parameters, history of diabetes, cancer, cardiovascular and chronic pulmonary diseases and medications in use. These were used to identify subtypes of patients with similar characteristics through hierarchical clustering based on Gower distance. Using multivariable Cox regressions, these clusters were then tested for association with mortality and modification of effect by treatment with HCQ.\n\nWe identified two clusters, one of 3,913 younger patients with lower circulating inflammation levels and better renal function, and one of 483 generally older and more comorbid subjects, more prevalently men and smokers. The latter group was at increased death risk adjusted by HCQ (HR[CI95%] = 3.80[3.08-4.67]), while HCQ showed an independent inverse association (0.51[0.43-0.61]), as well as a significant influence of cluster*HCQ interaction (p<0.001). This was driven by a differential association of HCQ with mortality between the high (0.89[0.65-1.22]) and the low risk cluster (0.46[0.39-0.54]). These effects survived adjustments for additional medications in use and were concordant with associations with disease severity and outcome.\n\nThese findings suggest a particularly beneficial effect of HCQ within low risk Covid-19 patients and may contribute clarifying the current controversy on HCQ efficacy in Covid-19 treatment.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Augusto Di Castelnuovo", - "author_inst": "Mediterranea Cardiocentro, Naples, Italy" - }, - { - "author_name": "Alessandro Gialluisi", - "author_inst": "IRCCS Neuromed" - }, - { - "author_name": "- The COVID-19 RISK and Treatments (CORIST) Collaboration", - "author_inst": "" - }, - { - "author_name": "Licia Iacoviello", - "author_inst": "Universita dell'Insubria, Varese, Italy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.26.21250533", "rel_title": "Lumipulse G SARS-CoV-2 Ag Assay Evaluation for SARS-CoV-2 Antigen Detection Using 594 Nasopharyngeal Swab Samples from Different Testing Groups", @@ -960762,6 +962546,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.26.21250543", + "rel_title": "The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera.", + "rel_date": "2021-01-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250543", + "rel_abs": "One year in the coronavirus disease 2019 (COVID-19) pandemic, the first vaccines are being rolled out under emergency use authorizations. It is of great concern that newly emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can escape antibody-mediated protection induced by previous infection or vaccination through mutations in the spike protein. The glutamate (E) to Lysine (K) substitution at position 484 (E484K) in the receptor binding domain (RBD) of the spike protein is present in the rapidly spreading variants of concern belonging to the B.1.351 and P.1 lineages. We performed in vitro microneutralization assays with both the USA-WA1/2020 virus and a recombinant (r)SARS-CoV-2 virus that is identical to USA-WA1/2020 except for the E484K mutation introduced in the spike RBD. We selected 34 sera from study participants based on their SARS-CoV-2 spike ELISA antibody titer (negative [N=4] versus weak [N=8], moderate [N=11] or strong positive [N=11]). In addition, we included sera from five individuals who received two doses of the Pfizer SARS-CoV-2 vaccine BNT162b2. Serum neutralization efficiency was lower against the E484K rSARS-CoV-2 (vaccination samples: 3.4 fold; convalescent low IgG: 2.4 fold, moderate IgG: 4.2 fold and high IgG: 2.6 fold) compared to USA-WA1/2020. For some of the convalescent donor sera with low or moderate IgG against the SARS-CoV-2 spike, the drop in neutralization efficiency resulted in neutralization ID50 values similar to negative control samples, with low or even absence of neutralization of the E484K rSARS-CoV-2. However, human sera with high neutralization titers against the USA-WA1/2020 strain were still able to neutralize the E484K rSARS-CoV-2. Therefore, it is important to aim for the highest titers possible induced by vaccination to enhance protection against newly emerging SARS-CoV-2 variants. Two vaccine doses may be needed for induction of high antibody titers against SARS-CoV-2. Postponing the second vaccination is suggested by some public health authorities in order to provide more individuals with a primer vaccination. Our data suggests that this may leave vaccinees less protected against newly emerging variants.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Sonia Jangra", + "author_inst": "Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA" + }, + { + "author_name": "Chengjin Ye", + "author_inst": "Texas Biomedical Research Institute, San Antonio, TX, USA" + }, + { + "author_name": "Raveen Rathnasinghe", + "author_inst": "Department of Microbiology, Graduate School of Biomedical Sciences, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New " + }, + { + "author_name": "Daniel Stadlbauer", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA" + }, + { + "author_name": "- Personalized Virology Initiative (PVI) Study Group", + "author_inst": "" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA" + }, + { + "author_name": "Viviana Simon", + "author_inst": "Department of Microbiology, Global Health and Emerging Pathogens Institute, Department of Medicine -Division of Infectious Diseases, Icahn School of Medicine at" + }, + { + "author_name": "Luis Martinez-Sobrido", + "author_inst": "Texas Biomedical Research Institute, San Antonio, TX, USA" + }, + { + "author_name": "Adolfo Garcia-Sastre", + "author_inst": "Department of Microbiology, Global Health and Emerging Pathogens Institute, Department of Medicine -Division of Infectious Diseases, The Tisch Cancer Institute," + }, + { + "author_name": "Michael Schotsaert", + "author_inst": "Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.26.21250557", "rel_title": "Covid-19 positive test cycle threshold trends predict covid-19 mortality in Rhode Island", @@ -961961,41 +963800,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.27.21250521", - "rel_title": "Induction of labour during the COVID-19 pandemic: a national survey of impact on practice in the UK", - "rel_date": "2021-01-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.27.21250521", - "rel_abs": "BackgroundInduction of labour (IOL) is one of the most commonly performed interventions in maternity care, with outpatient cervical ripening increasingly offered as an option for women undergoing IOL. The COVID-19 pandemic has changed the context of practice and the option of returning home for cervical ripening may now assume greater significance. This work aimed to examine whether and how the COVID-19 pandemic has changed practice around IOL in the UK.\n\nMethodWe used an online questionnaire to survey senior obstetricians and midwives at all 156 UK NHS Trusts and Boards that currently offer maternity services. Responses were analysed to produce descriptive statistics, with free text responses analysed using a conventional content analysis approach.\n\nFindingsResponses were received from 92 of 156 UK Trusts and Boards, a 59% response rate. Many Trusts and Boards reported no change to their IOL practice, however 23% reported change in methods used for cervical ripening; 28% a change in criteria for home cervical ripening; 28% stated that more women were returning home during cervical ripening; and 24% noted changes to womens response to recommendations for IOL. Much of the change was reported as happening in response to attempts to minimise hospital attendance and restrictions on birth partners accompanying women.\n\nConclusionsThe pandemic has changed practice around induction of labour, although this varied significantly between NHS Trusts and Boards. There is a lack of formal evidence to support decision-making around outpatient cervical ripening: the basis on which changes were implemented and what evidence was used to inform decisions is not clear.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Mairi Harkness", - "author_inst": "University of Stirling" - }, - { - "author_name": "Cassandra Yuill", - "author_inst": "City, University of London" - }, - { - "author_name": "Helen Cheyne", - "author_inst": "University of Stirling" - }, - { - "author_name": "Sarah Stock", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Christine McCourt", - "author_inst": "City, University of London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2021.01.27.21250153", "rel_title": "The prevalence of olfactory dysfunction and its associated factors in patients with COVID-19 infection", @@ -962132,6 +963936,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.27.21250612", + "rel_title": "The effectiveness of the first dose of BNT162 b 2 vaccine in reducing SARS-CoV-2 infection 13-24 days after immunization: real-world evidence", + "rel_date": "2021-01-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.27.21250612", + "rel_abs": "BackgroundBNT162b2 vaccines showed high efficacy against COVID-19 in a randomised controlled phase-III trial. A vaccine effectiveness evaluation in real life settings is urgently needed, especially given the global disease surge. Hence, we assessed the short-term effectiveness of the first dose of BNT162b2-vaccine against SARS-CoV-2 infection. Given the BNT162b2 Phase-III results, we hypothesized that the cumulative incidence of SARS-CoV-2 infection among vaccinees will decline after 12 days following immunization compared to the incidence during the preceding days.\n\nMethodsWe conducted a retrospective cohort study using data from 2{middle dot}6 million-member state-mandated health provider in Israel. Study population consisted of all members aged 16 or above years who were vaccinated with BNT162b2-vaccine between December/19/2020 and January/15/2021. We collected information regarding medical history and positive SARS-CoV-2 polymerase chain reaction test from days after first dose to January/17/2021. Daily and cumulative infection rates in days 13-24 were compared to days 1-12 after first dose using Kaplan-Meier survival analysis and generalized linear models.\n\nFindingsData of 503,875 individuals (mean age 59{middle dot}7 years SD=14{middle dot}7, 47{middle dot}8% males) were analysed, of whom 351,897 had 13-24 days of follow-up. The cumulative incidence of SARS-CoV-2 infection was 0{middle dot}57% (n=2484) during days 1-12 and 0{middle dot}27% (n=614) in days 13-24. A 51{middle dot}4% relative risk reduction (RRR) was calculated in weighted-average daily incidence of SARS-CoV-2 infection from 43{middle dot}41-per-100,000(SE=12{middle dot}07) in days 1-12 to 21{middle dot}08-per-100,000(SE=6{middle dot}16) in days 13-24 following immunization. The decrement in incidence was evident from day 18 after first dose. Similar RRRs were calculated in individuals aged 60 or above (44.5%), younger individuals (50.2%), females (50.0%) and males (52.1%). Findings were similar in sub-populations and patients with various comorbidities.\n\nConclusionsWe demonstrated an effectiveness of 51% of BNT162b2 vaccine against SARS-CoV-2 infection 13-24 days after immunization with the first dose. Immunization with the second dose should be continued to attain the anticipated protection.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for follow-up studies regarding the effectiveness of BNT162b2 mRNA Covid-19 Vaccine without any language restrictions. The search terms were (BNT162b2 OR mRNA Covid-19 Vaccine) AND (effectiveness OR real-world OR phase IV) until Jan 15, 2021. We found no relevant observational studies among humans. We also assessed Phase II and Phase III clinical trials with BNT162b2 mRNA vaccine.\n\nAdded value of this studyTo our knowledge, this is the first and largest phase IV study on the effectiveness of the BNT162b2 mRNA COVID-19 vaccine in real-world settings. Our findings showed that the first dose of the vaccine is associated with an approximately 51% reduction in the incidence of PCR-confirmed SARS-CoV-2 infections at 13 to 24 days after immunization compared to the rate during the first 12 days. Similar levels of effectiveness were found across age groups, sex, as well as among individuals residing in Arab or ultra-orthodox Jewish communities that display an increased COVID-19 risk.\n\nImplications of all the available evidenceThe study results indicate that in real life the first dose of the new BNT162b2 mRNA COVID-19 vaccine confers around 50% protection against overall SARS-CoV-2 infections (symptomatic or asymptomatic). Together our findings and the 95% efficacy shown in the phase III trial, suggest that the BNT162b2 vaccine should be administered in two doses to achieve maximum protection and impact in terms of disease burden reduction and possibly reducing SARS-CoV-2 transmission. COVID-19 vaccines should be urgently deployed globally.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Gabriel Chodcik", + "author_inst": "Maccabitech" + }, + { + "author_name": "Lilac Tene", + "author_inst": "Maccabi Healthcare Services" + }, + { + "author_name": "Tal Patalon", + "author_inst": "KSM, Maccabi Healthcare Services" + }, + { + "author_name": "Sivan Gazit", + "author_inst": "KSM, Maccabi Healthcare Services" + }, + { + "author_name": "Amir Ben-Tov", + "author_inst": "Maccabi Healthcare Services" + }, + { + "author_name": "Dani Cohen", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Khitam Muhsen", + "author_inst": "Tel Aviv University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.26.21250561", "rel_title": "SARS-CoV-2 antigenemia/viremia masks seroconversion in a COVID-19 patient", @@ -963863,85 +965710,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.26.21250506", - "rel_title": "The Association Between Hypoglycemic Agents and Clinical Outcomes of COVID-19 in Patients with Diabetes: A Systematic Review and Meta-Analysis", - "rel_date": "2021-01-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250506", - "rel_abs": "BackgroundDuring the current Coronavirus Disease 2019 (COVID-19) pandemic, diabetic patients face disproportionately more. Anti-inflammatory effects of hypoglycemic agents have been reported, and their beneficial or harmful effects in patients with diabetes and COVID-19 remain controversial.\n\nPurposeThis study was performed to clarify this association.\n\nData SourcesRelevant literature was searched on China National Knowledge Infrastructure (CNKI), Wanfang Data Knowledge Service Platform, Chinese periodical service platform VIP Database, Sinomed (China Biology Medicine, CBM), MedRxiv, PubMed, ScienceDirect, Web of Science, Ovid Databases (LWW), Springer Link, Wiley Online Library, Oxford Academic, Nature Press Group, Cochrane Library and BMJ Evidence-Based Medicine up to November 14, 2020.\n\nStudy SelectionOnly observational studies of hypoglycemic agents vs. drugs or therapy without hypoglycemic agents in adult diabetic patients with COVID-19 were included.\n\nData ExtractionData of death and poor composite outcomes were extracted.\n\nData SynthesisThe pooled effects were calculated using the fixed-effects or random-effects models based on heterogeneity assessment.\n\nLimitationMost studies were retrospective cohort studies with relative weak capability to verify causality.\n\nConclusionHome use of metformin might be beneficial in decreasing mortality in diabetic patients infected with SARS-CoV-2. There is insufficient evidence to conclude that metformin and other hypoglycemic agents are associated with poor composite outcomes. More prospective studies, especially RCTs are needed.\n\nRegistration-PROSPEROCRD42020221951.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Tiantia Han", - "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University" - }, - { - "author_name": "Shaodi Ma", - "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University" - }, - { - "author_name": "Chenyu Sun", - "author_inst": "AMITA Health Saint Joseph Hospital Chicago" - }, - { - "author_name": "Huimei Zhang", - "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University" - }, - { - "author_name": "Guangbo Qu", - "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University" - }, - { - "author_name": "Yue Chen", - "author_inst": "Department of Clinical Medicine, School of the First Clinical Medicine, Anhui Medical University" - }, - { - "author_name": "Ce Cheng", - "author_inst": "The University of Arizona College of Medicine at South Campus" - }, - { - "author_name": "Eric L. Chen", - "author_inst": "Internal Medicine, AMITA Health Saint Joseph Hospital Chicago" - }, - { - "author_name": "Mubashir Ayaz Ahmed", - "author_inst": "Internal Medicine, AMITA Health Saint Joseph Hospital Chicago" - }, - { - "author_name": "Keun Young Kim", - "author_inst": "Internal Medicine, AMITA Health Saint Joseph Hospital Chicago" - }, - { - "author_name": "Reveena Manem", - "author_inst": "Internal Medicine, AMITA Health Saint Joseph Hospital Chicago" - }, - { - "author_name": "Mengshi Chen", - "author_inst": "Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University" - }, - { - "author_name": "Zhichun Guo", - "author_inst": "Massachusetts college of Pharmacy and Health sciences" - }, - { - "author_name": "Hongru Yang", - "author_inst": "Massachusetts college of Pharmacy and Health sciences" - }, - { - "author_name": "Yue Yan", - "author_inst": "Massachusetts college of Pharmacy and Health sciences" - }, - { - "author_name": "Qin Zhou", - "author_inst": "Radiation Oncology, Mayo Clinic" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "endocrinology" - }, { "rel_doi": "10.1101/2021.01.25.21250040", "rel_title": "COVID-19-related disruptions to routine vaccination services in India: perspectives from pediatricians", @@ -964154,6 +965922,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.01.26.21250246", + "rel_title": "Lack of trust and social media echo chambers predict COVID-19 vaccine hesitancy", + "rel_date": "2021-01-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250246", + "rel_abs": "As COVID-19 vaccines are rolled out across the world, there are growing concerns about the role that trust, belief in conspiracy theories and spread of misinformation through social media impact vaccine hesitancy. We use a nationally representative survey of 1,476 adults in the UK between December 12 to 18, 2020 and five focus groups conducted in the same period. Trust is a core predictor, with distrust in vaccines in general and mistrust in government raising vaccine hesitancy. Trust in health institutions and experts and perceived personal threat are vital, with focus groups revealing that COVID-19 vaccine hesitancy is driven by a misunderstanding of herd immunity as providing protection, fear of rapid vaccine development and side effects, belief the virus is man- made and related to population control. Particularly those who obtain information from relatively unregulated social media sources such as YouTube that have recommendations tailored by watch history are less likely to be willing to become vaccinated. Those who hold general conspiratorial beliefs are less willing to be vaccinated. Since an increasing number of individuals use social media for gathering health information, interventions require action from governments, health officials and social media companies. More attention needs to help people understand their own risks, unpack complex concepts and fill knowledge voids.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Will Jennings", + "author_inst": "University of Southampton" + }, + { + "author_name": "Gerry Stoker", + "author_inst": "University of Southampton" + }, + { + "author_name": "Hannah Willis", + "author_inst": "University of Southampton" + }, + { + "author_name": "Viktor Valgardsson", + "author_inst": "University of Southampton" + }, + { + "author_name": "Jenn Gaskell", + "author_inst": "University of Southampton" + }, + { + "author_name": "Daniel Devine", + "author_inst": "University of Oxford" + }, + { + "author_name": "Lawrence Mckay", + "author_inst": "University of Southampton" + }, + { + "author_name": "Melinda C Mills", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.01.26.21250420", "rel_title": "Outcomes of Ivermectin in the treatment of COVID-19: a systematic review and meta-analysis", @@ -965593,37 +967408,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.21.21249496", - "rel_title": "Management of conductive deafness from Otitis Media with Effusion (known as glue ear) in children using bone conduction headsets when grommet operations were unavailable during COVID-19.", - "rel_date": "2021-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.21249496", - "rel_abs": "BackgroundOtitis Media with Effusion (OME) causing hearing impairments affects [~]1 in 10 children starting school in UK/ Europe. 80% have at least one episode with most having conductive hearing loss. Studies showed children with OME hear better with bone conducting headsets. During COVID-19 we investigated whether children with deafness secondary OME, without access to audiology or grommet surgery, could be aided with bone conduction kits and the HearGlueEar app.\n\nMethodsStarting July 2020, during COVID-19, children aged 3-11 years with OME and on a grommet waiting list were invited to a single arm, prospective study. They received the kit, instructions and HearGlueEar app by post. By 3 weeks parents were asked to charge and pair the devices, attend a remote consultation and complete an OMQ-14 questionnaire. Remote follow-up lasted 3 months. Outcomes: ability to use the equipment, complete the questionnaire about childs hearing and behaviour before and with the equipment, declining grommet surgery or where deafness resolved, and give opinion about the intervention.\n\nFindings26 children enrolled. Families used the kit at home and school. Most found remote consultations positive and convenient. OMQ-14 responses were 90% positive. Comments were: \"Other people have said, wow his speech is clearer.\", \"It is making a real difference at home.\", \"He said over and over again, \"I can hear everybody, wow, wow, wow.\", \"It is no exaggeration to say this has made an astronomical improvement to his quality of life\". One child reported \"I can hear my best friend again\". \"She is getting on really well with the headphones - pairing them with the iPad at home is simply brilliant.\" Three families continued with the headset to avoid grommets.\n\nInterpretationPosting a bone conduction kit, HearGlueEar app and remote consultation is effective support for children with deafness secondary to OME.\n\nFundingNone", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Tamsin Mary Holland Brown", - "author_inst": "Cambridgeshire Community Services NHS Trust" - }, - { - "author_name": "Isobel Fitzgerald OConnor", - "author_inst": "Cambridge University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Jessica Bewick", - "author_inst": "Cambridge University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Colin Morley", - "author_inst": "Cambridge University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.01.20.21250204", "rel_title": "Rule of thumb in human intelligence for assessing the COVID-19 outbreak in Japan", @@ -965812,6 +967596,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.23.21250325", + "rel_title": "Evaluation of a Commercial Culture-free Neutralization Antibody Detection Kit for Severe Acute Respiratory Syndrome-Related Coronavirus-2 and Comparison with an Anti-RBD ELISA Assay", + "rel_date": "2021-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.23.21250325", + "rel_abs": "BackgroundSARS-CoV-2 surrogate neutralization assays that obviate the need for viral culture offer substantial advantages regarding throughput and cost. The cPass SARS-CoV-2 Neutralization Antibody Detection Kit (Genscript) is the first such commercially available assay, detecting antibodies that block RBD/ACE-2 interaction. We aimed to evaluate cPass to inform its use and assess its added value compared to anti-RBD ELISA assays.\n\nMethodsSerum reference panels comprising 205 specimens were used to compare cPass to plaque-reduction neutralization test (PRNT) and a pseudotyped lentiviral neutralization (PLV) assay for detection of neutralizing antibodies. We assessed the correlation of cPass with an ELISA detecting anti-RBD IgG, IgM, and IgA antibodies at a single timepoint and across intervals from onset of symptoms of SARS-CoV-2 infection.\n\nResultsCompared to PRNT-50, cPass sensitivity ranged from 77% - 100% and specificity was 95% - 100%. Sensitivity was also high compared to the pseudotyped lentiviral neutralization assay (93% [95%CI 85-97]), but specificity was lower (58% [95%CI 48-67]). Highest agreement between cPass and ELISA was for anti-RBD IgG (r=0.823). Against the pseudotyped lentiviral neutralization assay, anti-RBD IgG sensitivity (99% [95%CI 94-100]) was very similar to that of cPass, but overall specificity was lower (37% [95%CI 28-47]). Against PRNT-50, results of cPass and anti-RBD IgG were nearly identical.\n\nConclusionsThe added value of cPass compared to an IgG anti-RBD ELISA was modest.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Jesse Papenburg", + "author_inst": "Montreal Children's Hospital" + }, + { + "author_name": "Matthew P Cheng", + "author_inst": "McGill University" + }, + { + "author_name": "Rachel Corsini", + "author_inst": "McGill Interdisciplinary Initiative in Infection and Immunity" + }, + { + "author_name": "Chelsea Caya", + "author_inst": "McGill University Health Centre - Research Institute" + }, + { + "author_name": "Emelissa J Mendoza", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Kathy J Manguiat", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "L Robbin Lindsay", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Heidi Wood", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Michael Drebot", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Antonia Dibernardo", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Gerasimos Zaharatos", + "author_inst": "Optilab Montreal - McGill University Health Centre" + }, + { + "author_name": "Ren\u00e9e Bazin", + "author_inst": "H\u00e9ma-Qu\u00e9bec" + }, + { + "author_name": "Romain Gasser", + "author_inst": "CRCHUM / Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Mehdi Benlarbi", + "author_inst": "CRCHUM" + }, + { + "author_name": "Gabrielle Gendron-Lepage", + "author_inst": "CRCHUM" + }, + { + "author_name": "Guillaume Beaudoin-Bussi\u00e8res", + "author_inst": "CRCHUM" + }, + { + "author_name": "J\u00e9r\u00e9mie Pr\u00e9vost", + "author_inst": "CRCHUM / Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Andr\u00e9s Finzi", + "author_inst": "CRCHUM, Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Momar Ndao", + "author_inst": "McGill University" + }, + { + "author_name": "Cedric P Yansouni", + "author_inst": "McGill University Health Centre" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.22.21250328", "rel_title": "Seroprevalence and attainment of herd immunity against SARS CoV-2: A modelling study", @@ -967427,57 +969306,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.23.21250370", - "rel_title": "Patients with Asthma and Chronic Obstructive Pulmonary Disease (COPD) have increased levels of plasma inflammatory mediators upregulated in severe COVID-19", - "rel_date": "2021-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.23.21250370", - "rel_abs": "BackgroundChronic obstructive pulmonary disease (COPD) is associated with increased risk of severe COVID-19, but the mechanisms are unclear. Besides, patients with severe COVID-19 have been reported to have increased levels of several immune mediators.\n\nObjectiveTo perform an immunoproteomic profiling of dysregulated plasma proteins in patients with asthma and COPD and to evaluate their relationship with biomarkers of severe COVID-19.\n\nMethodsNinety-two proteins were quantified in 315 plasma samples from adult subjects (age 40-90 years) including 118 asthmatics, 99 COPD patients and 98 healthy controls, that have been recruited in two reference pneumology clinics in Colombia before the beginning of the COVID-19 pandemic. Protein levels were compared between each disease group and healthy controls.\n\nSignificant proteins were compared to the gene signatures of SARS-CoV-2 infection reported in the \"COVID-19 Drug and Gene Set Library\" and with known protein biomarkers of severe COVID-19.\n\nResultsForty-one plasma proteins showed differences between patients and controls. Asthmatic patients have increased levels in IL-6 while COPD patients have a broader systemic inflammatory dysregulation driven by HGF, OPG, and several chemokines (CXCL9, CXCL10, CXCL11, CX3CL1, CXCL1, MCP-3, MCP-4, CCL3, CCL4 and CCL11). These proteins are involved in chemokine signaling pathways related with response to viral infections and some, were found up-regulated upon SARS-CoV-2 experimental infection of Calu-3 cells as reported in the COVID-19 Related Gene Sets database. An increase of HPG, CXCL9, CXCL10, IL-6, MCP-3, TNF and EN-RAGE has also been found in patients with severe COVID-19.\n\nConclusionsCOPD patients have altered levels of plasma proteins that have been reported increased in patients with severe COVID-19. Our study suggests that COPD patients have a systemic dysregulation in chemokine networks (including HGF and CXCL9) that could make them more susceptible to severe COVID-19. Our study also suggest that IL-6 levels are increased in some asthmatics and this may influence their immune response to COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Nathalie Acevedo", - "author_inst": "Instituto de Investigaciones Inmunologicas, Universidad de Cartagena" - }, - { - "author_name": "Jose Miguel Escamilla-Gil", - "author_inst": "Instituto de Investigaciones Inmunologicas, Universidad de Cartagena" - }, - { - "author_name": "Hector Espinoza", - "author_inst": "Universidad de Cartagena, Facultad de Ingenieria" - }, - { - "author_name": "Ronald Regino", - "author_inst": "Instituto de Investigaciones Inmunologicas, Universidad de Cartagena" - }, - { - "author_name": "Jonathan Ramirez", - "author_inst": "Instituto de Investigaciones Inmunologicas, Universidad de Cartagena" - }, - { - "author_name": "Lucila Florez De Arco", - "author_inst": "Clinica Respitaroria y de Alergias" - }, - { - "author_name": "Rodolfo Dennis", - "author_inst": "Fundacion Cardioinfantil" - }, - { - "author_name": "Carlos Torres-Duque", - "author_inst": "Fundacion Neumologica Colombiana" - }, - { - "author_name": "Luis Caraballo", - "author_inst": "Instituto de Investigaciones Inmunologicas, Universidad de Cartagena" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.01.25.21250233", "rel_title": "Contamination of air and surfaces in workplaces with SARS-CoV-2 virus: a systematic review", @@ -967814,6 +969642,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.25.21250440", + "rel_title": "Non-Congruent SARS-CoV-2 Waves in England", + "rel_date": "2021-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.25.21250440", + "rel_abs": "Examination of the chronology, location and size of waves of SARS-CoV-2 infection across England could shed light on the inter-play between the 1st and the 2nd Waves. From mid-October onwards such an analysis becomes increasingly difficult due to the emergence of a new strain (VOC-202012/01) and in light of the differential implementation of lockdown measures and tiers. Therefore, we sought to examine trends and correlations in virus prevalence and covid-related deaths spanning the start of the UK pandemic in March 2020 through to early November 2020 - i.e., including the first growth period of the 2nd Wave. We found striking regional relationships between the 1st and the 2nd Wave that are difficult to explain other than by involving some role for changing levels of immunity in the population affecting the progression of the pandemic.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Anthony J Brookes", + "author_inst": "University of Leicester, UK" + }, + { + "author_name": "Allyson Pollock", + "author_inst": "Newcastle University, UK" + }, + { + "author_name": "Danny Dorling", + "author_inst": "University of Oxford, UK" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.24.21250387", "rel_title": "Identification of COVID-19 Subtypes Based on Immunogenomic Profiling", @@ -969261,33 +971116,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.01.25.428191", - "rel_title": "Variant and mutation analysis of SARS-CoV-2 genomes isolated from the Kingdom of Bahrain", - "rel_date": "2021-01-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.25.428191", - "rel_abs": "The challenges imposed by the ongoing outbreak of severe acute respiratory syndrome coronavirus-2 affects every aspect of our modern world, ranging from our health to our socio-economic needs. Our existence highly depends on the vaccines availability, which demands in-depth research of the available strains and their mutations. In this work, we have analyzed all the available SERS-CoV2 genomes isolated from the Kingdom of Bahrain in terms of their variance and origin analysis. We have predicted various known and unique mutations in the SERS-CoV2 isolated from Bahrain. The complexity of the phylogenetic tree and dot plot representation of the strains mentioned above with other isolates of Asia indicates the versatility and multiple origins of Bahrains SERS-CoV2 isolates. We have also identified two high impact spike mutations from these strains which increase the virulence of SARS-CoV2. Our research could have a high impact on vaccine development and distinguishes the source of SERS-CoV2 in the Kingdom of Bahrain.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Khalid M bindayna", - "author_inst": "Arabian gulf university" - }, - { - "author_name": "Abdel Halim Deifalla", - "author_inst": "Arabian gulf uninversity" - }, - { - "author_name": "Hicham Ezzat Mohammed Mokbel", - "author_inst": "Arabian gulf uninversity" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.01.25.428137", "rel_title": "Increased Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7 to Antibody Neutralization", @@ -969552,6 +971380,117 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2021.01.26.428207", + "rel_title": "Kinetics and correlates of the neutralizing antibody response to SARS-CoV-2", + "rel_date": "2021-01-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.26.428207", + "rel_abs": "A detailed understanding of antibody-based SARS-CoV-2 immunity has critical implications for overcoming the COVID-19 pandemic and for informing on vaccination strategies. In this study, we evaluated the dynamics of the SARS-CoV-2 antibody response in a cohort of 963 recovered individuals over a period of 10 months. Investigating a total of 2,146 samples, we detected an initial SARS-CoV-2 antibody response in 94.4% of individuals, with 82% and 79% exhibiting serum and IgG neutralization, respectively. Approximately 3% of recovered patients demonstrated exceptional SARS-CoV-2 neutralizing activity, defining them as elite neutralizers. These individuals also possessed effective cross-neutralizing IgG antibodies to SARS-CoV-1 without any known prior exposure to this virus. By applying multivariate statistical modeling, we found that sero-reactivity, age, time since disease onset, and fever are key factors predicting SARS-CoV-2 neutralizing activity in mild courses of COVID-19. Investigating longevity of the antibody response, we detected loss of anti-spike reactivity in 13% of individuals 10 months after infection. Moreover, neutralizing activity had an initial half-life of 6.7 weeks in serum versus 30.8 weeks in purified IgG samples indicating the presence of a more stable and long-term memory IgG B cell repertoire in the majority of individuals recovered from COVID-19. Our results demonstrate a broad spectrum of the initial SARS-CoV-2 neutralizing antibody response depending on clinical characteristics, with antibodies being maintained in the majority of individuals for the first 10 months after mild course of COVID-19.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Kanika Vanshylla", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne" + }, + { + "author_name": "Veronica Di Cristianziano", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne" + }, + { + "author_name": "Franziska Kleipass", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne" + }, + { + "author_name": "Felix Dewald", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne" + }, + { + "author_name": "Philipp Schommers", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne" + }, + { + "author_name": "Lutz Gieselmann", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne" + }, + { + "author_name": "Henning Gruell", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne" + }, + { + "author_name": "Maike Schlotz", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne" + }, + { + "author_name": "Meryem S Ercanoglu", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne" + }, + { + "author_name": "Ricarda Stumpf", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne" + }, + { + "author_name": "Petra Mayer", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne" + }, + { + "author_name": "Eva Heger", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne" + }, + { + "author_name": "Wibke Johannis", + "author_inst": "Institute for Clinical Chemistry, Faculty of Medicine and University Hospital Cologne, University of Cologne" + }, + { + "author_name": "Carola Horn", + "author_inst": "Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne" + }, + { + "author_name": "Isabelle Suarez", + "author_inst": "Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne" + }, + { + "author_name": "Norma Jung", + "author_inst": "Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne" + }, + { + "author_name": "Susanne Salomon", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne" + }, + { + "author_name": "Kirsten Eberhardt", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne" + }, + { + "author_name": "Gerd Faetkenheuer", + "author_inst": "Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne" + }, + { + "author_name": "Nico Pfeifer", + "author_inst": "Methods in Medical Informatics, Department of Computer Science, University of Tuebingen" + }, + { + "author_name": "Ralf Eggeling", + "author_inst": "Methods in Medical Informatics, Department of Computer Science, University of Tuebingen" + }, + { + "author_name": "Max Augustin", + "author_inst": "Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne" + }, + { + "author_name": "Clara Lehmann", + "author_inst": "Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne" + }, + { + "author_name": "Florian Klein", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.01.26.428302", "rel_title": "40 minutes RT-qPCR Assay for Screening Spike N501Y and HV69-70del Mutations", @@ -970991,57 +972930,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.21.21250226", - "rel_title": "Determinants of the incidence and mortality rates of COVID-19 during the first six months of the pandemic; A cross-country study", - "rel_date": "2021-01-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.21250226", - "rel_abs": "COVID-19 pandemic raises an extraordinary challenge to the healthcare systems globally. The governments are taking key measures to constrain the corresponding health, social, and economic impacts, however, these measures vary depending on the nature of the crisis and country-specific circumstances.\n\nObjectivesConsidering different incidence and mortality rates across different countries, we aimed at explaining variance of these variables by performing accurate and precise multivariate analysis with aid of suitable predictors, accordingly, the model would proactively guide the governmental responses to the crisis.\n\nMethodsUsing linear and exponential time series analysis, this research aimed at studying the incidence and mortality rates of COVID-19 in 18 countries during the first six months of the pandemic, and further utilize multivariate techniques to explain the variance in monthly exponential growth rates of cases and deaths with aid of a set of different predictors: the recorded Google mobility trends towards six categories of places, daily average temperature, daily humidity, and key socioeconomic attributes of each country.\n\nResultsThe analysis showed that changes in mobility trends were the most significant predictors of the incidence and mortality rates, temperature and humidity were also significant but to a much lesser extent, on the other hand, the socioeconomic attributes did not contribute significantly to explaining different incidence and mortality rates across countries.\n\nConclusionChanges in mobility trends across countries dramatically affected the incidence and mortality rates across different countries, thus, it might be used as a proxy measure of contact frequency.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Noha Asem", - "author_inst": "Faculty of Medicine, Cairo University" - }, - { - "author_name": "Ahmed Mohamed Ramadan", - "author_inst": "DataClin CRO, Egypt" - }, - { - "author_name": "Mohamed Hassany", - "author_inst": "Ministry of Health and Population, Egypt" - }, - { - "author_name": "Ramy Mohamed Ghazy", - "author_inst": "High Institute of Public Health, Alexandria, Egypt" - }, - { - "author_name": "Mohamed Abdallah", - "author_inst": "Medical Research Division, National Research Center, Giza, Egypt" - }, - { - "author_name": "Eman Gamal", - "author_inst": "Ministry Of Health and Population" - }, - { - "author_name": "Shimaa Hassan", - "author_inst": "Ministry of Health and Population" - }, - { - "author_name": "Nehal Kamal", - "author_inst": "Children Cancer Hospital (CCHE) 57357" - }, - { - "author_name": "Hala Zaid", - "author_inst": "Ministry of Health and Population, Egypt" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.24.21250416", "rel_title": "Social, economic, and environmental factors influencing the basic reproduction number of COVID-19 across countries", @@ -971302,6 +973190,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.01.22.21249968", + "rel_title": "An external validation of the QCovid risk prediction algorithm for risk of mortality from COVID-19 in adults: national validation cohort study in England", + "rel_date": "2021-01-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.22.21249968", + "rel_abs": "BackgroundTo externally validate a risk prediction algorithm (QCovid) to estimate mortality outcomes from COVID-19 in adults in England.\n\nMethodsPopulation-based cohort study using the ONS Public Health Linked Data Asset, a cohort based on the 2011 Census linked to Hospital Episode Statistics, the General Practice Extraction Service Data for pandemic planning and research, radiotherapy and systemic chemotherapy records. The primary outcome was time to COVID-19 death, defined as confirmed or suspected COVID-19 death as per death certification. Two time periods were used: (a) 24th January to 30th April 2020; and (b) 1st May to 28th July 2020. We evaluated the performance of the QCovid algorithms using measures of discrimination and calibration for each validation time period.\n\nFindingsThe study comprises 34,897,648 adults aged 19-100 years resident in England. There were 26,985 COVID-19 deaths during the first time-period and 13,177 during the second. The algorithms had good calibration in the validation cohort in both time periods with close correspondence of observed and predicted risks. They explained 77.1% (95% CI: 76.9% to 77.4%) of the variation in time to death in men in the first time-period (R2); the D statistic was 3.76 (95% CI: 3.73 to 3.79); Harrells C was 0.935 (0.933 to 0.937). Similar results were obtained for women, and in the second time-period. In the top 5% of patients with the highest predicted risks of death, the sensitivity for identifying deaths in the first time period was 65.9% for men and 71.7% for women. People in the top 20% of predicted risks of death accounted for 90.8% of all COVID-19 deaths for men and 93.0% for women.\n\nInterpretationThe QCovid population-based risk algorithm performed well, showing very high levels of discrimination for COVID-19 deaths in men and women for both time periods. It has the potential to be dynamically updated as the pandemic evolves and therefore, has potential use in guiding national policy.\n\nFundingNational Institute of Health Research\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSPublic policy measures and clinical risk assessment relevant to COVID-19 need to be aided by rigorously developed and validated risk prediction models. A recent living systematic review of published risk prediction models for COVID-19 found most models are subject to a high risk of bias with optimistic reported performance, raising concern that these models may be unreliable when applied in practice. A population-based risk prediction model, QCovid risk prediction algorithm, has recently been developed to identify adults at high risk of serious COVID-19 outcomes, which overcome many of the limitations of previous tools.\n\nAdded value of this studyCommissioned by the Chief Medical Officer for England, we validated the novel clinical risk prediction model (QCovid) to identify risks of short-term severe outcomes due to COVID-19. We used national linked datasets from general practice, death registry and hospital episode data for a population-representative sample of over 34 million adults. The risk models have excellent discrimination in men and women (Harrells C statistic>0.9) and are well calibrated. QCovid represents a new, evidence-based opportunity for population risk-stratification.\n\nImplications of all the available evidenceQCovid has the potential to support public health policy, from enabling shared decision making between clinicians and patients in relation to health and work risks, to targeted recruitment for clinical trials, and prioritisation of vaccination, for example.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Vahe Nafilyan", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Ben Humberstone", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Nisha Metha", + "author_inst": "Office of the Chief Medical Officer" + }, + { + "author_name": "Ian Diamond", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Luke Lorenzi", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Piotr Pawelek", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Ryan Schofield", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Jasper Morgan", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Paul Brown", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Ronan Lyons", + "author_inst": "Swansea University" + }, + { + "author_name": "Aziz Sheikh", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Julia Hippisley-Cox", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.01.24.21250397", "rel_title": "Using an Ecological and Biological Framing for an Anti-racist Covid-19 Approach", @@ -972873,37 +974824,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.01.23.427885", - "rel_title": "Variation analysis of SARS-CoV-2 complete sequences from Iran", - "rel_date": "2021-01-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.23.427885", - "rel_abs": "The SARS-CoV-2 is a new emerging coronavirus initially reported in China at the late December 2019 and rapidly spread to the whole of the world. To date, 1261903 total case and 55830 deaths are reported from Iran as 8 January. In this study, we investigated all the complete sequences of SARS-CoV-2 that publicly reported from Iran. Twenty-four sequences between March to September 2020 were analyzed to identify genome variations and phylogenetic relationships. Furthermore, we assessed the amino acid changes related to the spike glycoprotein as an important viral factor associated with the entry to the host cells and as a vaccine target. Most of the variations are occurred in the ORF1ab, S, N, intergenic and ORF7 regions. The analysis of spike protein mutations demonstrated that D614G mutation could be detected from the May and beyond. Phylogenetic analysis showed that most of the circulated viruses in Iran are belong to the B.4 lineage. Although, we found a limited number of variants associated to the B.1 lineage carrying D614G mutation. Furthermore, we detected a variant characterize as the B.1.36 lineage with sixteen mutations in the spike protein region. This study showed the frequency of the viral populations in Iran as September, therefore, there is an emergent need to genomic surveillance to track viral lineage shift in the country beyond the September. These data would help to predict future situation and apply better strategy to control of the pandemic.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jale Moradi", - "author_inst": "Assistant Professor, Microbiology Department, Faculty of Medicine, Kermanshah university of Medical Sciences, Iran" - }, - { - "author_name": "Mohsen Moghoofei", - "author_inst": "Assistant Professor, Microbiology Department, Faculty of Medicine, Kermanshah university of Medical Sciences, Iran" - }, - { - "author_name": "Amir Houshang Alvandi", - "author_inst": "Associate Professor, Microbiology Department, Faculty of Medicine, Kermanshah university of Medical Sciences, Iran" - }, - { - "author_name": "Ramin Abiri", - "author_inst": "Associate Professor, Microbiology Department, Faculty of Medicine, Kermanshah university of Medical Sciences, Iran" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.01.24.427089", "rel_title": "Meta-analysis reveals consistent immune response patterns in COVID-19 infected patients at single-cell resolution", @@ -973124,6 +975044,141 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.01.21.20240887", + "rel_title": "The psychosocial impact of the COVID-19 pandemic on 4,378 UK healthcare workers and ancillary staff: initial baseline data from a cohort study collected during the first wave of the pandemic.", + "rel_date": "2021-01-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.20240887", + "rel_abs": "ObjectivesThis study reports preliminary findings on the prevalence of, and factors associated with, mental health and wellbeing outcomes of healthcare workers during the early months (April-June) of the COVID-19 pandemic in the UK.\n\nMethodsPreliminary cross-sectional data were analysed from a cohort study (n=4,378). Clinical and non-clinical staff of three London-based NHS Trusts (UK), including acute and mental health Trusts, took part in an online baseline survey. The primary outcome measure used is the presence of probable common mental disorders (CMDs), measured by the General Health Questionnaire (GHQ-12). Secondary outcomes are probable anxiety (GAD-7), depression (PHQ-9), Post-Traumatic Stress Disorder (PTSD) (PCL-6), suicidal ideation (CIS-R), and alcohol use (AUDIT). Moral injury is measured using the Moray Injury Event Scale (MIES).\n\nResultsAnalyses showed substantial levels of CMDs (58.9%, 95%CI 58.1 to 60.8), and of PTSD (30.2%, 95%CI 28.1 to 32.5) with lower levels of depression (27.3%, 95%CI 25.3 to 29.4), anxiety (23.2%, 95%CI 21.3 to 25.3), and alcohol misuse (10.5%, 95%CI, 9.2 to 11.9). Women, younger staff, and nurses tended to have poorer outcomes than other staff, except for alcohol misuse. Higher reported exposure to moral injury (distress resulting from violation of ones moral code) was strongly associated with increased levels of CMDs, anxiety, depression, PTSD symptoms, and alcohol misuse.\n\nConclusionsOur findings suggest that mental health support for healthcare workers should consider those demographics and occupations at highest risk. Rigorous longitudinal data are needed in order to respond to the potential long-term mental health impacts of the pandemic.\n\nHighlightsO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LILarge-scale population studies report increased prevalence of depression, anxiety, and psychological distress during the COVID-19 pandemic.\nC_LIO_LIEvidence from previous epidemics indicates a high and persistent burden of adverse mental health outcomes among healthcare workers.\nC_LI\n\nWhat are the new findings?O_LISubstantial levels of probable common mental disorders and post-traumatic stress disorder were found among healthcare workers.\nC_LIO_LIGroups at increased risk of adverse mental health outcomes included women, nurses, and younger staff, as well as those who reported higher levels of moral injury.\nC_LI\n\nHow might this impact on policy or clinical practice in the foreseeable future?O_LIThe mental health offering to healthcare workers must consider the interplay of demographic, social, and occupational factors.\nC_LIO_LIAdditional longitudinal research that emphasises methodological rigor, namely with use of standardised diagnostic interviews to establish mental health diagnoses, is necessary to better understand the mental health burden, identify those most at risk, and provide appropriate support without pathologizing ordinary distress responses.\nC_LI", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Danielle Lamb", + "author_inst": "Department of Applied Health Research, UCL, 1-19 Torrington Place, London, WC1E 7HB" + }, + { + "author_name": "Sam Gnanapragasam", + "author_inst": "South London and Maudsley NHS Foundation Trust, London, UK" + }, + { + "author_name": "Neil Greenberg", + "author_inst": "Health Protection Research Unit, King's College London, Weston Education Centre, 10 Cutcombe Road, London, SE5 9RJ" + }, + { + "author_name": "Rupa Bhundia", + "author_inst": "Department of Psychological Medicine, King's College London, London, UK." + }, + { + "author_name": "Ewan Carr", + "author_inst": "Department of Biostatistics and Health Informatics, King's College London, London, UK" + }, + { + "author_name": "Matthew Hotopf", + "author_inst": "National Institute of Health Research Biomedical Research Centre at the South London and Maudsley NHS Foundation Trust." + }, + { + "author_name": "Reza Razavi", + "author_inst": "1 Lambeth Palace Rd, South Bank, London, SE1 7EU" + }, + { + "author_name": "Rosalind Raine", + "author_inst": "Dept of Applied Health Research, UCL" + }, + { + "author_name": "Sean Cross", + "author_inst": "Department of Psychological Medicine, King's College Hospital. Denmark Hill. SE5 9RS" + }, + { + "author_name": "Amy Dewar", + "author_inst": "Guy's and St Thomas' NHS Foundation Trust" + }, + { + "author_name": "Mary Docherty", + "author_inst": "Department of Psychological Medicine, King's College Hospital. Denmark Hill. SE5 9RS" + }, + { + "author_name": "Sarah Dorrington", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, King's College London" + }, + { + "author_name": "Stephani Hatch", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, King's College London" + }, + { + "author_name": "Charlotte Wilson-Jones", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, King's College London" + }, + { + "author_name": "Daniel Leightley", + "author_inst": "King's Centre for Military Health Research, Department of Psychological Medicine, King's College London, London, UK. AND Department of Psychological Medicine, K" + }, + { + "author_name": "Ira Madan", + "author_inst": "Guy's and St Thomas' NHS Foundation Trust, London" + }, + { + "author_name": "Sally Marlow", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, King's College London" + }, + { + "author_name": "Isabel McMullen", + "author_inst": "Department of Psychological Medicine, King's College Hospital, South London and Maudsley NHS Foundation Trust" + }, + { + "author_name": "Anne Marie Rafferty", + "author_inst": "Adult Nursing, King's College London" + }, + { + "author_name": "Martin Parsons", + "author_inst": "Mental Health Liaison Team, King's College Hospital" + }, + { + "author_name": "Catherine Polling", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, King's College London" + }, + { + "author_name": "Danai Serfioti", + "author_inst": "King's Centre for Military Health Research, King's College London, Room 307, Weston Education Centre, 10 Cutcombe Road, London SE5 9RJ" + }, + { + "author_name": "Helen Gaunt", + "author_inst": "University Hospital of Leciester NHS Trust. Groby Road Leciester LE4 9QP" + }, + { + "author_name": "Peter Aitken", + "author_inst": "Devon Partnership NHS Trust, Trust HQ, R&D, Dryden Road, Exeter, Devon, EX2 5AF" + }, + { + "author_name": "Joanna Morris-Bone", + "author_inst": "Avon & Wiltshire Mental Health Partnership NHS Trust, R&D, Fromeside, Blackberry Hill Hospital, Bristol, BS16 1EG" + }, + { + "author_name": "Chloe Simela", + "author_inst": "Guy's and St Thomas' NHS Foundation Trust, London" + }, + { + "author_name": "Veronica French", + "author_inst": "Nottinghamshire Healthcare NHS Foundation Trust" + }, + { + "author_name": "Rachel Harris", + "author_inst": "Cornwall Partnership Foundation NHS Trust/ Research and Innovation Team" + }, + { + "author_name": "Sharon A.M. Stevelink", + "author_inst": "King's Centre for Military Health Research, Department of Psychological Medicine, King's College London, London, UK. AND Department of Psychological Medicine, K" + }, + { + "author_name": "Simon Wessely", + "author_inst": "Department of Psychological Medicine, King's College London, Weston Education, Denmark Hill, London, SE5 9JR" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.01.21.21250117", "rel_title": "Symptoms of anxiety and depression in relation to work patterns during the first wave of the COVID-19 epidemic in Philadelphia PA: a cross-sectional survey", @@ -974255,45 +976310,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.01.21.427315", - "rel_title": "DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins", - "rel_date": "2021-01-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.21.427315", - "rel_abs": "MotivationRecent efforts to computationally identify inhibitors for SARS-CoV-2 proteins have largely ignored the issue of receptor flexibility. We have implemented a computational tool for ensemble docking with the SARS-CoV-2 proteins, including the main protease (Mpro), papain-like protease (PLpro) and RNA-dependent RNA polymerase (RdRp).\n\nResultsEnsembles of other SARS-CoV-2 proteins are being prepared and made available through a user-friendly docking interface. Plausible binding modes between conformations of a selected ensemble and an uploaded ligand are generated by DINC, our parallelized meta-docking tool. Binding modes are scored with three scoring functions, and account for the flexibility of both the ligand and receptor. Additional details on our methods are provided in the supplementary material.\n\nAvailabilitydinc-covid.kavrakilab.org\n\nSupplementary informationDetails on methods for ensemble generation and docking are provided as supplementary data online.\n\nContactgeancarlo.zanatta@ufc.br, kavraki@rice.edu", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sarah Hall-Swan", - "author_inst": "Rice University" - }, - { - "author_name": "Dinler A Antunes", - "author_inst": "Rice University" - }, - { - "author_name": "Didier Devaurs", - "author_inst": "University of Grenoble Alpes" - }, - { - "author_name": "Mauricio M Rigo", - "author_inst": "Rice University" - }, - { - "author_name": "Lydia E Kavraki", - "author_inst": "Rice University" - }, - { - "author_name": "Geancarlo Zanatta", - "author_inst": "Federal University of Cear\u00e1" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.01.22.427737", "rel_title": "Human embryonic stem cell-derived cardiomyocytes express SARS-CoV-2 host entry proteins: screen to identify inhibitors of infection", @@ -974678,6 +976694,37 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.01.22.427813", + "rel_title": "CCR1 regulatory variants linked to pulmonary macrophage recruitment in severe COVID-19", + "rel_date": "2021-01-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.22.427813", + "rel_abs": "Genome-wide association studies have identified 3p21.31 as the main risk locus for severe disease in COVID-19 patients, although underlying biological mechanisms remain elusive. We performed a comprehensive epigenomic dissection of the 3p21.31 locus, identifying a CTCF-dependent tissue-specific 3D regulatory chromatin hub that controls the activity of several tissue-homing chemokine receptor (CCR) genes in monocytes and macrophages. Risk SNPs colocalized with regulatory elements and were linked to increased expression of CCR1, CCR2 and CCR5 in monocytes and macrophages. As excessive organ infiltration of inflammatory monocytes and macrophages is a hallmark of severe COVID-19, our findings provide a rationale for the genetic association of 3p21.31 variants with elevated risk of hospitalization upon SARS-CoV-2 infection.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Bernard Stikker", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Gregoire Stik", + "author_inst": "Centre for Genomic Regulation (CRG)" + }, + { + "author_name": "Rudi W. Hendriks", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Ralph Stadhouders", + "author_inst": "Erasmus MC" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.01.22.427830", "rel_title": "Exploring the natural origins of SARS-CoV-2", @@ -975833,37 +977880,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, - { - "rel_doi": "10.1101/2021.01.16.21249935", - "rel_title": "The Socioeconomic Impact of COVID-19 in Urban Informal Settlements", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.16.21249935", - "rel_abs": "The COVID-19 pandemic has reached almost every corner of the world. Without a pharmaceutical solution, governments have been forced to implement regulations and public policies to control social behavior and prevent the spread of the virus. There is dramatic evidence of the social and economic effects of these measures and their disparate impact on vulnerable communities. Individuals living in urban informal settlements are in a structurally disadvantaged position to cope with a health crisis such as the COVID-19 pandemic. This paper examines the socioeconomic impact of the crisis brought by the pandemic in informal settlements in Chile. We use a three-wave panel study to compare the situation in informal settlements before and during the health crisis. We show that households living in informal settlements are paying a high toll. Their employment loss is dramatic, substantially larger than the loss reported in the general population, and has particularly affected the inmigrant population. We also find that the pandemic has triggered neighborhood cooperation within the settlements. Targeted government assistance programs have reached these communities; however, this groups coverage is not enough to counteract the magnitude of the crisis. Our results suggest that governments, the non-profit sector, and the community need to urgently provide economic support and protections to individuals living in informal settlements and consider this opportunity for long-term improvements in these marginalized communities.\n\nHighlightsO_LIGovernments have implemented large-scale non-pharmaceutical interventions to control the spread of the COVID-19 pandemic\nC_LIO_LIThese measures have had dramatic social and economic effects on the population, particularly affecting vulnerable communities\nC_LIO_LIIndividuals living in urban informal settlements are in a structurally disadvantaged position to cope with this crisis\nC_LIO_LIUsing panel data, we document a dramatic employment loss among informal settlements dwellers, substantially larger than the general population\nC_LIO_LIThe pandemic has also triggered neighborhood cooperation within the settlements as well as targeted government assistance, but not enough to counteract the magnitude of the economic loss\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Diego Gil", - "author_inst": "Escuela de Gobierno, Pontificia Universidad Catolica de Chile, Santiago, Chile" - }, - { - "author_name": "Patricio Dominguez", - "author_inst": "Department of Research, Inter-American Development Bank, Washington DC" - }, - { - "author_name": "Eduardo A Undurraga", - "author_inst": "Escuela de Gobierno, Pontificia Universidad Catolica de Chile, Santiago, Chile" - }, - { - "author_name": "Eduardo Valenzuela", - "author_inst": "Department of Sociology, Pontificia Universidad Catolica de Chile, Santiago, Chile" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.18.21250025", "rel_title": "COVID-19 in 823 Transplant patients: A Systematic Scoping Review", @@ -976040,6 +978056,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.01.15.20248217", + "rel_title": "Hidden Parameters impacting resurgence of SARS-CoV-2 Pandemic", + "rel_date": "2021-01-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.15.20248217", + "rel_abs": "The spread of the COVID-19 virus has had an enormous impact on the worlds health and socioeconomic system. While lockdowns, which severely limit the movement of the population, have been implemented in March 2020 and again recently, the psychological and economic cost are severe. Removal of these restrictions occurred with varying degrees of success.\n\nTo study the resurgence of the virus in some communities we consider an epidemiological model, SIR-SD-L, that incorporates introduction of new population due to the removal of lockdown and identify parameters that impact the spread of the virus. This compartmental model of the epidemic incorporates a social distance metric based on progression of the infections; it models the dynamic propensity of infection spread based on the current infections relative to the susceptible population. The model is validated using data on growth of infections, hospitalizations and death, considering 24 counties in multiple US states and a categorization of the lockdown removal policies after the first lockdown. Model parameters, which include a compartment for the isolated population, are used to determine the rate at which the susceptible population increases to fit the rate of infections. Along with social distancing mandates, we identify active infections and the susceptible population as important factors in the resurgence of infections. We measure the efficacy of the lockdown removal policy via a ratio, PIR, which evaluates to less than 1 for counties where social distancing measures were mandated and which delayed complete re-opening of closed spaces like bars and restaurants. For other counties this ratio is greater than 1.\n\nWe also studied infection growth in the 24 US counties with respect to a release policy derived from CDC guidelines and compared against strategies that delay the removal of lockdown.\n\nOur results illustrate that guidelines for deciding when lockdown rules are to be relaxed should consider the current state of the infectious population and the remaining susceptible population, hidden parameters that are deducible from models such as SIR-SD-L, and not limit policy considerations to the rate of new infections alone. This is especially true for counties where the growth rate of the virus is initially slow and misleading. Emphasis on social distancing is critical.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Yi Zhang", + "author_inst": "Illinois Institute of Technology" + }, + { + "author_name": "Sanjiv Kapoor", + "author_inst": "Illinois Institute of Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.01.17.21249970", "rel_title": "Optimizing SARS-CoV-2 vaccination strategies in France: Results from a stochastic agent-based model", @@ -977279,69 +979318,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2021.01.18.21249414", - "rel_title": "Temporal Trends in COVID-19 associated AKI from March to December 2020 in New York City", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.18.21249414", - "rel_abs": "Acute Kidney Injury (AKI) is among the most common complications of Coronavirus Disease 2019 (COVID-19). Throughout 2020 pandemic, the clinical approach to COVID-19 has progressively improved, but it is unknown how these changes have affected AKI incidence and severity. In this retrospective analysis, we report the trend over time of COVID-19 associated AKI and need of renal replacement therapy in a large health system in New York City, the first COVID-19 epicenter in United States.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Sergio Dellepiane", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Akhil Vaid", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Suraj K Jaladanki", - "author_inst": "Icahn School of Medicine at Mount Sinai (ISMMS)" - }, - { - "author_name": "Ishan Paranjpe", - "author_inst": "Ican School of Medicine at Mount Sinai" - }, - { - "author_name": "Stevn Coca", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Zahi Fayad", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Alexander Charney", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Erwin P Bottinger", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "John Cijiang He", - "author_inst": "Icahn School of Medicineat Mount Sinai" - }, - { - "author_name": "Benjamin S Glicksberg", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Lili Chan", - "author_inst": "ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI" - }, - { - "author_name": "Girish Nadkarni", - "author_inst": "Mount Sinai Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2021.01.18.21249976", "rel_title": "Covid-19 respiratory protection: the filtration efficiency assessment of decontaminated FFP2 masks responding to associated shortages", @@ -977726,6 +979702,253 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.19.21249921", + "rel_title": "A comprehensive antigen production and characterization study for easy-to-implement, highly specific and quantitative SARS-CoV-2 antibody assays", + "rel_date": "2021-01-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.19.21249921", + "rel_abs": "Antibody tests are essential tools to investigate humoral immunity following SARS-CoV-2 infection. While first-generation antibody tests have primarily provided qualitative results with low specificity, accurate seroprevalence studies and tracking of antibody levels over time require highly specific, sensitive and quantitative test setups. Here, we describe two quantitative ELISA antibody tests based on the SARS-CoV-2 spike receptor-binding domain and the nucleocapsid protein. Comparative expression in bacterial, insect, mammalian and plant-based platforms enabled the identification of new antigen designs with superior quality and high suitability as diagnostic reagents. Both tests scored excellently in clinical validations with multi-centric specificity and sensitivity cohorts and showed unprecedented correlation with SARS-CoV-2 neutralization titers. Orthogonal testing increased assay specificity to 99.8%, thereby enabling robust serodiagnosis in low-prevalence settings. The inclusion of a calibrator permits accurate quantitative monitoring of antibody concentrations in samples collected at different time points during the acute and convalescent phase of COVID-19.", + "rel_num_authors": 58, + "rel_authors": [ + { + "author_name": "Miriam Klausberger", + "author_inst": "University of Natural Resources and Life Sciences (BOKU) Vienna" + }, + { + "author_name": "Mark Duerkop", + "author_inst": "Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Helmuth Haslacher", + "author_inst": "Department of Laboratory Medicine, Medical University of Vienna, Austria" + }, + { + "author_name": "Gordana Wozniak-Knopp", + "author_inst": "Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Monika Cserjan-Puschmann", + "author_inst": "Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Thomas Perkmann", + "author_inst": "Department of Laboratory Medicine, Medical University of Vienna, Austria" + }, + { + "author_name": "Nico Lingg", + "author_inst": "Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Patricia Pereira Aguilar", + "author_inst": "Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Elisabeth Laurent", + "author_inst": "Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Jelle De Vos", + "author_inst": "Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Manuela Hofer", + "author_inst": "Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria" + }, + { + "author_name": "Barbara Holzer", + "author_inst": "Austrian Agency for Health and Food Safety (AGES), Department for Animal Health, Moedling, Austria" + }, + { + "author_name": "Maria Stadler", + "author_inst": "Institute of Immunology, University of Veterinary Medicine Vienna, Austria" + }, + { + "author_name": "Gabriele Manhart", + "author_inst": "Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria" + }, + { + "author_name": "Klemens Vierlinger", + "author_inst": "Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria" + }, + { + "author_name": "Margot Egger", + "author_inst": "Department of Laboratory Medicine, Konventhospital Barmherzige Brueder Linz and Ordensklinikum Linz Barmherzige Schwestern, Linz, Austria" + }, + { + "author_name": "Lisa Milchram", + "author_inst": "Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria" + }, + { + "author_name": "Elisabeth Gludovacz", + "author_inst": "Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Nicolas Marx", + "author_inst": "Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Christoph Koeppl", + "author_inst": "Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Christopher Tauer", + "author_inst": "Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Juergen Beck", + "author_inst": "Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Daniel Maresch", + "author_inst": "BOKU Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences, Vienna, Austria" + }, + { + "author_name": "Clemens Gruenwald-Gruber", + "author_inst": "BOKU Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences, Vienna, Austria" + }, + { + "author_name": "Florian Strobl", + "author_inst": "enGenes Biotech GmbH, Vienna, Austria" + }, + { + "author_name": "Peter Satzer", + "author_inst": "Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Gerhard Stadlmayr", + "author_inst": "Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Ulrike Vavra", + "author_inst": "Department of Applied Genetics and Cell Biology (DAGZ), University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Jasmin Huber", + "author_inst": "Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria" + }, + { + "author_name": "Markus Wahrmann", + "author_inst": "Department of Medicine III, Division of Nephrology and Dialysis, Medical University Vienna, Austria" + }, + { + "author_name": "Farsad Eskandary", + "author_inst": "Department of Medicine III, Division of Nephrology and Dialysis, Medical University Vienna, Austria" + }, + { + "author_name": "Marie-Kathrin Breyer", + "author_inst": "Department of Respiratory and Critical Care Medicine and Ludwig Boltzmann Institute for Lung Health, Otto Wagner Hospital, Vienna, Austria" + }, + { + "author_name": "Daniela Sieghart", + "author_inst": "Division of Rheumatology, Department of Medicine III, Medical University of Vienna, Austria" + }, + { + "author_name": "Peter Quehenberger", + "author_inst": "Department of Laboratory Medicine, Medical University of Vienna, Austria" + }, + { + "author_name": "Gerda Leitner", + "author_inst": "Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Austria" + }, + { + "author_name": "Robert Strassl", + "author_inst": "Department of Laboratory Medicine, Medical University of Vienna, Austria" + }, + { + "author_name": "Alexander E Egger", + "author_inst": "Central Institute for Medical and Chemical Laboratory Diagnosis, Innsbruck University Hospital, Innsbruck, Austria" + }, + { + "author_name": "Christian Irsara", + "author_inst": "Central Institute for Medical and Chemical Laboratory Diagnosis, Innsbruck University Hospital, Innsbruck, Austria" + }, + { + "author_name": "Andrea Griesmacher", + "author_inst": "Central Institute for Medical and Chemical Laboratory Diagnosis, Innsbruck University Hospital, Innsbruck, Austria" + }, + { + "author_name": "Gregor Hoermann", + "author_inst": "Central Institute for Medical and Chemical Laboratory Diagnosis, Innsbruck University Hospital, Innsbruck, Austria" + }, + { + "author_name": "Guenter Weiss", + "author_inst": "Department of Internal Medicine II, Innsbruck Medical University, Austria" + }, + { + "author_name": "Rosa Bellmann-Weiler", + "author_inst": "Department of Internal Medicine II, Innsbruck Medical University, Austria" + }, + { + "author_name": "Judith Loeffler-Ragg", + "author_inst": "Department of Internal Medicine II, Innsbruck Medical University, Austria" + }, + { + "author_name": "Nicole Borth", + "author_inst": "Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Richard Strasser", + "author_inst": "Department of Applied Genetics and Cell Biology (DAGZ), University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Alois Jungbauer", + "author_inst": "Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Rainer Hahn", + "author_inst": "Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Juergen Mairhofer", + "author_inst": "enGenes Biotech GmbH, Vienna, Austria" + }, + { + "author_name": "Boris Hartmann", + "author_inst": "Austrian Agency for Health and Food Safety (AGES), Department for Animal Health, Moedling, Austria" + }, + { + "author_name": "Nikolaus B Binder", + "author_inst": "Technoclone Herstellung von Diagnostika und Arzneimitteln GmbH, Vienna, Austria" + }, + { + "author_name": "Gerald Striedner", + "author_inst": "Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Lukas Mach", + "author_inst": "Department of Applied Genetics and Cell Biology (DAGZ), University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + }, + { + "author_name": "Andreas Weinhaeusl", + "author_inst": "Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria" + }, + { + "author_name": "Benjamin Dieplinger", + "author_inst": "Department of Laboratory Medicine, Konventhospital Barmherzige Brueder Linz and Ordensklinikum Linz Barmherzige Schwestern, Linz, Austria" + }, + { + "author_name": "Florian Grebien", + "author_inst": "Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria" + }, + { + "author_name": "Wilhelm Gerner", + "author_inst": "Institute of Immunology, University of Veterinary Medicine Vienna, Austria" + }, + { + "author_name": "Christoph J Binder", + "author_inst": "Department of Laboratory Medicine, Medical University of Vienna, Austria" + }, + { + "author_name": "Reingard Grabherr", + "author_inst": "Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.19.21250094", "rel_title": "Diagnosis of SARS-Cov-2 infection using specimens other than naso- and oropharyngeal swabs: a systematic review and meta-analysis", @@ -979101,37 +981324,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.19.21250139", - "rel_title": "Overcrowding and Exposure to Secondhand Smoke Increase Risk for COVID-19 Infection Among Latinx Families in Greater San Francisco Bay Area", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.19.21250139", - "rel_abs": "BackgroundThe novel coronavirus (COVID-19) has disproportionately impacted the Latinx community in the United States. Environmental risk factors, including community level pollution burden and exposure to smoking and secondhand smoke, have not been evaluated in relation to risk for infection with COVID-19.\n\nMethodsWe evaluated self-reported infection rates of COVID-19 in three, preexisting, longitudinal, Latinx family cohorts in the San Francisco Bay Area from May through September 2020 (N=383 households, 1,875 people). All households were previously recruited during pregnancy and postpartum at Zuckerberg San Francisco General Hospital (ZSFG) and UCSF Benioff before the pandemic. For the COVID-19 sub-study, participants responded to a 15-minute telephonic interview where we assessed food consumption patterns, housing and employment status, and history of COVID-19 infection based on community and hospital-based testing. We also evaluated secondhand smoke exposure based on previously collected self-reported data. Environmental pollution exposure was determined from census tract residence using Californias EnviroScreen 2.0 data. Non-parametric tests and multiple logistic regression were used to assess possible associations and independent predictors of COVID-19 infection.\n\nResultsIn the combined Latinx, Eating and Diabetes Cohort (LEAD) and Hispanic, Eating and Nutrition (HEN) cohorts there was a 7.6% household infection rate (14/183) with a lower rate of 3.5% (7/200) in the Telomeres at Birth (TAB) cohort. Larger household size increased risk for infection (OR, 1.43 (95%CI 1.10-1.87)) in the combined LEAD/HEN cohorts and increasing number of children trended towards significance in the TAB cohort (OR 1.82, 95% CI 0.98-3.37). Any exposure to secondhand smoke in the household also trended towards increasing risk after adjusting for household size and other exposures (OR 3.20, 95%CI 0.80-12.73) and (OR 4.37, 95% CI 0.80-23.70). We did not find any associations between neighborhood pollution level based on census track location and risk of infection. Furthermore, we found weak evidence between dietary exposure and risk of COVID-19 infection after adjusting for possible confounders.\n\nConclusionCrowding as indicated by household size increases risk for COVID-19 infection in Latinx families. Exposure to secondhand smoke may also increase risk for COVID-19 through increased coughing, respiratory impairment and increased travel of virus on smoke particles. Public policy and health interventions need to ensure that multiunit residential complexes prevent any exposure to secondhand smoke.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Andrea DeCastro Mendez", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Milagro Escobar", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Maria Romero Encinas", - "author_inst": "University of California,San Francisco" - }, - { - "author_name": "Janet Wojcicki", - "author_inst": "UCSF" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.19.21250137", "rel_title": "A Label-Free SARS-CoV-2 Surrogate Virus Neutralization Test and a Longitudinal Study of Antibody Characteristics in COVID-19 Patients", @@ -979264,6 +981456,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.19.21250100", + "rel_title": "Impact of immediate and preferential relaxation of social and travel restrictions for vaccinated people on the spreading dynamics of COVID-19 : a model-based analysis", + "rel_date": "2021-01-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.19.21250100", + "rel_abs": "BackgroundFour COVID-19 vaccine candidates developed by Pfizer, Moderna, University of Oxford/ Astra Zeneca (also Oxford/ Serum Institute of India) and ICMR/ Bharat Biotech have been granted emergency use authorization in the democratic world following established clinical trial procedures in their respective countries. Vaccination of the general public is expected to begin in several weeks. We consider the question of whether people who have received the vaccine can be selectively and immediately cleared to return to normal activities, including hassle-free travel.\n\nMethodsWe use a delay differential equation model developed previously by our group to calculate the effects of vaccinee \"immunity passports\" on the spreading trajectories of the disease. We consider default virus strains as well as high-transmissibility variants such as B1.1.7 in our analysis.\n\nResultsWe find that with high vaccine efficacy of 80 percent or greater, vaccinees may be immediately cleared for normal life with no significant increase in case counts. Free travel of such vaccinees between two regions should not jeopardize the infection control performance of either. At current vaccine administration rates, it may be eight months or more before COVID-19 transmission is significantly reduced or eliminated. With lower vaccine efficacy of approximately 60 percent however, social as well as travel restrictions for vaccinees may need to remain in place until transmission of the disease is eliminated.\n\nConclusionsDesigning high-efficacy vaccines with easily scalable manufacturing and distribution capacity should remain on the priority list in academic as well as industrial circles. Performance of all vaccines should continue to be monitored in real time during vaccination drive with a view to analysing socio-demographic determinants if any of efficacy, and optimizing distribution accordingly. A speedy and efficacious vaccination drive will provide the smoothest path out of the pandemic with the least additional caseloads, death toll and socioeconomic cost.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "B Shayak", + "author_inst": "Cornell University" + }, + { + "author_name": "Mohit Manoj Sharma", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Anand Kumar Mishra", + "author_inst": "Cornell University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.19.21250116", "rel_title": "The Association of COVID-19 Incidence with Sport and Face Mask Use in United States High School Athletes", @@ -981075,97 +983294,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.01.17.425424", - "rel_title": "Large scale genomic and evolutionary study reveals SARS-CoV-2 virus isolates from Bangladesh strongly correlate with European origin and not with China.", - "rel_date": "2021-01-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.17.425424", - "rel_abs": "RationaleThe global public health is in serious crisis due to emergence of SARS-CoV-2 virus. Studies are ongoing to reveal the genomic variants of the virus circulating in various parts of the world. However, data generated from low- and middle-income countries are scarce due to resource limitation. This study was focused to perform whole genome sequencing of 151 SARS-CoV-2 isolates from COVID-19 positive Bangladeshi patients. The goal of this study was to identify the genomic variants among the SARS-CoV-2 virus isolates in Bangladesh, to determine the molecular epidemiology and to develop a relationship between host clinical trait with the virus genomic variants.\n\nMethodSuspected patients were tested for COVID-19 using one step commercial qPCR kit for SARS-CoV-2 Virus. Viral RNA was extracted from positive patients, converted to cDNA which was amplified using Ion AmpliSeq SARS-CoV-2 Research Panel. Massive parallel sequencing was carried out using Ion AmpliSeq Library Kit Plus. Assembly of raw data is done by aligning the reads to a pre-defined reference genome (NC_045512.2) while retaining the unique variations of the input raw data by creating a consensus genome. A random forest-based association analysis was carried out to correlate the viral genomic variants with the clinical traits present in the host.\n\nResultAmong the 151 viral isolates, we observed the 413 unique variants. Among these 8 variants occurred in more than 80 % of cases which include 241C to T, 1163A to T, 3037C to T,14408C to T, 23403A to G, 28881G to A, 28882 G to A, and finally the 28883G to C. Phylogenetic analysis revealed a predominance of variants belonging to GR clade, which have a strong geographical presence in Europe, indicating possible introduction of the SARS-CoV-2 virus into Bangladesh through a European channel. However, other possibilities like a route of entry from China cannot be ruled out as viral isolate belonging to L clade with a close relationship to Wuhan reference genome was also detected. We observed a total of 37 genomic variants to be strongly associated with clinical symptoms such as fever, sore throat, overall symptomatic status, etc. (Fishers Exact Test p-value<0.05). The most mention-worthy among those were the 3916CtoT (associated with causing sore throat, p-value 0.0005), the 14408C to T (associated with protection from developing cough, p-value= 0.027), and the 28881G to A, 28882G to A, and 28883G to C variant (associated with causing chest pain, p-value 0.025).\n\nConclusionTo our knowledge, this study is the first large scale phylogenomic studies of SARS-CoV-2 virus circulating in Bangladesh. The observed epidemiological and genomic features may inform future research platform for disease management, vaccine development and epidemiological study.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Mohammad Fazle Alam Rabbi", - "author_inst": "University of Dhaka" - }, - { - "author_name": "Md. Imran Khan", - "author_inst": "DNA Solution Ltd." - }, - { - "author_name": "Saam Hasan", - "author_inst": "DNA Solution Ltd." - }, - { - "author_name": "Mauricio Chalita", - "author_inst": "Chun Lab Inc." - }, - { - "author_name": "Kazi Nadim Hasan", - "author_inst": "North South University" - }, - { - "author_name": "Abu Sufian", - "author_inst": "DNA Solution Ltd." - }, - { - "author_name": "Md. Bayejid Hosen", - "author_inst": "Dhaka Medical College" - }, - { - "author_name": "Mohammed Nafiz Imtiaz Polol", - "author_inst": "DNA Solution Ltd." - }, - { - "author_name": "Jannatun Naima", - "author_inst": "DNA Solution Ltd." - }, - { - "author_name": "Kihyun Lee", - "author_inst": "Chun Lab Inc." - }, - { - "author_name": "Yeong Ouk Kim", - "author_inst": "Chun Lab Inc." - }, - { - "author_name": "Mamudul Hasan Razu", - "author_inst": "Designated Reference Institute for Chemical Measurements" - }, - { - "author_name": "Mala Khan", - "author_inst": "Designated Reference Institute for Chemical Measurements" - }, - { - "author_name": "Md. Mizanur Rahman", - "author_inst": "NIPRO JMI Pharma" - }, - { - "author_name": "Jongsik Chun", - "author_inst": "Chun Lab Inc." - }, - { - "author_name": "Md. Abdul Khaleque", - "author_inst": "North South University" - }, - { - "author_name": "Nur A Hasan", - "author_inst": "Ezbiome Inc." - }, - { - "author_name": "Rita R Colwell", - "author_inst": "University of Maryland" - }, - { - "author_name": "Sharif Akhteruzzaman", - "author_inst": "University of Dhaka" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2021.01.18.427092", "rel_title": "A national analysis of trends in COVID-19 infection and clinical management in Veterans Health Administration medical facilities", @@ -982006,6 +984134,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.13.21249645", + "rel_title": "Metabolic markers distinguish COVID-19 from other intensive care patients and show potential to stratify for disease risk", + "rel_date": "2021-01-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.13.21249645", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is a viral infection affecting multiple organ systems of great significance for metabolic processes. Thus. there is increasing interest in metabolic and lipoprotein signatures of the disease and early analyses have demonstrated metabolic pattern typical for atherosclerotic and hepatic damage in COVID-19 patients. However, it remains unclear whether these are specific for COVID-19 or a general marker of critical illness. To answer this question, we have analyzed 276 serum samples from 92 individuals using NMR metabolomics, including longitudinally collected samples from 5 COVID-19 and 11 cardiogenic shock intensive care patients, 18 SARS-CoV-2 antibody-positive individuals, and 58 healthy controls.\n\nCOVID-19 patients showed a distinct metabolic serum profile, including changes typical for severe dyslipidemia and a deeply altered metabolic status compared to healthy controls. Specifically, VLDL parameters, IDL particles, large-sized LDL particles, and the ApoB100/ApoA1 ratio were significantly increased, whereas HDL fractions were decreased. Moreover, a similarly perturbed profile was apparent, even when compared to other ICU patients suffering from cardiogenic shock, highlighting the impact of COVID-19 especially on lipid metabolism and energy status. COVID-19 patients were separated with an AUROC of 1.0 when compared to both healthy controls and cardiogenic shock patients. Anti-SARS-CoV-2 antibody-positive individuals without acute COVID-19 did not show a significantly perturbed metabolic profile compared to age- and sex-matched healthy controls, but SARS-CoV-2 antibody-titers correlated significantly with metabolic parameters, including levels of glycine, ApoA2, and small-sized LDL and HDL subfractions. Our data suggest that NMR metabolic profiles are suitable for COVID-19 patient stratification and post-treatment monitoring.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Franziska Schmelter", + "author_inst": "Institute of Nutritional Medicine, University of Luebeck" + }, + { + "author_name": "Bandik Foeh", + "author_inst": "Institute of Nutritional Medicine, University of Luebeck" + }, + { + "author_name": "Alvaro Mallagray", + "author_inst": "Institute of Chemistry and Metabolomics, University of Luebeck" + }, + { + "author_name": "Johann Rahmoeller", + "author_inst": "Institute of Nutritional Medicine, University of Luebeck" + }, + { + "author_name": "Marc Ehlers", + "author_inst": "Institute of Nutritional Medicine, University of Luebeck" + }, + { + "author_name": "Selina Lehrian", + "author_inst": "Institute of Nutritional Medicine, University of Luebeck" + }, + { + "author_name": "Vera von Kopylow", + "author_inst": "Institute of Nutritional Medicine, University of Luebeck" + }, + { + "author_name": "Inga Kuensting", + "author_inst": "Institute of Nutritional Medicine, University of Luebeck" + }, + { + "author_name": "Anne Sophie Lixenfeld", + "author_inst": "Institute of Nutritional Medicine, University of Luebeck" + }, + { + "author_name": "Emily Martin", + "author_inst": "Institute of Nutritional Medicine, University of Luebeck" + }, + { + "author_name": "Mohab Ragab", + "author_inst": "Institute of Nutritional Medicine, University of Luebeck" + }, + { + "author_name": "Max Borsche", + "author_inst": "Department of Infectious Diseases and Microbiology, University of Luebeck" + }, + { + "author_name": "Alexander Balck", + "author_inst": "Department of Infectious Diseases and Microbiology, University of Luebeck" + }, + { + "author_name": "Eva Juliane Vollstedt", + "author_inst": "Department of Infectious Diseases and Microbiology, University of Luebeck" + }, + { + "author_name": "Roza Meyer-Saraei", + "author_inst": "Department of Cardiology, Angiology and Intensive Care Medicine, University Heart Center Luebeck" + }, + { + "author_name": "Fabian Kreutzmann", + "author_inst": "Department of Cardiology, Angiology and Intensive Care Medicine, University Heart Center Luebeck" + }, + { + "author_name": "Ingo Eitel Eitel", + "author_inst": "Department of Cardiology, Angiology and Intensive Care Medicine, University Heart Center Luebeck" + }, + { + "author_name": "Stefan Taube Taube", + "author_inst": "Institute of Virology and Cell Biology, University of Luebeck, Luebeck" + }, + { + "author_name": "Christine Klein Klein", + "author_inst": "Institute of Neurogenetics, University of Luebeck" + }, + { + "author_name": "Alexander Katalinic Katalinic", + "author_inst": "Department of Infectious Diseases and Microbiology, University of Luebeck" + }, + { + "author_name": "Jan Rupp Rupp", + "author_inst": "Institute of Social Medicine and Epidemiology, University of Luebeck" + }, + { + "author_name": "Eckard Jantzen Jantzen", + "author_inst": "Research and Development Department, GALAB Laboratories GmbH" + }, + { + "author_name": "Tobias Graf", + "author_inst": "Department of Cardiology, Angiology and Intensive Care Medicine, University Heart Center Luebeck" + }, + { + "author_name": "Christian Sina", + "author_inst": "Institute of Nutritional Medicine, University of Luebeck" + }, + { + "author_name": "Ulrich L Guenther", + "author_inst": "Institute of Chemistry and Metabolomics, University of Luebeck" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.01.15.21249810", "rel_title": "SARS-CoV-2 seropositivity and seroconversion in patients undergoing active cancer-directed therapy", @@ -983564,33 +985807,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.13.20249064", - "rel_title": "Optimising SARS-CoV-2 pooled testing strategies on social networks for low-resource settings", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.13.20249064", - "rel_abs": "Controlling the COVID-19 pandemic is an urgent global challenge. The rapid geographic spread of SARS-CoV-2 directly reflects the social structure. Before effective vaccines and treatments are widely available, we have to rely on alternative, non-pharmaceutical interventions, including frequency testing, contact tracing, social distancing, mask wearing, and hand-washing, as public health practises to slow down the spread of the disease. However frequent testing is the key in the absence of any alternative. We propose a network approach to determine the optimal low resources setting oriented pool testing strategies that identifies infected individuals in a small number of tests and few rounds of testing, at low prevalence of the virus. We simulate stochastic infection curves on societies under quarantine. Allowing some social interaction is possible to keep the COVID-19 curve flat. However, similar results can be strategically obtained searching and isolating infected persons to preserve a healthier social structure. Here, we analyze which are the best strategies to contain the virus applying an algorithm that combine samples and testing them in groups [1]. A relevant parameter to keep infection curves flat using this algorithm is the dairy frequency of testing at zones where a high infection rate is reported. On the other hand, the algorithm efficiency is low for random search of infected people.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Karina I Mazzitello", - "author_inst": "University of Mar del Plata, ICYTE-CONICET" - }, - { - "author_name": "Yi Jiang", - "author_inst": "Department of Mathematics and Statistics, Georgia State University, Atlanta, GA 30303, USA" - }, - { - "author_name": "Constancio Miguel Arizmendi", - "author_inst": "Universidad Nacional de Mar del Plata, ICYTE, Argentina" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.14.21249853", "rel_title": "The Use of Procalcitonin as an Antimicrobial Stewardship Tool and a Predictor of Disease Severity in COVID-19", @@ -983731,6 +985947,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.01.15.426526", + "rel_title": "In vivo structure and dynamics of the RNA genome of SARS-Cov-2", + "rel_date": "2021-01-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.15.426526", + "rel_abs": "The SARS-CoV-2 coronavirus, which causes the COVID-19 pandemic, is one of the largest positive strand RNA viruses. Here we developed a simplified SPLASH assay and comprehensively mapped the in vivo RNA-RNA interactome of SARS-CoV-2 RNA during the viral life cycle. We observed canonical and alternative structures including 3-UTR and 5-UTR, frameshifting element (FSE) pseudoknot and genome cyclization in cells and in virions. We provide direct evidence of interactions between Transcription Regulating Sequences (TRS-L and TRS-Bs), which facilitate discontinuous transcription. In addition, we reveal alternative short and long distance arches around FSE, forming a \"high-order pseudoknot\" embedding FSE, which might help ribosome stalling at frameshift sites. More importantly, we found that within virions, while SARS-CoV-2 genome RNA undergoes intensive compaction, genome cyclization is weakened and genome domains remain stable. Our data provides a structural basis for the regulation of replication, discontinuous transcription and translational frameshifting, describes dynamics of RNA structures during life cycle of SARS-CoV-2, and will help to develop antiviral strategies.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Yan Zhang", + "author_inst": "Beijing institute of Biotechnology, Beijing, China" + }, + { + "author_name": "Kun Huang", + "author_inst": "Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China" + }, + { + "author_name": "Dejian Xie", + "author_inst": "Wuhan Frasergen Bioinformatics Co., Ltd, Wuhan, China" + }, + { + "author_name": "Jian You Lau", + "author_inst": "MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom" + }, + { + "author_name": "Wenlong Shen", + "author_inst": "Beijing institute of Biotechnology, Beijing, China" + }, + { + "author_name": "Ping Li", + "author_inst": "Beijing institute of Biotechnology, Beijing, China" + }, + { + "author_name": "Dong Wang", + "author_inst": "Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China" + }, + { + "author_name": "Zhong Zou", + "author_inst": "Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China" + }, + { + "author_name": "Shu Shi", + "author_inst": "Beijing institute of Biotechnology, Beijing, China" + }, + { + "author_name": "Hongguang Ren", + "author_inst": "Beijing institute of Biotechnology, Beijing, China" + }, + { + "author_name": "Meilin Jin", + "author_inst": "Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China" + }, + { + "author_name": "Grzegorz Kudla", + "author_inst": "MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom" + }, + { + "author_name": "Zhihu Zhao", + "author_inst": "Beijing institute of Biotechnology, Beijing, China" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2021.01.14.426521", "rel_title": "Structural characterization of cocktail-like targeting polysaccharides from Ecklonia kurome Okam and their anti-SARS-CoV-2 activities in vitro", @@ -985518,49 +987801,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2021.01.13.21249460", - "rel_title": "Physicians' Reactions to COVID-19: The Results of an International Internet Survey", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.13.21249460", - "rel_abs": "ObjectivesPhysicians across the world have been disproportionately affected by the COVID-19 pandemic. This study was designed and conducted to assess the emotional, cognitive, and behavioural reactions of physicians to the initial phase of the COVID-19 pandemic.\n\nMaterials and methodsAn online survey questionnaire using the google forms platform was constructed by the authors. The items in the questionnaire were based on clinical experience, relevant literature review and discussion with peers. A list of issues that were deemed as essential components of the experience of the pandemic relevant to physicians was arrived at. Thereafter these issues were operationalized into question form and hosted on the google forms platform. The link to this questionnaire was circulated by the authors among their peer groups in the month of April 2020.\n\nResultsWe received 295 responses and 3 were unusable. Most of the responses were from India, the United States of America, Australia, Canada and the United Kingdom. About 60% of the respondents identified themselves as frontline and had a decade of clinical experience. Most respondents reported being anxious due to the pandemic and also observed the same in their peers and families. A majority also observed changes in behaviour in self and others and advanced a variety of reasons and concerns. A sense of duty was the most commonly employed coping mechanism.\n\nConclusionPhysicians are not immune from information and misinformation, or cues in the environment. Behavioural choices are not always predicted by knowledge but by a combination of knowledge, emotional state, personality and environment. Healthcare settings need to be ready for emergencies and should focus on reducing uncertainty in physicians. These factors may also be gainfully used in the mental health promotion of physicians in COVID-19 care roles.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Parul Aneja", - "author_inst": "UPMC Pinnacle" - }, - { - "author_name": "Inderjit Singh", - "author_inst": "Roche Diabetes Care Inc." - }, - { - "author_name": "Bhupinder Singh", - "author_inst": "University of Illinois college of Medicine" - }, - { - "author_name": "Pardeep Singh Kundi", - "author_inst": "Vancouver General Hospital" - }, - { - "author_name": "Inderbir Singh", - "author_inst": "Essex Partnership University MHS Foundation Trust, UK" - }, - { - "author_name": "Sanjana Kathiravan", - "author_inst": "PGIMER, Chandigarh" - }, - { - "author_name": "Shubh Mohan Singh", - "author_inst": "PGIMER, Chandigarh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.01.11.21249324", "rel_title": "A national survey of potential acceptance of COVID-19 vaccines in healthcare workers in Egypt", @@ -985737,6 +987977,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2021.01.14.21249793", + "rel_title": "Real-Time Electronic Health Record Mortality Prediction During the COVID-19 Pandemic: A Prospective Cohort Study", + "rel_date": "2021-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.14.21249793", + "rel_abs": "BackgroundThe SARS-CoV-2 virus has infected millions of people, overwhelming critical care resources in some regions. Many plans for rationing critical care resources during crises are based on the Sequential Organ Failure Assessment (SOFA) score. The COVID-19 pandemic created an emergent need to develop and validate a novel electronic health record (EHR)-computable tool to predict mortality.\n\nResearch QuestionsTo rapidly develop, validate, and implement a novel real-time mortality score for the COVID-19 pandemic that improves upon SOFA.\n\nStudy Design and MethodsWe conducted a prospective cohort study of a regional health system with 12 hospitals in Colorado between March 2020 and July 2020. All patients >14 years old hospitalized during the study period without a do not resuscitate order were included. Patients were stratified by the diagnosis of COVID-19. From this cohort, we developed and validated a model using stacked generalization to predict mortality using data widely available in the EHR by combining five previously validated scores and additional novel variables reported to be associated with COVID-19-specific mortality. We compared the area under the receiver operator curve (AUROC) for the new model to the SOFA score and the Charlson Comorbidity Index.\n\nResultsWe prospectively analyzed 27,296 encounters, of which 1,358 (5.0%) were positive for SARS-CoV-2, 4,494 (16.5%) included intensive care unit (ICU)-level care, 1,480 (5.4%) included invasive mechanical ventilation, and 717 (2.6%) ended in death. The Charlson Comorbidity Index and SOFA scores predicted overall mortality with an AUROC of 0.72 and 0.90, respectively. Our novel score predicted overall mortality with AUROC 0.94. In the subset of patients with COVID-19, we predicted mortality with AUROC 0.90, whereas SOFA had AUROC of 0.85.\n\nInterpretationWe developed and validated an accurate, in-hospital mortality prediction score in a live EHR for automatic and continuous calculation using a novel model, that improved upon SOFA.\n\nTake Home PointsO_ST_ABSStudy QuestionC_ST_ABSCan we improve upon the SOFA score for real-time mortality prediction during the COVID-19 pandemic by leveraging electronic health record (EHR) data?\n\nResultsWe rapidly developed and implemented a novel yet SOFA-anchored mortality model across 12 hospitals and conducted a prospective cohort study of 27,296 adult hospitalizations, 1,358 (5.0%) of which were positive for SARS-CoV-2. The Charlson Comorbidity Index and SOFA scores predicted all-cause mortality with AUROCs of 0.72 and 0.90, respectively. Our novel score predicted mortality with AUROC 0.94.\n\nInterpretationA novel EHR-based mortality score can be rapidly implemented to better predict patient outcomes during an evolving pandemic.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Peter D. Sottile MD", + "author_inst": "Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado School of Medicine" + }, + { + "author_name": "David J. Albers PhD", + "author_inst": "Section of Informatics and Data Science, Department of Pediatrics, University of Colorado School of Medicine" + }, + { + "author_name": "Peter E. DeWitt PhD", + "author_inst": "Section of Informatics and Data Science, Department of Pediatrics, University of Colorado School of Medicine" + }, + { + "author_name": "Seth Russell MS", + "author_inst": "Data Science to Patient Value Initiative, University of Colorado School of Medicine" + }, + { + "author_name": "J. N. Stroh PhD", + "author_inst": "Department of Bioengineering, University of Colorado Denver College of Engineering, Design, and Computing" + }, + { + "author_name": "David P. Kao MD", + "author_inst": "Divisions of Cardiology and Bioinformatics/Personalized Medicine, Department of Medicine, University of Colorado School of Medicine" + }, + { + "author_name": "Bonnie Adrian PhD", + "author_inst": "UCHealth Clinical Informatics and University of Colorado College of Nursing" + }, + { + "author_name": "Matthew E. Levine BA", + "author_inst": "Department of Computational and Mathematical Sciences, California Institute of Technology" + }, + { + "author_name": "Ryan Mooney MS", + "author_inst": "UCHealth Hospital System" + }, + { + "author_name": "Lenny Larchick BA", + "author_inst": "UCHealth Hospital System" + }, + { + "author_name": "Jean S. Kutner MD, MSPH", + "author_inst": "Division of General Internal Medicine, Department of Medicine, University of Colorado School of Medicine, Chief Medical Officer, University of Colorado Hospital" + }, + { + "author_name": "Matthew K. Wynia MD", + "author_inst": "Center for Bioethics and Humanities, University of Colorado and Department of Medicine, University of Colorado School of Medicine" + }, + { + "author_name": "Jeffrey J. Glasheen MD", + "author_inst": "Division of Hospital Medicine, Department of Medicine, University of Colorado School of Medicine and Chief Quality Officer, UCHealth" + }, + { + "author_name": "Tellen D. Bennett MD, MS", + "author_inst": "Sections of Informatics and Data Science and Critical Care Medicine, Department of Pediatrics, University of Colorado School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.01.12.21249581", "rel_title": "Dynamical Pool-Size Optimization for the SARS-CoV-2 PCR Test", @@ -987256,57 +989567,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.14.426652", - "rel_title": "Natural SARS-CoV-2 infection in kept ferrets, Spain", - "rel_date": "2021-01-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.14.426652", - "rel_abs": "We found SARS-CoV-2 RNA in 6 of 71 ferrets (8.4%) and isolated the virus from one rectal swab. Natural SARS-CoV-2 infection does occur in kept ferrets, at least under circumstances of high viral circulation in the human population. However, small ferret collections are probably unable to maintain prolonged virus circulation.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Christian Gortazar", - "author_inst": "Universidad de Castilla La Mancha" - }, - { - "author_name": "Sandra Barroso-Arevalo", - "author_inst": "Universidad Complutense" - }, - { - "author_name": "Elisa Ferreras", - "author_inst": "Universidad de Castilla La Mancha" - }, - { - "author_name": "Julio Isla", - "author_inst": "Sabiotec" - }, - { - "author_name": "Gabriela de la Fuente", - "author_inst": "Sabiotec" - }, - { - "author_name": "Belen Rivera", - "author_inst": "Universidad Complutense" - }, - { - "author_name": "Lucas Dominguez", - "author_inst": "Universidad Complutense de Madrid" - }, - { - "author_name": "Jose de la Fuente", - "author_inst": "IREC" - }, - { - "author_name": "Jose M Vizcaino", - "author_inst": "Universidad Complutense" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.01.08.21249273", "rel_title": "Modeling the COVID-19 transmission in Italy: The roles of asymptomatic cases, social distancing, and lockdowns", @@ -987619,6 +989879,157 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.01.13.426626", + "rel_title": "A highly thermotolerant, trimeric SARS-CoV-2 receptor binding domain derivative elicits high titers of neutralizing antibodies", + "rel_date": "2021-01-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.13.426626", + "rel_abs": "The Receptor Binding Domain (RBD) of SARS-CoV-2 is the primary target of neutralizing antibodies. We designed a trimeric, highly thermotolerant glycan engineered RBD by fusion to a heterologous, poorly immunogenic disulfide linked trimerization domain derived from cartilage matrix protein. The protein expressed at a yield of [~]80-100 mg/liter in transiently transfected Expi293 cells, as well as CHO and HEK293 stable cell lines and formed homogeneous disulfide-linked trimers. When lyophilized, these possessed remarkable functional stability to transient thermal stress of upto 100 {degrees}C and were stable to long term storage of over 4 weeks at 37 {degrees}C unlike an alternative RBD-trimer with a different trimerization domain. Two intramuscular immunizations with a human-compatible SWE adjuvanted formulation, elicited antibodies with pseudoviral neutralizing titers in guinea pigs and mice that were 25-250 fold higher than corresponding values in human convalescent sera. Against the beta (B.1.351) variant of concern (VOC), pseudoviral neutralization titers for RBD trimer were [~] three-fold lower than against wildtype B.1 virus. RBD was also displayed on a designed ferritin-like Msdps2 nanoparticle. This showed decreased yield and immunogenicity relative to trimeric RBD. Replicative virus neutralization assays using mouse sera demonstrated that antibodies induced by the trimers neutralized all four VOC to date, namely B.1.1.7, B.1.351, P.1 and B.1.617.2 without significant differences. Trimeric RBD immunized hamsters were protected from viral challenge. The excellent immunogenicity, thermotolerance, and high yield of these immunogens suggest that they are a promising modality to combat COVID-19, including all SARS-CoV-2 VOC to date.", + "rel_num_authors": 34, + "rel_authors": [ + { + "author_name": "Sameer Kumar Malladi", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Unnatiben Rajeshbhai Patel", + "author_inst": "Mynvax Private Limited" + }, + { + "author_name": "Raju S Rajmani", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Randhir Singh", + "author_inst": "Mynvax Private Limited" + }, + { + "author_name": "Suman Pandey", + "author_inst": "Mynvax Private Limited" + }, + { + "author_name": "Sahil Kumar", + "author_inst": "Institute of Microbial Technology," + }, + { + "author_name": "Sara Khaleeq", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Petrus Jansen van Vuren", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation (CSIRO)" + }, + { + "author_name": "Shane S Riddell", + "author_inst": "CSIRO Australian Centre for Disease Preparedness" + }, + { + "author_name": "Sarah Goldie", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation (CSIRO)" + }, + { + "author_name": "Savitha Gayathri", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Debajyoti Chakraborty", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Parismita Kalita", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Ishika Pramanick", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Nupur Agarwal", + "author_inst": "Mynvax Private Limited" + }, + { + "author_name": "Poorvi Reddy", + "author_inst": "Mynvax Private Limited" + }, + { + "author_name": "Nidhi Girish", + "author_inst": "Mynvax Private Limited" + }, + { + "author_name": "Aditya Upadhyaya", + "author_inst": "Mynvax Private Limited" + }, + { + "author_name": "Mohammad Suhail Khan", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Kawkab Kanjo", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Madhuraj Bhat", + "author_inst": "Mynvax Private Limited" + }, + { + "author_name": "Shailendra Mani", + "author_inst": "Translational Health Science and Technology Instituteealth" + }, + { + "author_name": "Sankar Bhattacharyya", + "author_inst": "Translational Health Science and Technology Institute" + }, + { + "author_name": "Samreen Siddiqui", + "author_inst": "Max Super Speciality Hospital" + }, + { + "author_name": "Akansha Tyagi", + "author_inst": "Max Super Speciality Hospital" + }, + { + "author_name": "Sujeet Jha", + "author_inst": "Max Super Speciality Hospital" + }, + { + "author_name": "Rajesh Pandey", + "author_inst": "Council of Scientific & Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB)" + }, + { + "author_name": "Shashank Tripathi", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Somnath Dutta", + "author_inst": "Indian Institute of Science Bangalore" + }, + { + "author_name": "Alexander J. McAuley", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation" + }, + { + "author_name": "Nagendrakumar Balasubramanian Singanallur", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation (CSIRO)" + }, + { + "author_name": "Seshadri S Vasan", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation" + }, + { + "author_name": "Rajesh P. Ringe", + "author_inst": "Institute of Microbial Technology" + }, + { + "author_name": "Raghavan Varadarajan", + "author_inst": "Indian Institute of Science" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.01.13.426628", "rel_title": "Susceptibility of white-tailed deer (Odocoileus virginianus) to SARS-CoV-2", @@ -989138,101 +991549,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.11.21249547", - "rel_title": "Impact of the Coronavirus Disease (COVID-19) on the Mental Health and Physical Activity of Pharmacy Students at the University of Zambia: A Cross-Sectional Study", - "rel_date": "2021-01-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.11.21249547", - "rel_abs": "BackgroundThe novel coronavirus disease (COVID-19) is a serious global health problem that has negatively impacted the mental health of students.\n\nMethodsWe conducted an online descriptive cross-sectional study among 273 undergraduate pharmacy students at the University of Zambia. A partial proportional odds regression model was used to determine the predictors of anxiety. All statistical tests were set at 95% confidence level (p<0.05).\n\nResultsA response rate of 70% was obtained with the majority of the students being female 51.6%. Of the 273 respondents, 23.8% did not experience anxiety, 34.4% experienced mild anxiety, 24.9% experienced moderate anxiety while 16.9% experienced severe anxiety about COVID-19. It was also found that 61.2% of students reported that their attention to mental health increased during the COVID-19 pandemic whereas 44.3% reported an increased resting time with a significant reduction in relaxation 51.3% and physical activity 45.4% time. Factors that affected mental health included; reduced family care (OR: 2.27; 95% CI: 1.09-4.74), not changing attention to mental health (OR: 0.33; 95% CI: 0.18-0.62), being in the final year of study (OR: 0.33; 95% CI: 0.13-0.84), reduced time of resting (OR: 2.10; 95% CI: 1.26-3.50) and feeling helpless (OR: 0.42; 95% CI:0.23-0.75).\n\nConclusionCOVID-19 negatively impacted the mental health and physical activity of pharmacy students at the University of Zambia. This can have negative health and academic outcomes for students going forward. Higher learning institutions and key stakeholders should implement measures to aid students to recover from the impact of COVID-19 on their mental health and physical activity.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Steward Mudenda", - "author_inst": "University of Zambia" - }, - { - "author_name": "Moses Mukosha", - "author_inst": "University of Zambia" - }, - { - "author_name": "Chiluba Mwila", - "author_inst": "University of Zambia" - }, - { - "author_name": "Zikria Saleem", - "author_inst": "University of Lahore" - }, - { - "author_name": "Aubrey Chichoni Kalungia", - "author_inst": "University of Zambia" - }, - { - "author_name": "Derick Munkombwe", - "author_inst": "University of Zambia" - }, - { - "author_name": "Victor Daka", - "author_inst": "Copperbelt University" - }, - { - "author_name": "Bwalya Angel Witika", - "author_inst": "DDT College of Medicine" - }, - { - "author_name": "Martin Kampamba", - "author_inst": "University of Zambia" - }, - { - "author_name": "Misheck Chileshe", - "author_inst": "Mary Begg Health Services" - }, - { - "author_name": "Christabel Hikaambo", - "author_inst": "University of Zambia" - }, - { - "author_name": "Maisa Kasanga", - "author_inst": "Zhengzhou University, College of Public Health" - }, - { - "author_name": "Webrod Mufwambi", - "author_inst": "University of Zambia" - }, - { - "author_name": "Ruth Lindizyani Mfune", - "author_inst": "Copperbelt University" - }, - { - "author_name": "Scott Kaba Matafwali", - "author_inst": "Copperbelt University" - }, - { - "author_name": "Angela Gono Bwalya", - "author_inst": "University of Zambia" - }, - { - "author_name": "David Chimbizgani Banda", - "author_inst": "Chreso University" - }, - { - "author_name": "Akashi Gupta", - "author_inst": "Ramniranjan Jhunjhunwala College" - }, - { - "author_name": "Maureen Nkandu Phiri", - "author_inst": "University of Zambia" - }, - { - "author_name": "Eustarckio Kazonga", - "author_inst": "University of Lusaka" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.11.21249626", "rel_title": "Aerosol tracer testing in the cabin of wide-bodied Boeing 767 and 777 aircraft to simulate exposure potential of infectious particulate such as SARS-CoV-2", @@ -989489,6 +991805,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, + { + "rel_doi": "10.1101/2021.01.12.21249608", + "rel_title": "The impact of the coronavirus disease 2019 (COVID-19) pandemic on university students' dietary intake, physical activity, and sedentary behaviour", + "rel_date": "2021-01-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.12.21249608", + "rel_abs": "University students are a vulnerable group for poor dietary intake, insufficient physical activity and sedentary behaviour. The purpose of this study was to examine the impact of COVID-19 on university students dietary intake, physical activity and sedentary behaviour. Participants were students (n=125) from the Universities of Saskatchewan and Regina. An online questionnaire was administered retrospectively (for pre-pandemic) and prospectively (during the pandemic) to examine students dietary intake, physical activity and sedentary behaviour. Overall, nutrient and caloric intakes were significantly reduced (p<0.05) during the pandemic, and alcohol intake increased (p=0.03). Before the pandemic, 16% and 54% of the participants were meeting the Canadian 24-Hour Movement Guidelines for Adults (18-64 years) of 150 minutes of moderate-vigorous physical activity and 8 hours or less of sedentary activity respectively. Only 10% met the guidelines for physical activity while 30% met the guidelines for sedentary behaviour during the pandemic. The minutes per week spent engaging in moderate to vigorous physical activity during the pandemic decreased by approximately 20% (p<0.001). The hours spent in sedentary activities increased by 3 hours per day (p<0.001). Our findings confirm that during the pandemic, students inadequate dietary intake, high alcohol consumption, low physical activity and high sedentary behaviour were significantly compounded.\n\nNoveltyO_LIDuring COVID-19, the nutrient and caloric intakes of university students decreased, and alcohol intake increased significantly.\nC_LIO_LIUniversity students physical activity levels decreased, and sedentary activity increased significantly during COVID-19.\nC_LIO_LIDuring COVID-19 students did not engage in sufficient physical activity to offset the increased sedentary behaviour.\nC_LI", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Leandy Bertrand", + "author_inst": "College of Kinesiology, University of Saskatchewan" + }, + { + "author_name": "Keely A Shaw", + "author_inst": "College of Kinesiology, University of Saskatchewan" + }, + { + "author_name": "Jongbum Ko", + "author_inst": "College of Kinesiology, University of Saskatchewan" + }, + { + "author_name": "Dalton Deprez", + "author_inst": "College of Kinesiology, University of Saskatchewan" + }, + { + "author_name": "Philip D Chilibeck", + "author_inst": "College of Kinesiology, University of Saskatchewan" + }, + { + "author_name": "Gordon A Zello", + "author_inst": "College of Pharmacy and Nutrition, University of Saskatchewan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nutrition" + }, { "rel_doi": "10.1101/2021.01.11.21249526", "rel_title": "Hospital load and increased COVID-19 related mortality - a nationwide study in Israel", @@ -990728,73 +993083,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.09.21249515", - "rel_title": "Impact of Residential Neighborhood and Race/Ethnicity on Outcomes of Hospitalized Patients with COVID-19 in the Bronx", - "rel_date": "2021-01-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.09.21249515", - "rel_abs": "The socially vulnerable have been most affected due to the COVID-19 pandemic, similar to the aftermath of any major disaster. Racial and social minorities are experiencing a disproportionate burden of morbidity and mortality.\n\nThe aim of this study was to evaluate the impact of residential location/community and race/ethnicity on outcomes of COVID-19 infection among hospitalized patients within the Bronx. This was a single center retrospective observational cohort study that included SARS-CoV2 positive adult residents of the Bronx (stratified as residents of South Bronx vs Rest of Bronx) hospitalized between March-May 2020. Data extracted from hospital electronic medical records included residential addresses, race, comorbidities, and insurance details. Comorbidity burden other clinical and laboratory details were also assessed to determine their correlation to COVID-19 severity of illness and outcomes of mortality and length of stay.\n\nAs expected, the COVID-19 pandemic differentially affected outcomes in those in the more socially disadvantaged area of the South Bronx versus the rest of the Bronx borough. Residents of the South Bronx had a significantly higher comorbidity burden and had public insurance to access medical care in comparison to the remainder of the Bronx. Interestingly, for the patient population studied there was no observed difference in 30-day mortality by race/ethnicity among those infected with COVID- 19 in spite of the increased disease burden observed.\n\nThis adds an interesting perspective to the current literature, and highlights the need to address the social/economic factors contributing to health access disparity to reduce the adverse impact of COVID-19 in these communities.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Dwayvania Miller", - "author_inst": "Lincoln Mental and Medical Health Center" - }, - { - "author_name": "Amara Sarwal", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Bo Yu", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Edgar Gomez", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Victor Perez-Gutierrez", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Marcia Gossai", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Elisenda Valdez", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Astrid Mendez", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Sarah Chaudry", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Usha Venugopal", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Vihren Dimitrov", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Moiz Kasubhai", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Vidya Menon", - "author_inst": "Lincoln Medical and Mental Health Center" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.09.21249505", "rel_title": "Wastewater Virus Detection Complements Clinical COVID-19 Testing to Limit Spread of Infection at Kenyon College", @@ -991027,6 +993315,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.10.21249382", + "rel_title": "Epidemiological impact of prioritizing SARS-CoV-2 vaccination by antibody status: Mathematical modeling analyses", + "rel_date": "2021-01-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.10.21249382", + "rel_abs": "BackgroundVaccines against SARS-CoV-2 have been developed, but their availability falls far short of global needs. This study aimed to investigate the impact of prioritizing available doses on the basis of recipient antibody status, that is by exposure status, using Qatar as an example.\n\nMethodsVaccination impact was assessed under different scale-up scenarios using a deterministic meta-population mathematical model describing SARS-CoV-2 transmission and disease progression in the presence of vaccination.\n\nResultsFor a vaccine that protects against infection with an efficacy of 95%, half as many vaccinations were needed to avert one infection, disease outcome, or death by prioritizing antibody-negative individuals for vaccination. Prioritization by antibody status reduced incidence at a faster rate and led to faster elimination of infection and return to normalcy. Further prioritization by age group amplified the gains of prioritization by antibody status. Gains from prioritization by antibody status were largest in settings where the proportion of the population already infected at the commencement of vaccination was 30-60%, which is perhaps where most countries will be by the time vaccination programs are up and running. For a vaccine that only protects against disease and not infection, vaccine impact was reduced by half, whether this impact was measured in terms of averted infections or disease outcomes, but the relative gains from using antibody status to prioritize vaccination recipients were similar.\n\nConclusionsMajor health, societal, and economic gains can be achieved more quickly by prioritizing those who are antibody-negative while doses of the vaccine remain in short supply.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Houssein H. Ayoub", + "author_inst": "Qatar University, Doha, Qatar" + }, + { + "author_name": "Hiam Chemaitelly", + "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar" + }, + { + "author_name": "Monia Makhoul", + "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar" + }, + { + "author_name": "Zaina Al Kanaani", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Einas Al Kuwari", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Adeel A Butt", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Peter Coyle", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Andrew Jeremijenko", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Anvar Hassan Kaleeckal", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Ali Nizar Latif", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Riyazuddin Mohammad Shaik", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Hanan F. Abdul Rahim", + "author_inst": "Qatar University, Doha, Qatar" + }, + { + "author_name": "Gheyath K. Nasrallah", + "author_inst": "Qatar University, Doha, Qatar" + }, + { + "author_name": "Hadi M. Yassine", + "author_inst": "Qatar University, Doha, Qatar" + }, + { + "author_name": "Mohamed G. Al Kuwari", + "author_inst": "Primary Health Care Corporation, Doha, Qatar" + }, + { + "author_name": "Hamad Eid Al Romaihi", + "author_inst": "Ministry of Public Health, Doha, Qatar" + }, + { + "author_name": "Mohamed H. Al-Thani", + "author_inst": "Ministry of Public Health, Doha, Qatar" + }, + { + "author_name": "Roberto Bertollini", + "author_inst": "Ministry of Public Health, Doha, Qatar" + }, + { + "author_name": "Abdullatif Al Khal", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Laith J Abu-Raddad", + "author_inst": "Weill Cornell Medicine-Qatar" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.09.21249384", "rel_title": "International risk of the new variant COVID-19 importations originating in the United Kingdom", @@ -992558,81 +994941,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.01.11.426218", - "rel_title": "Modular basis for potent SARS-CoV-2 neutralization by a prevalent VH1-2-derived antibody class", - "rel_date": "2021-01-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.11.426218", - "rel_abs": "Antibodies with heavy chains that derive from the VH1-2 gene constitute some of the most potent SARS-CoV-2-neutralizing antibodies yet identified. To provide insight into whether these genetic similarities inform common modes of recognition, we determined structures of the SARS-CoV-2 spike in complex with three VH1-2-derived antibodies: 2-15, 2-43, and H4. All three utilized VH1-2-encoded motifs to recognize the receptor-binding domain (RBD), with heavy chain N53I enhancing binding and light chain tyrosines recognizing F486RBD. Despite these similarities, class members bound both RBD-up and -down conformations of the spike, with a subset of antibodies utilizing elongated CDRH3s to recognize glycan N343 on a neighboring RBD - a quaternary interaction accommodated by an increase in RBD separation of up to 12 [A]. The VH1-2-antibody class thus utilizes modular recognition encoded by modular genetic elements to effect potent neutralization, with VH-gene component specifying recognition of RBD and CDRH3 component specifying quaternary interactions.\n\nHighlightsO_LIDetermine structures of VH1-2-derived antibodies 2-43, 2-15, and H4 in complex with SARS-CoV-2 spike\nC_LIO_LIDefine a multi-donor VH1-2-antibody class with modular components for RBD and quaternary recognition\nC_LIO_LIReveal structural basis of RBD-up and RBD-down recognition within the class\nC_LIO_LIShow somatic hypermutations and avidity to be critical for potency\nC_LIO_LIDelineate changes in spike conformation induced by CDRH3-mediated quaternary recognition\nC_LI", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Micah Rapp", - "author_inst": "Columbia University" - }, - { - "author_name": "Yicheng Guo", - "author_inst": "Columbia University" - }, - { - "author_name": "Eswar Reddy Reddem", - "author_inst": "Columbia University" - }, - { - "author_name": "Lihong Liu", - "author_inst": "Columbia University" - }, - { - "author_name": "Pengfei Wang", - "author_inst": "Columbia University" - }, - { - "author_name": "Jian Yu", - "author_inst": "Columbia University" - }, - { - "author_name": "Gabriele Cerutti", - "author_inst": "Columbia University" - }, - { - "author_name": "Jude Bimela", - "author_inst": "Columbia University" - }, - { - "author_name": "Fabiana Bahna", - "author_inst": "Columbia University" - }, - { - "author_name": "Seetha Mannepalli", - "author_inst": "Columbia University" - }, - { - "author_name": "Baoshan Zhang", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Peter D. Kwong", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "David D. Ho", - "author_inst": "Columbia University" - }, - { - "author_name": "Lawrence Shapiro", - "author_inst": "Columbia University" - }, - { - "author_name": "Zizhang Sheng", - "author_inst": "Columbia University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.01.09.426032", "rel_title": "Immunogenicity and efficacy of the COVID-19 candidate vector vaccine MVA SARS 2 S in preclinical vaccination", @@ -992949,6 +995257,37 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.01.11.426227", + "rel_title": "Microsecond simulation unravel the structural dynamics of SARS-CoV-2 Spike-C-terminal cytoplasmic tail (residues 1242-1273)", + "rel_date": "2021-01-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.11.426227", + "rel_abs": "All available SARS-CoV-2 spike protein crystal and cryo-EM structures have shown missing electron densities for cytosolic C-terminal regions. Generally, the missing electron densities point towards the intrinsically disordered nature of the protein region. This curiosity has led us to investigate the C terminal cytosolic region of the spike glycoprotein of SARS-CoV-2 in isolation. The cytosolic regions is supposed to be from 1235-1273 residues or 1242-1273 residues depending on what prediction tool we use. Therefore, we have demonstrated the structural conformation of cytosolic region and its dynamics through computer simulations up to microsecond timescale using OPLS and CHARMM forcefields. The simulations have revealed the unstructured conformation of cytosolic region. Also, in temperature dependent replica-exchange molecular dynamics simulations it has shown its conformational dynamics. Further, we have validated our computational observations with circular dichroism (CD) spectroscopy-based experiments and found its signature spectra at 198 nm which is also adding the analysis as its intrinsically disordered nature. We believe that our findings will surely help us understand the structure-function relationship of the spike proteins cytosolic region.\n\nGraphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Prateek Kumar", + "author_inst": "Indian Institute of Technology Mandi" + }, + { + "author_name": "Taniya Bhardwaj", + "author_inst": "Indian Institute of Technology Mandi" + }, + { + "author_name": "Neha Garg", + "author_inst": "Banaras Hindu University, Varanasi" + }, + { + "author_name": "Rajanish Giri", + "author_inst": "Indian Institute of Technology Mandi" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.01.10.426114", "rel_title": "The hyperlipidaemic drug fenofibrate significantly reduces infection by SARS-CoV-2 in cell culture models", @@ -994860,41 +997199,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.06.21249272", - "rel_title": "Integrated Vaccination and Non-Pharmaceutical Interventions based Strategies in Ontario, Canada, as a Case Study: a Mathematical Modeling Study", - "rel_date": "2021-01-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.06.21249272", - "rel_abs": "BackgroundRecently, two \"Coronavirus disease 2019\" (COVID-19) vaccine products have been authorized in Canada. It is of crucial importance to model an integrated/combined package of non-pharmaceutical (physical/social distancing) and pharmaceutical (immunization) public health control measures.\n\nMethodsA modified epidemiological, compartmental SIR model was utilized and fit to the cumulative COVID-19 case data for the province of Ontario, Canada, from September 8, 2020 to December 8, 2020. Different vaccine roll-out strategies were simulated until 75 percent of the population is vaccinated, including a no-vaccination scenario. We compete these vaccination strategies with relaxation of non-pharmaceutical interventions. Non-pharmaceutical interventions were supposed to remain enforced and began to be relaxed on either January 31, March 31, or May 1, 2021.\n\nResultsBased on projections from the data and long-term extrapolation of scenarios, relaxing the public health measures implemented by re-opening too early would cause any benefits of vaccination to be lost by increasing case numbers, increasing the effective reproduction number above 1 and thus increasing the risk of localized outbreaks. If relaxation is, instead, delayed and 75 percent of the Ontarian population gets vaccinated by the end of the year, re-opening can occur with very little risk.\n\nInterpretationRelaxing non-pharmaceutical interventions by re-opening and vaccine deployment is a careful balancing act. Our combination of model projections from data and simulation of different strategies and scenarios, can equip local public health decision- and policy-makers with projections concerning the COVID-19 epidemiological trend, helping them in the decision-making process.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Matthew Betti", - "author_inst": "Mount Allison University" - }, - { - "author_name": "Nicola Bragazzi", - "author_inst": "York University" - }, - { - "author_name": "Jane Heffernan", - "author_inst": "York University" - }, - { - "author_name": "Jude Dvezela Kong", - "author_inst": "York University" - }, - { - "author_name": "Angie Raad", - "author_inst": "York University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.06.21249349", "rel_title": "Identifying silent COVID-19 infections among children is critical for controlling the pandemic", @@ -995275,6 +997579,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.07.21249353", + "rel_title": "Inherent random fluctuations in COVID-19 outbreaks may explain rapid growth of new mutated virus variants", + "rel_date": "2021-01-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.07.21249353", + "rel_abs": "A new virus variant of SARS-COV-2 has had a profound impact on society while governments have taken action to limit its impacts by enforcing lockdowns and limiting spread from the UK to other countries. Variants with mutations in the virus genome are likely to occur, but do not always associate to significant changes in the biology of the virus, or the disease. For the variant VOC 202012/01 (also referred to as B.1.1.7), however, preliminary reports indicate it may be more transmissible. Here we use a simulation model calibrated to the inherent random fluctuating transmission pattern of COVID-19 to investigate what the probability may be for detecting more transmissible virus variants post facto. We find that post facto identification of successful virus variants of SARS-COV-2 are likely to exhibit growth rates that are substantially larger than the average growth rate. This finding has implications for interpreting growth rate and transmissibility of new virus variants.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Kenneth Bodin", + "author_inst": "Umea University" + }, + { + "author_name": "Joacim Rocklov", + "author_inst": "Umea University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.06.21249365", "rel_title": "Modeling the effect of vaccination strategies in an Excel spreadsheet: The rate of vaccination, and not only the vaccination coverage, is a determinant for containing COVID-19 in urban areas", @@ -996533,49 +998860,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.01.08.425825", - "rel_title": "Artemisia annua L. extracts prevent in vitro replication of SARS-CoV-2", - "rel_date": "2021-01-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.08.425825", - "rel_abs": "Ethnopharmacological relevanceArtemisia annua L. has been used for millennia in Southeast Asia to treat \"fever\". Many infectious microbial and viral diseases have been shown to respond to A. annua and communities around the world use the plant as a medicinal tea, especially for treating malaria.\n\nAim of the StudySARS-CoV-2 (the cause of Covid-19) globally has infected and killed millions of people. Because of the broad-spectrum antiviral activity of artemisinin that includes blockade of SARS-CoV-1, we queried whether A. annua suppressed SARS-CoV-2.\n\nMaterials and MethodsUsing Vero E6 and Calu-3 cells, we measured anti viral activity SARS-CoV-2 activity against fully infectious virusof dried leaf extracts of seven cultivars of A. annua sourced from four continents. IC50s were calculated and defined as (the concentrations that inhibited viral replication by 50%.) and CC50s (the concentrations that kill 50% of cells) were calculated.\n\nResultsHot-water leaf extracts based on artemisinin, total flavonoids, or dry leaf mass showed antiviral activity with IC50 values of 0.1-8.7 M, 0.01-0.14 g, and 23.4-57.4 g, respectively. Antiviral efficacy did not correlate with artemisinin or total flavonoid contents of the extracts. One dried leaf sample was >12 years old, yet the hot-water extract was still found to be active. The UK and South African variants, B1.1.7 and B1.351, were similarly inhibited. While all hot water extracts were effective, concentrations of artemisinin and total flavonoids varied by nearly 100-fold in the extracts. Artemisinin alone showed an estimated IC50 of about 70 M, and the clinically used artemisinin derivatives artesunate, artemether, and dihydroartemisinin were ineffective or cytotoxic at elevated micromolar concentrations. In contrast, the antimalarial drug amodiaquine had an IC50 = 5.8 M. Extracts had minimal effects on infection of Vero E6 or Calu-3 cells by a reporter virus pseudotyped by the SARS-CoV-2 spike protein. There was no cytotoxicity within an order of magnitude above the antiviral IC90 values.\n\nConclusionsA. annua extracts inhibit SARS-CoV-2 infection, and the active component(s) in the extracts is likely something besides artemisinin or a combination of components that block virus infection at a step downstream of virus entry. Further studies will determine in vivo efficacy to assess whether A. annua might provide a cost-effective therapeutic to treat SARS-CoV-2 infections.\n\nList of compounds studiedAmodiaquine\nArtemisinin\nArtesunate\nArtemether\nDeoxyartemisinin\nDihydroartemisinin\n\n\nHighlightsO_LIArtemisia annua is effective in stopping replication of SARS-CoV-2 including 2 new variants.\nC_LIO_LIThe anti-viral effect does not correlate to artemisinin, nor to the total flavonoid content.\nC_LIO_LIThe anti-viral mechanism does not appear to involve blockade virus entry into cell.\nC_LIO_LIThe plant offers two additional benefits: a decreased inflammatory response and blunting of fibrosis.\nC_LIO_LIA. annua may provide a safe, low-cost alternative for treating patients infected with SARS-CoV-2.\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Manoj S Nair", - "author_inst": "Columbia University" - }, - { - "author_name": "Yaoxing Huang", - "author_inst": "Columbia University" - }, - { - "author_name": "David A Fidock", - "author_inst": "Columbia University" - }, - { - "author_name": "Stephen J Polyak", - "author_inst": "University of Washington" - }, - { - "author_name": "Jessica Wagoner", - "author_inst": "University of Washington" - }, - { - "author_name": "Melissa Towler", - "author_inst": "Worcester Polytechnic Institute" - }, - { - "author_name": "Pamela Weathers", - "author_inst": "Worcester Polytechnic Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.01.08.425915", "rel_title": "Ad26.COV2.S-elicited immunity protects against G614 spike variant SARS-CoV-2 infection in Syrian hamsters and does not enhance respiratory disease in challenged animals with breakthrough infection after sub-optimal vaccine dosing", @@ -996856,6 +999140,61 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2021.01.07.425745", + "rel_title": "New targets for drug design: Importance of nsp14/nsp10 complex formation for the 3'-5' exoribonucleolytic activity on SARS-CoV-2", + "rel_date": "2021-01-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.07.425745", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has triggered a global pandemic with devastating consequences for health-care and social-economic systems. Thus, the understanding of fundamental aspects of SARS-CoV-2 is of extreme importance.\n\nIn this work, we have focused our attention on the viral ribonuclease (RNase) nsp14, since this protein was considered one of the most interferon antagonists from SARS-CoV-2, and affects viral replication. This RNase is a multifunctional protein that harbors two distinct activities, an N-terminal 3-to-5 exoribonuclease (ExoN) and a C-terminal N7-methyltransferase (N7-MTase), both with critical roles in coronaviruses life cycle. Namely, SARS-CoV-2 nsp14 ExoN knockout mutants are non-viable, indicating nsp14 as a prominent target for the development of antiviral drugs.\n\nNsp14 ExoN activity is stimulated through the interaction with the nsp10 protein, which has a pleiotropic function during viral replication. In this study, we have performed the first biochemical characterization of the complex nsp14-nsp10 from SARS-CoV-2. Here we confirm the 3-5 exoribonuclease and MTase activities of nsp14 in this new Coronavirus, and the critical role of nsp10 in upregulating the nsp14 ExoN activity in vitro. Furthermore, we demonstrate that SARS-CoV-2 nsp14 N7-MTase activity is functionally independent of the ExoN activity. The nsp14 MTase activity also seems to be independent of the presence of nsp10 cofactor, contrarily to nsp14 ExoN.\n\nUntil now, there is no available structure for the SARS-CoV-2 nsp14-nsp10 complex. As such, we have modelled the SARS-CoV-2 nsp14-nsp10 complex based on the 3D structure of the complex from SARS-CoV (PDB ID 5C8S). We also have managed to map key nsp10 residues involved in its interaction with nsp14, all of which are also shown to be essential for stimulation of the nsp14 ExoN activity. This reinforces the idea that a stable interaction between nsp10 and nsp14 is strictly required for the nsp14-mediated ExoN activity of SARS-CoV-2, as observed for SARS-CoV.\n\nWe have studied the role of conserved DEDD catalytic residues of SARS-CoV-2 nsp14 ExoN. Our results show that motif I of ExoN domain is essential for the nsp14 function contrasting to the functionality of these conserved catalytic residues in SARS-CoV, and in the Middle East respiratory syndrome coronavirus (MERS). The differences here revealed can have important implications regarding the specific pathogenesis of SARS-CoV-2.\n\nThe nsp10-nsp14 interface is a recognized attractive target for antivirals against SARS-CoV-2 and other coronaviruses. This work has unravelled a basis for discovering inhibitors targeting the specific amino acids here reported, in order to disrupt the assembly of this complex and interfere with coronaviruses replication.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Margarida Saramago", + "author_inst": "ITQB NOVA" + }, + { + "author_name": "C\u00e1tia B\u00e1rria", + "author_inst": "ITQB NOVA" + }, + { + "author_name": "Vanessa Costa", + "author_inst": "ITQB NOVA" + }, + { + "author_name": "Caio S. Souza", + "author_inst": "ITQB NOVA" + }, + { + "author_name": "Sandra C. Viegas", + "author_inst": "ITQB NOVA" + }, + { + "author_name": "Susana Domingues", + "author_inst": "ITQB NOVA" + }, + { + "author_name": "Diana Lousa", + "author_inst": "ITQB NOVA" + }, + { + "author_name": "Cl\u00e1udio M. Soares", + "author_inst": "ITQB NOVA" + }, + { + "author_name": "Cec\u00edlia M. Arraiano", + "author_inst": "ITQB NOVA" + }, + { + "author_name": "Rute G. Matos", + "author_inst": "ITQB NOVA" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.01.07.425674", "rel_title": "CpG-adjuvanted stable prefusion SARS-CoV-2 spike protein protected hamsters from SARS-CoV-2 challenge", @@ -998291,61 +1000630,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.06.21249314", - "rel_title": "Impaired performance of SARS-CoV-2 antigen-detecting rapid tests at elevated temperatures", - "rel_date": "2021-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.06.21249314", - "rel_abs": "Rapid antigen-detecting tests (Ag-RDTs) can complement molecular diagnostics for COVID-19. The recommended temperature for storage of SARS-CoV-2 Ag-RDTs ranges between 5-30{degrees}C. In many countries that would benefit from SARS-CoV-2 Ag-RDTs, mean temperatures exceed 30{degrees}C. We assessed analytical sensitivity and specificity of eleven commercially available SARS-CoV-2 Ag-RDTs using different storage and operational temperatures, including (i) long-term storage and testing at recommended conditions, (ii) recommended storage conditions followed by 10 minutes exposure to 37{degrees}C and testing at 37{degrees}C and (iii) 3 weeks storage followed by testing at 37{degrees}C. The limits of detection of SARS-CoV-2 Ag-RDTs under recommended conditions ranged from 8.2x105-7.9x107 genome copies/ml of infectious SARS-CoV-2 cell culture supernatant. Despite long-term storage at recommended conditions, 10 minutes pre-incubation of Ag-RDTs and testing at 37{degrees}C resulted in about ten-fold reduced sensitivity for 46% of SARS-CoV-2 Ag-RDTs, including both Ag-RDTs currently listed for emergency use by the World Health Organization. After 3 weeks of storage at 37{degrees}C, 73% of SARS-CoV-2 Ag-RDTs exhibited about ten-fold reduced sensitivity. Specificity of SARS-CoV-2 Ag-RDTs using cell culture-derived human coronaviruses HCoV-229E and HCoV-OC43 was not affected by storage and testing at 37{degrees}C. In summary, short- and long-term exposure to elevated temperatures likely impairs sensitivity of several SARS-CoV-2 Ag-RDTs that may translate to false-negative test results at clinically relevant virus concentrations compatible with inter-individual transmission. Ensuring appropriate transport and storage conditions, and development of tests that are more robust across temperature fluctuations will be important for accurate use of SARS-CoV-2 Ag-RDTs in tropical settings.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Verena Claudia Haage", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Edmilson Ferreira de Oliveira-Filho", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Andres Moreira-Soto", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Arne K\u00fchne", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Carlo Fischer", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Jilian Sacks", - "author_inst": "Foundation for Innovative New Diagnostics" - }, - { - "author_name": "Victor Max Corman", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Marcel A. M\u00fcller", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Christian Drosten", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Jan Felix Drexler", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.05.21249131", "rel_title": "Ivermectin shows clinical benefits in mild to moderate Covid19 disease: A randomised controlled double blind dose response study in Lagos.", @@ -998510,6 +1000794,57 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.01.05.425420", + "rel_title": "COVID-19 virtual patient cohort reveals immune mechanisms driving disease outcomes", + "rel_date": "2021-01-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.05.425420", + "rel_abs": "To understand the diversity of immune responses to SARS-CoV-2 and distinguish features that predispose individuals to severe COVID-19, we developed a mechanistic, within-host mathematical model and virtual patient cohort. Our results indicate that virtual patients with low production rates of infected cell derived IFN subsequently experienced highly inflammatory disease phenotypes, compared to those with early and robust IFN responses. In these in silico patients, the maximum concentration of IL-6 was also a major predictor of CD8+ T cell depletion. Our analyses predicted that individuals with severe COVID-19 also have accelerated monocyte-to-macrophage differentiation that was mediated by increased IL-6 and reduced type I IFN signalling. Together, these findings identify biomarkers driving the development of severe COVID-19 and support early interventions aimed at reducing inflammation.\n\nAuthor summaryUnderstanding of how the immune system responds to SARS-CoV-2 infections is critical for improving diagnostic and treatment approaches. Identifying which immune mechanisms lead to divergent outcomes can be clinically difficult, and experimental models and longitudinal data are only beginning to emerge. In response, we developed a mechanistic, mathematical and computational model of the immunopathology of COVID-19 calibrated to and validated against a broad set of experimental and clinical immunological data. To study the drivers of severe COVID-19, we used our model to expand a cohort of virtual patients, each with realistic disease dynamics. Our results identify key processes that regulate the immune response to SARS-CoV-2 infection in virtual patients and suggest viable therapeutic targets, underlining the importance of a rational approach to studying novel pathogens using intra-host models.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Adrianne L. Jenner", + "author_inst": "CHU Sainte-Justine Research Centre, Department of Mathematics and Statistics, Universite de Montreal" + }, + { + "author_name": "Rosemary A. Aogo", + "author_inst": "Department of Pediatrics, University of Tennessee Health Science Center" + }, + { + "author_name": "Sofia Alfonso", + "author_inst": "Department of Physiology, McGill University" + }, + { + "author_name": "Vivienne Crowe", + "author_inst": "Department of Mathematics and Statistics, Concordia University" + }, + { + "author_name": "Amanda P. Smith", + "author_inst": "Department of Pediatrics, University of Tennessee Health Science Center" + }, + { + "author_name": "Penelope A. Morel", + "author_inst": "Department of Immunology, University of Pittsburgh" + }, + { + "author_name": "Courtney L. Davis", + "author_inst": "Natural Science Division, Pepperdine University" + }, + { + "author_name": "Amber M. Smith", + "author_inst": "Department of Pediatrics, University of Tennessee Health Science Center" + }, + { + "author_name": "Morgan Craig", + "author_inst": "CHU Sainte-Justine Research Centre, Department of Mathematics and Statistics, Universite de Montreal" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.01.05.425516", "rel_title": "RNA-protein interaction analysis of SARS-CoV-2 5'- and 3'-untranslated regions identifies an antiviral role of lysosome-associated membrane protein-2", @@ -999725,65 +1002060,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.30.20249062", - "rel_title": "Outbreak or pseudo-outbreak? Integrating SARS-CoV-2 sequencing to validate infection control practices in an end stage renal disease facility", - "rel_date": "2021-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.30.20249062", - "rel_abs": "BackgroundThe COVID-19 pandemic of 2020 poses a particularly high risk for End Stage Renal Disease (ESRD) patients and led to a need for facility-wide control plans to prevent introduction and spread of infection within ESRD facilities. Rapid identification of clusters of contemporaneous cases is essential, as these may be indicative of within-facility spread. Nevertheless, in a setting of high community COVID-19 prevalence, a series of ESRD patients may test positive at around the same time without their shared ESRD facility being the nexus for disease spread. Here we describe a series of five cases occurring within an eleven-day period in November 2020 in a hospital-based 32-station ESRD facility in southwest Wisconsin, the subsequent facility-wide testing, and the use of genetic sequence analysis of positive specimens to evaluate whether these cases were linked.\n\nMethodsFour patient cases and one staff case were identified in symptomatic individuals by RT-PCR. Facility-wide screening was initiated at the request of local public health and conducted using Abbot BinaxNOW antigen tests. SARS-CoV-2 genome sequences were obtained from residual diagnostic test specimens using an amplicon-based approach on an Ion Torrent S5 sequencer.\n\nResultsResidual specimens from 4 of 5 cases were available for sequence analysis. Each sequence was very clearly genetically distinct from the others, indicating that these contemporaneous cases were not linked. Facility-wide screening of 47 staff and 107 patients did not identify any additional cases.\n\nConclusionsThese data indicate that despite the outward appearance of a case cluster, the facility did not experience within-facility spread nor serve as the epicenter of a new outbreak, suggesting that the enacted rigorous infection control procedures (screening, masking, distancing) practiced stringently by patients and staff were sufficient to permit dialysis to proceed safely in a very high-risk population under pressure from increasing community spread. These data also demonstrate the utility of rapid turnaround SARS-CoV-2 sequencing in outbreak investigations in settings like ESRD facilities.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Bridget L Pfaff", - "author_inst": "Gundersen Health System" - }, - { - "author_name": "Craig S Richmond", - "author_inst": "Gundersen Medical Foundation" - }, - { - "author_name": "Arick P Sabin", - "author_inst": "Gundersen Health System" - }, - { - "author_name": "Deena M Athas", - "author_inst": "Gundersen Health System" - }, - { - "author_name": "Jessica C Adams", - "author_inst": "Gundersen Health System" - }, - { - "author_name": "Megan E Meller", - "author_inst": "Gundersen Health System" - }, - { - "author_name": "Kumari Usha", - "author_inst": "Gundersen Health System" - }, - { - "author_name": "Sarah A Schmitz", - "author_inst": "Gundersen Health System" - }, - { - "author_name": "Brian J Simmons", - "author_inst": "Gundersen Health System" - }, - { - "author_name": "Andrew J Borgert", - "author_inst": "Gundersen Medical Foundation" - }, - { - "author_name": "Paraic A Kenny", - "author_inst": "Gundersen Medical Foundation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.03.21249175", "rel_title": "Modelling COVID -19 Transmission in a Hemodialysis Centre Using Simulation Generated Contacts Matrices", @@ -1000028,6 +1002304,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2020.12.31.20249084", + "rel_title": "Hospitalization as reliable indicator of second wave COVID-19 pandemic in eight European countries", + "rel_date": "2021-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.31.20249084", + "rel_abs": "Time dependent reproduction number (Rt) is one of the most popular parameters to track the impact of COVID-19 pandemic. However, especially at the initial stages, Rt can be highly underestimated because of remarkable differences between the actual number of infected people and the daily incidence of people who are tested positive. Here, we present the analysis of daily cumulative number of hospitalized (HP) and intensive care unit (ICU) patients both in space and in time in the early phases of second wave COVID-19 pandemic across eight different European countries, namely Austria, Belgium, Czech Republic, France, Italy, Portugal, Spain, and United Kingdom. We derive simple model equations to fit the time dependence of these two variables where exponential behavior is observed. Growth rate constants of HP and ICU are listed, providing country-specific parameters able to estimate the burden of SARS-COV-2 infection before extensive containment measures take place. Our quantitative parameters, fully related to hospitalizations, are disentangled from the capacity range of the screening campaign, for example the number of swabs, and they cannot be directly biased by the actual number of infected people. This approach can give an array of reliable indicators which can be used by governments and healthcare systems to monitor the dynamics of COVID-19 epidemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Mattia Allieta", + "author_inst": "Ronin Institute, Montclair, NJ, USA" + }, + { + "author_name": "Davide Rossi Sebastiano", + "author_inst": "Neurophysiology Unit IRCCS-Neurological Institute Carlo Besta via Celoria 11, 20133, Milan, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.31.20249106", "rel_title": "Optimizing testing for COVID-19 in India", @@ -1001187,49 +1003486,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.12.29.20248869", - "rel_title": "High levels of plasminogen activator inhibitor-1, tissue plasminogen activator and fibrinogen in patients with severe COVID-19", - "rel_date": "2021-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.29.20248869", - "rel_abs": "We measured plasma levels of fibrinogen, plasminogen, tissue plasminogen activator (t-PA) and plasminogen activation inhibitor 1 (PAI-1) in blood from 37 patients with severe coronavirus disease-19 (COVID-19) and 23 controls. PAI-1, t-PA and fibrinogen levels were significantly higher in the COVID-19 group. Increased levels of PAI-1 likely result in lower plasmin activity and hence decreased fibrinolysis. These observations provide a partial explanation for the fibrin- mediated increase in blood viscosity and hypercoagulability that has previously been observed in COVID-19. Our data suggest that t-PA administration may be problematic, but that other interventions designed to enhance fibrinolysis might prove useful in the treatment of the coagulopathy that is often associated with severe COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "David Cabrera-Garcia", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Andrea Miltiades", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Samantha M Parsons", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Katerina Elisman", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Mohammad Taghi Mansouri", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Gebhard Wagener", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Neil L Harrison", - "author_inst": "Columbia University Irving Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2020.12.29.20248975", "rel_title": "COVID-19: Can early home treatment with Azithromycin alone or with Zinc help prevent hospitalisation, death, and long-COVID-19? A review", @@ -1001450,6 +1003706,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.28.20248950", + "rel_title": "COVID-19 vaccine hesitancy worldwide: a systematic review of vaccine acceptance rates", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.28.20248950", + "rel_abs": "IntroductionUtility of vaccine campaigns to control coronavirus disease 2019 (COVID-19) is not merely dependent on vaccine efficacy and safety. Vaccine acceptance among the general public and the healthcare workers, appears to have a decisive role for successful control of the pandemic.\n\nAimTo provide an up-to-date assessment of COVID-19 vaccination acceptance rates worldwide.\n\nMethodsA systematic search of the peer-reviewed English survey literature indexed in PubMed was done on December 25, 2020. Results from 30 studies, met the inclusion criteria and formed the basis for final COVID-19 vaccine acceptance estimates. Results of an additional recent survey from Jordan and Kuwait was considered in this review as well.\n\nResultsSurvey studies on COVID-19 vaccine acceptance rates were found from 33 different countries. Among adults representing the general public, the highest COVID-19 vaccine acceptance rates were found in Ecuador (97.0%), Malaysia (94.3%), Indonesia (93.3%) and China (91.3%). On the other hand, the lowest COVID-19 vaccine acceptance rates were found in Kuwait (23.6%), Jordan (28.4%), Italy (53.7), Russia (54.9%), Poland (56.3%), US (56.9%), and France (58.9%). Only eight surveys among healthcare workers (doctors, nurses) were found, with vaccine acceptance rates ranging from 27.7% in the Democratic Republic of the Congo to 78.1% in Israel. In a majority of survey studies among the general public (62%), the acceptance of COVID-19 vaccination showed a level of [≥] 70%.\n\nConclusionsLow rates of COVID-19 vaccine acceptance were reported in the Middle East, Russia, Africa and several European countries. This could represent a major problem in the global efforts that aim to control the current COVID-19 pandemic. More studies are recommended to address the scope of COVID-19 vaccine hesitancy. Such studies are particularly needed in the Middle East Africa, Eastern Europe, Central Asia, Middle and Latin America.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC=\"FIGDIR/small/20248950v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (30K):\norg.highwire.dtl.DTLVardef@141e966org.highwire.dtl.DTLVardef@423aa6org.highwire.dtl.DTLVardef@186d8dorg.highwire.dtl.DTLVardef@1c0450e_HPS_FORMAT_FIGEXP M_FIG C_FIG COVID-19 vaccine acceptance rates worldwideFor countries with more than one survey study, the vaccine acceptance rate of the latest survey was used in this graph. The estimates were also based on studies from the general population, except in the following cases were no studies from the general public were found (Australia: parents/guardians; DRC: healthcare workers; Hong Kong: healthcare workers; Malta: healthcare workers).", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Malik Sallam", + "author_inst": "University of Jordan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.28.20248552", "rel_title": "COVID-19 ARDS is characterized by a dysregulated host response that differs from cytokine storm and may be modified by dexamethasone", @@ -1002729,29 +1005004,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.28.20248936", - "rel_title": "Lockdown Effects on Sars-CoV-2 Transmission - The evidence from Northern Jutland", - "rel_date": "2021-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.28.20248936", - "rel_abs": "The exact impact of lockdowns and other NPIs on Sars-CoV-2 transmission remain a matter of debate as early models assumed 100% susceptible homogenously transmitting populations, an assumption known to overestimate counterfactual transmission, and since most real epidemiological data are subject to massive confounding variables. Here, we analyse the unique case-controlled epidemiological dataset arising from the selective lockdown of parts of Northern Denmark, but not others, as a consequence of the spread of mink-related mutations in November 2020. Our analysis shows that while infection levels decreased, they did so before lockdown was effective, and infection numbers also decreased in neighbour municipalities without mandates. Direct spill-over to neighbour municipalities or the simultaneous mass testing do not explain this. Instead, control of infection pockets possibly together with voluntary social behaviour was apparently effective before the mandate, explaining why the infection decline occurred before and in both the mandated and non-mandated areas. The data suggest that efficient infection surveillance and voluntary compliance make full lockdowns unnecessary at least in some circumstances.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Kasper Planeta Kepp", - "author_inst": "Technical University of Denmark" - }, - { - "author_name": "Christian Bjornskov", - "author_inst": "Aarhus University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.30.20248908", "rel_title": "Unsupervised Discovery of Risk Profiles on Negative and Positive COVID-19 Hospitalized Patients", @@ -1002860,6 +1005112,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.30.20248929", + "rel_title": "Antemortem vs. postmortem histopathological and ultrastructural findings in paired transbronchial biopsies and lung autopsy samples from three patients with confirmed SARS-CoV-2 infection", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.30.20248929", + "rel_abs": "BackgroundAcute respiratory distress syndrome (ARDS) is the major cause of death in coronavirus disease 2019 (COVID-19). Multiple autopsy-based reports of COVID-19 lung pathology describe diffuse alveolar damage (DAD), organizing pneumonia (OP) and fibrotic change, but data on early pathological changes as well as during progression of the disease are rare.\n\nResearch questionComparison of histopathological and ultrastructural findings in paired transbronchial biopsies (TBBs) and autopsy material from three patients with confirmed SARS-CoV-2-infection.\n\nMethodsWe prospectively enrolled 3 patients with confirmed SARS-CoV-2 infection. Full clinical evaluation was performed including high-resolution computed tomography (HR-CT). We took TBBs at different time points during the disease and autopsy tissue samples after the patients death.\n\nResultsSARS-CoV-2 was detected by RT-PCR and/or FISH in all TBBs. Lung histology revealed pneumocyte hyperplasia and capillary congestion in one patient who died short after hospital admission with detectable virus in 1/2 autopsy samples from the lung. SARS-CoV-2 was detected in 2/2 autopsy samples from a patient with a fulminant course of the disease and very short latency between biopsy and autopsy, both showing widespread DAD. In a third patient with a prolonged course, i.e. five weeks of ICU treatment with ECMO, autopsy samples showed extensive interstitial fibrosis without detectable virus by RT-PCR and/or FISH.\n\nInterpretationWe report the course of COVID-19 in paired TBB and autopsy samples from three patients at an early stage, in rapidly progressive and in a prolonged disease course. Our findings illustrate vascular, organizing and fibrotic patterns of COVID-19-induced lung injury and suggest an early spread of SARS-CoV-2 from the upper airways to the lung periphery with diminishing viral load during disease.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Daniel Gagiannis", + "author_inst": "Department of Pulmonology, Bundeswehrkrankenhaus Ulm, 89081 Ulm, Oberer Eselsberg 40, Germany" + }, + { + "author_name": "Vincent G Umathum", + "author_inst": "Institute of Pathology and Molecular Pathology, Bundeswehrkrankenhaus Ulm, 89081 Ulm, Oberer Eselsberg 40, Germany" + }, + { + "author_name": "Wilhelm Bloch", + "author_inst": "Department of Molecular and Cellular Sport Medicine, German Sport University Cologne, 50933 Cologne, Am Sportpark Muengersdorf 6, Germany" + }, + { + "author_name": "Conn Rother", + "author_inst": "Department of Hematology and Oncology, Bundeswehrkrankenhaus Ulm, 89081 Ulm, Oberer Eselsberg 40, Germany" + }, + { + "author_name": "Marcel Stahl", + "author_inst": "Department of Pulmonology, Bundeswehrkrankenhaus Ulm, 89081 Ulm, Oberer Eselsberg 40, Germany" + }, + { + "author_name": "Hanno M Witte", + "author_inst": "Department of Hematology and Oncology, Bundeswehrkrankenhaus Ulm, 89081 Ulm, Oberer Eselsberg 40, Germany" + }, + { + "author_name": "Sonja Djudjaj", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, 52074 Aachen, Pauwelsstrasse 30, Germany" + }, + { + "author_name": "Peter Boor", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, 52074 Aachen, Pauwelsstrasse 30, Germany" + }, + { + "author_name": "Konrad Steinestel", + "author_inst": "Bundeswehrkrankenhaus Ulm" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.12.29.20248994", "rel_title": "Respiratory and non-respiratory manifestations in children admitted with COVID 19 in Rio de Janeiro city, Brazil", @@ -1004043,33 +1006346,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.02.20248940", - "rel_title": "Brazilian model estimation for SARS-CoV-2 peak contagion (BMESPC): first and second wave", - "rel_date": "2021-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.02.20248940", - "rel_abs": "With newer data for SARS-CoV-2 and entering the second wave of contagion required the improvement of the forecasting model, structuring its model to forecast the peak of the first and second contagion wave in Brazil. The Brazilian model estimation for SARS-CoV-2 peak contagion (BMESPC) was structured, capable of estimating the peak of contagion for SARS-CoV-2 in the first and second waves, as the main objective of this work. Using the BMESPC model, it was possible to estimate, with a certain reliability degree, the peak of contagion for the first and second waves in Brazil, with one day difference from the real to the forecast. While at the state level, the calculated confidence interval proved to be more accurate. In this way, it is possible to use BMESPC to forecast the peak of contagion for several regions, provided that the necessary structure and calibration are respected.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Guilherme Asai", - "author_inst": "University of Illinois at Urbana Champaing" - }, - { - "author_name": "Andre Kuroiva", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Manuella Lucca Terra", - "author_inst": "University of Sao Paulo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.03.20248715", "rel_title": "Humoral and cell-mediated response in colostrum after exposure to severe acute respiratory syndrome coronavirus 2", @@ -1004458,6 +1006734,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.03.21249162", + "rel_title": "SARS-CoV-2 induces a durable and antigen specific humoral immunity after asymptomatic to mild COVID-19 infection", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.03.21249162", + "rel_abs": "Current SARS-CoV-2 serological assays generate discrepant results, and the longitudinal characteristics of antibodies targeting various antigens after asymptomatic to mild COVID-19 are yet to be established. This longitudinal cohort study including 1965 healthcare workers, of which 381 participants exhibited antibodies against the SARS-CoV-2 spike antigen at study inclusion, reveal that these antibodies remain detectable in most participants, 96%, at least four months post infection, despite having had no or mild symptoms. Virus neutralization capacity was confirmed by microneutralization assay in 91% of study participants at least four months post infection. Contrary to antibodies targeting the spike protein, antibodies against the nucleocapsid protein were only detected in 80% of previously anti-nucleocapsid IgG positive healthcare workers. Both anti-spike and anti-nucleocapsid IgG levels were significantly higher in previously hospitalized COVID-19 patients four months post infection than in healthcare workers four months post infection (p=2*10-23 and 2*10-13 respectively). Although the magnitude of humoral response was associated with disease severity, our findings support a durable and functional humoral response after SARS-CoV-2 infection even after no or mild symptoms. We further demonstrate differences in antibody kinetics depending on the antigen, arguing against the use of the nucleocapsid protein as target antigen in population-based SARS-CoV-2 serological surveys.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Sebastian Havervall", + "author_inst": "Department of Clinical Sciences, Karolinska Institute, Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "August Jernbom Falk", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Jonas Klingstrom", + "author_inst": "Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden" + }, + { + "author_name": "Henry Ng", + "author_inst": "Department of Medical Cell Biology, Uppsala University, SciLifeLab, Uppsala, Sweden" + }, + { + "author_name": "Nina Greilert Norin", + "author_inst": "Department of Clinical Sciences, Karolinska Institute, Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Lena Gabrielsson", + "author_inst": "Department of Clinical Sciences, Karolinska Institute, Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Ann-Christine Salomonsson", + "author_inst": "Department of Clinical Sciences, Karolinska Institute, Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Eva Isaksson", + "author_inst": "Department of Clinical Sciences, Karolinska Institute, Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Ann-Sofie Rudberg", + "author_inst": "Department of Neurology, Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Cecilia Hellstrom", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Eni Andersson", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Jennie Olofsson", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Lovisa Skoglund", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Jamil Yousef", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Elisa Pin", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Wanda Christ", + "author_inst": "Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden" + }, + { + "author_name": "Mikaela Olausson", + "author_inst": "Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden" + }, + { + "author_name": "My Hedhammar", + "author_inst": "Division of Protein Technology, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden" + }, + { + "author_name": "Hanna Tegel", + "author_inst": "Division of Protein Technology, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden" + }, + { + "author_name": "Sara Mangsbo", + "author_inst": "Department of Pharmaceutical Biosciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden" + }, + { + "author_name": "Mia Phillipson", + "author_inst": "Department of Medical Cell Biology, Uppsala University, SciLifeLab, Uppsala, Sweden" + }, + { + "author_name": "Anna Manberg", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Sophia Hober", + "author_inst": "Division of Protein Technology, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden" + }, + { + "author_name": "Peter Nilsson", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Charlotte Thalin", + "author_inst": "Department of Clinical Sciences, Karolinska Institute, Danderyd Hospital, Stockholm, Sweden" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.03.21249169", "rel_title": "The Impact of the November 2020 English National Lockdown on COVID-19 case counts", @@ -1005877,49 +1008268,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.12.28.20248920", - "rel_title": "Determinants of in-hospital mortality in COVID-19; a prospective cohort study from Pakistan", - "rel_date": "2021-01-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.28.20248920", - "rel_abs": "A prospective cohort study was conducted at the Indus Hospital Karachi, Pakistan between March and June 2020 to describe the determinants of mortality among hospitalized COVID-19 patients. 186 adult patients were enrolled and all-cause mortality was found to be 36% (67/186). Those who died were older and more likely to be males (p<0.05). Temperature and respiratory rate were higher among non-survivors while Oxygen saturation was lower (p<0.05). Serum CRP, D-dimer and IL-6 were higher while SpO2 was lower on admission among non-survivors (p<0.05). Non-survivors had higher SOFA and CURB-65 scores while thrombocytopenia, lymphopenia and severe ARDS was more prevalent among them (p<0.05). Use of non-invasive ventilation in emergency room, ICU admission and invasive ventilation were associated with mortality in our cohort (p<0.05). Length of hospital stay and days of intubation were longer in non-survivors (p<0.05). Use of azithromycin, hydroxychloroquine, steroids, tocilizumab, antibiotics, IVIG or anticoagulation showed no mortality benefit (p>0.05). Multivariable logistic regression showed that age > 60 years, oxygen saturation <93% on admission, pro-calcitonin > 2 ng/ml, unit rise in temperature and SOFA score, ICU admission and sepsis during hospital stay were associated with higher odds of mortality. Larger prospective studies are needed to further strengthen these findings.\n\nKey FindingsO_LIAge greater than 60 years is associated with in-hospital mortality among COVID-19 patients\nC_LIO_LIOxygen saturation less than 93% and ICU admission are associated with higher odds of mortality\nC_LIO_LIInflammatory markers including CRP, Ferritin and IL-6 were significantly higher among non-survivors\nC_LIO_LISerum pro-calcitonin greater than 2 ng/ml and sepsis during hospital stay are associated with higher odds of mortality among COVID-19 patients\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Samreen Sarfaraz", - "author_inst": "The Indus Hospital" - }, - { - "author_name": "Quratulain Shaikh", - "author_inst": "The Indus Hospital" - }, - { - "author_name": "Syed Ghazanfar Saleem", - "author_inst": "The Indus Hospital" - }, - { - "author_name": "Anum Rahim", - "author_inst": "The Indus Hospital" - }, - { - "author_name": "Fivzia Farooq Herekar", - "author_inst": "The Indus Hospital" - }, - { - "author_name": "Samina Junejo", - "author_inst": "The Indus Hospital" - }, - { - "author_name": "Aneela Hussain", - "author_inst": "The Indus Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.27.20248896", "rel_title": "Vaccination and Non-Pharmaceutical Interventions: when can the UK relax about COVID-19?", @@ -1006100,6 +1008448,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.27.20248894", + "rel_title": "Prevalence and clinical profile of SARS-CoV-2 infection among farmworkers in Monterey County, California: June-November, 2020", + "rel_date": "2021-01-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.27.20248894", + "rel_abs": "As essential personnel, United States farmworkers have continued working in-person throughout the COVID-19 pandemic. We undertook prospective surveillance of SARS-CoV-2 infection and antibody prevalence among farmworkers in Californias Salinas Valley from 15 June to 30 November, 2020. Over this period, we observed 22.1% (1514/6864) positivity for current SARS-CoV-2 by nucleic acid detection among farmworkers tested at federally-qualified migrant and community health clinics, as compared to 17.2% (1255/7305) among other adults from the same communities (risk ratio, 1.29; 95% confidence interval, 1.20-1.37). In a nested study enrolling 1,115 farmworkers, prevalence of current infection was 27.7% among farmworkers reporting [≥]1 potential COVID-19 symptom, and 7.2% among farmworkers without symptoms (adjusted odds ratio 4.17; 2.86-6.09). Prevalence of anti-SARS-CoV-2 IgG antibodies increased from 10.5% (6.0-18.4%) between 16 July-31 August to 21.2% (16.6-27.4%) between 1-30 November. The high observed prevalence of infection among farmworkers underscores the need for vaccination and other preventive interventions.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Joseph A Lewnard", + "author_inst": "University of California Berkeley" + }, + { + "author_name": "Ana M Mora", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Oguchi Nkwocha", + "author_inst": "Clinica de Salud del Valle de Salinas" + }, + { + "author_name": "Katherine Kogut", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Stephen Rauch", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Norma Morga", + "author_inst": "Clinica de Salud del Valle de Salinas" + }, + { + "author_name": "Samantha Hernandez", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Marcus P Wong", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Karen Huen", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Kristin Andrejko", + "author_inst": "University of California at Berkeley" + }, + { + "author_name": "Nicholas P Jewell", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Kimberly L Parra", + "author_inst": "University of Arizona" + }, + { + "author_name": "Nina Holland", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Eva Harris", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Maximiliano Cuevas", + "author_inst": "Clinica de Salud del Valle de Salinas" + }, + { + "author_name": "Brenda Eskenazi", + "author_inst": "University of California, Berkeley" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.27.20232934", "rel_title": "A renewal equation model to assess roles andlimitations of contact tracing for diseaseoutbreak control", @@ -1007231,25 +1009658,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2020.12.24.20248842", - "rel_title": "Simulating Retarded SEIRS model for COVID-19: will the second epidemic happen?", - "rel_date": "2020-12-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.24.20248842", - "rel_abs": "In this paper, we want to simulate the COVID-19 epidemic according to the Retarded SEIRS model. One of the main questions in the human mind is whether the COVID-19 epidemic will happen again. Therefore, a criterion must be set for the occurrence or non-occurrence of the disease. With the Retarded SEIRS model and this criterion, we can predict whether the Covid-19 will re-emerge. So far, a large number of researches that have been presented in scientific groups or communities have been based on the SIR or SEIR model. But we assume that each recovered individual is immune to the disease for a limited time, and then will be susceptible again. As we know, this assumption was also true for SARS.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Hamid Pour Mohammad", - "author_inst": "Sharif University of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.24.20248814", "rel_title": "S gene dropout patterns in SARS-CoV-2 tests suggest spread of the H69del/V70del mutation in the US.", @@ -1007506,6 +1009914,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.25.20248851", + "rel_title": "Genomic Diversity of the SARS-CoV-2 in Turkey and the Impact of Virus Genome Mutations on Clinical Outcomes", + "rel_date": "2020-12-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.25.20248851", + "rel_abs": "COVID-19 is a viral respiratory disease caused by SARS-CoV-2 infection. Global efforts of genomic surveillance of the virus give chance to track the spread of the pandemic. Global emergence of some viral mutations called attention and various studies have been suggested about increased infectivity of the virus. Herein, we sequenced viral genomes isolated from 184 patients in Istanbul and analyzed clinical metadata for the investigation of any viral mutation which affects the disease course of the host. We did not detect any viral mutations affecting the disease outcome in our cohort. Besides, we observed intra-host mutations in 76% of the isolates. Insertion/deletion and stop-gain mutations are also significantly less common among intra-host variants compared to consensus viral genome mutations. Longitudinal genomic surveillance is essential for timely detection of any lineages that might affect clinical outcome, the performance of diagnostic assays, or even the immunological escape of the virus.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Ilker Karacan", + "author_inst": "Istanbul Medeniyet University" + }, + { + "author_name": "Tugba Kizilboga Akgun", + "author_inst": "Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences" + }, + { + "author_name": "Nihat Bugra Agaoglu", + "author_inst": "Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences" + }, + { + "author_name": "Payam Zolfagharian", + "author_inst": "Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences" + }, + { + "author_name": "Mehtap Aydin", + "author_inst": "Department of Microbiology, Umraniye Training and Research Hospital, University of Health Sciences" + }, + { + "author_name": "Gizem Alkurt", + "author_inst": "Genomic Laboratory (GLAB), Umraniye Teaching and Research Hospital, University of Health Sciences" + }, + { + "author_name": "Jale Yildiz", + "author_inst": "Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences" + }, + { + "author_name": "Betsi Kose", + "author_inst": "Genomic Laboratory (GLAB), Umraniye Teaching and Research Hospital, University of Health Sciences" + }, + { + "author_name": "Nisan Denizce Can", + "author_inst": "Department of Molecular Biology and Genetics, Istanbul Technical University" + }, + { + "author_name": "Ayse Serra Ozel", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Umraniye Training and Research Hospital, University of Health Sciences" + }, + { + "author_name": "Nilsun Altunal", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Umraniye Training and Research Hospital, University of Health Sciences" + }, + { + "author_name": "Arzu Irvem", + "author_inst": "Department of Microbiology, Umraniye Training and Research Hospital, University of Health Sciences" + }, + { + "author_name": "Yasemin Kendir Demirkol", + "author_inst": "Department of Pediatric Genetics, Umraniye Training and Research Hospital, University of Health Sciences" + }, + { + "author_name": "Ozlem Akgun Dogan", + "author_inst": "Department of Pediatric Genetics, Umraniye Training and Research Hospital, University of Health Sciences" + }, + { + "author_name": "Levent Doganay", + "author_inst": "Genomic Laboratory (GLAB), Umraniye Teaching and Research Hospital, University of Health Sciences" + }, + { + "author_name": "Gizem Dinler Doganay", + "author_inst": "Department of Molecular Biology and Genetics, Istanbul Technical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.25.20248860", "rel_title": "Will Proton Pump Inhibitors Lead to a Higher Risk of COVID-19 Infection and Progression to Severe Disease? A Meta-analysis", @@ -1008899,49 +1011386,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.12.27.424507", - "rel_title": "Losartan promotes cell survival following SARS-CoV-2 infection in vitro", - "rel_date": "2020-12-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.27.424507", - "rel_abs": "IntroductionCoronavirus disease 2019 (COVID-19) can be associated with mortality and high morbidity worldwide. There is an extensive effort to control infection and disease caused by SARS-CoV-2. This study addressed the hypothesis that angiotensin II type I receptor blocker, Losartan, may restrict pathogenesis caused by SARS-CoV-2 by decreasing viral-induced cytopathological changes by blocking angiotensin II type 1 receptor (AT1R), thus reducing the affinity of the virus for ACE2, and inhibiting papain-like protease of the virus.\n\nMethodLosartan inhibitory effect on deubiquitination and deISGylation properties of papain-like protease was investigated using a fluorescence method and gel shift analysis determining its inhibitory effects.\n\nThe inhibitory effect of Losartan on SARS-CoV-2 cell replication was investigated both when losartan was added to the cell culture 1 hour before (pre-infection group) and 1 hour after (post-infection group) SARS-CoV-2 infection of Vero E6 cells.\n\nResultsLosartan treatment of Vero E6 cells prior to and after SARS-CoV-2 infection reduced SARS-CoV-2 replication by 80% and 70% respectively. Losartan was not a strong deubiquitinase and deISGylase inhibitor of PLpro.\n\nConclusionLosartan added pre- and post-infection to the Vero E6 cell culture significantly prevents cell destruction and replication by SARS-CoV2. Losartan has low side-effects, is readily available, and can be produced at high levels globally, all features of a promising drug in treatment of COVID-19 if validated by clinical trials.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Reza Nejat", - "author_inst": "Bazarganan Hospital" - }, - { - "author_name": "Ahmad Shahir Sadr", - "author_inst": "Cheragh Medical Institute and Hospital" - }, - { - "author_name": "Brendan T. Freitas", - "author_inst": "University of Georgia, Athens, Georgia 30602, USA" - }, - { - "author_name": "Jackelyn Crabtree", - "author_inst": "University of Georgia, Athens, Georgia 30602, USA" - }, - { - "author_name": "Scott D. Pegan", - "author_inst": "University of Georgia, Athens, Georgia 30602, USA" - }, - { - "author_name": "Ralph A. Tripp", - "author_inst": "University of Georgia, Athens, Georgia 30602, USA" - }, - { - "author_name": "David J. Najafi", - "author_inst": "alliance retina consultants" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.12.28.424554", "rel_title": "Human neutralizing antibodies against SARS-CoV-2 require intact Fc effector functions and monocytes for optimal therapeutic protection", @@ -1009218,6 +1011662,49 @@ "type": "confirmatory results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2020.12.26.424429", + "rel_title": "Analysis and Forecasting of Global of RT-PCR Primers for SARS-CoV-2", + "rel_date": "2020-12-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.26.424429", + "rel_abs": "Rapid tests for active SARS-CoV-2 infections rely on reverse transcription polymerase chain reaction (RT-PCR). RT-PCR uses reverse transcription of RNA into complementary DNA (cDNA) and amplification of specific DNA (primer and probe) targets using polymerase chain reaction (PCR). The technology makes rapid and specific identification of the virus possible based on sequence homology of nucleic acid sequence and is much faster than tissue culture or animal cell models. However the technique can lose sensitivity over time as the virus evolves and the target sequences diverge from the selective primer sequences. Different primer sequences have been adopted in different geographic regions. As we rely on these existing RT-PCR primers to track and manage the spread of the Coronavirus, it is imperative to understand how SARS-CoV-2 mutations, over time and geographically, diverge from existing primers used today. In this study, we analyze the performance of the SARS-CoV-2 primers in use today by measuring the number of mismatches between primer sequence and genome targets over time and spatially. We find that there is a growing number of mismatches, an increase by 2% per month, as well as a high specificity of virus based on geographic location.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Gowri Nayar", + "author_inst": "IBM Research" + }, + { + "author_name": "Ed Seabolt", + "author_inst": "IBM Research" + }, + { + "author_name": "Mark Kunitomi", + "author_inst": "IBM Research" + }, + { + "author_name": "Akshay Agarwal", + "author_inst": "IBM Research" + }, + { + "author_name": "Kristen L. Beck", + "author_inst": "IBM Research" + }, + { + "author_name": "Vandana Mukherjee", + "author_inst": "IBM Research" + }, + { + "author_name": "James Kaufman", + "author_inst": "IBM Research" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.12.28.424533", "rel_title": "Rapid inactivation in vitro of SARS-CoV-2 in saliva by black tea and green tea", @@ -1010721,53 +1013208,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.12.23.424231", - "rel_title": "Genomic diversity of SARS-CoV-2 can be accelerated by a mutation in the nsp14 gene", - "rel_date": "2020-12-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.23.424231", - "rel_abs": "Coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), encode a proofreading exonuclease, nonstructural protein 14 (nsp14), that helps ensure replication competence at a low evolutionary rate compared with other RNA viruses. In the current pandemic, SARS-CoV-2 has accumulated diverse genomic mutations including in nsp14. Here, to clarify whether amino acid substitutions in nsp14 affect the genomic diversity and evolution of SARS-CoV-2, we searched for amino acid substitutions in nature that may interfere with nsp14 function. We found that viruses carrying a proline-to-leucine change at position 203 (P203L) have a high evolutionary rate and that a recombinant SARS-CoV-2 virus with the P203L mutation acquired more diverse genomic mutations than wild-type virus during its replication in hamsters. Our findings suggest that substitutions, such as P203L, in nsp14 may accelerate the genomic diversity of SARS-CoV-2, contributing to virus evolution during the pandemic.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Kosuke Takada", - "author_inst": "Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Mahoko Takahashi Ueda", - "author_inst": "Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University" - }, - { - "author_name": "Shintaro Shichinohe", - "author_inst": "Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Yurie Kida", - "author_inst": "Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Chikako Ono", - "author_inst": "Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Yoshiharu Matsuura", - "author_inst": "Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Tokiko Watanabe", - "author_inst": "Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "So Nakagawa", - "author_inst": "Department of Molecular Life Science, Tokai University School of Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.12.23.424283", "rel_title": "The SARS-CoV-2 S1 spike protein mutation N501Y alters the protein interactions with both hACE2 and human derived antibody: A Free energy of perturbation study", @@ -1010936,6 +1013376,61 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.12.26.424442", + "rel_title": "Establishment of a well-characterized SARS-CoV-2 lentiviral pseudovirus neutralization assay using 293T cells with stable expression of ACE2 and TMPRSS2", + "rel_date": "2020-12-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.26.424442", + "rel_abs": "Pseudoviruses are useful surrogates for highly pathogenic viruses because of their safety, genetic stability, and scalability for screening assays. Many different pseudovirus platforms exist, each with different advantages and limitations. Here we report our efforts to optimize and characterize an HIV-based lentiviral pseudovirus assay for screening neutralizing antibodies for SARS-CoV-2 using a stable 293T cell line expressing human angiotensin converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). We assessed different target cells, established conditions that generate readouts over at least a two-log range, and confirmed consistent neutralization titers over a range of pseudovirus input. Using reference sera and plasma panels, we evaluated assay precision and showed that our neutralization titers correlate well with results reported in other assays. Overall, our lentiviral assay is relatively simple, scalable, and suitable for a variety of SARS-CoV-2 entry and neutralization screening assays.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Sabari Nath Neerukonda", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Russell Vassell", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Rachel Herrup", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Shufeng Liu", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Tony Wang", + "author_inst": "U.S. Food and Drug Administration" + }, + { + "author_name": "Kazuyo Takeda", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Ye Yang", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Tsai-Lien Lin", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Wei Wang", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Carol D. Weiss", + "author_inst": "US Food and Drug Administration" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.26.424422", "rel_title": "Extensive High-Order Complexes within SARS-CoV-2 Proteome Revealed by Compartmentalization-Aided Interaction Screening", @@ -1012531,105 +1015026,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.12.23.20248612", - "rel_title": "Coronavirus GenBrowser for monitoring adaptive evolution and transmission of SARS-CoV-2", - "rel_date": "2020-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.23.20248612", - "rel_abs": "Genomic epidemiology is important to study the COVID-19 pandemic and more than two million SARS-CoV-2 genomic sequences were deposited into public databases. However, the exponential increase of sequences invokes unprecedented bioinformatic challenges. Here, we present the Coronavirus GenBrowser (CGB) based on a highly efficient analysis framework and a movie maker strategy. In total, 1,002,739 high quality genomic sequences with the transmission-related metadata were analyzed and visualized. The size of the core data file is only 12.20 MB, efficient for clean data sharing. Quick visualization modules and rich interactive operations are provided to explore the annotated SARS-CoV-2 evolutionary tree. CGB binary nomenclature is proposed to name each internal lineage. The pre-analyzed data can be filtered out according to the user-defined criteria to explore the transmission of SARS-CoV-2. Different evolutionary analyses can also be easily performed, such as the detection of accelerated evolution and on-going positive selection. Moreover, the 75 genomic spots conserved in SARS-CoV-2 but non-conserved in other coronaviruses were identified, which may indicate the functional elements specifically important for SARS-CoV-2. The CGB not only enables users who have no programming skills to analyze millions of genomic sequences, but also offers a panoramic vision of the transmission and evolution of SARS-CoV-2.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Dalang Yu", - "author_inst": "Shanghai Institute of Nutrition and Health" - }, - { - "author_name": "Xiao Yang", - "author_inst": "Shanghai Institute of Nutrition and Health" - }, - { - "author_name": "Bixia Tang", - "author_inst": "Beijing Institute of Genomics (China National Center for Bioinformation)" - }, - { - "author_name": "Yi-Hsuan Pan", - "author_inst": "East China Normal University" - }, - { - "author_name": "Jianing Yang", - "author_inst": "Shanghai Institute of Nutrition and Health" - }, - { - "author_name": "Guangya Duan", - "author_inst": "Beijing Institute of Genomics (China National Center for Bioinformation)" - }, - { - "author_name": "Junwei Zhu", - "author_inst": "Beijing Institute of Genomics (China National Center for Bioinformation)" - }, - { - "author_name": "Zi-Qian Hao", - "author_inst": "Shanghai Institute of Nutrition and Health" - }, - { - "author_name": "Hailong Mu", - "author_inst": "Shanghai Institute of Nutrition and Health" - }, - { - "author_name": "Long Dai", - "author_inst": "Shanghai Institute of Nutrition and Health" - }, - { - "author_name": "Wangjie Hu", - "author_inst": "Shanghai Institute of Nutrition and Health" - }, - { - "author_name": "Mochen Zhang", - "author_inst": "Beijing Institute of Genomics (China National Center for Bioinformation)" - }, - { - "author_name": "Ying Cui", - "author_inst": "Beijing Institute of Genomics (China National Center for Bioinformation)" - }, - { - "author_name": "Tong Jin", - "author_inst": "Beijing Institute of Genomics (China National Center for Bioinformation)" - }, - { - "author_name": "Cuiping Li", - "author_inst": "Beijing Institute of Genomics (China National Center for Bioinformation)" - }, - { - "author_name": "Lina Ma", - "author_inst": "Beijing Institute of Genomics (China National Center for Bioinformation)" - }, - { - "author_name": "- Language translation team", - "author_inst": "" - }, - { - "author_name": "Xiao Su", - "author_inst": "Institut Pasteur of Shanghai" - }, - { - "author_name": "Guo-Qing Zhang", - "author_inst": "Shanghai Institute of Nutrition and Health" - }, - { - "author_name": "Wenming Zhao", - "author_inst": "Beijing Institute of Genomics (China National Center for Bioinformation)" - }, - { - "author_name": "Haipeng Li", - "author_inst": "Shanghai Institute of Nutrition and Health" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.12.17.20248360", "rel_title": "Identifying communities at risk for COVID-19-related burden across 500 U.S. Cities and within New York City", @@ -1012882,6 +1015278,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.22.20223651", + "rel_title": "Toward a COVID-19 testing policy: where and how to test when the purpose is to isolate silent spreaders", + "rel_date": "2020-12-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.22.20223651", + "rel_abs": "BackgroundTo stop pandemics, such as COVID-19, infected individuals should be detected, treated if needed, and -to prevent contacts with susceptible individuals-isolated. Because most infected individuals may be asymptomatic, when testing misses such cases, epidemics may growth exponentially, inducing a high number of deaths. In contrast, a relatively low number of COVID-19 related deaths may occur when both symptomatic and asymptomatic cases are tested.\n\nMethodsTo evaluate these hypotheses, a method composed of three elements was evaluated, which included: (i) county- and country-level geo-referenced data, (ii) cost-benefit related considerations, and (iii) temporal data on mortality or test positivity (TP). TP is the percentage of infections found among tested individuals. Temporal TP data were compared to the tests/case ratio (T/C ratio) as well as the number of tests performed/million inhabitants (tests/mi) and COVID-19 related deaths/million inhabitants (deaths/mi).\n\nFindingsTwo temporal TP profiles were distinguished, which, early, displayed low ([~] 1 %) and/or decreasing TP percentages or the opposite pattern, respectively. Countries that exhibited >10 TP % expressed at least ten times more COVID-19 related deaths/mi than low TP countries. An intermediate pattern was identified when the T/C ratio was explored. Geo-referenced, TP-based analysis discovered municipalities where selective testing would be more cost-effective than alternatives.\n\nInterpretationsWhen TP is low and/or the T/C ratio is high, testing detects asymptomatic cases and the number of COVID-19 related deaths/mi is low. Geo-referenced TP data can support cost-effective, site-specific policies. TP promotes the prompt cessation of epidemics and fosters science-based testing policies.\n\nFundingNone\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSTo map this field, bibliographic searches were conducted in the Web of Science, which included the following results: (i) COVID-19 (95,133 hits), (ii) SARS COV-2 (33,680 hits), (iii) testing policy and COVID-19 (939 hits), (iv) testing policy and SARS COV-2 (340 hits), (v) testing policy and COVID-19 and asymptomatic (80 hits), (vi) testing policy and SARS COV-2 and asymptomatic (54 hits); (vii) test positivity and COVID-19 and validation (7 hits), and (viii) test positivity and SARS CoV-2 and validation (5 hits). Therefore, before this study, testing policy in relation to asymptomatic cases as well as test positivity represented a very low proportion (between [~]1 thousandth to [~] 1 ten thousandth) of all publications. While many articles distinguished between diagnostic and screening tests, no paper was found in which testing policy is mentioned as part of a process ultimately designed to isolate all infected individuals. The few articles that mentioned test positivity only investigated symptomatic cases. These quanti/qualitative assessments led the authors to infer that neither testing policy nor test positivity had been adequately validated and/or investigated.\n\nAdded value of this studyWe provide the first validation of test positivity as an estimate of disease prevalence under rapidly changing conditions: in pandemics, disease prevalence may vary markedly within short periods of time. We also address a double limitation of control campaigns against COVID-19, namely: it is unknown who and where to test. Asymptomatic cases are not likely to seek medical assistance: while they feel well, they silently spread this pandemic. Because they represent approximately half of all infected individuals, they are a large, moving, and invisible target. Where to find them is also unknown because (i) randomized testing is likely to fail and (ii) testing is very limited. Usually, the locations where infected people reside are not randomly distributed but geographically clustered, and, up to now less than four persons per thousand inhabitants are tested on a given day. However, by combining geo-referenced test positivity data with cost-benefit considerations, we generate approaches not only likely to induce high benefits without increasing costs but also free of assumptions: we measure bio-geography as it is.\n\nImplications of all the available evidenceThe fact that asymptomatic cases were not tested in many countries may explain the exponential growth and much higher number of deaths observed in those countries. Ineffective testing (and, therefore, ineffective isolation) can also result from the absence of geo-referenced data analysis. Because the geographical location where people reside, work, study, or shop is not a random event, the analysis of small greographical areas is essential. Only when actual geographical relationships are observed, optimal (cost-benefit oriented) testing policies can be devised.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ariel L Rivas", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Almira L Hoogesteijn", + "author_inst": "Centro de Investigacion y de Estudios Avanzados (CINVESTAV), Merida, Mexico" + }, + { + "author_name": "James Hittner", + "author_inst": "College of Charleston" + }, + { + "author_name": "Marc HV van Regenmortel", + "author_inst": "University of Vienna, Austria; and Higher School of Biotechnology, University of Strasbourg, France & French National Research Center (CNRS), France" + }, + { + "author_name": "Prakasha Kempaiah", + "author_inst": "Loyola University Stritch School of Medicine" + }, + { + "author_name": "Paris Vogazianos", + "author_inst": "European University, Cyprus & Stremble Ventures LTD, Limassol, Cyprus" + }, + { + "author_name": "Athos Antoniades", + "author_inst": "Stremble Ventures LTD, Limassol, Cyprus" + }, + { + "author_name": "Jose PL Febles", + "author_inst": "Centro de Investigacion y de Estudios Avanzados (CINVESTAV), Merida, Mexico" + }, + { + "author_name": "Folorunso Oludayo Fasina", + "author_inst": "Food and Agriculture Organization of the United Nations" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.22.20248741", "rel_title": "Analysis of genome characteristics and transmission of SARS-CoV-2 strains in North-East of Romania during the first COVID-19 outbreak", @@ -1014261,20 +1016708,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2020.12.24.424322", - "rel_title": "Inferring Toll-Like Receptor induced epitope subunit vaccine candidate against SARS-CoV-2: A Reverse Vaccinology approach", - "rel_date": "2020-12-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.24.424322", - "rel_abs": "Toll-Like Receptors (TLRs) are a group of Pattern Recognition Receptors (PRRs) which bind to the exogenous pathogen associated molecular patterns (PAMPs) like other PRRs; hence the main function is to sense the harmness and mediate the innate immune response to pathogens. TLRs play an important role in innate immune responses to infection. The host has evolved to use other TLR and PAMP agonists as agents to stimulate a protective inflammatory immune response against infection. Because only a small number of doses are given, TLR agonists appear to have greater potential and fewer safety concerns than other uses as vaccine adjuvants. In the present days, development of peptides targeting immune response can be approved for survival in biological monitoring systems before vaccine exposures. Peptide vaccines are easy to synthesize, more stable and relatively safe. In addition, production of peptides becomes simple, easily reproducible, fast and cost effective. Getting vaccinated against Covid-19, which has become a pandemic in the human population, is the most practical way to control the outbreak. The new coronavirus does not contain a drug or vaccine to prevent it from spreading to humans. To getting a proper vaccine candidate against the novel coronavirus, the present study used the reverse vaccinology approach by using a complete set of SARS-CoV-2 proteins; such as: Spike, Envelope, Nucleocapsid, Membrane, NSPs, and ORFs to extract the antigenic elements that produce B-cell, T-cell and IFN positive epitopes. These epitopes with precise binding to the Toll-Like receptors (1-10) have developed epitope based vaccine candidates. We have prioritized a set of epitopes based on their antigenicity, allergenicity, sequence conservation and projected population coverage world-wide. The selected epitopes were employed for in-silico docking interactions with Toll-Like receptors and molecular dynamic simulation confirmed the stability of the vaccine candidates resulting epitope of spike proteins with both the TLR 7 and 8 shows the best binding affinity. We believe that this ideal epitope vaccine candidate could enhance the immune response of the host and reduce the reinfection risk.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.12.23.424232", "rel_title": "Remdesivir-Ivermectin combination displays synergistic interaction with improved in vitro antiviral activity against SARS-CoV-2", @@ -1014515,6 +1016948,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.23.424177", + "rel_title": "Identification of COVID-19-relevant transcriptional regulatory networks and associated kinases as potential therapeutic targets", + "rel_date": "2020-12-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.23.424177", + "rel_abs": "Identification of transcriptional regulatory mechanisms and signaling networks involved in the response of host to infection by SARS-CoV-2 is a powerful approach that provides a systems biology view of gene expression programs involved in COVID-19 and may enable identification of novel therapeutic targets and strategies to mitigate the impact of this disease. In this study, we combined a series of recently developed computational tools to identify transcriptional regulatory networks involved in the response of epithelial cells to infection by SARS-CoV-2, and particularly regulatory mechanisms that are specific to this virus. In addition, using network-guided analyses, we identified signaling pathways that are associated with these networks and kinases that may regulate them. The results identified classical antiviral response pathways including Interferon response factors (IRFs), interferons (IFNs), and JAK-STAT signaling as key elements upregulated by SARS-CoV-2 in comparison to mock-treated cells. In addition, comparing SARS-Cov-2 infection of airway epithelial cells to other respiratory viruses identified pathways associated with regulation of inflammation (MAPK14) and immunity (BTK, MBX) that may contribute to exacerbate organ damage linked with complications of COVID-19. The regulatory networks identified herein reflect a combination of experimentally validated hits and novel pathways supporting the computational pipeline to quickly narrow down promising avenue of investigations when facing an emerging and novel disease such as COVID-19.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Chen Su", + "author_inst": "McGill University" + }, + { + "author_name": "Simon Rousseau", + "author_inst": "McGill University & The Research Institute of the McGill University Health Centre" + }, + { + "author_name": "Amin Emad", + "author_inst": "McGill University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2020.12.22.423940", "rel_title": "No evidence for human monocyte-derived macrophage infection and antibody-mediated enhancement of SARS-CoV-2 infection", @@ -1016118,45 +1018578,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.18.20248499", - "rel_title": "Mental Disorder Prevalence Among Populations Impacted by Coronavirus Pandemics: A Multilevel Meta-Analytic Study of COVID-19, MERS & SARS", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248499", - "rel_abs": "ObjectiveThrough a systematic review and meta-analysis of research on COVID-19, severe acute respiratory syndrome (SARS) and middle east respiratory syndrome (MERS) pandemics, we investigated whether mental disorder prevalence: (a) was elevated among populations impacted by coronavirus pandemics (relative to unselected populations reported in the literature), and (b) varied by disorder (undifferentiated psychiatric morbidity, anxiety, depressive, posttraumatic stress disorders [PTSD]) and impacted population (community, infected/recovered, healthcare provider, quarantined).\n\nMethodFrom 68 publications (N=87,586 participants), 808 estimates were included in a series of multilevel meta-analyses/regressions including random effects to account for estimates nested within studies.\n\nResultsMedian summary point prevalence estimates varied by disorder and population. Psychiatric morbidity (20%-56%), PTSD (10-26%) and depression (9-27%) were most prevalent in most populations. The highest prevalence of each disorder was found among infected/recovered adults (18-56%), followed by healthcare providers (11-28%) and community adults (11-20%). Prevalence estimates were often notably higher than reported for unselected samples. Sensitivity analyses demonstrated that overall prevalence estimates moderately varied by pandemic, study location, and mental disorder measure type.\n\nConclusionCoronavirus pandemics are associated with multiple mental disorders in several impacted populations. Needed are investigations of causal links between specific pandemic-related stressors, threats, and traumas and mental disorders.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Matthew Boden", - "author_inst": "VA Palo Alto Health Care System Menlo Park Division" - }, - { - "author_name": "Nicole Cohen", - "author_inst": "University of Kansas" - }, - { - "author_name": "Jessilyn Froelich", - "author_inst": "VA Palo Alto Healthcare System" - }, - { - "author_name": "Katherine Hoggatt", - "author_inst": "San Francisco VA Medical Center" - }, - { - "author_name": "Hoda Abdel Magid", - "author_inst": "Stanford University" - }, - { - "author_name": "Swapandeep Mushiana", - "author_inst": "University of San Francisco" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.12.16.423122", "rel_title": "Immune-Based Prediction of COVID-19 Severity and Chronicity Decoded Using Machine Learning", @@ -1016353,6 +1018774,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.12.20.423682", + "rel_title": "Analysis of 46,046 SARS-CoV-2 whole-genomes leveraging principal component analysis (PCA)", + "rel_date": "2020-12-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.20.423682", + "rel_abs": "Since the beginning of the global SARS-CoV-2 pandemic, there have been a number of efforts to understand the mutations and clusters of genetic lines of the SARS-CoV-2 virus. Until now, phylogenetic analysis methods have been used for this purpose. Here we show that Principal Component Analysis (PCA), which is widely used in population genetics, can not only help us to understand existing findings about the mutation processes of the virus, but can also provide even deeper insights into these processes while being less sensitive to sequencing gaps. Here we describe a comprehensive analysis of a 46,046 SARS-CoV-2 genome sequence dataset downloaded from the GISAID database in June of this year.\n\nSummaryPCA provides deep insights into the analysis of large data sets of SARS-CoV-2 genomes, revealing virus lineages that have thus far been unnoticed.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Christiane Scherer", + "author_inst": "Evangelisches Klinikum Bethel" + }, + { + "author_name": "James Grover", + "author_inst": "Golden Helix Inc, Bozeman, Montana, United States" + }, + { + "author_name": "Darby Kameraad", + "author_inst": "Golden Helix, Inc, Bozeman, Montana, United States" + }, + { + "author_name": "Gabe Rudy", + "author_inst": "Golden Helix, Inc, Bozeman, Montana, United States" + }, + { + "author_name": "Andreas Scherer", + "author_inst": "Golden Helix, Inc, Bozeman, Montana, United States" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.12.20.20248572", "rel_title": "An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility", @@ -1017680,25 +1020136,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.21.20248605", - "rel_title": "Modeling the flow of the COVID-19 in Germany: The cohort SEIR model based on the system dynamics approach", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248605", - "rel_abs": "This study develops a computer simulation in understanding the flow of the COVID-19 in Germany between January 2020 and July 2020. This aims to analyze not only the flow of the COVID-19 but also the efficacy of taken measures during the given period. The computer model is based on the SEIR concept and it is based on the system dynamics approach in which some uncertain parameters are estimated through the calibration process. Moreover, the SEIR computer model is developed by considering different flows of COVID-19 cases in older and young people in Germany. This study successfully reproduces similar patterns of infected, recovered, and death cases. Moreover, as the SEIR model can successfully reproduce similar patterns, the SEIR model can be a basis to estimate other resources such as health workers, and bed capacities.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Muhamad Khairulbahri", - "author_inst": "Bandung Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.20.20248581", "rel_title": "Early empirical assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020", @@ -1017915,6 +1020352,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.12.21.20248607", + "rel_title": "Time use and social mixing during and around festive periods: Potential changes in the age distribution of COVID-19 cases from increased intergenerational interactions", + "rel_date": "2020-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248607", + "rel_abs": "RationaleAmid the ongoing coronavirus disease 2019 (COVID-19) pandemic in which many countries have adopted physical distancing measures, tiered restrictions, and episodic \"lockdowns,\" the impact of potentially increased social mixing during festive holidays on the age distribution of new COVID-19 cases remains unclear.\n\nObjectiveWe aimed to gain insights into possible changes in the age distribution of COVID-19 cases in the UK after temporarily increased intergenerational interactions in late December 2020.\n\nMethodWe modelled changes in time use and social mixing based on age-stratified contact rates using historical nationally-representative surveys and up-to-date Google mobility data from four weeks before and after the festive period. We explored changes in the effective reproduction number and the age distribution of cases, in four scenarios: (1) \"normal\": time use and contact patterns as observed historically, (2) \"pre-lockdown\": patterns as seen before the lockdown in November 2020, (3) \"lockdown\": patterns restricted as in November 2020, and (4) \"festive break\": similar to 3 but with social visits over the holiday period as in 1.\n\nResultsAcross ages, the estimated Reff decreases during the festive break in scenarios 1-3 and returns to pre-holiday levels in scenarios 2-3, while remaining relatively stable in scenario 4. Relative incidence is likely to decrease in children aged 0-15 but increase in other ages. Changes in age distribution were large during the holidays, and are likely to start before the holidays for individuals aged 16-24 years in scenarios 1-3.\n\nConclusionsOur modelling findings suggest that increased contacts during the festive period may shift the age distribution of COVID-19 cases from children towards adults. Given that COVID-19-related hospitalisations and deaths rise by age, more intergenerational mixing risks an increased burden in the period following the holidays.\n\nHighlightsO_LIHome visits are associated with increased intergenerational mixing.\nC_LIO_LIThe effective reproduction number is likely to remain stable or even reduce slightly due to a reduction in contacts at work and school.\nC_LIO_LIRelative incidence is likely to become lower in children, but higher in the\nC_LIO_LIolder (more vulnerable) age groups around the holiday period, which could lead to increased health care burden.\nC_LI", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Edwin van Leeuwen", + "author_inst": "Public Health England" + }, + { + "author_name": "Frank G. Sandmann", + "author_inst": "Public Health England; London School of Hygiene &Tropical Medicine" + }, + { + "author_name": "Rosalind M. Eggo", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "- PHE Joint modelling group", + "author_inst": "" + }, + { + "author_name": "Peter J. White", + "author_inst": "Public Health England; Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.21.20248467", "rel_title": "Experiences of the COVID-19 pandemic: cross-sectional analysis of risk perceptions and mental health in a student cohort", @@ -1019790,37 +1022262,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.21.20248621", - "rel_title": "A Systematic Review and Network Meta-Analysis for COVID-19 Treatments", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248621", - "rel_abs": "BackgroundNumerous interventions for coronavirus disease 2019 (COVID-19) have been investigated by randomized controlled trials (RCTs). This systematic review and Bayesian network meta-analysis (NMA) aim to provide a comprehensive evaluation of efficacy of available treatments for COVID-19.\n\nMethodsWe searched for candidate COVID-19 studies in WHO COVID-19 Global Research Database, PubMed, PubMed Central, LitCovid, Proquest Central and Ovid up to December 19, 2020. RCTs for suspected or confirmed COVID-19 patients were included, regardless of publication status or demographic characteristics. Bayesian NMA with fixed effects was conducted to estimate the effect sizes using posterior means and 95% equal-tailed credible intervals (CrIs), while that with random effects was carried out as well for sensitivity analysis. Bayesian hierarchical models were used to estimate effect sizes of treatments grouped by their drug classifications.\n\nResultsWe identified 96 eligible RCTs with a total of 51187 patients. Compared with the standard of care (SOC), this NMA showed that dexamethasone led to lower risk of mortality with an odds ratio (OR) of 0.85 (95% CrI [0.76, 0.95]; moderate certainty) and lower risk of mechanical ventilation (MV) with an OR of 0.68 (95% CrI [0.56, 0.83]; low certainty). For hospital discharge, remdesivir (OR 1.37, 95% CrI [1.15, 1.64]; moderate certainty), dexamethasone (OR 1.20, 95% CrI [1.08, 1.34]; low certainty), interferon beta (OR 2.15, 95% CrI [1.26, 3.74]; moderate certainty), tocilizumab (OR 1.40, 95% CrI [1.05, 1.89]; moderate certainty) and baricitinib plus remdesivir (OR 1.75, 95% CrI [1.28, 2.39]; moderate certainty) could all increase the discharge rate respectively. Recombinant human granulocyte colony-stimulating factor indicated lower risk of MV (OR 0.20, 95% CrI [0.10, 0.40]; moderate certainty); and patients receiving convalescent plasma resulted in better viral clearance (OR 2.28, 95% CrI [1.57, 3.34]; low certainty). About two-thirds of the studies included in this NMA were rated as high risk of bias, and the certainty of evidence was either low or very low for most of the comparisons.\n\nConclusionThe Bayesian NMA identified superiority of several COVID-19 treatments over SOC in terms of mortality, requirement of MV, hospital discharge and viral clearance. These results provide a comprehensive comparison of current COVID-19 treatments and shed new light on further research and discovery of potential COVID-19 treatments.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Chenyang Zhang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Huaqing Jin", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Yifeng Wen", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Guosheng Yin", - "author_inst": "The University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.21.20248288", "rel_title": "Comparative analysis of loop-mediated isothermal amplification (LAMP)-based assays for rapid detection of SARS-CoV-2 genes", @@ -1020017,6 +1022458,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.19.20248513", + "rel_title": "Clustering and longitudinal change in SARS-CoV-2 seroprevalence in school-children: prospective cohort study of 55 schools in Switzerland", + "rel_date": "2020-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.19.20248513", + "rel_abs": "Background and aimsThe facilitating role of schools in SARS-CoV-2 infection spread is still debated and the potential of school closures to mitigate transmission unclear. In autumn 2020, Switzerland experienced one of the highest second waves of the SARS-CoV-2 pandemic in Europe while keeping schools open, thus offering a high-exposure environment to study SARS-CoV-2 infections in schools. The aim of this study was to examine longitudinal change in SARS-CoV-2 seroprevalence in children and the evolution of clustering within classes and schools from June to November, 2020, in a prospective cohort study of school children in the canton of Zurich, Switzerland.\n\nMethodsChildren from randomly selected schools and classes, stratified by district, were invited to participate in serological testing of SARS-CoV-2 in June-July and October-November 2020. Parents of children filled questionnaires on sociodemographic and health-related questions. 55 schools and 275 classes within them were enrolled, with 2603 children participating in the first, and 2552 in the second testing (age range 6-16 years). We evaluated longitudinal changes of seroprevalence in districts and investigated clustering of seropositive cases within classes and schools.\n\nResultsOverall SARS-CoV-2 seroprevalence was 2.4% (95% CrI 1.4%-3.6%) in summer and 4.5% (95% CrI 3.2%-6.0%) in not previously seropositive children in late autumn, leading to estimated 7.8% (95% CrI 6.2%-9.5%) of ever seropositive children, without significant differences among lower, middle and upper school levels. Among the 2223 children with serology tested twice, 28 (40%) of previously seropositive were negative, and 109 (5%) previously negative became seropositive. Seroprevalence was not different between school levels or sexes, but varied across districts (1.7% to 15.0%). Between June-July and October-November 2020, the ratio of diagnosed to newly seropositive children was 1 to 8. At least one newly seropositive child was detected in 47 of 55 schools and 90 of 275 classes. Among 130 classes with high participation rate, 0, 1-2 or [≥]3 seropositive children were present in 73 (56%), 50 (38%) and 7 (5%) classes, respectively. Class level explained slightly more variation of individual serological results (standard deviation of random effects (SD) 0.97) than school level (SD 0.61) in the multilevel logistic regression models. Symptoms were reported for 22% of seronegative and 29% of newly seropositive children since summer.\n\nConclusionsUnder a regimen of open schools with some preventive measures in place since August, clustering of seropositive cases occurred in very few classes and not across entire schools despite a clear increase in seropositive children during a period of high transmission of SARS-CoV-2.\n\nTrial registrationClinicalTrials.gov NCT04448717. https://clinicaltrials.gov/ct2/show/NCT04448717", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Agne Ulyte", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Thomas Radtke", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Irene A Abela", + "author_inst": "Institute of Medical Virology, University of Zurich" + }, + { + "author_name": "Sarah R Haile", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Christoph Berger", + "author_inst": "University Children Hospital Zurich" + }, + { + "author_name": "Michael Huber", + "author_inst": "Institute of Medical Virology, University of Zurich" + }, + { + "author_name": "Merle Schanz", + "author_inst": "Institute of Medical Virology, University of Zurich" + }, + { + "author_name": "Magdalena Schwarzmueller", + "author_inst": "Institute of Medical Virology, University of Zurich" + }, + { + "author_name": "Alexandra Trkola", + "author_inst": "Institute of Medical Virology, University of Zurich" + }, + { + "author_name": "Jan Fehr", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich; Division of Infectious Diseases & Hospital Epidemiology, University Hospital " + }, + { + "author_name": "Milo A. Puhan", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Susi Kriemler", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.22.20248604", "rel_title": "A longitudinal seroprevalence study in a large cohort of working adults reveals that neutralising SARS-CoV-2 RBD-specific antibodies persist for at least six months independent of the severity of symptoms", @@ -1021712,69 +1024216,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.12.20.422693", - "rel_title": "A recombinant protein SARS-CoV-2 candidate vaccine elicits high-titer neutralizing antibodies in macaques.", - "rel_date": "2020-12-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.20.422693", - "rel_abs": "Vaccines that generate robust and long-lived protective immunity against SARS-CoV-2 infection are urgently required. We assessed the potential of vaccine candidates based on the SARS-CoV-2 spike in cynomolgus macaques (M. fascicularis) by examining their ability to generate spike binding antibodies with neutralizing activity. Antigens were derived from two distinct regions of the spike S1 subunit, either the N-terminal domain (NTD) or an extended C-terminal domain containing the receptor-binding domain (RBD) and were fused to the human IgG1 Fc domain. Three groups of 2 animals each were immunized with either antigen, alone or in combination. The development of antibody responses was evaluated through 20 weeks post-immunization. A robust IgG response to the spike protein was detected as early as 2 weeks after immunization with either protein and maintained for over 20 weeks. Sera from animals immunized with antigens derived from the RBD were able to prevent binding of soluble spike proteins to the ACE2 receptor, shown by in vitro binding assays, while sera from animals immunized with the NTD alone lacked this activity. Crucially, sera from animals immunized with the RBD but not the NTD had potent neutralizing activity against SARS-CoV-2 pseudotyped virus, with titers in excess of 10,000, greatly exceeding that typically found in convalescent humans. Neutralizing activity persisted for more than 20 weeks. These data support the utility of spike subunit-based antigens as a vaccine for use in humans.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Gary Baisa", - "author_inst": "Intuitive Biosciences, Inc." - }, - { - "author_name": "David Rancour", - "author_inst": "Lytic Solutions" - }, - { - "author_name": "Keith Mansfield", - "author_inst": "Novartis Institutes for Biomedical Research" - }, - { - "author_name": "Monika Burns", - "author_inst": "Novartis Institutes for Biomedical Research" - }, - { - "author_name": "Lori Martin", - "author_inst": "Novartis Institutes for Biomedical Research" - }, - { - "author_name": "Daise Cunha", - "author_inst": "Covance Greenfield Laboratories" - }, - { - "author_name": "Jessica Fischer", - "author_inst": "Covance Greenfield Laboratories" - }, - { - "author_name": "Frauke Muecksch", - "author_inst": "Laboratory of Retrovirology, The Rockefeller University" - }, - { - "author_name": "Theodora Hatziioannou", - "author_inst": "Laboratory of Retrovirology, The Rockefeller University" - }, - { - "author_name": "Paul Bieniasz", - "author_inst": "Howard Hughes Medical Institute, The Rockefeller University" - }, - { - "author_name": "Frtiz Schomburg", - "author_inst": "Lytic Solutions" - }, - { - "author_name": "Kimberly Luke", - "author_inst": "Intuitive Biosciences, Inc." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.12.20.423603", "rel_title": "Fatty Acid Synthase inhibition prevents palmitoylation of SARS-CoV2 SpikeProtein and improves survival of mice infected with murine hepatitis virus.", @@ -1021963,6 +1024404,161 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.12.20.423708", + "rel_title": "Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes in COVID-19 convalescent plasma", + "rel_date": "2020-12-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.20.423708", + "rel_abs": "Although humoral immunity is essential for control of SARS-CoV-2, the molecular composition, binding epitopes and effector functions of the immunoglobulin G (IgG) antibodies that circulate in blood plasma following infection are unknown. Proteomic deconvolution of the circulating IgG repertoire (Ig-Seq1) to the spike ectodomain (S-ECD2) in four convalescent study subjects revealed that the plasma response is oligoclonal and directed predominantly (>80%) to S-ECD epitopes that lie outside the receptor binding domain (RBD). When comparing antibodies directed to either the RBD, the N-terminal domain (NTD) or the S2 subunit (S2) in one subject, just four IgG lineages (1 anti-S2, 2 anti-NTD and 1 anti-RBD) accounted for 93.5% of the repertoire. Although the anti-RBD and one of the anti-NTD antibodies were equally potently neutralizing in vitro, we nonetheless found that the anti-NTD antibody was sufficient for protection to lethal viral challenge, either alone or in combination as a cocktail where it dominated the effect of the other plasma antibodies. We identified in vivo protective plasma anti-NTD antibodies in 3/4 subjects analyzed and discovered a shared class of antibodies targeting the NTD that utilize unmutated or near-germline IGHV1-24, the most electronegative IGHV gene in the human genome. Structural analysis revealed that binding to NTD is dominated by interactions with the heavy chain, accounting for 89% of the entire interfacial area, with germline residues uniquely encoded by IGHV1-24 contributing 20% (149 [A]2). Together with recent reports of germline IGHV1-24 antibodies isolated by B-cell cloning3,4 our data reveal a class of shared IgG antibodies that are readily observed in convalescent plasma and underscore the role of NTD-directed antibodies in protection against SARS-CoV-2 infection.", + "rel_num_authors": 35, + "rel_authors": [ + { + "author_name": "William N Voss", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Yixuan J Hou", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Nicole V Johnson", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Jin Eyun Kim", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "George Delidakis", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Andrew P Horton", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Foteini Bartzoka", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Chelsea J Paresi", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Yuri Tanno", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Shawn A Abbasi", + "author_inst": "U.S. Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Whitney Pickens", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Katia George", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Daniel R Boutz", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Dalton M Towers", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Jonathan R McDaniel", + "author_inst": "Biomedicine Design, Pfizer" + }, + { + "author_name": "Daniel Billick", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Jule Goike", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Lori Rowe", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Dhwani Batra", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Jan Pohl", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Justin Lee", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Shivaprakash Gangappa", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Suryaprakash Sambhara", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Michelle Gadush", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Nianshuang Wang", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Maria D Person", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Brent L Iverson", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Jimmy D Gollihar", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "John Dye", + "author_inst": "U.S. Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Andrew Herbert", + "author_inst": "U.S. Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Ralph S Baric", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Jason S McLellan", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "George Georgiou", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Jason J Lavinder", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Gregory C Ippolito", + "author_inst": "University of Texas at Austin" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.21.423787", "rel_title": "Binding strength and hydrogen bond numbers between Covid-19 RBD and HVR of antibody", @@ -1023445,85 +1026041,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2020.12.18.20248447", - "rel_title": "Epidemiological feature, viral shedding, and antibody seroconversion among asymptomatic carriers and symptomatic/ presymptomatic COVID-19 patients", - "rel_date": "2020-12-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248447", - "rel_abs": "Novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pandemic. However, data concerning the epidemiological features, viral shedding, and antibody dynamics between asymptomatic SARS-CoV-2 carriers and COVID-19 patients remain controversial. We enrolled 193 subjects infected with SARS-CoV-2 in Ningbo and Zhoushan, Zhejiang, China from January 21 to March 6, 2020. All subjects were followed up to monitor the dynamics of immunoglobulin M (IgM) and IgG against SARS-CoV-2. Of those, 31 were asymptomatic carriers, 149 were symptomatic patients, and 14 were presymptomatic patients. Compared to symptomatic patients, asymptomatic carriers were younger and had higher levels of white blood cell and lymphocyte, lower levels of C-reactive protein and viral load, and shorter viral shedding duration. Conversion of IgM from positive to negative was shorter in asymptomatic carriers than in COVID-19 patients (P=0.030). The proportion of those persistently seropositive for IgG was higher in COVID-19 patients than in asymptomatic carriers (P=0.037). Viral load was higher in symptomatic than presymptomatic patients. Viral shedding was longer in presymptomatic patients than in asymptomatic carriers. Conclusively, asymptomatic carriers have a higher antiviral immunity to clear SARS-CoV-2 than do symptomatic patients and this antiviral immunity is not contributable to humoral immunity.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Yi Chen", - "author_inst": "Ningbo Municipal center for disease control and prevention" - }, - { - "author_name": "Ping Li", - "author_inst": "Second Military Medical University" - }, - { - "author_name": "Yibo Ding", - "author_inst": "Second Military Medical University" - }, - { - "author_name": "Miao Liu", - "author_inst": "Center of Disease Control and Prevention of Putuo district, Zhoushan" - }, - { - "author_name": "Leijie Liu", - "author_inst": "Center of Disease Control and Prevention of Putuo district, Zhoushan" - }, - { - "author_name": "Bo Yi", - "author_inst": "Ningbo Municipal center for disease control and prevention" - }, - { - "author_name": "Ting Wu", - "author_inst": "Second Military Medical University" - }, - { - "author_name": "Hongjun Dong", - "author_inst": "Ningbo Municipal center for disease control and prevention" - }, - { - "author_name": "Xuying Lao", - "author_inst": "Ningbo Municipal center for disease control and prevention" - }, - { - "author_name": "Keqing Ding", - "author_inst": "Ningbo Municipal center for disease control and prevention" - }, - { - "author_name": "Haibo Wang", - "author_inst": "Ningbo Municipal center for disease control and prevention" - }, - { - "author_name": "Dongliang Zhang", - "author_inst": "Ningbo Municipal center for disease control and prevention" - }, - { - "author_name": "Xiaojie Tan", - "author_inst": "Second Military Medical University" - }, - { - "author_name": "Zhongfa Wang", - "author_inst": "Center of Disease Control and Prevention of Putuo district, Zhoushan" - }, - { - "author_name": "Guozhang Xu", - "author_inst": "Ningbo Municipal center for disease control and prevention" - }, - { - "author_name": "Guangwen Cao", - "author_inst": "Second Military Medical University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.18.423106", "rel_title": "Furin cleaves SARS-CoV-2 spike-glycoprotein at S1/S2 and S2'for viral fusion/entry: indirect role for TMPRSS2", @@ -1023860,6 +1026377,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.12.18.423509", + "rel_title": "Fast and scalable lipid nanoparticle formulation of niclosamide (nano NCM) effectively inhibits SARS-CoV-2 replication in vitro", + "rel_date": "2020-12-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.18.423509", + "rel_abs": "As exemplified by the COVID-19 pandemic, highly infective respiratory viruses can spread rapidly in the population because of lack of effective approaches to control viral replication and spread. Niclosamide (NCM) is an old anthelminthic drug (World Health Organization essential medicine list) with pleiotropic pharmacological activities. Several recent publications demonstrated that NCM has broad antiviral activities and potently inhibits viral replication, including replication of SARS-CoV-2, SARS-CoV, and dengue viruses. Unfortunately, NCM is almost completely insoluble in water, which limits its clinical use. We developed a highly scalable and cost-effective nanoparticle formulation of NCM (nano NCM) using only FDA-approved excipient and demonstrated potency against SARS-CoV-2 infection in cells (Vero E6 and ACE2-expressing lung epithelium cells). Our ultimate goal is to develop the nano NCM formulation for treatment of COVID-19 patients.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Guankui Wang", + "author_inst": "University of Colorado" + }, + { + "author_name": "Hanmant Gaikwad", + "author_inst": "University of Colorado" + }, + { + "author_name": "Mary K McCarthy", + "author_inst": "University of Colorado" + }, + { + "author_name": "Mercedes Gonzalez-Juarrero", + "author_inst": "Colorado State University" + }, + { + "author_name": "Yue Li", + "author_inst": "University of Colorado" + }, + { + "author_name": "Michael Armstrong", + "author_inst": "University of Colorado" + }, + { + "author_name": "Nichole Reisdorf", + "author_inst": "University of Colorado" + }, + { + "author_name": "Thomas E Morrison", + "author_inst": "University of Colorado" + }, + { + "author_name": "Dmitri Simberg", + "author_inst": "University of Colorado" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2020.12.18.423524", "rel_title": "Longitudinal omics in Syrian hamsters integrated with human data unravel complexity of moderate immune responses to SARS-CoV-2", @@ -1025183,25 +1027751,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.16.20248139", - "rel_title": "The Persistence of Vaccine Hesitancy: COVID-19 Vaccination Intention", - "rel_date": "2020-12-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.16.20248139", - "rel_abs": "Building public trust and willingness to vaccinate against COVID-19 is as important as developing an effective vaccine. However, a significant minority of the public are unwilling or hesitant to take a COVID-19 vaccine, when available. A nationally representative sample survey (N=1040) was conducted in July 2020 in New Zealand to identify factors associated with COVID-19 vaccine intention. Trust in experts and general vaccine hesitancy were significantly associated with COVID-19 vaccine intention. A communication campaign from trusted scientific experts, with information that addresses prevailing concerns about vaccines, is likely to help increase COVID-19 vaccine uptake.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Jagadish Thaker", - "author_inst": "Massey University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.12.16.20248180", "rel_title": "Seroprevalence of anti-SARS-CoV-2 IgG antibodies, risk factors for infection and associated symptoms in Geneva, Switzerland: a population-based study", @@ -1025766,6 +1028315,41 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.12.18.423420", + "rel_title": "A new concept on anti-SARS-CoV-2 vaccines: strong CD8+ T-cell immune response in both spleen and lung induced in mice by endogenously engineered extracellular vesicles", + "rel_date": "2020-12-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.18.423420", + "rel_abs": "Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 is spreading rapidly in the absence of validated tools to control the growing epidemic besides social distancing and masks. Many efforts are ongoing for the development of vaccines against SARS-CoV-2 since there is an imminent need to develop effective interventions for controlling and preventing SARS-CoV-2 spread. Essentially all vaccines in most advanced phases are based on the induction of antibody response against either whole or part of spike (S) protein. Differently, we developed an original strategy to induce CD8+ T cytotoxic lymphocyte (CTL) immunity based on in vivo engineering of extracellular vesicles (EVs). We exploited this technology with the aim to identify a clinical candidate defined as DNA vectors expressing SARS-CoV-2 antigens inducing a robust CD8+ T-cell response. This is a new vaccination approach employing a DNA expression vector encoding a biologically inactive HIV-1 Nef protein (Nefmut) showing an unusually high efficiency of incorporation into EVs even when foreign polypeptides are fused to its C-terminus. Nanovesicles containing Nefmut-fused antigens released by muscle cells are internalized by antigen-presenting cells leading to cross-presentation of the associated antigens thereby priming of antigen-specific CD8+ T-cells. To apply this technology to a design of anti-SARS-CoV-2 vaccine, we recovered DNA vectors expressing the products of fusion between Nefmut and four viral antigens, namely N- and C-terminal moieties of S (referred to as S1 and S2), M, and N. All fusion products are efficiently uploaded in EVs. When the respective DNA vectors were injected in mice, a strong antigen-specific CD8+ T cell immunity was generated. Most important, high levels of virus-specific CD8+ T cells were found in bronchoalveolar lavages of immunized mice. Co-injection of DNA vectors expressing the diverse SARS-CoV-2 antigens resulted in additive immune responses in both spleen and lung. EVs engineered with SARS-CoV-2 antigens proved immunogenic also in the human system through cross-priming assays carried out with ex vivo human cells. Hence, DNA vectors expressing Nefmut-based fusion proteins can be proposed as anti-SARS-CoV-2 vaccine candidates.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Flavia Ferrantelli", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Chiara Chiozzini", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Francesco Manfredi", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Patrizia Leone", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Maurizio Federico", + "author_inst": "Istituto Superiore di Sanita" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.18.423418", "rel_title": "Human Surfactant Protein D Binds S1 and Receptor Binding Domain of Spike protein and acts as an entry inhibitor of SARS-CoV-2 Pseudotyped viral particles in vitro", @@ -1027145,53 +1029729,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.16.20248166", - "rel_title": "Using Administrative Data to Incorporate Age and Sex-Dependent Resource Use for COVID-19 Acute Care Resource Use Simulations in Ontario, Canada", - "rel_date": "2020-12-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.16.20248166", - "rel_abs": "As the COVID-19 pandemic has progressed, more local data has become available, enabling a more granular modeling approach. In March 2020, we developed a COVID-19 Resource Estimator (CORE) model to estimate the acute care resource use in Ontario, Canada. In this paper, we describe the evolution of CORE2.0 to incorporate age, sex, and time-dependent acute care resource use, length of stay, and mortality to simulate hospital occupancy. Demographics (e.g., age and sex) of infected cases are informed by 4-month averages between March-June, and July-October using 10-year age groups. The probability of hospitalization, ICU admission, and requiring mechanical ventilation are all age and sex-dependent. LOS for each acute care level ranges from 5.7 to 16.15 days in the ward, 6.5 to 10.7 days in the ICU without ventilation, and 14.8 to 21.6 days on the ventilator, depending on month of infection. We calibrated some LOS components to reported ward and ICU occupancy between June 15 and October 31, 2020. Furthermore, we demonstrate the use of CORE2.0 for a regional analysis of Region of Waterloo, Ontario, Canada to simulate the ward bed, ICU bed, and ventilator occupancies for 30 days starting December 2020 for three case trajectory scenarios. Moving forward, this model has become highly flexible and customizable to data updates, and can better inform acute care planning and public measures as the pandemic progresses.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Stephen Mac", - "author_inst": "Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada" - }, - { - "author_name": "Raphael Ximenes", - "author_inst": "Toronto Health Economics and Technology Assessment (THETA) Collaborative, University Health Network, Toronto, Canada" - }, - { - "author_name": "Kali Barrett", - "author_inst": "University Health Network, Toronto, Canada" - }, - { - "author_name": "Yasin A Khan", - "author_inst": "University Health Network, Toronto, Canada" - }, - { - "author_name": "Petros Pechlivanoglou", - "author_inst": "Hospital for Sick Children, Toronto, Canada" - }, - { - "author_name": "Juan David Rios", - "author_inst": "Hospital for Sick Children, Toronto, Canada" - }, - { - "author_name": "David MJ Naimark", - "author_inst": "University of Toronto" - }, - { - "author_name": "Beate Sander", - "author_inst": "University Health Network" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.16.20248357", "rel_title": "Understanding the net benefit of antigen-based rapid diagnostic tests for COVID-19: An enhanced decision-curve analysis", @@ -1027456,6 +1029993,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.16.20214106", + "rel_title": "Transmission of SARS-CoV-2 before and after symptom onset: impact of nonpharmaceutical interventions in China", + "rel_date": "2020-12-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.16.20214106", + "rel_abs": "Nonpharmaceutical interventions, such as contact tracing and quarantine, are currently the primary means of controlling the spread of SARS-CoV-2; however, it remains uncertain which interventions are most effective at reducing transmission at the population level. Using serial interval data from before and after the rollout of nonpharmaceutical interventions in China, we estimate that the relative frequency of presymptomatic transmission increased from 34% before the rollout to 71% afterward. The shift touward earlier transmission indicates a disproportionate reduction in transmission post-symptom onset. We estimate that, following the rollout of nonpharmaceutical interventions, transmission post-symptom onset was reduced by 82% whereas presymptomatic transmission decreased by only 16%. These findings suggest that interventions which limit opportunities for transmission in the later stages of infection, such as contact tracing and isolation, may have been particularly effective at reducing transmission of SARS-CoV-2.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Mary Bushman", + "author_inst": "Harvard University" + }, + { + "author_name": "Colin J. Worby", + "author_inst": "Broad Institute" + }, + { + "author_name": "Hsiao-Han Chang", + "author_inst": "National Tsing Hua University" + }, + { + "author_name": "Moritz U.G. Kraemer", + "author_inst": "University of Oxford" + }, + { + "author_name": "William P. Hanage", + "author_inst": "Harvard University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.16.20248310", "rel_title": "COVID19 is a seasonal climate-driven disease across both hemispheres", @@ -1028679,149 +1031251,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.14.20247874", - "rel_title": "Rapid detection of SARS-CoV-2 with Cas13", - "rel_date": "2020-12-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.14.20247874", - "rel_abs": "Rapid nucleic acid testing is a critical component of a robust infrastructure for increased disease surveillance. Here, we report a microfluidic platform for point-of-care, CRISPR-based molecular diagnostics. We first developed a nucleic acid test which pairs distinct mechanisms of DNA and RNA amplification optimized for high sensitivity and rapid kinetics, linked to Cas13 detection for specificity. We combined this workflow with an extraction-free sample lysis protocol using shelf-stable reagents that are widely available at low cost, and a multiplexed human gene control for calling negative test results. As a proof-of-concept, we demonstrate sensitivity down to 40 copies/L of SARS-CoV-2 in unextracted saliva within 35 minutes, and validated the test on total RNA extracted from patient nasal swabs with a range of qPCR Ct values from 13-35. To enable sample-to-answer testing, we integrated this diagnostic reaction with a single-use, gravity-driven microfluidic cartridge followed by real-time fluorescent detection in a compact companion instrument. We envision this approach for Diagnostics with Coronavirus Enzymatic Reporting (DISCoVER) will incentivize frequent, fast, and easy testing.", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Shreeya Agrawal", - "author_inst": "Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA." - }, - { - "author_name": "Alison Fanton", - "author_inst": "Department of Bioengineering, University of California, Berkeley, CA" - }, - { - "author_name": "Sita S. Chandrasekaran", - "author_inst": "Department of Bioengineering, University of California, Berkeley, CA" - }, - { - "author_name": "B\u00e9r\u00e9nice Charrez", - "author_inst": "University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA" - }, - { - "author_name": "Arturo M. Escajeda", - "author_inst": "Wainamics Inc., Pleasanton, CA, USA." - }, - { - "author_name": "Sungmin Son", - "author_inst": "Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA." - }, - { - "author_name": "Roger Mcintosh", - "author_inst": "Wainamics Inc., Pleasanton, CA, USA." - }, - { - "author_name": "Abdul Bhuiya", - "author_inst": "Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA." - }, - { - "author_name": "Mar\u00eda D\u00edaz de Le\u00f3n Derby", - "author_inst": "Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA." - }, - { - "author_name": "Neil A. Switz", - "author_inst": "Department of Physics and Astronomy, San Jos\u00e9 State University, San Jos\u00e9, CA, USA" - }, - { - "author_name": "Maxim Armstrong", - "author_inst": "Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA" - }, - { - "author_name": "Andrew R. Harris", - "author_inst": "Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA." - }, - { - "author_name": "Noam Prywes", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley , California 94704 , United States." - }, - { - "author_name": "Maria Lukarska", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley, CA, USA" - }, - { - "author_name": "Scott B. Biering", - "author_inst": "Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Dylan C. J. Smock", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley, CA, USA" - }, - { - "author_name": "Amanda Mok", - "author_inst": "Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Gavin J. Knott", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA" - }, - { - "author_name": "Qi Dang", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Erik Van Dis", - "author_inst": "Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA" - }, - { - "author_name": "Eli Dugan", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley, CA, USA" - }, - { - "author_name": "Shin Kim", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley, CA, USA" - }, - { - "author_name": "Tina Y. Liu", - "author_inst": "Department of Molecular and Cell Biology, University of California, Berkeley, California, USA" - }, - { - "author_name": "- IGI Testing Consortium", - "author_inst": "" - }, - { - "author_name": "Eva Harris", - "author_inst": "Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-3370 USA" - }, - { - "author_name": "Sarah A. Stanley", - "author_inst": "School of Public Health, University of California, Berkeley, CA 94720, USA" - }, - { - "author_name": "Liana F. Lareau", - "author_inst": "Department of Bioengineering, University of California, Berkeley, CA" - }, - { - "author_name": "Ming X. Tan", - "author_inst": "Wainamics Inc., Pleasanton, CA, USA." - }, - { - "author_name": "Daniel A. Fletcher", - "author_inst": "Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA." - }, - { - "author_name": "Jennifer A. Doudna", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA." - }, - { - "author_name": "David F. Savage", - "author_inst": "Department of Molecular and Cell Biology, University of California, Berkeley, California, USA" - }, - { - "author_name": "Patrick D. Hsu", - "author_inst": "Department of Bioengineering, University of California, Berkeley, CA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.14.20248209", "rel_title": "The Presence of Ambulatory Hypoxia as an Early Predictor of Moderate to Severe COVID-19 Disease", @@ -1028962,6 +1031391,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.14.20248186", + "rel_title": "Vaccine Prioritisation Using Bluetooth Exposure Notification Apps", + "rel_date": "2020-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.14.20248186", + "rel_abs": "After vaccinating health care workers and vulnerable groups against COVID-19, authorities will need to decide how to vaccinate everyone else. Prioritising individuals with more contacts can be disproportionately effective, in theory, but identifying these individuals is difficult. Here we show that the technology underlying Bluetooth exposure notification applications, such as used for digital contact tracing, can be leveraged to prioritise vaccination based on individual contact data. Our approach is based on the insight that these apps also act as local sensing devices measuring each users total exposure time to other users, thereby enabling the implementation of a previously impossible strategy that prioritises potential super-spreaders. Furthermore, by generalising percolation theory and introducing a novel measure of vaccination efficiency, we demonstrate that this \"hot-spotting\" strategy can achieve herd immunity with up to half as many vaccines as a non-targeted strategy, and is attractive even for relatively low rates of app usage.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Mark D Penney", + "author_inst": "University of Waterloo & Perimeter Institute for Theoretical Physics" + }, + { + "author_name": "Yigit Yargic", + "author_inst": "Perimeter Institute for Theoretical Physics" + }, + { + "author_name": "Lee Smolin", + "author_inst": "Perimeter Institute for Theoretical Physics" + }, + { + "author_name": "Edward W Thommes", + "author_inst": "Sanofi Pasteur, University of Guelph and York University" + }, + { + "author_name": "Madhur Anand", + "author_inst": "University of Guelph" + }, + { + "author_name": "Chris T Bauch", + "author_inst": "University of Waterloo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.15.20248247", "rel_title": "Large differences in community COVID-19 testing across geographic areas in a Swedish region with 385,000 inhabitants", @@ -1030629,49 +1033097,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.12.16.423002", - "rel_title": "EXPERIMENTAL INVESTIGATION OF PULSE STERILIZATION OF VIRAL INFECTION", - "rel_date": "2020-12-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.16.423002", - "rel_abs": "The results of experimental investigations of the effect of high-intensity pulsed UV radiation on the influenza virus type A (H1N1) are presented. The research methodology is developed and the structure of the experiments is described. An end-face plasma accelerator was used as a radiation source, which provides a power pulsed discharge in an open atmosphere. The high efficiency of inactivation of the infectiousness of the virus was shown within a short period of time. The possibility of providing urgent 100% sterilization of a viral infection has been shown for the first time. A model for calculating the efficiency of pulse sterilization has been developed. The prospects for the application of pulse sterilization technology to combat coronavirus infection are considered.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Volodymyr I Chumakov", - "author_inst": "Kharkiv National University of Radioelectronics" - }, - { - "author_name": "Mykhailo Ostryzhny", - "author_inst": "Kharkiv National University of Radioelectronics" - }, - { - "author_name": "Oksana Kharchenko", - "author_inst": "Kharkiv National University of Radioelectronics" - }, - { - "author_name": "Krystina Naumenko", - "author_inst": "Danylo Zabolotny Institute of Microbiology and Virology of the National Academy of Science of Ukraine" - }, - { - "author_name": "Svitlana Zagorodnya", - "author_inst": "Danylo Zabolotny Institute of Microbiology and Virology of the National Academy of Science of Ukraine," - }, - { - "author_name": "Vasiliy Muraveinyk", - "author_inst": "Independed scholar" - }, - { - "author_name": "Aleksandr Tarasevich", - "author_inst": "Independent scholar" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2020.12.16.423071", "rel_title": "One Year of SARS-CoV-2: How Much Has the Virus Changed?", @@ -1030820,6 +1033245,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.15.20244160", + "rel_title": "The role of metabolic comorbidity in COVID-19 mortality of middle-aged adults. The case of Mexico.", + "rel_date": "2020-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.15.20244160", + "rel_abs": "BackgroundIn contrast to developed countries, in Mexico more than half of COVID-19 deaths have occurred in adults <65-years-old, with at least a million years of life lost to premature mortality (YLL) in eight months. Mexico has a young population but a high prevalence of metabolic diseases like obesity and diabetes that contribute to COVID-19 adverse outcomes. COVID-19 could be particularly risky in population with specific comorbidity combinations that havent been analyzed.\n\nMethodsTo explore what contributes to the high COVID-19 mortality in Mexican middle-aged adults, we calculated age-stratified COVID-19 case fatality rates, YLL and relative risk (RR) of 9 comorbidities and 23 comorbidity combinations in a retrospective Mexican cohort with 905,579 PCR-confirmed COVID-19 cases/89,167 deaths, until Nov/2/2020.\n\nFindingsChronic kidney disease (CKD) had the highest RR for COVID-19 fatality, followed by diabetes and immunosuppression, that in turn had higher RR than obesity or hypertension as single comorbidities. The combination diabetes/hypertension with or without obesity had RR as high as CKD as a single comorbidity (>3 in <60-year-olds). Notably, the RR of comorbidities decreased with age, tending to values near 1 after age 60; suggesting that in Mexico, comorbidities increase COVID-19 fatality mostly in young and middle-aged adults. Our analysis suggests that advanced metabolic disease, marked by multimorbidity (more than one chronic disease per individual) or diabetes before age 60, contribute particularly to the younger age of COVID-19 fatalities in Mexico. Around 38% of YLL to COVID-19, were attributable to the synergy between COVID-19 and pre-existing diseases, mainly combinations between obesity, diabetes and hypertension. Yet, [1/4] of deaths and 1/3 of YLL have occurred in individuals without known comorbidities.\n\nConclusionsThe Mexican COVID-19 outbreak illustrates that middle-aged adults 45-64-yo can have high COVID-19 mortality during large outbreaks, especially if they present chronic metabolic comorbidities, but also in their absence, making them an important group of concern after elders. COVID-19 mortality in middle-aged adults is likely proportional to the gradual decline in health that accompanies ageing, which presents earlier in poorer populations that also get more exposed to SARS-CoV-2 and have less access to specialized medical attention.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Lenin Dominguez-Ramirez", + "author_inst": "Universidad de las Americas Puebla" + }, + { + "author_name": "Francisco Rodriguez-Perez", + "author_inst": "Instituto Mexicano del Seguro Social (IMSS), Centro de Investigacion Biomedica de Oriente (CIBIOR)" + }, + { + "author_name": "Francisca Sosa-Jurado", + "author_inst": "Instituto Mexicano del Seguro Social (IMSS), Centro de Investigacion Biomedica de Oriente (CIBIOR)" + }, + { + "author_name": "Gerardo Santos-Lopez", + "author_inst": "Instituto Mexicano del Seguro Social (IMSS), Centro de Investigacion Biomedica de Oriente (CIBIOR)" + }, + { + "author_name": "Paulina Cortes-Hernandez", + "author_inst": "Instituto Mexicano del Seguro Social (IMSS), Centro de Investigacion Biomedica de Oriente (CIBIOR)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.16.20248325", "rel_title": "The impact of working during the Covid-19 pandemic on health care workers and first responders: mental health, function, and professional retention", @@ -1032231,53 +1034691,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.12.14.20248152", - "rel_title": "SARS-CoV-2 among migrants and forcibly displaced populations: a rapid systematic review", - "rel_date": "2020-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.14.20248152", - "rel_abs": "The economic and health consequences of the COVID-19 pandemic pose a particular threat to vulnerable groups, such as migrants, particularly forcibly displaced populations. The aim of this review is (i) to synthesise the evidence on risk of infection and transmission among migrants, refugees, asylum seekers and internally displaced populations, and (ii) the effect of lockdown measures on these populations. We searched MEDLINE and WOS, preprint servers, and pertinent websites between 1st December 2019 and 26th June 2020. The included studies showed a high heterogeneity in study design, population, outcome and quality. The incidence risk of SARS-CoV-2 varied from 0{middle dot}12% to 2{middle dot}08% in non-outbreak settings and from 5{middle dot}64% to 21{middle dot}15% in outbreak settings. Migrants showed a lower hospitalisation rate compared to non-migrants. Negative impacts on mental health due to lockdown measures were found across respective studies. However, findings show a tenuous and heterogeneous data situation, showing the need for more robust and comparative study designs.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Maren Hintermeier", - "author_inst": "Section for Health Equity Studies and Migration, Department of General Practice and Health Services Research, University Hospital Heidelberg, Germany" - }, - { - "author_name": "Hande Gencer", - "author_inst": "Leibniz-Institute for Prevention Research and Epidemiology (BIPS), Department Prevention and Evaluation, Unit Social Epidemiology, Bremen, Germany" - }, - { - "author_name": "Katja Kajikhina", - "author_inst": "Robert Koch Institute, Unit 28 Social Determinants of Health, Department of Health monitoring and Epidemiology, Berlin, Germany" - }, - { - "author_name": "Sven Rohleder", - "author_inst": "Department of Population Medicine and Health Services Research, School of Public Health, Bielefeld University & Section for Health Equity Studies and Migration," - }, - { - "author_name": "Claudia Santos-Hoevener", - "author_inst": "Robert Koch Institute, Unit 28 Social Determinants of Health, Department of Health monitoring and Epidemiology, Berlin, Germany" - }, - { - "author_name": "Marie Tallarek", - "author_inst": "Department of Public Health, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany" - }, - { - "author_name": "Jacob Spallek", - "author_inst": "Department of Public Health, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany" - }, - { - "author_name": "Kayvan Bozorgmehr", - "author_inst": "Department of Population Medicine and Health Services Research, School of Public Health, Bielefeld University & Section for Health Equity Studies and Migration," - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.13.20248142", "rel_title": "COVID-19 vaccines that reduce symptoms but do not block infection need higher coverage and faster rollout to achieve population impact", @@ -1032498,6 +1034911,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.10.20235747", + "rel_title": "Human Safety, Tolerability, and Pharmacokinetics of a Novel Broad-Spectrum Oral Antiviral Compound, Molnupiravir, with Activity Against SARS-CoV-2", + "rel_date": "2020-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.10.20235747", + "rel_abs": "Molnupiravir, EIDD-2801/MK-4482, the prodrug of the ribonucleoside analog {beta}-d-N4-hydroxycytidine (NHC), has activity against a number of RNA viruses including severe acute respiratory syndrome coronavirus 2, severe acute respiratory syndrome coronavirus, Middle East respiratory syndrome coronavirus, seasonal and pandemic influenza viruses, and respiratory syncytial virus.\n\nSingle and multiple doses of molnupiravir were evaluated in this first-in-human, phase 1, randomized, double-blind, placebo-controlled study in healthy volunteers, which included evaluation of the effect of food on pharmacokinetics.\n\nEIDD-1931 appeared rapidly in plasma, with a median time of maximum observed concentration of 1.00 to 1.75 hours, and declined with a geometric half-life of approximately 1 hour, with a slower elimination phase apparent following multiple doses or higher single doses (7.1 hours at the highest dose tested). Mean maximum observed concentration and area under the concentration versus time curve increased in a dose-proportional manner, and there was no accumulation following multiple doses. When administered in a fed state, there was a decrease in the rate of absorption, but no decrease in overall exposure.\n\nMolnupiravir was well tolerated. Fewer than half of subjects reported an adverse event, the incidence of adverse events was higher following administration of placebo, and 93.3% of adverse events were mild. One discontinued early due to rash. There were no serious adverse events and there were no clinically significant findings in clinical laboratory, vital signs, or electrocardiography. Plasma exposures exceeded expected efficacious doses based on scaling from animal models; therefore, dose escalations were discontinued before a maximum tolerated dose was reached.\n\nClinical trial identifierThis study was registered at ClinicalTrials.gov with the identifier NCT04392219.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Wendy P Painter", + "author_inst": "Ridgeback Biotherapeutics LP" + }, + { + "author_name": "Wayne Holman", + "author_inst": "Ridgeback Biotherapeutics LP" + }, + { + "author_name": "James A Bush", + "author_inst": "Covance Clinical Research Unit Limited" + }, + { + "author_name": "Firas Almazedi", + "author_inst": "Covance Clinical Research Unit Limited" + }, + { + "author_name": "Hamzah Malik", + "author_inst": "Covance Clinical Research Unit Limited" + }, + { + "author_name": "Nicola C.J.E. Eraut", + "author_inst": "Covance Clinical Research Unit Limited" + }, + { + "author_name": "Merribeth J Morin", + "author_inst": "Ridgeback Biotherapeutics LP" + }, + { + "author_name": "Laura J Szewczyk", + "author_inst": "Ridgeback Biotherapeutics LP" + }, + { + "author_name": "George R Painter III", + "author_inst": "Emory University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.13.20248143", "rel_title": "Decay of Fc-dependent antibody functions after mild to moderate COVID-19", @@ -1034061,65 +1036525,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.13.422589", - "rel_title": "Profiling of oral microbiota and cytokines in COVID-19 patients", - "rel_date": "2020-12-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.13.422589", - "rel_abs": "SARS-CoV-2 presence has been recently demonstrated in the sputum or saliva, suggesting how the shedding of viral RNA outlasts the end of symptoms. Recent data from transcriptome analysis show that oral cavity mucosa harbors high levels of ACE2 and TMPRSS2, highlighting its role as a double-edged sword for SARS-CoV-2 body entrance or interpersonal transmission. In the present study, for the first time, we demonstrate the oral microbiota structure and inflammatory profile of COVID-19 patients. Hospitalized COVID-19 patients and matched healthy controls underwent naso/oral-pharyngeal and oral swabs. Microbiota structure was analyzed by 16S rRNA V2 automated targeted sequencing, while oral and sera concentrations of 27 cytokines were assessed using magnetic bead-based multiplex immunoassays. A significant diminution in species richness was observed in COVID-19 patients, along with a marked difference in beta-diversity. Species such as Prevotella salivae and Veillonella infantium were distinctive for COVID-19 patients, while Neisseria perflava and Granulicatella elegans were predominant in controls. Interestingly, these two groups of oral species oppositely clustered within the bacterial network, defining two distinct Species Interacting Group (SIGs). Pro-inflammatory cytokines were distinctive for COVID-19 in both oral and serum samples, and we found a specific bacterial consortium able to counteract them, following a novel index called C4 firstly proposed here. We even introduced a new parameter, named CytoCOV, able to predict COVID-19 susceptibility for an unknown subject at 71% of power with an AUC equal to 0.995. This pilot study evidenced a distinctive oral microbiota composition in COVID-19 subjects, with a definite structural network in relation to secreted cytokines. Our results would pave the way for a theranostic approach in fighting COVID-19, trying to enlighten the intimate relationship among microbiota and SARS-CoV-2 infection.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Valerio Iebba", - "author_inst": "University of Trieste" - }, - { - "author_name": "Nunzia Zanotta", - "author_inst": "Laboratory of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health-IRCCS Burlo-Garofolo, Trieste, Italy." - }, - { - "author_name": "Giuseppina Campisciano", - "author_inst": "Laboratory of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health-IRCCS Burlo-Garofolo, Trieste, Italy." - }, - { - "author_name": "Verena Zerbato", - "author_inst": "Infectious Diseases Department, Udine University, 33100 Udine, Italy." - }, - { - "author_name": "Stefano Di Bella", - "author_inst": "Department of Medical, Surgical and Health Sciences, University of Trieste, Piazzale Europa, 1, 34127 Trieste, Italy." - }, - { - "author_name": "Carolina Cason", - "author_inst": "Laboratory of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health-IRCCS Burlo-Garofolo, Trieste, Italy." - }, - { - "author_name": "Sara Morassut", - "author_inst": "Laboratory of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health-IRCCS Burlo-Garofolo, Trieste, Italy." - }, - { - "author_name": "Roberto Luzzati", - "author_inst": "Department of Medical, Surgical and Health Sciences, University of Trieste, Piazzale Europa, 1, 34127 Trieste, Italy." - }, - { - "author_name": "Marco Confalonieri", - "author_inst": "Pulmonology Department, University Hospital of Cattinara, 34149 Trieste, Italy." - }, - { - "author_name": "Anna Teresa Palamara", - "author_inst": "IRCCS San Raffaele Pisana, 00166 Rome, Italy; Department of Public Health and Infectious Diseases, Sapienza University of Rome, Laboratory Affiliated to Institu" - }, - { - "author_name": "Manola Comar", - "author_inst": "Laboratory of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health-IRCCS Burlo-Garofolo, Trieste, Italy." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.12.13.420406", "rel_title": "Identification of bis-benzylisoquinoline alkaloids as SARS-CoV-2 entry inhibitors from a library of natural products in vitro", @@ -1034320,6 +1036725,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.12.14.422710", + "rel_title": "Surface proteins of SARS-CoV-2 drive airway epithelial cells to induce interferon-dependent inflammation", + "rel_date": "2020-12-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.14.422710", + "rel_abs": "SARS-CoV-2, the virus that has caused the COVID-19 pandemic, robustly activates the host immune system in critically ill patients. Understanding how the virus engages the immune system will facilitate the development of needed therapeutic strategies. Here we demonstrate both in vitro and in vivo that the SARS-CoV-2 surface proteins Spike (S) and Envelope (E) activate the key immune signaling interferon (IFN) pathway in both immune and epithelial cells independent of viral infection and replication. These proteins induce reactive oxidative species generation and increases in human and murine specific IFN-responsive cytokines and chemokines, similar to their upregulation in critically ill COVID-19 patients. Induction of IFN signaling is dependent on canonical but discrepant inflammatory signaling mediators as the activation induced by S is dependent on IRF3, TBK1, and MYD88 while that of E is largely MYD88 independent. Furthermore, these viral surface proteins, specifically E, induced peribronchial inflammation and pulmonary vasculitis in a mouse model. Finally we show that the organized inflammatory infiltrates are dependent on type I IFN signaling, specifically in lung epithelial cells. These findings underscore the role of SARS-CoV-2 surface proteins, particularly the understudied E protein, in driving cell specific inflammation and their potential for therapeutic intervention.\n\nAuthor SummarySARS-CoV-2 robustly activates widespread inflammation, but we do not understand mechanistically how the virus engages the immune system. This knowledge will facilitate the development of critically needed therapeutic strategies to promote beneficial immune responses will dampening harmful inflammation. Here we demonstrate that SARS-CoV-2 surface proteins spike and envelope alone activated innate cell function and the interferon signaling pathway. This activation occurred in both immune and epithelial cells, and mechanistic studies demonstrated dependence on known key inflammatory signaling mediators, IRF3, TBK1, and MYD88. In animal studies, we showed that these viral surface proteins induce epithelial cell IFN-dependent lung pathology, reminiscent to acute COVID-19 pulmonary infection. These findings underscore the need for further investigation into the role of SARS-CoV-2 surface proteins, particularly the understudied E protein, in driving cell specific inflammation.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Gautam Anand", + "author_inst": "Washington University in Saint Louis" + }, + { + "author_name": "Alexandra M Perry", + "author_inst": "Washington University in Saint Louis" + }, + { + "author_name": "Celeste L Cummings", + "author_inst": "Washington University in Saint Louis" + }, + { + "author_name": "Emma St. Raymond", + "author_inst": "Washington University in Saint Louis" + }, + { + "author_name": "Regina A Clemens", + "author_inst": "Washington University in Saint Louis" + }, + { + "author_name": "Ashley L Steed", + "author_inst": "Washington University in Saint Louis" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.14.420133", "rel_title": "Targeting Scavenger Receptor Type B-1 (SR-B1) and Cholesterol Inhibits Entry of SARS-CoV-2 Pseudovirus in Cell Culture", @@ -1035746,121 +1038190,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.04.20243949", - "rel_title": "The burden of active infection and anti-SARS-CoV-2 IgG antibodies in the general population: Results from a statewide survey in Karnataka, India", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.04.20243949", - "rel_abs": "BackgroundGlobally, the routinely used case-based reporting and IgG serosurveys underestimate the actual prevalence of COVID-19. Simultaneous estimation of IgG antibodies and active SARS-CoV-2 markers can provide a more accurate estimation.\n\nMethodsA cross-sectional survey of 16416 people covering all risk groups was done between 3-16 September 2020 using the state of Karnatakas infrastructure of 290 hospitals across all 30 districts. All participants were subjected to simultaneous detection of SARS-CoV-2 IgG using a commercial ELISA kit, SARS-CoV-2 antigen using a rapid antigen detection test (RAT), and reverse transcription-polymerase chain reaction (RT-PCR) for RNA detection. Maximum-likelihood estimation was used for joint estimation of the adjusted IgG, active, and total prevalence, while multinomial regression identified predictors.\n\nFindingsThe overall adjusted prevalence of COVID-19 in Karnataka was 27 {middle dot}3% (95% CI: 25 {middle dot}7-28 {middle dot}9), including IgG 16 {middle dot}4% (95% CI: 15 {middle dot}1 - 17 {middle dot}7) and active infection 12 {middle dot}7% (95% CI: 11 {middle dot}5-13 {middle dot}9). The case-to-infection ratio was 1:40, and the infection fatality rate was 0 {middle dot}05%. Influenza-like symptoms or contact with a COVID-19 positive patient are good predictors of active infection. The RAT kits had higher sensitivity (68%) in symptomatic participants compared to 47% in asymptomatic.\n\nInterpretationThis is the first comprehensive survey providing accurate estimates of the COVID-19 burden anywhere in the world. Further, our findings provide a reasonable approximation of population immunity threshold levels. Using the RAT kits and following the syndromic approach can be useful in screening and monitoring COVID-19. Leveraging existing surveillance platforms, coupled with appropriate methods and sampling framework, renders our model replicable in other settings.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Giridhara R Babu", - "author_inst": "Indian Institute of Public Health, Public Health Foundation of India, Bangalore" - }, - { - "author_name": "Rajesh Sundaresan", - "author_inst": "Indian Institute of Science, Bengaluru" - }, - { - "author_name": "Siva Athreya", - "author_inst": "Indian Statistical Institute Bangalore Centre" - }, - { - "author_name": "Jawaid Akhtar", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Pankaj Kumar Pandey", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Parimala S Maroor", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Padma MR", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Lalitha R", - "author_inst": "UNICEF, India" - }, - { - "author_name": "Mohammed Shariff", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Lalitha Krishnappa", - "author_inst": "MS Ramaiah Medical College" - }, - { - "author_name": "CN Manjunath", - "author_inst": "Sri Jayadeva Institute of Cardiovascular Sciences and Research" - }, - { - "author_name": "MK Sudarshan", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Gururaj G", - "author_inst": "National Institute of Mental Health and Neurosciences" - }, - { - "author_name": "Ranganath TS", - "author_inst": "Bangalore Medical College and Research Institute" - }, - { - "author_name": "Vasanth Kumar DE", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Pradeep Banandur", - "author_inst": "National Institute of Mental Health and Neurosciences" - }, - { - "author_name": "Deepa R", - "author_inst": "Indian Institute of Public Health Bengaluru, Public Health Foundation of India" - }, - { - "author_name": "Shilpa Shiju", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Eunice Lobo", - "author_inst": "Indian Institute of Public Health Bengaluru, Public Health Foundation of India" - }, - { - "author_name": "Asish Satapathy", - "author_inst": "WHO NPSP, India" - }, - { - "author_name": "Lokesh Alahari", - "author_inst": "WHO NPSP, India" - }, - { - "author_name": "Prameela", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Vinitha T", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Anita Desai", - "author_inst": "National Institute of Mental Health and Neurosciences" - }, - { - "author_name": "V Ravi", - "author_inst": "National Institute of Mental Health and Neurosciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.08.20246314", "rel_title": "Antibody landscape against SARS-CoV-2 proteome revealed significant differences between non-structural/ accessory proteins and structural proteins", @@ -1036073,6 +1038402,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.08.20246074", + "rel_title": "The impact of the COVID-19 pandemic on college students' health and financial stability in New York City: Findings from a population-based sample of City University of New York (CUNY) students", + "rel_date": "2020-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.08.20246074", + "rel_abs": "Understanding the effect of the coronavirus disease 2019 (COVID-19) pandemic on students health and financial stability is important to establish effective interventions to mitigate these effects, which may have long-term consequences on their health and wellbeing. Public universities in urban centers represent a substantial proportion of college students in the United States. We implemented a cross-sectional population-based online survey of 2,282 students in a large, public university in New York City in April 2020. We created weights to account for non-response and used Poisson regression with robust standard errors to estimate adjusted prevalence ratios (aPR) for factors associated with mental health outcomes. Students experienced high rates of anxiety/depression and financial instability due to the pandemic. Half of the students reported anxiety/depression (54.5%) and an increased need for mental health services (49.0%) as a result of the COVID-19 pandemic. The majority (81.1%) reported loss of household income, and half (49.8%) reported worries about losing housing. High levels of food (aPR=1.4, 95% CI 1.2, 1.6) and housing (aPR=1.3, 95% CI 1.2, 1.4) insecurity were the strongest predictors of anxiety/depression. Household and personal experiences with possible COVID-19 symptoms were also associated with anxiety/depression or the need for increased mental health services. Addressing student needs at public urban universities requires an integrated holistic approach that targets urgent mental health and economic needs related to the impact of COVID-19. Students who become infected need mental health services as well as health monitoring.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Heidi E Jones", + "author_inst": "CUNY School of Public Health" + }, + { + "author_name": "Meredith Manze", + "author_inst": "CUNY School of Public Health" + }, + { + "author_name": "Victoria Ngo", + "author_inst": "CUNY School of Public Health" + }, + { + "author_name": "Patricia Lamberson", + "author_inst": "Healthy CUNY" + }, + { + "author_name": "Nicholas Freudenberg", + "author_inst": "CUNY School of Public Health & Healthy CUNY" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.08.20246173", "rel_title": "Impact of Convalescent Plasma Transfusion (CCP) In Patients With Previous Circulating Neutralizing Antibodies (nAb) to COVID-19", @@ -1037660,45 +1040024,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.09.20246629", - "rel_title": "Optimal test allocation strategy for COVID-19", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.09.20246629", - "rel_abs": "Testing for active SARS-CoV-2 infections is key to controlling the spread of the virus and preventing severe disease. A central public health challenge is defining test allocation strategies in the presence of limited resources. Inthis paper, we provide a mathematical framework for defining anoptimal strategy for allocating viral tests. The framework accounts for imperfect test results, selective testing in certain high-risk patient populations, practical constraints in terms of budget and/or total number of available tests, and the purpose of testing. Our method is not only useful for detecting infected cases, but can also be used for long-time surveillance to monitor for new outbreaks, which will be especially important during ongoing vaccine distribution across the world. In our proposed approach, tests can be allocated across population strata defined by symptom severity and other patient characteristics, allowing the test allocation plan to prioritize higher risk patient populations. We illustrate our framework using historical data from the initial wave of the COVID-19 outbreak in New York City. We extend our proposed method to address the challenge of allocating two different types of tests with different costs and accuracy (for example, the expensive but more accurate RT-PCR test versus the cheap but less accurate rapid antigen test), administered under budget constraints. We show how this latter framework can be useful to reopening of college campuses where university administrators are challenged with finite resources for community surveillance. We provide a R Shiny web application allowing users to explore test allocation strategies across a variety of pandemic scenarios. This work can serve as a useful tool for guiding public health decision-making at a community level and adapting to different stages of an epidemic, and it has broader relevance beyond the COVID-19 outbreak.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Jiacong Du", - "author_inst": "University of Michigan" - }, - { - "author_name": "Lauren J Beesley", - "author_inst": "University of Michigan" - }, - { - "author_name": "Seunggeun Lee", - "author_inst": "Graduate School of Data Science, Seoul National University, Republic of Korea" - }, - { - "author_name": "Xiang Zhou", - "author_inst": "University of Michigan" - }, - { - "author_name": "Walter Dempsey", - "author_inst": "University of Michigan" - }, - { - "author_name": "Bhramar Mukherjee", - "author_inst": "University of Michigan" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.09.20246538", "rel_title": "The trade-off between mobility and vaccination for COVID-19 control: a metapopulation modeling approach", @@ -1037867,6 +1040192,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.12.10.20246959", + "rel_title": "First and second waves of coronavirus disease-19: A comparative study in hospitalized patients in Reus, Spain", + "rel_date": "2020-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.10.20246959", + "rel_abs": "Many countries have seen a two-wave pattern in reported cases of coronavirus disease-19 during the 2020 pandemic, with a first wave during spring followed by the current second wave in late summer and autumn. Empirical data show that the characteristics of the effects of the virus do vary between the two periods. Differences in age range and severity of the disease have been reported, although the comparative characteristics of the two waves still remain largely unknown. Those characteristics are compared in this study using data from two equal periods of 3 and a half months. The first period, between 15th March and 30th June, corresponding to the entire first wave, and the second, between 1st July and 15th October, corresponding to part of the second wave, still present at the time of writing this article. Two hundred and four patients were hospitalized during the first period, and 264 during the second period. Patients in the second wave were younger and the duration of hospitalization and case fatality rate were lower than those in the first wave. In the second wave, there were more children, and pregnant and post-partum women. The most frequent signs and symptoms in both waves were fever, dyspnea, pneumonia, and cough, and the most relevant comorbidities were cardiovascular diseases, type 2 diabetes mellitus, and chronic neurological diseases. Patients from the second wave more frequently presented renal and gastrointestinal symptoms, were more often treated with non-invasive mechanical ventilation and corticoids, and less often with invasive mechanical ventilation, conventional oxygen therapy and anticoagulants. Several differences in mortality risk factors were also observed. These results might help to understand the characteristics of the second wave and the behaviour and danger of SARS-CoV-2 in the Mediterranean area and in Western Europe. Further studies are needed to confirm our findings.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Simona Iftime", + "author_inst": "HUSJR" + }, + { + "author_name": "Ana F L\u00f3pez-Azcona", + "author_inst": "HUSJR" + }, + { + "author_name": "Immaculada Vallverdu", + "author_inst": "HUSJR" + }, + { + "author_name": "Salvador Hernandez-Flix", + "author_inst": "HUSJR" + }, + { + "author_name": "Gabriel de Febrer", + "author_inst": "HUSJR" + }, + { + "author_name": "Sandra Parra", + "author_inst": "HUSJR" + }, + { + "author_name": "Anna Hern\u00e1ndez-Aguilera", + "author_inst": "HUSJR" + }, + { + "author_name": "Francesc Riu", + "author_inst": "HUSJR" + }, + { + "author_name": "Jorge Joven", + "author_inst": "HUSJR" + }, + { + "author_name": "Jordi Camps", + "author_inst": "Hospital Universitari Sant Joan de Reus" + }, + { + "author_name": "Antoni Castro", + "author_inst": "HUSJR" + }, + { + "author_name": "- REUSCOVID Study Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.09.20239467", "rel_title": "SARS-CoV-2 Viral Load in Saliva Rises Gradually and to Moderate Levels in Some Humans", @@ -1039502,69 +1041890,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.10.417758", - "rel_title": "EVs analysis in the COVID-19 era: insights on serum inactivation protocols towards downstream isolation and analysis", - "rel_date": "2020-12-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.10.417758", - "rel_abs": "Since the outbreak of COVID-19 crisis, the handling of biological samples from confirmed or suspected SARS-CoV-2 positive individuals demanded the use of inactivation protocols to ensure laboratory operators safety. While not standardized, these practices can be roughly divided in two categories, namely heat inactivation and solvent-detergent treatments. As such, these routine procedures should also apply to samples intended for Extracellular Vesicles (EVs) analysis. Assessing the impact of virus inactivating pre-treatments is therefore of pivotal importance, given the well-known variability introduced by different pre-analytical steps on downstream EVs isolation and analysis. Arguably, shared guidelines on inactivation protocols tailored to best address EVs-specific requirements will be needed among the EVs community, yet deep investigations in this direction havent been reported so far.\n\nIn the attempt of sparking interest on this highly relevant topic, we here provide preliminary insights on SARS-CoV-2 inactivation practices to be adopted prior serum EVs analysis by comparing solvent/detergent treatment vs. heat inactivation. Our analysis entailed the evaluation of EVs recovery and purity along with biochemical, biophysical and biomolecular profiling by means of Nanoparticle Tracking Analysis, Western Blotting, Atomic Force Microscopy, miRNA content (digital droplet PCR) and tetraspanin assessment by microarrays. Our data suggest an increase in ultracentrifugation (UC) recovery following heat-treatment, however accompanied by a marked enrichment in EVs-associated contaminants. On the contrary, solvent/detergent treatment is promising for small EVs (< 150 nm range), yet a depletion of larger vesicular entities was detected. This work represents a first step towards the identification of optimal serum inactivation protocols targeted to EVs analysis.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Roberto Frigerio", - "author_inst": "National Research Council of Italy" - }, - { - "author_name": "Angelo Music\u00f2", - "author_inst": "National Research Council of Italy" - }, - { - "author_name": "Marco Brucale", - "author_inst": "National Research Council of Italy" - }, - { - "author_name": "Andrea Ridolfi", - "author_inst": "National Research Council of Italy" - }, - { - "author_name": "Silvia Galbiati", - "author_inst": "IRCSS Ospedale San Raffaele" - }, - { - "author_name": "Riccardo Vago", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Greta Bergamaschi", - "author_inst": "National Research Council of Italy" - }, - { - "author_name": "Anna Ferretti", - "author_inst": "National Research Council of Italy" - }, - { - "author_name": "Marcella Chiari", - "author_inst": "National Research Council of Italy" - }, - { - "author_name": "Francesco Valle", - "author_inst": "National Research Council of Italy" - }, - { - "author_name": "Alessandro Gori", - "author_inst": "National Research Council of Italy" - }, - { - "author_name": "Marina Cretich", - "author_inst": "Consiglio Nazionale delle Ricerche" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.12.11.416818", "rel_title": "Duplex formation between the template and the nascent strand in the transcription-regulating sequences determines the site of template switching in SARS - CoV-2", @@ -1040029,6 +1042354,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.12.10.418855", + "rel_title": "Identification of eight SARS-CoV-2 ORF7a deletion variants in 2,726 clinical specimens", + "rel_date": "2020-12-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.10.418855", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ORF7a, the ortholog of SARS-CoV ORF7a, is a type I transmembrane protein and plays an important role in virus-host interactions. Deletion variants in ORF7a may influence virulence, but only a few such isolates have been reported. Here, we report 8 unique ORF7a deletion variants of 6 to 96 nucleotides in length identified from 2,726 clinical specimens collected in March of 2020.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sun Hee Rosenthal", + "author_inst": "Quest Diagnostics" + }, + { + "author_name": "Ron M Kagan", + "author_inst": "Quest Diagnostics Infectious Disease" + }, + { + "author_name": "Anna Gerasimova", + "author_inst": "Quest Diagnostics Nichols Institute" + }, + { + "author_name": "Ben Anderson", + "author_inst": "Quest Diagnostics Nichols Institute" + }, + { + "author_name": "David grover", + "author_inst": "Quest Diagnostics Nichols Institute" + }, + { + "author_name": "Michael Hua", + "author_inst": "Quest Diagnostics Nichols Institute" + }, + { + "author_name": "Renius Owen", + "author_inst": "Quest Diagnostics Nichols Institute" + }, + { + "author_name": "Felicitas Lacbawan", + "author_inst": "Quest Diagnostics Nichols Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.10.420489", "rel_title": "A traditional Chinese medicine, Respiratory Detox Shot (RDS), inhibits the infection of SARS-CoV, SARS-CoV-2, and the Influenza A virus in vitro", @@ -1041456,85 +1043828,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.08.20245811", - "rel_title": "Six-month antibody response to SARS-CoV-2 in healthcare workers assessed by virus neutralisation and commercial assays", - "rel_date": "2020-12-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.08.20245811", - "rel_abs": "We conducted a prospective study in healthcare workers (n=296) of the University Hospital of Lyon, France. Serum samples (n=296) collected six months after disease onset were tested using three commercial assays: the Wantai Ab assay detecting total antibodies against the receptor binding domain (RBD) of the S protein, the bioMerieux Vidas assay detecting IgG to the RBD and the Abbott Architect assay detecting IgG to the N protein. The neutralising antibody (NAb) titre was also determined for all samples with a virus neutralisation assay (VNA) using live virus. The positivity rate was 100% with the Wantai assay, 84.8% with the bioMerieux assay and 55.4% with the Abbott assay. Only 51% of HCWs were positive for the presence of NAb. Less than 10 % of HCWs had a NAb titre greater than 80. At a neutralising titre of 80, the area under the curves [IC 95%] was 0.71 [0.62-0.81], 0.75 [0.65-0.85] and 0.95 [0.92-0.97] for Wantai, Abbott and Vidas respectively. The data presented herein suggest that commercial assays detecting antibodies against the N protein must not be used in long-term seroprevalence surveys while the Wantai assay could be useful for this purpose. VNA should remain the gold standard to assess the protective antibody response, but some commercial assays could be used as first-line screening of long-term presence of NAb.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Antonin Bal", - "author_inst": "Hospices civils de Lyon" - }, - { - "author_name": "Mary-Anne Trabaud", - "author_inst": "HCL" - }, - { - "author_name": "Jean-Baptiste Fassier", - "author_inst": "HCL" - }, - { - "author_name": "Muriel Rabilloud", - "author_inst": "HCL" - }, - { - "author_name": "Kahina Saker", - "author_inst": "HCL" - }, - { - "author_name": "Carole Langlois", - "author_inst": "HCL" - }, - { - "author_name": "Nicolas Guibert", - "author_inst": "HCL" - }, - { - "author_name": "Constance d'Aubarede", - "author_inst": "HCL" - }, - { - "author_name": "Adele Paul", - "author_inst": "HCL" - }, - { - "author_name": "Dulce Alfaiate", - "author_inst": "HCL" - }, - { - "author_name": "Amelie Massardier", - "author_inst": "HCL" - }, - { - "author_name": "Virginie Pitiot", - "author_inst": "HCL" - }, - { - "author_name": "Florence Morfin", - "author_inst": "HCL" - }, - { - "author_name": "Bruno Lina", - "author_inst": "HCL" - }, - { - "author_name": "Bruno Pozzetto", - "author_inst": "CHU de Saint-Etienne" - }, - { - "author_name": "Sophie Trouillet-Assant", - "author_inst": "Hospices Civils de Lyon" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.08.20245910", "rel_title": "SARS-CoV-2 infections in kindergartens and associated households at the start of the second wave in Berlin, Germany - a cross sectional study", @@ -1041699,6 +1043992,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.08.20245803", + "rel_title": "A Selective Increase in OC Symptoms is Driving Information Seeking and Guideline Adherence During the Covid-19 Pandemic", + "rel_date": "2020-12-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.08.20245803", + "rel_abs": "BackgroundIncreased mental health problems as a reaction to stressful life events, such as the Covid-19 pandemic, are common. Critically, successful adaptation helps reduce such symptoms to baseline, preventing long-term psychiatric disorders. It is thus important to understand whether and which psychiatric symptoms only show transient elevations, and which persist long-term and become chronically heightened. At particular risk for the latter trajectory are disorders with symptoms directly affected by the pandemic, such as obsessive-compulsive disorder.\n\nMethodsIn this longitudinal large-scale study (N=416), we assessed how obsessive-compulsive (OC), anxiety, and depression symptoms changed throughout the course of the first pandemic wave in a sample of the general UK public. We further examined how these symptoms affected pandemic-related information seeking and adherence to governmental guidelines.\n\nFindingsAll psychiatric domains were initially elevated, but showed distinct adaptation patterns. Depression scores decreased during the first pandemic wave, however, OC symptoms further increased, even after the end of lockdown. These OC symptoms were directly linked to Covid-related information seeking which gave rise to higher adherence to government guidelines.\n\nInterpretationThe rise and persistence of OC symptoms, despite the ease of Covid-19 restrictions, shows that OCD is disproportionally and chronically affected by the pandemic. This is particularly worrying with regards to the long-term impact of the Covid-19 pandemic on public mental health and indicates that patients with OCD may require particular treatment efforts.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Alisa Maria Loosen", + "author_inst": "University College London" + }, + { + "author_name": "Vasilisa Skvortsova", + "author_inst": "University College London" + }, + { + "author_name": "Tobias U. Hauser", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.12.08.20245829", "rel_title": "Prevalence of anxiety and depressive symptoms among physicians during the COVID-19 pandemic in Bangladesh: a cross-sectional study", @@ -1043225,89 +1045545,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.08.416339", - "rel_title": "Natural SARS-CoV-2 infections, including virus isolation, among serially tested cats and dogs in households with confirmed human COVID-19 cases in Texas, USA", - "rel_date": "2020-12-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.08.416339", - "rel_abs": "The natural infections and epidemiological roles of household pets in SARS-CoV-2 transmission are not understood. We conducted a longitudinal study of dogs and cats living with at least one SARS-CoV-2 infected human in Texas and found 47.1% of 17 cats and 15.3% of 59 dogs from 25.6% of 39 households were positive for SARS-CoV-2 via RT-PCR and genome sequencing or neutralizing antibodies. Virus was isolated from one cat. The majority (82.4%) of infected pets were asymptomatic. Re-sampling of one infected cat showed persistence of viral RNA at least 32 d-post human diagnosis (25 d-post initial test). Across 15 antibody-positive animals, titers increased (33.3%), decreased (33.3%) or were stable (33.3%) over time. A One Health approach is informative for prevention and control of SARS-CoV-2 transmission.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Sarah A Hamer", - "author_inst": "Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, USA" - }, - { - "author_name": "Alex Pauvolid-Correa", - "author_inst": "Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, USA" - }, - { - "author_name": "Italo B Zecca", - "author_inst": "Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, USA" - }, - { - "author_name": "Edward Davila", - "author_inst": "Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, USA" - }, - { - "author_name": "Lisa D Auckland", - "author_inst": "Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, USA" - }, - { - "author_name": "Christopher M Roundy", - "author_inst": "Department of Entomology, Texas A&M University and AgriLife Research, Texas, USA" - }, - { - "author_name": "Wendy Tang", - "author_inst": "Department of Entomology, Texas A&M University and AgriLife Research, Texas, USA" - }, - { - "author_name": "Mia K Torchetti", - "author_inst": "National Veterinary Services Laboratories, USDA APHIS VS, Ames, IA, USA" - }, - { - "author_name": "Mary Lea Killian", - "author_inst": "National Veterinary Services Laboratories, USDA APHIS VS, Ames, IA, USA" - }, - { - "author_name": "Melinda Jenkins-Moore", - "author_inst": "National Veterinary Services Laboratories, USDA APHIS VS, Ames, IA, USA" - }, - { - "author_name": "Katie Mozingo", - "author_inst": "National Veterinary Services Laboratories, USDA APHIS VS, Ames, IA, USA" - }, - { - "author_name": "Yao Akpalu", - "author_inst": "Brazos County Health Department, Bryan, Texas, USA" - }, - { - "author_name": "Ria R Ghai", - "author_inst": "U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA" - }, - { - "author_name": "Jessica R Spengler", - "author_inst": "U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA" - }, - { - "author_name": "Casey Barton Behravesh", - "author_inst": "U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA" - }, - { - "author_name": "Rebecca Fischer", - "author_inst": "School of Public Health, Texas A&M University, Texas, USA" - }, - { - "author_name": "Gabriel L Hamer", - "author_inst": "Department of Entomology, Texas A&M University and AgriLife Research, Texas, USA." - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "zoology" - }, { "rel_doi": "10.1101/2020.12.08.415836", "rel_title": "Anti-SARS-CoV-2 activity of Andrographis paniculata extract and its major component Andrographolide in human lung epithelial cells and cytotoxicity evaluation in major organ cell representatives", @@ -1043500,6 +1045737,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.12.07.415422", + "rel_title": "Circular RNA profiling reveals abundant and diverse circRNAs of SARS-CoV-2, SARS-CoV and MERS-CoV origin", + "rel_date": "2020-12-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.07.415422", + "rel_abs": "Circular RNAs (circRNAs) encoded by DNA genomes have been identified across host and pathogen species as parts of the transcriptome. Accumulating evidences indicate that circRNAs play critical roles in autoimmune diseases and viral pathogenesis. Here we report that RNA viruses of the Betacoronavirus genus of Coronaviridae, SARS-CoV-2, SARS-CoV and MERS-CoV, encode a novel type of circRNAs. Through de novo circRNA analyses of publicly available coronavirus-infection related deep RNA-Sequencing data, we identified 351, 224 and 2,764 circRNAs derived from SARS-CoV-2, SARS-CoV and MERS-CoV, respectively, and characterized two major back-splice events shared by these viruses. Coronavirus-derived circRNAs are more abundant and longer compared to host genome-derived circRNAs. Using a systematic strategy to amplify and identify back-splice junction sequences, we experimentally identified over 100 viral circRNAs from SARS-CoV-2 infected Vero E6 cells. This collection of circRNAs provided the first line of evidence for the abundance and diversity of coronavirus-derived circRNAs and suggested possible mechanisms driving circRNA biogenesis from RNA genomes. Our findings highlight circRNAs as an important component of the coronavirus transcriptome.\n\nSummaryWe report for the first time that abundant and diverse circRNAs are generated by SARS-CoV-2, SARS-CoV and MERS-CoV and represent a novel type of circRNAs that differ from circRNAs encoded by DNA genomes.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Shaomin Yang", + "author_inst": "College of Pharmacy and College of Life Science and Technology, Jinan University," + }, + { + "author_name": "Hong Zhou", + "author_inst": "Department of Microbiology, Howard University College of Medicine" + }, + { + "author_name": "Ruth Cruz-Cosme", + "author_inst": "Department of Microbiology, Howard University College of Medicine" + }, + { + "author_name": "Mingde Liu", + "author_inst": "Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agriculture and Environmental Sciences, Department of V" + }, + { + "author_name": "Xiaoyu Niu", + "author_inst": "Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agriculture and Environmental Sciences, Department of V" + }, + { + "author_name": "Jiayu Xu", + "author_inst": "Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agriculture and Environmental Sciences, Department of V" + }, + { + "author_name": "Yaolan Li", + "author_inst": "College of Pharmacy and College of Life Science and Technology, Jinan University" + }, + { + "author_name": "Qiuhong Wang", + "author_inst": "Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agriculture and Environmental Sciences, Department of V" + }, + { + "author_name": "Hua Zhu", + "author_inst": "Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University" + }, + { + "author_name": "Qiyi Tang", + "author_inst": "Howard.edu" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.08.415505", "rel_title": "Binding of SARS-CoV-2 spike protein to ACE2 is disabled by thiol-based drugs; evidence from in vitro SARS-CoV-2 infection studies.", @@ -1044590,57 +1046882,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.04.20243741", - "rel_title": "SARS-CoV-2 infection and COVID-19 severity in individuals with prior seasonal coronavirus infection.", - "rel_date": "2020-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.04.20243741", - "rel_abs": "A sizable fraction of healthy blood donors have cross-reactive T cells to SARS-CoV-2 peptides due to prior infection with seasonal coronavirus. Understanding the role of cross-reactive T cells in immunity to SARS-CoV-2 has implications for managing the COVID-19 pandemic. We show that individuals with documented history of seasonal coronavirus have a similar SARS-CoV-2 infection rate and COVID-19 severity as those with no prior history of seasonal coronavirus. Our findings suggest prior infection with seasonal coronavirus does not provide immunity to subsequent infection with SARS-CoV-2.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Saurabh Gombar", - "author_inst": "Stanford University" - }, - { - "author_name": "Timothy Bergquist", - "author_inst": "University of Washington" - }, - { - "author_name": "Vikas Pejaver", - "author_inst": "University of Washington" - }, - { - "author_name": "Noah Hammarlund", - "author_inst": "University of Washington" - }, - { - "author_name": "Kanagavel Murugesan", - "author_inst": "Stanford University" - }, - { - "author_name": "Sean Mooney", - "author_inst": "University of Washington" - }, - { - "author_name": "Nigam Shah", - "author_inst": "Stanford University" - }, - { - "author_name": "Benjamin Pinsky", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Niaz Banaei", - "author_inst": "Stanford Univ" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.05.20244673", "rel_title": "Handling and accuracy of four rapid antigen tests for the diagnosis of SARS-CoV-2 compared to RT-qPCR.", @@ -1044885,6 +1047126,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.05.20244541", + "rel_title": "IgG Antibodies against SARS-CoV-2 Correlate with Days from Symptom Onset, Viral Load and IL-10", + "rel_date": "2020-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.05.20244541", + "rel_abs": "The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in a pandemic of the respiratory disease coronavirus disease 2019 (COVID-19). Antibody testing is essential to identify persons exposed to the virus and potentially in predicting disease immunity. 183 COVID-19 patients (68 of whom required mechanical ventilation) and 41 controls were tested for plasma IgG, IgA and IgM against the SARS-CoV-2 S1, S2, receptor binding domain (RBD) and N proteins using the MILLIPLEX(R) SARS-CoV-2 Antigen Panel. Plasma cytokines were concurrently measured using the MILLIPLEX(R) MAP Human Cytokine/Chemokine/Growth Factor Panel A. As expected the 183 COVID-19 positive patients had high levels of IgG, IgA and IgM anti-SARS-CoV-2 antibodies against each of the viral proteins. Sensitivity of anti-S1 IgG increased from 60% to 93% one week after symptom onset. S1-IgG and S1-IgA had specificities of 98% compared to the 41 COVID-19 negative patients. The 68 ventilated COVID-19 positive patients had higher antibody levels than the 115 COVID-19 positive patients who were not ventilated. IgG antibody levels against S1 protein had the strongest positive correlation to days from symptom onset. There were no statistically significant differences in IgG, IgA and IgM antibodies against S1 based on age. We found that patients with the highest levels of anti-SARS-CoV-2 antibodies had the lowest viral load in the nasopharynx. Finally there was a correlation of high plasma IL-10 with low anti-SARS-CoV-2 antibodies. Anti-SARS-CoV-2 antibody levels, as measured by a novel antigen panel, increased within days after symptom onset, achieving > 90% sensitivity and specificity within one week, and were highest in patients who required mechanical ventilation. Antibody levels were inversely associated with viral load but did not differ as a function of age. The correlation of high IL-10 with low antibody response suggests a potentially suppressive role of this cytokine in the humoral immune response in COVID-19.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Mary K Young", + "author_inst": "University of Virginia, School of Medicine" + }, + { + "author_name": "Christine Kornmeier", + "author_inst": "MilliporeSigma" + }, + { + "author_name": "Rebecca M Carpenter", + "author_inst": "University of Virginia, School of Medicine" + }, + { + "author_name": "Nick R Natale", + "author_inst": "University of Virginia" + }, + { + "author_name": "Jennifer M Sasson", + "author_inst": "University of Virginia, School of Medicine" + }, + { + "author_name": "Michael D Solga", + "author_inst": "University of Virginia" + }, + { + "author_name": "Amy J Mathers", + "author_inst": "University of Virginia, School of Medicine" + }, + { + "author_name": "Melinda D Poulter", + "author_inst": "University of Virginia, School of Medicine" + }, + { + "author_name": "Xiao Qiang", + "author_inst": "MilliporeSigma" + }, + { + "author_name": "William A. Petri Jr.", + "author_inst": "University of Virginia, School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.04.20241059", "rel_title": "Sensitive detection and quantification of SARS-CoV-2 in saliva", @@ -1046268,65 +1048564,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.12.04.411736", - "rel_title": "Genetic variability in COVID-19-related genes in the Brazilian population", - "rel_date": "2020-12-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.04.411736", - "rel_abs": "SARS-CoV-2 employs the angiotensin-converting enzyme 2 (ACE2) receptor and the transmembrane serine protease (TMPRSS2) to infect human lung cells. Previous studies have suggested that different host genetic backgrounds in ACE2 and TMPRSS2 could contribute to differences in the rate of infection or severity of COVID-19. Recent studies also showed that variants in 15 genes related to type I interferon immunity to influenza virus could predispose to life-threatening COVID-19 pneumonia. Additional genes (SLC6A20, LZTFL1, CCR9, FYCO1, CXCR6, XCR1, IL6, CTSL, ABO, and FURIN) and HLA alleles have also been implicated in response to infection with SARS-CoV-2. Currently, Brazil has recorded the third-highest number of COVID-19 patients worldwide. We aim to investigate the genetic variation present in COVID-19-related genes in the Brazilian population. We analysed 27 candidate genes and HLA alleles in 954 admixed Brazilian exomes. We used the information available in two public databases (http://www.bipmed.org and http://abraom.ib.usp.br/), and additional exomes from individuals born in southeast Brazil, the region with the highest number of COVID-19 patients in the country. Variant allele frequencies were compared with the 1000 Genomes Project phase 3 (1KGP) and the gnomAD databases. We found 395 non-synonymous variants; of these, 325 were also found in the 1000 Genome Project phase 3 (1KGP) and/or gnomAD. Six of these variants were previously reported as putatively influencing the rate of infection or clinical prognosis for COVID-19. The remaining 70 variants were identified exclusively in the Brazilian sample, with a mean allele frequency of 0.0025. In silico prediction of the impact in protein function revealed that three of these rare variants were pathogenic. Furthermore, we identified HLA alleles that were previously associated with COVID-19 response at loci DQB1 and DRB1. Our results showed genetic variability common to other populations, but also rare and ultra-rare variants exclusively found in the Brazilian population. These findings could potentially lead to differences in the rate of infection or response to infection by SARS-CoV-2 and should be further investigated in patients with the disease.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Rodrigo Secolin", - "author_inst": "University of Campinas (UNICAMP). School of Medical Sciences. Department of Medical Genetics and Genomic Medicine" - }, - { - "author_name": "Tania K de Araujo", - "author_inst": "University of Campinas (UNICAMP). School of Medical Sciences. Department of Medical Genetics and Genomic Medicine" - }, - { - "author_name": "Marina C. Gonsales", - "author_inst": "University of Campinas (UNICAMP). School of Medical Sciences. Department of Medical Genetics and Genomic Medicine" - }, - { - "author_name": "Cristiane S. Rocha", - "author_inst": "University of Campinas (UNICAMP). School of Medical Sciences. Department of Medical Genetics and Genomic Medicine" - }, - { - "author_name": "Michel Satya Naslavsky", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Luiz De Marco", - "author_inst": "Federal University of Minas Gerais (UFMG)" - }, - { - "author_name": "Maria Bicalho", - "author_inst": "Federal University of Minas Gerais (UFMG)" - }, - { - "author_name": "Vinicius L Vazquez", - "author_inst": "Barretos Cancer Hospital" - }, - { - "author_name": "Mayana Zatz", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Wilson A Silva Jr.", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Iscia Lopes-Cendes", - "author_inst": "University of Campinas - UNICAMP" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.12.04.410092", "rel_title": "Ribavirin shows antiviral activity against SARS-CoV-2 and downregulates the activity of TMPRSS2 and the expression of ACE2 in vitro", @@ -1046611,6 +1048848,149 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.01.20241364", + "rel_title": "Post-infectious inflammatory disease in MIS-C features elevated cytotoxicity signatures and autoreactivity that correlates with severity", + "rel_date": "2020-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20241364", + "rel_abs": "Multisystem inflammatory syndrome in children (MIS-C) is a life-threatening post-infectious complication occurring unpredictably weeks after mild or asymptomatic SARS-CoV2 infection in otherwise healthy children. Here, we define immune abnormalities in MIS-C compared to adult COVID-19 and pediatric/adult healthy controls using single-cell RNA sequencing, antigen receptor repertoire analysis, unbiased serum proteomics, and in vitro assays. Despite no evidence of active infection, we uncover elevated S100A-family alarmins in myeloid cells and marked enrichment of serum proteins that map to myeloid cells and pathways including cytokines, complement/coagulation, and fluid shear stress in MIS-C patients. Moreover, NK and CD8 T cell cytotoxicity genes are elevated, and plasmablasts harboring IgG1 and IgG3 are expanded. Consistently, we detect elevated binding of serum IgG from severe MIS-C patients to activated human cardiac microvascular endothelial cells in culture. Thus, we define immunopathology features of MIS-C with implications for predicting and managing this SARS-CoV2-induced critical illness in children.", + "rel_num_authors": 32, + "rel_authors": [ + { + "author_name": "Anjali Ramaswamy", + "author_inst": "Department of Immunobiology, Yale University School of Medicine" + }, + { + "author_name": "Nina N. Brodsky", + "author_inst": "Department of Immunobiology, Yale University School of Medicine; Department of Pediatrics, Yale University School of Medicine" + }, + { + "author_name": "Tomokazu S. Sumida", + "author_inst": "Department of Immunobiology, Yale University School of Medicine; Department of Neurology, Yale University School of Medicine" + }, + { + "author_name": "Michela Comi", + "author_inst": "Department of Immunobiology, Yale University School of Medicine; Department of Neurology, Yale University School of Medicine" + }, + { + "author_name": "Hiromitsu Asashima", + "author_inst": "Department of Immunobiology, Yale University School of Medicine; Department of Neurology, Yale University School of Medicine" + }, + { + "author_name": "Kenneth B. Hoehn", + "author_inst": "Department of Pathology, Yale University School of Medicine" + }, + { + "author_name": "Ningshan Li", + "author_inst": "Department of Biostatistics, Yale School of Public Health" + }, + { + "author_name": "Yunqing Liu", + "author_inst": "Department of Biostatistics, Yale School of Public Health" + }, + { + "author_name": "Aagam Shah", + "author_inst": "Department of Internal Medicine (Cardiology), Yale University School of Medicine; Department of Computer Science, Yale University" + }, + { + "author_name": "Neal G. Ravindra", + "author_inst": "Department of Internal Medicine (Cardiology), Yale University School of Medicine; Department of Computer Science, Yale University" + }, + { + "author_name": "Jason Bishai", + "author_inst": "Department of Internal Medicine (Cardiology), Yale University School of Medicine; Department of Computer Science, Yale University" + }, + { + "author_name": "Alamzeb Khan", + "author_inst": "Department of Pediatrics, Yale University School of Medicine" + }, + { + "author_name": "William Lau", + "author_inst": "NIH Center for Human Immunology (CHI), NIH; Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH." + }, + { + "author_name": "Brian Sellers", + "author_inst": "NIH Center for Human Immunology (CHI), NIH" + }, + { + "author_name": "Neha Bansal", + "author_inst": "NIH Center for Human Immunology (CHI), NIH; Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH" + }, + { + "author_name": "Rachel Sparks", + "author_inst": "Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH" + }, + { + "author_name": "Avraham Unterman", + "author_inst": "Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine" + }, + { + "author_name": "Victoria Habet", + "author_inst": "Department of Pediatrics, Yale University School of Medicine" + }, + { + "author_name": "Andrew J. Rice", + "author_inst": "Department of Immunobiology, Yale University School of Medicine" + }, + { + "author_name": "Jason Catanzaro", + "author_inst": "Department of Pediatrics, Yale University School of Medicine" + }, + { + "author_name": "Harsha Chandnani", + "author_inst": "Department of Pediatrics, Loma Linda School of Medicine" + }, + { + "author_name": "Merrick Lopez", + "author_inst": "Department of Pediatrics, Loma Linda School of Medicine" + }, + { + "author_name": "Naftali Kaminski", + "author_inst": "Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine" + }, + { + "author_name": "Charles S. Dela Cruz", + "author_inst": "Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine" + }, + { + "author_name": "John S. Tsang", + "author_inst": "NIH Center for Human Immunology (CHI), NIH; Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH." + }, + { + "author_name": "Zuoheng Wang", + "author_inst": "Department of Biostatistics, Yale School of Public Health" + }, + { + "author_name": "Xiting Yan", + "author_inst": "Department of Biostatistics, Yale School of Public Health; Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine" + }, + { + "author_name": "Steven H. Kleinstein", + "author_inst": "Department of Pathology, Yale University School of Medicine; Interdepartmental Program in Computational Biology and Bioinformatics, Yale University" + }, + { + "author_name": "David van Dijk", + "author_inst": "Department of Internal Medicine (Cardiology), Yale University School of Medicine; Department of Computer Science, Yale University" + }, + { + "author_name": "Richard W. Pierce", + "author_inst": "Department of Pediatrics, Yale University School of Medicine" + }, + { + "author_name": "David A. Hafler", + "author_inst": "Department of Immunobiology, Yale University School of Medicine; Department of Neurology, Yale University School of Medicine" + }, + { + "author_name": "Carrie L. Lucas", + "author_inst": "Department of Immunobiology, Yale University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.11.30.20236570", "rel_title": "THE THERAPEUTIC POTENTIAL OF IVERMECTIN FOR COVID-19: A REVIEW OF MECHANISMS AND EVIDENCE", @@ -1048186,37 +1050566,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.12.03.20243352", - "rel_title": "Association between Participation in Government Subsidy Program for Domestic Travel and Symptoms Indicative of COVID-19 Infection", - "rel_date": "2020-12-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.03.20243352", - "rel_abs": "ImportanceAs countermeasures against the economic downturn caused by the coronavirus 2019 (COVID-19) pandemic, many countries have introduced or considering financial incentives for people to engage in economic activities such as travel and use restaurants. Japan has implemented a large-scale, nationwide government-funded program that subsidizes up to 50% of all travel expenses since July 2020 with the aim of reviving the travel industry. However, it remains unknown as to how such provision of government subsidies for travel impacted the COVID-19 pandemic.\n\nObjectiveTo investigate the association between participation in government subsidies for domestic travel in Japan and the incidence of COVID-19 infections.\n\nDesign, Setting, and ParticipantsUsing the data from a large internet survey conducted between August 25 and September 30, 2020, in Japan, we examined whether individuals who used subsidies experienced a higher likelihood of symptoms indicative of the COVID-19 infection.\n\nExposureParticipation in the government subsidy program for domestic travel.\n\nMain Outcomes and MeasuresFive symptoms indicative of the COVID-19 infection (high fever, sore throat, cough, headache, and smell and taste disorder) within the past one month of the survey.\n\nResultsOf the 25,482 respondents (50.3% [12,809] women; mean [SD] age, 48.4 [17.4] years), 3,289 (12.9%) participated in the subsidy program at the time of survey. After adjusting for potential confounders, we found that participants in the subsidy program exhibited higher incidence of high fever (adjusted rate, 4.8% for participants vs. 3.7% for non-participants; adjusted odds ratio [aOR], 1.90; 95%CI, 1.42-2.54; p<0.001), sore throat (19.8% vs. 11.3%; aOR, 2.09; 95%CI, 1.37-3.20; p=0.002), cough (19.1% vs. 11.2%; aOR 1.96; 95%CI, 1.27-3.02; p=0.007), headache (29.1% vs. 25.5%; aOR, 1.24; 95%CI, 1.07-1.43; p=0.007), and smell and taste disorder (2.6% vs. 1.8%; aOR 1.98; 95%CI; 1.15-3.40; p=0.01) compared with non-participants.\n\nConclusion and RelevanceThe participants of government subsidies for domestic travel experienced a higher incidence of symptoms indicative of the COVID-19 infection.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Atsushi Miyawaki", - "author_inst": "The University of Tokyo" - }, - { - "author_name": "Takahiro Tabuchi", - "author_inst": "Cancer Control Center, Osaka International Cancer Institute" - }, - { - "author_name": "Yasutake Tomata", - "author_inst": "Faculty of Health and Social Services, Kanagawa University of Human Services" - }, - { - "author_name": "Yusuke Tsugawa", - "author_inst": "UCLA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.12.03.20243345", "rel_title": "Long Covid and the role of physical activity: a qualitative study", @@ -1048357,6 +1050706,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.03.20239863", + "rel_title": "Detailed disease progression of 213 patients hospitalized with Covid-19 in the Czech Republic: An exploratory analysis", + "rel_date": "2020-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.03.20239863", + "rel_abs": "We collected a multi-centric retrospective dataset of patients (N = 213) who were admitted to ten hospitals in Czech Republic and tested positive for SARS-CoV-2. The dataset contains baseline patient characteristics, breathing support required, pharmacological treatment received and multiple markers on daily resolution. Patients in the dataset were treated with hydroxychloroquine (N = 108), azithromycin (N = 72), favipiravir (N = 9), convalescent plasma (N = 7), dexamethasone (N = 4) and remdesivir (N = 3), often in combination. Most patients were admitted during the first wave of the epidemic. To explore association between treatments and patient outcomes we performed multiverse analysis, observing how the conclusions change between defensible choices of statistical model, predictors included in the model and other analytical degrees of freedom. Weak evidence to constrain the potential efficacy of azithromycin and favipiravir can be extracted from the data. Additionally, we performed external validation of several proposed prognostic models for Covid-19 severity showing that they mostly perform unsatisfactorily on our dataset.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Martin Modrak", + "author_inst": "Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic" + }, + { + "author_name": "Paul-Christian Burkner", + "author_inst": "University of Stuttgart, Germany" + }, + { + "author_name": "Tomas Sieger", + "author_inst": "Dept. of Cybernetics, Faculty of Electrical Engineering, Czech Technical University in Prague, Czech Republic" + }, + { + "author_name": "Tomas Slisz", + "author_inst": "Department of Respiratory Medicine, 1st Faculty of Medicine, Charles University; Thomayer Hospital, Prague, Czech Republic" + }, + { + "author_name": "Martina Vasakova", + "author_inst": "Department of Respiratory Medicine, 1st Faculty of Medicine, Charles University; Thomayer Hospital, Prague, Czech Republic" + }, + { + "author_name": "Grigorij Meseznikov", + "author_inst": "Motol University Hospital, Prague, Czech Republic" + }, + { + "author_name": "Luis Fernando Casas-Mendez", + "author_inst": "Motol University Hospital, Prague, Czech Republic" + }, + { + "author_name": "Jaromir Vajter", + "author_inst": "Motol University Hospital, Prague, Czech Republic" + }, + { + "author_name": "Jan Taborsky", + "author_inst": "AGEL Hospital Novy Jicin, Novy Jicin, Czech Republic" + }, + { + "author_name": "Viktor Kubricht", + "author_inst": "Kralovske Vinohrady University Hospital, Prague, Czech Republic" + }, + { + "author_name": "Daniel Suk", + "author_inst": "General University Hospital in Prague, Czech Republic" + }, + { + "author_name": "Jan Horejsek", + "author_inst": "General University Hospital in Prague, Czech Republic" + }, + { + "author_name": "Martin Jedlicka", + "author_inst": "Military Hospital Olomouc, Olomouc, Czech Republic" + }, + { + "author_name": "Adriana Mifkova", + "author_inst": "Military Hospital Olomouc, Olomouc, Czech Republic" + }, + { + "author_name": "Adam Jaros", + "author_inst": "Na Homolce Hospital, Prague, Czech Republic" + }, + { + "author_name": "Miroslav Kubiska", + "author_inst": "Department of Infectious Diseases and Travel Medicine, Faculty of Medicine in Pilsen, Charles University, University Hospital in Pilsen, Pilsen, Czech Republic" + }, + { + "author_name": "Jana Vachalova", + "author_inst": "Department of Infectious Diseases and Travel Medicine, Faculty of Medicine in Pilsen, Charles University, University Hospital in Pilsen, Pilsen, Czech Republic" + }, + { + "author_name": "Robin Sin", + "author_inst": "Department of Infectious Diseases and Travel Medicine, Faculty of Medicine in Pilsen, Charles University, University Hospital in Pilsen, Pilsen, Czech Republic" + }, + { + "author_name": "Marketa Veverkova", + "author_inst": "Horovice Hospital, Horovice, Czech Republic" + }, + { + "author_name": "Zbysek Pospisil", + "author_inst": "Trebic Hospital, Trebic, Czech Republic" + }, + { + "author_name": "Julie Vohryzkova", + "author_inst": "2nd Faculty of Medicine, Charles University in Prague" + }, + { + "author_name": "Rebeka Pokrievkova", + "author_inst": "3rd Faculty of Medicine, Charles University in Prague" + }, + { + "author_name": "Kristian Hrusak", + "author_inst": "2nd Faculty of Medicine, Charles University in Prague" + }, + { + "author_name": "Kristina Christozova", + "author_inst": "2nd Faculty of Medicine, Charles University in Prague" + }, + { + "author_name": "Vianey Leos-Barajas", + "author_inst": "Department of Statistical Sciences, University of Toronto" + }, + { + "author_name": "Karel Fiser", + "author_inst": "Department of Bioinformatics, 2nd Faculty of Medicine, Charles University in Prague" + }, + { + "author_name": "Tomas Hyanek", + "author_inst": "Na Homolce Hospital, Prague, Czech Republic" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.03.20238840", "rel_title": "Galectin antagonist use in mild cases of SARS-CoV-2 cases; pilot feasibility randomised, open label, controlled trial", @@ -1049672,25 +1052144,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2020.11.30.20241224", - "rel_title": "COVID-19 Trends in Florida K-12 Schools, August 10 - November 14, 2020", - "rel_date": "2020-12-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20241224", - "rel_abs": "Data collected from 38 states from August 3 - November 15, 2020 showed more than 250,000 confirmed student and staff cases of SARS-CoV-2 in K-12 schools1. Yet, analysis of COVID-19 case data in USA schools has been extremely limited2,3. To date, no large-scale or state-wide analyses by school level and grade has been published, opening a wide gap in understanding COVID-19 in American schools. A large-scale assessment of available data and trends could provide a baseline for understanding the virus in the K-12 learning environment and dispel misconceptions about the prevalence of COVID-19 in schools.\n\nTable of Contents SummaryUsing the most comprehensive database of K-12 COVID-19 case data in the country, Florida provides clues for understanding student and staff cases in schools.\n\nWhats known on this subjectFlorida schools began reopening to in-person instruction in August have reported more than 18,000 student and staff cases of COVID-19 as of November 14, 2020. Incidence of COVID-19 cases in K-12 students and staff is of urgent public health concern.\n\nWhat this study addsCOVID-19 cases reported in Florida schools were most influenced by community case rates, district mask policies, and percent of students attending face-to-face. Student case rates were highest in high schools (12.5 per 1,000).", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Rebekah D Jones", - "author_inst": "The Covid Monitor" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.30.20239095", "rel_title": "Establishment of CORONET; COVID-19 Risk in Oncology Evaluation Tool to identify cancer patients at low versus high risk of severe complications of COVID-19 infection upon presentation to hospital", @@ -1049979,6 +1052432,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, + { + "rel_doi": "10.1101/2020.12.01.20242099", + "rel_title": "Is the end near? When the different countries will surmount COVID-19 pandemic: new approach applying physical, mathematical and game theory models.", + "rel_date": "2020-12-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20242099", + "rel_abs": "In the year 2020 COVID-19 pandemic was a global issue that changed mankinds lifestyle. Since then, when we will control the pandemic and recover our normal life has become the paramount question to be answered, and it needs to be solved. One problem is that there are wealthy countries, with very good health care systems and scientific resources while others barely dedicate 100 US $ per citizen per year, rich countries could cooperate at different levels with poorer ones. In such a diverse context classic epidemiology models, excellent for predicting short term evolution of the pandemic at a local level are not as suitable for long term predictions at a global scale specially if the data they use are of questionable accuracy. Alternatively, big data and AI approaches have been tried. There is an option that can be more effective. Physics applies predictive models about the duration of an event based on analysing the dynamics of the time evolution of the event itself. These models can be used alongside with probabilistic and game theory models that consider different degrees of cooperation. By means of the physics Delta-t argument and a game theory model (cooperate versus defector) we calculate when different countries may control COVID-19 pandemic. In a non-cooperate model, those countries with more resources and best manage the pandemic will have it under control between May and September 2021, whereas those with no resources will suffer the pandemic until at least October 2023. On the other hand, a strong cooperative model will allow that the majority could control the COVID-19 pandemic between October 2021 and November 2022.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Javier Garcia Garcia de Alcaniz", + "author_inst": "Veterinary Faculty Complutense University Madrid Genetics Department" + }, + { + "author_name": "Victoria Lopez-Rodas Sr.", + "author_inst": "Veterinary Faculty Complutense University Madrid Genetics Department" + }, + { + "author_name": "Eduardo Costas Sr.", + "author_inst": "Veterinary Faculty UCM" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.01.20241695", "rel_title": "Which COVID policies are most effective? A Bayesian analysis of COVID-19 by jurisdiction", @@ -1051026,85 +1053506,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.02.408823", - "rel_title": "A single intranasal or intramuscular immunization with chimpanzee adenovirus vectored SARS-CoV-2 vaccine protects against pneumonia in hamsters.", - "rel_date": "2020-12-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.02.408823", - "rel_abs": "The development of an effective vaccine against SARS-CoV-2, the etiologic agent of COVID-19, is a global priority. Here, we compared the protective capacity of intranasal and intramuscular delivery of a chimpanzee adenovirus-vectored vaccine encoding a pre-fusion stabilized spike protein (ChAd-SARS-CoV-2-S) in Golden Syrian hamsters. While immunization with ChAd-SARS-CoV-2-S induced robust spike protein specific antibodies capable or neutralizing the virus, antibody levels in serum were higher in hamsters immunized by an intranasal compared to intramuscular route. Accordingly, ChAd-SARS-CoV-2-S immunized hamsters were protected against a challenge with a high dose of SARS-CoV-2. After challenge, ChAd-SARS-CoV-2-S-immunized hamsters had less weight loss and showed reductions in viral RNA and infectious virus titer in both nasal swabs and lungs, and reduced pathology and inflammatory gene expression in the lungs, compared to ChAd-Control immunized hamsters. Intranasal immunization with ChAd-SARS-CoV-2-S provided superior protection against SARS-CoV-2 infection and inflammation in the upper respiratory tract. These findings support intranasal administration of the ChAd-SARS-CoV-2-S candidate vaccine to prevent SARS-CoV-2 infection, disease, and possibly transmission.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Traci Bricker", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Tamarand Darling", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Ahmed Hassan", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Houda Harastani", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Allison Soung", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Xiaoping Jiang", - "author_inst": "Washington University in St. Louis School of Medicine" - }, - { - "author_name": "Ya-Nan Dai", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Haiyan Zhao", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Lucas Adams", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Michael Holtzman", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Adam Bailey", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "James Brett Case", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Daved Fremont", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Robyn S Klein", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Michael Diamond", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Adrianus Boon", - "author_inst": "Washington University in St Louis" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.12.02.408575", "rel_title": "In Vitro Analysis of the Anti-viral Potential of nasal spray constituents against SARS-CoV-2", @@ -1051389,6 +1053790,41 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2020.12.02.409037", + "rel_title": "SARS-CoV-2 in Brazil: analysis of molecular variance and genetic diversity in viral haplotypes found in the states of Rio de Janeiro, Sao Paulo, Parana and Tocantins", + "rel_date": "2020-12-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.02.409037", + "rel_abs": "In this work, 18 sequences of the SARS-CoV-2 virus were used, from four Brazilian states (Rio de Janeiro, Sao Paulo, Parana and Tocantins) with 09, 04, 04, 8 and 01 haplotypes, respectively, with lengths ranging from 234 to 29,903 bp. All sequences were publicly available on the National Biotechnology Information Center (NCBI) platform and were previously aligned with the MEGA X software, where all gaps and ambiguous sites were extracted for the construction of the phylogenetic tree. Of the 301 sites analyzed, 68% varied, 131 of which were parsimonium-informative sites. Phylogenetic analyses revealed the presence of two distinct subgroups, corroborated by the high FST (80%). The high degree of polymorphism found among these samples helped to establish a clear pattern of non-genetic structuring, based on the time of divergence between the groups. All molecular variance estimators confirmed that there was no consensus in the conservation of the studied sequences, also indicating a high variation for the protein products of the virus. In a highly miscegenational and diverse population such as the Brazilian population, this observation draws our attention to the need for an urgent increase in public health actions, awareness strategies, hygiene and distancing practices and not the other way around.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Rosane Maria de Albuquerque", + "author_inst": "Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA" + }, + { + "author_name": "Eduarda Doralice Alves Braz Da Silva", + "author_inst": "Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA" + }, + { + "author_name": "Dallynne Barbara Ramos Venancio", + "author_inst": "Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA" + }, + { + "author_name": "Robson da Silva Ramos", + "author_inst": "Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA" + }, + { + "author_name": "Pierre Teodosio Felix Sr.", + "author_inst": "Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.12.03.409763", "rel_title": "SARS-CoV-2 D614 and G614 spike variants impair neuronal synapses and exhibit differential fusion ability", @@ -1052504,49 +1054940,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.30.20241232", - "rel_title": "Bridging the gaps in test interpretation of SARS-CoV-2 through Bayesian network modelling", - "rel_date": "2020-12-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20241232", - "rel_abs": "BackgroundIn the absence of an established gold standard, an understanding of the testing cycle from individual exposure to test outcome report is required to guide the correct interpretation of SARS-CoV-2 reverse transcriptase real-time polymerase chain reaction (RT-PCR) results and optimise the testing processes. Bayesian network (BN) models have been used within healthcare to bring clarity to complex problems. We use this modelling approach to construct a comprehensive framework for understanding the real world predictive value of individual RT-PCR results.\n\nMethodsWe elicited knowledge from domain experts to describe the test process from viral exposure to interpretation of the laboratory test, through a facilitated group workshop. A preliminary model was derived based on the elicited knowledge, then subsequently refined, parameterised and validated with a second workshop and one-on-one discussions.\n\nResultsCausal relationships elicited describe the interactions of multiple variables and their impact on a RT-PCR result. Some interactions are infrequently observable and accounted for across the testing cycle such as pre-testing factors, sample collector experience and RT-PCR platform. By setting the input variables as evidence for a given subject and preliminary parameterisation, three scenarios were simulated to demonstrate potential uses of the model.\n\nConclusionsThe core value of this model is a deep understanding of the total testing cycle, bridging the gap between a persons true infection status and their test outcome. This model can be adapted to different settings, testing modalities and pathogens, adding much needed nuance to the interpretations of results.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Yue Wu", - "author_inst": "The University of Sydney" - }, - { - "author_name": "David Foley", - "author_inst": "Perth Childrens Hospital" - }, - { - "author_name": "Jessica Ramsay", - "author_inst": "Telethon Kids Institute" - }, - { - "author_name": "Owen Woodberry", - "author_inst": "Monash University" - }, - { - "author_name": "Steven Mascaro", - "author_inst": "Monash University" - }, - { - "author_name": "Ann E Nicholson", - "author_inst": "Monash University" - }, - { - "author_name": "Tom Snelling", - "author_inst": "The university of Sydney" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.30.20241208", "rel_title": "Rapid and accurate point-of-care testing for SARS-CoV2 antibodies", @@ -1052851,6 +1055244,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.30.20241331", + "rel_title": "Serological prevalence of SARS-CoV-2 infection and associated factors in health care workers in a \"non-COVID\" hospital in Mexico City", + "rel_date": "2020-12-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20241331", + "rel_abs": "In spite of high mortality from COVID-19, in Mexico the number of confirmed cases and diagnostic tests per million population are lower than for other comparable countries, which leads to uncertainty about the actual extent of the pandemic. In Mexico City, healthcare workers represent an important fraction of individuals with SARS-CoV-2 infection. This work aims to estimate the frequency of antibodies to SARS-CoV-2 and identify associated factors in healthcare workers at a large hospital in Mexico City. We conducted a serological survey in a non-COVID national referral teaching hospital. We selected a representative sample of 300 individuals. Blood samples were collected and questionnaires were applied between August 10th and September 9th, 2020. ELISA results indicate a serological prevalence of SARS-CoV-2 infection of 13.0%. Working in the janitorial and security groups, having an educational level below a university degree, and living with a larger number of people, were also identified as sociodemographic factors that increase the risk of having SARS-CoV-2 infection. Thus, less favored socioeconomic groups are at significantly higher risk of experiencing SARS-CoV-2 infection. Even in healthcare workers there is still a majority of individuals that are seronegative, and thus the risk of continued epidemic waves and mortality remains high.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Esteban Cruz-Arenas", + "author_inst": "Epidemiological Vigilance Unit, Instituto Nacional de Rehabilitacion \"Luis Guillermo Ibarra Ibarra\"" + }, + { + "author_name": "Elizabeth Cabrera-Ruiz", + "author_inst": "Instituto Nacional de Rehabilitacion \"Luis Guillermo Ibarra Ibarra\"" + }, + { + "author_name": "Sara Laguna-Barcenas", + "author_inst": "Instituto Nacional de Rehabilitacion \"Luis Guillermo Ibarra Ibarra\"" + }, + { + "author_name": "Claudia A. Colin-Castro", + "author_inst": "Infectious Diseases Division, Instituto Nacional de Rehabilitacion \"Luis Guillermo Ibarra Ibarra\"" + }, + { + "author_name": "Tatiana Chavez", + "author_inst": "Epidemiological Vigilance Unit, Instituto Nacional de Rehabilitacion \"Luis Guillermo Ibarra Ibarra\"" + }, + { + "author_name": "Rafael Franco-Cendejas", + "author_inst": "Infectious Diseases Division, Instituto Nacional de Rehabilitacion \"Luis Guillermo Ibarra Ibarra\"" + }, + { + "author_name": "Clemente Ibarra", + "author_inst": "Instituto Nacional de Rehabilitacion \"Luis Guillermo Ibarra Ibarra\"" + }, + { + "author_name": "Javier Perez-Orive", + "author_inst": "Instituto Nacional de Rehabilitacion \"Luis Guillermo Ibarra Ibarra\"" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.30.20239566", "rel_title": "Smart Investment of Virus RNA Testing Resources to Enhance Covid-19 Mitigation", @@ -1054706,101 +1057146,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.12.01.407148", - "rel_title": "Mucosal Associated Invariant T (MAIT) Cell Responses Differ by Sex in COVID-19", - "rel_date": "2020-12-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.01.407148", - "rel_abs": "Sexual dimorphisms in immune responses contribute to coronavirus disease 2019 (COVID-19) outcomes, yet the mechanisms governing this disparity remain incompletely understood. We carried out sex-balanced sampling of peripheral blood mononuclear cells from confirmed COVID-19 inpatients and outpatients, uninfected close contacts, and healthy controls for 36-color flow cytometry and single cell RNA-sequencing. Our results revealed a pronounced reduction of circulating mucosal associated invariant T (MAIT) cells in infected females. Integration of published COVID-19 airway tissue datasets implicate that this reduction represented a major wave of MAIT cell extravasation during early infection in females. Moreover, female MAIT cells possessed an immunologically active gene signature, whereas male counterparts were pro-apoptotic. Collectively, our findings uncover a female-specific protective MAIT profile, potentially shedding light on reduced COVID-19 susceptibility in females.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Chen Yu", - "author_inst": "Duke University" - }, - { - "author_name": "Sejiro Littleton", - "author_inst": "Duke University" - }, - { - "author_name": "Nicholas Giroux", - "author_inst": "Duke University" - }, - { - "author_name": "Rose Mathew", - "author_inst": "Duke University" - }, - { - "author_name": "Shengli Ding", - "author_inst": "Duke University" - }, - { - "author_name": "Joan Kalnitsky", - "author_inst": "Duke University" - }, - { - "author_name": "Elizabeth Petzold", - "author_inst": "Duke University" - }, - { - "author_name": "Hong Chung", - "author_inst": "Duke University" - }, - { - "author_name": "Grecia rivera Palomino", - "author_inst": "Duke University" - }, - { - "author_name": "Tomer Rotstein", - "author_inst": "Duke University" - }, - { - "author_name": "Rui Xi", - "author_inst": "Duke University" - }, - { - "author_name": "Emily R Ko", - "author_inst": "Duke University" - }, - { - "author_name": "Ephraim L Tsalik", - "author_inst": "Duke University" - }, - { - "author_name": "gregory sempowski", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Thomas N Denny", - "author_inst": "Duke University" - }, - { - "author_name": "Thomas W Burke", - "author_inst": "Duke University" - }, - { - "author_name": "Micah T McClain", - "author_inst": "Duke University" - }, - { - "author_name": "Christopher W. Woods", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Xiling Shen", - "author_inst": "Duke University" - }, - { - "author_name": "Daniel R Saban", - "author_inst": "Duke University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.12.01.407007", "rel_title": "Multimodal Single-Cell Omics Analysis of COVID-19 Sex Differences in Human Immune Systems", @@ -1055069,6 +1057414,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.25.20238915", + "rel_title": "Alcohol Consumption is Associated with Poor Prognosis in Obese Patients with COVID-19: a Mendelian Randomization Study using UK Biobank", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20238915", + "rel_abs": "BackgroundAcute and chronic alcohol abuse have adverse impacts on both the innate and adaptive immune response, which may result in reduced resistance to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection and promote the progression of coronavirus disease 2019 (COVID-19). However, there are no large population-based data evaluating potential causal associations between alcohol consumption and COVID-19.\n\nMethodWe conducted a Mendelian randomization study using data from UK Biobank to explore the association between alcohol consumption and risk of SARS-CoV-2 infection and serious clinical outcomes in patients with COVID-19. A total of 12,937 participants aged 50-83 who tested for SARS-CoV-2 between 16 March to 27 July 2020 (12.1% tested positive) were included in the analysis. The exposure factor was alcohol consumption. Main outcomes were SARS-CoV-2 positivity and death in COVID-19 patients. We generated weighted and unweighted allele scores using three genetic variants (rs1229984, rs1260326, and rs13107325) and applied the allele scores as the instrumental variables to assess the effect of alcohol consumption on outcomes. Analyses were conducted separately for white participates with and without obesity.\n\nResultsOf the 12,937 participants, 4,496 were never or infrequent drinkers and 8,441 were frequent drinkers. (including 1,156 light drinkers, 3,795 moderate drinkers, and 3,490 heavy drinkers). Both logistic regression and Mendelian randomization analyses found no evidence that alcohol consumption was associated with risk of SARS-CoV-2 infection in participants either with (OR=0.963, 95%CI 0.800-1.159; q =1.000) or without obesity (OR=0.891, 95%CI 0.755-1.053; q =.319). However, frequent drinking (HR=1.565, 95%CI 1.012-2.419; q =.079), especially heavy drinking (HR=2.071, 95%CI 1.235-3.472; q =.054), was associated with higher risk of death in patients with obesity and COVID-19, but not in patients without obesity. Notably, the risk of death in frequent drinkers with obesity increased slightly with the average amount of alcohol consumed weekly (HR=1.480, 95%CI 1.059-2.069; q =.099).\n\nConclusionsOur findings suggested alcohol consumption may had adverse effects on the progression of COVID-19 in white participants with obesity, but was not associate with susceptibility to SARS-CoV-2 infection.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Xiude Fan", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Zhengwen Liu", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Kyle L Poulsen", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Xiaoqin Wu", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Tatsunori Miyata", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Srinivasan Dasarathy", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Daniel M. Rotroff", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Laura E Nagy", + "author_inst": "Cleveland Clinic" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.28.20240325", "rel_title": "Seroprevalence of anti-SARS-COV-2 antibodies in blood donors from Nuevo Leon state, Mexico, during the beginning of the COVID-19 pandemic", @@ -1056288,29 +1058680,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.26.20239434", - "rel_title": "The evolving worldwide dynamic state of the COVID-19 outbreak", - "rel_date": "2020-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.26.20239434", - "rel_abs": "The dynamic characterization of the COVID-19 outbreak is critical to implement effective actions for its control and eradication but the information available at a global scale is not sufficiently reliable to be used directly. Here, we integrate multiple data sources through dynamical constraints to quantify its temporal evolution and controllability around the world and within the United States. Overall, the numbers of actively infectious individuals have remained high beyond targeted controllability, with worldwide estimates of 10.24 million on November 24, 2020, totaling in 266.1 million cumulative infections growing at a rate of 11.12 million new infections per week. The actively infectious population reached a local maximum of 7.33 million on July 16, 2020 and remained virtually stagnant at a global scale, with growth rates for most countries around zero that compensated each other, until reverting to net growth on September 22, 2020. We validated the approach, contrasting with prevalence data and the effects of nonpharmaceutical interventions, and we identified general patterns of recession, stabilization, and resurgence. The diversity of dynamic behaviors of the outbreak across countries is paralleled by those of states and territories in the United States, converging to remarkably similar global states in both cases. Our results offer precise insights into the dynamics of the outbreak and an efficient avenue for the estimation of the prevalence rates over time.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Jose M. G. Vilar", - "author_inst": "Biofisika Intitute (CSIC-UPV/EHU) and Ikerbasque" - }, - { - "author_name": "Leonor Saiz", - "author_inst": "University of California, Davis" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.26.20239418", "rel_title": "Predictors of QT Interval Prolongation in Critically-ill Patients with SARS-CoV-2 Infection Treated with Hydroxychloroquine", @@ -1056487,6 +1058856,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.26.20239368", + "rel_title": "Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.26.20239368", + "rel_abs": "The effective reproductive number Re is a key indicator of the growth of an epidemic. Since the start of the SARS-CoV-2 pandemic, many methods and online dashboards have sprung up to monitor this number through time. However, these methods are not always thoroughly tested, correctly placed in time, or are overly confident during high incidence periods. Here, we present a method for timely estimation of Re, applied to COVID-19 epidemic data from 170 countries. We thoroughly evaluate the method on simulated data, and present an intuitive web interface for interactive data exploration. We show that, in early 2020, in the majority of countries the estimated Re dropped below 1 only after the introduction of major non-pharmaceutical interventions. For Europe the implementation of non-pharmaceutical interventions was broadly associated with reductions in the estimated Re. Globally though, relaxing non-pharmaceutical interventions had more varied effects on subsequent Re estimates. Our framework is useful to inform governments and the general public on the status of epidemics in their country, and is used as the official source of Re estimates for SARS-CoV-2 in Switzerland. It further allows detailed comparison between countries and in relation to covariates such as implemented public health policies, mobility, behaviour, or weather data.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jana S Huisman", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Jeremie Scire", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Daniel C Angst", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Richard A Neher", + "author_inst": "University of Basel" + }, + { + "author_name": "Sebastian Bonhoeffer", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Tanja Stadler", + "author_inst": "ETH Zurich" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.27.20239087", "rel_title": "Dietary supplements during the COVID-19 pandemic: insights from 1.4M users of the COVID Symptom Study app - a longitudinal app-based community survey", @@ -1057822,29 +1060230,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.11.27.20239970", - "rel_title": "Willingness to vaccinate against COVID-19 in the US: Longitudinal evidence from a nationally representative sample of adults from April-October 2020", - "rel_date": "2020-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.27.20239970", - "rel_abs": "IntroductionVaccines against COVID-19 have been developed in unprecedented time. However, the effectiveness of any vaccine is dictated by the proportion of the population willing to be vaccinated. In this observational population-based study we examined intentions to be vaccinated against COVID-19 over the course of the pandemic.\n\nMethodsWe analyzed longitudinal data from a nationally representative sample of 7,547 US adults enrolled in the Understanding America Study (UAS). Participants reporting being willing, undecided and unwilling to get vaccinated against coronavirus across 13 assessments conducted from April-October, 2020. Public attitudes to vaccination against the coronavirus were also assessed.\n\nResultsWillingness to vaccinate declined from 71% in April to 53.6% in October. This was explained by an increase in the percentage of participants undecided about vaccinating (from 10.5% to 14.4%) and the portion of the sample unwilling to vaccinate (from 18.5% to 32%). The population subgroups most likely to be undecided/unwilling to vaccinate were those without a degree (undecided: RRR=2.47, 95% CI: 2.04-3.00; unwilling: RRR=1.92, 95% CI: 1.67-2.20), Black participants (undecided: RRR=2.18, 95% CI: 1.73-2.74; unwilling: RRR=1.98, 95% CI: 1.63-2.42), and females (undecided: RRR=1.41, 95% CI: 1.20-1.65; unwilling: RRR=1.29, 95% CI: 1.14-1.46). Those aged 65+, those on high incomes, and other race/ethnicity participants were least likely to be undecided or unwilling to vaccinate. Concerns about potential side effects of a vaccine were common.\n\nConclusionsIntentions to be vaccinated against coronavirus have declined rapidly during the pandemic and close to half of Americans are undecided or unwilling to be vaccinated.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Michael Daly", - "author_inst": "Maynooth University" - }, - { - "author_name": "Eric Robinson", - "author_inst": "University of Liverpool" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.29.20240614", "rel_title": "AI4CoV: Matching COVID-19 Patients to Treatment Options Using Artificial Intelligence", @@ -1057997,6 +1060382,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.29.20237875", + "rel_title": "CLINICAL TRIALS IN COVID-19 MANAGEMENT & PREVENTION: A META-EPIDEMIOLOGICAL STUDY EXAMINING METHODOLOGICAL QUALITY", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.29.20237875", + "rel_abs": "BackgroundThe coronavirus disease (Covid-19) pandemic has produced a large number of clinical trial reports with unprecedented rapidity, raising concerns about methodological quality and potential for research waste.\n\nObjectivesTo describe the characteristics of randomized clinical trials (RCTs) investigating prophylaxis or treatment of Covid-19 infection and examine the effect of trial characteristics on whether the study reported a statistically significant effect on the primary outcome(s).\n\nStudy DesignMeta-epidemiological study of Covid-19 treatment and prophylaxis RCTs.\n\nEligibility criteriaEnglish-language RCTs (peer-reviewed or preprint) that evaluated pharmacologic agents or blood products compared to standard care, placebo, or an active comparator among participants with suspected or confirmed Covid-19 or at risk for Covid-19. We excluded trials of vaccines or traditional herbal medicines.\n\nInformation sourcesWe searched 25 databases in the US Centre for Disease Control Downloadable Database from January 1 to October 21, 2020.\n\nTrial appraisal and synthesis methodsWe extracted trial characteristics including number of centres, funding sources (industry versus non-industry), and sample size. We assessed risk of bias (RoB) using the modified Cochrane RoB 2.0 Tool. We used descriptive statistics to summarize trial characteristics and logistic regression to evaluate the association between RoB due to the randomization process, centre status (single vs. multicentre), funding source, and sample size, and statistically significant effect in the primary outcome.\n\nResultsWe included 91 RCTs (46,802 participants) evaluating Covid-19 therapeutic drugs (n = 76), blood products (n = 9) or prophylactic drugs (n = 6). Of these, 40 (44%) were single-centre, 23 (25.3%) enrolled < 50 patients, and 28 (30.8%) received industry funding. RoB varied across trials, with high or probably high overall RoB in 75 (82.4%) trials, most frequently due to deviations from the intended protocol (including blinding) and randomization processes. Thirty-eight trials (41.8%) found a statistically significant effect in the primary outcome. RoB due randomization (odds ratio [OR] 3.77, 95% confidence interval [CI], 1.47 to 9.72) and single centre trials (OR 3.15, 95% CI, 1.25 to 7.97) were associated with higher likelihood of finding a statistically significant effect.\n\nConclusionsThere was high variability in RoB amongst Covid-19 trials. RoB attributed to the randomization process and single centre status were associated with a three-fold increase in the odds of finding a statistically significant effect. Researchers, funders, and knowledge users should remain cognizant of the impact of study characteristics, including RoB, on trial results when designing, conducting, and appraising Covid-19 trials.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Kimia Honarmand", + "author_inst": "Western University" + }, + { + "author_name": "Jeremy Penn", + "author_inst": "McMaster University" + }, + { + "author_name": "Arnav Agarwal", + "author_inst": "McMaster University" + }, + { + "author_name": "Reed Siemieniuk", + "author_inst": "McMaster University" + }, + { + "author_name": "Romina Brignardello-Petersen", + "author_inst": "McMaster University" + }, + { + "author_name": "Jessica Bartoszko", + "author_inst": "McMaster University" + }, + { + "author_name": "Dena Zeraatkar", + "author_inst": "McMaster University" + }, + { + "author_name": "Thomas Agoritsas", + "author_inst": "McMaster University" + }, + { + "author_name": "Karen Burns", + "author_inst": "McMaster University" + }, + { + "author_name": "Shannon Fernando", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Farid Foroutan", + "author_inst": "University Health Network" + }, + { + "author_name": "Long Ge", + "author_inst": "Lanzhou University" + }, + { + "author_name": "Francois Lamontagne", + "author_inst": "Universite de Sherbrooke" + }, + { + "author_name": "Mario Alejandro Jiminez-Mora", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Srinivas Murthy", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Juan Jose Yepes-Nunez", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Per Olav Vandvik", + "author_inst": "University of Oslo" + }, + { + "author_name": "Zhikang Ye", + "author_inst": "University Health Network" + }, + { + "author_name": "Bram Rochwerg", + "author_inst": "McMaster University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.29.20240549", "rel_title": "Nationwide SARS-CoV-2 Surveillance Study for Sewage and Sludges of Wastewater Treatment Plants in Turkey", @@ -1059416,37 +1061892,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.11.25.20238766", - "rel_title": "The psychosocial impact on frontline health and social care professionals in the UK during the COVID-19 pandemic: a qualitative interview study.", - "rel_date": "2020-11-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20238766", - "rel_abs": "ObjectivesTo explore the psychosocial well-being of health and social care professionals working during the COVID-19 pandemic.\n\nDesignThis was a qualitative study deploying in-depth, individual interviews, which were audio-recorded and transcribed verbatim. Thematic analysis was used for coding.\n\nParticipantsThis study involved 25 participants from a range of frontline professions in health and social care.\n\nSettingInterviews were conducted over the phone or video call, depending on participant preference.\n\nResultsFrom the analysis, we identified 5 overarching themes: communication challenges, work-related stressors, support structures, personal growth, and individual resilience. The participants expressed difficulties such as communication challenges and changing work conditions, but also positive factors such as increased team unity at work, and a greater reflection on what matters in life.\n\nConclusionsThis study provides evidence on the support needs of health and social care professionals amid continued and future disruptions caused by the pandemic. It also elucidates some of the successful strategies (such as mindfulness, hobbies, restricting news intake, virtual socialising activities) deployed by health and social care professionals that can support their resilience and well-being and be used to guide future interventions.\n\nStrengths and limitations of this studyO_LIThis is the first study in the UK to interview both health and social care professionals working in a range of settings on their experiences working through COVID-19.\nC_LIO_LIThis study used a strong theoretical approach to inform the topic guide, and one-to-one interviews allowed in-depth analysis of the psychosocial experiences of health and social care professionals, complementing the wider availability of quantitative evidence.\nC_LIO_LIWe interviewed a wide range of professions, which provided breadth of experience but might limit the specificity of findings.\nC_LIO_LIGiven the fluctuating nature of the pandemic, attitudes of health and social care professionals may change over time. This can be challenging to capture during a single interview, however we did ask questions on how their experience had progressed longitudinally.\nC_LIO_LIOur sample may have been biased towards people who had more free time to participate and so were coping better than others. However, our sample still described a number of stressful experiences during the pandemic, and it is also possible that workers who were frustrated or stressed wished to express their views.\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Henry Aughterson", - "author_inst": "University College London" - }, - { - "author_name": "Alison Mckinlay", - "author_inst": "University College London" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - }, - { - "author_name": "Alexandra Burton", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.25.20238675", "rel_title": "Autosomal Dominant Polycystic Kidney Disease does not significantly alter major COVID-19 outcomes among veterans", @@ -1059675,6 +1062120,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.24.20238295", + "rel_title": "The Relationship between Weekly Periodicity and COVID-19 Progression", + "rel_date": "2020-11-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20238295", + "rel_abs": "COVID-19 is extraordinary both as once-in-a-lifetime pandemic and having abundant real-time case data, thus providing an extraordinary opportunity for timely independent analysis and novel perspectives. We investigate the weekly periodicity in the daily reported new cases and new deaths with the implied relationships to the societal and institutional responses using autocorrelation and Fourier transformation. The results show significant linear correlations between the weekly periodicity and the total cases and deaths, ranging from 50% to 84% for sizable groups of countries with population normalized deaths spanning nearly three orders of magnitude, from a few to approaching a thousand per million. In particular, the Strength Indicator of the periodicity in the new cases, defined by the autocorrelation with a 7-day lag, is positively correlated strongly to the total deaths per million in respective countries. The Persistence Indicator of the periodicity, defined as the average of three autocorrelations with 7-, 14- and 21-day lags, is an overall better indicator of the progression of the pandemic. For longer time series, Fourier transformation gives similar results. This analysis begins to fill the gap in modeling and simulation of epidemics with the inclusion of high frequency modulations, in this case most likely from human behaviors and institutional practices, and reveals that they can be highly correlated to the magnitude and duration of the pandemic. The results show that there is significant need to understand the causes and effects of the periodicity and its relationship to the progression and outcome of the pandemic, and how we could adapt our strategies and implementations to reduce the extent of the impact of COVID-19.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Sophia Li", + "author_inst": "Massachusetts Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.25.20236224", "rel_title": "The Impact of COVID-19 on Care Seeking Behavior of Patients at Tertiary Care Follow-up Clinics: A Cross-Sectional Telephone Survey. Addis Ababa, Ethiopia.", @@ -1060586,37 +1063050,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.11.24.20237040", - "rel_title": "Rapid environmental monitoring, capture, and destruction activities of SARS-CoV-2 during the Covid-19 health emergency", - "rel_date": "2020-11-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20237040", - "rel_abs": "ObjectivesSARS-CoV-2 pandemic is a health emergency for occupational healthcare workers at COVID19 hospital wards in Italy. The objective of the study was to investigate if U-Earth AIRcel bioreactors were effective in monitoring and improving air quality via detection, capture, and destruction of the SARS-CoV-2 virus, reducing the risk of transmission among healthcare workers.\n\nMethodsU-Earth AIRcel bioreactors are a demonstrated effective biomonitoring system. We implemented a methodological approach wherein they were placed at various hospitals treating COVID-19 patients in Italy. The detection of the SARS-CoV-2 virus was achieved through rapid biomonitoring testing of the solutes from the AIRcel bioreactors via SARS-CoV-2 rapid test antigen and consecutive reverse transcription-polymerase chain reaction (RT-PCR) analysis with the multiplex platform (XABT) and the Real-Time PCR Rotor-Gene.\n\nResultsThe marked presence of the SARS-CoV-2 virus was found in multiple water samples via the detection of ORF1ab + N and/or E gene involved in gene expression and cellular signaling of the SARS-CoV virus. The AIRcel bioreactors were able to neutralize the virus effectively as traces of the viruses were no longer found in multiple solute samples after an overnight period.\n\nConclusionsTransmission of COVID-19 via bio-aerosols, transmitted by infected patients, remains a viable threat for health workers. AIRcel bioreactors allow for rapid biomonitoring testing for early virus detection within the environment, reducing the risk of exponential contagion exposure and maintaining good air quality without endangering health workers. This same protocol can also be extended to public spaces as a bio-monitoring tool for hotpots early detection.\n\nKey messagesO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LITransmission of SARS-CoV-2 virus via bio-aerosols is a threat to health care workers. Only few studies have conducted investigations on how to limit the spread of the virus via air purifiers.\nC_LIO_LIExisting studies show a higher risk to health care workers serving at COVID-19 wards with a higher risk of viral transmission.\nC_LI\n\nWhat are the new findings?O_LIIn this study, SARS-CoV-2 virus traces were captured by U-Earth air purifier bioreactor units placed at several hospitals in Italy.\nC_LIO_LIAIRcel bioreactors achieved early detection of the SARS-CoV-2 virus within the environment via rapid biomonitoring testing.\nC_LIO_LIAIRcel bioreactors have proved effective in biomonitoring via the detection, capture, and destruction of SARS-CoV-2 virus through reverse transcription-polymerase chain reaction (RT-PCR) analysis with the multiplex platform (XABT) Multiple Real-Time PCR Rotor-Gene.\nC_LI\n\nHow might this impact on policy or clinical practice in the foreseeable future?O_LIThis study shows the need for effective surveillance and biomonitoring to contain the spread of the SARS-CoV-2 virus. AIRcel bioreactors, an effective occupational surveillance system, can reduce the transmission of the virus to health care workers serving COVID-19 infected patients at hospital wards.\nC_LIO_LIAIRcel bioreactors can also be used in public spaces and other settings, such as schools, to increase the speed of detection of the SARS-CoV-2 virus and improve control of the environment, thereby decreasing the exponential growth of the pandemic.\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Roberto Marchetti", - "author_inst": "Laboratori Clodia Diagnostics & Services" - }, - { - "author_name": "Martina Stella", - "author_inst": "Laboratori Clodia Diagnostics & Services" - }, - { - "author_name": "Debjyoti Talukdar", - "author_inst": "Teerthanker Mahaveer University, Moradabad Campus" - }, - { - "author_name": "Rosaria Erika Pileci", - "author_inst": "U-Earth Biotech Ltd" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.11.19.20234237", "rel_title": "Association of Toll-like receptor 7 variants with life-threatening COVID-19 disease in males", @@ -1060945,6 +1063378,189 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.25.20229088", + "rel_title": "Use of dialysis, tracheostomy, and extracorporeal membrane oxygenation among 240,392 patients hospitalized with COVID-19 in the United States", + "rel_date": "2020-11-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20229088", + "rel_abs": "ObjectiveTo estimate the proportion of patients hospitalized with COVID-19 who undergo dialysis, tracheostomy, and extracorporeal membrane oxygenation (ECMO).\n\nDesignA network cohort study.\n\nSettingSix databases from the United States containing routinely-collected patient data: HealthVerity, Premier, IQVIA Open Claims, Optum EHR, Optum SES, and VA-OMOP.\n\nPatientsPatients hospitalized with a clinical diagnosis or a positive test result for COVID-19.\n\nInterventionsDialysis, tracheostomy, and ECMO.\n\nMeasurements and Main Results240,392 patients hospitalized with COVID-19 were included (22,887 from HealthVerity, 139,971 from IQVIA Open Claims, 29,061 from Optum EHR, 4,336 from OPTUM SES, 36,019 from Premier, and 8,118 from VA-OMOP). Across the six databases, 9,703 (4.04% [95% CI: 3.96% to 4.11%]) patients received dialysis, 1,681 (0.70% [0.67% to 0.73%]) had a tracheostomy, and 398 (0.17% [95% CI: 0.15% to 0.18%]) patients underwent ECMO over the 30 days following hospitalization. Use of ECMO was generally concentrated among patients who were younger, male, and with fewer comorbidities except for obesity. Tracheostomy was used for a similar proportion of patients regardless of age, sex, or comorbidity. While dialysis was used for a similar proportion among younger and older patients, it was more frequent among male patients and among those with chronic kidney disease.\n\nConclusionUse of dialysis among those hospitalized with COVID-19 is high at around 4%. Although less than one percent of patients undergo tracheostomy and ECMO, the absolute numbers of patients who have undergone these interventions is substantial and can be expected to continue grow given the continuing spread of the COVID-19.", + "rel_num_authors": 42, + "rel_authors": [ + { + "author_name": "Edward Burn", + "author_inst": "1) Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain 2)Centre for Statistics in M" + }, + { + "author_name": "Anthony G. Sena", + "author_inst": "1) Janssen Research & Development, Titusville, NJ, USA 2) Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" + }, + { + "author_name": "Albert Prats-Uribe", + "author_inst": "Centre for Statistics in Medicine, NDORMS, University of Oxford, Uk" + }, + { + "author_name": "Matthew Spotnitz", + "author_inst": "Department of Biomedical Informatics, Columbia University, New York, NY, US," + }, + { + "author_name": "Scott DuVall", + "author_inst": "University of Utah School of Medicine, Salt Lake City, UT, US" + }, + { + "author_name": "Kristine E. Lynch", + "author_inst": "1) Department of Veterans Affairs, Salt Lake City, UT, US 2) Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA," + }, + { + "author_name": "Michael E. Matheny", + "author_inst": "1)Tennessee Valley Healthcare System, Veterans Affairs Medical Center, Nashville, TN, USA, 2) Department of Biomedical Informatics, Vanderbilt University Medica" + }, + { + "author_name": "Fredrik Nyberg", + "author_inst": "School of Public Health and Community Medicine,, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden" + }, + { + "author_name": "Waheed-Ul-Rahman Ahmed", + "author_inst": "1) Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, OX3 7LD" + }, + { + "author_name": "Osaid Alser", + "author_inst": "Massachusetts General Hospital, Harvard Medical School, Boston, USA," + }, + { + "author_name": "Heba Alghoul", + "author_inst": "Faculty of Medicine, Islamic University of Gaza, Palestine," + }, + { + "author_name": "Thamir Alshammari", + "author_inst": "Medication Safety Research Chair, King Saud University , Riyadh, Saudi Arabia" + }, + { + "author_name": "Lin Zhang", + "author_inst": "1) School of Population Medicine and Public Health, Peking Union Medical College and Chinese Academy of Medical Sciences 2)School of Population and Global Hea" + }, + { + "author_name": "Paula Casajust", + "author_inst": "Real-World Evidence, Trial Form Support, Barcelona, Spain" + }, + { + "author_name": "Carlos Areia", + "author_inst": "Nuffield Department of Clinical Neurosciences, University of Oxford" + }, + { + "author_name": "Karishma Shah", + "author_inst": "Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Botnar Research Centre, Oxford, UK" + }, + { + "author_name": "Christian Reich", + "author_inst": "Real World Solutions, IQVIA, Cambridge, MA USA," + }, + { + "author_name": "Clair Blacketer", + "author_inst": "Janssen Research & Development, Titusville, NJ, USA," + }, + { + "author_name": "Alan Andryc", + "author_inst": "Janssen Research & Development, Titusville, NJ, USA," + }, + { + "author_name": "Stephen Fortin", + "author_inst": "Janssen Research & Development, Titusville, NJ, USA," + }, + { + "author_name": "Karthik Natarajan", + "author_inst": "Department of Biomedical Informatics, Columbia University, New York, NY, US," + }, + { + "author_name": "Mengchun Gong", + "author_inst": "Southern Medical University, Guangzhou, China" + }, + { + "author_name": "Asieh Golozar", + "author_inst": "1) Regeneron Pharmaceuticals, NY US 2) Johns Hopkins Bloomberg School of Public Health, Baltimore, MD US" + }, + { + "author_name": "Daniel Morales", + "author_inst": "Division of Population Health and Genomics, University of Dundee" + }, + { + "author_name": "Peter Rijnbeek", + "author_inst": "Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" + }, + { + "author_name": "Vignesh Subbian", + "author_inst": "College of Engineering, The University of Arizona, Tucson, Arizona, USA," + }, + { + "author_name": "Elena Roel", + "author_inst": "Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain," + }, + { + "author_name": "Martina Recalde", + "author_inst": "1) Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain 2) Universitat Autonoma de Ba" + }, + { + "author_name": "Jennifer C.E. Lane", + "author_inst": "Centre for Statistics in Medicine, NDORMS, University of Oxford, UK" + }, + { + "author_name": "David Vizcaya", + "author_inst": "Bayer Pharmaceuticals, Sant Joan Despi, Spain," + }, + { + "author_name": "Jose D. Posada", + "author_inst": "Department of Medicine, Stanford University" + }, + { + "author_name": "Nigam H. Shah", + "author_inst": "Department of Medicine, Stanford University," + }, + { + "author_name": "Jitendra Jonnagaddala", + "author_inst": "School of Public Health and Community Medicine, UNSW Sydney," + }, + { + "author_name": "Lana Yin Hui Lai", + "author_inst": "Division of Cancer Sciences, School of Medical Sciences, University of Manchester" + }, + { + "author_name": "Francesc Xavier Aviles-Jurado", + "author_inst": "1) Otorhinolaryngology Head-Neck Surgery Department, Hospital Clinic, IDIBAPS Universitat de Barcelona, Barcelona, Spain 2)Agencia de Gestio d Ajuts Universita" + }, + { + "author_name": "George Hripcsak", + "author_inst": "Department of Biomedical Informatics, Columbia University, New York, NY, US" + }, + { + "author_name": "Marc A. Suchard", + "author_inst": "Department of Biostatistic, UCLA Fielding School of Public Health, University of California, Los Angeles" + }, + { + "author_name": "Otavio T. Ranzani", + "author_inst": "1) Barcelona Institute for Global Health, ISGlobal, Barcelona, Spain, 2) Pulmonary Division, Heart Institute (InCor, Hospital das Clinicas, Faculdade de Medici" + }, + { + "author_name": "Patrick Ryan", + "author_inst": "1) Janssen Research & Development, Titusville, NJ, USA 2) Columbia University, New York, NY, US" + }, + { + "author_name": "Daniel Prieto-Alhambra", + "author_inst": "Centre for Statistics in Medicine, NDORMS, University of Oxford," + }, + { + "author_name": "Kristin Kostka", + "author_inst": "Real World Solutions, IQVIA, Cambridge, MA USA," + }, + { + "author_name": "Talita Duarte-Salles", + "author_inst": "Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.25.20234195", "rel_title": "Are we ready for COVID-19's Golden Passport? Insights from a Global Physician Survey", @@ -1062632,101 +1065248,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.11.25.398008", - "rel_title": "Global analysis of protein-RNA interactions in SARS-CoV-2 infected cells reveals key regulators of infection", - "rel_date": "2020-11-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.25.398008", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19. SARS-CoV-2 relies on cellular RNA-binding proteins (RBPs) to replicate and spread, although which RBPs control SARS-CoV-2 infection remains largely unknown. Here, we employ a multi-omic approach to identify systematically and comprehensively which cellular and viral RBPs are involved in SARS-CoV-2 infection. We reveal that the cellular RNA-bound proteome is remodelled upon SARS-CoV-2 infection, having widespread effects on RNA metabolic pathways, non-canonical RBPs and antiviral factors. Moreover, we apply a new method to identify the proteins that directly interact with viral RNA, uncovering dozens of cellular RBPs and six viral proteins. Amongst them, several components of the tRNA ligase complex, which we show regulate SARS-CoV-2 infection. Furthermore, we discover that available drugs targeting host RBPs that interact with SARS-CoV-2 RNA inhibit infection. Collectively, our results uncover a new universe of host-virus interactions with potential for new antiviral therapies against COVID-19.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Wael Kamel", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland (UK); Department of Biochemistry, University of Oxford, South " - }, - { - "author_name": "Marko Noerenberg", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland (UK); Department of Biochemistry, University of Oxford, South " - }, - { - "author_name": "Berati Cerikan", - "author_inst": "Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partne" - }, - { - "author_name": "Honglin Chen", - "author_inst": "Department of Biochemistry, University of Oxford, South Parks road, OX1 3QU, Oxford, UK" - }, - { - "author_name": "Aino I. J\u00e4rvelin", - "author_inst": "Department of Biochemistry, University of Oxford, South Parks road, OX1 3QU, Oxford, UK" - }, - { - "author_name": "Mohamed Kammoun", - "author_inst": "German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany" - }, - { - "author_name": "Jeff Lee", - "author_inst": "Department of Biochemistry, University of Oxford, South Parks road, OX1 3QU, Oxford, UK" - }, - { - "author_name": "Ni Shuai", - "author_inst": "German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany" - }, - { - "author_name": "Manuel Garcia-Moreno", - "author_inst": "Department of Biochemistry, University of Oxford, South Parks road, OX1 3QU, Oxford, UK" - }, - { - "author_name": "Anna Andrejeva", - "author_inst": "Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA" - }, - { - "author_name": "Michael J. Deery", - "author_inst": "Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA" - }, - { - "author_name": "Christopher J. Neufeldt", - "author_inst": "Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partne" - }, - { - "author_name": "Mirko Cortese", - "author_inst": "Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partne" - }, - { - "author_name": "Michael L. Knight", - "author_inst": "Sir William Dunn School of Pathology, University of Oxford, South Parks road, OX1 3RE, Oxford, UK" - }, - { - "author_name": "Kathryn S. Lilley", - "author_inst": "Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA" - }, - { - "author_name": "Javier Martinez", - "author_inst": "Center of Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Dr. Bohr-Gasse 9/2, 1030, Vienna, Austria" - }, - { - "author_name": "Ilan Davis", - "author_inst": "Department of Biochemistry, University of Oxford, South Parks road, OX1 3QU, Oxford, UK" - }, - { - "author_name": "Ralf Bartenschlager", - "author_inst": "Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partne" - }, - { - "author_name": "Shabaz Mohammed", - "author_inst": "Department of Biochemistry, University of Oxford, South Parks road, OX1 3QU, Oxford, UK; Department of Chemistry, Chemistry Research Laboratory, Mansfield Road," - }, - { - "author_name": "Alfredo Castello", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland (UK); Department of Biochemistry, University of Oxford, South " - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.11.21.20236216", "rel_title": "Use of alternative RNA storage and extraction reagents and development of a hybrid PCR-based method for SARS-CoV-2 detection", @@ -1062903,6 +1065424,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.11.23.20236711", + "rel_title": "Statistical Analyses of the Public Health and Economic Performance of Nordic Countries in Response to the COVID-19 Pandemic", + "rel_date": "2020-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.23.20236711", + "rel_abs": "AimTo compare trends and undertake statistical analyses of differences in public health performance (confirmed cases and fatalities) of Nordic countries; Denmark, Finland, Norway and Sweden, and New Zealand, in response to the COVID-19 pandemic.\n\nMethodsPer capita trends in total cases and per capita fatalities were analysed and difference-in-difference statistical tests undertaken to assess whether differences in stringency of mandated social distancing (SD) measures, testing rates and border closures explain cross-country differences.\n\nResultsSweden is a statistical outlier, relative to its Nordic neighbours, for both per capita cases and per capita fatalities associated with COVID-19 but not in terms of the reduction in economic growth. Swedens public health differences, compared to its Nordic neigbours, are partially explained by differences in terms of international border closures and the level of stringency of SD measures (including testing) implemented from early March to June 2020.\n\nConclusionsWe find that: one, early imposition of full international travel restrictions combined with high levels of government-mandated stringency of SD reduced the per capita cases and per capita fatalities associated with COVID-19 in 2020 in the selected countries and, two, in Nordic countries, less stringent government-mandated SD is not associated with higher quarterly economic growth.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Daniel Gordon", + "author_inst": "University of Calgary" + }, + { + "author_name": "R. Quentin Grafton", + "author_inst": "The Australian National University" + }, + { + "author_name": "Stein Ivar Steinshamn", + "author_inst": "Norwegian School of Economics" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.11.23.20236828", "rel_title": "HIV infection alters SARS-CoV-2 responsive immune parameters but not clinical outcomes in COVID-19 disease", @@ -1064294,33 +1066842,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.24.20237644", - "rel_title": "Excess mortality across regions of Europe during the first wave of the COVID-19 pandemic - impact of the winter holiday travelling and government responses", - "rel_date": "2020-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20237644", - "rel_abs": "BackgroundThis aggregated population study of 219 regions in 11 European countries investigated the effect of the seemingly quasi-randomly assigned school winter holiday week on excess mortality associated with the COVID-19 pandemic during spring 2020. A secondary aim was to evaluate the impact of stringency and timing of the government responses to the early inflow of infected cases.\n\nMethodsRegional data on mortality week 14-23 in 2020 compared with the same period 2015-2019 were retrieved from Eurostat and national statistical agencies. Data on initial government responses were obtained from the Oxford COVID-19 Government Response Tracker. Variance-weighted least square regression was used with further adjustment for population density and age distribution.\n\nResultsBeing a region with winter holiday exclusively in week 9 was in the adjusted analysis associated with 16 weekly excess deaths (95% confidence interval 13 to 20) per million inhabitants, which corresponds to 38% of the excess mortality during the study period in these regions. A more stringent response implemented in week 11, corresponding to 10 additional units on the 0-100 ordinal scale, was associated with 20 fewer weekly deaths (95% confidence interval 18 to 22) per million inhabitants.\n\nConclusionsTravelling during winter holiday in week 9 was an amplifying event that contributed importantly to the excess mortality observed in the study area during the spring 2020. Timely government responses to the resulting early inflow of cases was associated with lower excess mortality.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jonas Bjork", - "author_inst": "Lund University" - }, - { - "author_name": "Kristoffer Mattisson", - "author_inst": "Lund University" - }, - { - "author_name": "Anders Ahlbom", - "author_inst": "Karolinska Institute" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.23.20237487", "rel_title": "How closely is COVID-19 related to HCoV, SARS, and MERS? : Clinical comparison of coronavirus infections and identification of risk factors influencing the COVID-19 severity using common data model (CDM)", @@ -1064613,6 +1067134,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, + { + "rel_doi": "10.1101/2020.11.24.20237586", + "rel_title": "The experience of distress during the COVID-19 outbreak: a cross-country examination on the fear of COVID-19 and the sense of loneliness", + "rel_date": "2020-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20237586", + "rel_abs": "ObjectivesTo examine gender, age and cross-country differences in fear of COVID-19 and sense of loneliness during the lockdown, by comparing people from countries with a high rate of infections and deaths (i.e. Spain and Italy) and from countries with a mild spread of infection (i.e. Croatia, Serbia, Slovakia, Slovenia, Bosnia and Herzegovina).\n\nMethodsA total of 3876 participants (63% female) completed an online survey on \"Everyday life practices in COVID-19 time\" in April 2020, including measures of fear of COVID-19 and loneliness.\n\nResultsMales and females of all age groups in countries suffering from a strong impact of the COVID-19 pandemic reported higher fear of COVID-19 and sense of loneliness. In less endangered countries females and elder stated more symptoms than males and younger; in Spanish and Italian sample the pattern of differences is considerably more complex.\n\nConclusionFuture research should thoroughly examine different age and gender groups. The analysis of emotional well-being in groups at risk of mental health issues can help to lessen the long term social and economic costs due to the COVID-19 outbreak.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Gianluca Lo Coco", + "author_inst": "University of Palermo" + }, + { + "author_name": "Ambra Gentile", + "author_inst": "University of Palermo" + }, + { + "author_name": "Ksenija Bosnar", + "author_inst": "University of Zagreb" + }, + { + "author_name": "Ivana Milovanovic", + "author_inst": "University of Novi Sad" + }, + { + "author_name": "Antonino Bianco", + "author_inst": "University of Palermo" + }, + { + "author_name": "Patrik Drid", + "author_inst": "University of Novi Sad" + }, + { + "author_name": "Sasa Pisot", + "author_inst": "Institute for Kinesiology Research Scientific Research Center Koper" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.11.23.20235465", "rel_title": "Mobile outreach testing for COVID-19 in twenty homeless shelters in Toronto, Canada", @@ -1065936,41 +1068500,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.21.20236117", - "rel_title": "Antibody persistency and dynamic trend after SARS-CoV-2 infection over 8 months", - "rel_date": "2020-11-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.21.20236117", - "rel_abs": "An improved understanding of the immunity offered by the antibodies developed against SARS-CoV-2 is critical for the development of diagnostic tests and vaccines. Our study aimed at the longitudinal analysis of antibody presence, persistence and its trend over a period of eight months in a group of COVID-19 recovered patients who tested positive by real-time quantitative PCR for SARS-CoV-2 in the period between the 18th and 30th of March, 2020. The subjects were divided into two groups based on disease severity: mild and moderately-severe. The MAGLUMI 2019-nCoV lgM/lgG chemiluminescent analytical system (CLIA) assay was used to analyse the antibody titres. Robust IgG antibody persistency was demonstrated in 76.7 % of the subjects (23 out of 30) at eight months post-infection. The results of this study highlight an important point in terms of the association between humoral immune response and disease severity. Patients who might have experienced a relatively moderate-severe infection may develop a robust immunity that could persist for a longer duration.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Puya Dehgani-Mobaraki", - "author_inst": "Associazione Naso Sano, Italy" - }, - { - "author_name": "Asiya Kamber Zaidi", - "author_inst": "Mahatma Gandhi Memorial Medical College , Indore, India and Member of Associazione Naso Sano,Italy" - }, - { - "author_name": "Annamaria Porreca", - "author_inst": "Department of Economics, University \"G.d'Annunzio\", chieti-Pescara, Italy." - }, - { - "author_name": "Alessandro Floridi", - "author_inst": "Laboratory of Nuclear Lipid BioPathology, Centro Ricerche Analisi Biochimico Specialistiche, Perugia, Italy" - }, - { - "author_name": "Emanuela Floridi", - "author_inst": "Laboratory of Nuclear Lipid BioPathology, Centro Ricerche Analisi Biochimico Specialistiche, Perugia, Italy." - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.20.20231696", "rel_title": "Antibody response patterns in COVID-19 patients with different levels of disease severity-Japan", @@ -1066147,6 +1068676,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.20.20235341", + "rel_title": "Diagnostic accuracy of two commercial SARS-CoV-2 Antigen-detecting rapid tests at the point of care in community-based testing centers", + "rel_date": "2020-11-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.20.20235341", + "rel_abs": "BackgroundAntigen-detecting rapid diagnostic tests for SARS-CoV-2 offer new opportunities for the quick and laboratory-independent identification of infected individuals for control of the SARS-CoV-2 pandemic.\n\nMethodsWe performed a prospective, single-center, point of care validation of two antigen-detecting rapid diagnostic tests (Ag-RDT) in comparison to RT-PCR on nasopharyngeal swabs.\n\nFindingsBetween October 9th and 23rd, 2020, 1064 participants were enrolled. The PanbioCovid-19 Ag Rapid Test device (Abbott) was validated in 535 participants, with 106 positive Ag-RDT results out of 124 positive RT-PCR individuals, yielding a sensitivity of 85.5% (95% CI: 78.0-91.2). Specificity was 100.0% (95% CI: 99.1-100) in 411 RT-PCR negative individuals. The Standard Q Ag-RDT (SD Biosensor, Roche) was validated in 529 participants, with 170 positive Ag-RDT results out of 191 positive RT-PCR individuals, yielding a sensitivity of 89.0% (95%CI: 83.7-93.1). One false positive result was obtained in 338 RT-PCR negative individuals, yielding a specificity of 99.7% (95%CI: 98.4-100). For individuals presenting with fever 1-5 days post symptom onset, combined Ag-RDT sensitivity was above 95%.\n\nInterpretationWe provide an independent validation of two widely available commercial Ag-RDTs, both meeting WHO criteria of [≥]80% sensitivity and [≥]97% specificity. Although less sensitive than RT-PCR, these assays could be beneficial due to their rapid results, ease of use, and independence from existing laboratory structures. Testing criteria focusing on patients with typical symptoms in their early symptomatic period onset could further increase diagnostic value.\n\nFundingFoundation of Innovative Diagnostics (FIND), Fondation privee des HUG, Pictet Charitable Foundation.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Alice Berger", + "author_inst": "Division of Infectious Disease, Geneva University Hospitals, Geneva, Switzerland" + }, + { + "author_name": "Marie-Therese Ngo Nsoga", + "author_inst": "Division of Infectious Disease, Geneva University Hospitals, Geneva, Switzerland" + }, + { + "author_name": "Francisco Javier Perez Rodriguez", + "author_inst": "Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland" + }, + { + "author_name": "Yasmine Abi Aad", + "author_inst": "Division of Infectious Disease, Geneva University Hospitals, Geneva, Switzerland" + }, + { + "author_name": "Pascale Sattonnet", + "author_inst": "Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland" + }, + { + "author_name": "Ang\u00e8le Gayet-Ageron", + "author_inst": "CRC & Division of Clinical-Epidemiology, Department of Health and Community Medicine, University of Geneva & University Hospitals of Geneva" + }, + { + "author_name": "Cyril Jaksic", + "author_inst": "CRC & Division of Clinical-Epidemiology, Department of Health and Community Medicine, University of Geneva & University Hospitals of Geneva" + }, + { + "author_name": "Giulia Torriani", + "author_inst": "Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland" + }, + { + "author_name": "Erik Boehm", + "author_inst": "Division of Infectious Disease, Geneva University Hospitals, Geneva, Switzerland" + }, + { + "author_name": "Ilona Kronig", + "author_inst": "Division of Infectious Disease, Geneva University Hospitals, Geneva, Switzerland" + }, + { + "author_name": "Jilian A Sacks", + "author_inst": "Foundation for Innovative New Diagnostics, Geneva, Switzerland" + }, + { + "author_name": "Margaretha de Vos", + "author_inst": "Foundation for Innovative New Diagnostics, Geneva, Switzerland" + }, + { + "author_name": "Fr\u00e9d\u00e9rique Jacquerioz-Bausch", + "author_inst": "Department of Primary Care, Geneva University Hospitals, Geneva, Switzerland" + }, + { + "author_name": "Fran\u00e7ois Chappuis", + "author_inst": "Department of Primary Care, Geneva University Hospitals, Geneva, Switzerland" + }, + { + "author_name": "Laurent Kaiser", + "author_inst": "University of Geneva Hospitals" + }, + { + "author_name": "Manuel Schibler", + "author_inst": "University of Geneva Hospitals" + }, + { + "author_name": "Isabella Eckerle", + "author_inst": "Geneva Centre for Emerging Viral Diseases" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.18.20234161", "rel_title": "Peginterferon Lambda-1a for treatment of outpatients with uncomplicated COVID-19: a randomized placebo-controlled trial", @@ -1067398,81 +1070010,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2020.11.23.393967", - "rel_title": "Building a virtual summer research experience in cancer for high school and early undergraduate students: lessons from the COVID-19 pandemic", - "rel_date": "2020-11-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.23.393967", - "rel_abs": "BackgroundThe COVID-19 pandemic posed a unique challenge for summer research programs in 2020, particularly for programs aimed at hands-on experience for younger trainees. The Indiana University Melvin and Bren Simon Comprehensive Cancer Center supports two pipeline programs, which traditionally immerse high school juniors, seniors, and early undergraduate students from underrepresented populations in science in hands-on projects in cancer biology labs. However, due to social distancing policies during the pandemic and reduction of research operations, these students were not physically allowed on campus. Thus, the authors set out to strategically pivot to a wholly virtual curriculum and evaluate the Virtual Summer Research Experience in Cancer outcomes.\n\nMethodsThe virtual program included four components: 1. a core science and professional development curriculum led by high school teachers and senior undergraduates; 2. faculty-delivered didactic sessions on cancer science; 3. mentored, virtual research projects with research faculty; and 4. online networking events to encourage vertical mentoring. Outcomes data were measured using an 11-item Research Preparation scale, daily electronic feedback, and structured evaluation and feedback via Zoom weekly.\n\nResultsOutcome data suggested high self-reported satisfaction with the virtual program. Outcome data also revealed the importance of coordination between multiple entities for seamless program implementation. This includes the active recruitment and participation of high school teachers and further investment in information technology capabilities of institutions.\n\nConclusionsFindings reveal a path to educate and train high school and early undergraduate students in cancer research when hands-on, in-person training is not feasible. Virtual research experiences are not only useful to engage students during public health crises but can provide an avenue for cancer centers to expand their cancer education footprints to remotely located schools and universities with limited resources to provide such experiences to their students.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Timothy W Corson", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Shannon M Hawkins", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Elmer Sanders", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Jessica Byram", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Leigh-Ann Cruz", - "author_inst": "Riverside High School" - }, - { - "author_name": "Jacob Olson", - "author_inst": "Decatur Central High School" - }, - { - "author_name": "Emily Speidell", - "author_inst": "Decatur Central High School" - }, - { - "author_name": "Rose Schnabel", - "author_inst": "Indiana University" - }, - { - "author_name": "Adhitya Balaji", - "author_inst": "Indiana University" - }, - { - "author_name": "Osas Ogbeide", - "author_inst": "Indiana University" - }, - { - "author_name": "Julie Dinh", - "author_inst": "Indiana University" - }, - { - "author_name": "Amy Hinshaw", - "author_inst": "Lawrence Township Schools" - }, - { - "author_name": "Laura Cummings", - "author_inst": "Herron High School" - }, - { - "author_name": "Vicki Bonds", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Harikrishna Nakshatri", - "author_inst": "Indiana University School of Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "scientific communication and education" - }, { "rel_doi": "10.1101/2020.11.20.20235440", "rel_title": "Coagulation factors and COVID-19 severity: Mendelian randomization analyses and supporting evidence", @@ -1067669,6 +1070206,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.20.20235333", + "rel_title": "Is Standard Personal Protective Equipment Effective Enough To Prevent COVID-19 Transmission During Aerosol Generating Dental, Oral and Maxillofacial Procedures ? A Systematic Review", + "rel_date": "2020-11-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.20.20235333", + "rel_abs": "A systematic review was performed to answer the following questions: 1) Do dental, oral and maxillofacial (OMF) surgical procedures generate bioaerosols (and if so, which ones), which can result in transmission of COVID-19?; 2) Are aerosolized airborne droplets (and to which extent is splatter) in dental and OMF procedures infective?; 3) Is enhanced personal protective equipment (PPE) an essential to prevent spreading of COVID-19 during dental and OMF aerosol generating procedures (AGPs)? Authors performed a systematic review to retrieve all pertinent literature that assessed effectiveness of surgical mask vs respirators for protecting dental health care workers during dental and OMF AGPs surgical procedures. Additionally, studies which assessed potential aerosolization during dental, OMF and orthopaedic surgeries were retrieved. There is moderate evidence showing that ultrasonic scaling and bone drilling using high speed rotary instruments produces respirable aerosols. Additionally, there is very weak/inconclusive evidence to support the creation of infectious aerosols during dental procedures. According to available very weak/inconclusive evidence, transmission of SARS-CoV-2 via infective aerosol during AGPS, so far, must remain speculative and controversial. As, however, this is a probable opportunistic way of transmission which at least cannot be sufficiently excluded and therefore should not be dismissed out of hand prematurely, proper and equally important properly applied protective equipment (i.e., N95 respirators or FFP-2 masksv or above regarding mouth and nose protection) should always be used during AGPs.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Essam Ahmed Al-Moraissi", + "author_inst": "Thamar univeristy" + }, + { + "author_name": "Marwan abood", + "author_inst": "Regional Dental Center in Qassim" + }, + { + "author_name": "Nasser Alasseri", + "author_inst": "Department of Oral & Maxillofacial Surgery, Prince Sultan Military Medical City, Riyadh, Saudi Arabia" + }, + { + "author_name": "Frank Gunther", + "author_inst": "Medical Microbiology and Hygiene, Marburg University Hospital, Hans-Meerwein-Strasse 2, D-35043, Marburg, Germany" + }, + { + "author_name": "Andreas Neff", + "author_inst": ", Dept. of Oral and Maxillofacial Surgery, University Hospital Marburg UKGM GmbH, Marburg, Germany." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "dentistry and oral medicine" + }, { "rel_doi": "10.1101/2020.11.19.20234120", "rel_title": "Actionable druggable genome-wide Mendelian randomization identifies repurposingopportunities for COVID-19", @@ -1069760,81 +1072332,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.18.20233932", - "rel_title": "REACT-1 round 6 updated report: high prevalence of SARS-CoV-2 swab positivity with reduced rate of growth in England at the start of November 2020", - "rel_date": "2020-11-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20233932", - "rel_abs": "BackgroundEngland is now in the midst of its second wave of the COVID-19 pandemic. Multiple regions of the country are at high infection prevalence and all areas experienced rapid recent growth of the epidemic during October 2020.\n\nMethodsREACT-1 is a series of community surveys of SARS-CoV-2 RT-PCR swab-positivity in England designed to monitor the spread of the epidemic and thus increase situational awareness. Round 6 of REACT-1 commenced swab-collection on 16th October. A prior interim report included data from 16th to 25th October for 85,971 participants. Here, we report data for the entire round on 160,175 participants with swab results obtained up to 2nd November 2020.\n\nResultsOverall weighted prevalence of infection in the community in England was 1.3% or 130 people per 10,000 infected, up from 60 people per 10,000 in the round 5 report (18th September to 5th October 2020), doubling every 24 days on average since the prior round. The corresponding R number was estimated to be 1.2. Prevalence of infection was highest in North West (2.4%, up from 1.2%), followed by Yorkshire and The Humber (2.3% up from 0.84%), West Midlands (1.6% up from 0.60%), North East (1.5% up from 1.1%), East Midlands (1.3% up from 0.56%), London (0.97%, up from 0.54%), South West (0.80% up from 0.33%), South East (0.69% up from 0.29%), and East of England (0.69% up from 0.30%). Rapid growth in the South observed in the first half of round 6 was no longer apparent in the second half of round 6. We also observed a decline in prevalence in Yorkshire and The Humber during this period. Comparing the first and second halves of round 6, there was a suggestion of decline in weighted prevalence in participants aged 5 to 12 years and in those aged 25 to 44 years. While prevalence remained high, in the second half of round 6 there was suggestion of a slight fall then rise that was seen nationally and also separately in both the North and the South.\n\nConclusionThe impact of the second national lockdown in England is not yet known. We provide here a detailed description of swab-positivity patterns at national, regional and local scales for the period immediately preceding lockdown, against which future trends in prevalence can be evaluated.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Steven Riley", - "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" - }, - { - "author_name": "Kylie E. C. Ainslie", - "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" - }, - { - "author_name": "Oliver Eales", - "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" - }, - { - "author_name": "Caroline E. Walters", - "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" - }, - { - "author_name": "Haowei Wang", - "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" - }, - { - "author_name": "Christina Atchinson", - "author_inst": "School of Public Health, Imperial College London, UK" - }, - { - "author_name": "Claudio Fronterre", - "author_inst": "CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK" - }, - { - "author_name": "Peter J. Diggle", - "author_inst": "CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK" - }, - { - "author_name": "Deborah Ashby", - "author_inst": "School of Public Health, Imperial College London, UK" - }, - { - "author_name": "Christl A Donnelly", - "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" - }, - { - "author_name": "Graham Cooke", - "author_inst": "Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic" - }, - { - "author_name": "Wendy Barclay", - "author_inst": "Department of Infectious Disease, Imperial College London, UK" - }, - { - "author_name": "Helen Ward", - "author_inst": "School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear" - }, - { - "author_name": "Ara Darzi", - "author_inst": "Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a" - }, - { - "author_name": "Paul Elliott", - "author_inst": "School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.17.20231290", "rel_title": "Secondary Attack Rate (SAR) in household contacts of expired primary cases of COVID-19: A study from Western India", @@ -1070075,6 +1072572,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.18.20234039", + "rel_title": "The detection and stability of the SARS-CoV-2 RNA biomarkers in wastewater influent in Helsinki, Finland", + "rel_date": "2020-11-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20234039", + "rel_abs": "Wastewater-based surveillance of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is used to monitor the population-level prevalence of the COVID-19 disease. In many cases, due to lockdowns or analytical delays, the analysis of wastewater samples might only be possible after prolonged storage. In this study, the effect of storage conditions on the RNA copy numbers of the SARS-CoV-2 virus in wastewater influent was studied and compared to the persistence of norovirus over time at 4{degrees}C, -20{degrees}C, and -75{degrees}C using the reverse-transcription quantitative PCR (RT-qPCR) assays E-Sarbeco, N2, and norovirus GII. For the first time in Finland, the presence of SARS-CoV-2 RNA was tested in 24 h composite influent wastewater samples collected from Viikinmaki wastewater treatment plant, Helsinki, Finland. The detected and quantified SARS-CoV-2 RNA copy numbers of the wastewater sample aliquots taken during 19-20 April 2020 and stored for 29, 64, and 84 days remained surprisingly stable. In the stored samples, the SARS betacoronavirus and SARS-CoV-2 copy numbers, but not the norovirus GII copy numbers, seemed slightly higher when analyzed from the pre-centrifuged pellet--that is, the particulate matter of the influent--as compared with the supernatant (i.e., water fraction) used for ultrafiltration, although the difference was not statistically significant. Furthermore, when wastewater was spiked with SARS-CoV-2, linear decay at 4{degrees}C was observed on the first 28 days, while no decay was visible within 58 days at -20{degrees}C or -75{degrees}C. In conclusion, freezing temperatures should be used for storage when immediate SARS-CoV-2 RNA analysis from the wastewater influent is not possible. Analysis of the particulate matter of the sample, in addition to the water fraction, can improve the detection frequency.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Anna-Maria Hokajarvi", + "author_inst": "Finnish Institute for Health and Welfare, Expert Microbiology Unit, Kuopio, Finland" + }, + { + "author_name": "Annastiina Rytkonen", + "author_inst": "Finnish Institute for Health and Welfare, Expert Microbiology Unit, Kuopio, Finland" + }, + { + "author_name": "Ananda Tiwari", + "author_inst": "Finnish Institute for Health and Welfare, Expert Microbiology Unit, Kuopio, Finland" + }, + { + "author_name": "Ari Kauppinen", + "author_inst": "Finnish Institute for Health and Welfare, Expert Microbiology Unit, Kuopio, Finland; Current address: Finnish Food Authority, Laboratory and Research Division, " + }, + { + "author_name": "Sami Oikarinen", + "author_inst": "Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland" + }, + { + "author_name": "Kirsi-Maarit Lehto", + "author_inst": "Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland" + }, + { + "author_name": "Aino Kankaanpaa", + "author_inst": "Finnish Institute for Health and Welfare, Forensic Toxicology Unit, Helsinki, Finland" + }, + { + "author_name": "Teemu Gunnar", + "author_inst": "Finnish Institute for Health and Welfare, Forensic Toxicology Unit, Helsinki, Finland" + }, + { + "author_name": "Haider Al-Hello", + "author_inst": "Finnish Institute for Health and Welfare, Expert Microbiology Unit, Helsinki, Finland" + }, + { + "author_name": "Soile Blomqvist", + "author_inst": "Finnish Institute for Health and Welfare, Expert Microbiology Unit, Helsinki, Finland" + }, + { + "author_name": "Ilkka T Miettinen", + "author_inst": "Finnish Institute for Health and Welfare, Expert Microbiology Unit, Kuopio, Finland" + }, + { + "author_name": "Carita Savolainen-Kopra", + "author_inst": "Finnish Institute for Health and Welfare, Expert Microbiology Unit, Helsinki, Finland" + }, + { + "author_name": "Tarja Pitkanen", + "author_inst": "Finnish Institute for Health and Welfare, Expert Microbiology Unit, Kuopio, Finland; University of Helsinki, Faculty of Veterinary Medicine, Dept. Food Hygiene " + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.18.20233288", "rel_title": "CLINICAL APPLICATIONS OF MACHINE LEARNING ON COVID-19: THE USE OF A DECISION TREE ALGORITHM FOR THE ASSESSMENT OF PERCEIVED STRESS IN MEXICAN HEALTHCARE PROFESSIONALS.", @@ -1071694,41 +1074258,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.18.20234088", - "rel_title": "Knowledge and perceptions on COVID-19 among Senior High School students in Ghana: a cross-sectional study", - "rel_date": "2020-11-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20234088", - "rel_abs": "BackgroundThe COVID-19 pandemic is associated with high morbidity and mortality. In Ghana, policy interventions have been implemented by the Government to combat the pandemic. However, the knowledge and perceptions of Senior High School students are not investigated on the COVID-19 symptoms, transmission and the government policy measures.\n\nObjectivesThe present study surveyed senior high school students to assess their knowledge and perceptions of COVID-19 and the government policy measures to address the outbreak.\n\nMethodsThe study employed a descriptive cross-sectional study design to assess the knowledge and perceptions of senior high school students on the COVID-19 pandemic and the measures put in place to address it. 624 senior high school students aged 18 years old and above were surveyed. Descriptive analysis was performed to assess knowledge and perceptions of COVID-19 symptoms, mode of transmissions and prevention.\n\nFindingsMost students were knowledgeable about COVID-19 symptoms, transmission and preventive measures. Majority of the students obtained information about COVID-19 from television, radio, social media, and from family and friends. Overall, the students also demonstrated a positive perception towards COVID-19 mode of transmission and preventive measures.\n\nConclusionsOverall, senior high school students in the Bawku Municipality in Ghana demonstrated an appreciable level of knowledge and positive perception of COVID-19. Students cited television, radio, peer education and social media as their information sources for COVID-19. These media outlets should be prioritized in disseminating COVID 19 information to the public, especially students.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Isaac Bador kamal Lettor", - "author_inst": "Bawku Technical Institute" - }, - { - "author_name": "Paschal Awingura Apanga", - "author_inst": "University of Nevada, Reno, School of Community of Health Sciences, Reno, USA" - }, - { - "author_name": "Maxwell Tii Kumbeni", - "author_inst": "Ghana Health Service, Nabdam District Health Directorate, Nangodi, Ghana" - }, - { - "author_name": "Ramatu Akunvane", - "author_inst": "Nursing and Midwifery Training College, Zuarungu, Upper East Region, Ghana" - }, - { - "author_name": "Robert Akparibo", - "author_inst": "School of Health and Related Research (ScHARR), University of Sheffield, Sheffield, United Kingdom" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.19.20234716", "rel_title": "A precise measure of the impact of the first wave of Covid-19 on life expectancy. Regional differentials in Switzerland", @@ -1071893,6 +1074422,137 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.11.18.388413", + "rel_title": "Long-chain polyphosphates impair SARS-CoV-2 infection and replication: a route for therapy in man", + "rel_date": "2020-11-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.18.388413", + "rel_abs": "Anti-viral activities of long-chain inorganic polyphosphates (PolyPs) against severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection were investigated. In molecular docking analyses, PolyPs interacted with several conserved angiotensin-converting enzyme (ACE)2 and RNA-dependent RNA polymerase (RdRp) amino acids. We thus tested PolyPs for functional interactions in vitro in SARS-CoV-2-infected Vero E6, Caco2 and human primary nasal epithelial cells. Immunofluorescence, qPCR, direct RNA sequencing, FISH and Immunoblotting were used to determine virus loads and transcription levels of genomic(g)RNAs and sub-genomic(sg)RNAs. We show that PolyP120 binds to ACE2 and enhances its proteasomal degradation. PolyP120 shows steric hindrance of the genomic Sars-CoV-2-RNA/RdRP complex, to impair synthesis of positive-sense gRNAs, viral subgenomic transcripts and structural proteins needed for viral replication. Thus, PolyP120 impairs infection and replication of Korean and European (containing non-synonymous variants) SARS-CoV-2 strains. As PolyPs have no toxic activities, we envision their use as a nebulised formula for oropharyngeal delivery to prevent infections of SARS-CoV-2 and during early phases of antiviral therapy.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Veronica Ferrucci", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie mediche DMMBM, Via Pansini 5, 80131, Naples, Italy CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486," + }, + { + "author_name": "Young Kong Dae", + "author_inst": "Ginxen Co., Ltd., 2F, Daewoong Building, 17, Gangnam-daero 95-gil, Seocho-gu, Seoul, South Korea 00821022391373" + }, + { + "author_name": "Fatemeh Asadzadeh", + "author_inst": "CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145, Naples, Italy 00390813737830" + }, + { + "author_name": "Laura Marrone", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie mediche DMMBM, Via Pansini 5, 80131, Naples, Italy; CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486" + }, + { + "author_name": "Roberto Siciliano", + "author_inst": "CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145, Naples, Italy" + }, + { + "author_name": "Pellegrino Cerino", + "author_inst": "Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples" + }, + { + "author_name": "Giuseppina Criscuolo", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie mediche DMMBM, Via Pansini 5, 80131, Naples, Italy; CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486" + }, + { + "author_name": "Ida Pisano", + "author_inst": "CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145, Naples, Italy" + }, + { + "author_name": "Fabrizio Quarantelli", + "author_inst": "CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145, Naples, Italy" + }, + { + "author_name": "Barbara Izzo", + "author_inst": "CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145, Naples, Italy" + }, + { + "author_name": "Giovanna Fusco", + "author_inst": "Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy" + }, + { + "author_name": "Marika Comegna", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie mediche DMMBM, Via Pansini 5, 80131, Naples, Italy" + }, + { + "author_name": "Angelo Boccia", + "author_inst": "CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145, Naples, Italy" + }, + { + "author_name": "Maurizio Viscardi", + "author_inst": "Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy" + }, + { + "author_name": "Giorgia Borriello", + "author_inst": "Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy" + }, + { + "author_name": "Sergio Brandi", + "author_inst": "Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy" + }, + { + "author_name": "Bianca Maria Pierri", + "author_inst": "Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy" + }, + { + "author_name": "Claudia Tiberio", + "author_inst": "U.O.C. di Patologia Clinica Ospedale D. Cotugno, Azienda Sanitaria Ospedali dei Colli, Via Gaetano Quagliariello, 54, 80131, Naples, Italy" + }, + { + "author_name": "Luigi Atripaldi", + "author_inst": "U.O.C. di Patologia Clinica Ospedale D. Cotugno, Azienda Sanitaria Ospedali dei Colli, Via Gaetano Quagliariello, 54, 80131, Naples, Italy" + }, + { + "author_name": "Giovanni Paolella", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie mediche DMMBM, Via Pansini 5, 80131, Naples, Italy; CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486" + }, + { + "author_name": "Giuseppe Castaldo", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie mediche DMMBM, Via Pansini 5, 80131, Naples, Italy; CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486" + }, + { + "author_name": "Stefano Pascarella", + "author_inst": "University La Sapienza di Roma, Roma, Italy" + }, + { + "author_name": "Martina Bianchi", + "author_inst": "University La Sapienza di Roma, Roma, Italy" + }, + { + "author_name": "Rosa Della Monica", + "author_inst": "CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145, Naples, Italy" + }, + { + "author_name": "Lorenzo Chiariotti", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie mediche DMMBM, Via Pansini 5, 80131, Naples, Italy; CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486" + }, + { + "author_name": "Kyong Seop Yun", + "author_inst": "HAIM BIO Co. Ltd, Industrial Park, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, South Korea" + }, + { + "author_name": "Jae Ho Cheong", + "author_inst": "Department of Surgery, Yonsei University College of Medicine, Seoul, Korea 00821022391373" + }, + { + "author_name": "Hong Yeoul Kim", + "author_inst": "HAIM BIO Co. Ltd, Industrial Park, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, South Korea" + }, + { + "author_name": "Massimo Zollo", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie mediche DMMBM, Via Pansini 5, 80131, Naples, Italy; CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2020.11.18.388868", "rel_title": "Improved production of SARS-CoV-2 spike receptor-binding domain (RBD) for serology assays", @@ -1073228,93 +1075888,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.16.20232835", - "rel_title": "Convalescent COVID-19 patients are susceptible to endothelial dysfunction due to persistent immune activation", - "rel_date": "2020-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20232835", - "rel_abs": "The rapid rise of coronavirus disease 2019 patients who suffer from vascular events after their initial recovery is expected to lead to a worldwide shift in disease burden. We aim to investigate the impact of COVID-19 on the pathophysiological state of blood vessels in convalescent patients. Here, convalescent COVID-19 patients with or without preexisting conditions (i.e. hypertension, diabetes, hyperlipidemia) were compared to non-COVID-19 patients with matched cardiovascular risk factors or healthy participants. Convalescent patients had elevated circulating endothelial cells (CECs), and those with underlying cardiovascular risk had more pronounced endothelial activation hallmarks (ICAM1, P-selectin or CX3CL1) expressed by CECs. Multiplex microbead-based immunoassays revealed some levels of cytokine production sustained from acute infection to recovery phase. Several proinflammatory and activated T lymphocyte-associated cytokines correlated positively with CEC measures, implicating cytokine-driven endothelial dysfunction. Finally, the activation markers detected on CECs mapped to the counter receptors (i.e. ITGAL, SELPLG, and CX3CR1) found primarily on CD8+ T cells and natural killer cells, suggesting that activated endothelial cells could be targeted by cytotoxic effector cells. Clinical trials in preventive therapy for post-COVID-19 vascular complications may be needed.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=69 SRC=\"FIGDIR/small/20232835v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (19K):\norg.highwire.dtl.DTLVardef@d34a61org.highwire.dtl.DTLVardef@1b82feeorg.highwire.dtl.DTLVardef@152ea88org.highwire.dtl.DTLVardef@a3b382_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Florence WJ Chioh", - "author_inst": "Nanyang Technological University Singapore, Lee Kong Chian School of Medicine" - }, - { - "author_name": "Siew-Wai Fong", - "author_inst": "Singapore Immunology Network, A*STAR" - }, - { - "author_name": "Barnaby Young", - "author_inst": "National Centre for Infectious Diseases, Singapore" - }, - { - "author_name": "Kan-Xing Wu", - "author_inst": "Nanyang Technological University Singapore, Lee Kong Chian School of Medicine" - }, - { - "author_name": "Anthony Siau", - "author_inst": "Nanyang Technological University Singapore" - }, - { - "author_name": "Shuba Krishnan", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "Yi-Hao Chan", - "author_inst": "Singapore Immunology Network" - }, - { - "author_name": "Louis LY Teo", - "author_inst": "National Heart Centre Singapore" - }, - { - "author_name": "Fei Gao", - "author_inst": "National Heart Centre Singapore" - }, - { - "author_name": "Ru San Tan", - "author_inst": "National Heart Centre Singapore" - }, - { - "author_name": "Liang Zhong", - "author_inst": "National Heart Centre Singapore" - }, - { - "author_name": "Angela SM Koh", - "author_inst": "National Heart Centre Singapore" - }, - { - "author_name": "Seow Yen Tan", - "author_inst": "Changi General Hospital" - }, - { - "author_name": "Paul A Tambyah", - "author_inst": "National University Hospital, Singapore" - }, - { - "author_name": "Laurent Renia", - "author_inst": "A-Star" - }, - { - "author_name": "Lisa F. P. Ng", - "author_inst": "Singapore Immunology Network" - }, - { - "author_name": "David Chien Boon Lye", - "author_inst": "National Centre of Infectious Diseases" - }, - { - "author_name": "Christine Cheung", - "author_inst": "Nanyang Technological University Singapore" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.11.17.20220681", "rel_title": "An efficient distributed algorithm with application to COVID-19 data from heterogeneous clinical sites", @@ -1073499,6 +1076072,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.17.20229583", + "rel_title": "Secondary transmission of COVID-19 in preschool and school settings after their reopening in northern Italy: a population-based study", + "rel_date": "2020-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.17.20229583", + "rel_abs": "BackgroundSchool closures was one of the main measures undertaken to reduce the number of social contacts during the first wave of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. We aimed to describe the data on secondary transmission of SARS-CoV-2 among students and teachers/personnel after the reopening of preschools and schools in Reggio Emilia, Italy.\n\nMethodsThis prospective population-based study included all consecutive cases leading to an investigation in 41 classes of 36 educational institutions (8 infant-toddler centres and preschools, 10 primary and 18 secondary schools) in the period September 1 - October 15, 2020, in Reggio Emilia province, Italy. We report the characteristics of the school, of the index case, including the possible source of infection, the number of contacts (students and teachers/personnel) that were identified and tested and the characteristics of secondary cases.\n\nResultsIn the study period, 994 students and 204 teachers were tested during related investigations due to notification of 43 primary cases (38 among students and 5 among teachers). Of these, 10 students and two teachers created 39 secondary cases, resulting in an attack rate of 3.9%. There were no secondary cases among teachers/stuff. Secondary transmission occurred in one primary school and 8 secondary schools. Except for two students and one teacher, the possible source of infection for all index cases was identified as they had all had previous contact with a positive case; the majority of secondary cases did not report any previous close contact with a positive case. The clusters ranged from one to 22 secondary cases.\n\nConclusionsTransmission at school occurred in a non-negligible number of cases, particularly in secondary schools. Prompt testing and isolation of classmates could probably reduce the risk of transmission in school settings.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Elisabetta Larosa", + "author_inst": "Public Health Unit, AUSL-IRCCS di Reggio Emilia, Reggio Emilia, Italy" + }, + { + "author_name": "Olivera Djuric", + "author_inst": "Epidemiology Unit, AUSL-IRCCS di Reggio Emilia, Reggio Emilia, Italy" + }, + { + "author_name": "Mariateresa Cassinadri", + "author_inst": "Public Health Unit, AUSL-IRCCS di Reggio Emilia, Reggio Emilia, Italy" + }, + { + "author_name": "Silvia Cilloni", + "author_inst": "Public Health Unit, AUSL-IRCCS di Reggio Emilia, Reggio Emilia, Italy" + }, + { + "author_name": "Eufemia Bisaccia", + "author_inst": "Public Health Unit, AUSL-RCCS di Reggio Emilia, Reggio Emilia, Italy" + }, + { + "author_name": "Massimo Vicentini", + "author_inst": "Epidemiology Unit, AUSL-IRCCS di Reggio Emilia, Reggio Emilia, Italy" + }, + { + "author_name": "Francesco Venturelli", + "author_inst": "Epidemiology Unit, AUSL-IRCCS di Reggio Emilia, Reggio Emilia, Italy" + }, + { + "author_name": "Paolo Giorgi Rossi", + "author_inst": "Epidemiology Unit, AUSL-IRCCS di Reggio Emilia, Reggio Emilia, Italy" + }, + { + "author_name": "Patrizio Pezzotti", + "author_inst": "Department of Infectious Diseases, ISS, Rome, Italy" + }, + { + "author_name": "Emanuela Bedeschi", + "author_inst": "Public Health Unit, AUSL-IRCCS di Reggio Emilia, Reggio Emilia, Italy" + }, + { + "author_name": "- Reggio Emilia Covid-19 Working Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.18.20233833", "rel_title": "COVID-19 patients and cancer in northern Italy", @@ -1074510,41 +1077142,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.17.20210211", - "rel_title": "The impacts of COVID-19 mitigation on dengue virus transmission: a modelling study", - "rel_date": "2020-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.17.20210211", - "rel_abs": "BackgroundThe COVID-19 pandemic has induced unprecedented reductions in human mobility and social contacts throughout the world. Because dengue virus (DENV) transmission is strongly driven by human mobility, behavioral changes associated with the pandemic have been hypothesized to impact dengue incidence. By discouraging human contact, COVID-19 control measures have also disrupted dengue vector control interventions, the most effective of which require entry into homes.\n\nMethodWe used an agent-based model with a realistic treatment of human mobility and vector control to investigate how and why dengue incidence could differ under a lockdown scenario with a proportion of the population sheltered at home.\n\nResultWe found that a lockdown in which 70% of the population sheltered at home led to a small average increase in cumulative DENV infections of up to 10%, depending on the time of year lockdown occurred. Lockdown had a more pronounced effect on the spatial distribution of DENV infections, with higher incidence under lockdown in regions with high mosquito abundance. Transmission was also more focused in homes following lockdown. The proportion of people infected in their own home rose from 54% under normal conditions to 66% under lockdown, and the household secondary attack rate rose from 0.109 to 0.128, a 17% increase. When we considered that lockdown measures could disrupt regular, city-wide vector control campaigns, the increase in incidence was more pronounced than with lockdown alone, especially if lockdown occurred at the optimal time for vector control.\n\nDiscussionOur results indicate that an unintended outcome of COVID-19 control measures may be to adversely alter the epidemiology of dengue. This observation has important implications for an improved understanding of dengue epidemiology and effective application of dengue vector control. When coordinating public health responses during a syndemic, it is important to monitor multiple infections and understand that an intervention against one disease may exacerbate another.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sean M. Cavany", - "author_inst": "University of Notre Dame" - }, - { - "author_name": "Guido Espa\u00f1a", - "author_inst": "University of Notre Dame" - }, - { - "author_name": "Gonzalo M Vazquez-Prokopec", - "author_inst": "Emory University" - }, - { - "author_name": "Thomas W Scott", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Alex Perkins", - "author_inst": "University of Notre Dame" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.16.20232900", "rel_title": "High throughput wastewater SARS-CoV-2 detection enables forecasting of community infection dynamics in San Diego county", @@ -1074777,6 +1077374,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.11.18.20233908", + "rel_title": "A sense of being needed: an interpretative phenomenological analysis of hospital-based allied health professionals' experiences during the COVID-19 pandemic", + "rel_date": "2020-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20233908", + "rel_abs": "BackgroundThe outbreak of COVID-19 has led to many hospitalizations in the Netherlands and worldwide. As a result, the work of hospital-based allied health professionals changed rapidly. In such a healthcare crisis, professionals may not be able to fulfill their own professional values regarding good care, resulting in ethical issues and moral distress. The aim of this study was to explore the lived experiences of allied health professionals working in hospitals during the COVID-19 pandemic, including the ethical issues and moral distress these professionals might have encountered.\n\nMethods and findingsLived experiences were collected in semi-structured interviews with 39 allied health professionals including dieticians, occupational therapists, physical therapists, and speech-language therapists, working in four different hospitals in the Netherlands. Interviews were held in June and July 2020, after waning of the first wave of COVID-19 spreading. Interpretative phenomenological analysis revealed four themes: a disease with great impact, personal health and safety, staying human in chaotic times and solidarity and changing roles. Participant experiences show that the virus and COVID-19 measures had a significant impact on the in-hospital working environment due to the massive downscaling of regular care, infection prevention measures and unknown risks to allied health professionals personal health. At the same time, participants experienced a certain freedom, which made room for authentic motives, connection and solidarity. Participants felt welcomed and appreciated at the COVID-19 wards and intensive care units, and were proud that they were able to fulfill their roles. The themes and accompanying ethical issues reflect a wide range of situations that were morally complex and led to moral distress.\n\nConclusionsTo diminish long-lasting negative impact of the COVID-19 pandemic and moral distress, employers should empathize with experiences of allied health professionals and create conditions for ethical reflection. Our data show that allied health professionals value professional autonomy. Creating room for professional autonomy makes them feel needed, connected and energized. However, the needs of allied health professionals may conflict with organizational rules and structures.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Roel van Oorsouw", + "author_inst": "Radboud university medical center, Radboud Institute for Health Sciences, Department of Rehabilitation, Nijmegen, the Netherlands" + }, + { + "author_name": "Anke Oerlemans", + "author_inst": "Radboud university medical center, Radboud Institute for Health Sciences, IQ healthcare, Nijmegen, the Netherlands" + }, + { + "author_name": "Emily Klooster", + "author_inst": "Radboud university medical center, Radboud Institute for Health Sciences, IQ healthcare, Nijmegen, the Netherlands; Deventer Hospital, Department of Rehabilitat" + }, + { + "author_name": "Manon van den Berg", + "author_inst": "Radboud university medical center, Department of Gastro-enterology and Hepatology-Dietetics and Intestinal Failure, Nijmegen, the Netherlands" + }, + { + "author_name": "Johanna Kalf", + "author_inst": "Radboud university medical center, Donders Center for Neuroscience, Department of Rehabilitation, Nijmegen, The Netherlands" + }, + { + "author_name": "Hester Vermeulen", + "author_inst": "Radboud university medical center, Radboud Institute for Health Sciences, IQ healthcare, Nijmegen, the Netherlands; HAN University of Applied Sciences, Faculty " + }, + { + "author_name": "Maud Graff", + "author_inst": "Radboud university medical center, Radboud institute for Health Sciences, Department of Rehabilitation, Nijmegen, the Netherlands" + }, + { + "author_name": "Philip van der Wees", + "author_inst": "Radboud university medical center, Radboud institute for Health Sciences, Department of Rehabilitation, Nijmegen, the Netherlands; Radboud university medical ce" + }, + { + "author_name": "Niek Koenders", + "author_inst": "Radboud university medical center, Radboud institute for Health Sciences, Department of Rehabilitation, Nijmegen, the Netherlands" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "rehabilitation medicine and physical therapy" + }, { "rel_doi": "10.1101/2020.11.17.20233023", "rel_title": "Resuming professional football during the Covid-19 pandemic in a country with high infection ratesA prospective cohort study", @@ -1076224,69 +1078872,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.11.17.386904", - "rel_title": "Preclinical evaluation of Imatinib does not support its use as an antiviral drug against SARS-CoV-2", - "rel_date": "2020-11-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.17.386904", - "rel_abs": "Following the emergence of SARS-CoV-2, the search for an effective and rapidly available treatment was initiated worldwide based on repurposing of available drugs. Previous reports described the antiviral activity of certain tyrosine kinase inhibitors (TKIs) targeting the Abelson kinase 2 against pathogenic coronaviruses. Imatinib, one of them, has more than twenty years of safe utilization for the treatment of hematological malignancies. In this context, Imatinib was rapidly evaluated in clinical trials against Covid-19. Here, we present the pre-clinical evaluation of Imatinib in multiple models. Our results indicated that Imatinib and another TKI, the Masitinib, exhibit an antiviral activity in VeroE6 cells. However, Imatinib was inactive in a reconstructed bronchial human airway epithelium model. In vivo, Imatinib therapy failed to impair SARS-CoV-2 replication in a golden Syrian hamster model despite high concentrations in plasma and in the lung. Overall, these results do not support the use of Imatinib and similar TKIs as antivirals in the treatment of Covid-19.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Franck Touret", - "author_inst": "Unite des Virus Emergents" - }, - { - "author_name": "Jean-Selim Driouich", - "author_inst": "Unite des Virus Emergents" - }, - { - "author_name": "Maxime Cochin", - "author_inst": "Unite des Virus Emergents" - }, - { - "author_name": "Paul Remy Petit", - "author_inst": "Unite des Virus Emergents" - }, - { - "author_name": "Magali Gilles", - "author_inst": "Unite des Virus Emergents" - }, - { - "author_name": "Karine Barthelemy", - "author_inst": "Unite des Virus Emergents" - }, - { - "author_name": "Gregory Moureau", - "author_inst": "Unite des Virus Emergents" - }, - { - "author_name": "Francois-Xavier MAHON", - "author_inst": "Institut BERGONIE" - }, - { - "author_name": "Denis Malvy", - "author_inst": "University of Bordeaux" - }, - { - "author_name": "Caroline Solas", - "author_inst": "Unite des Virus Emergents" - }, - { - "author_name": "Xavier de Lamballerie", - "author_inst": "Aix Marseille Univ, IRD French Institute of Research for Development, EHESP French School of Public Health & IHU Mediterranee Infection, APHM Public Hospitals o" - }, - { - "author_name": "Antoine Nougairede", - "author_inst": "Unite des Virus Emergents" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.11.16.20149377", "rel_title": "The effects of hypertension as an existing comorbidity on mortality rate in patients with COVID-19: a systematic review and meta-analysis.", @@ -1076563,6 +1079148,81 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.11.16.384040", + "rel_title": "A continuously self-sterilizing form of copper capable of 99% SARS-CoV-2 deactivation in 30 seconds.", + "rel_date": "2020-11-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.16.384040", + "rel_abs": "The coronavirus disease 2019 (COVID-19) has created an acute worldwide demand for sustained broadband pathogen suppression in households, hospitals, and public spaces. The US recently passed a new sad milestone of 500,000 deaths due to COVID-19, the highest rate anywhere in the world. In response, we have created a rapid-acting, self-sterilizing PPE configurations capable of killing SARS-CoV-2 and other microbes in seconds. The highly active material destroys pathogens faster than any conventional copper configuration. The material maintains its antimicrobial efficacy over sustained use and is shelf stable. We have performed rigorous testing in accordance with guidelines from U.S. governing authorities and believe that the material could offer broad spectrum, non-selective defense against most microbes via integration into masks and other protective equipment.\n\nSummaryA novel configuration of copper offering continued fast-acting protection against viruses and bacteria, including SARS-CoV-2.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Alfred A. Zinn", + "author_inst": "Kuprion, Inc. San Jose, CA 95134, USA" + }, + { + "author_name": "Mina Izadjoo", + "author_inst": "Integrated Pharma Services, Frederick, MD 21704, USA" + }, + { + "author_name": "Hosan Kim", + "author_inst": "Integrated Pharma Services, Frederick, MD 21704, USA" + }, + { + "author_name": "Kylene Kehn-Hall", + "author_inst": "Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Black" + }, + { + "author_name": "Caitlin Lehman", + "author_inst": "Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Black" + }, + { + "author_name": "Rachel L. Brody", + "author_inst": "Kuprion, Inc." + }, + { + "author_name": "Robert R. Roth", + "author_inst": "Kuprion, Inc. San Jose, CA 95134, USA" + }, + { + "author_name": "Augustin Vega", + "author_inst": "Kuprion, Inc. San Jose, CA 95134, USA" + }, + { + "author_name": "Khanh K. Nguyen", + "author_inst": "Kuprion, Inc. San Jose, CA 95134, USA" + }, + { + "author_name": "Nhi T. Ngo", + "author_inst": "Kuprion, Inc. San Jose, CA 95134, USA" + }, + { + "author_name": "Hannah T. Zinn", + "author_inst": "Kuprion, Inc. San Jose, CA 95134, USA" + }, + { + "author_name": "Lauren Panny", + "author_inst": "Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Black" + }, + { + "author_name": "Rafaela Flor", + "author_inst": "National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University, Manassas, VA, USA" + }, + { + "author_name": "Nicholas Antonopoulos", + "author_inst": "Kuprion, Inc. San Jose, CA 95134, USA" + }, + { + "author_name": "Randall M. Stoltenberg", + "author_inst": "Kuprion, Inc. San Jose, CA 95134, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.11.16.385849", "rel_title": "The Rhinolophus affinis bat ACE2 and multiple animal orthologs are functional receptors for bat coronavirus RaTG13 and SARS-CoV-2", @@ -1078314,49 +1080974,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2020.11.14.20231704", - "rel_title": "Impact of the COVID-19 pandemic on Older Adults Mental Health Services: a mixed methods study", - "rel_date": "2020-11-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.14.20231704", - "rel_abs": "PurposeThe Covid-19 pandemic is likely to have a significant impact on older adults mental health care. Our study aimed to explore staff perspectives on key challenges and innovations, to help inform the delivery of older adults mental health care in subsequent waves of the pandemic.\n\nMethodsA mixed methods online questionnaire developed by NIHR Mental Health Policy Research Unit (MHPRU) was used to gather staff perspectives on their challenges at work, problems faced by service users and their carers, and sources of help and support. Descriptive statistics were used for quantitative analysis and descriptive content analysis for qualitative analysis.\n\nResults158 participants, working in either community or inpatient settings, and from a range of professional disciplines, were included. For inpatient staff, a significant challenge was infection control. In the community, staff identified a lack of access to physical and social care as well as reduced contact with friends and families as being challenges for patients. Remote working was seen as a positive innovation along with Covid-19 related guidance from various sources and peer support.\n\nConclusionOur study, with a focus on staff and patient well-being, helps to inform service development for future waves of the pandemic. We discuss measures to improve infection control in inpatient settings, the role of voluntary organisations in supporting socially isolated community patients, the need for better integration of physical and mental health services at an organisational level, and the importance of training staff to support patients and their families with end of life planning.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Rohan Bhome", - "author_inst": "University College London" - }, - { - "author_name": "Jonathan Huntley", - "author_inst": "University College London" - }, - { - "author_name": "Christian Dalton-Locke", - "author_inst": "University College London" - }, - { - "author_name": "Norha Vera San Juan", - "author_inst": "King's College London" - }, - { - "author_name": "Sian Oram", - "author_inst": "King's College London" - }, - { - "author_name": "Una Foye", - "author_inst": "King's College London" - }, - { - "author_name": "Gill Livingston", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.11.14.20231142", "rel_title": "Capability impacts of the Covid-19 lockdown in association with mental well-being, social connections and existing vulnerabilities: an Austrian survey study", @@ -1078561,6 +1081178,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.11.13.20229625", + "rel_title": "Performance of SARS-CoV-2 Serology tests: Are they good enough?", + "rel_date": "2020-11-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.13.20229625", + "rel_abs": "BackgroundIn the emergency of the SARS-CoV-2 pandemic, great efforts were made to quickly provide serology testing to the medical community however, these methods have been introduced into clinical practice without the complete validation usually required by the regulatory organizations.\n\nMethodsSARS-CoV-2 patient samples (n=43) were analysed alongside pre-pandemic control specimen (n=50), confirmed respiratory infections (n=50), inflammatory polyarthritis (n=22) and positive for thyroid stimulating immunoglobulin (n=30). Imprecision, diagnostic sensitivity and specificity and concordance were evaluated on IgG serologic assays from EuroImmun, Epitope Diagnostics (EDI), Abbott Diagnostics and DiaSorin and a rapid IgG/IgM test from Healgen.\n\nResultsEDI and EuroImmun imprecision was 0.02-14.0% CV. Abbott and DiaSorin imprecision (CV) ranged from 5.2% - 8.1% and 8.2% - 9.6% respectively. Diagnostic sensitivity of the assays were 100% (CI: 80-100%) for Abbott, EDI and EuroImmun and 95% (CI: 73-100%) for DiaSorin at [≥]14 days post PCR. Only the Abbott assay had a diagnostic specificity of 100% (CI: 91-100%). EuroImmun cross-reacted in 3 non-SARS-CoV-2 respiratory infections and 2 controls. The DiaSorin displayed more false negative results and cross-reacted in six cases across all conditions tested. EDI had one cross-reactive sample. The Healgen rapid test showed excellent sensitivity and specificity. Overall, concordance of the assays ranged from 76.1% to 97.9%.\n\nConclusionsSerological tests for SARS-CoV-2 showed good analytical performance. The head-to-head analysis of samples revealed differences in results that may be linked to the use of nucleocapsid or spike proteins. The point of care device tested demonstrated adequate performance for antibody detection.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Isabelle Piec", + "author_inst": "University of East Anglia" + }, + { + "author_name": "Emma English", + "author_inst": "University of East Anglia" + }, + { + "author_name": "Mary Anette Thomas", + "author_inst": "Welsh External Quality Assessment Scheme (WEQAS)" + }, + { + "author_name": "Samir Darvisevic", + "author_inst": "Norfolk and Norwich University Hospital NHS Trust" + }, + { + "author_name": "William Duncan Fraser", + "author_inst": "University of East Anglia" + }, + { + "author_name": "William Garry John", + "author_inst": "Norfolk and Norwich University Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.11.13.20231365", "rel_title": "What is the relationship between validated frailty scores and mortality for adults with COVID-19 in acute hospital care? A systematic review.", @@ -1079952,77 +1082608,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.11.15.383463", - "rel_title": "SARS-CoV-2-specific T cell memory is long-lasting in the majority of convalsecent COVID-19 individuals", - "rel_date": "2020-11-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.15.383463", - "rel_abs": "An unaddressed key question in the current coronavirus disease 2019 (COVID-19) pandemic is the duration of immunity for which specific T cell responses against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are an indispensable element. Being situated in Wuhan where the pandemic initiated enables us to conduct the longest analyses of memory T cell responses against SARS-CoV-2 in COVID-19 convalescent individuals (CIs). Magnitude and breadth of SARS-CoV-2 memory CD4 and CD8 T cell responses were heterogeneous between patients but robust responses could be detected up to 9 months post disease onset in most CIs. Loss of memory CD4 and CD8 T cell responses were observed in only 16.13% and 25.81% of CIs, respectively. Thus, the overall magnitude and breadth of memory CD4 and CD8 T cell responses were quite stable and not inversely correlated with the time from disease onset. Interestingly, the only significant decrease in the response was found for memory CD4 T cells in the first 6-month post COVID-19 disease onset. Longitudinal analyses revealed that the kinetics of SARS-CoV-2 memory CD4 and CD8 T cell responses were quite heterogenous between patients. Loss of memory CD4 T cell responses was observed more frequently in asymptomatic cases than after symptomatic COVID-19. Interestingly, the few CIs in which SARS-CoV-2-specific IgG responses disappeared showed more durable memory CD4 T cell responses than CIs who remained IgG-positive for month. Collectively, we provide the first comprehensive characterization of the long-term memory T cell response in CIs, suggesting that SARS-CoV-2-specific T cell immunity is long-lasting in the majority of individuals.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Ziwei Li", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Jing Liu", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Hui Deng", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Xuecheng Yang", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Hua Wang", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Xuemei Feng", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Gennadiy Zelinskyy", - "author_inst": "Institute for Virology, University Hospital of Essen, University of Duisburg-Essen" - }, - { - "author_name": "Mirko Trilling", - "author_inst": "Institute for Virology, University Hospital of Essen, University of Duisburg-Essen" - }, - { - "author_name": "Kathrin Sutter", - "author_inst": "Institute for Virology, University Hospital of Essen, University of Duisburg-Essen" - }, - { - "author_name": "Mengji Lu", - "author_inst": "Institute for Virology, University Hospital of Essen, University of Duisburg-Essen" - }, - { - "author_name": "Baoju Wang", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Dongliang Yang", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Xin Zheng", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Jia Liu", - "author_inst": "Wuhan Union Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.11.16.385468", "rel_title": "Examining the Persistence of Human Coronaviruses on Fresh Produce", @@ -1080199,6 +1082784,33 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.11.15.383927", + "rel_title": "Transcriptome Profiling of different types of human respiratory tract cells infected by SARS-CoV-2 Highlight an unique Role for Inflammatory and Interferon Response", + "rel_date": "2020-11-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.15.383927", + "rel_abs": "The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease (COVID-19) at the end of 2019 has caused a large global outbreak and now become a major public health issue. Lack of data underlying how the human host interacts with SARS-CoV-2 virus. In the current study, We performed Venn-analysis, Gene ontology (GO), KEGG pathway analysis and Protein-protein interaction analysis of whole transcriptome studies with the aim of clarifying the genes and pathways potentially altered during human respiratory tract cells infected with SARS-CoV-2. We selected four studies through a systematic search of the Gene Expression Omnibus (GEO) database or published article about SARS-CoV-2 infection in different types of respiratory tract cells. We found 36 overlapping upregulated genes among different types of cells after viral infection. Further functional enrichment analysis revealed these DEGs are most likely involved in biological processes related to inflammatory response and response to cytokine, cell component related to extracellular space and I-kappaB/NF-kappaB complex, molecular function related to protein binding and cytokine activity. KEGG pathways analysis highlighted altered conical and casual pathways related to TNF, NF-kappa B, Cytokine-cytokine receptor interaction and IL17 signaling pathways during SARS-CoV-2 infection with CXCL1, CXCL2, CXCL3, CXCL8, CXCL10, IL32, CX3CL1, CCL20, IRF1, NFKB2 and NFKB1A up-regulated which may explain the inflammatory cytokine storms associated with severe cases of COVID-19.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Luping Lei", + "author_inst": "Beijing TongRen Hospital, Capital Medical University." + }, + { + "author_name": "Qiumei Cao", + "author_inst": "Beijing TongRen Hospital, Capital Medical University." + }, + { + "author_name": "Yu Wang", + "author_inst": "Beijing Geriatric Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "confirmatory results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.11.16.384743", "rel_title": "Recurrent mutations in SARS-CoV-2 genomes isolated from mink point to rapid host-adaptation", @@ -1082018,41 +1084630,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.12.20230748", - "rel_title": "Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: A Systematic Review and Meta-analysis", - "rel_date": "2020-11-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.12.20230748", - "rel_abs": "BackgroundNasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs.\n\nMethodsWe systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval October 1st, 2020) for comparative studies of alternative specimen types [saliva, oropharyngeal (OP), and nasal (NS) swabs] versus NP swabs for SARS-CoV-2 diagnosis using nucleic acid amplification testing (NAAT). A logistic-normal random-effects meta-analysis was performed to calculate % positive alternative-specimen, % positive NP, and % dual positives overall and in sub-groups. The QUADAS 2 tool was used to assess bias.\n\nResultsFrom 1,253 unique citations, we identified 25 saliva, 11 NS, 6 OP, and 4 OP/NS studies meeting inclusion criteria. Three specimen types captured lower % positives [NS (0.82, 95% CI: 0.73-0.90), OP (0.84, 95% CI: 0.57-1.0), saliva (0.88, 95% CI: 0.81 - 0.93)] than NP swabs, while combined OP/NS matched NP performance (0.97, 95% CI: 0.90-1.0). Absence of RNA extraction (saliva) and utilization of a more sensitive NAAT (NS) substantially decreased alternative-specimen yield.\n\nConclusionsNP swabs remain the gold standard for diagnosis of SARS-CoV-2, although alternative specimens are promising. Much remains unknown about the impact of variations in specimen collection, processing protocols, and population (pediatric vs. adult, late vs. early in disease course) and head-to head studies of sampling strategies are urgently needed.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Rose A Lee", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Joshua C Herigon", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Andrea Benedetti", - "author_inst": "McGill University" - }, - { - "author_name": "Nira R Pollock", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Claudia Denkinger", - "author_inst": "University of Heidelberg" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.12.20145318", "rel_title": "Critical care workers have lower seroprevalence of SARS-CoV-2 IgG compared with non-patient facing staff in first wave of COVID19.", @@ -1082281,6 +1084858,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.11.12.380931", + "rel_title": "The Preclinical Inhibitor GS441524 in Combination with GC376 Efficaciously Inhibited the Proliferation of SARS-CoV-2 in the Mouse Respiratory Tract", + "rel_date": "2020-11-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.12.380931", + "rel_abs": "The unprecedented coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a serious threat to global public health. Development of effective therapies against SARS-CoV-2 is urgently needed. Here, we evaluated the antiviral activity of a remdesivir parent nucleotide analog, GS441524, which targets the coronavirus RNA-dependent RNA polymerase enzyme, and a feline coronavirus prodrug, GC376, which targets its main protease, using a mouse-adapted SARS-CoV-2 infected mouse model. Our results showed that GS441524 effectively blocked the proliferation of SARS-CoV-2 in the mouse upper and lower respiratory tracts via combined intranasal (i.n.) and intramuscular (i.m.) treatment. However, the ability of high-dose GC376 (i.m. or i.n. and i.m.) was weaker than GS441524. Notably, low-dose combined application of GS441524 with GC376 could effectively protect mice against SARS-CoV-2 infection via i.n. or i.n. and i.m. treatment. Moreover, we found that the pharmacokinetic properties of GS441524 is better than GC376, and combined application of GC376 and GS441524 had a synergistic effect. Our findings support the further evaluation of the combined application of GC376 and GS441524 in future clinical studies.\n\nImportanceSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), which has seriously threatened global public health and economic development. Currently, effective therapies to treat COVID-19 are urgently needed. In this study, we assessed the efficacy of the preclinical inhibitors GC376 and GS441524 using a mouse-adapted SARS-CoV-2 infected mouse model for the first time. Our results showed that low-dose combined application of GC376 and GS441524 could effectively protect mice from HRB26M infection in the upper and lower respiratory tracts. Hence, the combined application should be developed and considered for future clinic practice.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yuejun Shi", + "author_inst": "Huazhong Agricultural University" + }, + { + "author_name": "Lei Shuai", + "author_inst": "Chinese Academy of Agricultural Sciences" + }, + { + "author_name": "Chong Wang", + "author_inst": "Chinese Academy of Agricultural Sciences" + }, + { + "author_name": "Yuanyuan Yan", + "author_inst": "Huazhong Agricultural University" + }, + { + "author_name": "Zhe Jiao", + "author_inst": "Huazhong Agricultural University" + }, + { + "author_name": "Fenglin Guo", + "author_inst": "Huazhong Agricultural University" + }, + { + "author_name": "Zhen F. Fu", + "author_inst": "Huazhong Agricultural University" + }, + { + "author_name": "Huanchun Chen", + "author_inst": "Huazhong Agricultural University" + }, + { + "author_name": "Zhi-Gao Bu", + "author_inst": "Harbin Veterinary Research Institute, CAAS" + }, + { + "author_name": "Guiqing Peng", + "author_inst": "Huazhong Agricultural University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.12.380816", "rel_title": "An evolutionary analysis of the SARS-CoV-2 genomes from the countries in the same meridian", @@ -1083504,29 +1086136,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.11.11.20229526", - "rel_title": "Universal Health Coverage and COVID-19 Pandemic: A Bangladesh Perspective", - "rel_date": "2020-11-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.11.20229526", - "rel_abs": "BackgroundLike many other countries around the world, Bangladesh adopts Universal Health Coverage (UHC) as a national aspiration. The central theme of its providing quality and affordable health services which is a significant element of social protection. This paper was aimed to provide a narrative understanding of the perspectives of UHC in Bangladesh towards COVID-19 based on the existing literature.\n\nMethodsWe conducted a review combining articles and abstracts with full HTML and PDF format. We searched Google Scholar, ScienceDirect and Google using multiple terms related to UHC, COVID-19 and Bangladesh without any date boundary and without any basis of types of studies, that is, all types of studies were scrutinized.\n\nResultsThis short description highlights that the current pandemic COVID-19 holds lessons that health systems and economies in several countries like Bangladesh are not in enough preparation to tackle a massive public health crisis. It reports the shortage of health workers, scarcity of personal protective equipment, limited and ineffective diagnostic facilities, inadequate infrastructure of health care facilities, scarcity of drugs, and underfunded health services. Further, COVID-19 pandemic highlights the countrys health system needs an ongoing rehab post-COVID-19 with strong coordination in governance, in health economics, in health systems, in information systems, as well as in community participation in health to achieve UHC.\n\nConclusionsAddressing the needs for UHC achievement, it is important to break down the access barriers and keeping up to date all the activities addressing public health crisis like COVID-19.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Most. Zannatul Ferdous", - "author_inst": "Jahangirnagar University" - }, - { - "author_name": "Ummay Soumayia Islam", - "author_inst": "Jahangirnagar University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2020.11.10.20229401", "rel_title": "Using Real World Data to Understand HIV and COVID-19 in the U.S.A. and Spain: Characterizing Co-Infected Patients Across the Care Cascade", @@ -1083899,6 +1086508,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.11.20229559", + "rel_title": "Secondary Household Covid-19 Transmission Modelling of Students Returning Home from University", + "rel_date": "2020-11-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.11.20229559", + "rel_abs": "We estimate the number of secondary Covid-19 infections caused by potentially infectious students returning from university to private homes with other occupants. Using a Monte-Carlo method and data derived from UK sources, we predict that an infectious student would, on average, infect 0.94 other household members. Or, as a rule of thumb, each infected student would generate (just less than) one secondary within-household infection. The total number of secondary cases for all returning students is dependent on the virus prevalence within the student population at the time of their departure from campus back home. Correspondingly, we provide results for prevalence ranging from 0.5% to 15%, which is based on observed minimum and maximum estimates from Cardiff Universitys asymptomatic testing service. Although the proposed estimation method is general and robust, the results are sensitive to the input data. We therefore provide Matlab code and a helpful online app (http://bit.ly/Secondary_infections_app) that can be used to estimate numbers of secondary infections based on local parameter values.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Paul R Harper", + "author_inst": "Cardiff University" + }, + { + "author_name": "Joshua W Moore", + "author_inst": "Cardiff University" + }, + { + "author_name": "Thomas E Woolley", + "author_inst": "Cardiff University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.11.20229062", "rel_title": "Longevity of seropositivity and neutralizing titers among SARS-CoV-2 infected individuals after 4 months from baseline: a population-based study in the province of Trento", @@ -1085454,69 +1088090,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.11.20230045", - "rel_title": "Impacts of the COVID-19 Pandemic on Cardiac Rehabilitation Delivery around the World", - "rel_date": "2020-11-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.11.20230045", - "rel_abs": "BackgroundTo investigate impacts of COVID-19 on CR delivery around the globe, including effects on providers and patients.\n\nMethodsIn this cross-sectional study, a piloted survey was administered to CR programs globally via REDCap from April-June/2020. The 50 members of the ICCPR and personal contacts facilitated program identification.\n\nResultsOverall, 1062(18.3% program response rate) responses were received from 70/111(63.1% country response rate) countries in the world with existent CR programs. Of these, 367(49.1%) programs reported they had stopped CR delivery, and 203(27.1%) stopped temporarily (mean=8.3{+/-}2.8weeks). Alternative models were delivered in 322(39.7%) programs, primarily through low-tech modes (n=226,19.3%). 353(30.2%) respondents were re-deployed, and 276 (37.3%) felt the need to work due to fear of losing their job, despite the perceived risk of contracting COVID-19 (mean=30.0%{+/-}27.4/100). 266(22.5%) reported anxiety, 241(20.4%) were concerned about exposing their family, 113(9.7%) reported increased workload to transition to remote delivery, and 105(9.0%) were juggling caregiving responsibilities during business hours. Patients were often contacting staff regarding grocery shopping for heart-healthy foods (n=333,28.4%), how to use technology to interact with the program (n=329,27.9%), having to stop their exercise because they have no place to exercise (n=303,25.7%), and their risk of death from COVID-19 due to pre-existing cardiovascular disease (n=249,21.2%). Respondents perceived staff (n=488,41.3%) and patient (n=453,38.6%) personal protective equipment, as well as COVID-19 screening (n=414,35.2%) and testing (n=411,35.0%) as paramount to in-person service resumption.\n\nConclusionApproximately 4400 programs ceased service delivery. Those that remain open are implementing new technologies to ensure their patients receive CR safely, despite the challenges.\n\nHighlights- COVID-19 has impacted cardiac rehabilitation (CR) delivery around the globe.\n- In this cross-sectional study, a survey was completed by 1062 (18.3%) CR programs from 70 (63.1%) countries.\n- The pandemic has resulted in cessation of [~]75% of CR programs, with others ceasing initiation of new patients, reducing components delivered, and/or changing of mode delivery with little opportunity for planning and training.\n- There is also significant psychosocial and economic impact on CR providers.\n- Alternative CR model (e.g. home-based, virtual) reimbursement advocacy is needed, to ensure safe, accessible secondary prevention delivery.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Gabriela Lima de Melo Ghisi", - "author_inst": "UHN Cardiovascular Prevention and Rehabilitation Program, Toronto, Ontario, Canada." - }, - { - "author_name": "Zhiming Xu", - "author_inst": "Shanghai Jiao Tong University Affiliated Sixth Peoples' Hospital, Shanghai, China (Mainland)." - }, - { - "author_name": "Xia Liu", - "author_inst": "Shanghai Jiao Tong University Affiliated Sixth Peoples' Hospital, Shanghai, China (Mainland)." - }, - { - "author_name": "Ana Mola", - "author_inst": "NYU Langone Health, New York City, USA." - }, - { - "author_name": "Robyn Gallagher", - "author_inst": "Sydney Nursing School, University of Sydney, Sydney, NSW, Australia." - }, - { - "author_name": "Abraham Samuel Babu", - "author_inst": "Department of Physiotherapy, Manipal College of Health Professions, Manipal Academy of Higher Education, Manipal, India" - }, - { - "author_name": "Colin Yeung", - "author_inst": "Department of Medicine, University of Saskatchewan, Regina, Saskatchewan, Canada." - }, - { - "author_name": "Susan Marzolini", - "author_inst": "UHN Cardiovascular Prevention and Rehabilitation Program, Toronto, Ontario, Canada." - }, - { - "author_name": "John Buckley", - "author_inst": "Centre for Active Living, University Centre Shrewsbury, Shrewsbury, UK." - }, - { - "author_name": "Paul Oh", - "author_inst": "UHN Cardiovascular Prevention and Rehabilitation Program, Toronto, Ontario, Canada." - }, - { - "author_name": "Aashish Contractor", - "author_inst": "Rehabilitation and Sports Medicine, Sir H. N. Reliance Foundation Hospital, Mumbai, India." - }, - { - "author_name": "Sherry L Grace", - "author_inst": "School of Kinesiology and Health Science, York University, Toronto, Canada; KITE & Peter Munk Cardiac Centre, University Health Network, University of Toronto." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.11.09.20228007", "rel_title": "Analysis of mitigation of Covid-19 outbreaks in workplaces and schools by hybrid telecommuting", @@ -1085653,6 +1088226,297 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.08.20228056", + "rel_title": "Protocol for a Sequential, Prospective Meta-Analysis to Describe COVID-19 in Pregnancy and Newborn Periods", + "rel_date": "2020-11-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.08.20228056", + "rel_abs": "We urgently need answers to basic epidemiological questions regarding SARS-CoV-2 infection in pregnant and postpartum women and its effect on their newborns. While many national registries, health facilities, and research groups are collecting relevant data, we need a collaborative and methodologically rigorous approach to better combine these data and address knowledge gaps, especially those related to rare outcomes. We propose that using a sequential, prospective meta-analysis (PMA) is the best approach to generate data for policy- and practice-oriented guidelines. As the pandemic evolves, additional studies identified retrospectively by the steering committee or through living systematic reviews will be invited to participate in this PMA. Investigators can contribute to the PMA by either submitting individual patient data or running standardized code to generate aggregate data estimates. For the primary analysis, we will pool data using two-stage meta-analysis methods. The meta-analyses will be updated as additional data accrue in each contributing study and as additional studies meet study-specific time or data accrual thresholds for sharing. At the time of publication, investigators of 25 studies, including more than 76,000 pregnancies, in 41 countries had agreed to share data for this analysis. Among the included studies, 12 have a contemporaneous comparison group of pregnancies without COVID-19, and four studies include a comparison group of non-pregnant women of reproductive age with COVID-19. Protocols and updates will be maintained publicly. Results will be shared with key stakeholders, including the World Health Organization (WHO) Maternal, Newborn, Child, and Adolescent Health (MNCAH) Research Working Group. Data contributors will share results with local stakeholders. Scientific publications will be published in open-access journals on an ongoing basis.", + "rel_num_authors": 69, + "rel_authors": [ + { + "author_name": "Emily R. Smith", + "author_inst": "Department of Global Health, George Washington University Milken Institute School of Public Health, Washington, DC, USA" + }, + { + "author_name": "Erin M Oakley", + "author_inst": "Department of Global Health, George Washington University Milken Institute School of Public Health, Washington, DC, USA" + }, + { + "author_name": "Siran He", + "author_inst": "Department of Global Health, George Washington University Milken Institute School of Public Health, Washington, DC, USA" + }, + { + "author_name": "Rebecca Zavala", + "author_inst": "Department of Global Health, George Washington University Milken Institute School of Public Health, Washington, DC, USA" + }, + { + "author_name": "Kacey Ferguson", + "author_inst": "Department of Global Health, George Washington University Milken Institute School of Public Health, Washington, DC, USA" + }, + { + "author_name": "Lior Miller", + "author_inst": "Department of Global Health, George Washington University Milken Institute School of Public Health, Washington, DC, USA" + }, + { + "author_name": "Gargi Wable Grandner", + "author_inst": "Department of Global Health, George Washington University Milken Institute School of Public Health, Washington, DC, USA" + }, + { + "author_name": "Ibukun-Oluwa Omolade Abejirinde", + "author_inst": "Department of Sexual and Reproductive Health and Research, World Health Organization, Geneva, Switzerland" + }, + { + "author_name": "Yalda Afshar", + "author_inst": "Division of Maternal Fetal Medicine, University of California Los Angeles, Los Angeles, CA, United States" + }, + { + "author_name": "Homa Ahmadzia", + "author_inst": "Division of Maternal-Fetal Medicine, The George Washington University School of Medicine and Health Sciences" + }, + { + "author_name": "Grace Aldrovandi", + "author_inst": "Department of Pediatrics, University of California Los Angeles, Los Angeles, CA, USA" + }, + { + "author_name": "Victor Akelo", + "author_inst": "US Centers for Disease Control and Prevention, Kisumu, Kenya" + }, + { + "author_name": "Beth A. Tippett Barr", + "author_inst": "US Centers for Disease Control and Prevention, Kisumu, Kenya" + }, + { + "author_name": "Elisa Bevilacqua", + "author_inst": "Department of Women and Child Health, Women Health Area, Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, Rome, Italy" + }, + { + "author_name": "Justin S. Brandt", + "author_inst": "Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, Rutgers Robert Wood Johnson Medical School, New Brunswick," + }, + { + "author_name": "Natalie Broutet", + "author_inst": "Department of Sexual and Reproductive Health and Research, World Health Organization, Geneva, Switzerland" + }, + { + "author_name": "Irene Fernandez Buhigas", + "author_inst": "Department of Obstetrics and Gynecology, Hospital Universitario de Torrej\u00f3n, Torrej\u00f3n de Ardoz, Madrid, Spain." + }, + { + "author_name": "Jorge Carrillo", + "author_inst": "Departmento de Obstetricia y Ginecologia, Clinica Alemana de Santiago, Facultad de Medicina Clinica Alemana-Universidad del Desarrollo, Santiago, Chile" + }, + { + "author_name": "Rebecca Clifton", + "author_inst": "Biostatistics Center, The George Washington University, Washington, DC, USA" + }, + { + "author_name": "Jeanne Conry", + "author_inst": "OBGYN, The International Federation of Gynecology and Obstetrics, London, United Kingdom" + }, + { + "author_name": "Erich Cosmi", + "author_inst": "Department of Woman's and Child's Health, Obstetrics and Gynecologic Clinic, University of Padua, Padua, Italy" + }, + { + "author_name": "Camille Delgado-L\u00f3pez", + "author_inst": "Surveillance for Emerging Threats to Mothers and Babies, Puerto Rico Department of Health, San Juan, Puerto Rico" + }, + { + "author_name": "Hema Divakar", + "author_inst": "Asian Research and Training Institute for Skill Transfer (ARTIST), Bengaluru, India" + }, + { + "author_name": "Amanda J. Driscoll", + "author_inst": "Center for Vaccine Development and Global Health, University of Maryland, School of Medicine, Baltimore, MD, USA" + }, + { + "author_name": "Guillaume Favre", + "author_inst": "Materno-fetal and Obstetrics Research Unit, Department Femme-M\u00e8re-Enfant, University Hospital, Lausanne, Switzerland" + }, + { + "author_name": "Valerie Flaherman", + "author_inst": "Department of Pediatrics, University of California San Francisco, CA, San Francisco, USA" + }, + { + "author_name": "Christopher Gale", + "author_inst": "Neonatal Medicine, School of Public Health, Faculty of Medicine, Imperial College London, United Kingdom" + }, + { + "author_name": "Maria del Mar Gil", + "author_inst": "Department of Obstetrics and Gynecology, Hospital Universitario de Torrej\u00f3n, Torrej\u00f3n de Ardoz, Madrid, Spain." + }, + { + "author_name": "Christine Godwin", + "author_inst": "Department of Sexual and Reproductive Health and Research, World Health Organization, Geneva, Switzerland" + }, + { + "author_name": "Sami Gottlieb", + "author_inst": "Department of Sexual and Reproductive Health and Research, World Health Organization, Geneva, Switzerland" + }, + { + "author_name": "Olivia Hernandez Bellolio", + "author_inst": "Gynecology and Obstetrics, Felix Bulnes Hospital and RedSalud Clinic, Santiago, Chile" + }, + { + "author_name": "Edna Kara", + "author_inst": "Department of Sexual and Reproductive Health and Research, World Health Organization, Geneva, Switzerland" + }, + { + "author_name": "Sammy Khagayi", + "author_inst": "Kenya Medical Research Institute-Center for Global Health Research, Kisumu Kenya" + }, + { + "author_name": "Caron Rahn Kim", + "author_inst": "Department of Sexual and Reproductive Health and Research, World Health Organization, Geneva, Switzerland" + }, + { + "author_name": "Marian Knight", + "author_inst": "National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Karen Kotloff", + "author_inst": "Center for Vaccine Development and Global Health, University of Maryland, School of Medicine, Baltimore, MD, USA" + }, + { + "author_name": "Antonio Lanzone", + "author_inst": "Department of Women and Child Health, Women Health Area, Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, Rome, Italy" + }, + { + "author_name": "Kirsty Le Doare", + "author_inst": "Medical Research Council /Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda" + }, + { + "author_name": "Christoph Lees", + "author_inst": "Department of Metabolism, Digestion, and Reproduction, Imperial College London, United Kingdom" + }, + { + "author_name": "Ethan Litman", + "author_inst": "Division of Maternal-Fetal Medicine, The George Washington University School of Medicine and Health Sciences" + }, + { + "author_name": "Erica M. Lokken", + "author_inst": "Department of Obstetrics and Gynecology, School of Medicine, University of Washington, USA" + }, + { + "author_name": "Valentina Laurita Longo", + "author_inst": "Catholic University of Sacred Hearth, Rome, Italy" + }, + { + "author_name": "Laura A. Magee", + "author_inst": "Department of Women and Childrens Health, School of Life Course Sciences, King's College London, United Kingdom" + }, + { + "author_name": "Raigam Jafet Martinez-Portilla", + "author_inst": "Clinical Research Division, National Institute of Perinatology, Mexico City, Mexico" + }, + { + "author_name": "Elizabeth McClure", + "author_inst": "Division of Statistics and Epidemiology, RTI International, NC, USA" + }, + { + "author_name": "Torri D. Metz", + "author_inst": "University of Utah Health, USA" + }, + { + "author_name": "Deborah Money", + "author_inst": "Department of Obstetrics and Gynecology, The University of British Columbia, Vancouver, Canada" + }, + { + "author_name": "Edward Mullins", + "author_inst": "Department of Metabolism, Digestion, and Reproduction, Imperial College London, United Kingdom" + }, + { + "author_name": "Jean B. Nachega", + "author_inst": "Department of Epidemiology and Center for Global Health, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA" + }, + { + "author_name": "Alice Panchaud", + "author_inst": "Institute of Primary Health Care (BIHAM), University of Bern, Bern, Switzerland" + }, + { + "author_name": "Rebecca Playle", + "author_inst": "Center for Trials Research, Cardiff University, Wales, United Kingdom" + }, + { + "author_name": "Liona C. Poon", + "author_inst": "Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong" + }, + { + "author_name": "Daniel Raiten", + "author_inst": "Pediatric Growth and Nutrition Branch, National Institute of Health, Bethesda, MD, USA" + }, + { + "author_name": "Lesley Regan", + "author_inst": "Federation International Federation Gynaecology & Obstetrics, Imperial College London United Kingdom" + }, + { + "author_name": "Gordon Rukundo", + "author_inst": "PeriCovid (PREPARE). Uganda Team, Makerere University. Johns Hopkins University Research Collaboration, Uganda" + }, + { + "author_name": "Jose Sanin-Blair", + "author_inst": "Maternal Fetal Unit. Universidad Pontificia Bolivariana. RECOGEST Study. Colombia." + }, + { + "author_name": "Marleen Temmerman", + "author_inst": "Department of Obstetrics and Gynecology, Aga Khan University, Nairobi, Kenya" + }, + { + "author_name": "Anna Thorson", + "author_inst": "Department of Sexual and Reproductive Health and Research, World Health Organization, Geneva, Switzerland" + }, + { + "author_name": "Soe Soe Thwin", + "author_inst": "Department of Sexual and Reproductive Health and Research, World Health Organization, Geneva, Switzerland" + }, + { + "author_name": "Jorge E. Tolosa", + "author_inst": "St Lukes University Health Network, Maternal Fetal Medicine, 701 Ostrum Street Suite 303, Bethlehem, PA USA" + }, + { + "author_name": "Julia Townson", + "author_inst": "Center for Trials Research, Cardiff University, Wales, United Kingdom" + }, + { + "author_name": "Miguel Valencia-Prado", + "author_inst": "Children with Special Medical Needs Division, Puerto Rico Department of Health, San Juan, Puerto Rico" + }, + { + "author_name": "Silvia Visentin", + "author_inst": "Department of Woman's and Child's Health, Obstetrics and Gynecologic Clinic, University of Padua, Padua, Italy" + }, + { + "author_name": "Peter von Dadelszen", + "author_inst": "Department of Women and Childrens Health, School of Life Course Sciences, King's College London, United Kingdom" + }, + { + "author_name": "Kristina Adams Waldorf", + "author_inst": "Department of Obstetrics and Gynecology, School of Medicine, University of Washington, USA" + }, + { + "author_name": "Clare Whitehead", + "author_inst": "Department of Maternal Fetal Medicine, University of Melbourne, Royal Womens Hospital, Parkville, VIC, Australia" + }, + { + "author_name": "Huixia Yang", + "author_inst": "Health Science Center, Peking University, Beijing, China" + }, + { + "author_name": "Kristian Thorlund", + "author_inst": "Department of Health Research Methods Evidence and Impact, McMaster University, Hamilton, ON, Canada" + }, + { + "author_name": "James M Tielsch", + "author_inst": "Department of Global Health, George Washington University Milken Institute School of Public Health, Washington, DC, USA" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.09.20228510", "rel_title": "Google Searches for Taste and Smell Loss Anticipate Covid-19 Epidemiology", @@ -1087248,57 +1090112,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.11.12.379958", - "rel_title": "Combined in silico docking and in vitro antiviral testing for drug repurposing identified lurasidone and elbasvir as SARS-CoV-2 and HCoV-OC43 inhibitors", - "rel_date": "2020-11-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.12.379958", - "rel_abs": "The current emergency of the novel coronavirus SARS-CoV-2 urged the need for broad-spectrum antiviral drugs as the first line of treatment. Coronaviruses are a large family of viruses that already challenged humanity in at least two other previous outbreaks and are likely to be a constant threat for the future. In this work we developed a pipeline based on in silico docking of known drugs on SARS-CoV RNA-dependent RNA polymerase combined with in vitro antiviral assays on both SARS-CoV-2 and the common cold human coronavirus HCoV-OC43. Results showed that certain drugs displayed activity for both viruses at a similar inhibitory concentration, while others were specific. In particular, the antipsychotic drug lurasidone and the antiviral drug elbasvir showed promising activity in the low micromolar range against both viruses with good selective index.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Mario Milani", - "author_inst": "CNR" - }, - { - "author_name": "Manuela Donalisio", - "author_inst": "Dipartimento di Scienze Cliniche e Biologiche Universita di Torino, Regione Gonzole, 10 I-10043 Orbassano Turin, Italy" - }, - { - "author_name": "Rafaela Milan Bonotto", - "author_inst": "Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology, Padriciano 99 I-34149 Trieste, Italy" - }, - { - "author_name": "Edoardo Schneider", - "author_inst": "High Throughput Screening facility of the International Centre for Genetic Engineering and Biotechnology, Padriciano 99 I-34149 Trieste, Italy" - }, - { - "author_name": "Irene Arduino", - "author_inst": "3Dipartimento di Scienze Cliniche e Biologiche Universita di Torino, Regione Gonzole, 10 I-10043 Orbassano (Turin), Italy" - }, - { - "author_name": "Francesco Boni", - "author_inst": "CNR-IBF, Istituto di Biofisica, Via Celoria 26, I-20133, Milano, Italy" - }, - { - "author_name": "David Lembo", - "author_inst": "Dipartimento di Scienze Cliniche e Biologiche Universita di Torino, Regione Gonzole, 10 I-10043 Orbassano (Turin), Italy" - }, - { - "author_name": "Alessandro Marcello", - "author_inst": "Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology, Padriciano 99 I-34149 Trieste, Italy" - }, - { - "author_name": "Eloise Mastrangelo", - "author_inst": "CNR-IBF, Istituto di Biofisica, Via Celoria 26, I-20133, Milano, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.11.11.375972", "rel_title": "ACE2-Targeting Monoclonal Antibody As A \"Pan\" Coronavirus Blocker In Vitro and In A Mouse Model", @@ -1087611,6 +1090424,29 @@ "type": "new results", "category": "ecology" }, + { + "rel_doi": "10.1101/2020.11.11.378828", + "rel_title": "Bifurcations and mutation hot-spots in the SARS-CoV-2 spike protein", + "rel_date": "2020-11-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.11.378828", + "rel_abs": "Novel topological methods are introduced to protein research. The aim is to identify hot-spot sites where a bifurcation can change the local topology of the protein backbone. Since the shape of a protein is intimately related to its biological function, a mutation that takes place at such a bifurcation hot-spot has an enhanced capacity to change the proteins biological function. The methodology applies to any protein but it is developed with the SARS-CoV-2 spike protein as a timely example. First, topological criteria are introduced to identify and classify potential mutation hot-spot sites along the protein backbone. Then, the expected outcome of a substitution mutation is estimated for a general class of hot-spots, by a comparative analysis of the backbone segments that surround the hot-spot sites. This analysis employs the statistics of commensurable amino acid fragments in the Protein Data Bank, in combination with general stereochemical considerations. It is observed that the notorious D614G substitution of the spike protein is a good example of such a mutation hot-spot. Several topologically similar examples are then analyzed in detail, some of them are even better candidates for a mutation hot-spot than D614G. The local topology of the recently observed N501Y mutation is also inspected, and it is found that this site is prone to a different kind of local topology changing bifurcation.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Xubiao Peng", + "author_inst": "Beijing Institute of Technology" + }, + { + "author_name": "Antti Juhani Niemi", + "author_inst": "Nordita/Stockholm University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.11.12.378422", "rel_title": "Massive X-ray screening reveals two allosteric drug binding sites of SARS-CoV-2 main protease", @@ -1089322,73 +1092158,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.11.07.20226837", - "rel_title": "Evaluating the Efficacy of Tocilizumab in Moderate to Severe COVID-19 with Progressive Illness despite Steroids: Identifying the Optimal Timing of its Administration in C3G study", - "rel_date": "2020-11-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.07.20226837", - "rel_abs": "BackgroundHigh mortality has been described in coronavirus disease 2019 (COVID-19) with cytokine release syndrome (CRS). Tocilizumab (TCZ), an interleukin-6 (IL-6) receptor antagonist may be associated with improved outcomes in such patients; however, the subgroups of patients who benefit the most need to be identified.\n\nObjectiveTo analyze the efficacy and optimal timing of administration of TCZ in moderate to severe COVID-19 with features of CRS, where the response to steroids was poor.\n\nMethodsThis is a retrospective study of 125 patients admitted between May 5 to July 31, 2020, in a tertiary care hospital in western India, with moderate to severe COVID-19 who were treated with TCZ along with steroids. The primary outcomes were the need for mechanical ventilation (MV) or death, and secondary outcomes were a decrease in oxygen requirement and inflammatory markers; the incidence of secondary infections, and renal or hepatic dysfunction. Kaplan Meier survival analysis and log rank test were used for evaluating primary outcomes. Secondary outcomes were analyzed using the Wilcoxon Signed-Rank test.\n\nResultsAmong 1081 patients admitted during the study period, 125 were administered TCZ (median age, 56 [95% CI 54 - 60] years; 100 [80%] male). The commonest symptoms were fever (96%), cough (64%), and dyspnea (48.8%). 78.4% patients had comorbidities (hypertension 51.2%, diabetes 43.2%, obesity 25.6% and chronic cardiac disease 13.6%). Of 117 patients who were treated with TCZ before requiring MV, 18.8% progressed to MV. Overall, 25% of the patients needed MV support. 65.3% of patients were discharged by day 14 after TCZ administration. Mortality was nil, 16.2%, 50%, and 62.5% in patients who received TCZ on room air, low flow oxygen, high flow nasal cannula (HFNC) and bilevel positive airway pressure (BiPAP), and MV respectively; overall 24.8% of patients died. Survival analysis showed no difference in outcome with respect to age and gender, while progression to MV showed a statistically significant reduction for the event death (90.9% of patients who progressed to MV died as compared to 6.3% who did not; log rank test with p < 0.0001). No adverse events were noticed.\n\nConclusionMortality was least in patients of COVID-19 with CRS who received TCZ while on low flow oxygen. When administered in the early hypoxemic phase, TCZ is associated with reduced mortality and decreased need for mechanical ventilation.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Surabhi Madan", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Manish Rana", - "author_inst": "GMERS Medical College, Sola" - }, - { - "author_name": "Rohan Gajjar", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Nitesh Shah", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Vipul Thakkar", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Bhagyesh Shah", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Pradip Dabhi", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Minesh Patel", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Hardik Shah", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Rashmi Chovatiya", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Maulik Soni", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Nirav Bapat", - "author_inst": "GMERS Medical College, Sola" - }, - { - "author_name": "Amit Patel", - "author_inst": "Care Institute of Medical Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.07.20227082", "rel_title": "A saliva-based RNA extraction-free workflow integrated with Cas13a for SARS-CoV-2 detection", @@ -1089653,6 +1092422,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.06.20227363", + "rel_title": "Performance of qualitative and quantitative antigen tests for SARS-CoV-2 in early symptomatic patients using saliva", + "rel_date": "2020-11-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.06.20227363", + "rel_abs": "BackgroundThe rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an urgent need for the prevention and containment of disease outbreaks in communities. Although the gold standard is polymerase chain reaction (PCR), antigen tests such as immunochromatographic assay (ICA) and chemiluminescent enzyme immunoassay (CLEIA) that can yield results within 30 minutes.\n\nMethodsWe evaluated performance of ICA and CLEIA using 34 frozen PCR-positive specimens (17 saliva and 17 nasopharyngeal swab) and 307 PCR-negative samples.\n\nResultsICA detected SARS-CoV-2 in only 14 (41%) samples, with positivity of 24% in saliva and 59% in NPS. Notably, ICA detected SARS-CoV-2 in 5 (83%) of 6 samples collected within 4 days after symptom onset. CLEIA detected SARS-CoV-2 in 31 (91%) samples, with positivity of 82% in saliva and 100% in NPS. CLEIA was negative in 3 samples with low viral load by PCR.\n\nConclusionsThese results suggest that use of ICA should be limited to earlier time after symptom onset and CLEIA is more sensitive and can be used in situations where quick results are required.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Isao Yokota", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Takayo Sakurazawa", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Junichi Sugita", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Sumio Iwasaki", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Keiko Yasuda", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Naoki Yamashita", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Shinichi Fujisawa", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Mutsumi Nishida", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Satoshi Konno", + "author_inst": "Hokkaido University Hospital" + }, + { + "author_name": "Takanori Teshima", + "author_inst": "Hokkaido University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.06.20227140", "rel_title": "Temporal Variations in the Intensity of Care Provided to Community and Nursing Home Residents Who Died of COVID-19 in Ontario, Canada", @@ -1090988,41 +1093812,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.07.20227512", - "rel_title": "Vitamin D - contrary to vitamin K - does not associate with clinical outcome in hospitalized COVID-19 patients", - "rel_date": "2020-11-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.07.20227512", - "rel_abs": "SARS-CoV-2 causes remarkably variable disease from asymptomatic individuals to respiratory insufficiency and coagulopathy. Vitamin K deficiency was recently found to associate with clinical outcome in a cohort of COVID-19 patients. Vitamin D has been hypothesized to reduce disease susceptibility by modulating inflammation, yet little is known about its role in disease severity. Considering the critical interaction between vitamin K and vitamin D in calcium and elastic fiber metabolism, we determined vitamin D status in the same cohort of 135 hospitalized COVID-19 patients by measuring blood 25(OH)D levels. We found no difference in vitamin D status between those with good and poor outcome (defined as intubation and/or death). Instead, we found vitamin D sufficient persons (25(OH)D >50 nmol/L) had accelerated elastic fiber degradation compared to those with mild deficiency (25(OH)D 25-50 nmol/L). Based on these findings, we hypothesize that vitamin D might have both favorable anti-inflammatory and unfavorable pro-calcification effects during COVID-19 and that vitamin K might compensate for the latter.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jona Walk", - "author_inst": "Canisius Wilhelmina Ziekenhuis" - }, - { - "author_name": "Anton SM Dofferhoff", - "author_inst": "Canisius Wilhelmina Ziekenhuis" - }, - { - "author_name": "Jody MW van den Ouweland", - "author_inst": "Canisius Wilhelmina Ziekenhuis" - }, - { - "author_name": "Henny van Daal", - "author_inst": "Canisius Wilhelmina Ziekenhuis" - }, - { - "author_name": "Rob Janssen", - "author_inst": "Canisius Wilhelmina Ziekenhuis" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.07.20201335", "rel_title": "Socio-economic disparities in social distancing during the COVID-19 pandemic in the United States", @@ -1091187,6 +1093976,49 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.11.08.372581", + "rel_title": "Resistance of endothelial cells to SARS-CoV-2 infection in vitro", + "rel_date": "2020-11-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.08.372581", + "rel_abs": "RationaleThe secondary thrombotic/vascular clinical syndrome of COVID-19 suggests that SARS-CoV-2 infects not only respiratory epithelium but also the endothelium activating thrombotic pathways, disrupting barrier function and allowing access of the virus to other organs of the body. However, a direct test of susceptibility to SARS-CoV-2 of authentic endothelial cell lines has not been performed.\n\nObjectiveTo determine infectibility of primary endothelial cell lines with live SARS-CoV-2 and pseudoviruses expressing SARS-CoV-2 spike protein.\n\nMethods and ResultsExpression of ACE2 and BSG pathways genes was determined in three types of endothelial cells; blood outgrowth, lung microvascular and aortic endothelial cells. For comparison nasal epithelial cells, Vero E6 cells (primate kidney fibroblast cell line) and HEK 293T cells (human embryonic kidney cells) transfected with either ACE2 or BSG were used as controls. Endothelial and Vero E6 cells were treated with live SARS-CoV-2 virus for 1 hour and imaged at 24 and 72 hours post infection. Pseudoviruses containing SARS-CoV-2, Ebola and Vesicular Stomatis Virus glycoproteins were generated and added to endothelial cells and HEK 239Ts for 2 hours and infection measured using luminescence at 48 hours post infection. Compared to nasal epithelial cells, endothelial cells expressed low or undetectable levels of ACE2 and TMPRSS2 but comparable levels of BSG, PPIA and PPIB. Endothelial cells showed no susceptibility to live SARS-CoV-2 or SARS-CoV-2 pseudovirus (but showed susceptibility to Ebola and Vesicular Stomatitis Virus). Overexpression of ACE2 but not BSG in HEK 239T cells conferred SARS-CoV-2 pseudovirus entry. Endothelial cells primed with IL-1{beta} remained resistant to SARS-CoV-2.\n\nConclusionEndothelial cells are resistant to infection with SARS-CoV-2 virus, in line with relatively low levels of ACE2 and TMPRSS2, suggesting that the vascular dysfunction and thrombosis seen in severe COVID-19 is a result of factors released by adjacent infected cells (e.g. epithelial cells) and/or circulating, systemic inflammatory mediators.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Blerina Ahmetaj-Shala", + "author_inst": "Imperial College London" + }, + { + "author_name": "Thomas P Peacock", + "author_inst": "Imperial College London" + }, + { + "author_name": "Laury Baillon", + "author_inst": "Imperial College London" + }, + { + "author_name": "Olivia Swann", + "author_inst": "Imperial College London" + }, + { + "author_name": "Hime Gashaw", + "author_inst": "Imperial College London" + }, + { + "author_name": "Wendy S Barclay", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jane A. Mitchell", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.11.09.374272", "rel_title": "Single cell transcriptomic re-analysis of immune cells in bronchoalveolar lavage fluids reveals the correlation of B cell characteristics and disease severity of patients with SARS-CoV-2 infection", @@ -1092965,41 +1095797,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.05.20226605", - "rel_title": "Alzheimer's and Parkinson's diseases predict different COVID-19 outcomes, a UK Biobank study", - "rel_date": "2020-11-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.05.20226605", - "rel_abs": "In December 2019, a coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began infecting humans causing a novel disease, coronavirus disease 19 (COVID-19). This was first described in the Wuhan province of the Peoples Republic of China. SARS-CoV-2 spread throughout the world causing a global pandemic. To date, thousands of cases of COVID-19 were reported in the United Kingdom, and over 45,000 patients have died. Some progress has been achieved in managing this disease, but the biological determinants of health, besides age, that affect COVID-19 infectivity and mortality are under scrutiny. Recent studies show that several medical conditions, including diabetes and hypertension, increase the risk of COVID-19 infection and death. The increased vulnerability of the elderly and those with comorbidities, together with the prevalence of neurodegenerative diseases with advanced age, led us to investigate the links between neurodegeneration and COVID-19. We analysed the primary health records of 13,338 UK individuals tested for COVID-19 between March and July 2020. We show that a pre-existing diagnosis of Alzheimers disease predicts the highest risk of COVID-19 infection and mortality among the elderly. In contrast, Parkinsons disease patients were found to be at increased risk of infection but not mortality from COVID-19. We conclude that there are disease-specific differences in COVID-19 susceptibility among patients affected by neurodegenerative disorders.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Yizhou Yu", - "author_inst": "University ofCambridge" - }, - { - "author_name": "Marco Travaglio", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Rebeka Popovic", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Nuno Santos Leal", - "author_inst": "University of Cambridge" - }, - { - "author_name": "L. Miguel Martins", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.06.20227017", "rel_title": "Predicting the impact of disruptions in lymphatic filariasis elimination programmes due to the outbreak of coronavirus disease (COVID-19) and possible mitigation strategies", @@ -1093320,6 +1096117,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.06.20225938", + "rel_title": "Validation of home oxygen saturations as a marker of clinical deterioration in patients with suspected COVID-19", + "rel_date": "2020-11-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.06.20225938", + "rel_abs": "BackgroundThe early identification of deterioration in suspected COVID-19 patients managed at home enables a more timely clinical intervention, which is likely to translate into improved outcomes. We undertook an analysis of COVID-19 patients conveyed by ambulance to hospital to investigate how oxygen saturation and measurements of other vital signs correlate to patient outcomes, to ascertain if clinical deterioration can be predicted with simple community physiological monitoring.\n\nMethodsA retrospective analysis of routinely collected clinical data relating to patients conveyed to hospital by ambulance was undertaken. We used descriptive statistics and predictive analytics to investigate how vital signs, measured at home by ambulance staff from the South Central Ambulance Service, correlate to patient outcomes. Information on patient comorbidities was obtained by linking the recorded vital sign measurements to the patients electronic health record at the Hampshire Hospitals NHS Foundation Trust. ROC analysis was performed using cross-validation to evaluate, in a retrospective fashion, the efficacy of different variables in predicting patient outcomes.\n\nResultsWe identified 1,080 adults with a COVID-19 diagnosis who were conveyed by ambulance to either Basingstoke & North Hampshire Hospital or the Royal Hampshire County Hospital (Winchester) between March 1st and July 31st and whose diagnosis was clinically confirmed at hospital discharge. Vital signs measured by ambulance staff at first point of contact in the community correlated with patient short-term mortality or ICU admission. Oxygen saturations were the most predictive of mortality or ICU admission (AUROC 0.772 (95 % CI: 0.712-0.833)), followed by the NEWS2 score (AUROC 0.715 (95 % CI: 0.670-0.760), patient age (AUROC 0.690 (95 % CI: 0.642-0.737)), and respiration rate (AUROC 0.662 (95 % CI: 0.599-0.729)). Combining age with the NEWS2 score (AUROC 0.771 (95 % CI: 0.718-0.824)) or the measured oxygen saturation (AUROC 0.820 (95 % CI: 0.785-0.854)) increased the predictive ability but did not reach significance.\n\nConclusionsInitial oxygen saturation measurements (on air) for confirmed COVID-19 patients conveyed by ambulance correlated with short-term (30-day) patient mortality or ICU admission, AUROC: 0.772 (95% CI: 0.712-0.833). We found that even small deflections in oxygen saturations of 1-2% below 96% confer an increased mortality risk in those with confirmed COVID at their initial community assessments.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Matthew Inada-Kim", + "author_inst": "Acute Medical Unit, Department of Acute Medicine, Hampshire Hospitals NHS Foundation Trust, Winchester, United Kingdom." + }, + { + "author_name": "Francis P Chmiel", + "author_inst": "School of Electronics and Computer Science, University of Southampton, Southampton, SO17 1BJ, UK" + }, + { + "author_name": "Michael J Boniface", + "author_inst": "School of Electronics and Computer Science, University of Southampton, Southampton, SO17 1BJ, UK" + }, + { + "author_name": "Helen Pocock", + "author_inst": "South Central Ambulance Service NHS Foundation Trust, Otterbourne, SO21 2RU, UK and Warwick Clinical Trials Unit, University of Warwick, Coventry, CV4 7AL, UK" + }, + { + "author_name": "John J. M. Black", + "author_inst": "South Central Ambulance Service NHS Foundation Trust, Otterbourne, SO21 2RU, UK and Emergency Department, Oxford University Hospitals NHS Foundation Trust OX3 9" + }, + { + "author_name": "Charles D Deakin", + "author_inst": "South Central Ambulance Service NHS Foundation Trust, Otterbourne, SO21 2RU, UK and Southampton Respiratory Biomedical Research Unit, National Institute for Hea" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2020.11.06.20226969", "rel_title": "Interventions targeting nonsymptomatic cases can be important to prevent local outbreaks: COVID-19 as a case-study", @@ -1094843,101 +1097679,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2020.11.04.20226191", - "rel_title": "Wastewater Analysis of SARS-CoV-2 as a Predictive Metric of Positivity Rate for a Major Metropolis", - "rel_date": "2020-11-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.04.20226191", - "rel_abs": "Wastewater monitoring for SARS-CoV-2 has been suggested as an epidemiological indicator of community infection dynamics and disease prevalence. We report wastewater viral RNA levels of SARS-CoV-2 in a major metropolis serving over 3.6 million people geographically spread over 39 distinct sampling sites. Viral RNA levels were followed weekly for 22 weeks, both before, during, and after a major surge in cases, and simultaneously by two independent laboratories. We found SARS-CoV-2 RNA wastewater levels were a strong predictive indicator of trends in the nasal positivity rate two-weeks in advance. Furthermore, wastewater viral RNA loads demonstrated robust tracking of positivity rate for populations served by individual treatment plants, findings which were used in real-time to make public health interventions, including deployment of testing and education strike teams.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Lauren B Stadler", - "author_inst": "Rice University" - }, - { - "author_name": "Katherine Ensor", - "author_inst": "Rice University" - }, - { - "author_name": "Justin R Clark", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Prashant Kalvapalle", - "author_inst": "Rice University" - }, - { - "author_name": "Zachary W LaTurner", - "author_inst": "Rice University" - }, - { - "author_name": "Lilian Mojica", - "author_inst": "Houston Health Department" - }, - { - "author_name": "Austen L Terwilliger", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Yue Zhuo", - "author_inst": "Rice University" - }, - { - "author_name": "Priyanka Ali", - "author_inst": "Rice University" - }, - { - "author_name": "Vasanthi Avadhanula", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Roberto Bertolusso", - "author_inst": "Rice University" - }, - { - "author_name": "Tessa Crosby", - "author_inst": "Rice University" - }, - { - "author_name": "Haroldo Hernandez Santos", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Marielle Hollstein", - "author_inst": "Rice University" - }, - { - "author_name": "Kyle Weesner", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "David M Zong", - "author_inst": "Rice University" - }, - { - "author_name": "David Persse", - "author_inst": "Houston Health Department" - }, - { - "author_name": "Pedro A Piedra", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Anthony W Maresso", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Loren Hopkins", - "author_inst": "Houston Health Department" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.04.20226092", "rel_title": "Nowcasting and forecasting provincial-level SARS-CoV-2 case positivity using google search data in South Africa", @@ -1095142,6 +1097883,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.11.05.20226415", + "rel_title": "Psychological resilience, coping behaviors, and social support among healthcare workers during the COVID-19 pandemic: a systematic review of quantitative studies", + "rel_date": "2020-11-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.05.20226415", + "rel_abs": "AimTo appraise and synthesize studies examining resilience, coping behaviours, and social support among healthcare workers during the coronavirus pandemic.\n\nBackgroundA wide range of evidence has shown that healthcare workers, currently on the frontlines in the fight against COVID-19, are not spared from the psychological and mental health-related consequences of the pandemic. Studies synthesizing the role of coping behaviours, resilience, and social support in safeguarding the mental health of healthcare workers during the pandemic is largely unknown.\n\nEvaluationThis is a systematic review with a narrative synthesis. A total of 31 articles were included in the review.\n\nKey IssuesHealthcare workers utilized both problem-centred and emotion-centred coping to manage the stress-associated with the coronavirus pandemic. Coping behaviours, resilience, and social support were associated with positive mental and psychological health outcomes.\n\nConclusionSubstantial evidence supports the effectiveness of coping behaviours, resilience, and social support to preserve psychological and mental health among healthcare workers during the COVID-19 pandemic.\n\nImplications for Nursing ManagementIn order to safeguard the mental health of healthcare workers during the pandemic, hospital and nursing administrators should implement proactive measures to sustain resilience in HCWs, build coping skills, and implement creative ways to foster social support in healthcare workers through theory-based interventions, supportive leadership, and fostering a resilient work environment.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Leodoro Labrague", + "author_inst": "Sultan Qaboos University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.04.20226126", "rel_title": "Post-acute COVID-19 syndrome negatively impacts health and wellbeing despite less severe acute infection", @@ -1096816,29 +1099576,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.11.04.368449", - "rel_title": "Thermodynamic evaluation of the impact of DNA mismatches in PCR-type SARS-CoV-2 primers and probes", - "rel_date": "2020-11-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.04.368449", - "rel_abs": "BackgroundDNA mismatches can affect the efficiency of PCR techniques if the intended target has mismatches in primers or probes regions. The accepted rule is that mismatches are detrimental as they reduce the hybridization temperatures, yet a more quantitative assessment is rarely performed.\n\nMethodsWe calculate the hybridization temperatures of primer/probe sets after aligning to SARS-COV-2, SARS-COV-1 and non-SARS genomes, considering all possible combinations of single, double and triple consecutive mismatches. We consider the mismatched hybridization temperature within a range of 5 {degrees}C to the fully matched reference temperature.\n\nResultsWe obtained the alignments of 19 PCR primers sets that were recently reported for the detection of SARS-CoV-2 and to 21665 SARS-CoV-2 genomes as well as 323 genomes of other viruses of the coronavirus family of which 10 are SARS-CoV-1. We find that many incompletely aligned primers become fully aligned to most of the SARS-CoV-2 when mismatches are considered. However, we also found that many cross-align to SARS-CoV-1 and non-SARS genomes.\n\nConclusionsSome primer/probe sets only align substantially to most SARS-CoV-2 genomes if mismatches are taken into account. Unfortunately, by the same mechanism, almost 75% of these sets also align to some SARS-CoV-1 and non-SARS viruses. It is therefore recommended to consider mismatch hybridization for the design of primers whenever possible, especially to avoid undesired cross-reactivity.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Pamella Miranda", - "author_inst": "Universidade Federal de Minas Gerais" - }, - { - "author_name": "Gerald Weber", - "author_inst": "Universidade Federal de Minas Gerais" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.11.03.20225425", "rel_title": "Per capita COVID-19 Case Rates are Lower in U.S. Counties Voting more Heavily Democratic in the 2016 Presidential Election, except not in States with a Republican Governor and Legislature", @@ -1097139,6 +1099876,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2020.11.03.20225375", + "rel_title": "Adaptive responses to SARS-CoV-2 infection linked to accelerated aging measures predict adverse outcomes in patients with severe COVID-19", + "rel_date": "2020-11-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.03.20225375", + "rel_abs": "INTRODUCTIONChronological age (CA) is a predictor of adverse COVID-19 outcomes; however, CA alone does not capture individual responses to SARS-CoV-2 infection. Here, we evaluated the influence of aging metrics PhenoAge and PhenoAgeAccel to predict adverse COVID-19 outcomes. Furthermore, we sought to model adaptive metabolic and inflammatory responses to severe SARS-CoV-2 infection using individual PhenoAge components.\n\nMETHODSIn this retrospective cohort study, we assessed cases admitted to a COVID-19 reference center in Mexico City. PhenoAge and PhenoAgeAccel were estimated using laboratory values at admission. Cox proportional hazards models were fitted to estimate risk for COVID-19 lethality and adverse outcomes (ICU admission, intubation, or death). To explore reproducible patterns which model adaptive responses to SARS-CoV-2 infection, we used k-means clustering using PhenoAge/PhenoAccelAge components.\n\nRESULTSWe included 1068 subjects of whom 401 presented critical illness and 204 died. PhenoAge was a better predictor of adverse outcomes and lethality compared to CA and SpO2 and its predictive capacity was sustained for all age groups. Patients with responses associated to PhenoAgeAccel>0 had higher risk of death and critical illness compared to those with lower values (log-rank p<0.001). Using unsupervised clustering we identified four adaptive responses to SARS-CoV-2 infection: 1) Inflammaging associated with CA, 2) metabolic dysfunction associated with cardio-metabolic comorbidities, 3) unfavorable hematological response, and 4) response associated with favorable outcomes.\n\nCONCLUSIONSAdaptive responses related to accelerated aging metrics are linked to adverse COVID-19 outcomes and have unique and distinguishable features. PhenoAge is a better predictor of adverse outcomes compared to CA.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Alejandro M\u00e1rquez-Salinas", + "author_inst": "Universidad Nacional Autonoma de Mexico" + }, + { + "author_name": "Carlos A. Ferm\u00edn-Mart\u00ednez", + "author_inst": "Universidad Nacional Autonoma de Mexico" + }, + { + "author_name": "Neftali Eduardo Antonio-Villa", + "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n \"Salvador Zubir\u00e1n\"" + }, + { + "author_name": "Arsenio Vargas-V\u00e1zquez", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Enrique C. Guerra", + "author_inst": "National Autonomous University of Mexico" + }, + { + "author_name": "Alejandro Campos-Mu\u00f1oz", + "author_inst": "UIEM, INCMNSZ" + }, + { + "author_name": "Lilian Zavala-Romero", + "author_inst": "Universidad Nacional Autonoma de Mexico" + }, + { + "author_name": "Roopa Mehta", + "author_inst": "UIEM, INCMNSZ" + }, + { + "author_name": "Jessica Paola Bahena-L\u00f3pez", + "author_inst": "Universidad Nacional Autonoma de Mexico" + }, + { + "author_name": "Edgar Ortiz-Brizuela", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Mar\u00eda Fernanda Gonz\u00e1lez-Lara", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Carla M Rom\u00e1n-Montes", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Bernardo A. Mart\u00ednez-Guerra", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Alfredo Ponce de Leon", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Jos\u00e9 Sifuentes-Osornio", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Luis Miguel Gut\u00e9irrez-Robledo", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Carlos A Aguilar-Salinas", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Omar Yaxmehen Bello-Chavolla", + "author_inst": "Instituto Nacional de Geriatria" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "geriatric medicine" + }, { "rel_doi": "10.1101/2020.11.04.20225698", "rel_title": "Early survey with bibliometric analysis on machine learning approaches in controlling coronavirus", @@ -1099038,89 +1101862,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.10.30.20223230", - "rel_title": "SARS-CoV-2 Seroprevalence in a Cohort of Asymptomatic, RT-PCR Negative Croatian First League Football Players", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20223230", - "rel_abs": "BackgroundDuring the COVID-19 pandemic the Croatian Football Federation has launched a new model of pre-season systematic examination of football players, emphasizing the diagnosis of asymptomatic SARS-CoV-2 infection and preventing further spread among the players.\n\nObjectivesThe aim of this study was to assess the prevalence and dynamics of SARS-CoV-2 IgA and IgG antibodies in the cohort of asymptomatic and SARS-CoV-2 PCR negative professional football players in the Croatian First Football League by using a commercial ELISA antibody assay in the paired serum samples taken 2 months apart.\n\nMethodsSerology testing was performed from May till July 2020 in a cohort of 305 asymptomatic football players and club staff members. RT-PCR for detection of SARS-CoV-2 from nasopharyngeal swabs was performed on three occasions, and Euroimmun ELISA for detection of IgA and IgG (S1 and NCP) antibodies was tested in paired serum samples in May and July.\n\nResultsAll RT-PCR results were negative. Sixty-one (20%) participants were reactive in one or two classes of antibodies at baseline and/or follow-up serology testing. IgA reactivity was found in 41 (13.4% [95% CI=10.7-17.7]) baseline sera and 42 (13.8% [95% CI=10.3-18.9]) follow-up sera. IgG to S1 protein was found in 6 (2% [95% CI=0.9-4.2]) participants at baseline and 1 (0.33% [95% CI=0.0006-1.83]) at follow-up. IgG to NCP was found in 2 (0.7% [95% CI=0.2-2.4]) participants at baseline and 8 (2.6% (95% CI=1.3-5.1]) participants at follow-up. Noticeable dynamics in the paired sera was observed in 18 (5.9%) participants (excluding borderline IgA results) or 32 (10.5%) (including IgA borderline results).\n\nConclusionVarious patterns of IgA and IgG reactivity were found in the paired serum samples. Based on serology dynamics we estimate that in 5.9%-10.5% of PCR negative football players asymptomatic exposure to SARS-CoV-2 during pandemics could not be excluded.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Adriana Vince", - "author_inst": "University Hospital for Infectious Diseases Dr. Fran Mihaljevic, Zagreb, Croatia School of Medicine University of Zagreb, Zagreb, Croatia" - }, - { - "author_name": "Renata Zadro", - "author_inst": "St. Catherine Specialty Hospital, Zabok/Zagreb, Croatia" - }, - { - "author_name": "Zvonimir Sostar", - "author_inst": "Public Health Institute Dr. Andrija Stampar, Department of Microbiology, Zagreb, Croatia" - }, - { - "author_name": "Suncanica Ljubin Sternak", - "author_inst": "Public Health Institute Dr. Andrija Stampar, Department of Microbiology, Zagreb, Croatia School of Medicine University of Zagreb, Zagreb, Croatia" - }, - { - "author_name": "Jasmina Vranes", - "author_inst": "Public Health Institute Dr. Andrija Stampar, Department of Microbiology, Zagreb, Croatia School of Medicine University of Zagreb, Zagreb, Croatia" - }, - { - "author_name": "Vedrana Skaro", - "author_inst": "Institute for Anthropological Research, Centre for Applied Bioanthropology, Laboratory for Molecular Anthropology, Zagreb, Croatia Genos Ltd, DNA Laboratory, Z" - }, - { - "author_name": "Petar Projic", - "author_inst": "Institute for Anthropological Research, Centre for Applied Bioanthropology, Laboratory for Molecular Anthropology, Zagreb, Croatia Genos Ltd, DNA Laboratory, Z" - }, - { - "author_name": "Vilim Molnar", - "author_inst": "St. Catherine Specialty Hospital, Zabok/Zagreb, Croatia" - }, - { - "author_name": "Vid Matisic", - "author_inst": "St. Catherine Specialty Hospital" - }, - { - "author_name": "Bruno Barsic", - "author_inst": "School of Medicine University of Zagreb, Zagreb, Croatia" - }, - { - "author_name": "Gordan Lauc", - "author_inst": "Genos Ltd, DNA Laboratory, Zagreb, Croatia University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia" - }, - { - "author_name": "Zvjezdana Lovric Makaric", - "author_inst": "Croatian Institute of Public Health, Zagreb, Croatia" - }, - { - "author_name": "Zoran Bahtijarevic", - "author_inst": "Childrens Hospital Zagreb, Zagreb, Croatia" - }, - { - "author_name": "Tomislav Vlahovic", - "author_inst": "Clinical Hospital Centre Sisters of Mercy, Clinic of Traumatology, Zagreb, Croatia" - }, - { - "author_name": "Sandra Sikic", - "author_inst": "Public Health Institute Dr. Andrija Stampar, Department of Microbiology, Zagreb, Croatia" - }, - { - "author_name": "Ozren Polasek", - "author_inst": "University of Split, Medical School, Split, Croatia" - }, - { - "author_name": "Dragan Primorac", - "author_inst": "St. Catherine Specialty Hospital, Zabok/Zagreb, Croatia Eberly College of Science, The Pennsylvania State University, University Park, PA, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "sports medicine" - }, { "rel_doi": "10.1101/2020.11.01.20217943", "rel_title": "CovidSIMVL - Agent-Based Modeling of Localized Transmission within a Heterogeneous Array of Locations: Motivation, Configuration and Calibration", @@ -1099305,6 +1102046,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.01.20223982", + "rel_title": "Filtration Performance Degradation of In-Use Masks by Vapors from Alcohol-Based Hand Sanitizers and the Mitigation Solutions", + "rel_date": "2020-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.01.20223982", + "rel_abs": "How often does one perform hand disinfection while wearing a mask? In the current COVID-19 pandemic, wearing masks and hand disinfection are widely adopted hygiene practices. However, our study indicated that exposure to the vapors from alcohol-based sanitizers during hand disinfection might degrade the filtration performance of the in-use masks, and the degradation worsened with the increasing number of hand disinfection. After five times of hand disinfection, the filtration efficiencies of surgical masks decreased by >8% for 400 and 500nm particles and by 3.68{+/-}1.83 % for 1m particles. This was attributed to the dissipation of electrostatic charges on the masks when exposed to the alcohol vapor generated during hand disinfection. Simple practice of vapor-avoiding hand disinfection could mitigate the effects of alcohol vapor, which was demonstrated on two brands of surgical masks. The vapor-avoiding hand disinfection is recommended to be included in the hygiene guide to maintain the mask performance.\n\nGraphic abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC=\"FIGDIR/small/20223982v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (21K):\norg.highwire.dtl.DTLVardef@16dc3a2org.highwire.dtl.DTLVardef@146d3e0org.highwire.dtl.DTLVardef@1003cb5org.highwire.dtl.DTLVardef@91b484_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Weidong He", + "author_inst": "Northeastern University" + }, + { + "author_name": "Yinghe Guo", + "author_inst": "Northeastern University" + }, + { + "author_name": "Jingxian Liu", + "author_inst": "Northeastern University" + }, + { + "author_name": "Yang Yue", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Jing Wang", + "author_inst": "ETH Zurich" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.10.30.20223586", "rel_title": "Lightweight Model For The Prediction of COVID-19 Through The Detection And Segmentation of Lesions in Chest CT Scans", @@ -1100552,65 +1103328,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.02.20224303", - "rel_title": "Randomized controlled trial of convalescent plasma therapy against standard therapy in patients with severe COVID-19 disease", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20224303", - "rel_abs": "BackgroundConvalescent plasma (CP) therapy in COVID-19 disease has been suggested to improve clinical outcome in severe disease. This pilot study was designed to inform the design of a definitive phase 3 clinical trial.\n\nMethodsThis was a prospective, interventional and randomized open label pilot trial involving 40 patients with COVID-19 who were requiring oxygen therapy and who had radiological evidence of pneumonia. Twenty COVID-19 patients received two 200ml transfusions of convalescent patient CP over 24 hours were compared with 20 patients who received routine care alone. The primary outcome was the requirement for ventilation. The secondary outcomes were white blood cell count, lactate dehydrogenase (LDH), C-reactive protein (CRP), Troponin, Ferritin, D-Dimer, procalcitonin, mortality rate at 28 days.\n\nResultsThe CP group were a higher risk group with higher ferritin levels (p<0.05) though respiratory indices did not differ. The primary outcome measure - ventilation - was required in 6 controls and 4 patients on CP (risk ratio 0.67 95% CI 0.22 - 2.0, p=0.72); mean time on ventilation was 10.5 days in the control against 8.2 days in patients on CP (p=0.81). There were no differences in secondary measures at the end of the study. Two patients died in the control and one patient in the CP arm.\n\nConclusionThere were no significant differences in the primary or secondary outcome measures between CP and standard therapy though fewer patients required ventilation and for a shorter period of time. The study showed that CP therapy appears to be safe and it is feasible to perform a definitive phase 3 clinical trial using this study protocol.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Manaf AlQahtani", - "author_inst": "Bahrain National Taskforce to Combat COVID-19, Bahrain Defense Force Hospital, Bahrain" - }, - { - "author_name": "Abdulkarim Abdulrahman", - "author_inst": "Bahrain National Taskforce to Combat COVID-19, Mohammed bin Khalifa Cardiac Centre, Bahrain" - }, - { - "author_name": "Abdulrahman AlMadani", - "author_inst": "Bahrain Defence Force Hospital, Bahrain" - }, - { - "author_name": "Salman Yousif AlAli", - "author_inst": "Bahrain Defence Force Hospital, Bahrain" - }, - { - "author_name": "Alaa Mahmood Al Zamrooni", - "author_inst": "Salmaniya Medical Complex, Bahrain" - }, - { - "author_name": "Amal Hejab", - "author_inst": "Bahrain National Taskforce to Combat COVID-19" - }, - { - "author_name": "Pearl Wasif", - "author_inst": "Royal College of Surgeons in Ireland-Bahrain" - }, - { - "author_name": "Ronan Conroy", - "author_inst": "Royal College of Surgeons in Ireland, Dublin, Ireland" - }, - { - "author_name": "Stephen Atkin", - "author_inst": "Royal College of Surgeons in Ireland - Bahrain" - }, - { - "author_name": "Sameer Otoom", - "author_inst": "Royal College of Surgeons in Ireland-Bahrain" - }, - { - "author_name": "Manal Abduljalil AlSayed", - "author_inst": "Bahrain Defence Force Hospital, Bahrain" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.31.20223776", "rel_title": "Cell phone mobility data reveals heterogeneity in stay-at-home behavior during the SARS-CoV-2 pandemic", @@ -1100907,6 +1103624,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2020.11.02.20224832", + "rel_title": "Preferential observation of large infectious disease outbreaks leads to consistent overestimation of intervention efficacy.", + "rel_date": "2020-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20224832", + "rel_abs": "Data from infectious disease outbreaks in congregate settings are often used to elicit clues about which types of interventions may be useful in other facilities. This is commonly done using before-and-after comparisons in which the infectiousness of pre-intervention cases is compared to that of post-intervention cases and the difference is attributed to intervention impact. In this manuscript, we show how a tendency to preferentially observe large outbreaks can lead to consistent overconfidence in how effective these interventions actually are. We show, in particular, that these inferences are highly susceptible to bias when the pathogen under consideration exhibits moderate-to-high amounts of heterogeneity in infectiousness. This includes important pathogens such as SARS-CoV-2, influenza, Noroviruses, HIV, Tuberculosis, and many others", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jon Zelner", + "author_inst": "University of Michigan School of Public Health" + }, + { + "author_name": "Nina B Masters", + "author_inst": "University of Michigan School of Public Health" + }, + { + "author_name": "Kelly Broen", + "author_inst": "University of Michigan School of Public Health" + }, + { + "author_name": "Eric Lofgren", + "author_inst": "Washington State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.02.20221309", "rel_title": "Seroprevalence of SARS-CoV-2 antibodies in Saint Petersburg, Russia: a population-based study", @@ -1102306,29 +1105054,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.11.03.20225227", - "rel_title": "Space-Time Covid-19 Bayesian SIR modeling in South Carolina", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.03.20225227", - "rel_abs": "The Covid-19 pandemic has spread across the world since the beginning of 2020. Many regions have experienced its effects. The state of South Carolina in the USA has seen cases since early March 2020 and a primary peak in early April 2020. A lockdown was imposed on April 6th but lifting of restrictions started on April 24th. The daily case and death data as reported by NCHS (deaths) via the New York Times GitHUB repository have been analyzed and approaches to modeling of the data are presented. Prediction is also considered and the role of asymptomatic transmission is assessed as a latent unobserved effect. Two different time periods are examined and one step prediction is provided.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Andrew B Lawson", - "author_inst": "Medical University of South Carolina" - }, - { - "author_name": "Joanne Kim", - "author_inst": "Medical University of South Carolina" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.30.20221440", "rel_title": "The relationship between anxiety, health, and potential stressors among adults in the United States during the COVID-19 pandemic", @@ -1102597,6 +1105322,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.11.02.20220038", + "rel_title": "Benefits and risks of zinc for adults during covid-19: rapid systematic review and meta-analysis of randomised controlled trials.", + "rel_date": "2020-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20220038", + "rel_abs": "ObjectiveTo evaluate the benefits and risks of any type of zinc intervention to prevent or treat SARS-CoV-2.\n\nDesignA living, systematic review and meta-analysis, incorporating rapid review methods.\n\nData sources17 English and Chinese databases and clinical trial registries were searched in April/May 2020, with additional covid-19 focused searches in June and August 2020.\n\nEligibilitycriteria and analysisRandomized control trials (RCTs) published in any language comparing zinc to a control to prevent or treat SARS-CoV-2. Other viral respiratory tract infections (RTIs) were included, but the certainty of evidence downgraded twice for indirectness. Screening, data extraction, risk of bias appraisal (RoB-2 tool) and verification was performed by calibrated, single reviewers. RCTs with adult populations were prioritised for analysis.\n\nResults123 RCTs were identified. None were specific to SARS-CoV-2 nor other coronaviruses. 28 RCTs evaluated oral (15-45mg daily), sublingual (45-300mg daily), or topical nasal (0.09-2.6 mg daily) zinc to prevent or treat nonspecific viral RTIs in 3,597 adults without zinc deficiency. Compared to placebo, zinc prevented 5 mild to moderate RTIs per 100 person-months, including in older adults (95% confidence interval 1 to 9) (number needed to treat (NTT)=20). There was no significant difference in the rates of non-serious adverse events (AE). For RTI treatment, a clinically important reduction in peak symptom severity scores was found for zinc compared to placebo (mean difference 1.2 points, 0.7 to 1.7), but not average daily symptom severity (standardised mean difference 0.2, 0.1 to 0.4). 19 fewer per 100 adults were at risk of remaining symptomatic over the first 7 days (2 to 38, NNT=5) and the mean duration of symptoms was 2 days shorter (0.2 to 3.5), however, there was substantial heterogeneity (I2 = 82% and 97%). 14 more per 100 experienced a non-serious AE (4 to 16, NNT=7) such as nausea, or mouth or nasal irritation. No differences in illness duration nor AE were found when zinc was compared to active controls. No serious AE, including copper deficiency, were reported by any RCT. Quality of life outcomes were not assessed. Confidence in these findings for SARS-CoV-2 is very low due to serious indirectness and some concerns about bias for most outcomes.\n\nConclusionsZinc is a potential therapeutic candidate for preventing and treating SARS-CoV-2, including older adults and adults without zinc deficiency (very low certainty). Zinc may also help to prevent other viral RTIs during the pandemic (moderate certainty) and reduce the severity and duration of symptoms (very low certainty). The pending results from seven RCTs evaluating zinc for SARS-CoV-2 will be tracked.\n\nSystematic review registrationPROSPERO CRD42020182044", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jennifer Hunter", + "author_inst": "Western Sydney University" + }, + { + "author_name": "Susan Arentz", + "author_inst": "Western Sydney University" + }, + { + "author_name": "Joshua Goldenberg", + "author_inst": "National University of Natural Medicine" + }, + { + "author_name": "Dominik Mertz", + "author_inst": "McMaster University" + }, + { + "author_name": "Guoyan Yang", + "author_inst": "Western Sydney University" + }, + { + "author_name": "Jennifer Beardsley", + "author_inst": "Independent Librarian, Seattle, USA" + }, + { + "author_name": "Stephen P Myers", + "author_inst": "Southern Cross University" + }, + { + "author_name": "Stephen Leeder", + "author_inst": "The University of Sydney" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.03.20216580", "rel_title": "Immune modulating drug MP1032 with SARS-CoV-2 antiviral activity in vitro: A potential multi-target approach for prevention and early intervention treatment of COVID-19.", @@ -1103792,41 +1106564,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.29.20207167", - "rel_title": "Gastroenterological and Hepatic Manifestations of Patients with COVID-19, Prevalence, Mortality by Country, and Intensive Care Admission Rate: Systematic Review and Meta-analysis.", - "rel_date": "2020-11-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.29.20207167", - "rel_abs": "Background & AimsPatient infected with the SARS-COV2 usually report fever and respiratory symptoms. However, multiple gastrointestinal (GI) manifestations such as diarrhea and abdominal pain has been described. The aim of this study was to evaluate the prevalence of GI, liver function test (LFT) abnormalities, and mortality of COVID-19 patients.\n\nMethodsWe performed a systematic review and meta-analysis of published studies that included cohort of patients infected with SARS-COV2 from December 1st, 2019 to July 1st, 2020. We collected data from the cohort of patients with COVID-19 by conducting a literature search using PubMed, Embase, Scopus, and Cochrane according to the preferred reporting Items for Systematic Reviews and MetaAnalyses (PRISMA) guidelines. We analyzed pooled data on the prevalence of overall and individual gastrointestinal symptoms, LFTs abnormalities and performed subanalyses to investigate the relationship between gastrointestinal symptoms, geographic location, fatality, and ICU admission.\n\nResultsThe available data of 17,802 positive patients for SARS-COV2 from 120 studies were included in our analysis. The most frequent manifestations were diarrhea (13.3%, 95% CI 12-16), nausea (9.1%, 95% CI 9-13) and elevated LFTs (23.7%, 95% CI 21- 27). The overall and GI fatality were 7.2% (95% CI 6 -10), and 1% (95% CI 1- 4) respectively. Subgroup analysis showed non statistically significant associations between GI symptoms/LFTs abnormalities and ICU admissions (OR=3.41, 95% CI 0.87 - 13.4). The GI mortality rate was 0.58% in China and 3.5% in the United States (95% CI 2 - 5).\n\nConclusionDigestive symptoms and LFTs abnormalities are common in COVID-19 patients. Our subanalysis shows that the presence of gastrointestinal and liver manifestations does not appear to affect mortality, or ICU admission rate. However, the mortality rate was higher in the United States compared to China.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Mohammad Shehab", - "author_inst": "Mubarak Hospital" - }, - { - "author_name": "Fatima Alrashed", - "author_inst": "MCPHS University" - }, - { - "author_name": "Sameera Shuaibi", - "author_inst": "Kuwait University" - }, - { - "author_name": "Dhuha Alajmi", - "author_inst": "Kuwait University" - }, - { - "author_name": "Alan Barkun", - "author_inst": "Mcgill University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2020.10.29.20215996", "rel_title": "''Necessity is the mother of invention'': Specialist palliative care service innovation and practice change in response to COVID-19. Results from a multi-national survey (CovPall)", @@ -1104019,6 +1106756,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.10.29.20222422", + "rel_title": "Avoiding versus contracting COVID-19: On the effectiveness of social distancing at the level of the individual", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.29.20222422", + "rel_abs": "Past research has established the value of social distancing as a means of deterring the spread of COVID-19 largely by examining aggregate level data. Locales in which efforts were undertaken to encourage distancing experienced reductions in their rate of transmission. However, these aggregate results tell us little about the effectiveness of social distancing at the level of the individual, which is the question addressed by the current research. Four months after participating in a study assessing their social distancing behavior, 2,120 participants indicated whether they had contracted COVID-19. Importantly, the assessment of social distancing involved not only a self-report measure of how strictly participants had followed social distancing recommendations, but also a series of virtual behavior measures of social distancing. These simulations presented participants with graphical depictions mirroring specific real-world scenarios, asking them to position themselves in relation to others in the scene. Individuals social distancing behavior, particularly as assessed by the virtual behavior measure, predicted whether they contracted COVID-19 during the intervening four months. This was true when considering only participants who reported having tested positively for the virus and when considering additional participants who, although untested, believed that they had contracted the virus. The findings offer a unique form of additional evidence as to why individuals should practice social distancing. What the individual does matters, not only for the health of the collective, but also for the specific individual.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Russell H Fazio", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Benjamin C. Ruisch", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Courtney A. Moore", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Javier A. Granados Samayoa", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Shelby T. Boggs", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Jesse T. Ladanyi", + "author_inst": "The Ohio State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.10.28.20221416", "rel_title": "COVID-19 Active Surveillance Simulation Case Study - Health and Economic Impacts of Active Surveillance in a School Environment", @@ -1105841,113 +1108617,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.10.30.20215301", - "rel_title": "Remdesivir-based therapy improved recovery of patients with COVID-19 in the SARSTer multicentre, real-world study", - "rel_date": "2020-11-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20215301", - "rel_abs": "BackgroundRemdesivir (RDV) is the only antiviral drug registered currently for treatment of COVID-19 after a few clinical trials with controversial results. The purpose of this study was to evaluate the effectiveness and safety of RDV in patients with COVID-19 in real world settings.\n\nMethodsPatients were selected from 1496 individuals included in the SARSTer national database; 122 of them received therapy with RDV and 211 were treated with lopinavir/ritonavir (LPV/r)-based therapy. The primary end-point of effectiveness was clinical improvement in the ordinal 8-point scale, which was defined as a 2-point decrease from baseline to 7, 14, 21 and 28 days of hospitalization. The secondary end-points of effectiveness included: death rate, rate of no clinical improvement within 28 days of hospitalization in the ordinal scale, rate of the need for constant oxygen therapy, duration of oxygen therapy, rate of the need for mechanical ventilation, total hospitalization time, and rate of positive RT PCR for SARS-CoV-2 after 30 days.\n\nFindingsSignificantly higher rates of clinical improvement, by 15% and 10% respectively, were observed after RDV treatment compared to LPV/r at days 21 and 28. The difference between regimens increased with worsening of oxygen saturation (SpO2) and depending on the baseline score from the ordinal scale. Statistically significant differences supporting RDV were also noted regarding the rate of no clinical improvement within 28 days of hospitalization and hospitalization duration in patients with baseline SpO2 [≤]90%. In the logistic regression model only the administration of remdesivir was independently associated with at least a 2-point improvement in the ordinal scale between baseline and day 21.\n\nInterpretationIn conclusion, data collected in this retrospective, observational, real world study supported use of remdesivir for treatment of SARS-CoV-2 infection particularly in patients with oxygen saturation [≤]95%.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Robert Flisiak", - "author_inst": "Department of Infectious Diseases and Hepatology, Medical University of Bialystok, Poland" - }, - { - "author_name": "Dorota Zarebska-Michaluk", - "author_inst": "Department of Infectious Diseases, Jan Kochanowski University, Kielce, Poland" - }, - { - "author_name": "Aleksandra Berkan-Kawinska", - "author_inst": "Department of Infectious Diseases and Hepatology, Medical University of Lodz, Lodz, Poland" - }, - { - "author_name": "Magdalena Tudrujek-Zdunek", - "author_inst": "Department of Infectious Diseases and Hepatology, Medical University of Lublin, Lublin, Poland" - }, - { - "author_name": "Magdalena Rogalska", - "author_inst": "Department of Infectious Diseases and Hepatology, Medical University of Bialystok, Bialystok, Poland" - }, - { - "author_name": "Anna Piekarska", - "author_inst": "Department of Infectious Diseases and Hepatology, Medical University of Lodz, Lodz, Poland" - }, - { - "author_name": "Dorota Kozielewicz", - "author_inst": "Department of Infectious Diseases and Hepatology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Poland" - }, - { - "author_name": "Krzysztof Klos", - "author_inst": "Department of Infectious Diseases and Allergology, Military Institute of Medicine, Warsaw, Poland" - }, - { - "author_name": "Marta Rorat", - "author_inst": "Department of Forensic Medicine, Wroclaw Medical University, Wroclaw, Poland & First Infectious Diseases Ward, Gromkowski Regional Specialist Hospital in Wrocla" - }, - { - "author_name": "Beata Bolewska", - "author_inst": "Department of Infectious Diseases, University of Medical Sciences, Poznan, Poland" - }, - { - "author_name": "Anna Szymanek-Pasternak", - "author_inst": "Department of Infectious Diseases and Hepatology, Wroclaw Medical University, Wroclaw, Poland" - }, - { - "author_name": "Wlodzimierz Mazur", - "author_inst": "Clinical Department of Infectious Diseases in Chorzow, Medical University of Silesia, Katowice, Poland" - }, - { - "author_name": "Beata Lorenc", - "author_inst": "Pomeranian Center of Infectious Diseases, Department of Infectious Diseases, Medical University of Gdansk, Gdansk, Poland" - }, - { - "author_name": "Regina Podlasin", - "author_inst": "Hospital of Infectious Diseases in Warsaw, Warsaw, Poland" - }, - { - "author_name": "Katarzyna Sikorska", - "author_inst": "Department of Tropical Medicine and Epidemiology, Medical University of Gdansk, Gdansk Poland" - }, - { - "author_name": "Barbara Oczko-Grzesik", - "author_inst": "Department of Infectious Diseases in Bytom, Medical University of Silesia, Katowice, Poland" - }, - { - "author_name": "Cezary Iwaszkiewicz", - "author_inst": "Department of Rheumatology and Osteoporosis, Jozef Strus Hospital in Poznan, Poland" - }, - { - "author_name": "Bartosz Szetela", - "author_inst": "Department of Infectious Diseases, Liver Diseases and Acquired Immune Deficiencies, Wroclaw Medical University, Wroclaw, Poland" - }, - { - "author_name": "Pawel Pabjan", - "author_inst": "Department of Infectious Diseases, Jan Kochanowski University, Kielce, Poland" - }, - { - "author_name": "Malgorzata Pawlowska", - "author_inst": "Department of Infectious Diseases and Hepatology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Poland" - }, - { - "author_name": "Krzysztof Tomasiewicz", - "author_inst": "Department of Infectious Diseases and Hepatology, Medical University of Lublin, Lublin, Poland" - }, - { - "author_name": "Joanna Polanska", - "author_inst": "Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland" - }, - { - "author_name": "Jerzy Jaroszewicz", - "author_inst": "Department of Infectious Diseases in Bytom, Medical University of Silesia, Katowice, Poland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.30.20222604", "rel_title": "Growth of respiratory droplets in cold and humid air", @@ -1106128,6 +1108797,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.30.20223081", + "rel_title": "Transmission routes of SARS-CoV-2 among healthcare workers of a French university hospital in Paris, France: a case-control study", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20223081", + "rel_abs": "In this case-control study on 564 healthcare workers of a university hospital in Paris (France), contacts without protection with COVID-19 patients or with colleagues were associated with infection with SARS-CoV-2, while working in a COVID-dedicated unit, using public transportation and having children kept in childcare facilities were not.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Adrien CONTEJEAN", + "author_inst": "Equipe Mobile d'Infectiologie, AP-HP, Hopital Cochin, F-75014 Paris, France" + }, + { + "author_name": "Jeremie LEPORRIER", + "author_inst": "Service de maladies infectieuses et tropicales, AP-HP, IHU Imagine, Hopital Necker-Enfants malades, F-75015 Paris, France" + }, + { + "author_name": "Etienne CANOUI", + "author_inst": "Equipe Mobile d'Infectiologie, AP-HP, Hopital Cochin, F-75014 Paris, France" + }, + { + "author_name": "Jacques FOURGEAUD", + "author_inst": "Laboratoire de virologie, AP-HP, Hopital Necker-Enfants malades, F-75015 Paris, France" + }, + { + "author_name": "Alice-Andree MARIAGGI", + "author_inst": "Departement de virologie, AP-HP, Hopital Cochin, F-75014 Paris, France" + }, + { + "author_name": "Fanny ALBY-LAURENT", + "author_inst": "Service de maladies infectieuses et tropicales, AP-HP, IHU Imagine, Hopital Necker-Enfants malades, F-75015 Paris, France" + }, + { + "author_name": "Emmanuel LAFONT", + "author_inst": "Service de maladies infectieuses et tropicales, AP-HP, IHU Imagine, Hopital Necker-Enfants malades, F-75015 Paris, France" + }, + { + "author_name": "Lauren BEAUDEAU", + "author_inst": "Equipe Mobile d'Infectiologie, AP-HP, Hopital Cochin, F-75014 Paris, France" + }, + { + "author_name": "Claire ROUZAUD", + "author_inst": "Service de maladies infectieuses et tropicales, AP-HP, IHU Imagine, Hopital Necker-Enfants malades, F-75015 Paris, France" + }, + { + "author_name": "Fabienne LECIEUX", + "author_inst": "Service de sante au travail, AP-HP, Hopital Cochin, F-75014 Paris, France" + }, + { + "author_name": "Agnes GREFFET", + "author_inst": "Service de sante au travail, AP-HP, Hopital Necker-Enfants malades, F-75015 Paris, France" + }, + { + "author_name": "Anne-Sophie L'HONNEUR", + "author_inst": "Departement de virologie, AP-HP, Hopital Cochin, F-75014 Paris, France" + }, + { + "author_name": "Jean-Marc TRELUYER", + "author_inst": "Pharmacology and Drug Evaluation in Children and Pregnant Women EA7323, Universite de Paris, Faculte de Medecine, F-75006 Paris, France" + }, + { + "author_name": "Fanny LANTERNIER", + "author_inst": "Service de maladies infectieuses et tropicales, AP-HP, IHU Imagine, Hopital Necker-Enfants malades, F-75015 Paris, France" + }, + { + "author_name": "Anne CASETTA", + "author_inst": "Equipe operationnelle d'hygiene hospitaliere, AP-HP, Hopital Cochin, F-75014 Paris, France" + }, + { + "author_name": "Pierre FRANGE", + "author_inst": "Laboratoire de microbiologie clinique, AP-HP, Hopital Necker-Enfants malades, F-75015 Paris," + }, + { + "author_name": "Marianne LERUEZ-VILLE", + "author_inst": "Laboratoire de virologie, AP-HP, Hopital Necker-Enfants malades, F-75015 Paris, France" + }, + { + "author_name": "Flore ROZENBERG", + "author_inst": "Departement de virologie, AP-HP, Hopital Cochin, F-75014 Paris, France" + }, + { + "author_name": "Olivier LORTHOLARY", + "author_inst": "Service de maladies infectieuses et tropicales, AP-HP, IHU Imagine, Hopital Necker-Enfants malades, F-75015 Paris, France" + }, + { + "author_name": "Solen KERNEIS", + "author_inst": "Equipe Mobile d'Infectiologie, AP-HP, Hopital Cochin, F-75014 Paris, France" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.30.20223180", "rel_title": "Risk perceptions and preventive practices of COVID-19 among healthcare professionals in public hospitals in Ethiopia", @@ -1107599,29 +1110363,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2020.11.02.350439", - "rel_title": "Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning", - "rel_date": "2020-11-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.02.350439", - "rel_abs": "The COVID-19 pandemic has demonstrated the serious potential for novel zoonotic coronaviruses to emerge and cause major outbreaks. The immediate animal origin of the causative virus, SARS-CoV-2, remains unknown, a notoriously challenging task for emerging disease investigations. Coevolution with hosts leads to specific evolutionary signatures within viral genomes that can inform likely animal origins. We obtained a set of 650 spike protein and 511 whole genome nucleotide sequences from 225 and 187 viruses belonging to the family Coronaviridae, respectively. We then trained random forest models independently on genome composition biases of spike protein and whole genome sequences, including dinucleotide and codon usage biases in order to predict animal host (of nine possible categories, including human). In hold-one-out cross-validation, predictive accuracy on unseen coronaviruses consistently reached [~]73%, indicating evolutionary signal in spike proteins to be just as informative as whole genome sequences. However, different composition biases were informative in each case. Applying optimised random forest models to classify human sequences of MERS-CoV and SARS-CoV revealed evolutionary signatures consistent with their recognised intermediate hosts (camelids, carnivores), while human sequences of SARS-CoV-2 were predicted as having bat hosts (suborder Yinpterochiroptera), supporting bats as the suspected origins of the current pandemic. In addition to phylogeny, variation in genome composition can act as an informative approach to predict emerging virus traits as soon as sequences are available. More widely, this work demonstrates the potential in combining genetic resources with machine learning algorithms to address long-standing challenges in emerging infectious diseases.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Liam Brierley", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Anna Fowler", - "author_inst": "University of Liverpool" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.11.01.363812", "rel_title": "Structural basis for repurpose and design of nucleoside drugs for treating COVID-19", @@ -1107894,6 +1110635,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.11.01.364364", + "rel_title": "Photocatalyst under visible light irradiation inactivates SARS-CoV-2 on an abiotic surface", + "rel_date": "2020-11-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.01.364364", + "rel_abs": "There is a worldwide attempt to develop prevention strategies against SARS-CoV-2 transmission. Here we examined the effectiveness of visible light-responsive photocatalyst RENECAT on the inactivation of SARS-CoV-2 under different temperatures and exposure durations. The viral activation on the photocatalyst-coated glass slides decreased from 5.93{+/-}0.38 logTCID50/ml to 3.05{+/-}0.25 logTCID50/ml after exposure to visible light irradiation for 6h at 20{degrees}C. On the other hand, lighting without the photocatalyst, or the photocatalyst-coat without lighting retained viral stability. Immunoblotting and electron microscopic analyses showed the reduced amounts of spike protein on the viral surface after the photocatalyst treatment. Our data suggest a possible implication of the photocatalyst on the decontamination of the SARS-CoV-2 in indoor environments, thereby preventing indirect viral spread.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Masashi Uema", + "author_inst": "National Institute of Health Sciences" + }, + { + "author_name": "Kenzo Yonemitsu", + "author_inst": "National Institute of Health Sciences" + }, + { + "author_name": "Yoshika Momose", + "author_inst": "National Institute of Health Sciences" + }, + { + "author_name": "Yoshikazu Ishii", + "author_inst": "Toho University School of Medicine" + }, + { + "author_name": "Kazuhiro Tateda", + "author_inst": "Toho University School of Medicine" + }, + { + "author_name": "Takao Inoue", + "author_inst": "National Institute of Health Sciences" + }, + { + "author_name": "Hiroshi Asakura", + "author_inst": "National Institute of Health Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.01.363739", "rel_title": "Temporal patterns in the evolutionary genetic distance of SARS-CoV-2 during the COVID-19 pandemic", @@ -1109217,81 +1112001,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.10.31.20223925", - "rel_title": "Viral genome sequencing places White House COVID-19 outbreak into phylogenetic context", - "rel_date": "2020-11-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.31.20223925", - "rel_abs": "In October 2020, an outbreak of at least 50 COVID-19 cases was reported surrounding individuals employed at or visiting the White House. Here, we applied genomic epidemiology to investigate the origins of this outbreak. We enrolled two individuals with exposures linked to the White House COVID-19 outbreak into an IRB-approved research study and sequenced their SARS-CoV-2 infections. We find these viral sequences are identical to each other, but are distinct from over 190,000 publicly available SARS-CoV-2 genomes. These genomes fall as part of a lineage circulating in the USA since April or May 2020 and detected in Virginia and Michigan. Looking forwards, sequencing of additional community SARS-CoV-2 infections collected in the USA prior to October 2020 may shed further light on its geographic ancestry. In sequencing of SARS-CoV-2 infections collected after October 2020, it may be possible to identify infections that likely descend from the White House COVID-19 outbreak.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Trevor Bedford", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Jennifer K. Logue", - "author_inst": "University of Washington" - }, - { - "author_name": "Peter D. Han", - "author_inst": "University of Washington" - }, - { - "author_name": "Caitlin R. Wolf", - "author_inst": "University of Washington" - }, - { - "author_name": "Chris D. Frazar", - "author_inst": "University of Washington" - }, - { - "author_name": "Benjamin Pelle", - "author_inst": "University of Washington" - }, - { - "author_name": "Erica Ryke", - "author_inst": "University of Washington" - }, - { - "author_name": "James Hadfield", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Jover Lee", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Mark J Rieder", - "author_inst": "University of Washington" - }, - { - "author_name": "Deborah A. Nickerson", - "author_inst": "University of Washington" - }, - { - "author_name": "Christina M. Lockwood", - "author_inst": "University of Washington" - }, - { - "author_name": "Lea M. Starita", - "author_inst": "University of Washington" - }, - { - "author_name": "Helen Y. Chu", - "author_inst": "University of Washington" - }, - { - "author_name": "Jay Shendure", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.01.363788", "rel_title": "Discovery of five HIV nucleoside analog reverse-transcriptase inhibitors (NRTIs) as potent inhibitors against the RNA-dependent RNA polymerase (RdRp) of SARS-CoV and 2019-nCoV", @@ -1109472,6 +1112181,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.19.20215673", + "rel_title": "Structural Entropy of Daily Number of COVID-19 Related Fatalities", + "rel_date": "2020-10-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.19.20215673", + "rel_abs": "A recently proposed temporal correlation-based- network framework applied on financial markets called Struc- tural Entropy has prompted us to utilize it as a means of analysis for COVID-19 fatalities across countries. Our observation on the resemblance of volatility of fluctuations of daily novel coronavirus related number of deaths to the daily stock exchange returns suggests the applicability of this approach.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Eren Unlu", + "author_inst": "Datategy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.27.20220863", "rel_title": "Retrospective in silico HLA predictions from COVID-19 patients reveal alleles associated with disease prognosis", @@ -1110939,145 +1113667,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2020.10.30.360115", - "rel_title": "PRAK-03202: A triple antigen VLP vaccine candidate against SARS CoV-2", - "rel_date": "2020-10-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.30.360115", - "rel_abs": "The rapid development of safe and effective vaccines against SARS CoV-2 is the need of the hour for the coronavirus outbreak. Here, we have developed PRAK-03202, the worlds first triple antigen VLP vaccine candidate in a highly characterized S. cerevisiae-based D-CryptTM platform, which induced SARS CoV-2 specific neutralizing antibodies in BALB/c mice. Immunizations using three different doses of PRAK-03202 induces antigen specific (Spike, envelope and membrane proteins) humoral response and neutralizing potential. PBMCs from convalescent patients, when exposed to PRAK-03202, showed lymphocyte proliferation and elevated IFN-{gamma} levels suggestive of conservation of epitopes and induction of T helper 1 (Th1)-biased cellular immune responses. These data support the clinical development and testing of PRAK-03202 for use in humans.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Saumyabrata Mazumder", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Ruchir Rastogi", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Avinash Undale", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Kajal Arora", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Nupur Mehrotra Arora", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Biswa Pratim Das Purkayastha", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Dilip Kumar", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Abyson Joseph", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Bhupesh Mali", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Vidya Bhushan Arya", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Sriganesh Kalyanaraman", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Abhishek Mukherjee", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Aditi Gupta", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Swaroop Potdar", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Sourav Singha Roy", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Deepak Parashar", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Jeny Paliwal", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Sudhir Kumar Singh", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Aelia Naqvi", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Apoorva Srivastava", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Manglesh Kumar Singh", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Devanand Kumar", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Sarthi Bansal", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Satabdi Rautray", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Indrajeet Singh", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Pankaj Fengade", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Bivekanand Kumar", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Manish Saini", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Kshipra Jain", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Reeshu Gupta", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Prabuddha K Kundu", - "author_inst": "Premas Biotech Pvt Ltd" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.10.30.352914", "rel_title": "Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses", @@ -1111190,6 +1113779,177 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.10.28.20217455", + "rel_title": "Anakinra To Prevent Respiratory Failure In COVID-19", + "rel_date": "2020-10-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20217455", + "rel_abs": "IntroductionThe management of pneumonia caused by SARS-CoV-2 should rely on early recognition of the risk for progression to severe respiratory failure (SRF) and its prevention. We investigated if early suPAR (soluble urokinase plasminogen activator receptor)-guided anakinra treatment could prevent COVID-19-assocated SRF.\n\nMethodsIn this open-label prospective trial, 130 patients admitted with SARS-CoV-2 pneumonia SARS-CoV-2 and suPAR levels [≥]6 g/l were assigned to subcutaneous anakinra 100mg once daily for 10 days. The primary outcome was the incidence of SRF at day 14. Secondary outcomes were 30-day mortality, changes in sequential organ failure assessment (SOFA) score, of cytokine-stimulation pattern and of circulating inflammatory mediators. Equal number of propensity score-matched comparators for comorbidities, severity on admission and standard-of care (SOC) were studied.\n\nResultsThe incidence of SRF was 22.3% (95% CI, 16.0-30.2%) among anakinra-treated patients and 59.2% (95% CI, 50.6-67.3%; P: 4.6 x 10-8) among SOC comparators (hazard ratio, 0.30; 95%CI, 0.20-0.46). 30-day mortality was 11.5% (95% CI, 7.1-18.2%) and 22.3% (95% CI, 16.0-30.2%) respectively (hazard ratio 0.49; 95% CI 0.25-0.97%; P: 0.041). Anakinra treatment was associated with decrease in SOFA score and in circulating interleukin (IL)-6, sCD163 and sIL2-R; the serum IL-10/IL-6 ratio on day 7 was inversely associated with the change in SOFA score. Duration of stay at the intensive care unit and at hospital was shortened compared to the SOC group; the cost of hospitalization was decreased.\n\nConclusionsEarly suPAR-guided anakinra treatment is associated with decrease of the risk for SRF and restoration of the pro- /anti-inflammatory balance.\n\nTrial RegistrationClinicalTrials.gov, NCT04357366", + "rel_num_authors": 39, + "rel_authors": [ + { + "author_name": "Evdoxia Kyriazopoulou", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Periklis Panagopoulos", + "author_inst": "Democritus University of Thrace" + }, + { + "author_name": "Simeon Metallidis", + "author_inst": "Aristotle University of Thessaloniki" + }, + { + "author_name": "George Dalekos", + "author_inst": "General University Hospital of Larissa" + }, + { + "author_name": "Garyfallia Poulakou", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Nikolaos Gatselis", + "author_inst": "General University Hospital of Larissa" + }, + { + "author_name": "Eleni Karakike", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Maria Saridaki", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Georgia Loli", + "author_inst": "Aristotle University of Thessaloniki" + }, + { + "author_name": "Aggelos Stefos", + "author_inst": "General University Hospital of Larissa" + }, + { + "author_name": "Danai Prasianaki", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Sarah Georgiadou", + "author_inst": "General University Hospital of Larissa" + }, + { + "author_name": "Olga Tsachouridou", + "author_inst": "Aristotle University of Thessaloniki" + }, + { + "author_name": "Vasileios Petrakis", + "author_inst": "Democritus University of Thrace" + }, + { + "author_name": "Konstantinos Tsiakos", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Maria Kosmidou", + "author_inst": "University of Ioannina" + }, + { + "author_name": "Vassiliki Lygoura", + "author_inst": "General University Hospital of Larissa" + }, + { + "author_name": "Maria Dareioti", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Haralampos Milionis", + "author_inst": "University of Ioannina" + }, + { + "author_name": "Ilias C Papanikolaou", + "author_inst": "General Hospital of Kerkyra" + }, + { + "author_name": "Karolina Akinosoglou", + "author_inst": "University of Patras" + }, + { + "author_name": "Dimitra-Melia Myrodia", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Areti Gravani", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Aliki Stamou", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Theologia Gkavogianni", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Konstantina Katrini", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Theodoros Marantos", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Ioannis P Trontzas", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Konstantinos Syrigos", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Lukas Chatzis", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Stamatios Chatzis", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Nikolaos Vechlidis", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Christina Avgoustou", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Stamatios Chalvatzis", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Miltiades Kyprianou", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Jos WM van der Meer", + "author_inst": "Radboud University Nijmegen" + }, + { + "author_name": "jesper eugen-olsen", + "author_inst": "Copenhagen University Hospital Hvidovre" + }, + { + "author_name": "Mihai Netea", + "author_inst": "Radboud University Nijmegen" + }, + { + "author_name": "Evangelos Giamarellos-Bourboulis", + "author_inst": "National and Kapodistrian University of Athens" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.28.359935", "rel_title": "Global Absence and Targeting of Protective Immune States in Severe COVID-19.", @@ -1113697,33 +1116457,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.25.20218735", - "rel_title": "A multiagent coronavirus model with territorial vulnerability parameters", - "rel_date": "2020-10-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.25.20218735", - "rel_abs": "We developed a simple and user-friendly simulator called MD Corona that is based on a multiagent model and describes the transmission dynamics of coronavirus for a given location considering three setting parameters: population density, social-isolation rate, and effective transmission probability. The latter is represented by the Coronavirus Protection Index (CPI) - a measurement of a given territorys vulnerability to the coronavirus that includes characteristics of the health system and socioeconomic development as well as infrastructure. The dynamic model also relies on other real epidemiological parameters. The model is calibrated by using immunity surveys and provides accurate predictions and indications of the different spread dynamic mechanisms. Our simulation studies clearly demonstrate the existence of multiple epidemic curves in the same city due to different vulnerabilities to the virus across regions. And it elucidates the phenomenon of the epidemic slowing despite a reduction in social-distancing policies, understood as a consequence of \"local protection bubbles.\" The simulator can be used for scientific outreach purposes, bringing science closer to the general public in order to raise awareness and increase engagement about the effectiveness of social distancing in reducing the transmissibility of the virus, but also to support effective actions to mitigate the spread of the virus.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Patricia Magalhaes", - "author_inst": "University of Bristol" - }, - { - "author_name": "Jose Paulo Guedes Pinto", - "author_inst": "Federal University of ABC (UFABC)" - }, - { - "author_name": "Diana Maritza Segura-Angel", - "author_inst": "Army Aviation School" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.27.20219436", "rel_title": "Childhood asthma outcomes during the COVID-19 pandemic: Findings from the PeARL multi-national cohort.", @@ -1114076,6 +1116809,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2020.10.27.20220566", + "rel_title": "Prevalence and outcomes of co-infection and super-infection with SARS-CoV-2 and other pathogens: A Systematic Review and Meta-analysis", + "rel_date": "2020-10-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.27.20220566", + "rel_abs": "IntroductionThe recovery of other respiratory viruses in patients with SARS-CoV-2 infection has been reported, either at the time of a SARS-CoV-2 infection diagnosis (co-infection) or subsequently (superinfection). However, data on the prevalence, microbiology and outcomes of co-infection and super infection are limited. The purpose of this study was to examine occurrence of respiratory co-infections and superinfections and their outcomes among patients with SARS-CoV-2 infection.\n\nPatients and MethodsWe searched literature databases for studies published from October 1, 2019, through June 11, 2020. We included studies that reported clinical features and outcomes of co-infection or super-infection of SARS-CoV-2 and other pathogens in hospitalized and non-hospitalized patients. We followed PRISMA guidelines and we registered the protocol with PROSPERO as: CRD42020189763.\n\nResultsOf 1310 articles screened, 48 were included in the random effects meta-analysis. The pooled prevalence of co-infection was 12% (95% confidence interval (CI): 6%-18%, n=29, I2=98%) and that of super-infection was 14% (95% CI: 9%-21%, n=18, I2=97%). Pooled prevalence of pathogen type stratified by co- or super-infection: viral co-infections, 4% (95% CI: 2%-7%); viral super-infections, 2% (95% CI: 0%-7%); bacterial co-infections, 4% (95% CI: 1%-8%); bacterial super-infections, 6% (95% CI: 2%-11%); fungal co-infections, 4% (95% CI: 1%-8%); and fungal super-infections, 4% (95% CI: 0%-11%). Compared to those with co-infections, patients with super-infections had a higher prevalence of mechanical ventilation [21% (95% CI: 13%-31%) vs. 7% (95% CI: 2%-15%)] and greater average length of hospital stay [mean=12.5 days, standard deviation (SD) =5.3 vs. mean=10.2 days, SD= 6.7].\n\nConclusionsOur study showed that as many as 14% of patients with COVID-19 have super-infections and 12% have co-infections. Poor outcomes were associated with super-infections. Our findings have implications for diagnostic testing and therapeutics, particularly in the upcoming respiratory virus season in the Northern Hemisphere.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jackson Ssentalo Musuuza", + "author_inst": "William S. Middleton Memorial Veterans Hospital" + }, + { + "author_name": "Lauren Watson", + "author_inst": "Division of Infectious Disease, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA" + }, + { + "author_name": "Vishala Parmasad", + "author_inst": "Division of Infectious Disease, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA" + }, + { + "author_name": "Nathan Putman-Buehler", + "author_inst": "Division of Infectious Disease, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA" + }, + { + "author_name": "Leslie Christensen", + "author_inst": "Ebling Library for the Health Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA" + }, + { + "author_name": "Nasia Safdar", + "author_inst": "Division of Infectious Disease, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.27.20211433", "rel_title": "Early Tocilizumab Dosing is Associated with Improved Survival In Critically Ill Patients Infected With Sars-CoV-2", @@ -1115195,25 +1117967,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2020.10.23.20218461", - "rel_title": "Detection and Segmentation of Lesion Areas in Chest CT Scans For The Prediction of COVID-19", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.23.20218461", - "rel_abs": "In this paper we compare the models for the detection and segmentation of Ground Glass Opacity and Consolidation in chest CT scans. These lesion areas are often associated both with common pneumonia and COVID-19. We train a Mask R-CNN model to segment these areas with high accuracy using three approaches: merging masks for these lesions into one, deleting the mask for Consolidation, and using both masks separately. The best model achieves the mean average precision of 44.68% using MS COCO criterion for instance segmentation across all accuracy thresholds. The classification model, COVID-CT-Mask-Net, which learns to predict the presence of COVID-19 vs common pneumonia vs control, achieves the 93.88% COVID-19 sensitivity, 95.64% overall accuracy, 95.06% common pneumonia sensitivity and 96.91% true negative rate on the COVIDx-CT test split (21192 CT scans) using a small fraction of the training data. We also analyze the effect of Non-Maximum Suppression of overlapping object predictions, both on the segmentation and classification accuracy. The full source code, models and pretrained weights are available on https://github.com/AlexTS1980/COVID-CT-Mask-Net.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Aram Ter-Sarkisov", - "author_inst": "City, University of London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.10.24.20218727", "rel_title": "DNA methylation and gene expression pattern of ACE2 and TMPRSS2 genes in saliva samples of patients with SARS-CoV-2 infection", @@ -1115426,6 +1118179,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.23.20217844", + "rel_title": "Standard blood laboratory results in SARS-CoV-19 positive patients: do they show a typical pattern?", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.23.20217844", + "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is current pandemic disease. Acute polymerase-chain-reaction is the gold standard test for this disease, is not available everywhere. Standard blood laboratory parameters may have diagnostic potential.\n\nMethodsWe evaluated standard blood laboratory parameters of 655 COVID-19 patients suspected to be infected with SARS-CoV-2, who underwent PCR testing in one of five hospitals in Vienna, Austria. Additionally, clinical characteristics and 28-day outcome were obtained from medical records. We compared standard blood laboratory parameters, clinical characteristics, and outcomes between positive and negative PCR-tested patients and evaluated the ability of those parameters to distinguish between groups.\n\nResultsOf the 590 study patients including 276 females and 314 males, aged between 20 and 100 years, 208 were tested positive by means of PCR. Patients with positive compared to negative PCR-tests had significantly lower levels of leukocytes, basophils, eosinophils, monocytes, and thrombocytes; while significantly higher levels were detected with hemoglobin, C-reactive-protein (CRP), neutrophil-to-lymphocyte ratio (NLR), activated-partial-thromboplastin-time (aPTT), creatine-kinase (CK), lactate-dehydrogenase (LDH), alanine-aminotransferase (ALT), aspartate-aminotransferase (AST), and lipase. Our multivariate model correctly classified 83.9% of cases with a sensitivity of 78.4%, specificity of 87.3%, positive predictive value of 79.5%, and negative predictive value of 86.6%. Decreasing leucocytes and eosinophils and increasing hemoglobin and CRP were significantly associated with an increased likelihood of being COVID-19 positive tested.\n\nConclusionsOur findings suggest that especially leucocytes, eosinophils, hemoglobin, and CRP are helpful to distinguish between COVID-19 positive and negative tested patients and that a certain blood pattern is able to predict PCR-results.\n\nSummaryDecreasing leucocytes and eosinophils and increasing hemoglobin and CRP were significantly associated with an increased likelihood of being COVID-19 positive tested. Each single parameter showed either a high sensitivity (leucocytes, eosinophils, CRP, monocytes, thrombocytes) or specificity (NLR, CK, ALT, lipase), or a sensitivity and specificity around 60% (Hb, LDH, AST).", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Rainer Thell", + "author_inst": "Donauspital Emergency Dep. Vienna" + }, + { + "author_name": "Jascha Zimmermann", + "author_inst": "Donauspital Emergency Department Vienna" + }, + { + "author_name": "Marton Szell", + "author_inst": "Donauspital Emergency Department Vienna" + }, + { + "author_name": "Sabine Tomez", + "author_inst": "Dep. of Lab. Medicine Donauspital Vienna" + }, + { + "author_name": "Philip Eisenburger", + "author_inst": "Krankenhaus Nord Emergency Dep." + }, + { + "author_name": "Anna Kreil", + "author_inst": "Rudolfstiftung Emergency Dept. Vienna" + }, + { + "author_name": "Moritz Haugk", + "author_inst": "Emerg. Dep. Krankenhaus Hietzing Vienna" + }, + { + "author_name": "Alexander Spiel", + "author_inst": "Emergency Dep. Wilhelminenspital Vienna" + }, + { + "author_name": "Amelie Blaschke", + "author_inst": "Emergency Dept. Donauspital Vienna" + }, + { + "author_name": "Anna Klicpera", + "author_inst": "Emergency Dept. Donauspital Vienna" + }, + { + "author_name": "Oskar Janata", + "author_inst": "Dept. of Hygiene, Donauspital Vienna" + }, + { + "author_name": "Walter Krugluger", + "author_inst": "Dep. of Lab. Medicine, Donauspital Vienna" + }, + { + "author_name": "Christian Sebesta", + "author_inst": "2. Med. Dept. Donauspital Vienna" + }, + { + "author_name": "Harald Herkner", + "author_inst": "Emerg. Dept. Gen. Hospital Vienna" + }, + { + "author_name": "Brenda Laky", + "author_inst": "Emergency Dept. Donauspital Vienna" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.24.20218701", "rel_title": "Clinical characteristics of Severe Acute Respiratory Syndrome by COVID-19 in Indigenous of Brazil", @@ -1116693,29 +1119521,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.20.20216085", - "rel_title": "COVIDTrach; a prospective cohort study of mechanically ventilated COVID-19 patients undergoing tracheostomy in the UK", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.20.20216085", - "rel_abs": "PurposeCOVIDTrach is a UK multi-centre prospective cohort study project evaluating the outcomes of tracheostomy in patients with COVID-19 receiving mechanical ventilation. It also examines the incidence of SARS-CoV-2 infection among healthcare workers involved in the procedure.\n\nMethodAn invitation to participate was sent to all UK NHS departments involved in tracheostomy in COVID-19 patients. Data was entered prospectively and clinical outcomes updated via an online database (REDCap). Clinical variables were compared with outcomes using multivariable regression analysis, with logistic regression used to develop a prediction model for mortality. Participants recorded whether any operators tested positive for SARS-CoV-2 within two weeks of the procedure.\n\nResultsThe cohort comprised 1605 tracheostomy cases from 126 UK hospitals. The median time from intubation to tracheostomy was 15 days (IQR 11, 21). 285 (18%) patients died following the procedure. 1229 (93%) of the survivors had been successfully weaned from mechanical ventilation at censoring and 1049 (81%) had been discharged from hospital. Age, inspired oxygen concentration, PEEP setting, pyrexia, number of days of ventilation before tracheostomy, C-reactive protein and the use of anticoagulation and inotropic support independently predicted mortality. Six reports were received of operators testing positive for SARS-CoV-2 within two weeks of the procedure.\n\nConclusionsTracheostomy appears to be safe in mechanically ventilated patients with COVID-19 and to operators performing the procedure and we identified clinical indicators that are predictive of mortality.\n\nFundingThe COVIDTrach project is supported by the Wellcome Trust UCL COVID-19 Rapid Response Award and the National Institute for Health Research.\n\nTrial registrationThe study is registered with ClinicalTrials.Gov (NCT04572438).", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "- COVIDTrach", - "author_inst": "" - }, - { - "author_name": "Nick JI Hamilton", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "otolaryngology" - }, { "rel_doi": "10.1101/2020.10.25.20219212", "rel_title": "Economic Losses Associated with COVID-19 Deaths in the United States", @@ -1116932,6 +1119737,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.26.20219428", + "rel_title": "Community prevalence of SARS-CoV-2 in England during April to September 2020: Results from the ONS Coronavirus Infection Survey", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219428", + "rel_abs": "BackgroundDecisions regarding the continued need for control measures to contain the spread of SARS-CoV-2 rely on accurate and up-to-date information about the number of people and risk factors for testing positive. Existing surveillance systems are not based on population samples and are generally not longitudinal in design.\n\nMethodsFrom 26 April to 19 September2020, 514,794 samples from 123,497 individuals were collected from individuals aged 2 years and over from a representative sample of private households from England. Participants completed a questionnaire and nose and throat swab were taken. The percentage of individuals testing positive for SARS-CoV-2 RNA was estimated over time using dynamic multilevel regression and post-stratification, to account for potential residual non-representativeness. Potential changes in risk factors for testing positive over time were also evaluated using multilevel regression models.\n\nFindingsBetween 26 April and 19 September 2020, in total, results were available from 514,794 samples from 123,497 individuals, of which 489 were positive overall from 398 individuals. The percentage of people testing positive for SARS-CoV-2 changed substantially over time, with an initial decrease between end of April and June, followed by low levels during the summer, before marked increases end of August and September 2020. Having a patient-facing role and working outside your home were important risk factors for testing positive in the first period but not (yet) in the second period of increased positivity rates, and age (young adults) being an important driver of the second period of increased positivity rates. A substantial proportion of infections were in individuals not reporting symptoms (53%-70%, dependent on calendar time).\n\nInterpretationImportant risk factors for testing positive varied substantially between the initial and second periods of higher positivity rates, and a substantial proportion of infections were in individuals not reporting symptoms, indicating that continued monitoring for SARS-CoV-2 in the community will be important for managing the epidemic moving forwards.\n\nFundingThis study is funded by the Department of Health and Social Care. KBP, ASW, EP and JVR are supported by the National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford in partnership with Public Health England (PHE) (NIHR200915). AG is supported by U.S. National Institute of Health and Office of Naval Research. ASW is also supported by the NIHR Oxford Biomedical Research Centre and by core support from the Medical Research Council UK to the MRC Clinical Trials Unit [MC_UU_12023/22] and is an NIHR Senior Investigator. The views expressed are those of the authors and not necessarily those of the National Health Service, NIHR, Department of Health, or PHE.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSUnprecedented control measures, such as national lockdowns, have been widely implemented to contain the spread of SARS-CoV-2. Decisions regarding the continued need for social distancing measures in the overall population, specific subgroups and geographic areas heavily rely on accurate and up-to-date information about the number of people and risk factors for testing positive. We searched PubMed and medRxiv and bioRxiv preprint servers up to 6 June 2020 for epidemiological studies using the terms \"SARS-CoV-2\" and \"prevalence\" or \"incidence\" without data or language restrictions. Most studies were small or had only information about current presence of the virus for a small subset of patients, or used data not representative of the community, such as hospital admissions, deaths or self-reported symptoms. Large population-based studies, such as the current study, are required to understand risk factors and the dynamics of the epidemic.\n\nAdded value of this studyThis is the first longitudinal community survey of SARS-CoV-2 infection at national and regional levels in the UK. With more than 500,000 swabs from more than 120,000 individuals this study provides robust evidence that the percentage of individuals from the general community in England testing positive for SARS-CoV-2 clearly declined between end of April and June 2020,, followed by consistently low levels during the summer, before marked increases end of August and September 2020. Risk factors for testing positive varied substantially between the initial and second periods of higher positivity rates, with having a patient-facing role and working outside your home being important risk factors in the first period but not (yet) in the second period, and age (young adults) being an important driver of the second period of increased positivity rates. Positive tests commonly occurred without symptoms being reported.\n\nImplications of all the available evidenceThe observed decline in the percentage of individuals testing positive adds to the increasing body of empirical evidence and theoretical models that suggest that the lockdown imposed on 23 March 2020 in England was associated, at least temporarily, with a decrease in infections. Important risk factors for testing positive varied substantially between the initial and second periods of higher positivity rates, and a substantial proportion of infections were in individuals not reporting symptoms, indicating that continued monitoring for SARS-CoV-2 in the community will be important for managing the epidemic moving forwards.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Koen B Pouwels", + "author_inst": "University of Oxford" + }, + { + "author_name": "Thomas House", + "author_inst": "University of Manchester" + }, + { + "author_name": "Emma Pritchard", + "author_inst": "University of Oxford" + }, + { + "author_name": "Julie V Robotham", + "author_inst": "Public Health England" + }, + { + "author_name": "Paul Birrell", + "author_inst": "Public Health England" + }, + { + "author_name": "Andrew Gelman", + "author_inst": "Columbia University" + }, + { + "author_name": "Karina-Doris Vihta", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nikola Bowers", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Ian Boreham", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Heledd Thomas", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "James Lewis", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Iain Bell", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "John I Bell", + "author_inst": "University of Oxford" + }, + { + "author_name": "John N Newton", + "author_inst": "Public Health England" + }, + { + "author_name": "Jeremy Farrar", + "author_inst": "Wellcome Trust" + }, + { + "author_name": "Ian Diamond", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Pete Benton", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Ann Sarah Walker", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.25.20219030", "rel_title": "High seroprevalence but short-lived immune response to SARS-CoV-2 infection in Paris", @@ -1118275,93 +1121167,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2020.10.26.20219600", - "rel_title": "Head-to-head comparison of SARS-CoV-2 antigen-detecting rapid test with self-collected anterior nasal swab versus professional-collected nasopharyngeal swab", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219600", - "rel_abs": "BackgroundTwo antigen-detecting rapid diagnostic tests (Ag-RDTs) are now approved through the WHO Emergency Use Listing procedure and can be performed at the point-of-care. However, both tests use nasopharyngeal (NP) swab samples. NP swab samples must be collected by trained healthcare personnel with protective equipment and are frequently perceived as uncomfortable by patients.\n\nMethodsThis was a manufacturer-independent, prospective diagnostic accuracy study with comparison of a supervised, self-collected anterior nose (AN) swab sample with a professional-collected NP swab sample, using a WHO-listed SARS-CoV-2 Ag-RDT, STANDARD Q COVID-19 Ag Test (SD Biosensor), which is also being distributed by Roche. The reference standard was RT-PCR from an oro-/nasopharyngeal swab sample. Percent positive and negative agreement as well as sensitivity and specificity were calculated.\n\nResultsAmong the 289 participants, 39 (13.5%) tested positive for SARS-CoV-2 by RT-PCR. The positive percent agreement of the two different sampling techniques for the Ag-RDT was 90.6% (CI 75.8-96.8). The negative percent agreement was 99.2% (CI 97.2-99.8). The Ag-RDT with AN sampling showed a sensitivity of 74.4% (29/39 PCR positives detected; CI 58.9-85.4) and specificity of 99.2% (CI 97.1-99.8) compared to RT-PCR. The sensitivity with NP sampling was 79.5% (31/39 PCR positives detected; CI 64.5-89.2) and specificity was 99.6% (CI 97.8-100). In patients with high viral load (>7.0 log 10 RNA SARS-CoV2/swab), the sensitivity of the Ag-RDT with AN sampling was 96% and 100% with NP sampling.\n\nConclusionSupervised self-sampling from the anterior nose is a reliable alternative to professional nasopharyngeal sampling using a WHO-listed SARS-CoV-2 Ag-RDT. Considering the ease-of-use of Ag-RDTs, self-sampling and potentially patient self-testing at home may be a future use case.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Andreas K. Lindner", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Olga Nikolai", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Franka Kausch", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Mia Wintel", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Franziska Hommes", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Maximilian Gertler", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Lisa Kr\u00fcger", - "author_inst": "Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany." - }, - { - "author_name": "Mary Gaeddert", - "author_inst": "Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany." - }, - { - "author_name": "Frank Tobian", - "author_inst": "Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany." - }, - { - "author_name": "Federica Lainati", - "author_inst": "Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany." - }, - { - "author_name": "Lisa K\u00f6ppel", - "author_inst": "Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany." - }, - { - "author_name": "Joachim Seybold", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Medical Dire" - }, - { - "author_name": "Victor M Corman", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Christian Drosten", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "J\u00f6rg Hofmann", - "author_inst": "Labor Berlin - Charit\u00e9 Vivantes GmbH, Berlin, Germany" - }, - { - "author_name": "Jilian Sacks", - "author_inst": "Foundation for Innovative New Diagnostics, Geneva, Switzerland" - }, - { - "author_name": "Frank Mockenhaupt", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Claudia M. Denkinger", - "author_inst": "Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.27.20220541", "rel_title": "A Scalable Saliva-based, Extraction-free RT-LAMP Protocol for SARS-Cov-2 Diagnosis", @@ -1118758,6 +1121563,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.26.20220137", + "rel_title": "A quantitative exploration of symptoms in COVID-19 patients: an observational cohort study", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20220137", + "rel_abs": "BackgroundAs the spreading of the COVID-19 around the global, we investigated the characteristics and changes of symptoms in COVID-19 patients.\n\nMethodsThis was an ambispective observational cohort study, and 133 confirmed COVID-19 patients were included and all symptoms over the course were analyzed qualitatively. The symptoms, their changes over the course in the cohort and in the different clinical types, etc. were illustrated. Differences in different periods and severities were analyzed through Chi square test, association with severity was analyzed through LASSO binomial logistic regression analysis. Inter-correlation and classification of symptoms were completed. Major symptoms were screened and their changes were illustrated.\n\nResultsA total of 43 symptoms with frequencies as 6067 in this cohort. Differences of symptoms in different stages and clinical types were significant. Expectoration, shortness of breath, dyspnea, diarrhea, poor appetite were positively but vomiting, waist discomfort, pharyngeal discomfort, acid reflux were negatively correlated with the combined-severe and critical type; dyspnea was correlated with the critical type. The 17 major symptoms were identified. The average daily frequency of symptoms per case was decreased continuously before the transition into the severe type and increased immediately one day before the transition and then decreased. It was decreased continuously before the transition date of the critical type and increased from the transition into the critical type to the next day and decreased thereafter. Dyspnea (P<0.001), shortness of breath (P<0.01) and chest distress (P<0.05) were correlated with death and their corresponding coefficient was 0.393, 0.258, 0.214, respectively.\n\nConclusionThe symptoms of COVID-19 patients mainly related to upper respiratory tract infection, cardiopulmonary function, and digestive system. The mild type and the early stage in other types mainly related to upper respiratory tract infection. The cardiopulmonary function and digestive system associated symptoms were found in all other types and stages. Dyspnea was correlated with critical type and dyspnea, shortness of breath, and chest distress were correlated with death. Respiratory dysfunction (or incompleteness) associated symptoms were the characteristic symptoms. The changes of symptoms did not synchronously with the changes of severity before the transition into the severe or critical type.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Gaojing Qu", + "author_inst": "Center of Evidence-Based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, Hubei, China" + }, + { + "author_name": "Junwen Chen", + "author_inst": "Department of Respiratory and Critical Care Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, Hubei, China" + }, + { + "author_name": "Guoxin Huang", + "author_inst": "Center of Evidence-Based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, Hubei, China" + }, + { + "author_name": "Meiling Zhang", + "author_inst": "Center of Evidence-Based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, Hubei, China" + }, + { + "author_name": "Hui Yu", + "author_inst": "Center of Evidence-Based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, Hubei, China" + }, + { + "author_name": "Haoming Zhu", + "author_inst": "Center of Evidence-Based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, Hubei, China" + }, + { + "author_name": "Lei Chen", + "author_inst": "Center of Evidence-Based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, Hubei, China" + }, + { + "author_name": "Dengru Wang", + "author_inst": "Yunnan Yanling Biological Technology co., LTD, Kunming 650224, Yunnan, China" + }, + { + "author_name": "Bin Pei", + "author_inst": "Center of Evidence-Based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, Hubei, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.26.20219725", "rel_title": "Declining prevalence of antibody positivity to SARS-CoV-2: a community study of 365,000 adults", @@ -1120557,29 +1123413,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.22.20217554", - "rel_title": "Extending the range of symptoms in a Bayesian Network for the Predictive Diagnosis of COVID-19", - "rel_date": "2020-10-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.22.20217554", - "rel_abs": "Emerging digital technologies have taken an unprecedented position at the forefront of COVID-19 management. This paper extends a previous Bayesian network designed to predict the probability of COVID-19 infection, based on a patients profile. The structure and prior probabilities have been amalgamated from the knowledge of peer-reviewed articles. The network accounts for demographics, behaviours and symptoms, and can mathematically identify multivariate combinations with the highest risk. Potential applications include patient triage in healthcare systems or embedded software for contact-tracing apps. Specifically, this paper extends the set of symptoms that are a marker for COVID-19 infection and the differential diagnosis of other conditions with similar presentations.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Rachel Butcher", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Norman Fenton", - "author_inst": "Queen Mary University of London" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.10.22.20217430", "rel_title": "Covid-19 and Socioeconomic Factors: Cross-country Evidence", @@ -1120736,6 +1123569,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.22.20217604", + "rel_title": "Coronavirus Disease (COVID-19) Global Prediction Using Hybrid Artificial Intelligence Method of ANN Trained with Grey Wolf Optimizer", + "rel_date": "2020-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.22.20217604", + "rel_abs": "An accurate outbreak prediction of COVID-19 can successfully help to get insight into the spread and consequences of infectious diseases. Recently, machine learning (ML) based prediction models have been successfully employed for the prediction of the disease outbreak. The present study aimed to engage an artificial neural network-integrated by grey wolf optimizer for COVID-19 outbreak predictions by employing the Global dataset. Training and testing processes have been performed by time-series data related to January 22 to September 15, 2020 and validation has been performed by time-series data related to September 16 to October 15, 2020. Results have been evaluated by employing mean absolute percentage error (MAPE) and correlation coefficient (r) values. ANN-GWO provided a MAPE of 6.23, 13.15 and 11.4% for training, testing and validating phases, respectively. According to the results, the developed model could successfully cope with the prediction task.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Sina Ardabili", + "author_inst": "University of Mohaghegh Ardabili" + }, + { + "author_name": "Amir MOSAVI", + "author_inst": "Obuda University" + }, + { + "author_name": "Shahab S. Band", + "author_inst": "Future Technology Research Center, College of Future, National Yunlin University of Science and Technology, 123 University Road, Section 3, Douliou, Yunlin 6400" + }, + { + "author_name": "Annamaria R. Varkonyi-Koczy", + "author_inst": "Institute of Automation, Obuda University, 1034 Budapest, Hungary varkonyi.koczy@uni-obuda.hu" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.22.20217513", "rel_title": "Measuring the Impact of Exposure to COVID-19 Vaccine Misinformation on Vaccine Intent in the UK and US", @@ -1121939,53 +1124803,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.10.21.20216804", - "rel_title": "Predictors of PTSD, depression and anxiety in UK frontline health and social care workers during COVID-19.", - "rel_date": "2020-10-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20216804", - "rel_abs": "BackgroundStudies have shown that working in frontline healthcare roles during epidemics and pandemics was associated with PTSD, depression, anxiety, and other mental health disorders.\n\nObjectivesThe objectives of this study were to identify demographic, work-related and other predictors for clinically significant PTSD, depression, and anxiety during the COVID-19 pandemic in UK frontline health and social care workers (HSCWs), and to compare rates of distress across different groups of HCSWs working in different roles and settings.\n\nMethodsA convenience sample (n=1194) of frontline UK HCSWs completed an online survey during the first wave of the pandemic (27 May - 23 July 2020). Participants worked in UK hospitals, nursing or care homes and other community settings. PTSD was assessed using the International Trauma Questionnaire (ITQ); Depression was assessed using the Patient Health Questionnaire-9 (PHQ-9); Anxiety was assessed using the Generalized Anxiety Disorder Scale (GAD-7).\n\nResultsNearly 58% of respondents met the threshold for clinically significant PTSD, anxiety or depression, and symptom levels were high across occupational groups and settings. Logistic regression analyses found that participants who were concerned about infecting others, who felt they could not talk with their managers, who reported feeling stigmatised and who had not had reliable access to personal protective equipment (PPE) were more likely to meet criteria for a clinically significant mental disorder. Being redeployed during the pandemic, and having had COVID were associated with higher odds for PTSD. Higher household income was associated with reduced odds for a mental disorder.\n\nConclusionsThis study identified predictors of clinically significant distress during COVID-19 and highlights the need for reliable access to PPE and further investigation of barriers to communication between managers and staff.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Talya Greene", - "author_inst": "University of Haifa" - }, - { - "author_name": "Jasmine Harju-Seppanen", - "author_inst": "University College London" - }, - { - "author_name": "Mariam Adjeniji", - "author_inst": "University College London" - }, - { - "author_name": "Charlotte Steel", - "author_inst": "University College London" - }, - { - "author_name": "Nick Grey", - "author_inst": "Sussex Partnership NHS Foundation Trust" - }, - { - "author_name": "Chris R Brewin", - "author_inst": "University College London" - }, - { - "author_name": "Michael A Bloomfield", - "author_inst": "University College London" - }, - { - "author_name": "Jo Billings", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.10.21.20217406", "rel_title": "Social and Psychiatric Effects of COVID-19 Pandemic and Distance Learning On High School Students: A Cross-Sectional Web-Based Survey Comparing Turkey and Denmark", @@ -1122134,6 +1124951,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.21.20217331", + "rel_title": "Requirements for the containment of COVID-19 disease outbreaks through periodic testing, isolation, and quarantine", + "rel_date": "2020-10-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20217331", + "rel_abs": "We employ individual-based Monte Carlo computer simulations of a stochastic SEIR model variant on a two-dimensional Newman-Watts small-world network to investigate the control of epidemic outbreaks through periodic testing and isolation of infectious individuals, and subsequent quarantine of their immediate contacts. Using disease parameters informed by the COVID-19 pandemic, we investigate the effects of various crucial mitigation features on the epidemic spreading: fraction of the infectious population that is identifiable through the tests; testing frequency; time delay between testing and isolation of positively tested individuals; and the further time delay until quarantining their contacts as well as the quarantine duration. We thus determine the required ranges for these intervention parameters to yield effective control of the disease through both considerable delaying the epidemic peak and massively reducing the total number of sustained infections.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ruslan I Mukhamadiarov", + "author_inst": "Virginia Tech" + }, + { + "author_name": "Shengfeng Deng", + "author_inst": "Central China Normal University" + }, + { + "author_name": "Shannon Serrao", + "author_inst": "Virginia Tech" + }, + { + "author_name": "Priyanka Priyanka", + "author_inst": "Virginia Tech" + }, + { + "author_name": "Lauren M Childs", + "author_inst": "Virginia Tech" + }, + { + "author_name": "Uwe C Tauber", + "author_inst": "Virginia Tech" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.23.353177", "rel_title": "Dysregulation of Pulmonary Responses in Severe COVID-19", @@ -1123481,97 +1126337,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.21.20216820", - "rel_title": "Seroprevalence of SARS-CoV-2 IgG antibodies in two regions of Estonia (KoroSero-EST-1)", - "rel_date": "2020-10-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20216820", - "rel_abs": "BackgroundIn Estonia, during the first wave of COVID-19 total number of cases confirmed by PCR was 13.3/10,000, similar in most regions, including capital Tallinn, but in the hotspot of Estonian epidemic, an island Saaremaa, the cumulative incidence was 166.1/10,000.\n\nAimWe aimed to determine the prevalence of SARS-CoV-2 IgG antibodies in these two regions, symptoms associated with infection and factors associated with antibody concentrations.\n\nMethodsParticipants were selected using stratified (formed by age decades) random sampling and recruited by general practitioners. IgG were determined from sera by four assays. Symptoms of acute respiratory illness associated with seropositivity were analyzed by multiple correspondence analysis, antibody concentrations by multiple linear regression.\n\nResultsTotal of 3608 individual were invited and 1960 recruited From May 8 to July 31, 2020. Seroprevalence was 1.5% (95% confidence interval (CI) 0.9-2.5) and 6.3% (95% CI 5.0-7.9), infection fatality rate 0.1% (95% CI 0.0-0.2) and 1.3% (95% CI 0.4-2.1) in Tallinn and Saaremaa, respectively. Of seropositive subjects 19.2% (14/73) had acute respiratory illness. Fever, diarrhea and the absence of cough and runny nose were associated with seropositivity in individuals aged 50 or more years. IgG concentrations were higher if fever, difficulty breathing, shortness of breath, chest pain or diarrhea was present, or hospitalization required.\n\nConclusionSimilarly to other European countries the seroprevalence of SARS-CoV-2 in Estonia was low even in the hotspot region Saaremaa suggesting that majority of population is still susceptible to SARS-CoV-2. Focusing only on respiratory symptoms may delay accurate diagnosis of SARS-CoV-2 infection.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Piia Jogi", - "author_inst": "Tartu University Hospital" - }, - { - "author_name": "Hiie Soeorg", - "author_inst": "University of Tartu" - }, - { - "author_name": "Diana Ingerainen", - "author_inst": "Family doctor center Jarveotsa" - }, - { - "author_name": "Mari Soots", - "author_inst": "Family doctor center Kuressaare" - }, - { - "author_name": "Freddy Lattekivi", - "author_inst": "University of Tartu" - }, - { - "author_name": "Paul Naaber", - "author_inst": "SYNLAB Eesti" - }, - { - "author_name": "Karolin Toompere", - "author_inst": "University of Tartu" - }, - { - "author_name": "Part Peterson", - "author_inst": "University of Tartu" - }, - { - "author_name": "Liis Haljasmagi", - "author_inst": "University of Tartu" - }, - { - "author_name": "Eva Zusinaite", - "author_inst": "University of Tartu" - }, - { - "author_name": "Hannes Vaas", - "author_inst": "Tartu University Hospital" - }, - { - "author_name": "Merit Pauskar", - "author_inst": "University of Tartu" - }, - { - "author_name": "Arina Shablinskaja", - "author_inst": "University of Tartu" - }, - { - "author_name": "Katrin Kaarna", - "author_inst": "University of Tartu" - }, - { - "author_name": "Heli Paluste", - "author_inst": "Ministry of Social Affairs of the Republic of Estonia" - }, - { - "author_name": "Kai Kisand", - "author_inst": "University of Tartu" - }, - { - "author_name": "Marje Oona", - "author_inst": "University of Tartu" - }, - { - "author_name": "Riina Janno", - "author_inst": "Tartu University Hospital" - }, - { - "author_name": "Irja Lutsar", - "author_inst": "University of Tartu" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.21.20216895", "rel_title": "Superspreading Events Without Superspreaders: Using High Attack Rate Events to Estimate N o forAirborne Transmission of COVID-19", @@ -1123736,6 +1126501,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.21.20216846", + "rel_title": "Prediction of the infection of COVID-19 in Bangladesh by classical SIR model", + "rel_date": "2020-10-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20216846", + "rel_abs": "The ongoing outbreak of the novel coronavirus (COVID-19) started from Wuhan, China, at the end of December 2019. It is one of the leading public health challenges in the world because of high transmissibility. The first patient of COVID-19 was officially reported on March 8, 2020, in Bangladesh. Using the epidemiological data up to October 17, 2020, we try to estimate the infectious size. In this paper, we used Classical SIR (Susceptible-Infected-Recovered), model. The epidemic has now spread to more than 216 countries around the world. The necessary reproduction number R0 of Bangladesh is 1.92. The primary data was collected from the Coronavirus (COVID-19) Dashboard (BANGLADESH: CASE TREND). In our analysis, the statistical parameters specify the best import to provide the predicted result. We projected that the epidemic curve pulling down in Bangladesh will start from the first week of November (November 4, 2020) and may end in the last week of July (July 24, 2021). It is also estimated that the start of acceleration on May 24, 2020, in 53 days, and the start of steady growth on September 10, 2020, in 109 days. The start of the ending phase of the epidemic may appear in the first week of November 2020, and the epidemic is expected to be finished by the last week of July 2021. However, these approximations may become invalid if a large variety of data occurs in upcoming days.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Sofi Mahmud Parvez", + "author_inst": "Department of Applied Mathematics, Noakhali Science and Technology University, Bangladesh" + }, + { + "author_name": "Faria Tabassum", + "author_inst": "Department of Applied Mathematics, Noakhali Science and Technology University, Bangladesh" + }, + { + "author_name": "H. M. Shahadat Ali", + "author_inst": "Department of Applied Mathematics, Noakhali Science and Technology University, Bangladesh" + }, + { + "author_name": "Md. Murad Hossain", + "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.21.20216721", "rel_title": "Patterns of Multimorbidity and Risk of Severe SARS-CoV-2 Infection: an observational study in the U.K.", @@ -1125083,37 +1127879,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.10.22.328864", - "rel_title": "Databiology Lab CORONAHACK: Collection of Public COVID-19 Data", - "rel_date": "2020-10-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.22.328864", - "rel_abs": "COVID-19 has had an unprecedented global impact in health and economy affecting millions of persons world-wide. To support and enable a collaborative response from the global research communities, we created a data collection for different public sources for anonymized patient clinical data, imaging datasets, molecular data as nucleotide and protein sequences for the SARS-CoV-2 virus, reports of count of cases and deaths per city/country, and other economic indicators in Databiology Lab (https://www.lab.databiology.net/) where researchers could access these data assets and use the hundreds of available open source bioinformatic applications to analyze them. These data assets are regularly updated and was used in a successful virtual 3-day hackathon organized by Databiology Ltd and Mindstream-AI where hundreds of attendees to work collaboratively to analyze these data collections.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Juan Caballero Perez", - "author_inst": "Databiology Ltd" - }, - { - "author_name": "Carlos de Blas Perez", - "author_inst": "Databiology Ltd" - }, - { - "author_name": "Felipe Leza Alvarez", - "author_inst": "Databiology Ltd" - }, - { - "author_name": "Jose Manuel Caballero Contreras", - "author_inst": "Databiology Ltd" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.10.22.349522", "rel_title": "Analysis of SARS-CoV-2 ORF3a structure reveals chloride binding sites", @@ -1125418,6 +1128183,37 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2020.10.22.351056", + "rel_title": "Small-Molecule In Vitro Inhibitors of the Coronavirus Spike - ACE2 Protein-Protein Interaction as Blockers of Viral Attachment and Entry for SARS-CoV-2", + "rel_date": "2020-10-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.22.351056", + "rel_abs": "Inhibitors of the protein-protein interaction (PPI) between the SARS-CoV-2 spike protein and ACE2, which acts as a ligand-receptor pair that initiates the viral attachment and cellular entry of this coronavirus causing the ongoing COVID-19 pandemic, are of considerable interest as potential antiviral agents. While blockade of such PPIs with small molecules is more challenging than with antibodies, small-molecule inhibitors (SMIs) might offer alternatives that are less strain- and mutation-sensitive, suitable for oral or inhaled administration, and more controllable / less immunogenic. Here, we report the identification of SMIs of this PPI by screening our compound-library that is focused on the chemical space of organic dyes. Among promising candidates identified, several dyes (Congo red, direct violet 1, Evans blue) and novel drug-like compounds (DRI-C23041, DRI-C91005) inhibited the interaction of hACE2 with the spike proteins of SARS-CoV-2 as well as SARS-CoV with low micromolar activity in our cell-free ELISA-type assays (IC50s of 0.2-3.0 M); whereas, control compounds, such as sunset yellow FCF, chloroquine, and suramin, showed no activity. Protein thermal shift assays indicated that the SMIs identified here bind SARS-CoV-2-S and not ACE2. Selected promising compounds inhibited the entry of a SARS-CoV-2-S expressing pseudovirus into ACE2-expressing cells in concentration-dependent manner with low micromolar IC50s (6-30 M). This provides proof-of-principle evidence for the feasibility of small-molecule inhibition of PPIs critical for coronavirus attachment/entry and serves as a first guide in the search for SMI-based alternative antiviral therapies for the prevention and treatment of diseases caused by coronaviruses in general and COVID-19 in particular.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Damir Bojadzic", + "author_inst": "Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, USA" + }, + { + "author_name": "Oscar Alcazar", + "author_inst": "Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, USA" + }, + { + "author_name": "Jinshui Chen", + "author_inst": "Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, USA" + }, + { + "author_name": "Peter Buchwald", + "author_inst": "University of Miami" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2020.10.19.20215483", "rel_title": "Deep learning segmentation model for automated detection of the opacity regions in the chest X-rays of the Covid-19 positive patients and the application for disease severity", @@ -1126712,101 +1129508,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.20.20213116", - "rel_title": "Prevalence of SARS-CoV-2 antibodies in France: results from nationwide serological surveillance", - "rel_date": "2020-10-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.20.20213116", - "rel_abs": "BackgroundAssessment of cumulative incidence of SARS-CoV-2 infections is critical for monitoring the course and the extent of the epidemic. As asymptomatic or mild cases were typically not captured by surveillance data in France, we implemented nationwide serological surveillance. We present estimates for prevalence of anti-SARS-CoV-2 antibodies in the French population and the proportion of infected individuals who developed potentially protective neutralizing antibodies throughout the first epidemic wave.\n\nMethodsWe performed serial cross-sectional sampling of residual sera over three periods: prior to (9-15 March), during (6-12 April) and following (11-17 May) a nationwide lockdown. Each sample was tested for anti-SARS-CoV-2 IgG antibodies targeting the Nucleoprotein and Spike using two Luciferase-Linked ImmunoSorbent Assays, and for neutralising antibodies using a pseudo-neutralisation assay. We fitted a general linear mixed model of seropositivity in a Bayesian framework to derive prevalence estimates stratified by age, sex and region.\n\nFindingsIn total, sera from 11 021 individuals were analysed. Nationwide seroprevalence of SARS-CoV-2 antibodies was estimated at 0.41% [0.05-0.88] mid-March, 4.14% [3.31-4.99] mid-April and 4.93% [4.02-5.89] mid-May. Approximately 70% of seropositive individuals had detectable neutralising antibodies. Seroprevalence was higher in regions where circulation occurred earlier and was more intense. Seroprevalence was lowest in children under 10 years of age (2.72% [1.10-4.87]).\n\nInterpretationSeroprevalence estimates confirm that the nationwide lockdown substantially curbed transmission and that the vast majority of the French population remains susceptible to SARS-CoV-2. Low seroprevalence in school age children suggests limited susceptibility and/or transmissibility in this age group. Our results show a clear picture of the progression of the first epidemic wave and provide a framework to inform the ongoing public health response as viral transmission is picking up again in France and globally.\n\nFundingSante publique France.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Stephane Le Vu", - "author_inst": "Sante publique France" - }, - { - "author_name": "Gabrielle Jones", - "author_inst": "Sante publique France" - }, - { - "author_name": "Francois Anna", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Thierry Rose", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Jean-Baptiste Richard", - "author_inst": "Sante publique France" - }, - { - "author_name": "Sibylle Bernard-Stoecklin", - "author_inst": "Sante publique France" - }, - { - "author_name": "Sophie Goyard", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Caroline Demeret", - "author_inst": "Institut pasteur" - }, - { - "author_name": "Olivier Helynck", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Corinne Robin", - "author_inst": "Cerba Healthcare Division" - }, - { - "author_name": "Virgile Monnet", - "author_inst": "Eurofins-Biomnis" - }, - { - "author_name": "Louise Perrin de Facci", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Marie-Noelle Ungeheuer", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Lucie Leon", - "author_inst": "Sante publique France" - }, - { - "author_name": "Yvonnick Guillois", - "author_inst": "Sante publique France" - }, - { - "author_name": "Laurent Filleul", - "author_inst": "Sante publique France" - }, - { - "author_name": "Pierre Charneau", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Daniel Levy-Bruhl", - "author_inst": "Sante publique France" - }, - { - "author_name": "Sylvie van der Werf", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Harold Noel", - "author_inst": "Sante publique France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.20.20215863", "rel_title": "Cognitive deficits in people who have recovered from COVID-19 relative to controls: An N=84,285 online study", @@ -1127063,6 +1129764,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.10.21.347799", + "rel_title": "Preclinical study of DNA vaccines targeting SARS-CoV-2", + "rel_date": "2020-10-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.21.347799", + "rel_abs": "To fight against the worldwide COVID-19 pandemic, the development of an effective and safe vaccine against SARS-CoV-2 is required. As potential pandemic vaccines, DNA/RNA vaccines, viral vector vaccines and protein-based vaccines have been rapidly developed to prevent pandemic spread worldwide. In this study, we designed plasmid DNA vaccine targeting the SARS-CoV-2 Spike glycoprotein (S protein) as pandemic vaccine, and the humoral, cellular, and functional immune responses were characterized to support proceeding to initial human clinical trials. After intramuscular injection of DNA vaccine encoding S protein with alum adjuvant (three times at 2-week intervals), the humoral immunoreaction, as assessed by anti-S protein or anti-receptor-binding domain (RBD) antibody titers, and the cellular immunoreaction, as assessed by antigen-induced IFN{gamma} expression, were up-regulated. In IgG subclass analysis, IgG2b was induced as the main subclass. Based on these analyses, DNA vaccine with alum adjuvant preferentially induced Th1-type T cell polarization. We confirmed the neutralizing action of DNA vaccine-induced antibodies via two different methods, a binding assay of RBD recombinant protein with angiotensin-converting enzyme 2 (ACE2), a receptor of SARS-CoV-2, and pseudovirus assay. Further B cell epitope mapping analysis using a peptide array showed that most vaccine-induced antibodies recognized the S2 and RBD subunits, but not the S1 subunit. In conclusion, DNA vaccine targeting the spike glycoprotein of SARS-CoV-2 might be an effective and safe approach to combat the COVID-19 pandemic.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Hiroki Hayashi", + "author_inst": "Osaka University" + }, + { + "author_name": "Jiao Sun", + "author_inst": "Osaka University" + }, + { + "author_name": "Yuka Yanagida", + "author_inst": "Osaka University" + }, + { + "author_name": "Takako Otera", + "author_inst": "Osaka University" + }, + { + "author_name": "Ritsuko Kubota-Kotetsu", + "author_inst": "Osaka University" + }, + { + "author_name": "Tatsuo Shioda", + "author_inst": "Osaka University" + }, + { + "author_name": "Chikako Ono", + "author_inst": "Osaka University" + }, + { + "author_name": "Yoshiharu Matsuura", + "author_inst": "Osaka University" + }, + { + "author_name": "Hisashi Arase", + "author_inst": "Osaka University" + }, + { + "author_name": "Shota Yoshida", + "author_inst": "Osaka University" + }, + { + "author_name": "Ryo Nakamaru", + "author_inst": "Osaka University" + }, + { + "author_name": "Ryoko Ide", + "author_inst": "Funpep" + }, + { + "author_name": "Akiko Tenma", + "author_inst": "Funpep" + }, + { + "author_name": "Sotaro Kawabata", + "author_inst": "Funpep" + }, + { + "author_name": "Takako Ehara", + "author_inst": "Funpep" + }, + { + "author_name": "Makoto Sakaguchi", + "author_inst": "Funpep" + }, + { + "author_name": "Hideki Tomioka", + "author_inst": "Funpep" + }, + { + "author_name": "Munehisa Shimamura", + "author_inst": "Osaka University" + }, + { + "author_name": "Sachiko Okamoto", + "author_inst": "Takara Bio" + }, + { + "author_name": "Yasunori Amaishi", + "author_inst": "Takara Bio" + }, + { + "author_name": "Hideto Chono", + "author_inst": "Takara Bio" + }, + { + "author_name": "Junichi Mineno", + "author_inst": "Takara Bio" + }, + { + "author_name": "Takao Komatsuno", + "author_inst": "Anges" + }, + { + "author_name": "Yoshimi Saito", + "author_inst": "Anges" + }, + { + "author_name": "Hiromi Rakugi", + "author_inst": "Osaka University" + }, + { + "author_name": "Ryuichi Morishita", + "author_inst": "Osaka University" + }, + { + "author_name": "Hironori Nakagami", + "author_inst": "Osaka University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.10.21.347690", "rel_title": "Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP", @@ -1128210,53 +1131034,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.10.15.20213371", - "rel_title": "Impact of SARS-CoV-2 on Seasonal Respiratory Viruses: A Tale of Two Large Metropolitan Centers in the United States", - "rel_date": "2020-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.15.20213371", - "rel_abs": "To assess the impact of the SARS-CoV-2 pandemic on seasonal respiratory viruses, absolute case counts and viral reproductive rates from 2019-2020 were compared against previous seasons. Our findings suggest that the public health measures implemented to reduce SARS-CoV-2 transmission significantly reduced the transmission of other respiratory viruses.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Amy C Sherman", - "author_inst": "Division of Infectious Diseases, Brigham and Women's Hospital" - }, - { - "author_name": "Ahmed Babiker", - "author_inst": "Division of Infectious Diseases, Emory University School of Medicine" - }, - { - "author_name": "Andrew J Sieben", - "author_inst": "Emory University" - }, - { - "author_name": "Alexander Pyden", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center" - }, - { - "author_name": "James Steinberg", - "author_inst": "Division of Infectious Diseases, Emory University School of Medicine" - }, - { - "author_name": "Colleen S Kraft", - "author_inst": "Division of Infectious Diseases, Emory University School of Medicine" - }, - { - "author_name": "Katia Koelle", - "author_inst": "Department of Biology, Emory University" - }, - { - "author_name": "Sanjat Kanjilal", - "author_inst": "Division of Infectious Diseases, Brigham and Women's Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.15.20213512", "rel_title": "COVID-19 neutralizing antibodies predict disease severity and survival", @@ -1128689,6 +1131466,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.10.15.20212308", + "rel_title": "Indirect effects of the COVID-19 pandemic on paediatric health-care use and severe disease: a retrospective national cohort study", + "rel_date": "2020-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.15.20212308", + "rel_abs": "BackgroundSevere disease directly associated with SARS-CoV-2 infection in children is rare. However, the indirect consequences of the COVID-19 pandemic on paediatric health have not been fully quantified. We examined paediatric health-care utilisation, incidence of severe disease, and mortality during the lockdown period in Scotland.\n\nMethodsThis national retrospective cohort study examined national data for emergency childhood primary and secondary care utilisation following national lockdown on March 23, 2020. To determine whether social distancing measures and caregiver behavioural changes were associated with delayed care-seeking and increased disease severity on presentation, unplanned, emergency admissions requiring invasive mechanical ventilation for the two national Paediatric Intensive Care Units (PICUs) were analysed. PICU admissions were grouped by diagnostic category, and disease severity on presentation calculated. National statutory death records were consulted to establish childhood mortality rates and causes of death. For all observations, the lockdown period was compared to equivalent dates in 2016-2019.\n\nFindingsWe identified 273,455 unscheduled primary care attendances; 462,437 emergency department attendances; 54,076 emergency hospital admissions; 413 PICU emergency admissions; and 415 deaths during the lockdown study period and equivalent dates in previous years. The rates of emergency presentations to primary and secondary care fell during lockdown in comparison to previous years. Emergency PICU admissions for children requiring invasive mechanical ventilation also fell, with an odds ratio of 0{middle dot}52 for chance of admission during lockdown (95% CI 0{middle dot}37-0{middle dot}73, p < 0{middle dot}001). Clinical severity scores did not suggest children were presenting with more advanced disease. The greatest reduction in PICU admissions was for diseases of the respiratory system; those for injury, poisoning or other external causes were equivalent to previous years. Mortality during lockdown did not change significantly compared to 2016-2019.\n\nInterpretationNational lockdown led a reduction in paediatric emergency care utilisation, without associated evidence of severe harm.\n\nFundingNone\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSData on the indirect effects of the COVID-19 pandemic on children at a population level are limited. We searched PubMed and medRxiv on October 13, 2020, for studies published from Jan 1, 2020 examining the indirect effects of non-pharmaceutical interventions (NPIs), and associated changes in caregiver health-care seeking behaviour, on the risk of severe paediatric disease and death. We used the search terms COVID-19, SARS-CoV-2, non-pharmaceutical interventions, indirect, and children, as well as manually searching references in other relevant papers. Terms were searched individually and in combination as necessary, with no language restrictions. We identified one study that modelled the indirect effects of the COVID-19 pandemic on child deaths in low- and middle-income countries. Other studies analysed in isolation the effects of NPIs and other behavioural changes on emergency department attendances, hospital admission rates, paediatric intensive care unit (PICU) admission rates, or the incidence of specific presentations, such as asthma exacerbations. Some case series described delayed care-seeking for children with non-SARS-CoV-2 disease. We did not identify any national studies examining the indirect effects of the COVID-19 pandemic on the incidence of severe paediatric disease and mortality.\n\nAdded value of this studyThis national study quantified the changes following national lockdown in Scotland on March 23, 2020. We examined data for unscheduled primary care and emergency department attendances, emergency hospital admissions, emergency paediatric intensive care unit (PICU) admissions requiring invasive mechanical ventilation, and paediatric mortality. Rates were compared with previous years. We found a reduction in paediatric emergency care utilisation rates associated with national lockdown. This reduction is likely to be due to a combination of changes in health care seeking behavior, and a fall in overall burden of paediatric infectious disease. These measures did not appear to have been associated with evidence of severe harm to children in Scotland, as evidenced by severity scores on presentation to PICU or mortality.\n\nImplications of all the available evidenceThis is the first comprehensive population-based assessment at a national level of the indirect effects of the COVID-19 pandemic on severe paediatric morbidity and mortality. Despite a significant reduction in health-care utilisation rates, we did not find associated evidence of severe harm. This study will assist policy makers, health-care providers and the public in evaluating the effects of lockdown on the risk of severe paediatric disease at a population level.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Thomas C Williams", + "author_inst": "Department of Paediatric Respiratory and Sleep Medicine, Royal Hospital for Children and Young People, Edinburgh" + }, + { + "author_name": "Clare MacRae", + "author_inst": "Usher Institute, University of Edinburgh" + }, + { + "author_name": "Olivia Swann", + "author_inst": "Department of Child Life and Health, University of Edinburgh" + }, + { + "author_name": "Haris Haseeb", + "author_inst": "Department of Paediatric Respiratory and Sleep Medicine, Royal Hospital for Children and Young People, Edinburgh" + }, + { + "author_name": "Steve Cunningham", + "author_inst": "Department of Paediatric Respiratory and Sleep Medicine, Royal Hospital for Children and Young People, Edinburgh" + }, + { + "author_name": "Philip Davies", + "author_inst": "Department of Paediatric Respiratory and Sleep Medicine, Royal Hospital for Children, Glasgow" + }, + { + "author_name": "Neil Gibson", + "author_inst": "Department of Paediatric Respiratory and Sleep Medicine, Royal Hospital for Children, Glasgow" + }, + { + "author_name": "Christopher Lamb", + "author_inst": "Critical Care, Royal Hospital for Children, Glasgow" + }, + { + "author_name": "Richard Levin", + "author_inst": "Critical Care, Royal Hospital for Children, Glasgow" + }, + { + "author_name": "Catherine McDougall", + "author_inst": "Department of Paediatric Respiratory and Sleep Medicine, Royal Hospital for Children and Young People, Edinburgh" + }, + { + "author_name": "Jillian McFadzean", + "author_inst": "Critical Care, Royal Hospital for Children and Young People, Edinburgh" + }, + { + "author_name": "Ian Piper", + "author_inst": "Critical Care, Royal Hospital for Children and Young People, Edinburgh" + }, + { + "author_name": "Alastair Turner", + "author_inst": "Critical Care, Royal Hospital for Children, Glasgow" + }, + { + "author_name": "Steve Turner", + "author_inst": "University of Aberdeen" + }, + { + "author_name": "Margrethe Van Dijke", + "author_inst": "Critical Care, Royal Hospital for Children and Young People, Edinburgh" + }, + { + "author_name": "Don Urquhart", + "author_inst": "Department of Paediatric Respiratory and Sleep Medicine, Royal Hospital for Children and Young People, Edinburgh" + }, + { + "author_name": "Bruce Guthrie", + "author_inst": "Usher Institute, University of Edinburgh" + }, + { + "author_name": "Ross Langley", + "author_inst": "Department of Paediatric Respiratory and Sleep Medicine, Royal Hospital for Children, Glasgow" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.10.15.20213645", "rel_title": "A Comparative Analysis of System Features Used in the TREC-COVID Information Retrieval Challenge", @@ -1129900,69 +1132764,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, - { - "rel_doi": "10.1101/2020.10.18.20214221", - "rel_title": "Structural and metabolic brain abnormalities in COVID-19 patients with sudden loss of smell", - "rel_date": "2020-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.18.20214221", - "rel_abs": "ObjectivesSudden loss of smell is a very common symptom of coronavirus disease 19 (COVID-19). This study characterizes the structural and metabolic cerebral correlates of dysosmia in patients with COVID-19.\n\nMethodsStructural brain magnetic resonance imaging (MRI) and positron emission tomography with [18F]-fluorodeoxyglucose (FDG-PET) were prospectively acquired simultaneously on a hybrid PET-MR in twelve patients (2 males, 10 females, mean age: 42.6 years, age range: 23-60 years) with sudden dysosmia and positive detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on nasopharyngeal swab specimens. FDG-PET data were analysed using a voxel-based approach and compared with that of a group of healthy subjects.\n\nResultsBilateral blocking of the olfactory cleft was observed in six patients, while subtle olfactory bulb asymmetry was found in three patients. No MRI signal abnormality downstream of the olfactory tract was observed. Heterogeneous (decrease or increase) glucose metabolism abnormalities were observed in core olfactory and high-order neocortical areas. A modulation of regional cerebral glucose metabolism by the severity and the duration of COVID-19-related dysosmia was disclosed using correlation analyses.\n\nConclusionsThis PET-MR study shows that sudden loss of smell in COVID-19 is not related to central involvement due to SARS-CoV-2 neuroinvasiveness. Loss of smell is associated with heterogeneous cerebral metabolic changes in core olfactory and high-order cortical areas likely related to combined processes of deafferentation and active functional reorganisation secondary to the lack of olfactory stimulation.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Maxime Niesen", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Nicola Trotta", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Antoine Noel", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Tim Coolen", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Georges Fayad", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Gil Leurkin-Sterk", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Isabelle Delpierre", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Sophie Henrard", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Niloufar Sadeghi", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Jean-Christophe Goffard", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Serge Goldman", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Xavier De Ti\u00e8ge", - "author_inst": "CUB Hopital Erasme" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2020.10.17.20214429", "rel_title": "SARS-CoV-2 infection among patients with multiple sclerosis; A cross-sectional study", @@ -1130083,6 +1132884,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2020.10.16.20214023", + "rel_title": "Age-Stratified SARS-CoV-2 Infection Fatality Rates in New York City estimated from serological data", + "rel_date": "2020-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.16.20214023", + "rel_abs": "ImportanceCOVID-19 has killed hundreds of thousands of people in the US and >1 million globally. Estimating the age-specific infection fatality rate (IFR) of SARS-CoV-2 for different populations is crucial for assessing the fatality of COVID-19 and for appropriately allocating limited vaccine supplies to minimize mortality.\n\nObjectiveTo estimate IFRs for COVID-19 in New York City and compare them to IFRs from other countries.\n\nDesign, Setting, ParticipantsWe used data from a published serosurvey of 5946 individuals 18 years or older conducted April 19-28, 2020 with time series of COVID-19 confirmed cases and deaths for five age-classes from the New York City Department of Health and Mental Hygiene. We inferred age-specific IFRs using a Bayesian framework that accounted for the distribution of delay between infection and seroconversion and infection and death.\n\nMain Outcome and MeasureInfection fatality rate.\n\nResultsWe found that IFRs increased approximately 77-fold with age, with a nearly linear increase on a log scale, from 0.07% (0.055%-0.086%) in 18-44 year olds to 5.4% (4.3%-6.3%) in individuals 75 and older. New York City IFRs were higher for 18-44 year olds and 45-64 year olds (0.58%; 0.45%-0.75%) than Spanish, English, and Swiss populations, but IFRs for 75+ year olds were lower than for English populations and similar to Spanish and Swiss populations.\n\nConclusions and RelevanceThese results suggest that the age-specific fatality of COVID-19 differs among developed countries and raises questions about factors underlying these differences.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSHow do age-specific infection fatality rates (IFR) for COVID-19 in the U.S. compare to other populations?\n\nFindingsWe estimated age-specific IFRs of SARS-CoV-2 using seroprevalence data and deaths in New York City. IFRs increased more than 75-fold with age, from 0.07% in 18-45 year olds to 5.3% in individuals over 75. IFRs in New York City were higher than IFRs in England, Geneva, France and Spain for individuals younger than 64 years old, but similar for older individuals.\n\nMeaningThe age-specific fatality of COVID-19 varies significantly among developed nations for unknown reasons.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Chloe G Rickards", + "author_inst": "University of California, Santa Cruz" + }, + { + "author_name": "A. Marm Kilpatrick", + "author_inst": "University of California, Santa Cruz" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.17.20214205", "rel_title": "Composition of the immunoglobulin G glycome associates with the severity of COVID-19", @@ -1131650,37 +1134474,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.10.18.344622", - "rel_title": "An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants", - "rel_date": "2020-10-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.18.344622", - "rel_abs": "The spike S of SARS-CoV-2 recognizes ACE2 on the host cell membrane to initiate entry. Soluble decoy receptors, in which the ACE2 ectodomain is engineered to block S with high affinity, potently neutralize infection and, due to close similarity with the natural receptor, hold out the promise of being broadly active against virus variants without opportunity for escape. Here, we directly test this hypothesis. We find an engineered decoy receptor, sACE22.v2.4, tightly binds S of SARS-associated viruses from humans and bats, despite the ACE2-binding surface being a region of high diversity. Saturation mutagenesis of the receptor-binding domain (RBD) followed by in vitro selection, with wild type ACE2 and the engineered decoy competing for binding sites, failed to find S mutants that discriminate in favor of the wild type receptor. Variant N501Y in the RBD, which has emerged in a rapidly spreading lineage (B.1.1.7) in England, enhances affinity for wild type ACE2 20-fold but remains tightly bound to engineered sACE22.v2.4. We conclude that resistance to engineered decoys will be rare and that decoys may be active against future outbreaks of SARS-associated betacoronaviruses.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Kui K Chan", - "author_inst": "Orthogonal Biologics, Inc." - }, - { - "author_name": "Timothy JC Tan", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Krishna K Narayanan", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Erik Procko", - "author_inst": "University of Illinois at Urbana-Champaign" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.10.19.343954", "rel_title": "Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium", @@ -1132073,6 +1134866,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.14.20212993", + "rel_title": "White blood cells and severe COVID-19: a Mendelian randomization study", + "rel_date": "2020-10-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212993", + "rel_abs": "Increasing evidence shows that white blood cells are associated with the risk of coronavirus disease 2019 (COVID-19), but the direction and causality of this association are not clear. To evaluate the causal associations between various white blood cell traits and the COVID-19 susceptibility and severity, we conducted two-sample bidirectional Mendelian Randomization (MR) analyses with summary statistics from the largest and most recent genome-wide association studies. Our MR results indicated causal protective effects of higher basophil count, basophil percentage of white blood cells, and myeloid white blood cell count on severe COVID-19, with odds ratios (OR) per standard deviation increment of 0.75 (95% CI: 0.60-0.95), 0.70 (95% CI: 0.54-0.92), and 0.85 (95% CI: 0.73-0.98), respectively. Neither COVID-19 severity nor susceptibility was associated with white blood cell traits in our reverse MR results. Genetically predicted high basophil count, basophil percentage of white blood cells, and myeloid white blood cell count are associated with a lower risk of developing severe COVID-19. Individuals with a lower genetic capacity for basophils are likely at risk, while enhancing the production of basophils may be an effective therapeutic strategy.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Yitang Sun", + "author_inst": "Department of Genetics, University of Georgia, Athens, GA" + }, + { + "author_name": "Jingqi Zhou", + "author_inst": "Department of Genetics, University of Georgia, Athens, GA; School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China" + }, + { + "author_name": "Kaixiong Ye", + "author_inst": "Department of Genetics, University of Georgia, Athens, GA; Institute of Bioinformatics, University of Georgia, Athens, GA" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.14.20212167", "rel_title": "Anxiety Levels among Healthcare Professionals during Covid-19 Pandemic: A Multifactorial Study", @@ -1133243,77 +1136063,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.14.20212415", - "rel_title": "CoViD-19, learning from the past: A wavelet and cross-correlation analysis of the epidemic dynamics looking to emergency calls and Twitter trends in Italian Lombardy region", - "rel_date": "2020-10-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212415", - "rel_abs": "The first case of Coronavirus Disease 2019 in Italy was detected on February the 20th in Lombardy region. Since that date, Lombardy has been the most affected Italian region by the epidemic, and its healthcare system underwent a severe overload during the outbreak. From a public health point of view, therefore, it is fundamental to provide healthcare services with tools that can reveal possible new health system stress periods with a certain time anticipation, which is the main aim of the present study. Moreover, the sequence of law decrees to face the epidemic and the large amount of news generated in the population feelings of anxiety and suspicion. Considering this whole complex context, it is easily understandable how people \"overcrowded\" social media with messages dealing with the pandemic, and emergency numbers were overwhelmed by the calls. Thus, in order to find potential predictors of possible new health system overloads, we analysed data both from Twitter and emergency services comparing them to the daily infected time series at a regional level. Particularly, we performed a wavelet analysis in the time-frequency plane, to finely discriminate over time the anticipation capability of the considered potential predictors. In addition, a cross-correlation analysis has been performed to find a synthetic indicator of the time delay between the predictor and the infected time series. Our results show that Twitter data are more related to social and political dynamics, while the emergency calls trends can be further evaluated as a powerful tool to potentially forecast new stress periods. Since we analysed aggregated regional data, and taking into account also the huge geographical heterogeneity of the epidemic spread, a future perspective would be to conduct the same analysis on a more local basis.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Bruno Alessandro Rivieccio", - "author_inst": "Department of Laboratory Medicine, Division of Anatomic Pathology, Niguarda Hospital, Milan, Italy" - }, - { - "author_name": "Alessandra Micheletti", - "author_inst": "Department of Environmental Science and Policy, University of Milan, Milan, Italy" - }, - { - "author_name": "Manuel Maffeo", - "author_inst": "Department of Biomedical Sciences for Health, University of Milan, Milan, Italy" - }, - { - "author_name": "Matteo Zignani", - "author_inst": "Department of Computer Science, University of Milan, Milan, Italy" - }, - { - "author_name": "Alessandro Comunian", - "author_inst": "Department of Earth Sciences, University of Milan, Milan, Italy" - }, - { - "author_name": "Federica Nicolussi", - "author_inst": "Department of Economics, Management and Quantitative Methods & Data Science Research Center, University of Milan, Milan, Italy" - }, - { - "author_name": "Silvia Salini", - "author_inst": "Department of Economics, Management and Quantitative Methods & Data Science Research Center, University of Milan, Milan, Italy" - }, - { - "author_name": "Giancarlo Manzi", - "author_inst": "Department of Economics, Management and Quantitative Methods & Data Science Research Center, University of Milan, Milan, Italy" - }, - { - "author_name": "Francesco Auxilia", - "author_inst": "Department of Biomedical Sciences for Health, University of Milan, Milan, Italy; ASST FBF-Sacco, Milan, Italy" - }, - { - "author_name": "Mauro Giudici", - "author_inst": "Department of Earth Sciences, University of Milan, Milan, Italy" - }, - { - "author_name": "Giovanni Naldi", - "author_inst": "Department of Environmental Science and Policy, University of Milan, Milan, Italy" - }, - { - "author_name": "Sabrina Gaito", - "author_inst": "Department of Computer Science, University of Milan, Milan, Italy" - }, - { - "author_name": "Silvana Castaldi", - "author_inst": "Department of Biomedical Sciences for Health, University of Milan, Milan, Italy; Fondazione IRCCS Ca Granda Ospedale Maggiore, Milan, Italy" - }, - { - "author_name": "Elia Biganzoli", - "author_inst": "Department of Clinical Sciences and Community Health & Data Science Research Center, University of Milan, Milan, Italy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.14.20212555", "rel_title": "Multi-organ impairment in low-risk individuals with long COVID", @@ -1133626,6 +1136375,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.14.20212431", + "rel_title": "How to remove the testing bias in CoV-2 statistics", + "rel_date": "2020-10-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212431", + "rel_abs": "BACKGROUNDPublic health measures and private behaviour are based on reported numbers of SARS-CoV-2 infections. Some argue that testing influences the confirmed number of infections.\n\nOBJECTIVES/METHODSDo time series on reported infections and the number of tests allow one to draw conclusions about actual infection numbers? A SIR model is presented where the true numbers of susceptible, infectious and removed individuals are unobserved. Testing is also modelled.\n\nRESULTSOfficial confirmed infection numbers are likely to be biased and cannot be compared over time. The bias occurs because of different reasons for testing (e.g. by symptoms, representative or testing travellers). The paper illustrates the bias and works out the effect of the number of tests on the number of reported cases. The paper also shows that the positive rate (the ratio of positive tests to the total number of tests) is uninformative in the presence of non-representative testing.\n\nCONCLUSIONSA severity index for epidemics is proposed that is comparable over time. This index is based on Covid-19 cases and can be obtained if the reason for testing is known.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Klaus Waelde", + "author_inst": "Johannes Gutenberg University Mainz" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.16.342410", "rel_title": "Drug synergy of combinatory treatment with remdesivir and the repurposed drugs fluoxetine and itraconazole effectively impairs SARS-CoV-2 infection in vitro", @@ -1135013,57 +1137781,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.10.15.339838", - "rel_title": "Inhibition of SARS-CoV-2 viral entry in vitro upon blocking N- and O-glycan elaboration", - "rel_date": "2020-10-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.15.339838", - "rel_abs": "The Spike protein of SARS-CoV-2, its receptor binding domain (RBD), and its primary receptor ACE2 are extensively glycosylated. The impact of this post-translational modification on viral entry is yet unestablished. We expressed different glycoforms of the Spike-protein and ACE2 in CRISPR-Cas9 glycoengineered cells, and developed corresponding SARS-CoV-2 pseudovirus. We observed that N- and O-glycans had only minor contribution to Spike-ACE2 binding. However, these carbohydrates played a major role in regulating viral entry. Blocking N-glycan biosynthesis at the oligomannose stage using both genetic approaches and the small molecule kifunensine dramatically reduced viral entry into ACE2 expressing HEK293T cells. Blocking O-glycan elaboration also partially blocked viral entry. Mechanistic studies suggest multiple roles for glycans during viral entry. Among them, inhibition of N-glycan biosynthesis enhanced Spike-protein proteolysis. This could reduce RBD presentation on virus, lowering binding to host ACE2 and decreasing viral entry. Overall, chemical inhibitors of glycosylation may be evaluated for COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Qi Yang", - "author_inst": "State University of New York, Buffalo, NY, USA" - }, - { - "author_name": "Thomas A. Hughes", - "author_inst": "State University of New York, Buffalo, NY, USA" - }, - { - "author_name": "Anju Kelkar", - "author_inst": "State University of New York, Buffalo, NY, USA" - }, - { - "author_name": "Xinheng Yu", - "author_inst": "State University of New York, Buffalo, NY, USA" - }, - { - "author_name": "Kai Cheng", - "author_inst": "State University of New York, Buffalo, NY, USA" - }, - { - "author_name": "Sheldon J. Park", - "author_inst": "State University of New York, Buffalo, NY, USA" - }, - { - "author_name": "We-Chiao Huang", - "author_inst": "State University of New York, Buffalo, NY, USA" - }, - { - "author_name": "Jonathan F. Lovell", - "author_inst": "State University of New York, Buffalo, NY, USA" - }, - { - "author_name": "Sriram Neelamegham", - "author_inst": "State University of New York, Buffalo, NY, USA" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.10.14.339952", "rel_title": "Multiplexed proteomics and imaging of resolving and lethal SARS-CoV-2 infection in the lung", @@ -1135340,6 +1138057,81 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.10.15.340794", + "rel_title": "Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs", + "rel_date": "2020-10-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.15.340794", + "rel_abs": "The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, poses a severe threat to humanity. Rapid and comprehensive analysis of both pathogen and host sequencing data is critical to track infection and inform therapies. In this study, we performed unbiased metatranscriptomic analysis of clinical samples from COVID-19 patients using a newly-developed RNA-seq library construction method (TRACE-seq), which utilizes tagmentation activity of Tn5 on RNA/DNA hybrids. This approach avoids the laborious and time-consuming steps in traditional RNA-seq procedure, and hence is fast, sensitive and convenient. We demonstrated that TRACE-seq allowed integrated characterization of full genome information of SARS-CoV-2, putative pathogens causing coinfection, antibiotic resistance and host response from single throat swabs. We believe that the integrated information will deepen our understanding of pathogenesis and improve diagnostic accuracy for infectious diseases.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Bo Lu", + "author_inst": "Peking University" + }, + { + "author_name": "Yi Yan", + "author_inst": "Chinese Academy of Sciences" + }, + { + "author_name": "Liting Dong", + "author_inst": "Peking University" + }, + { + "author_name": "Lingling Han", + "author_inst": "GrandOmics Biosciences" + }, + { + "author_name": "Yawei Liu", + "author_inst": "The First Medical Center of PLA General Hospital" + }, + { + "author_name": "Junping Yu", + "author_inst": "Chinese Academy of Sciences" + }, + { + "author_name": "Jianjun Chen", + "author_inst": "Chinese Academy of Sciences" + }, + { + "author_name": "Danyang Yi", + "author_inst": "Peking University" + }, + { + "author_name": "Meiling Zhang", + "author_inst": "Peking University" + }, + { + "author_name": "Chao Wang", + "author_inst": "GrandOmics Biosciences" + }, + { + "author_name": "Runkun Wang", + "author_inst": "GrandOmics Biosciences" + }, + { + "author_name": "Dengpeng Wang", + "author_inst": "GrandOmics Biosciences" + }, + { + "author_name": "Hongping Wei", + "author_inst": "Chinese Academy of Sciences" + }, + { + "author_name": "Di Liu", + "author_inst": "Chinese Academy of Sciences" + }, + { + "author_name": "Chengqi Yi", + "author_inst": "Peking University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.10.15.340604", "rel_title": "Quantitative Assays Reveal Cell Fusion at Minimal Levels of SARS-CoV-2 Spike Protein and Fusion-from-Without", @@ -1136395,49 +1139187,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.13.20211797", - "rel_title": "Use of antivirals and antibiotics for COVID-19 in Mexico City: A Real-World Multicenter Cohort Study", - "rel_date": "2020-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.13.20211797", - "rel_abs": "AimTo evaluate all-cause mortality risk in patients with laboratory-confirmed COVID-19 in Mexico City treated with repurposed antivirals and antibiotics.\n\nMethodsThis real-world retrospective cohort study contemplated 395,343 patients evaluated for suspected COVID-19 between February 24 and September 14, 2020 in 688 primary-to-tertiary medical units in Mexico City. Patients were included with a positive RT-PCR for SARS-CoV-2; those receiving unspecified antivirals, excluded; and antivirals prescribed in <30 patients, eliminated. Survival and mortality risks were determined for patients receiving antivirals, antibiotics, both, or none.\n\nResults136,855 patients were analyzed; mean age 44.2 (SD:16.8) years; 51.3% were men. 16.6% received antivirals (3%), antibiotics (10%), or both (3.6%). Antivirals studied were Oseltamivir (n=8414), Amantadine (n=319), Lopinavir-Ritonavir (n=100), Rimantadine (n=61), Zanamivir (n=39), and Acyclovir (n=36). Survival with antivirals (73.7%, p<0.0001) and antibiotics (85.8%, p<0.0001) was lower than no antiviral/antibiotic (93.6%). After multivariable adjustment, increased risk of death occurred with antivirals (HR=1.72, 95%CI:1.61-1.84) in ambulatory (HR=4.7, 95%CI:3.94-5.62) and non-critical (HR=2.03, 95%CI:1.86-2.21) patients. Oseltamivir increased mortality risk in the general population (HR=1.72, 95%CI:1.61-1.84), ambulatory (HR=4.79, 95%CI:4.01-5.75), non-critical (HR=2.05, 95%CI:1.88-2.23), and pregnancy (HR=8.35, 95%CI:1.77-39.30); as well as hospitalized (HR=1.13, 95%CI:1.01-1.26) and critical patients (HR:1.22, 95%CI:1.05-1.43) after propensity score-matching. Antibiotics were a risk factor in general population (HR=1.13, 95%CI:1.08-1.19) and pediatrics (HR=4.22, 95%CI:2.01-8.86), but a protective factor in hospitalized (HR=0.81, 95%CI:0.77-0.86) and critical patients (HR=0.67, 95%CI:0.63-0.72).\n\nConclusionsNo significant benefit for repurposed antivirals was observed; oseltamivir was associated with increased mortality. Antibiotics increased mortality risk in the general population but may increase survival in hospitalized and critical patients.\n\nWHAT IS ALREADY KNOWNO_LICurrent recommendations for using repurposed antivirals and antibiotics for COVID-19 are conflicting.\nC_LIO_LIFew antivirals (i.e. lopinavir-ritonavir) have been shown to provide no additional benefit for COVID-19 in clinical trials; other antivirals may be having widespread use in real-world settings without formal assessment in clinical trials.\nC_LIO_LIReal-world use of repurposed antivirals and antibiotics for COVID-19 in population-based studies have not been performed; important populations have been left largely understudied (ambulatory patients, pregnant women, and pediatrics).\nC_LI\n\nWHAT THIS STUDY ADDSO_LIThis is the first real-world observational study evaluating amantadine, rimantadine, zanamivir, and acyclovir for COVID-19; no registered studies to evaluate these drugs exist. Only one study has evaluated risk of death for oseltamivir. Lopinavir-ritonavir have been previously evaluated in clinical trials.\nC_LIO_LIRepurposed antivirals and antibiotics were commonly prescribed in 688 ambulatory units and hospitals of Mexico City despite unclear recommendations for their use out of clinical trials.\nC_LIO_LIOseltamivir was associated with increased mortality risk; other repurposed antivirals (zanamivir, amantadine, rimantadine, and acyclovir) had no significant and consistent impact on mortality. Antibiotics were associated with increased mortality risk in the general population but may increase survival in hospitalized and critical patients.\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Javier Mancilla-Galindo", - "author_inst": "Unidad de Investigacion UNAM-INC, Instituto Nacional de Cardiologia Ignacio Chavez" - }, - { - "author_name": "Jorge Oscar Garcia-Mendez", - "author_inst": "Departamento de Posgrado y Educacion Medica Continua, Instituto Nacional de Cancerologia." - }, - { - "author_name": "Jessica Marquez-Sanchez", - "author_inst": "Departamento de Infectologia, Instituto Nacional de Pediatria" - }, - { - "author_name": "Rodrigo Estefano Reyes-Casarrubias", - "author_inst": "Facultad de Medicina, Universidad Nacional Autonoma de Mexico." - }, - { - "author_name": "Eduardo Aguirre-Aguilar", - "author_inst": "Departamento de Atencion Institutcional Continua y Urgencias, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" - }, - { - "author_name": "Hector Isaac Rocha-Gonzalez", - "author_inst": "Seccion de Estudios de Posgrado e Investigacion, Escuela Superior de Medicina, Instituto Politecnico Nacional" - }, - { - "author_name": "Ashuin Kammar-Garcia", - "author_inst": "Departamento de Atencion Institucional Continua y Urgencias, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2020.10.13.20178483", "rel_title": "Automated chest radiograph diagnosis: A Twofer for tuberculosis and Covid-19", @@ -1136754,6 +1139503,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.10.13.20212183", + "rel_title": "Return to University Campuses Associated with 9% Increase in New COVID-19 Case Rate", + "rel_date": "2020-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.13.20212183", + "rel_abs": "The vast majority of colleges and universities across the United States are bringing students back for in-person instruction in the midst of the COVID-19 pandemic, despite the absence of an effective vaccine or other anti-viral therapeutic treatment. Using data from the New York Times and the American Community Survey, we assess the effect of this return to campus on viral case growth in counties with a significant college student population (\"college counties\") relative to non-college counties. We find a significant surge in new cases in a 21-day time frame in college counties, a finding consistent across U.S. Census divisions. These results suggest the need for institutions of higher education and the communities where these institutions reside work together quickly and effectively to mitigate viral transmission and to prevent overwhelming local healthcare infrastructure in college counties.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Grace Bagwell Adams", + "author_inst": "University of Georgia" + }, + { + "author_name": "Jerry Shannon", + "author_inst": "University of Georgia" + }, + { + "author_name": "Sarah Shannon", + "author_inst": "University of Georgia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.10.12.20211573", "rel_title": "Preventing COVID-19 spread in closed facilities by regular testing of employees - an efficient intervention in long-term care facilities and prisons", @@ -1138289,41 +1141065,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.13.20211839", - "rel_title": "Measurement of small droplet aerosol concentrations in public spaces using handheld particle counters", - "rel_date": "2020-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.13.20211839", - "rel_abs": "We investigate the role of aerosols in the transmission of SARS-CoV-2 in public spaces. Direct measurement of aerosol concentrations however has proven technically difficult; we propose the use of handheld particle counters as a novel and easily applicable method to measure aerosol concentrations. This allow us to perform measurements in typical public spaces, each differing in volume, number of people and ventilation rate. These data are used to estimate the relation between aerosol persistence time and the risk of infection with SARS-CoV-2.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "G Aernout Somsen", - "author_inst": "Cardiology Centers of the Netherlands" - }, - { - "author_name": "Cees van Rijn", - "author_inst": "Institute of Physics, University of Amsterdam" - }, - { - "author_name": "Stefan Kooy", - "author_inst": "Instute of Physics, University of Amsterdam" - }, - { - "author_name": "Reinout A Bem", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Daniel Bonn", - "author_inst": "Institute of Physics, University of Amsterdam" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.13.20211904", "rel_title": "Background and concurrent factors predicting non-adherence to public health preventive measures during the chronic phase of the COVID-19 pandemic", @@ -1138532,6 +1141273,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.10.14.339150", + "rel_title": "Therapeutic activity of an inhaled potent SARS-CoV-2 neutralizing human monoclonal antibody in hamsters", + "rel_date": "2020-10-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.14.339150", + "rel_abs": "SARS-CoV-2 infection results in viral burden in the upper and lower respiratory tract, enabling transmission and often leading to substantial lung pathology. Delivering the antiviral treatment directly to the lungs has the potential to improve lung bioavailability and dosing efficiency. As the SARS-CoV-2 Receptor Binding Domain (RBD) of the Spike (S) is increasingly deemed to be a clinically validated target, RBD-specific B cells were isolated from patients following SARS-CoV-2 infection to derive a panel of fully human monoclonal antibodies (hmAbs) that potently neutralize SARS-CoV-2. The most potent hmAb, 1212C2 was derived from an IgM memory B cell, has high affinity for SARS-CoV-2 RBD which enables its direct inhibition of RBD binding to ACE2. The 1212C2 hmAb exhibits in vivo prophylactic and therapeutic activity against SARS-CoV-2 in hamsters when delivered intraperitoneally, achieving a meaningful reduction in upper and lower respiratory viral burden and lung pathology. Furthermore, liquid nebulized inhale treatment of SARS-CoV-2 infected hamsters with as low as 0.6 mg/kg of inhaled dose, corresponding to approximately 0.03 mg/kg of lung deposited dose, mediated a reduction in respiratory viral burden that is below the detection limit, and mitigated lung pathology. The therapeutic efficacy achieved at an exceedingly low-dose of inhaled 1212C2 supports the rationale for local lung delivery and achieving dose-sparing benefits as compared to the conventional parenteral route of administration. Taken together, these results warrant an accelerated clinical development of 1212C2 hmAb formulated and delivered via inhalation for the prevention and treatment of SARS-CoV-2 infection.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Michael S Piepenbrink", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Jun-Gyu Park", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Fatai Oladunni", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Ashlesha Deshpande", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Madhubanti Basu", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Sanghita Sarkar", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Andreas Loos", + "author_inst": "Aridis Pharmaceuticals" + }, + { + "author_name": "Jennifer Woo", + "author_inst": "Aridis Pharmaceuticals" + }, + { + "author_name": "Phillip Lovalenti", + "author_inst": "Aridis Pharmaceuticals" + }, + { + "author_name": "Derek Sloan", + "author_inst": "Aridis Pharmaceuticals" + }, + { + "author_name": "Chengjin Ye", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Kevin Chiem", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Nathaniel B Erdmann", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Paul A Goepfert", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Vu L Truong", + "author_inst": "Aridis Pharmaceuticals" + }, + { + "author_name": "Mark R Walter", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Luis Martinez-Sobrido", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "James J Kobie", + "author_inst": "University of Alabama at Birmingham" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.10.14.335893", "rel_title": "Co-infection of influenza A virus enhances SARS-CoV-2 infectivity", @@ -1139790,65 +1142618,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.09.20208876", - "rel_title": "Using an Agent-Based Model to Assess K-12 School Re-openings Under Different COVID-19 Spread Scenarios - United States, School Year 2020/21", - "rel_date": "2020-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.09.20208876", - "rel_abs": "School-age children play a key role in the spread of airborne viruses like influenza due to the prolonged and close contacts they have in school settings. As a result, school closures and other non-pharmaceutical interventions were recommended as the first line of defense in response to the novel coronavirus pandemic (COVID-19). Assessing school reopening scenarios is a priority for states, administrators, parents, and children in order to balance educational disparities and negative population impacts of COVID-19. To address this challenge, we used an agent-based model that simulates communities across the United States including daycares, primary, and secondary schools to quantify the relative health outcomes of reopening schools. We explored different reopening scenarios including remote learning, in-person school, and several hybrid options that stratify the student population into cohorts (also referred to as split cohort) in order to reduce exposure and disease spread. In addition, we assessed the combined impact of reduced in-person attendance in workplaces (e.g., through differing degrees of reliance on telework and/or temporary workplace closings) and school reopening scenarios to quantify the potential impact of additional transmission pathways contributing to COVID-19 spread. Scenarios where split cohorts of students return to school in non-overlapping formats resulted in significant decreases in the clinical attack rate (i.e., the percentage of symptomatic individuals), potentially by as much as 75%. These split cohort scenarios have impacts which are only modestly lesser than the most impactful 100% distance learning scenario. Split cohort scenarios can also significantly avert the number of cases-approximately 60M and 28M-depending on the scenario, at the national scale over the simulated eight-month period. We found the results of our simulations to be highly dependent on the number of workplaces assumed to be open for in-person business, as well as the initial level of COVID-19 incidence within the simulated community. Our results show that reducing the number of students attending school leads to better health outcomes, and the split cohort option enables part-time in-classroom education while substantially reducing risk. The results of this study can support decisions regarding optimal school reopening strategies that at the population level balance education and the negative health outcomes of COVID-19.\n\nDisclaimerThis work was sponsored by the United States Centers for Disease Control and Prevention. Los Alamos National Laboratory, an affirmative action/equal opportunity employer, is operated by Triad National Security, LLC, for the National Nuclear Security Administration of the United States Department of Energy under contract # 19FED1916814CKC. Approved for public release: LA-UR-20-27982.\n\nThe findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention or Los Alamos National Laboratory.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Timothy C. Germann", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Manhong Z. Smith", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Lori Dauelsberg", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Geoffrey Fairchild", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Terece Turton", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Morgan E. Gorris", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Chrysm Watson Ross", - "author_inst": "University of New Mexico and Los Alamos National Laboratory" - }, - { - "author_name": "James P. Ahrens", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Daniel D. Hemphill", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Carrie Manore", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Sara Y Del Valle", - "author_inst": "Los Alamos National Laboratory" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.10.20210427", "rel_title": "Mathematical Modeling of COVID-19 pandemic in the African continent", @@ -1140425,6 +1143194,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.10.09.20210260", + "rel_title": "Group Testing with Homophily to Curb Epidemics with Asymptomatic Carriers", + "rel_date": "2020-10-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.09.20210260", + "rel_abs": "Contagion happens through heterogeneous interpersonal relations (homophily) which induce contamination clusters. Group testing is increasingly recognized as necessary to fight the asymptomatic transmission of the COVID-19. Still, it is plagued by false negatives. Homophily can be taken into account to design test pools that encompass potential contamination clusters. I show that this makes it possible to overcome the usual information-theoretic limits of group testing, which are based on an implicit homogeneity assumption. Even more interestingly, a multiple-step testing strategy combining this approach with advanced complementary exams for all individuals in pools identified as positive identifies asymptomatic carriers who would be missed even by costly exhaustive individual tests. Recent advances in group testing have brought large gains in efficiency, but within the bounds of the above cited information-theoretic limits, and without tackling the false negatives issue which is crucial for COVID-19. Homophily has been considered in the contagion literature already, but not in order to improve group testing.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Louis-Marie Harpedanne de Belleville", + "author_inst": "Paris School of Economics" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.10.10.20210591", "rel_title": "Predicting mortality of individual COVID-19 patients: A multicenter Dutch cohort", @@ -1142152,57 +1144940,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.08.20208785", - "rel_title": "Rapid and Low-cost Sampling for Detection of Airborne SARS-CoV-2 in Dehumidifier Condensate", - "rel_date": "2020-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.08.20208785", - "rel_abs": "Airborne spread of COVID-19 by infectious aerosol is all but certain. However, easily implemented approaches to assess the actual environmental threat are currently unavailable. We present a simple approach with the potential to rapidly provide information about the prevalence of SARS-CoV-2 in the atmosphere at any location. We used a portable dehumidifier as a readily available and affordable tool to collect airborne virus in the condensate. The dehumidifiers were deployed in selected locations of a hospital ward with patients reporting flu like symptoms which could possibly be due to COVID-19 over three separate periods of one week. Samples were analyzed frequently for both virus envelope protein and SARS-CoV-2 RNA. In several samples across separate deployments, condensate from dehumidifiers tested positive for the presence of SARS-CoV-2 antigens and confirmed using two independent assays. RNA was detected, but not attributable to SARS-CoV-2. Our results point to a facile pool testing method to sample air in any location in the world and assess the presence and concentration of the infectious agent in order to obtain quantitative risk assessment of exposure, designate zones as hot spots and minimize the need for individual testing which may often be time consuming, expensive and laborious.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Parikshit Moitra", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "Maha Alafeef", - "author_inst": "University ofMaryland School of Medicine and University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Ketan Dighe", - "author_inst": "University ofMaryland Baltimore County and University of Maryland School of Medicine" - }, - { - "author_name": "Priyanka Ray", - "author_inst": "University of Maryland Baltimore County and University of Maryland School of Medicine" - }, - { - "author_name": "James Chang", - "author_inst": "University of maryland Medical Center" - }, - { - "author_name": "Sai Sathish Ramamurthy", - "author_inst": "University of Maryland Baltimore County and Sri Sathya Sai Insistute of Higher Learning" - }, - { - "author_name": "Xudong Ge", - "author_inst": "University of Maryland Baltimore County" - }, - { - "author_name": "Dipanjan Pan", - "author_inst": "University of Maryland baltimore County and University of Maryland School of Medicine" - }, - { - "author_name": "Govind Rao", - "author_inst": "UMBC" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.08.20208991", "rel_title": "Covid Pandemic Analysis using Regression", @@ -1142339,6 +1145076,20 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.09.20209999", + "rel_title": "COVID-19 Disease Severity and Determinants among Ethiopian Patients: A study of the Millennium COVID-19 Care Center", + "rel_date": "2020-10-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.09.20209999", + "rel_abs": "BackgroundThe COVID-19 pandemic started a little later in Ethiopia than Europe and most of the initial cases were reported to have a milder disease course and a favorable outcome. This changed as the disease spread into the population and the more vulnerable began to develop severe disease. Understanding the risk factors for severe disease in Ethiopia was needed to provide optimal health care services in a resource limited setting.\n\nObjectiveThe study assessed COVID-19 patients admitted to Millennium COVID-19 Care Center in Ethiopia for characteristics associated with COVID-19 disease severity.\n\nMethodsA cross-sectional study was conducted from June to August 2020 among 686 randomly selected 686 patients. Chi-square test was used to detect the presence of a statistically significant difference in the characteristics of the patients based on disease severity (Mild vs Moderate vs Severe). A multinomial logistic regression model was used to identify risk factors of COVID-19 disease severity where Adjusted Odds ratio (AOR), 95% CIs for AOR and P-values were used for significance testing.\n\nResultsHaving moderate as compared with mild disease was significantly associated with having hypertension (AOR=2.30, 95%CI=1.27,4.18, p-value=0.006), diabetes mellitus (AOR=2.61, 95%CI=1.31,5.19, p-value=0.007 for diabetes mellitus), fever (AOR=6.12, 95%CI=2.94,12.72, p-value=0.0001) and headache (AOR=2.69, 95%CI=1.39,5.22, p-value=0.003). Similarly, having severe disease as compared with mild disease was associated with age group (AOR=4.43, 95%CI=2.49,7.85, p-value=0.0001 for 40-59 years and AOR=18.07, 95%CI=9.29,35.14, p-value=0.0001 for [≥] 60 years), sex (AOR=1.84, 95%CI=1.12,3.03, p-value=0.016), hypertension (AOR=1.97, 95%CI=1.08,3.59, p-value=0.028), diabetes mellitus (AOR=3.93, 95%CI=1.96,7.85, p-value=0.0001), fever (AOR=13.22, 95%CI=6.11, 28.60, p-value=0.0001) and headache (AOR=4.82, 95%CI=2.32, 9.98, p-value=0.0001). In addition, risk factors of severe disease as compared with moderate disease were found to be significantly associated with age group (AOR=4.87, 95%CI=2.85, 8.32, p-value=0.0001 for 40-59 years and AOR=18.91, 95%CI=9.84,36.33, p-value=0.0001 for [≥] 60 years), fever (AOR=2.16, 95%CI=1.29,3.63, p-value=0.004) and headache (AOR=1.79, 95%CI=1.03, 3.11, p-value=0.039).\n\nConclusionsRisk factors associated with severe COVID-19 in Ethiopia are being greater than 60 years old, male, a diagnosis of hypertension, and diabetes mellitus, and the presence of fever and headache. This is consistent with severity indicators identified by WHO and suggests the initial finding of milder disease in Ethiopia may have been because the first people to get COVID-19 in Ethiopia were less than 60 years of age with fewer health problems.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.09.20209601", "rel_title": "Cleaning and Re-Use of cobas(R) 6800/8800 Processing Plates for the SARS-CoV-2 Assay", @@ -1143634,29 +1146385,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.08.20209064", - "rel_title": "Social Distancing with Movement Restrictions and the Effective Replication Number of COVID-19: Multi-Country Analysis Based on Phone Mobility Data", - "rel_date": "2020-10-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.08.20209064", - "rel_abs": "Linking phone mobility data to the effective replication number (Rt) could help evaluation of the impact of social distancing on the coronavirus disease 2019 (COVID-19) spread and estimate the time lag (TL) needed for the effect of movement restrictions to appear. We used a time-series analysis to discover how patterns of five indicators of mobility data relate to changes in Rt of 125 countries distributed over three groups based on Rt-mobility correlation. Group 1 included 71 countries in which Rt correlates negatively with residential and positively with other mobility indicators. Group 2 included 25 countries showing an opposite correlation pattern to Group 1. Group 3 included the 29 remaining countries. We chose the best-fit TL based on forecast and linear regression models. We used linear mixed models to evaluate how mobility indicators and the stringency index (SI) relate with Rt. SI reflects the strictness of governmental responses to COVID-19. With a median of 14 days, TLs varied across countries as well as across groups of countries. There was a strong negative correlation between SI and Rt in most countries belonging to Group 1 as opposed to Group 2. SI (units of 10%) associated with decreasing Rt in Group 1 [{beta} -0.15, 95% CI -0.15 - (-0.14)] and Group 3 [-0.05, -0.07 - (-0.03)], whereas, in Group 2, SI associated with increasing Rt (0.13, 0.11 - 0.16). Mobile phone mobility data could contribute evaluations of the impact of social distancing with movement restrictions on the spread of the COVID-19.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Mounir Ould Setti", - "author_inst": "University of Eastern Finland" - }, - { - "author_name": "Ari Voutilainen", - "author_inst": "University of Eastern Finland" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.10.20210492", "rel_title": "Transmission of SARS-CoV-2 from Children and Adolescents", @@ -1143949,6 +1146677,109 @@ "type": "confirmatory results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.10.10.334458", + "rel_title": "SARS-CoV-2 infects carotid arteries: implications for vascular disease and organ injury in COVID-19", + "rel_date": "2020-10-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.10.334458", + "rel_abs": "Stroke and central nervous system dysfunction are cardinal symptoms in critically ill corona virus disease 19 (COVID-19) patients. In an autopsy series of 32 COVID-19 patients, we investigated whether carotid arteries were infected with SARS-CoV-2 by employing genomic, virologic, histochemical and transcriptomic analyses. We show that SARS-CoV-2 productively infects and modulates vascular responses in carotid arteries. This finding has far reaching implications for the understanding and clinical treatment of COVID-19.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Susanne Pfefferle", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Thomas Guenther", + "author_inst": "Heinrich Pette Institute, Leibniz Institute for Experimental Virology" + }, + { + "author_name": "Victor Puelles", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Fabian Heinrich", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Dominik Noerz", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Manja Czech-Sioli", + "author_inst": "Universitatsklinikum Hamburg-Eppendorf" + }, + { + "author_name": "Alexander Carstens", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Susanne Krasemann", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Milagros Wong", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Lisa Oestereich", + "author_inst": "Bernhard Nocht Institute for Tropical Medicine" + }, + { + "author_name": "Tim Magnus", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Lena Allweiss", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Caroline Edler", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Ann-Sophie Schroeder", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Maura Dandri", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Tobias Huber", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Markus Glatzel", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Klaus Pueschel", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Adam Grundhoff", + "author_inst": "Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology" + }, + { + "author_name": "Marc Luetgehetmann", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Martin Aepfelbacher", + "author_inst": "University Medical Center HAmburg-Eppendorf" + }, + { + "author_name": "Nicole Fischer", + "author_inst": "University Medical Center Hamburg-Eppendorf" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.10.11.335406", "rel_title": "Unsupervised explainable AI for simultaneous molecular evolutionary study of forty thousand SARS-CoV-2 genomes", @@ -1145432,85 +1148263,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.07.20208645", - "rel_title": "Low zinc levels at clinical admission associates with poor outcomes in COVID-19", - "rel_date": "2020-10-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.07.20208645", - "rel_abs": "BackgroundBiomarkers to predict Coronavirus disease-19 (COVID-19) outcome early at infection are urgently needed to improve prognosis and treatment. Zinc balances immune responses and also has a proven direct antiviral action against some viruses. Importantly, zinc deficiency (ZD) is a common condition in elderly and individuals with chronic diseases, two groups with more severe COVID-19 outcomes. We hypothesize that serum zinc content (SZC) influences COVID-19 disease progression and thus might represent a useful biomarker.\n\nMethodsWe run a retrospective observational study with 249 COVID-19 patients admitted in Hospital del Mar. We have studied COVID-19 severity and progression attending to SZC at admission. In parallel we have studied SARS-CoV2 replication in the Vero E6 cell line modifying zinc concentrations.\n\nFindingsOur study demonstrates a correlation between serum zinc levels and COVID-19 outcome. Serum zinc levels lower than 50 {micro}g/dl at admission correlated with worse clinical presentation, longer time to reach stability and higher mortality. Our in vitro results indicate that low zinc levels favor viral expansion in SARS-CoV2 infected cells.\n\nInterpretationSZC is a novel biomarker to predict COVID-19 outcome. We encourage performing randomized clinical trials to study zinc supplementation as potential prophylaxis and treatment with people at risk of zinc deficiency.\n\nFundingSpanish Ministry of Science and Innovation, \"Maria de Maeztu\" Programme for Units of Excellence in R&D and Secretaria dUniversitats i Recerca del Departament dEconomia i Coneixement of the Generalitat de Catalunya. Instituto Carlos III Fondos de Investigaciones Sanitarias (FIS), CIBER on Frailty and Healthy Ageing and FEDER funds", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Marina Vogel", - "author_inst": "Laboratory of Molecular Physiology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain." - }, - { - "author_name": "Marc Tallo-Parra", - "author_inst": "Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain." - }, - { - "author_name": "Victor Herrera-Fernandez", - "author_inst": "Laboratory of Molecular Physiology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain." - }, - { - "author_name": "Gemma Perez-Vilaro", - "author_inst": "Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain." - }, - { - "author_name": "Miguel Chillon", - "author_inst": "Department of Biochemistry and Molecular Biology and Institute of Neurosciences, Edifici H, Universitat Autonoma de Barcelona, E-08193, Bellaterra, Spain." - }, - { - "author_name": "Xavier Nogues", - "author_inst": "Institut Mar d'Investigacions Mediques, Barcelona, Spain; Department of Internal Medicine, Hospital del Mar, Autonomous University of Barcelona, Spain; CIBERFES" - }, - { - "author_name": "Silvia Gomez-Zorrilla", - "author_inst": "Institut Mar d'Investigacions Mediques, Barcelona, Spain; Department of Infectious Diseases, Hospital del Mar, Autonomous University of Barcelona, Spain; CIBERF" - }, - { - "author_name": "Inmaculada Lopez-Montesinos", - "author_inst": "Institut Mar d'Investigacions Mediques, Barcelona, Spain; Department of Infectious Diseases, Hospital del Mar, Autonomous University of Barcelona, Spain; CIBERF" - }, - { - "author_name": "Judit Villar", - "author_inst": "Institut Mar d'Investigacions Mediques, Barcelona, Spain; Department of Infectious Diseases, Hospital del Mar, Autonomous University of Barcelona, Spain; CIBERF" - }, - { - "author_name": "Maria Luisa Sorli-Redo", - "author_inst": "Institut Mar d'Investigacions Mediques, Barcelona, Spain; Department of Infectious Diseases, Hospital del Mar, Autonomous University of Barcelona, Spain; CIBERF" - }, - { - "author_name": "Juan Pablo Horcajada", - "author_inst": "Institut Mar d'Investigacions Mediques, Barcelona, Spain; Department of Infectious Diseases, Hospital del Mar, Autonomous University of Barcelona, Spain; CIBERF" - }, - { - "author_name": "Natalia Garcia-Giralt", - "author_inst": "Institut Mar d'Investigacions Mediques, Barcelona, Spain; Department of Infectious Diseases, Hospital del Mar, Autonomous University of Barcelona, Spain; CIBERF" - }, - { - "author_name": "Julio Pascual", - "author_inst": "Institut Mar d'Investigacions Mediques, Barcelona, Spain; Department of Nephrology, Hospital del Mar, Autonomous University of Barcelona, Spain." - }, - { - "author_name": "Juana Diez", - "author_inst": "Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain." - }, - { - "author_name": "Ruben Vicente", - "author_inst": "Laboratory of Molecular Physiology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain." - }, - { - "author_name": "Robert Guerri-Fernandez", - "author_inst": "Institut Mar d'Investigacions Mediques, Barcelona, Spain; Department of Infectious Diseases, Hospital del Mar, Autonomous University of Barcelona, Spain; CIBERF" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.06.20208025", "rel_title": "Enoxaparin is associated with lower rates of thrombosis, kidney injury, and mortality than Unfractionated Heparin in hospitalized COVID patients", @@ -1145707,6 +1148459,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.10.07.20208595", + "rel_title": "When lockdown policies amplify social inequalities in COVID-19 infections. Evidence from a cross-sectional population-based survey in France.", + "rel_date": "2020-10-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.07.20208595", + "rel_abs": "ObjectivesTo assess social inequalities in the trends in COVID-19 infections following lockdown\n\nDesignA cross-sectional survey conducted among the general population in France in April 2020, during COVID-19 lockdown.\n\nParticipants10 401 participants aged 18-64, from a national cohort who lived in the three metropolitan French regions most affected by the first wave of COVID-19.\n\nMain outcomeThe main outcome was occurrence of possible COVID-19 symptoms, defined as the occurrence of sudden onset of cough, fever, dyspnea, ageusia and/or anosmia, that lasted more than three days in the 15 days before the survey. We used multinomial regression models to identify social and health factors related to possible COVID-19 before and during the lockdown.\n\nResultsIn all, 1,304 (13.0%; 95% CI: 12.0%-14.0%) reported cases of possible COVID-19. The effect of lockdown on the occurrence of possible COVID-19 was different across social hierarchies. The most privileged class individuals saw a significant decline in possible COVID-19 infections between the period prior to lockdown and during the lockdown (from 8.8% to 4.3%, P=0.0001) while the decline was less pronounced among working class individuals (6.9% before lockdown and 5.5% during lockdown, P=0.03). This differential effect of lockdown remained significant after adjusting for other factors including history of chronic disease. The odds of being contaminated during lockdown as opposed to the prior period increased by 57% among working class individuals (OR=1.57; 95% CI: 1.0-2.48). The same was true for those engaged in in-person professional activities during lockdown (OR=1.53; 95% CI: 1.03-2.29).\n\nInterpretationLockdown was associated with social inequalities in the decline in COVID-19 infections, calling for the adoption of preventive policies to account for living and working conditions. Such adoptions are critical to reduce social inequalities related to COVID-19, as working-class individuals also have the highest COVID-19 related mortality, due to higher prevalence of comorbidities.\n\nSection 1: What is already known on this topicSignificant differences in COVID-19 incidence by gender, class and race/ethnicity are recorded in many countries in the world. Lockdown measures implemented throughout the globe have been effective in reducing transmission risks.\n\nSection 2: What this study addsOur study shows that lockdowns impact was socially differentiated and has benefited the working classes the least. Such results underline the need to design COVID-19 preventive policies that take into account living and working conditions, as working-class individuals also have the highest COVID-19 related mortality, due to higher prevalence of comorbidities.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Nathalie BAJOS", + "author_inst": "INSERM" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.10.08.20209510", "rel_title": "Global projections of potential lives saved from COVID-19 through universal mask use", @@ -1147154,65 +1149925,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.07.20207282", - "rel_title": "COVID-19, Type-2 Diabetes, and Associated Health Outcomes in China: Results from a Nationwide Survey of 10,545 Adults", - "rel_date": "2020-10-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.07.20207282", - "rel_abs": "ObjectiveThis study examined the associations between type-2 diabetes (T2DM) and self-reported/familial COVID-19 infection and investigated health-related outcomes among those with diabetes during Chinas nationwide quarantine.\n\nMethodsThe 2020 China COVID-19 Survey was administered anonymously via social media (WeChat) across China. It was completed by 10,545 adults in all of mainland Chinas 31 provinces. The survey consisted of 74 items covering sociodemographic characteristics, preventive measures for COVID-19, lifestyle behaviors, and health-related outcomes during the period of quarantine. Regression models examined associations among study variables, adjusting for covariates.\n\nResultsDiabetes was associated with a six-fold increased risk of reporting COVID-19 infection among respondents or their family members. Among patients with diabetes, individuals who rarely wore masks had double the risk of suspected COVID-19 infection compared with those who always wore masks, with an inverse J-shaped relationship between face mask wearing and suspected COVID-19 infection. People with T2DM tended to have both poor knowledge of COVID-19 and poor compliance with preventive measures, despite perceiving a high risk of personal infection (40.0% among respondents reporting T2DM and 8.0% without T2DM). Only 54-55% of these respondents claimed to consistently practice preventive measures, including wearing face masks. Almost 60% of those with T2DM experienced food or medication shortages during the quarantine period, which was much higher than those without T2DM. Importantly, respondents who experienced medication shortages reported a 63% higher COVID-19 infection rate.\n\nConclusionsT2DM was associated with an increased risk of self-reported personal and family member COVID-19 infection, which is mitigated by consistent use of face masks.\n\nFundingThe project is supported in part by research grants from the China Medical Board (Grant number: 16-262), the National Key Research and Development Program of China (Grant Number: 2017YFC0907200 & 2017YFC0907201), the University Alliance of the Silk Road (Grant number: 2020LMZX002), and Xian Jiaotong University Global Health Institute.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSDuring the COVID-19 pandemic, it has become increasingly clear that the risk factors for initial infection and subsequent poor health outcomes include, but are not limited to, social vulnerability, economic status, older age, and obesity. While community-wide masking has been recommended by the World Health Organization to control COVID-19, its overall effectiveness has not been clearly evaluated.\n\nAdded value of this studyThrough an anonymous survey disseminated and promoted through WeChat, the largest social media platform in China, we sought to understand the impact of COVID-19 on the health, wellbeing, and health-related behaviors of adults in China. Specifically, this study examined how individuals with chronic diseases managed the threat, including their COVID-19 related knowledge, attitudes, and adherence to preventive measures such as wearing face masks, and their disease-related self-care.\n\nImplications of the available evidenceThis study demonstrates that type-2 diabetes mellitus is associated with an increased risk of COVID-19 infection, which is mitigated by consistent use of face masks.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Zumin Shi", - "author_inst": "Human Nutrition Department, College of Health Sciences, QU Health, Qatar University, Doha, Qatar" - }, - { - "author_name": "Alice Yan", - "author_inst": "Center for Advancing Population Science, Division of General Internal Medicine, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA" - }, - { - "author_name": "Paul Zimmet", - "author_inst": "Department of Diabetes, Central Clinical School, Monash University, Melbourne, Australia" - }, - { - "author_name": "Xiaoming Sun", - "author_inst": "Global Health Institute, School of Public Health, Xian Jiaotong University Health Science Center, Xian, China" - }, - { - "author_name": "Nayla Cristina do Vale Moreira", - "author_inst": "Faculty of Medicine, Federal University of Ceara (FAMED-UFC), Brazil" - }, - { - "author_name": "Lawrence J Cheskin", - "author_inst": "Department of Nutrition and Food Studies, George Mason University, Fairfax, VA 220030, USA" - }, - { - "author_name": "Liming Wang", - "author_inst": "National Center for Chronic and Non-communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China" - }, - { - "author_name": "Weidong Qu", - "author_inst": "Centers for Water and Health, Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fu" - }, - { - "author_name": "Hong Yan", - "author_inst": "School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China" - }, - { - "author_name": "Akhtar Hussain", - "author_inst": "Faculty of Health Sciences, Nord University, Norway; International Diabetes Federation. 166 Chaussee de La Hulpe B-1170, Brussels, Belgium" - }, - { - "author_name": "Youfa Wang", - "author_inst": "Global Health Institute, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.07.20208280", "rel_title": "A high-throughput microfluidic nano-immunoassay for detecting anti-SARS-CoV-2 antibodies in serum or ultra-low volume dried blood samples", @@ -1147417,6 +1150129,20 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.10.08.330456", + "rel_title": "idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates", + "rel_date": "2020-10-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.08.330456", + "rel_abs": "idCOV is a phylogenetic pipeline for quickly identifying the clades of SARS-CoV-2 virus isolates from raw sequencing data based on a selected clade-defining marker list. Using a public dataset, we show that idCOV can make equivalent calls as annotated by Nextstrain.org on all three common clade systems using user uploaded FastQ files directly. Web and equivalent command-line interfaces are available. It can be deployed on any Linux environment, including personal computer, HPC and the cloud. The source code is available at https://github.com/xz-stjude/idcov. A documentation for installation can be found at https://github.com/xz-stjude/idcov/blob/master/README.md.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.10.08.332544", "rel_title": "Neutralizing antibodies from early cases of SARS-CoV-2 infection offer cross-protection against the SARS-CoV-2 D614G variant.", @@ -1148732,125 +1151458,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.05.20206730", - "rel_title": "Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya", - "rel_date": "2020-10-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.05.20206730", - "rel_abs": "We generated 274 SARS-CoV-2 genomes from samples collected during the early phase of the Kenyan pandemic. Phylogenetic analysis identified 8 global lineages and at least 76 independent SARS-CoV-2 introductions into Kenyan coast. The dominant B.1 lineage (European origin) accounted for 82.1% of the cases. Lineages A, B and B.4 were detected from screened individuals at the Kenya-Tanzania border or returning travellers but did not lead to established transmission. Though multiple lineages were introduced in coastal Kenya within three months following the initial confirmed case, none showed extensive local expansion other than cases characterised by lineage B.1, which accounted for 45 of the 76 introductions. We conclude that the international points of entry were important conduits of SARS-CoV-2 importations. We speculate that early public health responses prevented many introductions leading to established transmission, but nevertheless a few undetected introductions were sufficient to give rise to an established epidemic.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "George Githinji", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Zaydah R deLaurent", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Khadija Said Mohamed", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Donwilliams O Omuoyo", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Peter M Macharia", - "author_inst": "Population Health Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya" - }, - { - "author_name": "John M Morobe", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Edward Otieno", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Samson M Kinyanjui", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Ambrose Agweyu", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Eric Maitha", - "author_inst": "Department of Health, Kilifi county" - }, - { - "author_name": "Ben Kitole", - "author_inst": "Department of Health, Kilifi county" - }, - { - "author_name": "Thani Suleiman", - "author_inst": "Department of Health, Mombasa county" - }, - { - "author_name": "Mohamed Mwakinangu", - "author_inst": "Department of Health, Kwale county" - }, - { - "author_name": "John Nyambu", - "author_inst": "Department of Health, Taita Taveta county" - }, - { - "author_name": "John Otieno", - "author_inst": "Department of Health, Lamu county" - }, - { - "author_name": "Barke Salim", - "author_inst": "Department of Health, Tana River county" - }, - { - "author_name": "Kadondi Kasera", - "author_inst": "Ministry of Health, Government of Kenya, Nairobi, Kenya" - }, - { - "author_name": "John Kiiru", - "author_inst": "Ministry of Health, Government of Kenya, Nairobi, Kenya" - }, - { - "author_name": "Rashid Aman", - "author_inst": "Ministry of Health, Government of Kenya, Nairobi, Kenya" - }, - { - "author_name": "Edwine Barasa", - "author_inst": "Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya" - }, - { - "author_name": "George Warimwe", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Philip Bejon", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Benjamin Tsofa", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Lynette Isabella Ochola-Oyier", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "D James Nokes", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Charles N Agoti", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.02.20205674", "rel_title": "Mental health symptoms in a cohort of hospital healthcare workers following the first peak of the Covid-19 pandemic in the United Kingdom.", @@ -1149003,6 +1151610,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2020.10.05.20205872", + "rel_title": "SARS-CoV-2 RNA detection using pooling of self-collected samples: Simple protocols may foster asymptomatic surveillance", + "rel_date": "2020-10-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.05.20205872", + "rel_abs": "1BackgroundSurveillance of COVID infection and isolation of infected individuals is one of the available tools to control the spread of SAR-CoV-2. Asymptomatic and pre symptomatic are responsible for substantial transmission. RNA or antigen tests are necessary to identify non-symptomatic individuals. We tested the feasibility of using samples pooling offering different collection alternatives (swab/throat wash/saliva) to volunteers of a public health institute.\n\nMethodsWe evaluated pool samples from frozen material from previously tested samples and a prospective collection from asymptomatic volunteers. Some collections were paired for comparison. Pools and some individual samples were extracted with QIAamp Viral RNA Mini Kit (Qiagen, USA) and/or Lucigen Quick Extract DNA extraction solution (BioSearch, USA) and submitted to rtPCR (Allplex, Seegene, Korea).\n\nResultsA total of 240 samples from 130 new collections and 37 samples with known result were evaluated. Pool CT was generally higher than individual samples. Lucigen extraction showed higher CT, including false negative results for samples with high CT at Qiagen extraction. Paired Swab and TW samples showed comparable results. No volunteer from negative pools reported any symptom in the 2-3 days after collection.\n\nConclusionsClinical samples pooling to detect SARS-CoV-2 RNA is feasible and an economical way to test for COVID-19, especially in surveillance strategies targeting more infectiousness, higher viremia individuals. The use of Lucigen reagents show lower sensibility that may lead to false negative results with lower viremia samples. Combining throat wash with saliva may provide and interesting self-collection alternative, but more comparative work is needed.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Giselle Ibette Silva Lopez Lopes", + "author_inst": "Adolfo Lutz Institute" + }, + { + "author_name": "Rita de Cassia Compagnoli Carmona", + "author_inst": "Adolfo Lutz Institution" + }, + { + "author_name": "Valeria Oliveira Silva", + "author_inst": "Pos Graduacao da Coordenadoria de Controle de Doencas do Estado de Sao Paulo" + }, + { + "author_name": "Cintia Mayumi Ahagon", + "author_inst": "Pos Graduacao da Coordenadoria de Controle de Doencas do Estado de Sao Paulo" + }, + { + "author_name": "Lincoln Spinazola do Prado", + "author_inst": "Adolfo Lutz Institute" + }, + { + "author_name": "Fabiana Cristina Pereira dos Santos", + "author_inst": "Adolfo Lutz Institute" + }, + { + "author_name": "Daniela Bernardes Borges da Silva", + "author_inst": "Adolfo Lutz Institute" + }, + { + "author_name": "Wiliam Nery Ribeiro", + "author_inst": "Adolfo Lutz Institue" + }, + { + "author_name": "Elaine Monteiro Matshuda", + "author_inst": "Pos Graduacao da Coordenadoria de Controle de Doencas do Estado de Sao Paulo" + }, + { + "author_name": "Auldrey Cilli", + "author_inst": "Adolfo Lutz Institute" + }, + { + "author_name": "Ana Maria Sardinha Afonso", + "author_inst": "Adolfo Lutz Institute" + }, + { + "author_name": "Margarete Aparecida Benaga Pinho", + "author_inst": "Adolfo Lutz Institute" + }, + { + "author_name": "Maria do Carmo Sampaio Tavare Timnetsky", + "author_inst": "Adolfo Lutz Institute" + }, + { + "author_name": "Luis Fernando de Macedo Brigido", + "author_inst": "Instituto Adolfo Lutz" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.05.20206664", "rel_title": "Antibody reactivity to SARS-CoV-2 in adults from the Vancouver metropolitan area, Canada", @@ -1150470,41 +1153148,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2020.10.04.20206680", - "rel_title": "Serological testing in addition to PCR screening for the re-opening of American colleges and universities: potential for cost-savings without compromising pandemic mitigation", - "rel_date": "2020-10-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.04.20206680", - "rel_abs": "ImportanceThe addition of a serological testing could reduce the overall testing costs of a PCR-based SARS-CoV-2 testing reopening plan for colleges/universities in the United States, without compromising the efficacy of the testing plan.\n\nObjectivesTo determine whether a college/university reopening SARS-CoV-2 testing plan that includes serological testing can be cost-saving compared to a PCR-only testing.\n\nDesign, Setting, and ParticipantsWe assessed costs of serological testing in addition to PCR testing under various scenarios of university sizes (2000, 10,000, and 40,000) and epidemic conditions (initial antibody prevalence 2.5-15%; cumulative SARS-CoV-2 incidence during the school year 5-30%) of SARS-CoV-2 in the United States. We estimated total testing costs and relative percentage of cost-savings of different screening (i.e. targeted/ universal) and testing (i.e. in-sourcing/out-sourcing) scenarios between September 2020-May 2021.\n\nMain Outcomes and MeasuresTesting costs of serological testing and PCR testing, Relative percentage of cost saving by including serology testing in addition to PCR testing.\n\nResultsIncluding baseline serology testing alongside routine regular PCR testing can reduce total test volumes and related costs throughout the school year. While the total testing cost is likely much lower if regular PCR testing is insourced compared to outsourced ($5 million vs $34 million for university size 10,000), including serologic testing could achieve the up to 20% cost-savings relative to PCR testing alone. The insourcing of serological testing when PCR testing is insourced can achieve greater cost-savings under high initial antibody prevalence (>5%) and cumulative incidence throughout the school year (>10%) at medium and large sized universities. If PCR testing is outsourced, however, the inclusion of serological testing becomes always preferred in most university sizes and epidemic conditions.\n\nConclusions and RelevanceWhile regular PCR testing alone is the preferred strategy for containing epidemics, including serology testing may help achieve cost-savings if outbreaks are anticipated, or if baseline seropositivity is high.\n\nKey Points (96/100)O_ST_ABSQuestionC_ST_ABSCan the addition of a serological testing reduce the overall testing costs of a PCR-based SARS-CoV-2 testing reopening plan for universities in the United States?\n\nFindingsThis costing study suggested that inclusion of serological testing in addition to outsourced PCR testing as part of a university re-opening strategy could achieve cost savings of up to 20%. The amount of savings, or additional costs, is dependent on insourcing or outsourcing of testing, epidemic conditions and university size.\n\nMeaningThe relative cost-savings depend strongly on whether PCR and/or serology are being insourced or outsourced, university sizes and cumulative incidence.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Youngji Jo", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Ruby Singh", - "author_inst": "Boston University" - }, - { - "author_name": "Gabriella Rao", - "author_inst": "Boston University" - }, - { - "author_name": "Sandro Galea", - "author_inst": "Boston University" - }, - { - "author_name": "Brooke E Nichols", - "author_inst": "Boston University School of Public Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.10.05.20206920", "rel_title": "Development of a customised data management system for a COVID-19-adapted colorectal cancer pathway", @@ -1150633,6 +1153276,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.10.03.20206193", + "rel_title": "Development and comparison of a novel multiple cross displacement amplification (MCDA) assay with other nucleic acid amplification methods for SARS-CoV-2 detection", + "rel_date": "2020-10-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.03.20206193", + "rel_abs": "The development of alternative isothermal amplification assays including multiple cross displacement amplification (MCDA) may address speed and portability limitations of real-time PCR (rt-PCR) methods for SARS-CoV-2 detection. We developed a novel SARS-CoV-2 MCDA assay and compared its speed and sensitivity to loop-mediated isothermal amplification (LAMP) and rt-PCR. Two MCDA assays targeting SARS-CoV-2 N gene and ORF1ab was designed. The fastest time to detection and sensitivity of MCDA was compared to LAMP and rt-PCR using DNA standards and transcribed RNA. For N gene, MCDA was faster than LAMP and rt-PCR by 10 and 20 minutes, respectively with fastest time to detection at 5.2 minutes. rt-PCR had highest sensitivity with limit of detection at 10 copies/{micro}l compared with MCDA (100 copies/{micro}l) and LAMP (500 copies/{micro}l). For ORF1ab, MCDA and LAMP had similar speed with fastest time to detection at 9.7 and 8.4 minutes, respectively. LAMP was more sensitive for ORF1ab detection with 50 copies/{micro}l compared to MCDA (500 copies/{micro}l). In conclusion, different nucleic acid amplification methods provide different advantages. MCDA is the fastest nucleic acid amplification method for SARS-CoV-2 while rt-PCR is the most sensitive. These advantages should be considered when determining the most suitable nucleic acid amplification methods for different applications.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Laurence Don Wai Luu", + "author_inst": "The University of New South Wales" + }, + { + "author_name": "Michael J Payne", + "author_inst": "The University of New South Wales" + }, + { + "author_name": "Xiaomei Zhang", + "author_inst": "The University of New South Wales" + }, + { + "author_name": "Lijuan Luo", + "author_inst": "The University of New South Wales" + }, + { + "author_name": "Ruiting Lan", + "author_inst": "The University of New South Wales" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.04.20206466", "rel_title": "Rapid SARS-CoV-2 antigen detection by immunofluorescence - a new tool to detect infectivity", @@ -1151800,85 +1154478,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.03.20206128", - "rel_title": "Characteristics and outcomes of hospitalized adults with COVID-19 in Nepal: a multicenter, prospective cohort study", - "rel_date": "2020-10-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.03.20206128", - "rel_abs": "IntroductionThere is limited data on clinical course and outcomes of hospitalized adults with COVID-19 in Nepal. Thus, it is imperative to characterize the features of this disease in the domestic context.\n\nMethodologyWe identified all adult patients with laboratory-confirmed COVID-19 admitted to five different hospitals in Nepal from June 15 to July 15, 2020. We collected epidemiological, socio-cultural and clinicopathologic data, and stratified the patients based on their symptom status.\n\nResultsThe study included 220 patients with an overall median age of 31.5 (25-37) years, and 181 (82.3%) were males. 159 (72.3%) were asymptomatic, and 163 (74.1%) were imported cases. Of 217 patients with the available data, 110 (50.7%) reported their annual household income less than 2000 US dollars, and 122 (56.2%) practiced Pranayama (yogic rhythmic breathing techniques) regularly. Eight patients (3.6%) required supplemental oxygen and two patients (0.9%) died. None of the patients who practiced Pranayama regularly required supplemental oxygen. Compared to asymptomatic patients, symptomatic patients had greater proportion of females (31.1% vs. 12.6%, p=0.001), imported cases (85.2% vs. 69.8%, p=0.02), illiterates (26.8% vs. 12.1%, p=0.01), alcohol users (43.3% vs. 24.5%, p=0.01), patients feeling stigmatized by society (45.8% vs. 22.6%, p=0.001), and had higher platelet count (253x 109/L vs. 185x109/L, p=0.02).\n\nConclusionsMost cases were imported, asymptomatic young males, with very few deaths. Pranayama practice was associated with protection against severe COVID-19, but more data is needed to substantiate this. The association of platelets count with symptom status in the Nepalese population needs further exploration.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Ashok Chaudhary", - "author_inst": "Seti Provincial Hospital, Dhangadhi, Nepal" - }, - { - "author_name": "Uday Narayan Singh", - "author_inst": "Narayani Hospital,Birgunj, Nepal" - }, - { - "author_name": "Pramod Paudel", - "author_inst": "Bharatpur Hospital, Bharatpur, Nepal" - }, - { - "author_name": "Niresh Thapa", - "author_inst": "Karnali Academy of Health Sciences, Jumla, Nepal" - }, - { - "author_name": "Kamal Khadka", - "author_inst": "Rapti Provincial Hospital, Tulsipur, Nepal" - }, - { - "author_name": "Prameshwar Kumar Sah", - "author_inst": "Narayani Hospital, Birgunj, Nepal" - }, - { - "author_name": "Sher Bahadur Kamar", - "author_inst": "Seti Provincial Hospital, Dhangadhi, Nepal" - }, - { - "author_name": "Jagadish Joshi", - "author_inst": "Seti Provincial Hospital, Dhangadhi, Nepal" - }, - { - "author_name": "Kamar Hasan Ansari", - "author_inst": "Seti Provincial Hospital, Dhangadhi, Nepal" - }, - { - "author_name": "Shree Ram Tiwari", - "author_inst": "Bharatpur Hospital, Bharatpur, Nepal" - }, - { - "author_name": "Sarbesh Sharma", - "author_inst": "Rapti Provincial Hospital, Tulsipur, Nepal" - }, - { - "author_name": "Sanjay Kumar Jaiswal", - "author_inst": "Anamnagar Diagnostic Center and Polyclinic, Kathmandu, Nepal" - }, - { - "author_name": "Ramesh Joshi", - "author_inst": "Seti Provincial Hospital, Dhangadhi, Nepal" - }, - { - "author_name": "Samikchya Baskota", - "author_inst": "Anamnagar Diagnostic Center and Polyclinic, Kathmandu, Nepal" - }, - { - "author_name": "Arjun Prasad Tiwari", - "author_inst": "Karnali Academy of Health Sciences, Jumla, Nepal" - }, - { - "author_name": "Hem Raj Pandey", - "author_inst": "Seti Provincial Hospital, Dhangadhi, Nepal" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.06.20207662", "rel_title": "Which factors should be included in triage? An online survey of the attitudes of the UK general public to pandemic triagedilemmas", @@ -1152035,6 +1154634,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.01.20204214", + "rel_title": "SARS-CoV-2 Inactivation Potential of Metal Organic Framework Induced Photocatalysis", + "rel_date": "2020-10-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.01.20204214", + "rel_abs": "As the world recovers from the lockdown imposed by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic, returning to shared indoor spaces is considered a formidable risk. It is now clear that transmission of SARS-CoV-2 is driven by respiratory microdroplets expelled by infected persons, which can become suspended in the air. Several layering technologies are being explored to mitigate indoor transmission in the hopes of re-opening business, schools and transportation systems. Here we coupled the water adsorptive and photocatalytic capacity of novel Metal Organic Frameworks (MOFs) to demonstrate the capture and inactivation of SARS-CoV-2. Discussion is given on the methods of analysis and the differences between the photocatalytic activity of several MOFs, and the difference between MOF induced photocatalysis and ultra violet photolysis of SARS-CoV-2. Our results are intended to provide support to industry looking for alternative methods secure indoor spaces.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jason Mathew Ornstein", + "author_inst": "framergy, Inc., College Station, TX, USA" + }, + { + "author_name": "Ray Ozdemir", + "author_inst": "framergy, Inc., College Station, TX, USA" + }, + { + "author_name": "Anne Boehme", + "author_inst": "framergy, Inc., College Station, TX, USA" + }, + { + "author_name": "Christian Serre", + "author_inst": "Institut des Materiaux Poreux de Paris, ESPCI Paris, Ecole Normale Superieure, PSL University, France" + }, + { + "author_name": "Farid Nouar", + "author_inst": "Institut des Materiaux Poreux de Paris, ESPCI Paris, Ecole Normale Superieure, PSL University, France" + }, + { + "author_name": "Joshua Santarpia", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "Vicki L. Herrera", + "author_inst": "National Strategic Research Institute, Omaha, NE, USA" + }, + { + "author_name": "Daniel N. Ackerman", + "author_inst": "National Strategic Research Institute, Omaha, NE, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.06.20207589", "rel_title": "Epidemic characteristics of respiratory viruses in hospitals in a Chinese city during the SARS-CoV-2 epidemic", @@ -1153338,41 +1155984,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.04.325266", - "rel_title": "Reference ontology and database annotation of the COVID-19 Open Research Dataset (CORD-19)", - "rel_date": "2020-10-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.04.325266", - "rel_abs": "The COVID-19 Open Research Dataset (CORD-19) was released in March 2020 to allow the machine learning and wider research community to develop techniques to answer scientific questions on COVID-19. The dataset consists of a large collection of scientific literature, including over 100,000 full text papers. Annotating training data to normalise variability in biological entities can improve the performance of downstream analysis and interpretation. To facilitate and enhance the use of the CORD-19 data in these applications, in late March 2020 we performed a comprehensive annotation process using named entity recognition tool, TERMite, along with a number of large reference ontologies and vocabularies including domains of genes, proteins, drugs and virus strains. The additional annotation has identified and tagged over 45 million entities within the corpus made up of 62,746 unique biomedical entities. The latest updated version of the annotated data, as well as older versions, is made openly available under GPL-2.0 License for the community to use at: https://github.com/SciBiteLabs/CORD19", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Oliver Giles", - "author_inst": "SciBite" - }, - { - "author_name": "Rachael Huntley", - "author_inst": "SciBite" - }, - { - "author_name": "Anneli Karlsson", - "author_inst": "SciBite" - }, - { - "author_name": "Jane Lomax", - "author_inst": "SciBite" - }, - { - "author_name": "James Malone", - "author_inst": "SciBite" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.10.03.20205278", "rel_title": "Validation of self-collected buccal swab and saliva as a diagnostic tool for COVID-19", @@ -1153605,6 +1156216,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.02.20205567", + "rel_title": "Impact of pathogen reduction technologies on immunological propertiesof the COVID-19 convalescent plasma", + "rel_date": "2020-10-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.02.20205567", + "rel_abs": "Background and ObjectivesCOVID-19 convalescent plasma is an experimental treatment against SARS-CoV-2. The aim of this study is to assess the impact of different pathogen reduction methods on the levels and virus neutralizing activity of the specific antibodies against SARS-CoV2 in convalescent plasma.\n\nMaterials and MethodsA total of 140 plasma doses collected by plasmapheresis from COVID-19 convalescent donors were subjected to pathogen reduction by three methods: methylene blue (M)/visible light, riboflavin (R)/UVB, and amotosalen (A)/UVA. To conduct a paired comparison, individual plasma doses were divided into 2 samples that were subjected to one of these methods. The titres of SARS-CoV2 neutralizing antibodies (NtAbs) and levels of specific immunoglobulins to RBD, S- and N- proteins of SARS-CoV-2 were measured before and after pathogen reduction.\n\nResultsThe methods reduced NtAbs titres differently: among units with the initial titre 80 or above, 81% of units remained unchanged and 19% decreased by one step after methylene blue; 60% were unchanged and 40% decreased by one step after amotosalen; after riboflavin 43% were unchanged and 50% (7% respectively) had a one- step (two-step respectively) decrease. Paired two-sample comparisons (M vs A, M vs R and A vs R) revealed that the largest statistically significant decrease in quantity and activity of the specific antibodies resulted from the riboflavin treatment.\n\nConclusionPathogen reduction with methylene blue or with amotosalen provides the greater likelihood of preserving the immunological properties of the COVID-19 convalescent plasma compared to riboflavin.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Alexander I Kostin", + "author_inst": "Sklifosovsky Research Institute for Emergency Medicine, Moscow, Russia" + }, + { + "author_name": "Maria N Lundgren", + "author_inst": "Department of Clinical Immunology and Transfusion Medicine, Office of Medical Services, Region Skane, Lund, Sweden" + }, + { + "author_name": "Andrey Y Bulanov", + "author_inst": "Sklifosovsky Research Institute for Emergency Medicine, Moscow, Russia" + }, + { + "author_name": "Elena A Ladygina", + "author_inst": "Sklifosovsky Research Institute for Emergency Medicine, Moscow, Russia" + }, + { + "author_name": "Karina Chirkova", + "author_inst": "Sklifosovsky Research Institute for Emergency Medicine, Moscow, Russia" + }, + { + "author_name": "Alexander Gintsburg", + "author_inst": "National Research Center of Epidemiology and Microbiology N.F. Gamaleya of the Ministry of Health of the Russian Federation, Moscow, Russia" + }, + { + "author_name": "Denis Logunov", + "author_inst": "National Research Center of Epidemiology and Microbiology N.F. Gamaleya of the Ministry of Health of the Russian Federation, Moscow, Russia" + }, + { + "author_name": "Inna Dolzhikova", + "author_inst": "National Research Center of Epidemiology and Microbiology N.F. Gamaleya of the Ministry of Health of the Russian Federation, Moscow, Russia" + }, + { + "author_name": "Dmitry Shcheblyakov", + "author_inst": "National Research Center of Epidemiology and Microbiology N.F. Gamaleya of the Ministry of Health of the Russian Federation, Moscow, Russia" + }, + { + "author_name": "Natalya V Borovkova", + "author_inst": "Sklifosovsky Research Institute for Emergency Medicine, Moscow, Russia" + }, + { + "author_name": "Mikhail A Godkov", + "author_inst": "Sklifosovsky Research Institute for Emergency Medicine, Moscow, Russia" + }, + { + "author_name": "Alexey I Bazhenov", + "author_inst": "Sklifosovsky Research Institute for Emergency Medicine, Moscow, Russia" + }, + { + "author_name": "Valery Shustov", + "author_inst": "0000-0002-9624-5883" + }, + { + "author_name": "Alina Bogdanova", + "author_inst": "Sklifosovsky Research Institute for Emergency Medicine, Moscow, Russia" + }, + { + "author_name": "Alina Kamalova", + "author_inst": "N.I. Pirogov Federal Russian National Research Medical University, Moscow, Russia" + }, + { + "author_name": "Vladimir Ganchin", + "author_inst": "Autonomous non-commercial organization Center of Analytical Development of the Social Sector, Moscow, Russia" + }, + { + "author_name": "Eugene Dombrovskiy", + "author_inst": "Autonomous non-commercial organization Center of Analytical Development of the Social Sector, Moscow, Russia" + }, + { + "author_name": "Stanislav Volkov", + "author_inst": "Centre for Mathematical Sciences, Lund University, Lund, Sweden" + }, + { + "author_name": "Nataliya E Drozdova", + "author_inst": "Sklifosovsky Research Institute for Emergency Medicine, Moscow, Russia" + }, + { + "author_name": "Sergey S Petrikov", + "author_inst": "Sklifosovsky Research Institute for Emergency Medicine, Moscow, Russia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.02.20206045", "rel_title": "Safety and efficacy of pharmacotherapy used for the management of COVID 19: A systematic review and meta-analysis of randomized control trials", @@ -1155204,77 +1157910,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.01.20205310", - "rel_title": "Prognostic accuracy of MALDI mass spectrometric analysis of plasma in COVID-19", - "rel_date": "2020-10-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.01.20205310", - "rel_abs": "PurposeSARS-CoV-2 infection poses a global public health problem. There is a critical need for improvements in the noninvasive prognosis of COVID-19. We hypothesized that matrix-assisted laser desorption ionization mass spectrometry (MALDI-TOF MS) analysis combined with bottom-up proteomic analysis of plasma proteins might identify features to predict high and low risk cases of COVID-19.\n\nPatients and MethodsWe used MALDI-TOF MS to analyze plasma small proteins and peptides isolated using C18 micro-columns from a cohort containing a total of 117 cases of high (hospitalized) and low risk (outpatients) cases split into training (n = 88) and validation sets (n= 29). The plasma protein/peptide fingerprint obtained was used to train the algorithm before validation using a blinded test cohort.\n\nResultsSeveral sample preparation, MS and data analysis parameters were optimized to achieve an overall accuracy of 85%, sensitivity of 90%, and specificity of 81% in the training set. In the blinded test set, this signature reached an overall accuracy of 93.1%, sensitivity of 87.5%, and specificity of 100%. From this signature, we identified two distinct regions in the MALDI-TOF profile belonging to the same proteoforms. A combination of 1D SDS-PAGE and quantitative bottom-up proteomic analysis allowed the identification of intact and truncated forms of serum amyloid A-1 and A-2 proteins. Conclusions: We found a plasma proteomic profile that discriminates against patients with high and low risk COVID-19. Proteomic analysis of C18-fractionated plasma may have a role in the noninvasive prognosis of COVID-19. Further validation will consolidate its clinical utility.\n\nKey messageO_ST_ABSWhat is the key question?C_ST_ABSDo individuals infected with SARS-CoV-2 harboring different degree of disease severity have a plasma protein profile that differentiate them and predict the COVID-19 outcome?\n\nWhat is the bottom line?In a series of 117 patients with COVID-19 divided in hospitalized (60) and outpatients (57), differential expression of serum amyloid A-1 (SAA1) and A-2 (SAA2) predict their outcome.\n\nWhy read on?The high mortality rate in SARS-CoV-2 infected individuals requires accurate markers for predicting COVID-19 severity. Plasma levels of SAA1 and SAA2 indicate higher risk of hospitalization and can be used to improve COVID-19 monitoring and therapy.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Lucas Cardoso Lazari", - "author_inst": "Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Fabio de Rose Ghilardi", - "author_inst": "Instituto de Medicina Tropical, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Livia Rosa-Fernandes", - "author_inst": "Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Diego M Assis", - "author_inst": "Bruker do Brasil, Atibaia, Sao Paulo, Brazil" - }, - { - "author_name": "Jose Carlos Nicolau", - "author_inst": "Heart Institute (InCor), University of Sao Paulo Medical School, Sao Paulo, Brazil" - }, - { - "author_name": "Veronica Feijoli Santiago", - "author_inst": "Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Talia F Dalcoquio", - "author_inst": "Heart Institute (InCor), University of Sao Paulo Medical School, Sao Paulo, Brazil" - }, - { - "author_name": "Claudia Blanes Angeli", - "author_inst": "Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Adriadne Justi Bertolin", - "author_inst": "Heart Institute (InCor), University of Sao Paulo Medical School, Sao Paulo, Brazil" - }, - { - "author_name": "Claudio Romero Farias Marinho", - "author_inst": "Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Carsten Wrenger", - "author_inst": "Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Edison Luiz Durigon", - "author_inst": "Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Rinaldo Focaccia Siciliano", - "author_inst": "Heart Institute (InCor), University of Sao Paulo Medical School, Sao Paulo, Brazil" - }, - { - "author_name": "Giuseppe Palmisano", - "author_inst": "Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.30.20204719", "rel_title": "Corticosteroid pulses for hospitalized patients with COVID-19. Effects on mortality and in-hospital stay.", @@ -1155459,6 +1158094,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.09.30.20199828", + "rel_title": "Exhaled aerosol increases with COVID-19 infection, and risk factors of disease symptom severity", + "rel_date": "2020-10-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.30.20199828", + "rel_abs": "Coronavirus disease-19 (COVID-19) transmits by droplets generated from surfaces of airway mucus during processes of respiration within hosts infected by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) virus. We studied respiratory droplet generation and exhalation in human and nonhuman primate subjects with and without COVID-19 infection to explore whether SARS-CoV-2 infection, and other changes in physiological state, translates into observable evolution of numbers and sizes of exhaled respiratory droplets in healthy and diseased subjects. In our observational cohort study of the exhaled breath particles of 74 healthy human subjects, and in our experimental infection study of eight nonhuman primates infected by aerosol with SARS-CoV-2, we found that exhaled aerosol particles increase one to three orders of magnitude with aging, high BMI, and COVID-19 infection. These variances appear to be related to changes in airway mucus surface composition and the propensity for mucus surfaces to breakup into small droplets during acts of breathing. We also observed that 20% of those participating in our human study accounted for 80% of the overall exhaled bioaerosol, reflecting a bioaerosol distribution analogous to a classical 20:80 super spreader distribution.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "David A Edwards", + "author_inst": "Sensory Cloud" + }, + { + "author_name": "Dennis Ausiello", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Robert Langer", + "author_inst": "MIT" + }, + { + "author_name": "Jonathan Salzman", + "author_inst": "Sensory Cloud" + }, + { + "author_name": "Tom Devlin", + "author_inst": "Sensory Cloud" + }, + { + "author_name": "Brandon J. Beddingfield", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Alyssa C. Fears", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Lara A. Doyle-Meyers", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Rachel K. Redmann", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Stephanie Z. Killeen", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "NIcholas J. Maness", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "CHAD J ROY", + "author_inst": "Tulane University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.10.01.20205112", "rel_title": "COVID-19 Pandemic in University Hospital: Is There an Effect on The Medical Interns?", @@ -1156946,65 +1159644,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.09.30.317818", - "rel_title": "SARS-CoV-2 Spike protein promotes hyper-inflammatory response that can be ameliorated by Spike-antagonistic peptide and FDA-approved ER stress and MAP kinase inhibitors in vitro", - "rel_date": "2020-10-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.30.317818", - "rel_abs": "SARS-CoV-2 infection causes an inflammatory cytokine storm and acute lung injury. Currently there are no effective antiviral and/or anti-inflammatory therapies. Here we demonstrate that 2019 SARS-CoV-2 spike protein subunit 1 (CoV2-S1) induces high levels of NF-{kappa}B activations, production of pro-inflammatory cytokines and mild epithelial damage, in human bronchial epithelial cells. CoV2-S1-induced NF-{kappa}B activation requires S1 interaction with human ACE2 receptor and early activation of endoplasmic reticulum (ER) stress, and associated unfolded protein response (UPR), and MAP kinase signalling pathways. We developed an antagonistic peptide that inhibits S1-ACE2 interaction and CoV2-S1-induced productions of pro-inflammatory cytokines. The existing FDA-approved ER stress inhibitor, 4-phenylburic acid (4-PBA), and MAP kinase inhibitors, trametinib and ulixertinib, ameliorated CoV2-S1-induced inflammation and epithelial damage. These novel data highlight the potentials of peptide-based antivirals for novel ACE2-utilising CoVs, while repurposing existing drugs may be used as treatments to dampen elevated inflammation and lung injury mediated by SARS-CoV-2.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Alan C-Y. Hsu", - "author_inst": "Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, New South Wales 2305, Australia" - }, - { - "author_name": "Guoqiang Wang", - "author_inst": "Department of Pathogen Biology, College of Basic Medical Science, Jilin University, Changchun 130021, China." - }, - { - "author_name": "Andrew T. Reid", - "author_inst": "Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, New South Wales 2305, Australia" - }, - { - "author_name": "Punnam Chander Veerati", - "author_inst": "Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, New South Wales 2305, Australia" - }, - { - "author_name": "Prabuddha S. Pathinayake", - "author_inst": "Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, New South Wales 2305, Australia" - }, - { - "author_name": "Katie Daly", - "author_inst": "Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, New South Wales 2305, Australia" - }, - { - "author_name": "Jemma R. Mayall", - "author_inst": "Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, New South Wales 2305, Australia" - }, - { - "author_name": "Philip M. Hansbro", - "author_inst": "Centenary UTS Centre for Inflammation, Centenary Institute, New South Wales 2050, Australia" - }, - { - "author_name": "Jay C. Horvat", - "author_inst": "Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, New South Wales 2305, Australia" - }, - { - "author_name": "Fang Wang", - "author_inst": "Department of Pathogen Biology, College of Basic Medical Science, Jilin University, Changchun 130021, China." - }, - { - "author_name": "Peter A. Wark", - "author_inst": "Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, New South Wales 2305, Australia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.09.30.320903", "rel_title": "SARS-CoV-2 viral budding and entry can be modeled using virus-like particles", @@ -1157173,6 +1159812,49 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.09.28.20203463", + "rel_title": "Efficacy of Famotidine for COVID-19: A Systematic Review and Meta-analysis", + "rel_date": "2020-09-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.28.20203463", + "rel_abs": "Background: Coronavirus Disease 2019 (COVID-19) pandemic continues unabated in many parts of the world. In the absence of any definite antiviral therapy except some benefit of remdesivir, there is an ongoing search for effective therapy. Famotidine has been shown to reduce mortality in hospitalized patients in a few studies. We conducted a systematic review on the use of famotidine in COVID-19. Methods: We searched the databases Medline, Embase, Cochrane CENTRAL and Medrxiv. Title/abstract screening, full text screening and data abstraction were carried out in by two reviewers. Case series, cohort studies and randomized trials were included. Results: Five studies were eligible for inclusion: all were retrospective cohort or case series. Low quality evidence suggests a likely clinical benefit for the use of famotidine in decreasing mortality in hospitalized patients with moderate to severe COVID-19. A meta-analysis of two cohort studies showed a statistically significant decrease in the composite outcome for death and intubation with famotidine (HR 0.44, 95% CI 0.27 to 0.73). Conclusion: Further evidence from RCTs is required for famotidine to treat COVID 19.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Rahul Sethia", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "Manya Prasad", + "author_inst": "NDMC Medical College, New Delhi, India" + }, + { + "author_name": "Soumya Jagannath", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "Neeraj Nischal", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India." + }, + { + "author_name": "Manish Soneja", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India." + }, + { + "author_name": "Pramod Garg", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India." + }, + { + "author_name": "Shalimar", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.28.20203489", "rel_title": "Mental health of undocumented college students during the COVID-19 pandemic", @@ -1158628,97 +1161310,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.30.20194290", - "rel_title": "Evaluation of high-throughput SARS-CoV-2 serological assays in a longitudinal cohort of mild COVID-19 patients: sensitivity, specificity and association with virus neutralization test", - "rel_date": "2020-09-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.30.20194290", - "rel_abs": "ObjectivesWe evaluated widely-used SARS-CoV-2 serological tests and their potential association with virus neutralization test (VNT) in a cohort of mild COVID-19 patients.\n\nMethodsA total of 439 specimens were longitudinally collected from 76 healthcare workers with RT-PCR-confirmed mild COVID-19. Nine serological assays developed by leading global companies (Abbott, DiaSorin, Siemens, Bio-Rad, Wantai, bioMerieux, Euroimmun) were assessed. For each test the sensitivity to detect SARS-CoV-2 antibodies was determined weekly after symptom onset. Correlation and concordance were assessed using the Spearman and Cohens Kappa coefficients, respectively. Positive percent agreement and negative percent agreement (NPA) with the VNT were also determined.\n\nResultsThe Wantai Total Ab assay targeting the receptor binding domain (RBD) within the S protein presented the best sensitivity at different times during the course of disease. The best correlation between antibody level and neutralizing antibody titer was found with the Euroimmun S1-based IgA assay (Spearman coefficient [95%CI]: 0.71 [0.61-0.79]). A moderate concordance (Kappa [95%CI]: 0.43[0.23-0.63]) as well as the lowest NPA (33%) was found between the Wantai Total Ab assay and the VNT. Compared to the Wantai Total Ab assay, other total Ab or IgG assays targeting the S or the RBD (bioMerieux, DiaSorin, Siemens,) were more concordant with the VNT (Kappa>0.7 for the three tests) and had a higher NPA (range: 90% to 97%).\n\nConclusionsAlthough some assays presented a better concordance with VNT than others, the present findings emphasize that commercialized serological tests including those targeting the RBD cannot substitute VNT for the assessment of functional antibody response.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Antonin Bal", - "author_inst": "Hospices civils de Lyon" - }, - { - "author_name": "Bruno Pozzetto", - "author_inst": "Laboratory of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, Saint-Etienne, France" - }, - { - "author_name": "Mary-Anne Trabaud", - "author_inst": "HCL" - }, - { - "author_name": "Vanessa Escuret", - "author_inst": "HCL" - }, - { - "author_name": "Muriel Rabilloud", - "author_inst": "HCL" - }, - { - "author_name": "Carole Langlois-jacques", - "author_inst": "HCL" - }, - { - "author_name": "Adele Paul", - "author_inst": "HCL" - }, - { - "author_name": "Nicolas Guibert", - "author_inst": "HCL" - }, - { - "author_name": "Constance d'Aubarede", - "author_inst": "HCL" - }, - { - "author_name": "Amelie Massardier", - "author_inst": "HCL" - }, - { - "author_name": "Nicole Fabien", - "author_inst": "HCL" - }, - { - "author_name": "David Goncalves", - "author_inst": "HCL" - }, - { - "author_name": "Andre Boibieux", - "author_inst": "HCL" - }, - { - "author_name": "Florence Morfin", - "author_inst": "HCL" - }, - { - "author_name": "Virginie Pitiot", - "author_inst": "HCL" - }, - { - "author_name": "Francois Gueyffier", - "author_inst": "HCL" - }, - { - "author_name": "Bruno Lina", - "author_inst": "HCL" - }, - { - "author_name": "Jean Baptiste Fassier", - "author_inst": "HCL" - }, - { - "author_name": "Sophie Assant", - "author_inst": "HCL" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.30.20201830", "rel_title": "Geospatial Analysis of Individual and Community-Level Socioeconomic Factors Impacting SARS-CoV-2 Prevalence and Outcomes", @@ -1158875,6 +1161466,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.09.29.20204289", + "rel_title": "Identification of biological correlates associated with respiratory failure in COVID-19", + "rel_date": "2020-09-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.29.20204289", + "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) is a global public health concern. Recently, a genome-wide association study (GWAS) was performed with participants recruited from Italy and Spain by an international consortium group.\n\nMethodsSummary GWAS statistics for 1610 patients with COVID-19 respiratory failure and 2205 controls were downloaded. In the current study, we analyzed the summary statistics with the information of loci and p-values for 8,582,968 single-nucleotide polymorphisms (SNPs), using gene ontology analysis to determine the top biological processes implicated in respiratory failure in COVID-19 patients.\n\nResultsWe considered the top 708 SNPs, using a p-value cutoff of 5x10-5, which were mapped to the nearest genes, leading to 144 unique genes. The list of genes was input into a curated database to conduct gene ontology and protein-protein interaction (PPI) analyses. The top ranked biological processes were wound healing, epithelial structure maintenance, muscle system processes, and cardiac-relevant biological processes with a false discovery rate < 0.05. In the PPI analysis, the largest connected network consisted of 8 genes. Through literature search, 7 out of the 8 genes were found to be implicated in both pulmonary and cardiac diseases.\n\nConclusionGene ontology and protein-protein interaction analyses identified cardio-pulmonary processes that may partially explain the risk of respiratory failure in COVID-19 patients.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Jung Hun Oh", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Allen Tannenbaum", + "author_inst": "Stony Brook University" + }, + { + "author_name": "Joseph Deasy", + "author_inst": "Memorial Sloan Kettering Cancer Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.09.29.20204172", "rel_title": "The Challenge of Forecasting Demand of Medical Resources and Supplies During a Pandemic: A Comparative Evaluation of Three Surge Calculators for COVID-19", @@ -1160730,41 +1163348,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.28.20203190", - "rel_title": "Predictors of symptomatic laboratory-confirmed SARS-COV-2 reinfection", - "rel_date": "2020-09-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.28.20203190", - "rel_abs": "ObjectiveTo identify factors predicting symptomatic laboratory-positive SARS-COV-2 reinfection.\n\nMethodWe conducted a nationwide retrospective cohort study and data from 99,993 confirmed cases of COVID-19 were analyzed.\n\nResultsThe overall risk of reinfection (28 or more elapsed days between both episodes onset) was 0.21%, and older subjects and those with mild primary disease were at reduced risk of reinfection. Healthcare workers and immunosuppressed or renal patients had at greater risk of SARS-COV-2 reinfection.\n\nConclusionsIf replicated in other populations, these results may be useful to prioritize efforts focusing on the reduction of SARS-COV-2 spread and the related burden.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "EFREN MURILLO-ZAMORA", - "author_inst": "INSTITUTO MEXICANO DEL SEGURO SOCIAL" - }, - { - "author_name": "CARLOS M HERNANDEZ-SUAREZ", - "author_inst": "UNIVERSIDAD DE COLIMA" - }, - { - "author_name": "AGUSTIN LUGO-RADILLO", - "author_inst": "CONACYT-FACULTAD DE MEDICINA Y CIRUGIA, UNIVERSIDAD AUTONOMA BENITO JUAREZ DE OAXACA" - }, - { - "author_name": "FELIPE AGUILAR-SOLLANO", - "author_inst": "UNIVERSIDAD DE COLIMA. PROGRAMA DE MAESTRIA EN CIENCIAS MEDICAS." - }, - { - "author_name": "OLIVER MENDOZA-CANO", - "author_inst": "UNIVERSIDAD DE COLIMA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.29.20203760", "rel_title": "Which early indicator allows for a better understanding of the evolution of the COVID-19 epidemic in France?", @@ -1160861,6 +1163444,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.28.20202978", + "rel_title": "A steady trickle-down from metro districts and improving epidemic-parameters characterize the increasing COVID-19 cases in India", + "rel_date": "2020-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.28.20202978", + "rel_abs": "BackgroundBy mid-September of 2020, the number of daily new infections in India crossed 95, 000. We aimed to characterize the spatio-temporal shifts in the disease burden as the infections rose during the first wave of COVID-19.\n\nMethodsWe gathered the publicly available district-level (equivalent of counties) granular data for the 15 April to 31 August 2020 period. We used the epidemiological data from 186 districts with the highest case burden as of August 31, 559, 566 active cases and 2, 715, 656 cumulative infections, and the governing epidemic parameters were estimated by fitting it to a susceptible-asymptomatic-infected-recovered-dead (SAIRD) model. The space-time trends in the case burden and epidemic parameters were analyzed. When the physical proximity of the districts did not explain the spreading patterns, we developed a metric for accessibility of the districts via air and train travel. The districts were categorized as large metro, metro, urban and sub-urban and the spatial shifts in case burden were analyzed.\n\nResultsThe center of the burden of the current-active infections which on May 15 was in the large metro districts with easy international access shifted continuously and smoothly towards districts which could be accessed by domestic airports and by trains. A linear trend-analysis showed a continuous improvement in the governing epidemic parameters consistently across the four categories of districts. The reproduction numbers improved from 1.77 {+/-} 0.58 on May 15 to 1.07 {+/-} 0.13 on August 31 in large metro districts (p-Value of trend 0.0001053); and from 1.58 {+/-} 0.39 on May 15 to 0.94 {+/-} 0.11 on August 31 in sub-urban districts (p-Value of trend 0.0067). The recovery rate per infected person per day improved from 0.0581 {+/-} 0.009 on May 15 to 0.091 {+/-} 0.010 on August 31 in large metro districts (p-Value of trend 0.26 x 10-12); and from 0.059 {+/-} 0.011 on May 15 to 0.100 {+/-} 0.010 on August 31 in sub-urban districts (p-Value of trend 0.12 x 10-16). The death rate of symptomatic individuals which includes the case-fatality-rate as well as the time from symptoms to death, consistently decreased from 0.0025 {+/-} 0.0014 on May 15 to 0.0013 {+/-} 0.0003 on August 31 in large metro districts (p-Value of trend 0.0010); and from 0.0018 {+/-} 0.0008 on May 15 to 0.0014 {+/-} 0.0003 on August 31 in sub-urban districts (p-Value of trend 0.2789).\n\nConclusionsAs the daily infections continued to rise at a national level, the \"center\" of the pandemic-burden shifted smoothly and predictably towards smaller sized districts in a clear hierarchical fashion of accessibility from an international travel perspective. This observed trend was meant to serve as an alert to re-organize healthcare resources towards remote districts. The geographical spreading patterns continue to be relevant as the second wave of infections began in March 2021 with a center in the mid-range districts.\n\nFundingNone", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Santosh Ansumali", + "author_inst": "Jawaharlal Nehru Center for Advanced Scientific Research" + }, + { + "author_name": "Aloke Kumar", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Samarth Agrawal", + "author_inst": "Jawaharlal Nehru Center for Advanced Scientific Research" + }, + { + "author_name": "H J Shashank", + "author_inst": "Jawaharlal Nehru Center for Advanced Scientific Research" + }, + { + "author_name": "Meher K Prakash", + "author_inst": "Jawaharlal Nehru Centre for Advanced Scientific Research" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.28.20202937", "rel_title": "The potential contribution of face coverings to the control of SARS-CoV-2 transmission in schools and broader society in the UK: a modelling study", @@ -1162116,113 +1164734,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.25.20201921", - "rel_title": "Improved Sensitivity, Safety, and Rapidity of COVID-19 Tests by Replacing Viral Storage Solution with Lysis Buffer", - "rel_date": "2020-09-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.25.20201921", - "rel_abs": "Conducting numerous, rapid, and reliable PCR tests for SARS-CoV-2 is essential for our ability to monitor and control the current COVID-19 pandemic.\n\nHere, we tested the sensitivity and efficiency of SARS-CoV-2 detection in clinical samples collected directly into a mix of lysis buffer and RNA preservative, thus inactivating the virus immediately after sampling.\n\nWe tested 79 COVID-19 patients and 20 healthy controls. We collected two samples (nasopharyngeal swabs) from each participant: one swab was inserted into a test tube with Viral Transport Medium (VTM), following the standard guideline used as the recommended method for sample collection; the other swab was inserted into a lysis buffer supplemented with nucleic acid stabilization mix (coined NSLB).\n\nWe found that RT-qPCR tests of patients were significantly more sensitive with NSLB sampling, reaching detection threshold 2.1{+/-}0.6 (Mean{+/-}SE) PCR cycles earlier then VTM samples from the same patient. We show that this improvement is most likely since NSLB samples are not diluted in lysis buffer before RNA extraction. Re-extracting RNA from NSLB samples after 72 hours at room temperature did not affect the sensitivity of detection, demonstrating that NSLB allows for long periods of sample preservation without special cooling equipment. We also show that swirling the swab in NSLB and discarding it did not reduce sensitivity compared to retaining the swab in the tube, thus allowing improved automation of COVID-19 tests. Overall, we show that using NSLB instead of VTM can improve the sensitivity, safety, and rapidity of COVID-19 tests at a time most needed.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Oran Erster", - "author_inst": "Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel" - }, - { - "author_name": "Omer Shkedi", - "author_inst": "Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel" - }, - { - "author_name": "Gil Benedek", - "author_inst": "Hadassah Medical Center, Jerusalem, Israel" - }, - { - "author_name": "Eyal Zilber", - "author_inst": "Department of Internal Medicine, Sheba Medical Center, Tel Hashomer, Israel" - }, - { - "author_name": "Itay Varkovitzky", - "author_inst": "Directorate of Defense Research & Development, Israeli Ministry of Defense, Israel" - }, - { - "author_name": "Rachel Shirazi", - "author_inst": "Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel" - }, - { - "author_name": "Dorit Oriya Shorka", - "author_inst": "Hadassah Medical Center, Jerusalem, Israel" - }, - { - "author_name": "Yuval Cohen", - "author_inst": "Directorate of Defense Research & Development, Israeli Ministry of Defense, Israel" - }, - { - "author_name": "Tzahi Bar", - "author_inst": "Independent Researcher, Israel" - }, - { - "author_name": "Rafi Yechieli", - "author_inst": "Independent Researcher, Israel" - }, - { - "author_name": "Michal Tepperberg Oikawa", - "author_inst": "Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel" - }, - { - "author_name": "Dana Venkert", - "author_inst": "Department of Neurobiology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel" - }, - { - "author_name": "Michal Linial", - "author_inst": "Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel" - }, - { - "author_name": "Esther Oiknine-Djian", - "author_inst": "Hadassah Medical Center, Jerusalem, Israel" - }, - { - "author_name": "Michal Mandelboim", - "author_inst": "Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel; School of Public Health, Sackler" - }, - { - "author_name": "Zvi Livneh", - "author_inst": "Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel" - }, - { - "author_name": "Gilat Shenhav-Saltzman", - "author_inst": "Department of Internal Medicine, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Ella Mendelson", - "author_inst": "Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel; School of Public Health, Sackler" - }, - { - "author_name": "Dana Wolf", - "author_inst": "Hadassah Medical Center, Jerusalem, Israel" - }, - { - "author_name": "Moran Szwarcwort-Cohen", - "author_inst": "Virology Laboratory, Rambam Health Care Campus, Haifa, Israel" - }, - { - "author_name": "Orna Mor", - "author_inst": "Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel; School of Public Health, Sackler" - }, - { - "author_name": "Yair Lewis", - "author_inst": "Navina AI Medical Technologies, Tel Aviv, Israel" - }, - { - "author_name": "Danny Zeevi", - "author_inst": "Department of Biotechnology, Hadassah Academic College, Jerusalem, Israel" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.26.20201814", "rel_title": "Evolution of COVID-19 cases in selected low- and middle-income countries: past the herd immunity peak?", @@ -1162335,6 +1164846,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.26.20202150", + "rel_title": "Comparison of mental health service activity before and shortly after UK social distancing responses to the COVID-19 pandemic: February-March 2020", + "rel_date": "2020-09-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.26.20202150", + "rel_abs": "This study sought to provide an early description of mental health service activity before and after national implementation of social distancing for COVID-19. A time series analysis was carried out of daily service-level activity on data from a large mental healthcare provider in southeast London, from 01.02.2020 to 31.03.2020, comparing activity before and after 16.03.2020: i) inpatient admissions, discharges and numbers, ii) contact numbers and daily caseloads (Liaison, Home Treatment Teams, Community Mental Health Teams); iii) numbers of deaths for past and present patients. Daily face-to-face contact numbers fell for liaison, home treatment and community services with incomplete compensatory rises in non-face-to-face contacts. Daily caseloads fell for all services, apart from working age and child/adolescent community teams. Inpatient numbers fell 13.6% after 16th March, and daily numbers of deaths increased by 61.8%.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Robert Stewart", + "author_inst": "King's College London" + }, + { + "author_name": "Evangelia Martin", + "author_inst": "South London and Maudsley NHS Foundation Trust" + }, + { + "author_name": "Ioannis Bakolis", + "author_inst": "King's College London" + }, + { + "author_name": "Matthew Broadbent", + "author_inst": "King's College London" + }, + { + "author_name": "Nicola Byrne", + "author_inst": "South London and Maudsley NHS Foundation Trust" + }, + { + "author_name": "Sabine Landau", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.09.26.20202382", "rel_title": "Estimation of the fraction of COVID-19 infected people in U.S. states and countries worldwide", @@ -1163818,37 +1166368,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.09.25.20194431", - "rel_title": "The Use of Psychoactive Substances in the Context of the Covid-19 Pandemic in Brazil", - "rel_date": "2020-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.25.20194431", - "rel_abs": "BackgroundThe protocols for mitigating the transmission of Covid-19 seem to be a trigger for the use of psychoactive substances, as an individuals adaptive response to support this new way of being in the world. Objective: To investigate the use of psychoactive substances in the context of the Covid-19 pandemic in Brazil. Method: A cross-sectional and prospective observational study, undertaken in a virtual environment. An online survey was developed and employed through Google Forms to collect data. The survey was made available to participants on social networks, Facebook@, Whatsapp@, and Instagram@, linked to the research group, during the period 06/15/2020 to 07/15/2020. 1,145 individuals participated in the research. Results: The average age of the participants was 37 years old. They were mostly female, white, Brazilians, with a higher education level, with occupations in the health field, and had religion. They either maintained their family income or suffered a small income decrease. Moreover, they informed that they were caring for social isolation. The most used substances before and after the beginning of the Covid-19 pandemic were alcohol, tobacco, marijuana, although the use of these substances decreased (P< 0.001). Approximately 32% of the participants started using psychoactive substances in this period. Among them, most individuals started by their own initiative. Conclusions: For a better understanding of the pattern use of psychoactive substances during the Covid-19 pandemic and the adverse effects on human behavior and mental disorders, careful longitudinal studies must be developed, due to the great interest in the knowledge of adaptive responses when peoples lives are at risk.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Cesar Augusto Trinta Weber", - "author_inst": "Centro de Estudos Jose de Barros Falcao" - }, - { - "author_name": "Ingridi Teixeira Monteiro", - "author_inst": "Centro de Estudos Jose de Barros Falcao" - }, - { - "author_name": "Julia Medeiros Gehrke", - "author_inst": "Centro de Estudos Jose de Barros Falcao" - }, - { - "author_name": "Wagner Silva de Souza", - "author_inst": "Centro de Estudos Jose de Barros Falcao" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.09.25.20201616", "rel_title": "COVID-19 in Youth Soccer", @@ -1163997,6 +1166516,173 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.25.20201863", + "rel_title": "Deep Immune Profiling of MIS-C demonstrates marked but transient immune activation compared to adult and pediatric COVID-19", + "rel_date": "2020-09-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.25.20201863", + "rel_abs": "Pediatric COVID-19 following SARS-CoV-2 infection is associated with fewer hospitalizations and often milder disease than in adults. A subset of children, however, present with Multisystem Inflammatory Syndrome in Children (MIS-C) that can lead to vascular complications and shock, but rarely death. The immune features of MIS-C compared to pediatric COVID-19 or adult disease remain poorly understood. We analyzed peripheral blood immune responses in hospitalized SARS-CoV-2 infected pediatric patients (pediatric COVID-19) and patients with MIS-C. MIS-C patients had patterns of T cell-biased lymphopenia and T cell activation similar to severely ill adults, and all patients with MIS-C had SARS-CoV-2 spike-specific antibodies at admission. A distinct feature of MIS-C patients was robust activation of vascular patrolling CX3CR1+ CD8 T cells that correlated with use of vasoactive medication. Finally, whereas pediatric COVID-19 patients with acute respiratory distress syndrome (ARDS) had sustained immune activation, MIS-C patients displayed clinical improvement over time, concomitant with decreasing immune activation. Thus, non-MIS-C versus MIS-C SARS-CoV-2 associated illnesses are characterized by divergent immune signatures that are temporally distinct and implicate CD8 T cells in clinical presentation and trajectory of MIS-C.\n\nOne Sentence SummaryMIS-C is defined by generalized lymphocyte activation that corrects during hospitalization, including elevated plasmablast frequencies and marked activation of vascular patrolling CX3CR1+ CD8 T cells.", + "rel_num_authors": 38, + "rel_authors": [ + { + "author_name": "Laura Vella", + "author_inst": "University of Pennsylvania/Children's Hospital of Philadelphia" + }, + { + "author_name": "Josephine R. Giles", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Amy E. Baxter", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Derek A Oldridge", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Caroline Diorio", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "Leticia Kuri-Cervantes", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Cecile Alanio", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Maria Betina Pampena", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jennifer E Wu", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Zeyu Chen", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Yinghui Jane Huang", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Elizabeth M. Anderson", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Sigrid Gouma", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Kevin O. McNerney", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "Julie Chase", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "Chakkapong Burudpakdee", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "Jessica H. Lee", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "Sokratis A. Apostolidis", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Alexander C. Huang", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Divij Mathew", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Oliva Kuthuru", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Eileen C. Goodwin", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Madison E. Weirick", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Marcus J. Bolton", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Claudia P. Arevalo", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Andre Ramos", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Cristina Jasen", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "Heather M. Giannini", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Kurt DAndrea", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "- The UPenn COVID Processing Unit", + "author_inst": "" + }, + { + "author_name": "Nuala J. Meyer", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Edward M. Behrens", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "Hamid Bassiri", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "Scott E. Hensley", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "Sarah E. Henrickson", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "David T. Teachey", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "Michael R. Betts", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "E. John Wherry", + "author_inst": "University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.25.20201889", "rel_title": "Prioritising COVID-19 vaccination in changing social and epidemiological landscapes", @@ -1165264,41 +1167950,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.23.20200410", - "rel_title": "Review of clinical characteristics and laboratory findings of COVID-19 in children-Systematic review and Meta-analysis", - "rel_date": "2020-09-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.23.20200410", - "rel_abs": "OBJECTIVE: To conduct a systematic review and meta-analysis to assess the prevalence of various clinical symptoms and laboratory findings of COVID-19 in children. METHODS: PubMed, MEDLINE, and SCOPUS databases were searched to include studies conducted between January 1, 2020, and July 15, 2020 which reported data about clinical characteristics and laboratory findings in laboratory-confirmed diagnosis of COVID-19 in pediatric patients. Random effects meta-analysis using generalized linear mixed models was used to estimate the pooled prevalence. RESULTS: The most prevalent symptom of COVID-19 in children was 46.17% (95%CI 39.18-53.33%), followed by cough (40.15%, 95%CI 34.56-46.02%). Less common symptoms were found to be dyspnea, vomiting, nasal congestion/rhinorrhea, diarrhea, sore throat/pharyngeal congestion, headache, and fatigue. The prevalence of asymptomatic children was 17.19% (95%CI 11.02-25.82%). The most prevalent laboratory findings in COVID-19 children were elevated Creatinine Kinase (26.86%, 95%CI 16.15-41.19%) and neutropenia (25.76%, 95%CI 13.96-42.58%). These were followed by elevated LDH, thrombocytosis, lymphocytosis, neutrophilia, elevated D Dimer, Elevated CRP, elevated ESR, leukocytosis, elevated AST and leukopenia. There was a low prevalence of elevated ALT and lymphopenia in children with COVID- 19. CONCLUSIONS AND RELEVANCE: This study provides estimates of the pooled prevalence of various symptoms and laboratory findings of COVID-19 in the pediatric population.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Harmeet K Kharoud", - "author_inst": "Division of Epidemiology, School of Public Health, University of Minnesota, MN, USA" - }, - { - "author_name": "Rizwana Asim", - "author_inst": "Fatima Jinnah Medical University, Lahore, Pakistan" - }, - { - "author_name": "Lianne Siegel", - "author_inst": "Division of Biostatistics, School of Public Health, University of Minnesota" - }, - { - "author_name": "Lovepreet Chahal", - "author_inst": "School of Health Science Kwantlen Polytechnic University, Surrey, Canada" - }, - { - "author_name": "Gagan Deep Singh", - "author_inst": "Department of Internal Medicine, University of Connecticut, CT, USA" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.23.20198713", "rel_title": "Suitability of Two Rapid Lateral Flow Immunochromatographic Assays for Predicting SARS-CoV-2 Neutralizing Activity of Sera", @@ -1165695,6 +1168346,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.23.20165639", + "rel_title": "First phylogenetic analysis of Malian SARS-CoV-2 sequences provide molecular insights into the genomic diversity of the Sahel region", + "rel_date": "2020-09-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.23.20165639", + "rel_abs": "We are currently facing a pandemic of COVID-19, caused by a spillover from an animal-originating coronavirus to humans occuring in the Wuhan region, China, in December 2019. From China the virus has spread to 188 countries and regions worldwide, reaching the Sahel region on the 2nd of March 2020. Since whole genome sequencing (WGS) data is very crucial to understand the spreading dynamics of the ongoing pandemic, but only limited sequence data is available from the Sahel region to date, we have focused our efforts on generating the first Malian sequencing data available. Screening of 217 Malian patient samples for the presence of SARS-CoV-2 resulted in 38 positive isolates from which 21 whole genome sequences were generated. Our analysis shows that both, the early A (19B) and the fast evolving B (20A/C) clade, are present in Mali indicating multiple and independent introductions of the SARS-CoV-2 to the Sahel region.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Bourema Kouriba", + "author_inst": "Centre d'Infectiologie Charles Merieux du Mali, Bamako, Mali" + }, + { + "author_name": "Angela Duerr", + "author_inst": "Bundeswehr Institute of Microbiology, Munich, Germany" + }, + { + "author_name": "Alexandra Rehn", + "author_inst": "Bundeswehr Institute of Microbiology, Munich, Germany" + }, + { + "author_name": "Abdoul Karim Sangare", + "author_inst": "Centre d'Infectiologie Charles Merieux du Mali, Bamako, Mali" + }, + { + "author_name": "Brehima Youssouf Traoure", + "author_inst": "Centre d'Infectiologie Charles Merieux du Mali, Bamako, Mali" + }, + { + "author_name": "Malena S Bestehorn-Willmann", + "author_inst": "Bundeswehr Institute of Microbiology, Munich, Germany" + }, + { + "author_name": "Judicael LJ Ouedraogo", + "author_inst": "Centre d'Infectiologie Charles Merieux du Mali, Bamako, Mali" + }, + { + "author_name": "Asli Heitzer", + "author_inst": "Bundeswehr Institute of Microbiology, Munich, Germany" + }, + { + "author_name": "Elisabeth Sogodogo", + "author_inst": "Centre d'Infectiologie Charles Merieux du Mali, Bamako, Mali" + }, + { + "author_name": "Abderrhamane Maiga", + "author_inst": "Centre d'Infectiologie Charles Merieux du Mali, Bamako, Mali" + }, + { + "author_name": "Mathias C Walter", + "author_inst": "Bundeswehr Institute of Microbiology, Munich, Germany" + }, + { + "author_name": "Fee Zimmermann", + "author_inst": "Bundeswehr Institute of Microbiology, Munich, Germany" + }, + { + "author_name": "Roman Woelfel", + "author_inst": "Bundeswehr Institute of Microbiology, Munich, Germany" + }, + { + "author_name": "Markus H Antwerpen", + "author_inst": "Bundeswehr Institute of Microbiology, Munich, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.24.20200543", "rel_title": "Evidence for and level of herd immunity against SARS-CoV-2 infection: the ten-community study", @@ -1166930,45 +1169652,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.24.20201301", - "rel_title": "Psychological preparedness for pandemic (COVID-19) management: Perceptions of nurses and nursing students in India", - "rel_date": "2020-09-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.24.20201301", - "rel_abs": "IntroductionThe growing COVID-19 pandemic has posed a great threat to millions of people worldwide. Nurses and nursing students are an important group of health professionals who are most likely to face many challenges in this unprecedented scenario. The present study aimed at exploring the perception of nurses and nursing students regarding psychological preparedness for the pandemic (COVID-19) management.\n\nMaterials & MethodsThe study employed a quantitative cross-sectional online survey research design. Purposive sampling was used with an attempt to represent the entire nurses (i.e. nursing officers, nurse administrators and nursing teachers) and nursing students group of India. The survey link was shared to their email ID and they were invited to participate in the study. Data were collected using Psychological Preparedness for Disaster Threat Scale (PPDTS)-Modified, General Self Efficacy (GSE) Scale, Optimism Scale and Brief Resilient Coping Scale (BRS). Totally 685 responses were received and 676 forms were completed which were analyzed using SPSS software (version 24).\n\nResultsThe mean age of the subjects was 31.72 (SD=9.58) years. Around 20% of the subjects previously had some kind of psychological training and 4% of the subjects had taken care of persons with COVID-19. Findings revealed that mean score for PPDTS, GSE, BRCS and Optimism was 73.44 (SD=10.82, 33.19 (SD=5.23), 16.79 (SD=2.73) and 9.61 (SD=2.26) respectively indicating that the subjects had moderate level of psychological preparedness, self-efficacy and resilience but higher level of optimism. Psychological preparedness, self-efficacy, optimism and resilience were positively correlated to each other. Self-efficacy, optimism, and resilience emerged as predictors of psychological preparedness.\n\nConclusionThe findings suggested that self-efficacy, optimism and resilience can be considered as predictors for psychological preparedness in pandemic management. Appropriate training could influence self-efficacy while programs addressing resilience and coping may strengthen psychological preparedness which can help in further management of ongoing pandemic.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sailaxmi Gandhi", - "author_inst": "National Institute of Mental Health and Neurosciences" - }, - { - "author_name": "Maya Sahu", - "author_inst": "National Institute of Mental Health & Neuro Sciences" - }, - { - "author_name": "Radhakrishnan Govindan", - "author_inst": "National Institute of Mental Health and Neurosciences" - }, - { - "author_name": "Prasanthi Nattala", - "author_inst": "National Institute of Mental Health and Neurosciences" - }, - { - "author_name": "Paulomi M Sudhir", - "author_inst": "National Institute of Mental Health and Neurosciences" - }, - { - "author_name": "Rathi Balachandran", - "author_inst": "Ministry of Health & Family Welfare, Government of India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nursing" - }, { "rel_doi": "10.1101/2020.09.24.20201228", "rel_title": "Outcomes associated with SARS-CoV-2 viral clades in COVID-19", @@ -1167253,6 +1169936,117 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.09.25.309914", + "rel_title": "Prophylactic intranasal administration of a TLR2 agonist reduces upper respiratory tract viral shedding in a SARS-CoV-2 challenge ferret model", + "rel_date": "2020-09-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.25.309914", + "rel_abs": "Respiratory viruses such as coronaviruses represent major ongoing global threats, causing epidemics and pandemics with huge economic burden. Rapid spread of virus through populations poses an enormous challenge for outbreak control. Like all respiratory viruses, the most recent novel human coronavirus SARS-CoV-2, initiates infection in the upper respiratory tract (URT). Infected individuals are often asymptomatic, yet highly infectious and readily transmit virus. A therapy that restricts initial replication in the URT has the potential to prevent progression of severe lower respiratory tract disease as well as limiting person-to-person transmission.\n\nWe show that prophylactic intra-nasal administration of the TLR2/6 agonist INNA-051 in a SARS-CoV-2 ferret infection model effectively reduces levels of viral RNA in the nose and throat. The results of our study support clinical development of a therapy based on prophylactic TLR2/6 innate immune activation in the URT to reduce SARS-CoV-2 transmission and provide protection against COVID-19.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Pamela C Proud", + "author_inst": "Public Health England" + }, + { + "author_name": "Daphne Tsitoura", + "author_inst": "Ena Respiratory" + }, + { + "author_name": "Robert J Watson", + "author_inst": "Public Health England" + }, + { + "author_name": "Brendon Y. Chua", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Marilyn J Aram", + "author_inst": "Public Health England" + }, + { + "author_name": "Kevin R Bewley", + "author_inst": "Public Health England" + }, + { + "author_name": "Breeze E Cavell", + "author_inst": "Public Health England" + }, + { + "author_name": "Rebecca Cobb", + "author_inst": "Public Health England" + }, + { + "author_name": "Stuart Dowall", + "author_inst": "Public Health England" + }, + { + "author_name": "Susan A Fotheringham", + "author_inst": "Public Health England" + }, + { + "author_name": "Catherine MK Ho", + "author_inst": "Public Health England" + }, + { + "author_name": "Vanessa Lucas", + "author_inst": "Public Health England" + }, + { + "author_name": "Didier Ngabo", + "author_inst": "Public Health England" + }, + { + "author_name": "Emma Rayner", + "author_inst": "Public Health England" + }, + { + "author_name": "Kathryn A Ryan", + "author_inst": "Public Health England" + }, + { + "author_name": "Gillian S Slack", + "author_inst": "Public Health England" + }, + { + "author_name": "Stephen Thomas", + "author_inst": "Public Health England" + }, + { + "author_name": "Nadina I Wand", + "author_inst": "Public Health England" + }, + { + "author_name": "Paul Yeates", + "author_inst": "Public Health England" + }, + { + "author_name": "Christophe Demaison", + "author_inst": "Ena Respiratory" + }, + { + "author_name": "David C. Jackson", + "author_inst": "The Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Nathan W Bartlett", + "author_inst": "Viral Immunology and Respiratory Disease group and Priority Research Centre for Healthy Lungs, University of Newcastle and Hunter Medical Research Institute" + }, + { + "author_name": "Francesca Mercuri", + "author_inst": "Ena Respiratory" + }, + { + "author_name": "Miles W Carroll", + "author_inst": "Public Health England and Nuffield Dept of Medicine, Oxford University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.09.24.312553", "rel_title": "SARS-CoV-2 induces double-stranded RNA-mediated innate immune responses in respiratory epithelial derived cells and cardiomyocytes", @@ -1168660,105 +1171454,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2020.09.22.308965", - "rel_title": "Cross-reactive serum and memory B cell responses to spike protein in SARS-CoV-2 and endemic coronavirus infection", - "rel_date": "2020-09-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.22.308965", - "rel_abs": "Pre-existing immune responses to seasonal endemic coronaviruses could have profound consequences for antibody responses to SARS-CoV-2, either induced in natural infection or through vaccination. Such consequences are well established in the influenza and flavivirus fields. A first step to establish whether pre-existing responses can impact SARS-CoV-2 infection is to understand the nature and extent of cross-reactivity in humans to coronaviruses. We compared serum antibody and memory B cell responses to coronavirus spike (S) proteins from pre-pandemic and SARS-CoV-2 convalescent donors using a series of binding and functional assays. We found weak evidence of pre-existing SARS-CoV-2 cross-reactive serum antibodies in pre-pandemic donors. However, we found stronger evidence of pre-existing cross-reactive memory B cells that were activated on SARS-CoV-2 infection. Monoclonal antibodies (mAbs) isolated from the donors showed varying degrees of cross-reactivity with betacoronaviruses, including SARS and endemic coronaviruses. None of the cross-reactive mAbs were neutralizing except for one that targeted the S2 subunit of the S protein. The results suggest that pre-existing immunity to endemic coronaviruses should be considered in evaluating antibody responses to SARS-CoV-2.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Ge Song", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Wan-ting He", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Sean Callaghan", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Fabio Anzanello", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Deli Huang", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "James Ricketts", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Jonathan L. Torres", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Nathan Beutler", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Linghang Peng", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Sirena Vargas", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Jon Cassell", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Mara Parren", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Linlin Yang", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Caroline Ignacio", - "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." - }, - { - "author_name": "Davey M. Smith", - "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." - }, - { - "author_name": "James E. Voss", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "David Nemazee", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Andrew B. Ward", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Thomas Rogers", - "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." - }, - { - "author_name": "Dennis R. Burton", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Raiees Andrabi", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.09.23.309948", "rel_title": "Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK", @@ -1169079,6 +1171774,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, + { + "rel_doi": "10.1101/2020.09.21.20198804", + "rel_title": "A Brief Burnout Evaluation Scale (BBES) as a potential tool to prevent collapse of the health care task force during the COVID-19 pandemic", + "rel_date": "2020-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.21.20198804", + "rel_abs": "IntroductionIn the context of the COVID-19 pandemic, where overloaded health systems seem inevitable, there is a need for reliable, conceptually adequate, and easily applied measurement tools to identify health professionals at risk.\n\nObjectiveto present the preliminary psychometric properties of a Brief Burnout Evaluation Scale (BBES) and its association with important outcomes, i.e., moderate to severe depression and suicidal ideation.\n\nMethodsThe BBES has 4 Likert-type items and was tested as part of a cross-sectional study that included 401 medical students. Reliability analysis and validity studies were performed.\n\nResultsIn the parallel analysis, two factors were extracted, explaining 84.4% of the variance. The Cronbachs alpha was 0.78, showing high internal consistency. Considering a cut-off point of 12, the odds ratio for moderate to severe depression was 3.01 (CI 1.7-5.22; p<0.001) and for last month suicidal ideation 2.96 (CI 1.6-5.48).\n\nConclusionThe results suggest good psychometric characteristics for the BBES, thus reinforcing its utility as an assessment tool for evaluating the well-being or distress of health professionals. It carries with it the potential to implement early interventions and to prevent the descent into burnout so common today in the health care task force during the pandemic.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Tamires Martins Bastos", + "author_inst": "Universidade Federal do Rio Grande do Sul" + }, + { + "author_name": "Gabriela Massaro Carneiro Monteiro", + "author_inst": "Universidade Federal do Rio Grande do Sul" + }, + { + "author_name": "Rogerio Boff Borges", + "author_inst": "Hospital de Clinicas de Porto Alegre" + }, + { + "author_name": "Carolina Meira Moser", + "author_inst": "Universidade Federal do Rio Grande do Sul" + }, + { + "author_name": "Daniel Luccas Arenas", + "author_inst": "Universidade Federal do Rio Grande do Sul" + }, + { + "author_name": "Ana Margareth Bassols", + "author_inst": "Universidade Federal do Rio Grande do Sul" + }, + { + "author_name": "Pricilla Braga Laskoski", + "author_inst": "Universidade Federal do Rio Grande do Sul" + }, + { + "author_name": "Simone Hauck", + "author_inst": "Universidade Federal do Rio Grande do Sul" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.09.20.20198531", "rel_title": "Puerto Rico Health System Resilience After Hurricane Maria: Implications for Disaster Preparedness in the COVID-19 Era", @@ -1170466,25 +1173208,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.20.20198283", - "rel_title": "Exponential distribution of large excess death rates in Europe during the COVID-19 outbreak in the spring of 2020", - "rel_date": "2020-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.20.20198283", - "rel_abs": "Excess death rates E during the spring of 2020 are computed in N = 540 level 3 European territorial units for statistics --NUTS3 in Belgium (40), France (96), Italy (110), Netherlands (44), Spain (50), Sweden(21) and United Kingdom (179)-- from 2020 provisional week deaths, the population numbers for 2020, and observations in previous years (reference or baseline), all of them obtained from Eurostat web page.\n\nExcess death rates are classified in three tiers. Largest 27 excess death rates (tier 1, E > 1721x 10-6) were distributed exponentially with empirical complementary cumulative distribution function (empirical survival function) S following S {propto} 2-E/{varepsilon} with{varepsilon} 1 = 958(42) x 10-6. Tier 2 (the next 52 largest excess death rates, E < 1142 x 10-6 also distributed exponentially with{varepsilon} 2 = 379.5(89) x10-6. Tier 3 (smallest 460 excess death rates) were distributed normally.\n\nThe results suggests that when, within some regions, the outbreak is above a threshold, interaction with neighbouring region become less relevant and the outcomes --excess death rates-- become exponentially distributed as it happens with independent events.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Jose Maria Martin-Olalla", - "author_inst": "Universidad de Sevilla" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.22.20198275", "rel_title": "Knowledge, Attitude and Practice towards COVID-19 among people in Bangladesh during the pandemic: a cross-sectional study.", @@ -1170689,6 +1173412,205 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.09.22.20199703", + "rel_title": "Prognostic value of sTREM-1 in COVID-19 patients: a biomarker for disease severity and mortality", + "rel_date": "2020-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.22.20199703", + "rel_abs": "Background: The uncontrolled inflammatory response plays a critical role in the novel coronavirus disease (COVID-19) and triggering receptor expressed on myeloid cells-1 (TREM-1) is thought to be intricate to inflammatory signal amplification. This study aims to investigate the association between soluble TREM-1 (sTREM-1) and COVID-19 as a prognostic biomarker to predict the disease severity, lethality and clinical management.Methods: We enrolled 91 patients with COVID-19 in domiciliary care (44 patients) or in hospital care (47 patients), who were classified after admission into mild, moderate, severe and critical groups according to their clinical scores. As non-COVID-19 control, 30 healthy volunteers were included. Data on demographic, comorbidities and baseline clinical characteristics were obtained from their medical and nurse records. Peripheral blood samples were collected at admission and after hospitalization outcome to assess cytokine profile and sTREM-1 level by specific immunoassays Results: Within COVID-19 patients, the highest severity was associated with the most significant elevated plasma levels sTREM-1. Using receiver operating curve analysis (ROC), sTREM-1 was found to be predictive of disease severity (AUC= 0.988) and the best cut-off value for predicting in-hospital severity was [≥] 116.5 pg/mL with the sensitivity for 93.3% and specificity for 95.8%. We also described the clinical characteristics of these patients and explored the correlation with markers of the disease aggravation. The levels of sTREM-1 were positively correlated with IL-6, IL-10, blood neutrophils counts, and critical disease scoring (r= 0.68, p<0.0001). On the other hand, sTREM-1 level was significantly negative correlated with lymphocytes counting, and mild disease (r= -0.42, p<0.0001). Higher levels of sTREM-1 were related to poor outcome and death, patients who received dexamethasone tended to have lower sTREM-1 levels. Conclusion: Our results indicated that sTREM-1 in COVID-19 is associated with severe disease development and a prognostic marker for mortality. The use of severity biomarkers such as sTREM-1 together with patients clinical scores could improve the early recognition and monitoring of COVID-19 cases with higher risk of disease worsening. Key words: COVID-19; sTREM-1; Inflammation; Biomarker; Severity; Mortality.", + "rel_num_authors": 46, + "rel_authors": [ + { + "author_name": "Pedro V da Silva Neto", + "author_inst": "Departamento de Analises Clinicas, Toxicologicas e Bromatologicas. Faculdade de Ciencias Farmaceuticas de Ribeirao Preto FCFRP. Universidade de Sao Paulo USP, " + }, + { + "author_name": "Jonatan C S de Carvalho", + "author_inst": "Departamento de Analises Clinicas, Toxicologicas e Bromatologicas. Faculdade de Ciencias Farmaceuticas de Ribeirao Preto FCFRP. Universidade de Sao Paulo USP, " + }, + { + "author_name": "Vinicius E Pimentel", + "author_inst": "Departamento de Bioquimica e Imunologia. Faculdade de Medicina de Ribeirao Preto FMRP. Universidade de Sao Paulo USP, Ribeirao Preto, SP, Brazil" + }, + { + "author_name": "Malena M Perez", + "author_inst": "Departamento de Analises Clinicas, Toxicologicas e Bromatologicas. Faculdade de Ciencias Farmaceuticas de Ribeirao Preto FCFRP. Universidade de Sao Paulo USP, " + }, + { + "author_name": "Ingryd Carmona-Garcia", + "author_inst": "Escola de Enfermagem de Ribeirao Preto EERP. Universidade de Sao Paulo USP, Ribeirao Preto, SP, Brazil" + }, + { + "author_name": "Nicola T Neto", + "author_inst": "Escola de Enfermagem de Ribeirao Preto EERP. Universidade de Sao Paulo USP, Ribeirao Preto, SP, Brazil" + }, + { + "author_name": "Diana M Toro", + "author_inst": "Programa de Pos Graduacao em Imunologia Basica e Aplicada PPGIBA. Instituto de Ciencias Biologicas, Universidade Federal do Amazonas UFAM, Manaus, AM, Brazil" + }, + { + "author_name": "Camilla N S Oliveira", + "author_inst": "Departamento de Bioquimica e Imunologia. Faculdade de Medicina de Ribeirao Preto FMRP. Universidade de Sao Paulo USP, Ribeirao Preto, SP, Brazil." + }, + { + "author_name": "Thais F C Fraga-Silva", + "author_inst": "Departamento de Bioquimica e Imunologia. Faculdade de Medicina de Ribeirao Preto FMRP. Universidade de Sao Paulo USP, Ribeirao Preto, SP, Brazil." + }, + { + "author_name": "Cristiane M Milanezi", + "author_inst": "Departamento de Bioquimica e Imunologia. Faculdade de Medicina de Ribeirao Preto FMRP. Universidade de Sao Paulo USP, Ribeirao Preto, SP, Brazil." + }, + { + "author_name": "Lilian C Rodrigues", + "author_inst": "Departamento de Analises Clinicas, Toxicologicas e Bromatologicas. Faculdade de Ciencias Farmaceuticas de Ribeirao Preto FCFRP. Universidade de Sao Paulo USP, " + }, + { + "author_name": "Cassia F. S. L. Dias", + "author_inst": "Departamento de Analises Clinicas, Toxicologicas e Bromatologicas. Faculdade de Ciencias Farmaceuticas de Ribeirao Preto FCFRP. Universidade de Sao Paulo USP, " + }, + { + "author_name": "Ana C Xavier", + "author_inst": "Escola de Enfermagem de Ribeirao Preto EERP. Universidade de Sao Paulo USP, Ribeirao Preto, SP, Brazil" + }, + { + "author_name": "Giovanna S Porcel", + "author_inst": "Escola de Enfermagem de Ribeirao Preto EERP. Universidade de Sao Paulo USP, Ribeirao Preto, SP, Brazil" + }, + { + "author_name": "Isabelle C Guarneri", + "author_inst": "Escola de Enfermagem de Ribeirao Preto EERP. Universidade de Sao Paulo USP, Ribeirao Preto, SP, Brazil" + }, + { + "author_name": "Kamila Zaparoli", + "author_inst": "Escola de Enfermagem de Ribeirao Preto EERP. Universidade de Sao Paulo USP, Ribeirao Preto, SP, Brazil" + }, + { + "author_name": "Caroline T Garbato", + "author_inst": "Escola de Enfermagem de Ribeirao Preto EERP. Universidade de Sao Paulo USP, Ribeirao Preto, SP, Brazil" + }, + { + "author_name": "Jamille G M Argolo", + "author_inst": "Escola de Enfermagem de Ribeirao Preto EERP. Universidade de Sao Paulo USP, Ribeirao Preto, SP, Brazil" + }, + { + "author_name": "Angelo A F Junior", + "author_inst": "Escola de Enfermagem de Ribeirao Preto EERP. Universidade de Sao Paulo USP, Ribeirao Preto, SP, Brazil" + }, + { + "author_name": "Alessandro P de Amorim", + "author_inst": "Hospital Santa Casa de Misericordia de Ribeirao Preto, Ribeirao Preto, SP, Brazil." + }, + { + "author_name": "Augusto M Degiovani", + "author_inst": "Hospital Santa Casa de Misericordia de Ribeirao Preto, Ribeirao Preto, SP, Brazil." + }, + { + "author_name": "Dayane P da Silva", + "author_inst": "Hospital Santa Casa de Misericordia de Ribeirao Preto, Ribeirao Preto, SP, Brazil." + }, + { + "author_name": "Debora C Nepomuceno", + "author_inst": "Hospital Santa Casa de Misericordia de Ribeirao Preto, Ribeirao Preto, SP, Brazil." + }, + { + "author_name": "Rafael C da Silva", + "author_inst": "Hospital Santa Casa de Misericordia de Ribeirao Preto, Ribeirao Preto, SP, Brazil." + }, + { + "author_name": "Leticia F Constant", + "author_inst": "Hospital Santa Casa de Misericordia de Ribeirao Preto, Ribeirao Preto, SP, Brazil." + }, + { + "author_name": "Fatima M Ostini", + "author_inst": "Hospital Santa Casa de Misericordia de Ribeirao Preto, Ribeirao Preto, SP, Brazil." + }, + { + "author_name": "Marley R Feitosa", + "author_inst": "Departamento de Cirurgia e Anatomia, Faculdade de Medicina de Ribeirao Preto FMRP, Universidade de Sao Paulo (USP), Ribeirao Preto, SP, Brazil" + }, + { + "author_name": "Rogerio S Parra", + "author_inst": "Departamento de Cirurgia e Anatomia, Faculdade de Medicina de Ribeirao Preto FMRP, Universidade de Sao Paulo (USP), Ribeirao Preto, SP, Brazil" + }, + { + "author_name": "Fernando C Vilar", + "author_inst": "Departamento de Clinica Medica, Faculdade de Medicina de Ribeirao Preto FMRP, Universidade de Sao Paulo (USP), Ribeirao Preto, SP, Brazil." + }, + { + "author_name": "Gilberto G Gaspar", + "author_inst": "Departamento de Clinica Medica, Faculdade de Medicina de Ribeirao Preto FMRP, Universidade de Sao Paulo (USP), Ribeirao Preto, SP, Brazil." + }, + { + "author_name": "Jose J R da Rocha", + "author_inst": "Departamento de Cirurgia e Anatomia, Faculdade de Medicina de Ribeirao Preto FMRP, Universidade de Sao Paulo (USP), Ribeirao Preto, SP, Brazil" + }, + { + "author_name": "Omar Feres", + "author_inst": "Departamento de Cirurgia e Anatomia, Faculdade de Medicina de Ribeirao Preto FMRP, Universidade de Sao Paulo (USP), Ribeirao Preto, SP, Brazil" + }, + { + "author_name": "Rita C C Barbieri", + "author_inst": "Hospital Sao Paulo, Ribeirao Preto, SP, Brazil." + }, + { + "author_name": "Fabiani G Frantz", + "author_inst": "Departamento de Analises Clinicas, Toxicologicas e Bromatologicas. Faculdade de Ciencias Farmaceuticas de Ribeirao Preto FCFRP. Universidade de Sao Paulo USP, " + }, + { + "author_name": "Sandra R Maruyama", + "author_inst": "Departamento de Genetica e Evolucao, Centro de Ciencias Biologicas e da Saude Universidade Federal de Sao Carlos UFSCar, Sao Carlos, SP, Brazil" + }, + { + "author_name": "Elisa M S Russo", + "author_inst": "Departamento de Analises Clinicas, Toxicologicas e Bromatologicas. Faculdade de Ciencias Farmaceuticas de Ribeirao Preto FCFRP. Universidade de Sao Paulo USP, " + }, + { + "author_name": "Angelina L Viana", + "author_inst": "Escola de Enfermagem de Ribeirao Preto EERP. Universidade de Sao Paulo USP, Ribeirao Preto, SP, Brazil" + }, + { + "author_name": "Ana P M Fernandes", + "author_inst": "Escola de Enfermagem de Ribeirao Preto EERP. Universidade de Sao Paulo USP, Ribeirao Preto, SP, Brazil" + }, + { + "author_name": "Isabel K F M Santos", + "author_inst": "Departamento de Bioquimica e Imunologia. Faculdade de Medicina de Ribeirao Preto FMRP. Universidade de Sao Paulo USP, Ribeirao Preto, SP, Brazil." + }, + { + "author_name": "Vania L D Bonato", + "author_inst": "Departamento de Bioquimica e Imunologia. Faculdade de Medicina de Ribeirao Preto FMRP. Universidade de Sao Paulo USP, Ribeirao Preto, SP, Brazil." + }, + { + "author_name": "Marcelo Dias-Baruffi", + "author_inst": "Departamento de Analises Clinicas, Toxicologicas e Bromatologicas. Faculdade de Ciencias Farmaceuticas de Ribeirao Preto FCFRP. Universidade de Sao Paulo USP, " + }, + { + "author_name": "Adriana Malheiro", + "author_inst": "Programa de Pos Graduacao em Imunologia Basica e Aplicada PPGIBA. Instituto de Ciencias Biologicas, Universidade Federal do Amazonas UFAM, Manaus, AM, Brazil." + }, + { + "author_name": "Ruxana T Sadikot", + "author_inst": "Department of Veterans Affairs, Division of Pulmonary and Critical Care Medicine, Emory University, Atlanta, USA" + }, + { + "author_name": "Cristina R B Cardoso", + "author_inst": "Departamento de Analises Clinicas, Toxicologicas e Bromatologicas. Faculdade de Ciencias Farmaceuticas de Ribeirao Preto FCFRP. Universidade de Sao Paulo USP, " + }, + { + "author_name": "Lucia H Faccioli", + "author_inst": "Departamento de Analises Clinicas, Toxicologicas e Bromatologicas. Faculdade de Ciencias Farmaceuticas de Ribeirao Preto FCFRP. Universidade de Sao Paulo USP, " + }, + { + "author_name": "Carlos A Sorgi", + "author_inst": "Departamento de Quimica. Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto FFCLRP. Universidade de Sao Paulo USP, Ribeirao Preto, SP, Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.20.20198242", "rel_title": "First quarter chronicle of COVID-19: an attempt to measure governments response", @@ -1172276,145 +1175198,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.23.308239", - "rel_title": "The COVID-19 PHARMACOME: Rational Selection of Drug Repurposing Candidates from Multimodal Knowledge Harmonization", - "rel_date": "2020-09-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.23.308239", - "rel_abs": "The SARS-CoV-2 pandemic has challenged researchers at a global scale. The scientific communitys massive response has resulted in a flood of experiments, analyses, hypotheses, and publications, especially in the field of drug repurposing. However, many of the proposed therapeutic compounds obtained from SARS-CoV-2 specific assays are not in agreement and thus demonstrate the need for a singular source of COVID-19 related information from which a rational selection of drug repurposing candidates can be made. In this paper, we present the COVID-19 PHARMACOME, a comprehensive drug-target-mechanism graph generated from a compilation of 10 separate disease maps and sources of experimental data focused on SARS-CoV-2 / COVID-19 pathophysiology. By applying our systematic approach, we were able to predict the synergistic effect of specific drug pairs, such as Remdesivir and Thioguanosine or Nelfinavir and Raloxifene, on SARS-CoV-2 infection. Experimental validation of our results demonstrate that our graph can be used to not only explore the involved mechanistic pathways, but also to identify novel combinations of drug repurposing candidates.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Bruce T Schultz", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing SCAI" - }, - { - "author_name": "Andrea Zaliani", - "author_inst": "Fraunhofer Institute for Molecular Biology and Applied Ecology IME" - }, - { - "author_name": "Christian Ebeling", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing SCAI" - }, - { - "author_name": "Jeanette Reinshagen", - "author_inst": "Fraunhofer Institute for Molecular Biology and Applied Ecology IME" - }, - { - "author_name": "Denisa Bojkova", - "author_inst": "Institute of Medical Virology" - }, - { - "author_name": "Vanessa Lage-Rupprecht", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing SCAI" - }, - { - "author_name": "Reagon Karki", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing (SCAI)" - }, - { - "author_name": "Soeren Lukassen", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Yojana Gadiya", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing" - }, - { - "author_name": "Neal Giri Ravindra", - "author_inst": "Yale University" - }, - { - "author_name": "Sayoni Das", - "author_inst": "PrecisionLife Ltd." - }, - { - "author_name": "Shounak Baksi", - "author_inst": "Causality BioModels Pvt Ltd" - }, - { - "author_name": "Daniel Domingo-Fernandez", - "author_inst": "Fraunhofer SCAI" - }, - { - "author_name": "Manuel Lentzen", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing (SCAI)" - }, - { - "author_name": "Mark Strivens", - "author_inst": "PrecisionLife Ltd." - }, - { - "author_name": "Tamara Raschka", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing (SCAI)" - }, - { - "author_name": "Jindrich Cinatl Jr.", - "author_inst": "Klinikum der Goethe-Universitaet" - }, - { - "author_name": "Lauren Nicole DeLong", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing (SCAI)" - }, - { - "author_name": "Philip Gribbon", - "author_inst": "Fraunhofer Institute for Molecular Biology and Applied Ecology IME" - }, - { - "author_name": "Gerd Geisslinger", - "author_inst": "Fraunhofer Cluster of Excellence for Immune Mediated Diseases" - }, - { - "author_name": "Sandra Ciesek", - "author_inst": "Fraunhofer Institute for Molecular Biology and Applied Ecology IME" - }, - { - "author_name": "David van Dijk Jr.", - "author_inst": "Yale University" - }, - { - "author_name": "Steve Gardner", - "author_inst": "PrecisionLife Ltd" - }, - { - "author_name": "Alpha Tom Kodamullil", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing SCAI" - }, - { - "author_name": "Holger Froehlich", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing (SCAI)" - }, - { - "author_name": "Manuel Peitsch", - "author_inst": "Philip Morris International" - }, - { - "author_name": "Marc Jacobs", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing (SCAI)" - }, - { - "author_name": "Julia Hoeng", - "author_inst": "Philip Morris International (Switzerland)" - }, - { - "author_name": "Roland Eils", - "author_inst": "Charite Universitaetsmedizin Berlin & Berlin Institute of Health (BIH)" - }, - { - "author_name": "Carsten Claussen", - "author_inst": "Fraunhofer Institute for Molecular Biology and Applied Ecology IME" - }, - { - "author_name": "Martin Hofmann-Apitius", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing SCAI" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.09.18.20197582", "rel_title": "Ruling In and Ruling Out COVID-19: Computing SARS-CoV-2 Infection Risk From Symptoms, Imaging and Test Data.", @@ -1172567,6 +1175350,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.16.20195230", + "rel_title": "Vent-Lock: A 3D Printed Ventilator Multiplexer to Enhance the Capacity of Treating Patients with COVID-19", + "rel_date": "2020-09-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20195230", + "rel_abs": "Mechanical ventilators are essential to patients who become critically ill from acute respiratory distress syndrome (ARDS), and shortages have been reported due to the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We utilized cost-effective, on-demand 3D printing (3DP) technology to produce critical components for a novel ventilator multiplexer system, Vent-Lock, to split one ventilator or anesthesia gas machine between two patients. FloRest, a novel 3DP flow restrictor, provides clinicians control of tidal volumes and positive end expiratory pressure (PEEP), using the 3DP manometer adaptor to monitor pressures. We tested the ventilator splitter circuit in simulation centers between artificial lungs and used an anesthesia gas machine to successfully ventilate two swines. As one of the first studies to demonstrate splitting one anesthesia gas machine between two swines, we present proof-of-concept of a de novo, closed, multiplexing system, with flow restriction for individualized patient therapy. Our studies underscore that while possible, ventilator multiplexing is a complicated synergy between machine settings, circuit modification, and patient monitoring. Consequently, ventilator multiplexing is reserved only as a last emergency resource, by trained clinicians and respiratory therapists with ventilator operative experience.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Helen Xun", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Christopher Shallal", + "author_inst": "Department of Biomedical Engineering, Johns Hopkins University" + }, + { + "author_name": "Justin Unger", + "author_inst": "Department of Civil and Systems Engineering, Johns Hopkins University" + }, + { + "author_name": "Runhan Tao", + "author_inst": "Department of Biomedical Engineering, Johns Hopkins University" + }, + { + "author_name": "Alberto Torres", + "author_inst": "Department of Civil and Systems Engineering, Johns Hopkins University" + }, + { + "author_name": "Michael Vladimirov", + "author_inst": "Department of Civil and Systems Engineering, Johns Hopkins University" + }, + { + "author_name": "Jenna Frye", + "author_inst": "Maryland Institute College of Art" + }, + { + "author_name": "Mohit Singhala", + "author_inst": "Department of Mechanical Engineering, Johns Hopkins University" + }, + { + "author_name": "Brockett Horne", + "author_inst": "Maryland Institute College of Art" + }, + { + "author_name": "Pooja Yesantharao", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Bo Soo Kim", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Broc Burke", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Michael Montana", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Michael Talcott", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Bradford Winters", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Margaret Frisella", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Bradley Kushner", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Justin Sacks", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "James Guest", + "author_inst": "Department of Civil and Systems Engineering, Johns Hopkins University" + }, + { + "author_name": "Sung Hoon Kang", + "author_inst": "Department of Mechanical Engineering, Johns Hopkins University" + }, + { + "author_name": "Julie Caffrey", + "author_inst": "Johns Hopkins School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.09.19.20198028", "rel_title": "An improved method to estimate the effective reproduction number of the COVID-19 pandemic: lessons from its application in Greece", @@ -1173894,33 +1176776,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.09.22.308098", - "rel_title": "Rapid and efficient inactivation of surface dried SARS-CoV-2 by UV-C irradiation", - "rel_date": "2020-09-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.22.308098", - "rel_abs": "BackgroundThe SARS-CoV-2 pandemic urges for cheap, reliable, and rapid technologies for disinfection and decontamination. One frequently proposed method is UV-C irradiation. However, UV-C doses necessary to achieve inactivation of high-titer SARS-CoV-2 are poorly defined.\n\nMethodsUsing a box and two handheld systems designed to decontaminate objects and surfaces we evaluated the efficacy of 254 nm UV-C treatment to inactivate surface dried SARS-CoV-2.\n\nResultsDrying for two hours did not have a major impact on the infectivity of SARS-CoV-2, indicating that exhaled virus in droplets or aerosols stays infectious on surfaces at least for a certain amount of time. Short exposure of high titer surface dried virus (3-5*10^6 IU/ml) with UV-C light (16 mJ/cm2) resulted in a total inactivation of SARS-CoV-2. Dose-dependency experiments revealed that 3.5 mJ/cm2 were still effective to achieve a > 6-log reduction in viral titers whereas 1.75 mJ/cm2 lowered infectivity only by one order of magnitude.\n\nConclusionsOur results demonstrate that SARS-CoV-2 is rapidly inactivated by relatively low doses of UV-C irradiation. Furthermore, the data reveal that the relationship between UV-C dose and log-viral titer reduction of surface residing SARS-CoV-2 is non-linear. In the context of UV-C-based technologies used to disinfect surfaces, our findings emphasize the necessity to assure sufficient and complete exposure of all relevant areas by integrated UV-C doses of at least 3.5 mJ/cm2 at 254 nm. Altogether, UV-C treatment is an effective non-chemical possibility to decontaminate surfaces from high-titer infectious SARS-CoV-2.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Natalia Ruetalo", - "author_inst": "Institiute for Medical Virology, University Hospital Tuebingen, Germany" - }, - { - "author_name": "Ramona Businger", - "author_inst": "Institiute for Medical Virology, University Hospital Tuebingen, Germany" - }, - { - "author_name": "Michael Schindler", - "author_inst": "Institiute for Medical Virology, University Hospital Tuebingen, Germany" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.09.22.308023", "rel_title": "Humoral response to SARS-CoV-2 by healthy and sick dogs during COVID-19 pandemic in Spain.", @@ -1174153,6 +1177008,20 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.09.22.308338", + "rel_title": "NeutrobodyPlex - Nanobodies to monitor a SARS-CoV-2 neutralizing immune response", + "rel_date": "2020-09-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.22.308338", + "rel_abs": "As the COVID-19 pandemic escalates, the need for effective vaccination programs, therapeutic intervention, and diagnostic tools increases. Here, we identified 11 unique nanobodies (Nbs) specific for the SARS-CoV-2 spike receptor-binding domain (RBD) of which 8 Nbs potently inhibit the interaction of RBD with angiotensin-converting enzyme 2 (ACE2) as the major viral docking site. Following a detailed epitope determination and characterization of the binding mode by structural analysis, we constructed a hetero-bivalent Nb targeting two different epitopes within the RBD:ACE2 interface. This resulted in a high-affinity binder with a viral neutralization efficacy in the picomolar range. Using the bivalent Nb as a surrogate, we established a competitive multiplex binding assay (\"NeutrobodyPlex\") for detailed analysis of the presence and performance of neutralizing RBD-binding antibodies in the serum of convalescent or vaccinated patients. As demonstrated, the NeutrobodyPlex enables high-throughput screening and detailed analysis of neutralizing immune responses in infected or vaccinated individuals, helping to monitor immune status or guide vaccine design. This approach is easily transferrable to diagnostic laboratories worldwide.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.09.22.307975", "rel_title": "Mass cytometry and artificial intelligence define CD169 as a specific marker of SARS-CoV2-induced acute respiratory distress syndrome", @@ -1175496,53 +1178365,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2020.09.18.302901", - "rel_title": "SARS-CoV-2 Nsp1 suppresses host but not viral translation through a bipartite mechanism", - "rel_date": "2020-09-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.18.302901", - "rel_abs": "The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a highly contagious virus that underlies the current COVID-19 pandemic. SARS-CoV-2 is thought to disable various features of host immunity and cellular defense. The SARS-CoV-2 nonstructural protein 1 (Nsp1) is known to inhibit host protein translation and could be a target for antiviral therapy against COVID-19. However, how SARS-CoV-2 circumvents this translational blockage for the production of its own proteins is an open question. Here, we report a bipartite mechanism of SARS-CoV-2 Nsp1 which operates by: (1) hijacking the host ribosome via direct interaction of its C-terminal domain (CT) with the 40S ribosomal subunit and (2) specifically lifting this inhibition for SARS-CoV-2 via a direct interaction of its N-terminal domain (NT) with the 5 untranslated region (5 UTR) of SARS-CoV-2 mRNA. We show that while Nsp1-CT is sufficient for binding to 40S and inhibition of host protein translation, the 5 UTR of SARS-CoV-2 mRNA removes this inhibition by binding to Nsp1-NT, suggesting that the Nsp1-NT-UTR interaction is incompatible with the Nsp1-CT-40S interaction. Indeed, lengthening the linker between Nsp1-NT and Nsp1-CT of Nsp1 progressively reduced the ability of SARS-CoV-2 5 UTR to escape the translational inhibition, supporting that the incompatibility is likely steric in nature. The short SL1 region of the 5 UTR is required for viral mRNA translation in the presence of Nsp1. Thus, our data provide a comprehensive view on how Nsp1 switches infected cells from host mRNA translation to SARS-CoV-2 mRNA translation, and that Nsp1 and 5 UTR may be targeted for anti-COVID-19 therapeutics.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ming Shi Sr.", - "author_inst": "Harbin Institute of Technology" - }, - { - "author_name": "Longfei Wang", - "author_inst": "Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School" - }, - { - "author_name": "Pietro Fontana", - "author_inst": "Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School" - }, - { - "author_name": "Setu Vora", - "author_inst": "Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School," - }, - { - "author_name": "Ying Zhang", - "author_inst": "Program in Cellular and Molecular Medicine, Boston Childrens Hospital" - }, - { - "author_name": "Tian-Min Fu", - "author_inst": "Department of Biological Chemistry and Pharmacology, The Ohio State University" - }, - { - "author_name": "Judy Lieberman", - "author_inst": "Program in Cellular and Molecular Medicine, Boston Childrens Hospital" - }, - { - "author_name": "Hao Wu", - "author_inst": "Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.09.18.304493", "rel_title": "An immunodominance hierarchy exists in CD8+ T cell responses to HLA-A*02:01-restricted epitopes identified from the non-structural polyprotein 1a of SARS-CoV-2.", @@ -1175727,6 +1178549,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.09.15.20165886", + "rel_title": "Genetically proxied inhibition of interleukin-6 signaling: opposing associations with susceptibility to COVID-19 and pneumonia", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.15.20165886", + "rel_abs": "The inflammatory cytokine interleukin-6 (IL-6) is pivotal for orchestrating the immune response. Inhibitors of IL-6 signaling are being investigated as treatments for severe coronavirus disease 2019 (COVID-19). We conducted a Mendelian randomization study investigating the effect of IL-6 signaling on susceptibility to COVID-19 and pneumonia. Our results showed that genetically proxied inhibition of IL-6 signaling was associated with reduced risk of COVID-19, but also with increased risk of pneumonia. Respiratory disease is a main feature of severe COVID-19, and the potential of IL-6 signaling inhibitors to increase risk of pneumonia warrants vigilance and caution in their application to treat COVID-19.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Susanna C Larsson", + "author_inst": "Uppsala University" + }, + { + "author_name": "Stephen Burgess", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Dipender C Gill", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.09.14.20194605", "rel_title": "Strict lockdown versus flexible social distance strategy for COVID-19 disease: a cost-effectiveness analysis", @@ -1176998,45 +1179847,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.15.20194944", - "rel_title": "COVID-19 pandemic increased the magnitude of mortality risks associated with cold temperature in Italy: A nationwide time-stratified case-crossover study", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.15.20194944", - "rel_abs": "Abstract Backgrounds: The coronavirus disease 2019 (COVID-19) pandemic and some containment measures have changed many people lives and behaviours. Whether the pandemic could change the association between cold temperature and mortality remains unknown. Objectives: We aimed to assess whether the association between cold temperature and all-cause mortality in the pandemic period has changed compared to non-COVID-19 period (2015-2019) in Italy. Methods: We collected daily all-cause mortality data and meteorological data for 107 Italian provinces from 1, January 2015 to 31, May 2020. A time-stratified case-crossover design with the distributed lag non-linear model was used to examine the association between cold temperature and all-cause mortality during the first three months (from March to May in 2020) of the COVID-19 outbreak and the same months in 2015-2019. Results: The relative risk (RR) of all-cause mortality at extreme cold temperature (2.5th percentile of temperature at 3 {degrees}C) in comparison with the minimum mortality temperature (24 {degrees}C) was 4.75 [95% confidence interval (CI): 3.90-5.79] in the pandemic period, which is more than triple higher than RR [1.41 (95%CI: 1.33-1.50)] in the same months during 2015-2019. The shift in cold-mortality association was particularly significant for people aged 65-74 years [RR (95%CI): 5.98 (3.78-9.46) in 2020 versus 1.29 (1.10-1.51) in 2015-2019], 75-84 years [5.25 (3.79-7.26) versus 1.40 (1.25-1.56)], and [≥] 85 years [5.03 (3.90-6.51) versus 1.52 (1.39-1.66)], but not significant for those aged 0-64 years [1.95 (1.17-3.24) versus 1.24 (1.05-1.48)]. Conclusion: The findings suggest that the COVID-19 pandemic enhanced the risk of cold temperature on mortality in Italy, particularly among the elderly people. Further studies are warranted to understand the exact mechanism when detailed data are available.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Wenhua Yu", - "author_inst": "Monash University" - }, - { - "author_name": "Rongbin Xu", - "author_inst": "Monash Unviersity" - }, - { - "author_name": "Tingting Ye", - "author_inst": "Monash University" - }, - { - "author_name": "Chunlei Han", - "author_inst": "Binzhou Medical University" - }, - { - "author_name": "Shanshan Li", - "author_inst": "Monash University" - }, - { - "author_name": "Yuming Guo", - "author_inst": "Monash University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.15.20191957", "rel_title": "Adherence to the test, trace and isolate system: results from a time series of 21 nationally representative surveys in the UK (the COVID-19 Rapid Survey of Adherence to Interventions and Responses study)", @@ -1177249,6 +1180059,309 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.11.20187369", + "rel_title": "Longitudinal multi-omics analysis identifies responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20187369", + "rel_abs": "The pandemic spread of the potentially life-threatening disease COVID-19 requires a thorough understanding of the longitudinal dynamics of host responses. Temporal resolution of cellular features associated with a severe disease trajectory will be a pre-requisite for finding disease outcome predictors. Here, we performed a longitudinal multi-omics study using a two-centre German cohort of 13 patients (from Cologne and Kiel, cohort 1). We analysed the bulk transcriptome, bulk DNA methylome, and single-cell transcriptome (>358,000 cells, including BCR profiles) of peripheral blood samples harvested from up to 5 time points. The results from single-cell and bulk transcriptome analyses were validated in two independent cohorts of COVID-19 patients from Bonn (18 patients, cohort 2) and Nijmegen (40 patients, cohort 3), respectively. We observed an increase of proliferating, activated plasmablasts in severe COVID-19, and show a distinct expression pattern related to a hyperactive cellular metabolism of these cells. We further identified a notable expansion of type I IFN-activated circulating megakaryocytes and their progenitors, indicative of emergency megakaryopoiesis, which was confirmed in cohort 2. These changes were accompanied by increased erythropoiesis in the critical phase of the disease with features of hypoxic signalling. Finally, projecting megakaryocyte- and erythroid cell-derived co-expression modules to longitudinal blood transcriptome samples from cohort 3 confirmed an association of early temporal changes of these features with fatal COVID-19 disease outcome. In sum, our longitudinal multi-omics study demonstrates distinct cellular and gene expression dynamics upon SARS-CoV-2 infection, which point to metabolic shifts of circulating immune cells, and reveals changes in megakaryocytes and increased erythropoiesis as important outcome indicators in severe COVID-19 patients.", + "rel_num_authors": 72, + "rel_authors": [ + { + "author_name": "Joana P. Bernardes", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Neha Mishra", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Florian Tran", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany and Department of I" + }, + { + "author_name": "Thomas Bahmer", + "author_inst": "University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Lena Best", + "author_inst": "Institute for Experimental Medicine, University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Johanna I. Blase", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Dora Bordoni", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Jeanette Franzenburg", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany and Institute of Cl" + }, + { + "author_name": "Ulf Geisen", + "author_inst": "Section for Rheumatology, Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Jonathan Josephs-Spaulding", + "author_inst": "Institute for Experimental Medicine, University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Philipp Koehler", + "author_inst": "Department I of Internal Medicine, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany; German Center for Infection Res" + }, + { + "author_name": "Axel Kuenstner", + "author_inst": "Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany." + }, + { + "author_name": "Elisa Rosati", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Anna C. Aschenbrenner", + "author_inst": "Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany" + }, + { + "author_name": "Petra Bacher", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany and Institute of Im" + }, + { + "author_name": "Nathan Baran", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Teide Boysen", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Burkhard Brandt", + "author_inst": "Institute of Clinical Chemistry, University Medical Center Schleswig-Holstein, Germany" + }, + { + "author_name": "Niklas Bruse", + "author_inst": "Department of Intensive Care Medicine, Radboud University Medical Center, Nijmegen, Netherlands; Department of Internal Medicine and Radboud Center for Infectio" + }, + { + "author_name": "Jonathan Doerr", + "author_inst": "Section for Rheumatology, Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Andreas Draeger", + "author_inst": "Department of Computer Science, University of Tuebingen; German Center for Infection Research (DZIF), partner site Tuebingen, Germany" + }, + { + "author_name": "Gunnar Elke", + "author_inst": "Department of Anaesthesiology and Intensive Care Medicine, University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "David Ellinghaus", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Julia Fischer", + "author_inst": "Department I of Internal Medicine, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany; German Center for Infection Res" + }, + { + "author_name": "Michael Forster", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Andre Franke", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Soeren Franzenburg", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Norbert Frey", + "author_inst": "Department of Internal Medicine III, University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Anette Friedrichs", + "author_inst": "Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Janina Fuss", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Andreas Glueck", + "author_inst": "Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Jacob Hamm", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Finn Hinrichsen", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Marc P. Hoeppner", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Simon Imm", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Ralf Juenker", + "author_inst": "Institute of Clinical Chemistry, University Medical Center Schleswig-Holstein, Germany" + }, + { + "author_name": "Sina Kaiser", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Ying H. Kan", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Rainer Knoll", + "author_inst": "Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany" + }, + { + "author_name": "Christoph Lange", + "author_inst": "Division of Clinical Infectious Diseases, Research Center Borstel, Borstel; German Center for Infection Research (DZIF), TTU-TB, Borstel; International Health/I" + }, + { + "author_name": "Georg Laue", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Clemes Lier", + "author_inst": "Institute of Clinical Chemistry, University Medical Center Schleswig-Holstein, Germany" + }, + { + "author_name": "Matthias Lindner", + "author_inst": "Institute of Immunology, University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Georgios Marinos", + "author_inst": "Institute for Experimental Medicine, University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Robert Markewitz", + "author_inst": "Institute of Clinical Chemistry, University Medical Center Schleswig-Holstein, Germany" + }, + { + "author_name": "Jacob Nattermann", + "author_inst": "Hepatogastroenterology at the Department of Internal Medicine I, University of Bonn, Germany" + }, + { + "author_name": "Rainer Noth", + "author_inst": "Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Peter Pickkers", + "author_inst": "Department of Intensive Care Medicine, Radboud University Medical Center, Nijmegen, Netherlands; Department of Internal Medicine and Radboud Center for Infectio" + }, + { + "author_name": "Klaus F. Rabe", + "author_inst": "LungenClinic Grosshansdorf, Airway Research Centre North, German Centre for Lung Research, Grosshansdorf, Germany; Department of Medicine, Christian Albrechts U" + }, + { + "author_name": "Alina Renz", + "author_inst": "Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany" + }, + { + "author_name": "Christoph Roecken", + "author_inst": "Department of Pathology, University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Jan Rupp", + "author_inst": "Department of Infectious Diseases and Microbiology, University of Luebeck, Luebeck, Germany" + }, + { + "author_name": "Annika Schaffarzyk", + "author_inst": "Section for Rheumatology, Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Alexander Scheffold", + "author_inst": "Institute of Immunology, University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Jonas Schulte-Schrepping", + "author_inst": "Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany" + }, + { + "author_name": "Domagoj Schunck", + "author_inst": "Department for Emergency Medicine, University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Dirk Skowasch", + "author_inst": "Section of Pneumology, Department of Internal Medicine II, University Hospital Bonn, Bonn, Germany" + }, + { + "author_name": "Thomas Ulas", + "author_inst": "PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany, and University of Bonn, Bonn, Ger" + }, + { + "author_name": "Klaus-Peter Wandinger", + "author_inst": "Institute of Clinical Chemistry, University Medical Center Schleswig-Holstein, Germany" + }, + { + "author_name": "Michael Wittig", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Johannes Zimmermann", + "author_inst": "Institute for Experimental Medicine, University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Hauke Busch", + "author_inst": "Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany" + }, + { + "author_name": "Bimba F. Hoyer", + "author_inst": "Section for Rheumatology, Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Christoph Kaleta", + "author_inst": "Institute for Experimental Medicine, University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Jan Heyckendorf", + "author_inst": "Division of Clinical Infectious Diseases, Research Center Borstel, Borstel; German Center for Infection Research (DZIF), TTU-TB, Borstel; International Health/I" + }, + { + "author_name": "Matthijs Kox", + "author_inst": "21\tDepartment of Intensive Care Medicine, Radboud University Medical Center, Nijmegen, Netherlands; Department of Internal Medicine and Radboud Center for Infec" + }, + { + "author_name": "Jan Rybniker", + "author_inst": "Department I of Internal Medicine, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany; German Center for Infection Res" + }, + { + "author_name": "Stefan Schreiber", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany and Department of I" + }, + { + "author_name": "Joachim Schultze", + "author_inst": "Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany" + }, + { + "author_name": "Philip Rosenstiel", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "- HCA Lung Biological Network", + "author_inst": "" + }, + { + "author_name": "- Deutsche COVID-19 Omics Initiative (DeCOI)", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.15.20195263", "rel_title": "Clinical Thrombosis Rate was not Increased in a Cohort of Cancer Patients with COVID-19", @@ -1178724,105 +1181837,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.16.20196071", - "rel_title": "COVID-19 and human milk: SARS-CoV-2, antibodies, and neutralizing capacity", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20196071", - "rel_abs": "Background: It is not known whether SARS-CoV-2 can be transmitted from mother to infant during breastfeeding, and if so whether the benefits of breastfeeding outweigh this risk. This study was designed to evaluate 1) if SARS-CoV-2 RNA can be detected in milk and on the breast of infected women, 2) concentrations of milk-borne anti-SARS-CoV-2 antibodies, and 3) the capacity of milk to neutralize SARS-CoV-2 infectivity. Methods: We collected 37 milk samples and 70 breast swabs (before and after breast washing) from 18 women recently diagnosed with COVID-19. Samples were analyzed for SARS-CoV-2 RNA using RT-qPCR. Milk was also analyzed for IgA and IgG specific for the nucleocapsid protein, receptor binding domain (RBD), S2 subunit of the spike protein of SARS-CoV-2, as well as 2 seasonal coronaviruses using ELISA; and for its ability to neutralize SARS-CoV-2. Results: We did not detect SARS-CoV-2 RNA in any milk sample. In contrast, SARS-CoV-2 RNA was detected on several breast swabs, although only one was considered conclusive. All milk contained SARS-CoV-2-specific IgA and IgG, and levels of anti-RBD IgA correlated with SARS-CoV-2 neutralization. Strong correlations between levels of IgA and IgG to SARS-CoV-2 and seasonal coronaviruses were noted. Conclusions: Our data do not support maternal-to-child transmission of SARS-CoV-2 via milk; however, risk of transmission via breast skin should be further evaluated. Importantly, milk produced by infected mothers is a source of anti-SARS-CoV-2 IgA and IgG and neutralizes SARS-CoV-2 activity. These results support recommendations to continue breastfeeding during mild-to-moderate maternal COVID-19 illness.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Ryan M Pace", - "author_inst": "University of Idaho" - }, - { - "author_name": "Janet E Williams", - "author_inst": "University of Idaho" - }, - { - "author_name": "Kirsi M J\u00e4rvinen", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Mandy B Belfort", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Christina DW Pace", - "author_inst": "University of Idaho" - }, - { - "author_name": "Kimberly A Lackey", - "author_inst": "University of Idaho" - }, - { - "author_name": "Alexandra C Gogel", - "author_inst": "University of Idaho" - }, - { - "author_name": "Phuong Nguyen-Contant", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Preshetha Kanagaiah", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Theresa Fitzgerald", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Rita Ferri", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Bridget Young", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Casey Rosen-Carole", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Nichole Diaz", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Courtney Meehan", - "author_inst": "Washington State University" - }, - { - "author_name": "Beatrice Caffe", - "author_inst": "Washington State University" - }, - { - "author_name": "Mark Y Sangster", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "David J Topham", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Mark A McGuire", - "author_inst": "University of Idaho" - }, - { - "author_name": "Antti Seppo", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Michelle K McGuire", - "author_inst": "University of Idaho" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.16.20195446", "rel_title": "High-throughput quantitation of SARS-CoV-2 antibodies in a single-dilution homogeneous assay", @@ -1179083,6 +1182097,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.16.20195958", + "rel_title": "Physiological Effect of Prone Positioning in Mechanically Ventilated SARS- CoV-2 Infected Patients with Severe ARDS: Preliminary Analysis of an Observational Study", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20195958", + "rel_abs": "Prone position ventilation has been shown to decrease mortality and improve oxygenation in ARDS patients. With best of our knowledge, no study reported physiological effect of prone position in SARS-CoV-2 infected ARDS patients. In this prospective observational study, data of n=20 consecutive laboratory confirmed SARS-CoV-2 patients with severe ARDS as per Berlin definition was included. Data of 20 patients analyzed with a median (Interquartile range, IQR) age of 56 (45.5-67) y and median (IQR) P/F ratio of 56 (54-66) with a median (IQR) PEEP of 12 (12-14) before initiation of prone position. Seventy-five percentage (95% CI 53.1-88.8) patients were prone responders at 16h prone session and 50 (95% CI 29.9-70.1) % patients were sustained responders. There was a significant decrease in plateau airway pressure (p<0.0001), peak airway pressure (p<0.0001) and driving pressure(p<0.0001) and increase in static compliance (p=0.001), P/F ratio (p<0.0001), PaO2 (p=0.0002)and SpO2 (p=0.0004) at 4h and 16h since initiation of prone session and also after return of supine position. Prone position in SARS-CoV-2 infected severe ARDS patients is associated with improvement in lung compliance and oxygenation in two-third of the patients and persisted in half of the patients.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Avishek Roy", + "author_inst": "AIIMS, New Delhi" + }, + { + "author_name": "Srikant Behera", + "author_inst": "AIIMS, New Delhi" + }, + { + "author_name": "Aparna Pande", + "author_inst": "AIIMS, New Delhi" + }, + { + "author_name": "Anirban Bhattacharjee", + "author_inst": "AIIMS, New Delhi" + }, + { + "author_name": "Amrita Bhattacharyya", + "author_inst": "AIIMS, New Delhi" + }, + { + "author_name": "Dalim Kumar Baidya", + "author_inst": "AIIMS, New Delhi" + }, + { + "author_name": "Rahul Kumar Anand", + "author_inst": "AIIMS, New Delhi" + }, + { + "author_name": "Bikash Ranjan Ray", + "author_inst": "AIIMS, New Delhi" + }, + { + "author_name": "Rajeshwari Subramaniam", + "author_inst": "AIIMS, New Delhi" + }, + { + "author_name": "Souvik Maitra", + "author_inst": "AIIMS, New Delhi" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.09.18.20196980", "rel_title": "Relations between demographic, geographic, and environmental statistics, and the spread of novel coronavirus disease (COVID-19) in Italy", @@ -1180386,113 +1183455,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.09.17.20194860", - "rel_title": "High-risk exposure without personal protective equipment and infection with SARS-CoV-2 in healthcare workers: results of the CoV-CONTACT prospective cohort", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.17.20194860", - "rel_abs": "Objective: We aimed to estimate the risk of infection in Healthcare workers (HCWs) following a high-risk exposure without personal protective equipment (PPE). Methods: We conducted a prospective cohort in HCWs who had a high-risk exposure to SARS-CoV-2-infected subject without PPE. Daily symptoms were self-reported for 30 days, nasopharyngeal swabs for SARS-CoV-2 RT-PCR were performed at inclusion and at days 3, 5, 7 and 12, SARS-CoV-2 serology was assessed at inclusion and at day 30. Confirmed infection was defined by positive RT-PCR or seroconversion, and possible infection by one general and one specific symptom for two consecutive days. Results: Between February 5th and May 30th, 2020, 154 HCWs were enrolled within 14 days following one high-risk exposure to either a hospital patient (70/154; 46.1%) and/or a colleague (95/154; 62.5%). At day 30, 25.0% had a confirmed infection (37/148; 95%CI, 18.4%; 32.9%), and 43.9% (65/148; 95%CI, 35.9%; 52.3%) had a confirmed or possible infection. Factors independently associated with confirmed or possible SARS-CoV-2 infection were being a pharmacist or administrative assistant rather than being from medical staff (adjusted OR (aOR)=3.8, CI95%=1.3;11.2, p=0.01), and exposure to a SARS-CoV-2-infected patient rather than exposure to a SARS-CoV-2-infected colleague (aOR=2.6, CI95%=1.2;5.9, p=0.02). Among the 26 HCWs with a SARS-CoV-2-positive nasopharyngeal swab, 7 (26.9%) had no symptom at the time of the RT-PCR positivity. Conclusions: The proportion of HCWs with confirmed or possible SARS-CoV-2 infection was high. There were less occurrences of high-risk exposure with patients than with colleagues, but those were associated with an increased risk of infection.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Sarah Tubiana", - "author_inst": "APHP; Universite de Paris, INSERM, Paris, France" - }, - { - "author_name": "Charles Burdet", - "author_inst": "APHP; Universite de Paris, INSERM, Paris, France" - }, - { - "author_name": "Nadhira Houhou", - "author_inst": "APHP, Paris, France" - }, - { - "author_name": "Michael Thy", - "author_inst": "APHP, Paris, France" - }, - { - "author_name": "Pauline Manchon", - "author_inst": "APHP, Paris, France" - }, - { - "author_name": "Francois Blanquart", - "author_inst": "Universite de Paris, INSERM; College de France, France" - }, - { - "author_name": "Charlotte Charpentier", - "author_inst": "APHP; Universite de Paris, INSERM, Paris, France" - }, - { - "author_name": "Jeremie Guedj", - "author_inst": "Universite de Paris, INSERM, France" - }, - { - "author_name": "Loubna Alavoine", - "author_inst": "APHP, Paris, France" - }, - { - "author_name": "Sylvie Behillil", - "author_inst": "Institut Pasteur, Paris, France" - }, - { - "author_name": "Anne Leclercq", - "author_inst": "APHP, Paris, France" - }, - { - "author_name": "Jean-Christophe Lucet", - "author_inst": "APHP; Universite de Paris, INSERM, Paris, France" - }, - { - "author_name": "Yazdan Yazdanpanah", - "author_inst": "APHP; Universite de Paris, INSERM, Paris, France" - }, - { - "author_name": "Mickael Attia", - "author_inst": "Institut Pasteur, Paris, France" - }, - { - "author_name": "Caroline Demeret", - "author_inst": "Institut Pasteur, Paris, France" - }, - { - "author_name": "Thierry Rose", - "author_inst": "Institut Pasteur, Paris, France" - }, - { - "author_name": "Julia A Bielicki", - "author_inst": "University of Basel Children's Hospital, Basel, Switzerland" - }, - { - "author_name": "Patricia Bruijning-Verhagen", - "author_inst": "University Medical Center Utrecht,Utrecht, The Netherlands" - }, - { - "author_name": "Herman Goossens", - "author_inst": "University of Antwerp, Antwerp, Belgium" - }, - { - "author_name": "Diane Descamps", - "author_inst": "APHP; Universite de Paris, Paris, France" - }, - { - "author_name": "Sylvie van der Werf", - "author_inst": "Institut Pasteur, Paris, France" - }, - { - "author_name": "Bruno Lina", - "author_inst": "Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France" - }, - { - "author_name": "Xavier Duval", - "author_inst": "APHP; Universite de Paris, Paris, France" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.18.20195669", "rel_title": "How do the general population behave with facemasks to prevent COVID-19 in the community?", @@ -1180789,6 +1183751,149 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.17.20196212", + "rel_title": "Early Anti-SARS-CoV-2 Convalescent Plasma in Patients Admitted for COVID-19: A Randomized Phase II Clinical Trial", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.17.20196212", + "rel_abs": "Background: Convalescent plasma (CP), despite limited evidence on its efficacy, is being widely used as a compassionate therapy for hospitalized patients with COVID-19. We aimed to evaluate the efficacy and safety of early CP therapy in COVID-19 progression. Methods: Open-label, single-center, randomized clinical trial performed in an academic center in Santiago, Chile from May 10, 2020, to July 18, 2020, with final follow-up August 17, 2020. The trial included patients hospitalized within the first 7 days of COVID-19 symptoms onset, presenting risk factors for illness progression and not on mechanical ventilation. The intervention consisted in immediate CP (early plasma group) versus no CP unless developing pre-specified criteria of deterioration (deferred plasma group). Additional standard treatment was allowed in both arms. The primary outcome was a composite of mechanical ventilation, hospitalization for >14 days or death. Key secondary outcomes included: time to respiratory failure, days of mechanical ventilation, hospital length-of-stay, mortality at 30 days, and SARS-CoV-2 RT-PCR clearance rate. Results: Of 58 randomized patients (mean age, 65.8 years, 50% male), 57 (98.3%) completed the trial. A total of 13 (43.3%) participants from the deferred group received plasma based on clinical aggravation. We found no benefit in the primary outcome (32.1% vs 33.3%, OR 0.95, 95% CI 0.32-2.84, p>0.99) in the early versus deferred CP group. In-hospital mortality rate was 17.9% vs 6.7% (OR 3.04, 95% CI 0.54-17.2, p=0.25), mechanical ventilation 17.9% vs 6.7% (OR 3.04, 95% CI 0.54-17.2, p=0.25), and prolonged hospitalization 21.4% vs 30% (OR 0.64, 95%CI, 0.19-2.1, p=0.55) in early versus deferred CP group, respectively. Viral clearance rate on day 3 (26% vs 8%, p=0.20) and day 7 (38% vs 19%, p=0.37) did not differ between groups. Two patients experienced serious adverse events within 6 or less hours after plasma transfusion. Conclusion: Immediate addition of CP therapy in early stages of COVID-19 -compared to its use only in case of patient deterioration- did not confer benefits in mortality, length of hospitalization or mechanical ventilation requirement.", + "rel_num_authors": 32, + "rel_authors": [ + { + "author_name": "Mar\u00eda Elvira Balcells", + "author_inst": "Department of Infectious Diseases. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile." + }, + { + "author_name": "Luis Rojas", + "author_inst": "Department of Internal Medicine. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile" + }, + { + "author_name": "Nicole Le Corre", + "author_inst": "Department of Pediatric Infectious Diseases and Immunology. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile." + }, + { + "author_name": "Constanza Mart\u00ednez-Valdebenito", + "author_inst": "Diagnostic Virology Laboratory. Red de Salud UC Christus." + }, + { + "author_name": "Mar\u00eda Elena Ceballos", + "author_inst": "Department of Infectious Diseases. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile" + }, + { + "author_name": "Marcela Ferr\u00e9s", + "author_inst": "Department of Pediatric Infectious Diseases and Immunology. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile" + }, + { + "author_name": "Mayling Chang", + "author_inst": "Department of Hematology and Oncology. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile" + }, + { + "author_name": "Cecilia Vizcaya", + "author_inst": "Department of Pediatric Infectious Diseases and Immunology. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile." + }, + { + "author_name": "Sebasti\u00e1n Mondaca", + "author_inst": "Department of Hematology and Oncology. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile." + }, + { + "author_name": "\u00c1lvaro Huete", + "author_inst": "Department of Radiology. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile." + }, + { + "author_name": "Ricardo Castro", + "author_inst": "Department of Intensive Care Medicine. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile" + }, + { + "author_name": "Mauricio Sarmiento", + "author_inst": "Department of Hematology and Oncology. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile." + }, + { + "author_name": "Luis Villarroel", + "author_inst": "Department of Public Health. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile." + }, + { + "author_name": "Alejandra Pizarro", + "author_inst": "Department of Infectious Diseases. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile." + }, + { + "author_name": "Patricio Ross", + "author_inst": "Department of Internal Medicine. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile." + }, + { + "author_name": "Jaime Santander", + "author_inst": "Department of Psychiatry. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile." + }, + { + "author_name": "B\u00e1rbara Lara", + "author_inst": "Emergency Medicine Section. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile." + }, + { + "author_name": "Marcela Ferrada", + "author_inst": "Clinical Research Center. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile." + }, + { + "author_name": "Sergio Vargas-Salas", + "author_inst": "Department of Hematology and Oncology. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile." + }, + { + "author_name": "Carolina Beltr\u00e1n-Pavez", + "author_inst": "Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences. Faculty of Medicine. Universidad de Chile. HIV/AIDS Work Grou" + }, + { + "author_name": "Ricardo Soto-Rifo", + "author_inst": "Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile. HIV/AIDS Work Grou" + }, + { + "author_name": "Fernando Valiente-Echeverr\u00eda", + "author_inst": "Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile. HIV/AIDS Work Grou" + }, + { + "author_name": "Christian Caglevic", + "author_inst": "Instituto Oncol\u00f3gico Fundaci\u00f3n Arturo L\u00f3pez P\u00e9rez (FALP) Santiago, Chile" + }, + { + "author_name": "Mauricio Mahave", + "author_inst": "Instituto Oncol\u00f3gico Fundaci\u00f3n Arturo L\u00f3pez P\u00e9rez (FALP) Santiago, Chile" + }, + { + "author_name": "Carolina Selman", + "author_inst": "Instituto Oncol\u00f3gico Fundaci\u00f3n Arturo L\u00f3pez P\u00e9rez (FALP) Santiago, Chile" + }, + { + "author_name": "Raimundo Gazit\u00faa", + "author_inst": "Instituto Oncol\u00f3gico Fundaci\u00f3n Arturo L\u00f3pez P\u00e9rez (FALP) Santiago, Chile" + }, + { + "author_name": "Jos\u00e9 Luis Briones", + "author_inst": "Instituto Oncol\u00f3gico Fundaci\u00f3n Arturo L\u00f3pez P\u00e9rez (FALP) Santiago, Chile" + }, + { + "author_name": "Franz Villarroel-Espindola", + "author_inst": "Instituto Oncol\u00f3gico, Fundaci\u00f3n Arturo L\u00f3pez P\u00e9rez (FALP). Translational Medicine Research Laboratory, Fundaci\u00f3n Arturo L\u00f3pez P\u00e9rez (FALP), Chile" + }, + { + "author_name": "Carlos Balmaceda", + "author_inst": "Health Technology Assessment Unit, Clinical Research Center, School of Medicine, Pontificia Universidad Cat\u00f3lica de Chile" + }, + { + "author_name": "Manuel A. Espinoza", + "author_inst": "Department of Public Health. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile." + }, + { + "author_name": "Jaime Pereira", + "author_inst": "Department of Hematology and Oncology. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile." + }, + { + "author_name": "Bruno Nervi", + "author_inst": "Department of Hematology and Oncology. School of Medicine. Pontificia Universidad Cat\u00f3lica de Chile." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.17.20196469", "rel_title": "Renin-angiotensin system inhibitors and susceptibility to COVID-19 in patients with hypertension: a propensity score-matched cohort study in primary care", @@ -1182444,61 +1185549,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.09.16.300459", - "rel_title": "The flexibility of ACE2 in the context of SARS-CoV-2 infection", - "rel_date": "2020-09-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.16.300459", - "rel_abs": "The COVID-19 pandemic has swept over the world in the past months, causing significant loss of life and consequences to human health. Although numerous drug and vaccine developments efforts are underway, many questions remain outstanding on the mechanism of SARS-CoV-2 viral association to angiotensin-converting enzyme 2 (ACE2), its main host receptor, and entry in the cell. Structural and biophysical studies indicate some degree of flexibility in the viral extracellular Spike glycoprotein and at the receptor binding domain-receptor interface, suggesting a role in infection. Here, we perform all-atom molecular dynamics simulations of the glycosylated, full-length membrane-bound ACE2 receptor, in both an apo and spike receptor binding domain (RBD) bound state, in order to probe the intrinsic dynamics of the ACE2 receptor in the context of the cell surface. A large degree of fluctuation in the full length structure is observed, indicating hinge bending motions at the linker region connecting the head to the transmembrane helix, while still not disrupting the ACE2 homodimer or ACE2-RBD interfaces. This flexibility translates into an ensemble of ACE2 homodimer conformations that could sterically accommodate binding of the spike trimer to more than one ACE2 homodimer, and suggests a mechanical contribution of the host receptor towards the large spike conformational changes required for cell fusion. This work presents further structural and functional insights into the role of ACE2 in viral infection that can be exploited for the rational design of effective SARS-CoV-2 therapeutics.\n\nStatement of SignificanceAs the host receptor of SARS-CoV-2, ACE2 has been the subject of extensive structural and antibody design efforts in aims to curtail COVID-19 spread. Here, we perform molecular dynamics simulations of the homodimer ACE2 full-length structure to study the dynamics of this protein in the context of the cellular membrane. The simulations evidence exceptional plasticity in the protein structure due to flexible hinge motions in the head-transmembrane domain linker region and helix mobility in the membrane, resulting in a varied ensemble of conformations distinct from the experimental structures. Our findings suggest a dynamical contribution of ACE2 to the spike glycoprotein shedding required for infection, and contribute to the question of stoichiometry of the Spike-ACE2 complex.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Emilia P. Barros", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Lorenzo Casalino", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Zied Gaieb", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Abigail C Dommer", - "author_inst": "UC San Diego" - }, - { - "author_name": "Yuzhang Wang", - "author_inst": "State University of New York" - }, - { - "author_name": "Lucy Fallon", - "author_inst": "State University of New York" - }, - { - "author_name": "Lauren Raguette", - "author_inst": "State University of New York" - }, - { - "author_name": "Kellon Belfon", - "author_inst": "State University of New York" - }, - { - "author_name": "Carlos L. Simmerling", - "author_inst": "SUNY at Stony Brook" - }, - { - "author_name": "Rommie E. Amaro", - "author_inst": "UC San Diego" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.09.16.299537", "rel_title": "Mouse model for testing SARS-CoV-2 antivirals: Pharmacokinetics", @@ -1182703,6 +1185753,193 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.09.16.300277", + "rel_title": "Baricitinib treatment resolves lower airway inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques", + "rel_date": "2020-09-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.16.300277", + "rel_abs": "Effective therapeutics aimed at mitigating COVID-19 symptoms are urgently needed. SARS-CoV-2 induced hypercytokinemia and systemic inflammation are associated with disease severity. Baricitinib, a clinically approved JAK1/2 inhibitor with potent anti-inflammatory properties is currently being investigated in COVID-19 human clinical trials. Recent reports suggest that baricitinib may also have antiviral activity in limiting viral endocytosis. Here, we investigated the immunologic and virologic efficacy of baricitinib in a rhesus macaque model of SARS-CoV-2 infection. Viral shedding measured from nasal and throat swabs, bronchoalveolar lavages and tissues was not reduced with baricitinib. Type I IFN antiviral responses and SARS-CoV-2 specific T cell responses remained similar between the two groups. Importantly, however, animals treated with baricitinib showed reduced immune activation, decreased infiltration of neutrophils into the lung, reduced NETosis activity, and more limited lung pathology. Moreover, baricitinib treated animals had a rapid and remarkably potent suppression of alveolar macrophage derived production of cytokines and chemokines responsible for inflammation and neutrophil recruitment. These data support a beneficial role for, and elucidate the immunological mechanisms underlying, the use of baricitinib as a frontline treatment for severe inflammation induced by SARS-CoV-2 infection.", + "rel_num_authors": 43, + "rel_authors": [ + { + "author_name": "Timothy N Hoang", + "author_inst": "Emory University" + }, + { + "author_name": "Maria Pino", + "author_inst": "Emory University" + }, + { + "author_name": "Arun K Boddapati", + "author_inst": "Emory University" + }, + { + "author_name": "Elise G Viox", + "author_inst": "Emory University" + }, + { + "author_name": "Carly E Starke", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Amit A Upadhyay", + "author_inst": "Emory University" + }, + { + "author_name": "Sanjeev Gumber", + "author_inst": "Emory University" + }, + { + "author_name": "Kathleen Busman-Sahay", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Zachary Strongin", + "author_inst": "Emory University" + }, + { + "author_name": "Justin L Harper", + "author_inst": "Emory University" + }, + { + "author_name": "Gregory K Tharp", + "author_inst": "Emory University" + }, + { + "author_name": "Kathryn L Pellegrini", + "author_inst": "Emory University" + }, + { + "author_name": "Shannon Kirejczyk", + "author_inst": "Emory University" + }, + { + "author_name": "Keivan Zandi", + "author_inst": "Emory University" + }, + { + "author_name": "Sijia Tao", + "author_inst": "Emory University" + }, + { + "author_name": "Tristan R Horton", + "author_inst": "Emory University" + }, + { + "author_name": "Elizabeth N Beagle", + "author_inst": "Emory University" + }, + { + "author_name": "Ernestine A Mahar", + "author_inst": "Emory University" + }, + { + "author_name": "Michelle YH Lee", + "author_inst": "Emory University" + }, + { + "author_name": "Joyce Cohen", + "author_inst": "Emory University" + }, + { + "author_name": "Sherrie Jean", + "author_inst": "Emory University" + }, + { + "author_name": "Jennifer S Wood", + "author_inst": "Emory University" + }, + { + "author_name": "Fawn Connor-Stroud", + "author_inst": "Emory University" + }, + { + "author_name": "Rachelle L Stammen", + "author_inst": "Emory University" + }, + { + "author_name": "Olivia M Delmas", + "author_inst": "Emory University" + }, + { + "author_name": "Shelly Wang", + "author_inst": "Emory University" + }, + { + "author_name": "Kimberly A Cooney", + "author_inst": "Emory University" + }, + { + "author_name": "Michael N Sayegh", + "author_inst": "Emory University" + }, + { + "author_name": "Lanfang Wang", + "author_inst": "Emory Univeersity" + }, + { + "author_name": "Daniela Weiskopf", + "author_inst": "La Jolla Institute For Allergy & Immunology" + }, + { + "author_name": "Peter D Filev", + "author_inst": "Emory University" + }, + { + "author_name": "Jesse Waggoner", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Anne Piantadosi", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Sudhir P Kasturi", + "author_inst": "Emory University" + }, + { + "author_name": "Hilmi Al-Shakhshir", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Susan P Ribeiro", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Rafick P Sekaly", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Rebecca D Levit", + "author_inst": "Emory University" + }, + { + "author_name": "Jacob D Estes", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Thomas H Vanderford", + "author_inst": "Emory University" + }, + { + "author_name": "Raymond F Schinazi", + "author_inst": "Emory University" + }, + { + "author_name": "Steven E Bosinger", + "author_inst": "Emory University" + }, + { + "author_name": "Mirko Paiardini", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.09.16.297366", "rel_title": "Bromelain Inhibits SARS-CoV-2 Infection in VeroE6 Cells", @@ -1184018,73 +1187255,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.14.20194472", - "rel_title": "SARS-CoV-2 in wastewater settled solids is associated with COVID-19 cases in a large urban sewershed", - "rel_date": "2020-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.14.20194472", - "rel_abs": "Wastewater-based epidemiology (WBE) may be useful for informing public health response to viral diseases like COVID-19 caused by SARS-CoV-2. We quantified SARS-CoV-2 RNA in wastewater influent and primary settled solids in two wastewater treatment plants to inform the pre-analytical and analytical approaches, and to assess whether influent or solids harbored more viral targets. The primary settled solids samples resulted in higher SARS-CoV-2 detection frequencies than the corresponding influent samples. Likewise, SARS-CoV-2 RNA was more readily detected in solids using one-step digital droplet (dd)RT-PCR than with two-step RT-QPCR and two-step ddRT-PCR, likely owing to reduced inhibition with the one-step ddRT-PCR assay. We subsequently analyzed a longitudinal time series of 89 settled solids samples from a single plant for SARS-CoV-2 RNA as well as coronavirus recovery (bovine coronavirus) and fecal strength (pepper mild mottle virus, PMMoV) controls. SARS-CoV-2 RNA targets N1 and N2 concentrations correlate positively and significantly with COVID-19 clinical confirmed case counts in the sewershed. Together, the results demonstrate that measuring SARS-CoV-2 RNA concentrations in settled solids may be a more sensitive approach than measuring SARs-CoV-2 in influent.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Katherine Graham", - "author_inst": "Stanford University" - }, - { - "author_name": "Stephanie Loeb", - "author_inst": "Stanford University" - }, - { - "author_name": "Marlene Wolfe", - "author_inst": "Stanford University" - }, - { - "author_name": "David Catoe", - "author_inst": "SLAC National Accelerator Laboratory" - }, - { - "author_name": "Nasa Sinnott-Armstrong", - "author_inst": "Stanford University" - }, - { - "author_name": "Sooyeol Kim", - "author_inst": "Stanford University" - }, - { - "author_name": "Kevan Yamahara", - "author_inst": "Monterey Bay Aquarium Research Institute" - }, - { - "author_name": "Lauren Sassoubre", - "author_inst": "University of San Francisco" - }, - { - "author_name": "Lorelay Mendoza", - "author_inst": "Stanford University" - }, - { - "author_name": "Laura Roldan-Hernandez", - "author_inst": "Stanford University" - }, - { - "author_name": "Linlin Li", - "author_inst": "County of Santa Clara Public Health Department" - }, - { - "author_name": "Krista Wigginton", - "author_inst": "University of Michigan" - }, - { - "author_name": "Alexandria Boehm", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.14.20191759", "rel_title": "SARS-CoV-2 N-antigenemia: A new alternative to nucleic acid amplification techniques", @@ -1184445,6 +1187615,81 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.09.15.298067", + "rel_title": "Antibody potency, effector function and combinations in protection from SARS-CoV-2 infection in vivo", + "rel_date": "2020-09-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.15.298067", + "rel_abs": "SARS-CoV-2, the causative agent of COVID-19, is responsible for over 24 million infections and 800,000 deaths since its emergence in December 2019. There are few therapeutic options and no approved vaccines. Here we examine the properties of highly potent human monoclonal antibodies (hu-mAbs) in a mouse adapted model of SARS-CoV-2 infection (SARS-CoV-2 MA). In vitro antibody neutralization potency did not uniformly correlate with in vivo activity, and some hu-mAbs were more potent in combination in vivo. Analysis of antibody Fc regions revealed that binding to activating Fc receptors is essential for optimal protection against SARS-CoV-2 MA. The data indicate that hu-mAb protective activity is dependent on intact effector function and that in vivo testing is required to establish optimal hu-mAb combinations for COVID-19 prevention.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Alexandra Schaefer", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Frauke Muecksch", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Julio C.C. Lorenzi", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Sarah R. Leist", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Melissa Cipolla", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Stylianos Bournazos", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Fabian Schmidt", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Anna Gazumyan", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Ralph S. Baric", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Davide F. Robbiani", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Theodora Hatziioannou", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Jeffrey V. Ravetch", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Paul D. Bieniasz", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Michel C. Nussenzweig", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Timothy P. Sheahan", + "author_inst": "University of North Carolina at Chapel Hill" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.09.15.296228", "rel_title": "The Anti-histamine Azelastine, Identified by Computational Drug Repurposing, Inhibits SARS-CoV-2 Infection in Reconstituted Human Nasal Tissue In Vitro", @@ -1185632,125 +1188877,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.09.13.20193581", - "rel_title": "Rapid, accurate, nucleobase detection using FnCas9", - "rel_date": "2020-09-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.13.20193581", - "rel_abs": "Rapid detection of pathogenic sequences or variants in DNA and RNA through a point-of-care diagnostic approach is valuable for accelerated clinical prognosis as has been witnessed during the recent COVID-19 outbreak. Traditional methods relying on qPCR or sequencing are difficult to implement in settings with limited resources necessitating the development of accurate alternative testing strategies that perform robustly. Here, we present FnCas9 Editor Linked Uniform Detection Assay (FELUDA) that employs a direct Cas9 based enzymatic readout for detecting nucleotide sequences and identifying nucleobase identity without the requirement of trans-cleavage activity of reporter molecules. We demonstrate that FELUDA is 100% accurate in detecting single nucleotide variants (SNVs) including heterozygous carriers of a mutation and present a simple design strategy in the form of a web-tool, JATAYU, for its implementation. FELUDA is semi quantitative, can be adapted to multiple signal detection platforms and can be quickly designed and deployed for versatile applications such as infectious disease outbreaks like COVID-19. Using a lateral flow readout within 1h, FELUDA shows 100% sensitivity and 97% specificity across all range of viral loads in clinical samples. In combination with RT-RPA and a smartphone application True Outcome Predicted via Strip Evaluation (TOPSE), we present a prototype for FELUDA for CoV-2 detection at home.\n\nSingle sentence summaryA method to identify nucleotide sequence or nucleobase identity using FnCas9 and its implementation in the rapid and accurate diagnosis of SARS-CoV-2", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Mohd. Azhar", - "author_inst": "CSIR Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Rhythm Phutela", - "author_inst": "CSIR Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Manoj Kumar", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Asgar Hussain Ansari", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Riya Rauthan", - "author_inst": "CSIR Institute of Genomics and Integrative Biology, New Delhi" - }, - { - "author_name": "Sneha Gulati", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Namrata Sharma", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Dipanjali Sinha", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Saumya Sharma", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Sunaina Singh", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Sundaram Acharya", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Deepanjan Paul", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Poorti Kathpalia", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Meghali Aich", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Paras Sehgal", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Gyan Ranjan", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Rahul C Bhoyar", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "- Indian CoV2 Genomics & Genetic Epidemiology (IndiCovGEN) Consortium", - "author_inst": "" - }, - { - "author_name": "Khushboo Singhal", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Harsha Lad", - "author_inst": "CSIR-Sickle Cell Anemia Mission Laboratory, Chhattisgarh Institute of Medical Sciences, Bilaspur 495001, Chhattisgarh, India" - }, - { - "author_name": "Pradeep Kumar Patra", - "author_inst": "CSIR-Sickle Cell Anemia Mission Laboratory, Chhattisgarh Institute of Medical Sciences, Bilaspur 495001, Chhattisgarh, India" - }, - { - "author_name": "Govind Makharia", - "author_inst": "All India Institute of Medical Sciences, Ansari Nagar East, New Delhi 110029, India" - }, - { - "author_name": "Giriraj Ratan Chandak", - "author_inst": "CSIR-Center for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telengana 500007" - }, - { - "author_name": "Bala Pesala", - "author_inst": "CSIR-Central Electronics Engineering Research Institute, Chennai, India" - }, - { - "author_name": "Debojyoti Chakraborty", - "author_inst": "CSIR Institute of Genomics & Integrative Biology" - }, - { - "author_name": "Souvik Maiti", - "author_inst": "CSIR Institute of Genomics & Integrative Biology, New Delhi" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.09.13.20193722", "rel_title": "Sensing of COVID-19 Antibodies in Seconds via Aerosol Jet Printed Three Dimensional Electrodes", @@ -1185983,6 +1189109,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.09.10.20190017", + "rel_title": "Quantifying heterogeneity in SARS-CoV-2 transmission during the lockdown in India", + "rel_date": "2020-09-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.10.20190017", + "rel_abs": "The novel SARS-CoV-2 virus shows marked heterogeneity in its transmission. Here, we used data collected from contact tracing during the lockdown in Punjab, a major state in India, to quantify this heterogeneity, and to examine implications for transmission dynamics. We found evidence of heterogeneity acting at multiple levels: in the number of potentially infectious contacts per index case, and in the per-contact risk of infection. Incorporating these findings in simple mathematical models of disease transmission reveals that these heterogeneities act in combination to strongly influence transmission dynamics. Standard approaches, such as representing heterogeneity through secondary case distributions, could be biased by neglecting these underlying interactions between heterogeneities. We discuss implications for policy, and for more efficient contact tracing in resource-constrained settings such as India. Our results highlight how contact tracing, an important public health measure, can also provide important insights into epidemic spread and control.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Nimalan Arinaminpathy", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jishnu Das", + "author_inst": "Georgetown University" + }, + { + "author_name": "Tyler McCormick", + "author_inst": "University of Washington" + }, + { + "author_name": "Partha Mukhopadhyay", + "author_inst": "Centre for Policy Research, India" + }, + { + "author_name": "Neelanjan Sircar", + "author_inst": "Ashoka University, and Centre for Policy Research, India" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.13.20193508", "rel_title": "Slight reduction in SARS-CoV-2 exposure viral load due to masking results in a significant reduction in transmission with widespread implementation", @@ -1187166,41 +1190327,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.11.20193052", - "rel_title": "Adapting Lot Quality Assurance Sampling to accommodate imperfect tests: application to COVID-19 serosurveillance in Haiti", - "rel_date": "2020-09-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20193052", - "rel_abs": "Background: Lot Quality Assurance Sampling (LQAS), a tool used for monitoring health indicators in low resource settings resulting in \"high\" or \"low\" classifications, assumes that determination of the trait of interest is perfect. This is often not true for diagnostic tests, with imperfect sensitivity and specificity. Here, we develop Lot Quality Assurance Sampling for Imperfect Tests (LQAS-IMP) to address this issue and apply it to a COVID-19 serosurveillance study in Haiti. Development: As part of the standard LQAS procedure, the user specifies allowable classification errors for the system, which is defined by a sample size and decision rule. We show that when an imperfect diagnostic test is used, the classification errors are larger than specified. We derive a modified procedure, LQAS-IMP, that accounts for the sensitivity and specificity of a diagnostic test to yield correct classification errors. Application: At Zanmi Lasante health facilities in Haiti, the goal was to assess the prior circulation of COVID-19 among healthcare workers (HCWs) using a limited number of antibody tests. As the COVID-19 antibody tests were known to have imperfect diagnostic accuracy, we used the LQAS-IMP procedure to define valid systems for sampling at eleven hospitals in Haiti. Conclusions: The LQAS-IMP procedure accounts for imperfect sensitivity and specificity in system design; if the accuracy of a test is known, the use of LQAS-IMP extends LQAS to applications for indicators that are based on laboratory tests, such as COVID-19 antibodies.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Isabel R Fulcher", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Mary Clisbee", - "author_inst": "Zanmi Lasante" - }, - { - "author_name": "Wesler Lambert", - "author_inst": "Zanmi Lasante" - }, - { - "author_name": "Fernet Renand Leandre", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Bethany Hedt-Gauthier", - "author_inst": "Harvard Medical School" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.11.20192401", "rel_title": "Anakinra and Intravenous IgG versus Tocilizumab in the Treatment of COVID-19 Pneumonia", @@ -1187401,6 +1190527,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.09.11.20190520", + "rel_title": "SARS2 simplified scores to estimate risk of hospitalization and death among patients with COVID-19", + "rel_date": "2020-09-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20190520", + "rel_abs": "Although models have been developed for predicting severity of COVID-19 based on the medical history of patients, simplified risk prediction models with good accuracy could be more practical. In this study, we examined utility of simpler models for estimating risk of hospitalization of patients with COVID-19 and mortality of these patients based on demographic characteristics (sex, age, race, median household income based on zip code) and smoking status of 12,347 patients who tested positive at Mass General Brigham centers. The corresponding electronic health records were queried from 02/26/2020 to 07/14/2020 to construct derivation and validation cohorts. The derivation cohort was used to fit a generalized linear model for estimating risk of hospitalization within 30 days of COVID-19 diagnosis and mortality within approximately 3 months for the hospitalized patients. On the validation cohort, the model resulted in c-statistics of 0.77 [95% CI: 0.73-0.80] for hospitalization outcome, and 0.72 [95% CI: 0.69-0.74] for mortality among hospitalized patients. Higher risk was associated with older age, male sex, black ethnicity, lower socioeconomic status, and current/past smoking status. The model can be applied to predict risk of hospitalization and mortality, and could aid decision making when detailed medical history of patients is not easily available.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Hesam Dashti", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Elise Roche", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "David Bates", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Samia Mora", + "author_inst": "Brigham and Women's Hospital and Harvard Medical School" + }, + { + "author_name": "Olga Demler", + "author_inst": "Division of Preventive Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.12.293498", "rel_title": "Discovery of a Novel Inhibitor of Coronavirus 3CL Protease as a Clinical Candidate for the Potential Treatment of COVID-19", @@ -1188940,29 +1192101,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.10.20192120", - "rel_title": "Estimating the global reduction in transmission and rise in detection capacity of the novel coronavirus SARS-CoV-2 in early 2020", - "rel_date": "2020-09-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.10.20192120", - "rel_abs": "To better control the SARS-CoV-2 pandemic, it is essential to quantify the impact of control measures and the fraction of infected individuals that are detected. To this end we developed a deterministic transmission model based on the renewal equation and fitted the model to daily case and death data in the first few months of 2020 in 79 countries and states, representing more than 4 billions individuals. Based on a region-specific infected fatality ratio, we inferred the time-varying probability of case detection and the time-varying decline in transmissiblity. The model was validated by the good correlation between the predicted total number of infected and that found in serosurveys; and most importantly by the strong correlation between the inferred probability of detection and the number of daily tests per inhabitant, with 50% detection achieved with 0.003 daily tests per inhabitants. Most of the decline in transmission was explained by the reductions in transmissibility (social distancing), which avoided 107 deaths in the regions studied over the first four months of 2020. In contrast, symptom-based testing and isolation was not an efficient way to control the spread of the disease, as a large part of transmission happens before symptoms and only a small fraction of infected individuals was typically detected. We developed a phenomenological model to link the number of daily tests with the probability of detection and verified the prediction that increasing test capacity increases the probability of detection less than proportionally. Together these results suggest that little control can be achieved by symptom-based testing and isolation alone.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Antoine Belloir", - "author_inst": "Ecole Polytechnique" - }, - { - "author_name": "Francois Blanquart", - "author_inst": "CNRS" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.10.20191841", "rel_title": "The King's College London Coronavirus Health and Experiences of Colleagues at King's Study: SARS-CoV-2 antibody response in an occupational sample", @@ -1189179,6 +1192317,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, + { + "rel_doi": "10.1101/2020.09.09.20191593", + "rel_title": "Title: COVID-19Predict - Predicting Pandemic Trends.", + "rel_date": "2020-09-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.09.20191593", + "rel_abs": "BackgroundGiven the global public health importance of the COVID-19 pandemic, data comparisons that predict on-going infection and mortality trends across national, state and county-level administrative jurisdictions are vitally important. We have designed a COVID-19 dashboard with the goal of providing concise sets of summarized data presentations to simplify interpretation of basic statistics and location-specific current and short-term future risks of infection.\n\nMethodsWe perform continuous collection and analyses of publicly available data accessible through the COVID-19 dashboard hosted at Johns Hopkins University (JHU github). Additionally, we utilize the accumulation of cases and deaths to provide dynamic 7-day short-term predictions on these outcomes across these national, state and county administrative levels.\n\nFindingsCOVID-19Predict produces 2,100 daily predictions [or calculations] on the state level (50 States x3 models x7 days x2 cases and deaths) and 131,964 (3,142 Counties x3 models x7 days x2 cases and deaths) on the county level. To assess how robust our models have performed in making short-term predictions over the course of the pandemic, we used available case data for all 50 U.S. states spanning the period January 20 - August 16 2020 in a retrospective analysis. Results showed a 3.7% to -0.2% mean error of deviation from the actual case predictions to date.\n\nInterpretationOur transparent methods and admin-level visualizations provide real-time data reporting and forecasts related to on-going COVID-19 transmission allowing viewers (individuals, health care providers, public health practitioners and policy makers) to develop their own perspectives and expectations regarding public life activity decisions.\n\nFundingFinancial resources for this study have been provided by Case Western Reserve University.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jurgen Bosch", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Austin Wilson", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Karthik O'Neil", + "author_inst": "Andrews Osborne Academy" + }, + { + "author_name": "Pater A Zimmerman", + "author_inst": "Case Western Reserve University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.09.10.20190793", "rel_title": "The impact of asthma on mental health & wellbeing during COVID-19 lockdown", @@ -1190578,77 +1193747,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.09.11.20192591", - "rel_title": "Saliva as a potential clinical specimen for diagnosis of SARS-CoV-2", - "rel_date": "2020-09-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20192591", - "rel_abs": "Background It is almost nine months, still there is no sign to stop the spreading of the COVID-19 pandemic. Rapid and early detection of the virus is the master key to cease the rapid spread and break the human transmission chain. There are very few studies in search of an alternate and convenient diagnostic tool which can substitute nasopharyngeal swab (NPS) specimen for detection of SARS-CoV-2. We aimed to analyse the comparison and agreement between the feasibility of using the saliva in comparison to NPS for diagnosis of SARS-CoV-2. Methods A total number of 74 patients were enrolled for this study. We analysed and compared the NPS and saliva specimen collected within 48 h after the symptom onset. We used real time quantitative polymerase chain reaction (RT-qPCR), gene sequencing for the detection and determination SARS-CoV-2 specific genes. Phylogenetic tree was constructed to establish the isolation of viral RNA from saliva. We use Bland-Altman model to identify the agreement between two sampling methods. Findings This study shows a lower CT mean value for the detection of SARS-CoV-2 ORF1 gene (27.07; 95% CI, 25.62 to 28.52) in saliva methods than that of NPS (28.24; 95% CI, 26.62 to 29.85) sampling method. Bland-Altman analysis produces relatively smaller bias and high agreement between these specimen tools. Phylogenetic analysis with the RdRp and Spike gene confirmed the presence of SARS-CoV-2 in the saliva samples. Interpretation: In conclusion, our study highlights that saliva represents a promising tool in COVID-19 diagnosis and would reduce the exposure risk of frontline health workers which is one of biggest concern in primary healthcare settings.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Dr. Debdutta Bhattacharya", - "author_inst": "ICMR - Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Debaprasad Parai", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Usha Kiran Rout", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Rashmi Ranjan Nanda", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Srikanta Kanungo", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Girish Chandra Dash", - "author_inst": "ICMR-Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Subrat Kumar Palo", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Siddharth Giri", - "author_inst": "ICMR- Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Hari Ram Choudhary", - "author_inst": "ICMR- Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Jaya Singh Kshatri", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Jyotirmayee Turuk", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Bijay Mishra", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Saroj Dash", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Sanghamitra Pati", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.10.20192260", "rel_title": "Evaluating ten commercially-available SARS-CoV-2 rapid serological tests using the STARD (Standards for Reporting of Diagnostic Accuracy Studies) method.", @@ -1190869,6 +1193967,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.11.293449", + "rel_title": "Identifying zoonotic origin of SARS-CoV-2 by modeling the binding affinity between Spike receptor-binding domain and host ACE2", + "rel_date": "2020-09-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.11.293449", + "rel_abs": "Despite considerable research progress on SARS-CoV-2, the direct zoonotic origin (intermediate host) of the virus remains ambiguous. The most definitive approach to identify the intermediate host would be the detection of SARS-CoV-2-like coronaviruses in wild animals. However, due to the high number of animal species, it is not feasible to screen all the species in the laboratory. Given that the recognition of the binding ACE2 proteins is the first step for the coronaviruses to invade host cells, we proposed a computational pipeline to identify potential intermediate hosts of SARS-CoV-2 by modeling the binding affinity between the Spike receptor-binding domain (RBD) and host ACE2. Using this pipeline, we systematically examined 285 ACE2 variants from mammals, birds, fish, reptiles, and amphibians, and found that the binding energies calculated on the modeled Spike-RBD/ACE2 complex structures correlate closely with the effectiveness of animal infections as determined by multiple experimental datasets. Built on the optimized binding affinity cutoff, we suggested a set of 96 mammals, including 48 experimentally investigated ones, which are permissive to SARS-CoV-2, with candidates from primates, rodents, and carnivores at the highest risk of infection. Overall, this work not only suggested a limited range of potential intermediate SARS-CoV-2 hosts for further experimental investigation; but more importantly, it proposed a new structure-based approach to general zoonotic origin and susceptibility analyses that are critical for human infectious disease control and wildlife protection.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Xiaoqiang Huang", + "author_inst": "University of Michigan" + }, + { + "author_name": "Chengxin Zhang", + "author_inst": "University of Michigan" + }, + { + "author_name": "Robin Pearce", + "author_inst": "University of Michigan" + }, + { + "author_name": "Gilbert S Omenn", + "author_inst": "Univ of Michigan" + }, + { + "author_name": "Yang Zhang", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.09.11.292631", "rel_title": "A key linear epitope for a potent neutralizing antibody to SARS-CoV-2 S-RBD", @@ -1192136,53 +1195269,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.08.20189555", - "rel_title": "The Impact of COVID-19 Pandemic on The Preventive Services in Qatar", - "rel_date": "2020-09-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.08.20189555", - "rel_abs": "BackgroundIn March 2020, Qatar started reporting increased numbers of COVID-19 cases. At that stage, containment measures were put in place. The health authority in Qatar developed an emergency action plan to respond to the outbreak with the Primary Health Care as the main component of that response and suspended all non-urgent services including preventive health services. The aim of the retrospective analysis to measure the Impact of COVID 19 on the preventive services provided in Qatar.\n\nMethodsA retrospective data analysis was conducted for all the preventive services utilization volume across the 27 PHCC health centers from the 1st of January 2017 to the 31st of July 2020.\n\nResultsWith 17,012 no-show appointments, well-baby and Immunization services utilization demonstrated a reduction of 40% in May and started to come back to volumes higher than expected in June. The number of cancelled appointments for breast cancer and colorectal cancer screening programs were 3,481 and 5,854 respectively. The expected volumes demand has dropped by 100% in comparison to 2017 demand. Wellness services only met 20% of its projected utilization in April, however, the services picked up in June.\n\nConclusionThese findings will guide the public health policymakers to understand the effects COVID-19 on preventive services and the risk of having an increased number of outbreaks for childhood communicable disease, cancer cases with delayed diagnosis due to the screening services suspension. In addition, the plan will address the increased number of sedately behavior due to the services reduced utilization of wellness services.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ahmad Haj Bakri", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Mohamed Ghaith Al-Kuwari", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Mariam Ali Abdulmalik", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Hamad Rashid Al-Mudahka", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Wadha Ahmed Al-Baker", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Shaikha Sami Abushaikha", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Mujeeb Chettiyam Kandy", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "John Gibb", - "author_inst": "Primary Health Care Corporation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.09.20188482", "rel_title": "Adherence to COVID-19 pandemic prescribed recommendations, source of information and lockdown psychological impact of Nigeria social media users", @@ -1192315,6 +1195401,61 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.09.08.20190603", + "rel_title": "Sleep Disturbances, Anxiety, and Burnout during the COVID-19 Pandemic: a nationwide cross-sectional study in Brazilian Healthcare Professionals.", + "rel_date": "2020-09-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.08.20190603", + "rel_abs": "Study objectivesTo evaluate the impact of COVID-19 pandemic on sleep, anxiety, and Burnout in healthcare professionals.\n\nMethodsA survey was distributed using social media and organizational emails to Brazilian active healthcare professionals during the COVID-19 outbreak. We explored potential associated factors including age, gender, occupation, workplace, work hours, income, previous infection with COVID-19, recent/current contact with COVID-19 patients, regional number of incident deaths due to COVID-19, anxiety, and burnout. We evaluated new-onset or previous insomnia worsening (primary outcome), sleep quality, and duration (secondary outcomes).\n\nResultsA total of 4,384 health professionals from all regions of the country were included in the analysis (mean age: 44{+/-}12 years, 76% females, 53.8% physicians). Overall, 55.7% were assisting patients with COVID-19, and 9.2% had a previous COVID-19 infection. New-onset insomnia symptoms or previous insomnia worsening occurred in 41.4% of respondents in parallel to 13% (n=572) new pharmacological treatments for insomnia. Prevalent anxiety and burnout during the pandemic were observed in 44.2% and 21% of participants, respectively. Multivariate analyses showed that females (OR:1.756; 95% CI 1.487-2.075), weight change (decrease: OR:1.852; 95% CI 1.531-2.240; increase: OR:1.542; 95% CI 1.323-1.799), prevalent anxiety(OR:3.209; 95% CI 2.796-3.684), new-onset burnout (OR:1.986; 95% CI 1.677-2.352), family income reduction >30% (OR:1.366; 95% CI 1.140-1.636) and assisting patients with COVID-19 (OR:1.293; 95% CI 1.104-1.514) were independently associated with new-onset or worsening of previous insomnia.\n\nConclusionsWe observed a huge burden of insomnia in healthcare professionals during the COVID-19 pandemic. In this scenario, dedicated approaches for sleep health are highly desirable.\n\nStatement of SignificanceConsidering the stressful routine and risk of infection by COVID-19 among healthcare professionals, it is conceivable that sleep disturbances are significantly impaired during the pandemic. This nationwide survey conducted in Brazil found that 41.4% developed new-onset or worsening of previous insomnia symptoms. Moreover, 572 (13%) of respondents initiated pharmacological treatments for insomnia. Females, weight change, anxiety, Burnout development, family income reduction >30%, and recent/current care of patients with COVID-19 were independently associated with the development of insomnia or exacerbated previous insomnia symptoms. Considering the potential impact of insomnia on work performance/healthcare decisions as well as the potential long-term dependence of pharmacological treatments for insomnia, this study underscores the need for dedicated sleep and mental health programs for healthcare professionals.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Luciano Drager", + "author_inst": "Heart Institute (InCor)" + }, + { + "author_name": "Daniela Pachito", + "author_inst": "Hospital Sirio-Libanes" + }, + { + "author_name": "Claudia Moreno", + "author_inst": "Univ of Sao Paulo" + }, + { + "author_name": "Almir Tavares Jr.", + "author_inst": "Federal University of Minas Gerais" + }, + { + "author_name": "Silvia G. Conway", + "author_inst": "Univ of Sao Paulo" + }, + { + "author_name": "Marcia Assis", + "author_inst": "Hospital Sao Lucas" + }, + { + "author_name": "Danilo A. Sguillar", + "author_inst": "Federal University of Sao Paulo" + }, + { + "author_name": "Gustavo A. Moreira", + "author_inst": "Federal University of Sao Paulo" + }, + { + "author_name": "Andrea Bacelar", + "author_inst": "Carlos Bacelar Clinica" + }, + { + "author_name": "Pedro R. Genta", + "author_inst": "Univ of Sao Paulo" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.07.286344", "rel_title": "Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease", @@ -1193930,49 +1197071,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.07.20189860", - "rel_title": "Ongoing natural selection drives the evolution of SARS-CoV-2 genomes", - "rel_date": "2020-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.07.20189860", - "rel_abs": "SARS-CoV-2 is a new RNA virus affecting humans and spreads extensively through world populations since its first outbreak in late December, 2019. Whether the transmissibility and pathogenicity of SARS-CoV-2 is actively evolving, and driven by adaptation to the new host and environments is still unknown. Understanding the evolutionary mechanism underlying epidemiological and pathological characteristics of COVID-19 is essential for predicting the epidemic trend, and providing guidance for disease control and treatments. Interrogating 22,078 SARS-CoV-2 genome sequences of 84 countries, we demonstrate with convincing evidence that (i) SARS-CoV-2 genomes are overall conserved under purifying selection. (ii) Ongoing positive selection is actively driving the evolution of specific genes. Notably, genes related to coronavirus infection and host immune system defense are under adaptive evolution while genes related to viral RNA replication, transcription and translation are under purifying selection. A spatial and temporal landscape of 54 critical mutants is constructed based on their divergence among viral haplotype clusters, of which multiple mutants potentially conferring viral transmissibility, infectivity and virulence of SARS-CoV-2 are highlighted.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Qi Liu", - "author_inst": "Beijing Institute of Genomics, CAS" - }, - { - "author_name": "Shilei Zhao", - "author_inst": "Beijing Institute of Genomics, CAS" - }, - { - "author_name": "Yali Hou", - "author_inst": "Beijing Institute of Genomics, CAS" - }, - { - "author_name": "Wenmin Zhao", - "author_inst": "Beijing Institute of Genomics, CAS" - }, - { - "author_name": "Yimin Bao", - "author_inst": "Beijing Institute of Genomics, CAS" - }, - { - "author_name": "Yongbiao Xue", - "author_inst": "Beijing Institute of Genomics, CAS" - }, - { - "author_name": "Hua Chen", - "author_inst": "Beijing Institute of Genomics" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.07.20189597", "rel_title": "COVID-19 control across urban-rural gradients", @@ -1194113,6 +1197211,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, + { + "rel_doi": "10.1101/2020.09.08.20187559", + "rel_title": "The role of NIH funding in vaccine readiness; foundational research and NIH funding underlying candidate SARS-CoV-2 vaccines", + "rel_date": "2020-09-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.08.20187559", + "rel_abs": "This work characterizes the NIH contribution to vaccine technologies being employed in \"warp speed\" development of vaccines for COVID-19, as well as the lack of sustained NIH funding for published research against recognized epidemic threats. Using quantitative methods, we examined the advance of published research on ten of the vaccine technologies incorporated in the 165 candidate vaccines entering development through July 2020 as well as the NIH funding that supported this research. Live, attenuated virus, inactivated virus, and adjuvant technologies have been used in successful products since the 1950s and continue to exhibit steady advance. Synthetic (recombinant) vaccines, viral vectors, DNA, and TLR9 agonists as adjuvants emerged since the 1980s, and exhibit a logistic, \"S-curve\" pattern of growth characteristic of emerging technologies that have passed an analytically-defined established point. In contrast, mRNA, virus-like particle, and nanoparticle technologies show exponential growth characteristic of technologies short of their established points. The body of research and NIH funding for established and emerging vaccine technologies exhibited sustained growth through the late 2010s, supported by > 16,000 project years of NIH funding totaling over $17.2 billion (2000-2019), the majority through cooperative agreements and intramural programs. NIH funding for published research on vaccines for recognized zoonotic threats including coronavirus, Zika, Ebola, and dengue, however, has been inconsistent and reactive to disease outbreaks. These data are considered in the context of the high failure rate for candidate vaccines and evidence that technological maturity is a significant factor in the efficiency of product development. Sustained funding for both enabling technologies and vaccine development is essential to ensure a rapid response to COVID and future pandemic threats.\n\nSIGNIFICANCE STATEMENTThis work examines the advance of research and NIH funding for technologies being employed in \"warp speed\" development of COVID-19 vaccines in the context of evidence that mature technologies have a greater likelihood of generating successful products. We show that candidate vaccines for COVID-19 employ a variety of established and still-emerging technologies, and identify $17.2 billion in NIH funding for this research from 2000-2019. In contrast, NIH funding for published research for vaccines on recognized pandemic threats has been inconsistent. This work highlights the significance and scale of the NIH contribution to vaccine technologies and the lack of sustained initiatives for vaccine development.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Anthony E Kiszewski", + "author_inst": "Bentley University" + }, + { + "author_name": "Ekaterina I Galkina Cleary", + "author_inst": "Bentley University" + }, + { + "author_name": "Matthew J Jackson", + "author_inst": "Bentley University" + }, + { + "author_name": "Fred D Ledley", + "author_inst": "Bentley University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.09.08.20190488", "rel_title": "Comparative evaluation of six immunoassays for the detection of antibodies against SARS-CoV-2", @@ -1195368,97 +1198497,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.08.20190496", - "rel_title": "Systematic profiling of SARS-CoV-2 specific IgG epitopes at single amino acid resolution", - "rel_date": "2020-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.08.20190496", - "rel_abs": "SARS-CoV-2 specific IgG responses play critical roles for patients to recover from COVID-19, in-depth dissecting of the IgG responses on systems level is of great interest. Herein, we adopted a newly developed high-throughput epitope mapping technology (AbMap), analyzed 55 COVID-19 convalescent sera and 226 antibody samples enriched by specific proteins or peptides from these sera. We revealed three areas that are rich of IgG epitopes, two are on Spike protein but outside of RBD, and one is on Nucleocapsid protein. We identified 29 significant epitopes on Spike protein, from two of these significant epitopes, two critical epitope residues were found, i. e., D936 and P1263, which are highly related to the infectivity of SARS-CoV-2 In summary, we provided the first global map of IgG binding epitopes for SARS-CoV-2 at single amino acid resolution. This map will facilitate the precise development of therapeutic antibodies and vaccines.\n\nHIGHLIGHTSO_LIA map of SARS-CoV-2 specific IgG binding epitopes at single amino acid resolution\nC_LIO_LITwo areas outside of RBD that are rich of significant epitopes were identified\nC_LIO_LIOne area rich of significant epitopes was determined on Nucleocapsid protein\nC_LIO_LITwo critical epitope residues (D936 and P1263) on Spike protein are highly related to the infectivity of SARS-CoV-2\nC_LI", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Huan Qi", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Ming-liang Ma", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Jeremy Jiang", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Jian-ya Ling", - "author_inst": "Shandong University" - }, - { - "author_name": "Ling-yun Chen", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Hai-nan Zhang", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Dan-yun Lai", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Yang Li", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Zi-wen Guo", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Chuang-sheng Hu", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Shu-juan Guo", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Qing-feng Meng", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Yan Ren", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Wei Wang", - "author_inst": "Foshan Fourth Hospital" - }, - { - "author_name": "Xiao Yang", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Jie Zhou", - "author_inst": "Foshan Fourth Hospital" - }, - { - "author_name": "Xiao-dong Zhao", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Hua Li", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Sheng-ce Tao", - "author_inst": "Shanghai Jiao Tong University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.09.20191239", "rel_title": "COVID-19 Transmission Within Danish Households: A Nationwide Study from Lockdown to Reopening", @@ -1195715,6 +1198753,33 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.09.09.289488", + "rel_title": "Candidate screening of host cell membrane proteins involved in SARS-CoV-2 entry", + "rel_date": "2020-09-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.09.289488", + "rel_abs": "Coronavirus disease (COVID-19) represents a real threat to the global population, and understanding the biological features of the causative virus, i.e., severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is imperative for mitigating this threat. Analyses of proteins such as primary receptors and co-receptors (co-factors), which are involved in the entry of SARS-CoV-2 into host cells, will provide important clues to help control the virus. Here, we identified host cell membrane protein candidates present in proximity to the attachment sites of SARS-CoV-2 spike proteins, using proximity labeling and proteomic analysis. The identified proteins represent key candidate factors that may be required for viral entry. DPP4, Cadherin-17, and CD133 were found to co-localize with cell membrane-bound SARS-CoV-2 spike proteins in Caco-2 cells and thus showed potential as candidate factors. The experimental infection with a SARS-CoV-2 pseudovirus indicated a 2-fold enhanced infectivity in the CD133-ACE2-coexpressing HEK293T cells compared to that in HEK293T cells expressing ACE-2 alone. The information and resources regarding these co-receptor labeling and analysis techniques could be utilized for the development of antiviral agents against SARS-CoV-2 and other emerging viruses.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Norihiro Kotani", + "author_inst": "Saitama Medical University" + }, + { + "author_name": "Takanari Nakano", + "author_inst": "Saitama Medical University" + }, + { + "author_name": "Ryusuke Kuwahara", + "author_inst": "Okinawa Institute of Science and Technology Graduate University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.09.08.272328", "rel_title": "Potential impact on coagulopathy of gene variants of coagulation related proteins that interact with SARS-CoV-2", @@ -1197330,33 +1200395,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "orthopedics" }, - { - "rel_doi": "10.1101/2020.09.06.20189258", - "rel_title": "Superspreaders and High Variance Infectious Diseases", - "rel_date": "2020-09-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.06.20189258", - "rel_abs": "(Dated: September 6, 2020)\n\nA well-known characteristic of pandemics such as COVID-19 is the high level of transmission heterogeneity in the infection spread: not all infected individuals spread the disease at the same rate and some individuals (superspreaders) are responsible for most of the infections. To quantify this phenomenon requires the analysis of the effect of the variance and higher moments of the infection distribution. Working in the framework of stochastic branching processes, we derive an approximate analytical formula for the probability of an outbreak in the high variance regime of the infection distribution, verify it numerically and analyze its regime of validity in various examples. We show that it is possible for an outbreak not to occur in the high variance regime even when the basic reproduction number R0 is larger than one and discuss the implications of our results for COVID-19 and other pandemics.\n\nPACS numbers: 87.10.+e", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Shmuel Safra", - "author_inst": "Tel Aviv university" - }, - { - "author_name": "Yaron Oz", - "author_inst": "Tel Aviv university" - }, - { - "author_name": "Ittai Rubinstein", - "author_inst": "Tel Aviv University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.04.20188110", "rel_title": "Modelling the transmission of infectious diseases inside hospital bays: implications for Covid-19", @@ -1198537,6 +1201575,189 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.04.20188169", + "rel_title": "In severe COVID-19, SARS-CoV-2 induces a chronic, TGF-\u03b2-dominated adaptive immune response", + "rel_date": "2020-09-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20188169", + "rel_abs": "Here we have analyzed the dynamics of the adaptive immune response triggered by SARS-CoV-2 in severely affected COVID-19 patients, as reflected by activated B cells egressing into the blood, at the single cell level. Early on, before seroconversion in response to SARS-CoV-2 spike protein, activated peripheral B cells displayed a type 1 interferon-induced gene expression signature. After seroconversion, activated B cells lost this signature, expressed IL-21- and TGF-{beta}-induced gene expression signatures, and mostly IgG1 and IgA1. In the sustained immune reaction of the COVID-19 patients, until day 59, activated peripheral B cells shifted to expression of IgA2, reflecting instruction by TGF-{beta}. Despite the continued generation of activated B cells, those cells were not found in the lungs of deceased COVID-19 patients, nor did the IgA2 bind to dominant antigens of SARS-CoV-2. In severe COVID-19, SARS-CoV-2 thus triggers a chronic immune reaction distracted from itself and instructed by TGF-{beta}.", + "rel_num_authors": 42, + "rel_authors": [ + { + "author_name": "Marta Ferreira-Gomes", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Andrey Kruglov", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Pawel Durek", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Frederik Heinrich", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association," + }, + { + "author_name": "Caroline Tizian", + "author_inst": "Laboratory of Innate Immunity, Department of Microbiology and Infection Immunology, Charite-Universitaetsmedizin Berlin" + }, + { + "author_name": "Gitta Anne Heinz", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association," + }, + { + "author_name": "Anna Pascual-Reguant", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Weijie Du", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Ronja Mothes", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Chaofan Fan", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Stefan Frischbutter", + "author_inst": "Dermatological Allergology, Department of Dermatology and Allergy, Charite-Universitaetsmedizin Berlin" + }, + { + "author_name": "Katharina Habenicht", + "author_inst": "Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany" + }, + { + "author_name": "Lisa Budzinski", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Justus Ninnemann", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Peter K. Jani", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Gabriela Guerra", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Katrin Lehmann", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Mareen Matz", + "author_inst": "BIH Center for Regenerative Therapies (BCRT), Charite Universitaetsmedizin Berlin, Berlin, Germany." + }, + { + "author_name": "Lennard Ostendorf", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Lukas Heiberger", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Hyun-Dong Chang", + "author_inst": "1Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Sandy Bauherr", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Marcus Maurer", + "author_inst": "Dermatological Allergology, Department of Dermatology and Allergy, Charite-Universitaetsmedizin Berlin" + }, + { + "author_name": "Guenther Schoenrich", + "author_inst": "Institute of Virology, Charite-Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute" + }, + { + "author_name": "Martin Raftery", + "author_inst": "Institute of Virology, Charite-Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute" + }, + { + "author_name": "Tilmann Kallinich", + "author_inst": "Department of Pediatric Pulmonology, Immunology and Critical Care Medicine, Charite-Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, " + }, + { + "author_name": "Marcus Alexander Mall", + "author_inst": "Department of Pediatric Pulmonology, Immunology and Critical Care Medicine, Charite-Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, " + }, + { + "author_name": "Stefan Angermair", + "author_inst": "Department of Anesthesiology and Intensive Care Medicine, Campus Benjamin Franklin, Charite - Universitaetsmedizin Berlin, Corporate Member of Freie Universitae" + }, + { + "author_name": "Sascha Treskatsch", + "author_inst": "Department of Anesthesiology and Intensive Care Medicine, Campus Benjamin Franklin, Charite - Universitaetsmedizin Berlin, Corporate Member of Freie Universitae" + }, + { + "author_name": "Thomas Doerner", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Victor M Corman", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Andreas Diefenbach", + "author_inst": "Laboratory of Innate Immunity, Department of Microbiology and Infection Immunology, Charite-Universitaetsmedizin Berlin" + }, + { + "author_name": "Hans-Dieter Volk", + "author_inst": "BIH Center for Regenerative Therapies (BCRT), Charite Universitaetsmedizin Berlin, Berlin, Germany." + }, + { + "author_name": "Sefer Elezkurtaj", + "author_inst": "Institute of Pathology, Charite- Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institu" + }, + { + "author_name": "Thomas H. Winkler", + "author_inst": "Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany." + }, + { + "author_name": "Jun Dong", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Anja Erika Hauser", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Helena Radbruch", + "author_inst": "Department of Neuropathology, Charite-Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin In" + }, + { + "author_name": "Mario Witkowski", + "author_inst": "Laboratory of Innate Immunity, Department of Microbiology and Infection Immunology, Charite-Universitaetsmedizin Berlin, 12203 Berlin, Germany" + }, + { + "author_name": "Fritz Melchers", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Andreas Radbruch", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + }, + { + "author_name": "Mir-Farzin Mashreghi", + "author_inst": "Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.06.20189266", "rel_title": "Multiscale statistical physics of the Human-SARS-CoV-2 interactome", @@ -1200132,29 +1203353,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.04.20188326", - "rel_title": "Variations in state-level SARS-COV-2 testing recommendations in the United States, March-July 2020", - "rel_date": "2020-09-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20188326", - "rel_abs": "BackgroundState health departments have been responsible for prioritizing and allocating SARS-CoV-2 tests and vaccines. Testing and vaccination recommendations in the United States varied by state and over time, as did vaccine rollouts, COVID-19 cases, and estimates of excess mortality.\n\nMethodsWe compiled data about COVID-19 testing, cases, and deaths, and excess pneumonia + influenza + COVID-19 deaths to assess relationships between testing recommendations, per capita tests performed, epidemic intensity, and excess mortality during the early months of the COVID-19 pandemic in the United States. We compiled further data about state-level SARS-CoV-2 vaccination policies and doses administered during the early months of the vaccine rollout.\n\nResultsAs of July 2020, 16 states recommended testing asymptomatic members of the general public. The rate of COVID-19 tests reported in each state correlated with more inclusive testing recommendations and with higher epidemic intensity. Higher per capita testing was associated with more complete reporting of COVID-19 deaths, which is a fundamental requirement for analyzing the pandemic. Testing per capita during the first three months was associated with vaccination per capita in the first three months of rollout. Per capita vaccine doses in each state were not associated with adherence to national guidelines.\n\nConclusionsReported deaths due to COVID-19 likely represent an undercount of the true burden of the pandemic. States that struggled with testing rollout have also frequently struggled with vaccine rollout. Coordinated, consistent guidelines for COVID-19 testing and vaccine administration should be a high priority for state and national health systems.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Stephanie R Perniciaro", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Daniel M Weinberger", - "author_inst": "Yale School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.04.20188359", "rel_title": "COVID-19 superspreading in cities versus the countryside", @@ -1200279,6 +1203477,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.09.05.20187435", + "rel_title": "The dichotomous and incomplete adaptive immunity in COVID-19", + "rel_date": "2020-09-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.05.20187435", + "rel_abs": "The adaptive immunity that protects patients from coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is not well characterized. In particular, the asymptomatic patients have been found to induce weak and transient SARS-CoV-2 antibody responses, but the underlying mechanisms remain unknown; meanwhile, the protective immunity that guide the recovery of these asymptomatic patients is also not well studied. Here, we characterized SARS-CoV-2-specific B-cell and T-cell responses in 10 asymptomatic patients and 49 patients with other disease severity (mild, n = 10, moderate, n = 32, severe, n = 7) and found that asymptomatic or mild symptomatic patients failed to mount virus-specific germinal center (GC) B cell responses that result in robust and long-term humoral immunity, assessed by GC response indicators including follicular helper T (TFH) cell and memory B cell responses as well as serum CXCL13 levels. Alternatively, these patients mounted potent virus-specific TH1 and CD8+ T cell responses. In sharp contrast, patients of moderate or severe disease induced vigorous virus-specific GC B cell responses and associated TFH responses; however, the virus-specific TH1 and CD8+ T cells were minimally induced in these patients. These results therefore uncovered the protective immunity in COVID-19 patients and revealed the strikingly dichotomous and incomplete adaptive immunity in COVID-19 patients with different disease severity, providing important insights into rational design of COVID-19 vaccines.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Leiqiong Gao", + "author_inst": "Institute of Immunology, Third Military Medical University, Chongqing 400038, China." + }, + { + "author_name": "Jing Zhou", + "author_inst": "Institute of Immunology, Third Military Medical University, Chongqing 400038, China." + }, + { + "author_name": "Sen Yang", + "author_inst": "Chongqing Public Health Medical Center, Chongqing 400038, China." + }, + { + "author_name": "Xiangyu Chen", + "author_inst": "Institute of Immunology, Third Military Medical University, Chongqing 400038, China." + }, + { + "author_name": "Yang Yang", + "author_inst": "Institute of Immunology, Third Military Medical University, Chongqing 400038, China." + }, + { + "author_name": "Ren Li", + "author_inst": "State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150001, C" + }, + { + "author_name": "Zhiwei Pan", + "author_inst": "Institute of Immunology, Third Military Medical University, Chongqing 400038, China." + }, + { + "author_name": "Jing Zhao", + "author_inst": "Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China." + }, + { + "author_name": "Zhirong Li", + "author_inst": "Institute of Immunology, Third Military Medical University, Chongqing 400038, China." + }, + { + "author_name": "Qizhao Huang", + "author_inst": "Cancer Center, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, China." + }, + { + "author_name": "Jianfang Tang", + "author_inst": "Institute of Immunology, Third Military Medical University, Chongqing 400038, China." + }, + { + "author_name": "Li Hu", + "author_inst": "Institute of Immunology, Third Military Medical University, Chongqing 400038, China." + }, + { + "author_name": "Pinghuang Liu", + "author_inst": "Comparative Immunology Research Center, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China." + }, + { + "author_name": "Guozhong Zhang", + "author_inst": "Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China." + }, + { + "author_name": "Yaokai Chen", + "author_inst": "Chongqing Public Health Medical Center, Chongqing 400038, China." + }, + { + "author_name": "Lilin Ye", + "author_inst": "1Institute of Immunology, Third Military Medical University, Chongqing 400038, China." + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.09.05.20188458", "rel_title": "The association between COVID-19 and preterm delivery: A cohort study with a multivariate analysis", @@ -1201658,61 +1204935,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.03.20187377", - "rel_title": "Impact of baseline cases of cough and fever on UK COVID-19 diagnostic testing rates: estimates from the Bug Watch community cohort study", - "rel_date": "2020-09-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.03.20187377", - "rel_abs": "BackgroundDiagnostic testing forms a major part of the UKs response to the current COVID-19 pandemic with tests offered to people with a continuous cough, high temperature or anosmia. Testing capacity must be sufficient during the winter respiratory season when levels of cough and fever are high due to non-COVID-19 causes. This study aims to make predictions about the contribution of baseline cough or fever to future testing demand in the UK.\n\nMethodsIn this analysis of the Bug Watch prospective community cohort study, we estimated the incidence of cough or fever in England in 2018-2019. We then estimated the COVID-19 diagnostic testing rates required in the UK for baseline cough or fever cases for the period July 2020-June 2021. This was explored for different rates of the population requesting tests and four second wave scenarios and then compared to current national capacity.\n\nResultsThe baseline incidence of cough or fever in the UK is expected to rise rapidly from 154,554 (95%CI 103,083 - 231,725) cases per day in August 2020 to 250,708 (95%CI 181,095 - 347,080) in September, peaking at 444,660 (95%CI 353,084 - 559,988) in December. If 80% of baseline cough or fever cases request tests, average daily UK testing demand would exceed current capacity for five consecutive months (October 2020 to February 2021), with a peak demand of 147,240 (95%CI 73,978 - 239,502) tests per day above capacity in December 2020.\n\nConclusionsOur results show that current national COVID-19 testing capacity is likely to be exceeded by demand due to baseline cough and fever alone. This study highlights that the UKs response to the COVID-19 pandemic must ensure that a high proportion of people with symptoms request tests, and that testing capacity is immediately scaled up to meet this high predicted demand.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Max T Eyre", - "author_inst": "Centre of Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster, LA1 4YW, UK; Liverpool School of Tropical Med" - }, - { - "author_name": "Rachel Burns", - "author_inst": "Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK" - }, - { - "author_name": "Victoria Kirkby", - "author_inst": "Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK" - }, - { - "author_name": "Catherine Smith", - "author_inst": "Institute of Health Informatics, University College London, London, NW1 2DA, UK" - }, - { - "author_name": "Spiros Denaxas", - "author_inst": "Institute of Health Informatics, University College London, London, NW1 2DA, UK; Health Data Research UK, London, NW1 2DA, UK; The Alan Turing Institute, London" - }, - { - "author_name": "Vincent Nguyen", - "author_inst": "Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK; Institute of Epidemiology and Health Care" - }, - { - "author_name": "Andrew Hayward", - "author_inst": "Institute of Epidemiology and Health Care, University College London, London, WC1E 7HB, UK" - }, - { - "author_name": "Laura Shallcross", - "author_inst": "Institute of Health Informatics, University College London, London, NW1 2DA, UK" - }, - { - "author_name": "Ellen Fragaszy", - "author_inst": "Institute of Health Informatics, University College London, London, NW1 2DA, UK; Faculty of Epidemiology and Population Health, London School of Hygiene and Tro" - }, - { - "author_name": "Robert W Aldridge", - "author_inst": "Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.03.20187336", "rel_title": "Household Secondary Attack Rate in Gandhinagar district of Gujarat state from Western India", @@ -1201937,6 +1205159,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.09.03.20187807", + "rel_title": "Assessment of COVID-19 Pandemic in Nepal: A Lockdown Scenario Analysis", + "rel_date": "2020-09-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.03.20187807", + "rel_abs": "The Government of Nepal issued a nationwide lockdown from 24 March to 21 July 2020, prohibiting domestic and international travels, closure of the border and non-essential services. There were only two confirmed cases from 610 Reverse Transcription Polymerase Chain Reaction (RT-PCR) tests and no fatalities when the government introduced nationwide lockdown. This study aimed to explore the overall scenario of COVID-19 including spatial distribution of cases; government efforts, and impact on public health, socio-economy, and education during the lockdown in Nepal. We collated and analysed data using official figures from the Nepalese Ministry of Health and Population. Nepal had performed 7,791 RT-PCR tests for COVID-19, the highest number of tests during the lockdown. It has recorded its highest daily rise in coronavirus infections with a total of 740 new cases from the total of 4,483 RT-PCR tests performed on a single day. Nepal had reported a total of 17,994 positive cases and 40 deaths at the end of lockdown. The spatial distribution clearly shows that the cases were rapidly spreading from the southern part of the country where most points of entry and exit from India are located. To contain the spread of the virus, the government has also initiated various preventive measures and strategies during the lockdown. The Government of Nepal needs to allocate more resources, increase its capacity to test and trace, establish dedicated isolation and quarantine facility and impose local restrictions such as a local lockdown based on risk assessment rather than a nationwide lockdown.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Kusum Sharma", + "author_inst": "Science Hub" + }, + { + "author_name": "Amrit Banstola", + "author_inst": "Public Health Perspective Nepal" + }, + { + "author_name": "Rishi Ram Parajuli", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.09.04.20187922", "rel_title": "Viable virus aerosol propagation by PAP circuit leak and mitigation with a ventilated patient hood: a model for improving health care worker safety in the COVID-19 pandemic", @@ -1203268,45 +1206517,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.01.20186395", - "rel_title": "Age-dependence of healthcare interventions for SARS-CoV-2 infection in Ontario, Canada", - "rel_date": "2020-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20186395", - "rel_abs": "BackgroundPatient age is the most salient clinical indicator of risk from COVID-19. Age-specific distributions of known SARS-CoV-2 infections and COVID-19-related deaths are available for most countries. However, relatively little attention has been given to the age distributions of hospitalizations and serious healthcare interventions administered to COVID-19 patients. We examined these distributions in Ontario, Canada, in order to quantify the age-related impacts of COVID-19, and to identify potential risks should the healthcare system become overwhelmed with COVID-19 patients in the future.\n\nMethodsWe analysed known SARS-CoV-2 infection records from the integrated Public Health Information System (iPHIS) and the Toronto Public Health Coronavirus Rapid Entry System (CORES) between 23 January 2020 and 17 June 2020 (N = 30,546), and estimated the age distributions of hospitalizations, ICU admissions, intubations, and ventilations. We quantified the probability of hospitalization given known SARS-CoV-2 infection, and of survival given COVID-19-related hospitalization.\n\nResultsThe distribution of COVID-19-related hospitalizations peaks with a wide plateau covering ages 54-90, whereas deaths are sharply concentrated in very old ages, with a maximum at age 90. The estimated probability of hospitalization given known SARS-CoV-2 infection reaches a maximum of 32.0% at age 75 (95% CI 27.5%-36.7%). The probability of survival given COVID-19-related hospitalization is uncertain for children (due to small sample size), and near 100% for adults younger than 40. After age 40, survival of hospitalized COVID-19 patients declines substantially; for example, a hospitalized 50-year-old patient has a 90.4% chance of surviving COVID-19 (95% CI 81.9%-95.7%).\n\nInterpretationConcerted efforts to control the spread of SARS-CoV-2 have kept prevalence of the virus low in the population of Ontario. The healthcare system has not been overstretched, yet the probability of survival given hospitalization for COVID-19 has been lower than is generally recognized for patients over 40. If prevalence of the virus were to increase and healthcare capacities were to be exceeded, survival of individuals in the broad age range requiring acute care would be expected to decrease, potentially expanding the distribution of COVID-19-related deaths toward younger ages.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Irena Papst", - "author_inst": "Cornell University" - }, - { - "author_name": "Michael Li", - "author_inst": "McMaster University" - }, - { - "author_name": "David Champredon", - "author_inst": "University of Western Ontario" - }, - { - "author_name": "Benjamin M Bolker", - "author_inst": "McMaster University" - }, - { - "author_name": "Jonathan Dushoff", - "author_inst": "McMaster University" - }, - { - "author_name": "David J D Earn", - "author_inst": "McMaster University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.01.20185280", "rel_title": "SARS-CoV-2 Protein in Wastewater Mirrors COVID-19 Prevalence.", @@ -1203507,6 +1206717,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, + { + "rel_doi": "10.1101/2020.09.02.20186502", + "rel_title": "Real-time monitoring of COVID-19 dynamics using automated trend fitting and anomaly detection", + "rel_date": "2020-09-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20186502", + "rel_abs": "As several countries gradually release social distancing measures, rapid detection of new localised COVID-19 hotspots and subsequent intervention will be key to avoiding large-scale resurgence of transmission. We introduce ASMODEE (Automatic Selection of Models and Outlier Detection for Epidemics), a new tool for detecting sudden changes in COVID-19 incidence. Our approach relies on automatically selecting the best (fitting or predicting) model from a range of user-defined time series models, excluding the most recent data points, to characterise the main trend in an incidence. We then derive prediction intervals and classify data points outside this interval as outliers, which provides an objective criterion for identifying departures from previous trends. We also provide a method for selecting the optimal breakpoints, used to define how many recent data points are to be excluded from the trend fitting procedure. The analysis of simulated COVID-19 outbreaks suggest ASMODEE compares favourably with a state-of-art outbreak-detection algorithm while being simpler and more flexible. We illustrate our method using publicly available data of NHS Pathways reporting potential COVID-19 cases in England at a fine spatial scale, for which we provide a template automated analysis pipeline. ASMODEE is implemented in the free R package trendbreaker.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Thibaut Jombart", + "author_inst": "London School of Hygiene and Tropical Medicine (LSHTM)" + }, + { + "author_name": "Stephane Ghozzi", + "author_inst": "Department of Epidemiology, Helmholtz Centre for Infection Research, Brunswick, Lower Saxony, Germany" + }, + { + "author_name": "Dirk Schumacher", + "author_inst": "R Epidemics Consortium" + }, + { + "author_name": "Quentin Leclerc", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Mark Jit", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Stefan Flasche", + "author_inst": "LSHTM" + }, + { + "author_name": "Felix Greaves", + "author_inst": "Joint Biosecurity Centre" + }, + { + "author_name": "Tom Ward", + "author_inst": "Joint Biosecurity Centre" + }, + { + "author_name": "Rosalind M Eggo", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Emily Nightingale", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Sophie Meakin", + "author_inst": "LSHTM" + }, + { + "author_name": "Oliver J Brady", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "- Centre for Mathematical Modelling of Infectious Diseases COVID-19 Working Group", + "author_inst": "" + }, + { + "author_name": "Graham Medley", + "author_inst": "LSHTM" + }, + { + "author_name": "Michael Hohle", + "author_inst": "Department of Mathematics, Stockholm University, Sweden" + }, + { + "author_name": "John Edmunds", + "author_inst": "LSHTM" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.09.01.20186288", "rel_title": "A model assessing potential benefits of isolation and mass testing on COVID-19: the case of Nigeria", @@ -1204806,29 +1208095,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.02.20186676", - "rel_title": "Estimating the number of COVID-19 cases being introduced into British Higher Education Institutions during Autumn 2020", - "rel_date": "2020-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20186676", - "rel_abs": "It is estimated that 81% of the 163 UK Higher Educational Institutes (HEIs) have more than a 50% chance of having at least one COVID-19 case arriving on campus when considering all staff and students. Across all HEIs it is estimated that there will be a total of approximately 700 COVID-19 cases (95% CI: 640 - 750) arriving on campus of which 380 are associated from UK students, 230 from international and 90 from staff. This assumes all students will return to campus and that student numbers and where they come from are similar to previous years. According to the current UK government guidance approximately 237,370 students arriving on campus will be required to quarantine because they come from countries outwith designated travel corridors. Assuming quarantining is 100% efficient this will potentially reduce the overall number of cases by approximately 20% to 540 (95% CI: 500 - 590). Universities must plan for COVID-19 cases to arrive on campus and facilitate mitigations to reduce the spread of disease. It is likely that the first two weeks will be crucial to stop spread of introduced cases. Following that, the risk of introduction of new cases onto campus will be from interactions between students, staff and the local community as well as students travelling off campus for personal, educational or recreational reasons.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Francisco Perez-Reche", - "author_inst": "University of Aberdeen" - }, - { - "author_name": "Norval Strachan", - "author_inst": "University of Aberdeen" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.01.20182873", "rel_title": "Effects of Public Health Interventions on the Epidemiological Spread During the First Wave of the COVID-19 Outbreak in Thailand", @@ -1204997,6 +1208263,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.09.01.20186213", + "rel_title": "Performance of serum apolipoprotein-A1 as a sentinel of Covid-19", + "rel_date": "2020-09-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20186213", + "rel_abs": "BackgroundSince 1920, a decrease in serum cholesterol has been identified as a marker of severe pneumonia. We have assessed the performance of serum apolipoprotein-A1, the main transporter of HDL-cholesterol, to identify the early spread of coronavirus disease 2019 (Covid-19) in the general population and its diagnostic performance for the Covid-19.\n\nMethodsWe compared the daily mean serum apolipoprotein-A1 during the first 30 weeks of 2020 in a population that is routinely followed for a risk of liver fibrosis risk in the USA (183,112 sera) and in France (18,316 sera) in relation to a local increase in confirmed cases, and in comparison to the same period in 2019 (respectively 234,881 and 26,056 sera). We prospectively assessed the sensitivity of this marker in an observational study of 136 consecutive hospitalized cases and retrospectively evaluated its specificity in 7,481 controls representing the general population.\n\nResultsThe mean serum apolipoprotein-A1 levels in these populations began decreasing in January 2020, compared to the same 30 weeks in 2019. This decrease was highly correlated to and in parallel with the daily increase in confirmed Covid-19 cases in the following 30 weeks, in both France and USA, including the June and mid-July recovery periods in France. Apolipoprotein-A1 at the 1.25 g/L cutoff had a sensitivity of 90.6% (95%CI84.2-95.1) and a specificity of 96.1% (95.7-96.6%) for the diagnosis of Covid-19. The area under the characteristics curve was 0.978 (0.957-0.988), and outperformed haptoglobin and liver function tests. The adjusted risk ratio for survival without transfer to intensive care unit was 5.61 (95%CI 1.02-31.0;P=0.04).\n\nConclusionApolipoprotein-A1 could be both a sentinel of the pandemic in existing routine surveillance of the general population with no new blood sample, as well as a candidate predictor of suspected Covid-19 in multivariate analysis in cases with a negative virological test. NCT01927133, CER-2020-14.\n\nKey Points\n\nQuestionDoes serum apolipoprotein-A1 decrease could be a very early biomarker of SARS-CoV-2 pandemic?\n\nFindingsDuring the 30 weeks of 2020 we observed in two large cohorts of patients at risk of liver fibrosis a highly significant decrease of serum apolipoprotein-A1, not observed in previous years. This decrease was highly correlated to and in parallel with the daily increase in confirmed Covid-19 cases, including the recovery period.\n\nMeaningApolipoprotein-A1 could be used as a sentinel of the pandemic in existing routine surveillance of the general population.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Thierry Poynard", + "author_inst": "APHP Sorbonne University" + }, + { + "author_name": "Olivier Deckmyn", + "author_inst": "BioPredictive" + }, + { + "author_name": "Marika Rudler", + "author_inst": "APHP" + }, + { + "author_name": "Valentina Peta", + "author_inst": "BioPredictive" + }, + { + "author_name": "Yen Ngo", + "author_inst": "BioPredictive" + }, + { + "author_name": "Mathieu Vautier", + "author_inst": "APHP" + }, + { + "author_name": "Sepideh Akhavan", + "author_inst": "APHP" + }, + { + "author_name": "Vincent Calvez", + "author_inst": "APHP" + }, + { + "author_name": "Clemence Franc", + "author_inst": "BioPredictive" + }, + { + "author_name": "Jean Marie Castille", + "author_inst": "BioPredictive" + }, + { + "author_name": "Fabienne Drane", + "author_inst": "BioPredictive.com" + }, + { + "author_name": "Mehdi Sakka", + "author_inst": "APHP" + }, + { + "author_name": "Dominique Bonnefont-Rousselot", + "author_inst": "APHP" + }, + { + "author_name": "Jean Marc Lacorte", + "author_inst": "APHP" + }, + { + "author_name": "David Saadoun", + "author_inst": "APHP" + }, + { + "author_name": "Yves Allenbach", + "author_inst": "APHP" + }, + { + "author_name": "Olivier Benveniste", + "author_inst": "APHP" + }, + { + "author_name": "Frederique Gandjbakhch", + "author_inst": "APHP" + }, + { + "author_name": "Julien Mayaux", + "author_inst": "APHP" + }, + { + "author_name": "Olivier Lucidarme", + "author_inst": "APHP" + }, + { + "author_name": "Bruno Fautrel", + "author_inst": "APHP" + }, + { + "author_name": "Vlad Ratziu", + "author_inst": "INSERM" + }, + { + "author_name": "Chantal Housset", + "author_inst": "INSERM" + }, + { + "author_name": "Dominique Thabut", + "author_inst": "APHP" + }, + { + "author_name": "Patrice Cacoub", + "author_inst": "APHP" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.02.20186528", "rel_title": "Vaccination for some childhood diseases may impact the outcome of covid-19 infections", @@ -1206220,49 +1209601,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.30.20184705", - "rel_title": "Analyzing inherent biases in SARS-CoV-2 PCR and serological epidemiologic metrics", - "rel_date": "2020-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.30.20184705", - "rel_abs": "BackgroundProspective observational data show that infected persons with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remain polymerase chain reaction (PCR) positive for a prolonged duration, and that detectable antibodies develop slowly with time. We aimed to analyze how these effects can bias key epidemiological metrics used to track and monitor SARS-CoV-2 epidemics.\n\nMethodsAn age-structured mathematical model was constructed to simulate progression of SARS-CoV-2 epidemics in populations. PCR testing to diagnose infection and cross-sectional surveys to measure seroprevalence were also simulated. Analyses were conducted on simulated outcomes assuming a natural epidemic time course and an epidemic in presence of interventions.\n\nResultsThe prolonged PCR positivity biased the epidemiological measures. There was a lag of 10 days between the true epidemic peak and the actually-observed peak. Prior to epidemic peak, PCR positivity rate was 2-fold higher than that based only on current active infection, and half of those tested positive by PCR were in the prolonged PCR positivity stage after infection clearance. Post epidemic peak, PCR positivity rate poorly predicted true trend in active infection. Meanwhile, the prolonged PCR positivity did not appreciably bias estimation of the basic reproduction number R0. The time delay in development of detectable antibodies biased measured seroprevalence. The actually-observed seroprevalence substantially underestimated true prevalence of ever infection, with the underestimation being most pronounced around epidemic peak.\n\nConclusionsCaution is warranted in interpreting PCR and serological testing data, and any drawn inferences need to factor the effects of the investigated biases for an accurate assessment of epidemic dynamics.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Monia Makhoul", - "author_inst": "Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar" - }, - { - "author_name": "Farah Abou-Hijleh", - "author_inst": "Department of Public Health, College of Health Sciences, Academic Quality Affairs Office, QU Health, Qatar University, Doha, Qatar" - }, - { - "author_name": "Shaheen Seedat", - "author_inst": "Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar" - }, - { - "author_name": "Ghina R Mumtaz", - "author_inst": "Department of Epidemiology and Population Health, American University of Beirut, Beirut, Lebanon" - }, - { - "author_name": "Hiam Chemaitelly", - "author_inst": "Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar" - }, - { - "author_name": "Houssein Ayoub", - "author_inst": "Department of Mathematics, Statistics, and Physics, College of Arts and Sciences, Qatar University, Doha, Qatar" - }, - { - "author_name": "Laith J Abu-Raddad", - "author_inst": "Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.29.20184135", "rel_title": "Modeling the combined effect of digital exposure notification and non-pharmaceutical interventions on the COVID-19 epidemic in Washington state", @@ -1206491,6 +1209829,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.30.20184598", + "rel_title": "The Uncertain COVID-19 Spread Pattern in India: A Statistical Analysis of the Current Situation", + "rel_date": "2020-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.30.20184598", + "rel_abs": "There are standard techniques of forecasting the spread of pandemics. Uncertainty however is always associated with such forecasts. In this article, we are going to discuss the uncertain situation currently prevailing in the COVID-19 spread in India. For statistical analysis, we have considered the total number of cases for 60 consecutive days, from June 23 to August 21. We have seen that instead of taking data of all 60 days together, a better picture of uncertainty can be observed if we consider the data separately in three equal parts from June 23 to July 12, from July 13 to August 1, and from August 2 to August 21. For that we would first need to ascertain that the current spread pattern in India is almost exponential. Thereafter we shall show that the data regarding the total number of cases in India are not really behaving in an expected way, making forecasting the time to peak very difficult. We have found that the pandemic would perhaps change its pattern of growth from nearly exponential to nearly logarithmic, which we have earlier observed in the case of Italy, in less than 78 days starting from August 2.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Hemanta Kumar Baruah", + "author_inst": "The Assam Royal Global University, Guwahati, Assam, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.29.20184382", "rel_title": "Are COVID-19 proximity tracing apps working under real-world conditions? Indicator development and assessment of drivers for app (non-)use", @@ -1208130,57 +1211487,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.31.20185017", - "rel_title": "First snap-shot meta-analysis to estimate the prevalence of serum antibodies to SARS-CoV-2 in humans", - "rel_date": "2020-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.31.20185017", - "rel_abs": "BackgroundCOVID-19 is arguably the number-one public health concern worldwide, and efforts are now escalating to control its spread.\n\nObjectiveIn this study, we undertake a meta-analysis to estimate the global and regional anti-SARS-CoV-2 seroprevalence rates in humans and assess whether seroprevalence associates with geographical, climatic and socio-demographic factors.\n\nData sourcesWe systematically reviewed PubMed, Scopus, Embase, medRxiv and bioRxiv for peer-reviewed articles or preprints (up to 14 August 2020).\n\nStudy eligibility criteriaPopulation-based studies describing prevalence of anti-SARS-CoV-2 serum antibodies in general people.\n\nParticipantsgeneral people who were tested for prevalence of anti-SARS-CoV-2 serum antibodies.\n\nInterventionsThere were no interventions.\n\nMethodsWe used random-effects model to estimate pooled seroprevalence, and then extrapolated these findings to the global population (for 2020). Sub-group and meta-regression analyses explored potential sources of heterogeneity in the data and relationships between seroprevalence and socio-demographic, geographical and climatic factors.\n\nResultsIn total, 47 serological studies involving 399,265 people from 23 countries met the inclusion criteria. The pooled seroprevalence of SARS-CoV-2 in general people was estimated at 3.38% (95% CI, 3.05%-3.72%; 15,879/399,265). On a regional basis, we determined seroprevalence estimates of 5.27% (3.97-6.57%) in Northern Europe; 4.41% (2.20-6.61%) in Southern Europe; 4.41% (3.03- 5.79%) in North America; 3.17% (1.96-4.38%) in Western Europe; 2.02% (1.56-2.49%) in the Eastern Asia; and 1.45% (0.95-1.94%) in South America. Extrapolating to the 2020 world population, we estimated that 263,565,606 individuals had been exposed or infected with SARS-CoV-2 at the first wave of the pandemic. A significantly higher seroprevalence was related to higher income levels and human development indices, higher geographical latitudes and lower mean environmental temperatures.\n\nInterpretationThis study reinforces that SARS-CoV-2 infection is a very rapidly-spreading communicable disease and calls for routine surveys to constantly monitor temporal changes in seroprevalence around the globe.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Ali Rostami", - "author_inst": "Babol University of Medical Science" - }, - { - "author_name": "Mahdi Sepidarkish", - "author_inst": "Babol University of Medical Sciences" - }, - { - "author_name": "Mariska Leeflang", - "author_inst": "University of Amsterdam" - }, - { - "author_name": "Seyed Mohammad Riahi", - "author_inst": "Birjand University of Medical Sciences" - }, - { - "author_name": "Malihe Nourollahpour Shiadeh", - "author_inst": "Mazandaran University of Medical Sciences" - }, - { - "author_name": "Sahar Esfandyari", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Ali H Mokdad", - "author_inst": "University of Washington" - }, - { - "author_name": "Peter J. Hotez", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Robin B. Gasser", - "author_inst": "The University of Melbourne" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.31.20185587", "rel_title": "Health and economic effects of COVID-19 control in Australia: Modelling and quantifying the payoffs of hard versus soft lockdown", @@ -1208413,6 +1211719,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.31.20184895", + "rel_title": "Selecting COVID-19 Convalescent Plasma for Neutralizing Antibody Potency Using a High-capacity SARS-CoV-2 Antibody Assay", + "rel_date": "2020-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.31.20184895", + "rel_abs": "BACKGROUNDEfficacy of COVID-19 convalescent plasma (CCP) to treat COVID-19 is hypothesized to be associated with the concentration of neutralizing antibodies (nAb) to SARS-CoV-2. High capacity serologic assays detecting binding antibodies (bAb) have been developed, nAb assays are not adaptable to high-throughput testing. We sought to determine the effectiveness of using surrogate bAb signal-to-cutoff ratios (S/CO) in predicting nAb titers using a pseudovirus reporter viral particle neutralization (RVPN) assay.\n\nMETHODSCCP donor serum collected by 3 US blood collectors was tested with a bAb assay (Ortho Clinical Diagnostics VITROS Anti-SARS-CoV-2 Total, CoV2T) and a nAb RVPN assay. CoV2T prediction effectiveness at S/CO thresholds was evaluated for RVPN nAb NT50 titers using receiver operating characteristic analysis.\n\nRESULTS753 CCPs were tested with median CoV2T S/CO of 71.2 and median NT50 of 527.5. Proportions of CCP donors with NT50 over various target nAb titers were 86% [≥]1:80, 76% [≥]1:160, and 62%[≥]1:320. Increasing CoV2Ts reduced the sensitivity to predict NT50 titers, while specificity to identify those below thresholds increased. As the targeted NT50 increased, the positive predictive value fell with reciprocal increase in negative predictive value. S/CO thresholds were thus less able to predict target NT50 titers.\n\nCONCLUSIONSelection of a clinically effective nAb titer will impact availability of CCP. Product release with CoV2T assay S/CO thresholds must balance the risk of releasing products below target nAb titers with the cost of false negatives. A two-step testing scheme may be optimal, with nAb testing on CoV2T samples with S/COs below thresholds.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Erin Goodhue Meyer", + "author_inst": "American Red Cross" + }, + { + "author_name": "Graham Simmons", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Eduard Grebe", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Michael Gannett", + "author_inst": "OneBlood" + }, + { + "author_name": "Sergej Franz", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Orsolya Darst", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Clara Di Germanio", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Mars Stone", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Paul Contestable", + "author_inst": "Ortho Clinical Diagnostics" + }, + { + "author_name": "Alicia Prichard", + "author_inst": "OneBlood" + }, + { + "author_name": "Rita Reik", + "author_inst": "OneBlood" + }, + { + "author_name": "Ralph Vassallo", + "author_inst": "Vitalant" + }, + { + "author_name": "Pampee Young", + "author_inst": "American Red Cross" + }, + { + "author_name": "Michael Busch", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Phillip Williamson", + "author_inst": "Creative Testing Solutions" + }, + { + "author_name": "Larry Dumont", + "author_inst": "Vitalant Research Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.31.20185082", "rel_title": "Outcome of SARS-CoV-2 infection linked to MAIT cell activation and cytotoxicity: evidence for an IL-18 dependent mechanism", @@ -1209844,109 +1213229,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.09.01.278689", - "rel_title": "Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility", - "rel_date": "2020-09-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.01.278689", - "rel_abs": "A spike protein mutation D614G became dominant in SARS-CoV-2 during the COVID-19 pandemic. However, the mutational impact on viral spread and vaccine efficacy remains to be defined. Here we engineer the D614G mutation in the SARS-CoV-2 USA-WA1/2020 strain and characterize its effect on viral replication, pathogenesis, and antibody neutralization. The D614G mutation significantly enhances SARS-CoV-2 replication on human lung epithelial cells and primary human airway tissues, through an improved infectivity of virions with the spike receptor-binding domain in an \"up\" conformation for binding to ACE2 receptor. Hamsters infected with D614 or G614 variants developed similar levels of weight loss. However, the G614 virus produced higher infectious titers in the nasal washes and trachea, but not lungs, than the D614 virus. The hamster results confirm clinical evidence that the D614G mutation enhances viral loads in the upper respiratory tract of COVID-19 patients and may increases transmission. For antibody neutralization, sera from D614 virus-infected hamsters consistently exhibit higher neutralization titers against G614 virus than those against D614 virus, indicating that (i) the mutation may not reduce the ability of vaccines in clinical trials to protect against COVID-19 and (ii) therapeutic antibodies should be tested against the circulating G614 virus before clinical development.\n\nImportanceUnderstanding the evolution of SARS-CoV-2 during the COVID-19 pandemic is essential for disease control and prevention. A spike protein mutation D614G emerged and became dominant soon after the pandemic started. By engineering the D614G mutation into an authentic wild-type SARS-CoV-2 strain, we demonstrate the importance of this mutation to (i) enhanced viral replication on human lung epithelial cells and primary human airway tissues, (ii) improved viral fitness in the upper airway of infected hamsters, and (iii) increased susceptibility to neutralization. Together with clinical findings, our work underscores the importance of this mutation in viral spread, vaccine efficacy, and antibody therapy.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Jessica A Plante", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Yang Liu", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Jianying Liu", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Hongjie Xia", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Bryan A Johnson", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Kumari G Lokugamage", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Xianwen Zhang", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Antonio E Muruato", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Jing Zou", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Camila R Fontes-Garfias", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Divya Mirchandani", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Dionna Scharton", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "John P Bilello", - "author_inst": "Gilead" - }, - { - "author_name": "Zhiqiang Ku", - "author_inst": "University of Texas Health Science Center at Houston" - }, - { - "author_name": "Zhiqiang An", - "author_inst": "University of Texas Health Science Center at Houston" - }, - { - "author_name": "Birte Kalveram", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Alexander N Freiberg", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Vineet D Menachery", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Xuping Xie", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Kenneth S Plante", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Scott C Weaver", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Pei-Yong Shi", - "author_inst": "University of Texas Medical Branch" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.09.01.278366", "rel_title": "An intestinal cell type in zebrafish is the nexus for the SARS-CoV-2 receptor and the Renin-Angiotensin-Aldosterone System that contributes to COVID-19 comorbidities", @@ -1210131,6 +1213413,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.31.20185074", + "rel_title": "Fully automated detection and differentiation of pandemic and endemic coronaviruses (NL63, 229E, HKU1, OC43 and SARS-CoV-2) on the Hologic Panther Fusion", + "rel_date": "2020-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.31.20185074", + "rel_abs": "The Hologic Panther Fusion (PF) platform provides fully automated CE marked diagnostics for respiratory viruses, including recently SARS-coronavirus 2 by a transcription mediated amplification (TMA) assay, but not for the endemic human coronaviruses (hCoV). Therefore, a laboratory developed multiplexed RT-PCR protocol (LDT) that detects and differentiates the four hCoV NL63, 229E, HKU1 and OC43 was adapted on the PF.\n\nThe novel CE marked Aptima SARS-CoV-2 TMA and the LDT for hCoV were validated with 321 diagnostic specimens from the upper and lower respiratory tract in comparison to two SARS-CoV-2 RT-PCRs (PF E-gene LDT and genesig RT-PCR, 157 specimens) or the R-GENE hCoV / hParaFlu RT-PCR (164 specimens), respectively.\n\nFor the endemic hCoV, results were 96.3% concordant with two specimens discordantly positive in the PF and four specimens discordantly positive in the R-GENE assay. All discordantly positive samples had Ct values between 33 and 39. The PF hCoV LDT identified 23 hCoV positive specimens as NL63, 15 as 229E, 15 as HKU1 and 25 as OC43. The Aptima SARS-CoV-2 TMA gave 99.4 % concordant results compared to the consensus results with a single specimen discordantly positive. Moreover, 36 samples from proficiency testing panels were detected and typed correctly by both novel methods.\n\nIn conclusion, the SARS-CoV-2 TMA and the LDT for hCoV enhanced the diagnostic spectrum of the PF for all coronaviruses circulating globally for a multitude of diagnostic materials from the upper and lower respiratory tract.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Anne K Cordes", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "William M Rehrauer", + "author_inst": "University of Wisconsin School of Medicine and Public Health" + }, + { + "author_name": "Molly A Accola", + "author_inst": "University of Wisconsin Hospital and Clinics, Molecular Diagnostics Laboratory" + }, + { + "author_name": "Benno Woelk", + "author_inst": "LADR Medical Laboratory, Geesthacht" + }, + { + "author_name": "Birgitta Hilfrich", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Albert Heim", + "author_inst": "Hannover Medical School" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.02.280180", "rel_title": "Induction of a regulatory myeloid program in bacterial sepsis and severe COVID-19", @@ -1211826,61 +1215147,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.26.20182303", - "rel_title": "Risk factors for SARS-CoV-2 infection, hospitalisation, and death in Catalonia, Spain: a population-based cross-sectional study", - "rel_date": "2020-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.26.20182303", - "rel_abs": "OBJECTIVETo identify the different subpopulations that are susceptible for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and hospitalisation or death due to coronavirus disease 2019 (COVID-19) in Catalonia, Spain.\n\nDESIGNCross-sectional study.\n\nSETTINGData collected from the Catalan Health Surveillance System (CatSalut) in Catalonia, a region of Spain.\n\nPARTICIPANTSUsing data collected between 1 March and 1 June 2020, we conducted the following comparative analyses: people infected by SARS-CoV-2 (328 892) vs Catalonias entire population (7 699 568); COVID-19 cases who required hospitalisation (37 638) vs cases who did not require hospitalisation (291 254); and COVID-19 cases who died during the study period vs cases who did not die during the study period (12 287).\n\nMAIN OUTCOME MEASURESThree clinical outcomes related to COVID-19 (infection, hospitalisation, or death). We analysed sociodemographic and environment variables (such as residing in a nursing home) and the presence of previous comorbidities.\n\nRESULTSA total of 328 892 cases were considered to be infected with SARS-CoV-2 (4.27% of total population). The main risk factors for the diagnostic were: female gender (risk ratio [RR] =1.49; 95% confidence interval [95% CI] =1.48-1.50), age (4564 years old; RR=1.02; 95% CI=1.01-1.03), high comorbidity burden (GMA index) (RR=3.03; 95% CI=2.97-3.09), reside in a nursing home (RR=11.82; 95% CI=11.66-11.99), and smoking (RR=1.06; 95% CI=1.05-1.07). During the study period, there were 37 638 (11.4 %) hospitalisations due to COVID-19, and the risk factors were: male gender (RR=1.45; 95% CI=1.43-1.48), age > 65 (RR=2.38; 95% CI=2.28-2.48), very low individual income (RR=1.03; 95% CI=0.97-1.08), and high burden of comorbidities (GMA index) (RR=5.15; 95% CI=4.89-5.42). The individual comorbidities with higher burden were obesity (RR=1.23; 95% CI=1.20-1.25), chronic obstructive pulmonary disease (RR=1.19; 95% CI=1.15-1.22), heart failure (RR=1.19; 95% CI=1.16-1.22), diabetes mellitus (RR=1.07; 95% CI=1.04-1.10), and neuropsychiatric comorbidities (RR=1.06; 95% CI=1.03-1.10). A total of 12 287 deaths (3.73%) were attributed to COVID-19, and the main risk factors were: male gender (RR=1.73; 95% CI=1.67-1.81), age > 65 (RR=37.45; 95% CI=29.23-47.93), residing in a nursing home (RR=9.22; 95% CI=8.81-9.65), and high burden of comorbidities (GMA index) (RR=5.25; 95% CI=4.60-6.00). The individual comorbidities with higher burden were: heart failure (RR=1.21; 95% CI=1.16-1.22), chronic kidney disease (RR=1.17; 95% CI=1.13-1.22), and diabetes mellitus (RR=1.10; 95% CI=1.06-1.14). These results did not change significantly when we considered only PCR-positive patients.\n\nCONCLUSIONSFemale gender, age between 45 to 64 years old, high burden of comorbidities, and factors related to environment (nursing home) play a relevant role in SARS-CoV-2 infection and transmission. In addition, we found risk factors for hospitalisation and death due to COVID-19 that had not been described to date, including comorbidity burden, neuro-psychiatric disorders, and very low individual income. This study supports interventions for transmission control beyond stratify-and-shield strategies focused only on protecting those at risk of death. Future COVID-19 studies should examine the role of gender, the burden of comorbidities, and socioeconomic status in disease transmission, and should determine its relationship to workplaces, especially healthcare centres and nursing homes.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Judit Villar-Garcia", - "author_inst": "Medical Research Institute Hospital del Mar-IMIM, Barcelona, Spain" - }, - { - "author_name": "Rosa Maria Vivanco-Hidalgo", - "author_inst": "Agencia de Qualitat i Avaluacio Sanitaries de Catalunya, Barcelona, Spain" - }, - { - "author_name": "Montserrat Cleries", - "author_inst": "Area de sistemes de informacio, Servei Catala de la Salut, Generalitat de Catalunya Barcelona, Spain" - }, - { - "author_name": "Elisenda Martinez", - "author_inst": "Agencia de Qualitat i Avaluacio Sanitaries de Catalunya Barcelona,Spain" - }, - { - "author_name": "David Monterde", - "author_inst": "Sistemes de Informacio, Institut Catala de la Salut Barcelona,Spain" - }, - { - "author_name": "Pol Perez-Sust", - "author_inst": "Area de Sistemes de Informacio. Servei Catala de la Salut Barcelona, Spain" - }, - { - "author_name": "Luis Garcia-Eroles", - "author_inst": "Area de Sistemes de Informacio. Servei Catala de la Salut Barcelona, Spain" - }, - { - "author_name": "Carol Sais", - "author_inst": "Area de Sistemes de Informacio. Servei Catala de la Salut Barcelona, Spain" - }, - { - "author_name": "Montserrat Moharra", - "author_inst": "Agencia de Qualitat i Avaluacio Sanitaries de Catalunya, Barcelona, Spain" - }, - { - "author_name": "Emili Vela", - "author_inst": "Area de Sistemes de Informacio. Servei Catala de la Salut Barcelona, Spain" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.26.20182584", "rel_title": "A multipurpose machine learning approach to predict COVID-19 negative prognosis in Sao Paulo, Brazil", @@ -1212085,6 +1215351,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2020.08.26.20182840", + "rel_title": "On Statistical Power for Case-Control Host Genomic Studies of COVID-19", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.26.20182840", + "rel_abs": "The identification of genetic variation that directly impacts infection susceptibility and disease severity of COVID-19 is an important step towards risk stratification, personalized treatment plans, therapeutic and vaccine development and deployment. Given the importance of study design in infectious disease genetic epidemiology, we use simulation and draw on current estimates of exposure, infectivity and test accuracy of COVID-19 to demonstrate the feasibility of detecting host genetic factors associated with susceptibility and severity with published COVID-19 study designs. We demonstrate why studying susceptibility to SARS-CoV-2 infection could be futile at the early stages of the pandemic. Our insights can aid in the interpretation of genetic findings emerging in the literature and guide the design of future host genetic studies.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yu-Chung Lin", + "author_inst": "Department of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada" + }, + { + "author_name": "Jennifer D Brooks", + "author_inst": "Department of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada" + }, + { + "author_name": "Shelley B Bull", + "author_inst": "Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON" + }, + { + "author_name": "France Gagnon", + "author_inst": "Department of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada" + }, + { + "author_name": "Celia MT Greenwood", + "author_inst": "Gerald Bronfman Department of Oncology, Department of Epidemiology, Biostatistics & Occupational Health, Department of Human Genetics, McGill University, Montre" + }, + { + "author_name": "Rayjean J Hung", + "author_inst": "Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada." + }, + { + "author_name": "Jerald Lawless", + "author_inst": "Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, ON, Canada" + }, + { + "author_name": "Andrew Paterson", + "author_inst": "Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada" + }, + { + "author_name": "Lei Sun", + "author_inst": "Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada." + }, + { + "author_name": "Lisa J Strug", + "author_inst": "Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.08.28.20183699", "rel_title": "Do Lockdowns Bring about Additional Mortality Benefits or Costs? Evidence based on Death Records from 300 Million Chinese People", @@ -1213164,129 +1216485,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2020.08.28.20181883", - "rel_title": "Clinical, cerebrospinal fluid and neuroimaging findings in COVID-19 encephalopathy: a case series", - "rel_date": "2020-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.28.20181883", - "rel_abs": "ObjectiveTo describe the clinical, neurological, neuroimaging and cerebrospinal fluid (CSF) findings associated with encephalopathy in patients admitted to a COVID-19 tertiary reference center.\n\nMethodsWe retrospectively reviewed records of consecutive patients with COVID-19 evaluated by a consulting neurology team from March 30, 2020 through May 15, 2020.\n\nResultsFifty-five patients with confirmed SARS-CoV-2 were included, 43 of whom showed encephalopathy, and were further divided into mild, moderate and severe encephalopathy groups. Nineteen patients (44%) had undergone mechanical ventilation and received intravenous sedatives. Eleven (26%) patients were on dialysis. Laboratory markers of COVID-19 severity were very common in encephalopathy patients, but did not correlate with the severity of encephalopathy. Thirty-nine patients underwent neuroimaging studies, which showed mostly non-specific changes. One patient showed lesions possibly related to CNS demyelination. Four had suffered an acute stroke. SARS-CoV-2 was detected by RT-PCR in only one of 21 CSF samples. Two CSF samples showed elevated white blood cell count and all were negative for oligoclonal bands. In our case series the severity of encephalopathy correlated with higher probability of death during hospitalization (OR = 5.5 for each increment in the degree of encephalopathy, from absent (0) to mild (1), moderate (2) or severe (3), p<0.001).\n\nConclusionIn our consecutive series with 43 encephalopathy cases, neuroimaging and CSF analysis did not support the role of direct viral CNS invasion or CNS inflammation as the cause of encephalopathy.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Raphael Tuma", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Bruno Guedes", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Rafael Carra", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Bruno Iepsen", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Julia Rodrigues", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Antonio Edvan Camelo Filho", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Gabriel Kubota", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Maira Ferrari", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Adalberto Studart-Neto", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Mariana Oku", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Sara Terrim", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Cesar Lopes", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Carlos Eduardo Passos Neto", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Matheus Dalben", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Julia De Souza", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Jose Pedro Baima", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Tomas Da Silva", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Iago Perissinotti", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Maria da Graca Martin", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurradiologia" - }, - { - "author_name": "Marcia Goncalves", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Ida Fortini", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Jerusa Smid", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Tarso Adoni", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Leandro Lucatto", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurradiologia" - }, - { - "author_name": "Ricardo Nitrini", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Helio Gomes", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Luiz Henrique Castro", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2020.08.27.20183277", "rel_title": "DeepSOCIAL: Social Distancing Monitoring and Infection Risk Assessment in COVID-19 Pandemic", @@ -1213455,6 +1216653,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.30.20183889", + "rel_title": "Viral shedding dynamics reveals sputum as a reliable and cost-saving specimen for SARS-CoV-2 diagnosis within the first 10 days since symptom onset: A prospective cohort study", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.30.20183889", + "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome virus (SARS-CoV-2) is challenging global public health, due to an increasing demand for testing and the shortage of diagnostic supplies. Nasopharyngeal swab (NPS) is considered the optimal sample for SARS-CoV2 diagnosis and sputum (SPT) has been proposed as an economic alternative. However, the temporal concordance of diagnosis in NPS and SPT has not been addressed.\n\nMethodsThrough a longitudinal study we compared the shedding dynamics of SARS-CoV-2 RNA evaluated by RT-qPCR in serially collected SPT and NPS obtained from 82 ambulatory and hospitalized patients during acute infection and convalescence. The concordance during the follow-up and cost analysis between both collected specimens was evaluated.\n\nFindingsWe analyzed 379 samples, 177 NPS and 202 SPT. The highest proportion of positive samples was detected within the first 15 days after the symptoms onset. The median time of positivity was higher for NPS (median= 25 days) than SPT (median= 21 days). There was no significant difference in the median RT-qPCR CT values between both sample types. The temporal categorization of matched-paired samples indicated substantial correlation (r=0{middle dot}6023) and substantial agreement (87{middle dot}23%) during the first ten days since symptoms onset (kappa = 0{middle dot}697). A cost analysis demonstrated a significant saving when the SPT specimen was used.\n\nInterpretationSputum is a feasible and cost-saving alternative to NPS, providing an equivalent value for the detection and follow-up of SARS-CoV-2 RNA.\n\nFundingAgencia Nacional de Investigacion y Desarrollo (ANID) of Chile, NIH-NIAID USA.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Jorge E Levican-Asenjo", + "author_inst": "1Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile." + }, + { + "author_name": "Leonardo I Almonacid", + "author_inst": "Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile." + }, + { + "author_name": "Gonzalo Valenzuela", + "author_inst": "Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile." + }, + { + "author_name": "Tamara Garcia", + "author_inst": "Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile." + }, + { + "author_name": "Luis Rojas", + "author_inst": "Department of Internal Medicine, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile. Program of Pharmacology and Toxicology, School o" + }, + { + "author_name": "Eileen Serrano", + "author_inst": "Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile." + }, + { + "author_name": "Catalina Pardo-Roa", + "author_inst": "Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile." + }, + { + "author_name": "Erick Salinas", + "author_inst": "Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile" + }, + { + "author_name": "Maria J Avendano", + "author_inst": "Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile." + }, + { + "author_name": "Fabiola Perazzo", + "author_inst": "Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile." + }, + { + "author_name": "Luis A Diaz", + "author_inst": "Department of Gastroenterology, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile" + }, + { + "author_name": "Sebastian Valderrama", + "author_inst": "Department of Internal Medicine, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile." + }, + { + "author_name": "Marcos Ortega", + "author_inst": "Department of Intensive Care Medicine, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile. Department of Respiratory Medicine, School" + }, + { + "author_name": "Adriana Toro", + "author_inst": "Pediatric Service, Clinica UC San Carlos, Red Salud UC Christus, Faculty of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile." + }, + { + "author_name": "Viviana Montecinos", + "author_inst": "Department of Hematology-Oncology, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile." + }, + { + "author_name": "Arnoldo Riquelme", + "author_inst": "Department of Gastroenterology, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile." + }, + { + "author_name": "Rafael A. Medina", + "author_inst": "Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile. Department of Microbi" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.27.20183483", "rel_title": "Repeat testing for SARS-COV-2: Persistence of viral RNA is common, and clearance is slower in older age groups", @@ -1215182,25 +1218463,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.30.274506", - "rel_title": "From Face-to-Face to Online Modality: Implications for Undergraduate Learning While the World is Temporarily Closed in the Age of COVID-19", - "rel_date": "2020-08-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.30.274506", - "rel_abs": "The second half of the Spring 2020 semester has been an unprecedented time globally due to the ongoing coronavirus disease 2019 (COVID-19). COVID-19 pandemic has forced more than one billion students out of school, has disrupted the world and led all university courses switched to online instruction social distancing actions taken to limit the spread of the virus. The aim of the present study is to evaluate the pandemic related changes for undergraduate students, to assess their perspectives related to their learning, experiences in two courses, and to discuss the far-reaching potential implications for the upcoming summer and fall semesters. An electronic survey was conducted to gather data on the student perceptions and learning characteristics of this transition from face-to-face (F2F) to online at a medium-sized university in the Southeast in the Spring 2020 semester. Nearly 88% of the participants indicated that the COVID-19 pandemic impacted their education, while 19% indicated that they prefer online over F2F learning. Furthermore, the online modality significantly increased attendance in General Biology I. Our study also showed that the usage of live conferencing and digital applications increased due to the pandemic. The current research fills the gap in the existing literature by providing the first study on the effects of the ongoing COVID-19 pandemic on undergraduate learning and experiences in the most unique dual modality of the Spring 2020 semester.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Gokhan Hacisalihoglu", - "author_inst": "Florida A&M University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "scientific communication and education" - }, { "rel_doi": "10.1101/2020.08.25.20181347", "rel_title": "Correction of Daily Positivity Rates for contribution of various test protocols being used in a pandemic.", @@ -1215329,6 +1218591,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.08.25.20181453", + "rel_title": "Phosphate levels and pulmonary damage in COVID-19 patients based on CO-RADS scheme: is there any link between parathyroid gland and COVID-19?", + "rel_date": "2020-08-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.25.20181453", + "rel_abs": "BackgroundPreliminary studies of COVID-19 have provided some evidence that electrolyte disturbances may also be present in patients. In this study we aimed to evaluate the role of the arrival electrolytes and symptoms in prediction of Lung damage in CT scan based on the CO-RADS system.\n\nMethodsThis was a retrospective cross-sectional analytical study. We included patients with laboratory confirmed COVID-19 infection, June 15 to July 7. Patients were included in study if there were no previous history of kidney disease. Demographic, clinical characteristics, laboratory findings, and CO-RADS High-resolution computed tomography (HRCT) of lung report were collected. Univariate logistic regression was employed first to identify the effective, correlated items. All statistics were performed with SPSS version 18.0.\n\nResultsIn the current study, 36 (20 male- 16 female) patients with mean age of the 54.7{+/-}17.5 years old were studied. Most common symptom at the arrival was the Fever (52.8%), followed by Fatigue (18%), and dyspnea (44.4%). Computed tomography assessment revealed CO-RADS 2 in 4 (11.1%) patients, CORADS 3 in 1 (2.8%), CO-RADS 4 in 20 (55.6%), and CO-RADS 5 in 11 (30.6%) patients. In the comparison with the study groups based on the HRCT status (CO-RADS II,III vs. CO-RADS IV,V), patients with severe HRCT damage had significantly lower level of Phosphorus (P < 0.01). Univariate logistic regression analysis showed that only one factors was associated with HRCT damage status (Phosphorus, P=0.040). Phosphorus upper than 4.5 was associated with better HRCT results with OR ratio of 3.71 (X2(1)=5.69; p=0.017).\n\nConclusionOur study illustrates that higher phosphate levels may be associated with better CT scan of lung outcomes in COVID-19; while hypophosphatemia is associated with severe lung injuries. This could help clinicians to manage hospitalized patients and may link the COVID-19 and parathyroid gland.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Farshid Javdani", + "author_inst": "Jahrom University of Medical Sciences, Jahrom, Iran." + }, + { + "author_name": "Shima Parsa", + "author_inst": "Jahrom University of Medical Sciences, Jahrom, Iran." + }, + { + "author_name": "Heshmatollah Shakeri", + "author_inst": "Jahrom University of Medical Sciences, Jahrom, Iran" + }, + { + "author_name": "Naser Hatami", + "author_inst": "Jahrom University of Medical Sciences, Jahrom, Iran." + }, + { + "author_name": "Navid Kalani", + "author_inst": "Jahrom University of Medical Sciences, Jahrom, Iran" + }, + { + "author_name": "Marzieh Haghbeen", + "author_inst": "Jahrom University of Medical Sciences, Jahrom, Iran" + }, + { + "author_name": "Rahim Raufi", + "author_inst": "Jahrom University of Medical Sciences, Jahrom, Iran" + }, + { + "author_name": "Alireza Abbasi", + "author_inst": "Jahrom University of Medical Sciences, Jahrom, Iran" + }, + { + "author_name": "Pouyan Keshavarz", + "author_inst": "Jahrom University of Medical Sciences, Jahrom, Iran" + }, + { + "author_name": "Seyyed Abbas Hashemi", + "author_inst": "Mazandaran University of Medical Sciences, Sari, Iran." + }, + { + "author_name": "Amin shafiee", + "author_inst": "Jahrom University of Medical Sciences, Jahrom, Iran." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "endocrinology" + }, { "rel_doi": "10.1101/2020.08.25.20182048", "rel_title": "Twitter Interaction to Analyze Covid-19 Impact in Ghana, Africa from March to July", @@ -1217032,97 +1220353,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.25.20181198", - "rel_title": "The importance of supplementary immunisation activities to prevent measles outbreaks during the COVID-19 pandemic in Kenya", - "rel_date": "2020-08-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.25.20181198", - "rel_abs": "BackgroundThe COVID-19 pandemic has disrupted routine measles immunisation and supplementary immunisation activities (SIAs) in most countries including Kenya. We assessed the risk of measles outbreaks during the pandemic in Kenya as a case study for the African Region.\n\nMethodsCombining measles serological data, local contact patterns, and vaccination coverage into a cohort model, we predicted the age-adjusted population immunity in Kenya and estimated the probability of outbreaks when contact-reducing COVID-19 interventions are lifted. We considered various scenarios for reduced measles vaccination coverage from April 2020.\n\nFindingsIn February 2020, when a scheduled SIA was postponed, population immunity was close to the herd immunity threshold and the probability of a large outbreak was 22% (0-46). As the COVID-19 restrictions to physical contact are lifted, from December 2020, the probability of a large measles outbreak increased to 31% (8-51), 35% (16-52) and 43% (31-56) assuming a 15%, 50% and 100% reduction in measles vaccination coverage. By December 2021, this risk increases further to 37% (17-54), 44% (29-57) and 57% (48-65) for the same coverage scenarios respectively. However, the increased risk of a measles outbreak following the lifting of restrictions on contact can be overcome by conducting an SIA with [≥] 95% coverage in under-fives.\n\nInterpretationWhile contact restrictions sufficient for SAR-CoV-2 control temporarily reduce measles transmissibility and the risk of an outbreak from a measles immunity gap, this risk rises rapidly once physical distancing is relaxed. Implementing delayed SIAs will be critical for prevention of measles outbreaks once contact restrictions are fully lifted in Kenya.\n\nFundingThe United Kingdoms Medical Research Council and the Department for International Development", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Caroline Ngendo Mburu", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "John Ojal", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya & London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Rose Chebet", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Donald Akech", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Boniface Karia", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "James Tuju", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Antipa Sigilai", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Kaja Abbas", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Mark Jit", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Sebastian Funk", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Gaby Smits", - "author_inst": "National Institute of Public Health and the Environment (RIVM), The Netherlands" - }, - { - "author_name": "Pieter G.M van Gageldonk", - "author_inst": "National Institute of Public Health and the Environment (RIVM), The Netherlands" - }, - { - "author_name": "Fiona R.M van der Klis", - "author_inst": "National Institute of Public Health and the Environment (RIVM), The Netherlands" - }, - { - "author_name": "Collins Tabu", - "author_inst": "National Vaccine and Immunisation Programme, Ministry of Health, Kenya" - }, - { - "author_name": "D James Nokes", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya & School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Re" - }, - { - "author_name": "- LSHTM CMMID COVID-19 Working Group", - "author_inst": "" - }, - { - "author_name": "John Anthony Scott", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi Kenya & London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Stefan Flasche", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Ifedayo M. O Adetifa", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya & London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.25.20182113", "rel_title": "Post-infection depression, anxiety and PTSD: a retrospective cohort study with mild COVID-19 patients", @@ -1217371,6 +1220601,77 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2020.08.30.273979", + "rel_title": "Ebselen derivatives are very potent dual inhibitors of SARS-CoV-2 proteases - PLpro and Mpro in in vitro studies", + "rel_date": "2020-08-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.30.273979", + "rel_abs": "Proteases encoded by SARS-CoV-2 constitute a promising target for new therapies against COVID-19. SARS-CoV-2 main protease (Mpro, 3CLpro) and papain-like protease (PLpro) are responsible for viral polyprotein cleavage - a process crucial for viral survival and replication. Recently it was shown that 2-phenylbenzisoselenazol-3(2H)-one (ebselen), an organoselenium anti-inflammatory small-molecule drug, is a potent, covalent inhibitor of both the proteases and its potency was evaluated in enzymatic and anti-viral assays. In this study, we screened a collection of 23 ebselen derivatives for SARS-CoV-2 PLpro and Mpro inhibitors. Our studies revealed that ebselen derivatives are potent inhibitors of both the proteases. We identified three PLpro and four Mpro inhibitors superior to ebselen. Our work shows that ebselen constitutes a promising platform for development of new antiviral agents targeting both SARS-CoV-2 PLpro and Mpro.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Mikolaj Zmudzinski", + "author_inst": "Wroclaw University of Science and Technology" + }, + { + "author_name": "Wioletta Rut", + "author_inst": "Wroclaw University of Science and Technology" + }, + { + "author_name": "Kamila Olech", + "author_inst": "Wroclaw University of Science and Technology" + }, + { + "author_name": "Jaroslaw Granda", + "author_inst": "Wroclaw University of Science and Technology" + }, + { + "author_name": "Miroslaw Giurg", + "author_inst": "Wroclaw University of Science and Technology" + }, + { + "author_name": "Malgorzata Burda-Grabowska", + "author_inst": "Wroclaw University of Science and Technology" + }, + { + "author_name": "Linlin Zhang", + "author_inst": "University of Luebeck" + }, + { + "author_name": "Xinyuanyuan Sun", + "author_inst": "University of Lubeck" + }, + { + "author_name": "Zongyang Lv", + "author_inst": "Department of Biochemistry & Structural Biology University of Texas Health Science Center at San Antonio" + }, + { + "author_name": "Digant Nayak", + "author_inst": "Department of Biochemistry & Structural Biology University of Texas Health Science Center at San Antonio" + }, + { + "author_name": "Malgorzata Kesik-Brodacka", + "author_inst": "Research Network Lukasiewicz - Institute of Biotechnology and Antibiotics" + }, + { + "author_name": "Shaun Olsen", + "author_inst": "Department of Biochemistry & Structural Biology University of Texas Health Science Center at San Antonio" + }, + { + "author_name": "Rolf Hilgenfeld", + "author_inst": "University of Lubeck" + }, + { + "author_name": "Marcin Drag", + "author_inst": "Wroclaw University of Science and Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.08.31.270736", "rel_title": "ACE2 and SARS-CoV-2 Expression in the Normal and COVID-19 Pancreas", @@ -1219138,37 +1222439,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.08.27.270819", - "rel_title": "Elucidation of remdesivir cytotoxicity pathways through genome-wide CRISPR-Cas9 screening and transcriptomics", - "rel_date": "2020-08-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.27.270819", - "rel_abs": "The adenosine analogue remdesivir has emerged as a frontline antiviral treatment for SARS-CoV-2, with preliminary evidence that it reduces the duration and severity of illness1. Prior clinical studies have identified adverse events1,2, and remdesivir has been shown to inhibit mitochondrial RNA polymerase in biochemical experiments7, yet little is known about the specific genetic pathways involved in cellular remdesivir metabolism and cytotoxicity. Through genome-wide CRISPR-Cas9 screening and RNA sequencing, we show that remdesivir treatment leads to a repression of mitochondrial respiratory activity, and we identify five genes whose loss significantly reduces remdesivir cytotoxicity. In particular, we show that loss of the mitochondrial nucleoside transporter SLC29A3 mitigates remdesivir toxicity without a commensurate decrease in SARS-CoV-2 antiviral potency and that the mitochondrial adenylate kinase AK2 is a remdesivir kinase required for remdesivir efficacy and toxicity. This work elucidates the cellular mechanisms of remdesivir metabolism and provides a candidate gene target to reduce remdesivir cytotoxicity.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Lin Lin", - "author_inst": "Hubrecht Institute" - }, - { - "author_name": "Grace Yeo", - "author_inst": "MIT" - }, - { - "author_name": "Callie J Donahue", - "author_inst": "Boston University" - }, - { - "author_name": "Robert A Davey", - "author_inst": "Boston University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.08.26.269118", "rel_title": "Fractal signatures of SARS-CoV2 coronavirus, the indicator matrix, the fractal dimension and the 2D directional wavelet transform: A comparative study with SARS-CoV, MERS-CoV and SARS-like coronavirus.", @@ -1219297,6 +1222567,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.08.28.267567", + "rel_title": "A PCR amplicon-based SARS-CoV-2 replicon for antiviral screening", + "rel_date": "2020-08-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.28.267567", + "rel_abs": "The development of specific antiviral compounds to SARS-CoV-2 is an urgent task. One of the obstacles for the antiviral development is the requirement of biocontainment because infectious SARS-CoV-2 must be handled in a biosafety level-3 laboratory. Replicon, a non-infectious self-replicative viral RNA, could be a safe and effective tool for antiviral screening; however, SARS-CoV-2 replicon has not been reported yet. Herein, we generated a PCR-based SARS-CoV-2 replicon. Eight fragments covering the entire SARS-CoV-2 genome except S, E, and M genes were amplified with HiBiT-tag sequence by PCR. The amplicons were ligated and in vitro transcribed to RNA. The cells electroporated with the replicon RNA showed more than 3,000 times higher luminescence than MOCK control cells at 24 hours post-electroporation, indicating robust viral translation and RNA replication. The replication was drastically inhibited by remdesivir, an RNA polymerase inhibitor for SARS-CoV-2. The IC50 of remdesivir in this study was 0.29 M, generally consistent to the IC50 obtained using infectious SARS-CoV-2 in a previous study (0.77 M). Taken together, this system could be applied to the safe and effective antiviral screening without using infectious SARS-CoV-2. Because this is a transient replicon, further improvement including the establishment of stable cell line must be achieved.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Tomohiro Kotaki", + "author_inst": "Kobe University" + }, + { + "author_name": "Xuping Xie", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Pei-Yong Shi", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Masanori Kameoka", + "author_inst": "Kobe University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.28.267526", "rel_title": "Plasmablast-derived antibody response to acute SARS-CoV-2 infection in humans", @@ -1220619,41 +1223920,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2020.08.19.20178376", - "rel_title": "Preventing disease after exposure to COVID-19 using hydroxychloroquine: A summary of a protocol for exploratory re-analysis of age and time-nuanced effects.", - "rel_date": "2020-08-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20178376", - "rel_abs": "BACKGROUNDA recently published randomized trial (Boulware et al., 2020, NCT04308668) of hydroxychloroquine (HCQ) for post-exposure prophylaxis found a reduction in Covid-19 of 17%. In the context of ambitious powering to detect a 50% reduction, this non-statistically significant finding could translate to a reduction of 22,000/130,828 cases (CDC 8/12/20) among US health care workers (HCW), impacting trajectory and resource utilization models that drive decisions on lockdowns and social distancing.\n\nData found only in the appendix of Boulware et al. suggested greater differences in the effect HCQ among sub-groups. There were reductions (36%) in younger (<35 years) and increases (110%) in older (>50 years) subjects. Our preliminary analysis revealed a significant negative correlation (slope -0.211, CI -0.328-0.094, p=0.016) between treatment lag and disease reduction, reaching 49% when initiated within one day (RR 0.51, CI 0.176-1.46, p=0.249).\n\nThere were also differences in disease reduction by HCQ by type of exposure (HCW - 8% vs. household contacts - 31%; RR 0.691, CI 0.398-1.2). The definitions of exposure severity did not discriminate between the numbers or duration (> 10 minutes) of exposures. Differences between exposure types may result from younger HCW and higher risks in less trained household contacts with little access to advanced PPE. The ex-protocol use of zinc and ascorbic acid were likely confounders, as was the possibly active folate placebo.\n\nExploratory reanalysis of the raw dataset may inform an age- and stage- nuanced approach to COVID-19 using HCQ testable by prospective studies and may provide insight into the various proposed mechanisms of HCQ.\n\nOBJECTIVESTo conduct an exploratory re-analysis of the de-identified raw dataset from a randomized study of the use of HCQ for post-exposure prophylaxis of COVID-19 with view to further defining: a) The time dependent effect of HCQ, b) The age dependent effect of HCQ; c) The sub-stratification of time- and age-dependent effects by exposure type and risk level, as well as by the use of zinc and ascorbic acid. d) The design of future clinical trials to test the hypotheses generated by this study.\n\nMETHODSShould granularity of data (by age, time-lag, level and type of exposure) be greater than that originally reported, Fisher Exact test will be used to compare the incidence of COVID-19 in HCQ- and control groups, for each sub-group stratification. Since the degree of loss of data granularity due to de-identification is yet unknown, exploratory analyses involving other demographic characteristics cannot be planned. Where sufficient data granularity exists, univariate regression analyses will be conducted to examine the effect of age- and time lag on any effect of HCQ. The possibility will be explored of conducting multivariate Cox regression analyses with propensity score matching to examine observational data relating to the use of zinc and ascorbic acid.\n\nThis analysis will be expanded should a dataset from a similarly designed study (Mitja et al., 2020, NCT04304053), with directionally similar results, become available. This protocol was devised using the Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) incorporating the WHO Trial Registration Data Set.\n\nStudy StatusProtocol version 1.1 (August 19 2020)\n\nProtocol registered at: OSF Registries August 19 2020\n\nRegistration doi: https://doi.org/10.17605/OSF.IO/9RPYT", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "David M Wiseman", - "author_inst": "Synechion, Inc., Dallas, TX" - }, - { - "author_name": "Pierre Kory", - "author_inst": "Aurora St. Lukes Medical Center, Milwaukee, WI" - }, - { - "author_name": "Dan Mazzucco", - "author_inst": "ZSX Medical, Philadelphia, PA" - }, - { - "author_name": "Mayur S Ramesh", - "author_inst": "Henry Ford Hospital, Detroit, MI" - }, - { - "author_name": "Marcus Zervos", - "author_inst": "Henry Ford Hospital, Detroit, MI" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.24.20170175", "rel_title": "Evidence of SARS-CoV-2 transcriptional activity in cardiomyocytes of COVID-19 patients without clinical signs of cardiac involvement", @@ -1220922,6 +1224188,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.24.20180927", + "rel_title": "SARS-CoV-2 phylodynamics differentiates the effectiveness of non-pharmaceutical interventions", + "rel_date": "2020-08-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.24.20180927", + "rel_abs": "Quantifying the effectiveness of large-scale non-pharmaceutical interventions against COVID-19 is critical to adapting responses against future waves of the pandemic. By combining phylogenetic data of 5,198 SARS-CoV-2 genomes with the chronology of non-pharmaceutical interventions in 57 countries, we examine how interventions and combinations thereof alter the divergence rate of viral lineages, which is directly related to the epidemic reproduction number. Home containment and education lockdown had the largest independent impacts and were predicted to reduce the reproduction number by 35% and 26%, respectively. However, we find that in contexts with a reproduction number >2, no individual intervention is sufficient to stop the epidemic and increasingly stringent intervention combinations may be required. Our phylodynamic approach can complement epidemiological models to inform public health strategies against COVID-19.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Jean-Philippe Rasigade", + "author_inst": "University of Lyon" + }, + { + "author_name": "Anais Barray", + "author_inst": "University of Lyon" + }, + { + "author_name": "Julie Teresa Shapiro", + "author_inst": "University of Lyon" + }, + { + "author_name": "Charlene Coquisart", + "author_inst": "PSL University" + }, + { + "author_name": "Yoann Vigouroux", + "author_inst": "Sorbonne University" + }, + { + "author_name": "Antonin Bal", + "author_inst": "Hospices Civils de Lyon" + }, + { + "author_name": "Gregory Destras", + "author_inst": "Institut des Agents Infectieux - Hospices Civils de Lyon" + }, + { + "author_name": "Philippe Vanhems", + "author_inst": "Lyon University Hospitals" + }, + { + "author_name": "Bruno Lina", + "author_inst": "University of Lyon" + }, + { + "author_name": "Laurence Josset", + "author_inst": "University of Lyon" + }, + { + "author_name": "Thierry Wirth", + "author_inst": "PSL University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.24.20180919", "rel_title": "Sociodemographic disparities in knowledge, practices, and ability to comply with COVID-19 public health measures in Canada", @@ -1222493,61 +1225818,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.26.267831", - "rel_title": "SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolution", - "rel_date": "2020-08-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.26.267831", - "rel_abs": "Numerous factors have been identified to influence susceptibility to SARS-CoV-2 infection and disease severity. Cancer patients are more prone to clinically evolve to more severe COVID-19 conditions, but the determinants of such a more severe outcome remain largely unknown. We have determined the full-length SARS-CoV-2 genomic sequences of cancer patients and healthcare workers (HCW; non-cancer controls) by deep sequencing and investigated the within-host viral quasispecies of each infection, quantifying intrahost genetic diversity. Naso- and oropharyngeal SARS-CoV-2+ swabs from 57 cancer patients and 14 healthcare workers (HCW) from the Brazilian Cancer Institute were collected in April-May 2020. Complete genome amplification using ARTIC network V3 multiplex primers was performed followed by next-generation sequencing. Assemblies were conducted in Geneious R11, where consensus sequences were extracted and intrahost single nucleotide variants (iSNVs) were identified. Maximum likelihood phylogenetic analysis was performed using PhyMLv.3.0 and lineages were classified using Pangolin and CoV-GLUE. Phylogenetic analysis showed that all but one strain belonged to clade B1.1. Four genetically linked mutations known as the globally dominant SARS-CoV-2 haplotype (C241T, C3037T, C14408T and A23403G) were found in the majority of consensus sequences. SNV signatures of previously characterized Brazilian genomes were also observed in most samples. Another 85 SNVs were found at a lower frequency (1.4-19.7%). Cancer patients displayed a significantly higher intrahost viral genetic diversity compared to HCW (p = 0.009). Intrahost genetic diversity in cancer patients was independent of SARS-CoV-2 Ct values, and was not associated with disease severity, use of corticosteroids, or use of antivirals, characteristics that could influence viral diversity. Such a feature may explain, at least in part, the more adverse outcomes to which cancer/COVID-19 patients experience.\n\nAuthor SummaryCancer patients are more prone to clinically evolve to more severe COVID-19 conditions, but the determinants of such a more severe outcome remain largely unknown. In this study, phylogenetic and variation analysis of SARS-CoV-2 genomes from cancer patients and non-cancer healthcare workers at the Brazilian National Cancer Institute were characterized by deep sequencing. Viral genomes showed signatures characteristic of Brazilian viruses, consistent with the hypothesis of local, community transmission rather than virus importation from abroad. Despite most genomes in patients and healthcare workers belonging to the same lineage, intrahost variability was higher in cancer patients when compared to non-cancer counterparts. The intrahost genomic diversity analysis presented in our study highlights the relaxed evolution of SARS-CoV-2 in a vulnerable population of cancer patients. The high number of minor variations can result in the selection of immune escape variants, resistance to potential drugs, and/or increased pathogenicity. The impact of this higher intrahost variability over time warrants further investigation.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Juliana Siqueira", - "author_inst": "Instituto Nacional de Cancer" - }, - { - "author_name": "Livia R. Goes", - "author_inst": "Instituto Nacional de Cancer" - }, - { - "author_name": "Brunna M. Alves", - "author_inst": "Instituto Nacional de Cancer" - }, - { - "author_name": "Pedro S. de Carvalho", - "author_inst": "Instituto Nacional de Cancer" - }, - { - "author_name": "Claudia Cicala", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "James Arthos", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Jo\u00e3o P.B. Viola", - "author_inst": "Instituto Nacional de Cancer" - }, - { - "author_name": "Andr\u00e9ia C. de Melo", - "author_inst": "Instituto Nacional de Cancer" - }, - { - "author_name": "Marcelo A. Soares", - "author_inst": "Instituto Nacional de Cancer" - }, - { - "author_name": "INCA COVID-19 Task Force (names of participants listed in the acknowledgements section number of cha", - "author_inst": "" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.22.20179754", "rel_title": "Monitoring COVID-19 transmission risks by RT-PCR tracing of droplets in hospital and living environments", @@ -1222776,6 +1226046,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.08.23.20179838", + "rel_title": "Projecting COVID-19 disease severity in cancer patients using purposefully-designed machine learning", + "rel_date": "2020-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.23.20179838", + "rel_abs": "BackgroundAccurately predicting outcomes for cancer patients with COVID-19 has been clinically challenging. Numerous clinical variables have been retrospectively associated with disease severity, but the predictive value of these variables, and how multiple variables interact to increase risk, remains unclear.\n\nMethodsWe used machine learning algorithms to predict COVID-19 severity in 354 cancer patients at Memorial Sloan Kettering Cancer Center in New York City. Using clinical variables only collected on or before a patients COVID-19 positive date (time zero), we sought to classify patients into one of three possible future outcomes: Severe-early (the patient required high levels of oxygen support within 3 days of being tested positive for COVID-19), Severe-late (the patient required high levels of oxygen after 3 days), and Non-severe (the patient never required oxygen support).\n\nResultsOur algorithm classified patients into these classes with an AUROC ranging from 70-85%, significantly outperforming prior methods and univariate analyses. Critically, classification accuracy is highest when using a potpourri of clinical variables -- including patient demographics, pre-existing diagnoses, laboratory and radiological work, and underlying cancer type -- suggesting that COVID-19 in cancer patients comes with numerous, combinatorial risk factors.\n\nConclusionsOverall, we provide a computational tool that can identify high-risk patients early in their disease progression, which could aid in clinical decision-making and selecting treatment options.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Saket Navlakha", + "author_inst": "Cold Spring Harbor Laboratory" + }, + { + "author_name": "Sejal Morjaria", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Rocio Perez-Johnston", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Allen Zhang", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Ying Taur", + "author_inst": "Memorial Sloan Kettering Cancer Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.23.20179820", "rel_title": "Allocation of COVID-19 Vaccines Under Limited Supply", @@ -1224139,61 +1227444,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.22.20180042", - "rel_title": "Role of interfering substances in the survival of coronaviruses on surfaces and their impact on the efficiency of hand and surface disinfection", - "rel_date": "2020-08-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.22.20180042", - "rel_abs": "Contaminated environmental surfaces are considered to represent a significant vector for hospital-acquired viral infections. In this study, we have evaluated the impact of interfering substances on SARS-CoV-2 surface stability and virucidal efficiency of hand sanitizers and surface disinfectant. To this end, surface stability of SARS-CoV-2 was measured on stainless steel in different experimental conditions, with or without an artificial mucus/saliva mixture and compared against that of human coronavirus HCoV-229E and feline coronavirus FCoV. The impact of the mucus/saliva mixture on the virucidal efficiency of 3 commercial alcohol hand sanitizers and 1 surface chemical disinfectant against SARS-CoV-2, HCoV-229E and FCoV was then measured. Our results indicate that mucus/saliva mixture did not demonstrate a beneficial effect on the surface survival of tested viruses, with temperature being an important parameter. In addition, we demonstrated that interfering substances may play an important role in the virucidal efficacy of hand sanitizers and disinfectants, highlighting the need for adapted testing protocols that better reflect current \"real life\" conditions of use.\n\nHighlightsO_LIContaminated environmental surfaces are a significant vector for viral infections.\nC_LIO_LIWe studied the impact of interfering substances on SARS-CoV-2 surface stability and virucidal efficiency.\nC_LIO_LIMucus/saliva did not demonstrate a beneficial effect on viral surface stability, with temperature being an important parameter.\nC_LIO_LIInterfering substances are important for virucidal surface activity of disinfectants.\nC_LI", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Lea Szpiro", - "author_inst": "VirHealth" - }, - { - "author_name": "Andres Pizzorno", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Lauranne Durimel", - "author_inst": "VirHealth" - }, - { - "author_name": "Thomas Julien", - "author_inst": "Centre International de Recherche En Infectiologie" - }, - { - "author_name": "Aurelien Traversier", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Dounia Bouchami", - "author_inst": "VirHealth" - }, - { - "author_name": "Yana Marie", - "author_inst": "VirHealth" - }, - { - "author_name": "Manuel Rosa-Calatrava", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Olivier Terrier", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Vincent Moules", - "author_inst": "VirHealth" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.23.20177501", "rel_title": "Therapeutic Prospects for Th-17 Cell Immune Storm Syndrome and Neurological Symptoms in COVID-19: Thiamine Efficacy and Safety, In-vitro Evidence and Pharmacokinetic Profile", @@ -1224586,6 +1227836,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.20.20178772", + "rel_title": "Hydroxychloroquine in the treatment of outpatients with mildly symptomatic COVID-19: A multi-center observational study", + "rel_date": "2020-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.20.20178772", + "rel_abs": "BackgroundHydroxychloroquine has not been associated with improved survival among hospitalized COVID-19 patients in the majority of observational studies and similarly was not identified as an effective prophylaxis following exposure in a prospective randomized trial. We aimed to explore the role of hydroxychloroquine therapy in mildly symptomatic patients diagnosed in the outpatient setting.\n\nMethodsWe examined the association between outpatient hydroxychloroquine exposure and the subsequent progression of disease among mildly symptomatic non-hospitalized patients with documented SARS-CoV-2 infection. The primary outcome assessed was requirement of hospitalization. Data was obtained from a retrospective review of electronic health records within a New Jersey USA multi-hospital network. We compared outcomes in patients who received hydroxychloroquine with those who did not applying a multivariable logistic model with propensity matching.\n\nResultsAmong 1274 outpatients with documented SARS-CoV-2 infection 7.6% were prescribed hydroxychloroquine. In a 1067 patient propensity matched cohort, 21.6% with outpatient exposure to hydroxychloroquine were hospitalized, and 31.4% without exposure were hospitalized. In the primary multivariable logistic regression analysis with propensity matching there was an association between exposure to hydroxychloroquine and a decreased rate of hospitalization from COVID-19 (OR 0.53; 95% CI, 0.29, 0.95). Sensitivity analyses revealed similar associations. QTc prolongation events occurred in 2% of patients prescribed hydroxychloroquine with no reported arrhythmia events among those with data available.\n\nConclusionsIn this retrospective observational study of SARS-CoV-2 infected non-hospitalized patients hydroxychloroquine exposure was associated with a decreased rate of subsequent hospitalization. Additional exploration of hydroxychloroquine in this mildly symptomatic outpatient population is warranted.\n\nLay SummaryIn this observational study of 1,274 COVID-19 patients, hydroxychloroquine given as an outpatient treatment was associated with a 47% reduction in the hazard of hospitalization. Adverse events were not increased (2% QTc prolongation events, 0% arrhythmias). Further validation is required. Use of hydroxychloroquine to treat COVID-19 in the outpatient setting should be reserved for a clinical trial or after discussion with a physician regarding risks and benefits.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Andrew Ip", + "author_inst": "Division of Outcomes and Value Research, John Theurer Cancer Center at Hackensack University Medical Center" + }, + { + "author_name": "Jaeil Ahn", + "author_inst": "Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University" + }, + { + "author_name": "Yizhao Zhou", + "author_inst": "Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University" + }, + { + "author_name": "Andre H Goy", + "author_inst": "John Theurer Cancer Center at Hackensack University Medical Center" + }, + { + "author_name": "Eric Hansen", + "author_inst": "COTA" + }, + { + "author_name": "Andrew L Pecora", + "author_inst": "John Theurer Cancer Center at Hackensack University Medical Center" + }, + { + "author_name": "Brittany A Sinclaire", + "author_inst": "John Theurer Cancer Center at Hackensack University Medical Center" + }, + { + "author_name": "Urszula Bednarz", + "author_inst": "John Theurer Cancer Center at Hackensack University Medical Center" + }, + { + "author_name": "Michael Marafelias", + "author_inst": "John Theurer Cancer Center at Hackensack University Medical Center" + }, + { + "author_name": "Shivam Mathura", + "author_inst": "COTA" + }, + { + "author_name": "Ihor S Sawczuk", + "author_inst": "Hackensack Meridian Health, Hackensack Meridian School of Medicine" + }, + { + "author_name": "Joseph P Underwood III", + "author_inst": "Hackensack University Medical Center" + }, + { + "author_name": "David M Walker", + "author_inst": "Hackensack University Medical Center" + }, + { + "author_name": "Rajiv Prasad", + "author_inst": "Bayshore Medical Center" + }, + { + "author_name": "Robert L Sweeney", + "author_inst": "Jersey Shore University Medical Center" + }, + { + "author_name": "Marie G Ponce", + "author_inst": "Jersey Shore University Medical Center" + }, + { + "author_name": "Samuel LaCapra", + "author_inst": "JFK Medical Center" + }, + { + "author_name": "Frank J Cunningham", + "author_inst": "JFK Medical Center" + }, + { + "author_name": "Arthur G Calise", + "author_inst": "Hackensack Meridian Mountainside Medical Center" + }, + { + "author_name": "Bradley L Pulver", + "author_inst": "Ocean Medical Center" + }, + { + "author_name": "Dominic Ruocco", + "author_inst": "Palisades Medical Center" + }, + { + "author_name": "Greggory E Mojares", + "author_inst": "Pascack Valley Medical Center" + }, + { + "author_name": "Michael P Eagan", + "author_inst": "Raritan Bay Medical Center" + }, + { + "author_name": "Kristy L Ziontz", + "author_inst": "Riverview Medical Center" + }, + { + "author_name": "Paul Mastrokyriakos", + "author_inst": "Southern Ocean Medical Center" + }, + { + "author_name": "Stuart L Goldberg", + "author_inst": "Division of Outcomes and Value Research, John Theurer Cancer Center at Hackensack University Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.18.20177592", "rel_title": "Evaluation of nasopharyngeal swab collection techniques for nucleic acid recovery and participant experience: recommendations for COVID-19 diagnostics", @@ -1226060,37 +1229429,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2020.08.21.20166355", - "rel_title": "Platelet-to-lymphocyte ratio (PLR), a novel biomarker to predict the severity of COVID-19 patients: a systematic review and meta-analysis", - "rel_date": "2020-08-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.21.20166355", - "rel_abs": "BackgroundPlatelet-to-lymphocyte ratio (PLR), a novel inflammatory marker, has been suggested to be able to predict the severity of COVID-19 patients. This systematic review aims to evaluate the association between PLR levels on admission and the severity of COVID-19 patients.\n\nMethodsA systematic literature search was done on 23 July 2020 to identify peer-reviewed studies across four different databases (Ovid MEDLINE, EMBASE, SCOPUS, and the Cochrane Library), preprints from two databases (MedRxiv and SSRN), and grey literature from two databases (WHO COVID-19 Global Research Database and Center for Disease Control and Prevention COVID-19 Research Article). Research articles comparing the PLR value on admission in adult patients with COVID-19 with varying degrees of severity were included in the analysis. The following keywords were used for the search: \"COVID-19\", \"PLR\", \"severity\", and \"mortality\". The inverse variance method was used to calculate the pooled effect standardized mean difference (SMD) along with its 95% confidence interval (CI).\n\nResultsA total of seven studies were included in the meta-analysis, six of which were conducted in China. From a total of 998 participants included, 316 (31.7%) had severe diseases; and those in the severe group were generally older and had underlying diseases compared to the non-severe group. In comparison to non-severe patients, the meta-analysis showed that severe COVID-19 patients had higher PLR levels on admission (SMD 0.68; 95%CI 0.43-0.93; I2 =58%).\n\nConclusionHigh PLR levels on admission were associated with severe COVID-19 cases. Therefore, on-admission PLR level is a novel, cost-effective, and readily available biomarker with a promising prognostic role for determining the severity of COVID-19 patients.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Daniel Martin Simadibrata", - "author_inst": "Faculty of Medicine, Universitas Indonesia" - }, - { - "author_name": "Bashar Adi Wahyu Pandhita", - "author_inst": "Faculty of Medicine, Universitas Indonesia" - }, - { - "author_name": "Muammar Emir Ananta", - "author_inst": "Faculty of Medicine, Universitas Indonesia" - }, - { - "author_name": "Tamara Tango", - "author_inst": "Faculty of Medicine, Universitas Indonesia" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2020.08.21.20177923", "rel_title": "Prevalence and outcome of Covid-19 infection in cancer patients: a national VA study", @@ -1226371,6 +1229709,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.21.20167965", + "rel_title": "Implications of the school-household network structure on SARS-CoV-2 transmission under different school reopening strategies in England", + "rel_date": "2020-08-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.21.20167965", + "rel_abs": "BackgroundSchool closures are a well-established non-pharmaceutical intervention in the event of infectious disease outbreaks, and have been implemented in many countries across the world, including the UK, to slow down the spread of SARS-CoV-2. As governments begin to relax restrictions on public life there is a need to understand the potential impact that reopening schools may have on transmission.\n\nMethodsWe used data provided by the UK Department for Education to construct a network of English schools, connected through pairs of pupils resident at the same address. We used the network to evaluate the potential for transmission between schools, and for long range propagation across the network, under different reopening scenarios.\n\nResultsAmongst the options evaluated we found that reopening only Reception, Year 1 and Year 6 (4-6 and 10-11 year olds) resulted in the lowest risk of transmission between schools, with outbreaks within a single school unlikely to result in outbreaks in adjacent schools in the network. The additional reopening of Years 10 and 12 (14-15 and 16-17 year olds) resulted in an increase in the risk of transmission between schools comparable to reopening all primary school years (4-11 year olds). However, the majority of schools presented low risk of initiating widespread transmission through the school system. Reopening all secondary school years (11-18 year olds) resulted in large potential outbreak clusters putting up to 50% of households connected to schools at risk of infection if sustained transmission within schools was possible.\n\nConclusionsReopening secondary school years is likely to have a greater impact on community transmission than reopening primary schools in England. Keeping transmission within schools limited is essential for reducing the risk of large outbreaks amongst school-aged children and their household members.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "James D Munday", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Katharine Sherratt", + "author_inst": "London school of Hygiene and Tropical Medicine" + }, + { + "author_name": "Sophie Meakin", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Akira Endo", + "author_inst": "London School Of Hygiene and Tropical Medicine" + }, + { + "author_name": "Carl A. B. Pearson", + "author_inst": "London School Of Hygiene and Tropical Medicine" + }, + { + "author_name": "Joel Hellewell", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Sam Abbott", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Nikos Bosse", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "- CMMID COVID-19 Working Group", + "author_inst": "" + }, + { + "author_name": "Katherine Elizabeth Atkins", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Jacco Wallinga", + "author_inst": "Leiden University" + }, + { + "author_name": "W. John Edmunds", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Albert Jan van Hoek", + "author_inst": "RIVM" + }, + { + "author_name": "Sebastian Funk", + "author_inst": "London School of Hygiene & Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.21.20177857", "rel_title": "Homologous and heterologous antibodies to coronavirus 229E, NL63, OC43, HKU1, SARS, MERS and SARS-CoV-2 antigens in an age stratified cross-sectional serosurvey in a large tertiary hospital in The Netherlands", @@ -1227486,45 +1230895,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.20.20178822", - "rel_title": "COVID-19 Risk Perception Among U.S. Adults: Changes from February to May 2020", - "rel_date": "2020-08-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.20.20178822", - "rel_abs": "The COVID-19 pandemic continues to detrimentally impact the United States. Using a survey, we collected demographic and COVID-19 risk perception, behavior, knowledge, and attitude data from 672 adults across the U.S. in May 2020. These variables were compared with the results from a survey in February 2020. Participants who were older (55+ years; M = 6.3, SD = 2.0), identified as Native American/Alaska Native (M = 6.8, SD = 1.0) or Asian (M = 6.0, SD = 2.0), and those who had contracted (M = 6.8, SD = 2.0) or knew someone who had contracted COVID-19 (M = 6.2, SD = 1.7) reported higher perceived risk. Health behaviors, such as physical distancing, have shown to impact infectious disease trajectories. As the U.S. reopens its economy, public health officials and politicians must formulate culturally appropriate and evidence-based messaging and policies, based on the publics COVID-19 risk perceptions, to encourage preventive behaviors.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Amyn A Malik", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "SarahAnn M McFadden", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "Jad A Elharake", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "Obianuju Genevieve Aguolu", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "Mehr Shafiq", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "Saad B Omer", - "author_inst": "Yale Institute for Global Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.20.20178970", "rel_title": "Poor knowledge of COVID-19 and unfavourable perception of the response to the pandemic by healthcare workers at the Bafoussam Regional Hospital (West Region - Cameroon)", @@ -1227797,6 +1231167,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.19.20177550", + "rel_title": "This time is different: model-based evaluation of the implications of SARS-CoV-2 infection kinetics for disease control", + "rel_date": "2020-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20177550", + "rel_abs": "As the ongoing COVID-19 pandemic passes from an acute to a chronic situation, countries and territories are grappling with the issue of how to reopen safely. The unique kinetics of infectivity of SARS-CoV-2, with its significant presymptomatic transmission, presents an unprecedented challenge to our intuitions. In this context, a generalizable quantitative understanding of the impact of SARS-CoV-2 infectivity on disease control strategies is vital. We used a previously published time-dependent model of SARS-CoV-2 infectivity (He et al., 2020) to parameterize an epidemiological model of transmission, which was then used to explore the effect of various disease control measures. Our analysis suggests that using symptom-based isolation alone as a control strategy is ineffective in limiting the spread of COVID-19, in contrast to its effectiveness in other diseases, such as SARS and influenza. Additionally, timeliness of testing and tracing strategies to reduce time to isolation, along with widespread adoption of measures to limit transmission are critical for any containment strategy. Our findings suggest that for symptom-based isolation and testing strategies to be effective, reduced transmission is required, reinforcing the importance of measures to limit transmission. From a public health strategy perspective, our findings lend support to the idea that symptomatic isolation should not form the primary basis for COVID-19 disease control.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Kaitlyn E Johnson", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "Madison Stoddard", + "author_inst": "Fractal Therapeutics, Cambridge, MA" + }, + { + "author_name": "Ryan P Nolan", + "author_inst": "Halozyme Therapeutics, San Diego, CA" + }, + { + "author_name": "Douglas E White", + "author_inst": "Independent Researcher" + }, + { + "author_name": "Natasha Hochberg", + "author_inst": "Department of Epidemiology, Boston University School of Public Health" + }, + { + "author_name": "Arijit Chakravarty", + "author_inst": "Fractal Therapeutics, Cambridge, MA" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.19.20177188", "rel_title": "Transmission dynamics of COVID-19 in household and community settings in the United Kingdom", @@ -1229088,61 +1232497,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.08.19.20177980", - "rel_title": "Prevalence and correlation of symptoms and comorbidities in COVID-19 patients: A systematic review and meta-analysis", - "rel_date": "2020-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20177980", - "rel_abs": "BackgroundThe COVID-19 affected millions of people, and the patients present a constellation of symptoms and comorbidities. We aimed to chronicle the prevalence and correlations of symptoms and comorbidities, and associated covariates among the patients.\n\nMethodsWe performed a systematic review and meta-analysis [PROSPERO registration: CRD42020182677]. Databases [PubMed, SCOPUS, EMBASE, WHO, Semantic Scholar, and COVID-19 Primer] were searched for clinical studies published in English from January 1 to April 20, 2020. The pooled prevalence of symptoms and comorbidities were identified using the random effect model, and sub-groups analysis of patients age and locations were investigated. A multivariable factor analysis was also performed to show the correlation among symptoms, comorbidities and age of the COVID-19 patients.\n\nFindingsTwenty-nine articles [China (24); Outside of China (5)], with 4,884 COVID-19 patients were included in this systematic review. The meta-analysis investigated 33 symptoms, where fever [84%], cough/dry cough [61%], and fatigue/weakness [42%] were found frequent. Out of 43 comorbidities investigated, acute respiratory distress syndrome (ARDS) [61%] was a common condition, followed by hypertension [23%] and diabetes [12%]. According to the patients age, the prevalence of symptoms like fatigue/weakness, dyspnea/shortness of breath, and anorexia were highly prevalent in older adults [[≥]50 years] than younger adults [[≤]50 years]. Diabetes, hypertension, coronary heart disease, and COPD/lung disease were more prevalent comorbidities in older adults than younger adults. The patients from outside of China had significantly higher prevalence [p< 0.005] of diarrhea, fatigue, nausea, sore throat, and dyspnea, and the prevalent comorbidities in that region were diabetes, hypertension, coronary heart disease, and ARDS. The multivariable factor analysis showed positive association between a group of symptoms and comorbidities, and with the patients age.\n\nInterpretationEpitomizing the correlation of symptoms of COVID-19 with comorbidities and patients age would help clinicians effectively manage the patients.\n\nSummary boxO_TEXTBOXO_LSTWhat is already known?C_LSTO_LIThere is scarce evidence on the prevalence of all symptoms and comorbidities in COVID-19 infected older adults and patients from outside of China.\nC_LIO_LIPreviously published review studies excluded a wide range of symptoms and comorbidities from their analysis due to limited time-frame.\nC_LIO_LIStudy on the correlation of symptoms and comorbidity with age of the COVID-19 patients are not yet to be explored.\nC_LI\n\nO_LSTWhat are the new findings?C_LSTO_LIWe investigated all the reported symptoms [33] and comorbidity [43] where fever [84%], cough/dry cough [61%], fatigue/weakness [42%] and dyspnea/shortness of breath [ symptoms, and ARDS [61%], followed by hypertension [23%] and frequent comorbidity.\nC_LIO_LIKey findings, the fatigue/weakness, dyspnea/shortness of breath and anorexia were comparatively higher in older adults than younger adults, and the patients from outside of China had a higher prevalence diarrhoea, fatigue, nausea, sore throat, dyspnea, diabetes, hypertension, coronary heart disease and ARDS.\nC_LIO_LIKey findings, the symptoms comprising fever, dyspnea/shortness of breath, nausea, vomiting, abdominal pain, dizziness, anorexia and pharyngalgia; and the comorbidities including diabetes, hypertension, coronary heart disease, COPD/lung disease and ARDS were positively correlated with the COVID-19 patients age.\nC_LI\n\nO_LSTWhat do the new findings imply?C_LSTO_LIThese findings according to patients age and geographical variations may help the health care providers and policy makers.\nC_LIO_LIThis pioneering efforts in estimating the prevalence and correlations of all frequent symptoms and comorbidities will help the clinicians and disease practitioners like WHO to implement patient-centered interventions.\nC_LI\n\nC_TEXTBOX", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Mohammad Meshbahur Rahman", - "author_inst": "Biomedical Research Foundation, Dhaka-1230, Bangladesh" - }, - { - "author_name": "Badhan Bhattacharjee", - "author_inst": "Department of Biotechnology, BRAC University, Dhaka 1212, Bangladesh" - }, - { - "author_name": "Zaki Farhana", - "author_inst": "National Institute of Preventive and Social Medicine, Mohakhali, Dhaka-1212, Bangladesh" - }, - { - "author_name": "Mohammad Hamiduzzaman", - "author_inst": "College of Medicine & Public Health, Flinders University, South Australia, Australia." - }, - { - "author_name": "Muhammad Abdul Bake Chowdhury", - "author_inst": "Department of Emergency Medicine, University of Florida College of Medicine, FL 32608, USA." - }, - { - "author_name": "Mohammad Sorowar Hossain", - "author_inst": "Biomedical Research Foundation, Dhaka-1230, Bangladesh" - }, - { - "author_name": "Mahbubul H Siddiqee", - "author_inst": "Biomedical Research Foundation, Dhaka-1230, Bangladesh." - }, - { - "author_name": "Md. Ziaul Islam", - "author_inst": "Department of Community Medicine, National Institute of Preventive and Social Medicine, Mohakhali, Dhaka-1212, Bangladesh" - }, - { - "author_name": "Enayetur Raheem", - "author_inst": "Biomedical Research Foundation, Dhaka-1230, Bangladesh" - }, - { - "author_name": "Md. Jamal Uddin", - "author_inst": "Department of Statistics (Biostatistics and Epidemiology), Shahjalal University of Science & Technology, Sylhet-3114, Bangladesh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.20.20176529", "rel_title": "Preventing within household transmission of COVID-19: Is self-isolation outside the home feasible and acceptable?", @@ -1229367,6 +1232721,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.08.21.261727", + "rel_title": "The receptor binding domain of SARS-CoV-2 spike is the key target of neutralizing antibody in human polyclonal sera.", + "rel_date": "2020-08-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.21.261727", + "rel_abs": "Natural infection of SARS-CoV-2 in humans leads to the development of a strong neutralizing antibody response, however the immunodominant targets of the polyclonal neutralizing antibody response are still unknown. Here, we functionally define the role SARS-CoV-2 spike plays as a target of the human neutralizing antibody response. In this study, we identify the spike protein subunits that contain antigenic determinants and examine the neutralization capacity of polyclonal sera from a cohort of patients that tested qRT-PCR-positive for SARS-CoV-2. Using an ELISA format, we assessed binding of human sera to spike subunit 1 (S1), spike subunit 2 (S2) and the receptor binding domain (RBD) of spike. To functionally identify the key target of neutralizing antibody, we depleted sera of subunit-specific antibodies to determine the contribution of these individual subunits to the antigen-specific neutralizing antibody response. We show that epitopes within RBD are the target of a majority of the neutralizing antibodies in the human polyclonal antibody response. These data provide critical information for vaccine development and development of sensitive and specific serological testing.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Tara Steffen", + "author_inst": "Saint Louis University" + }, + { + "author_name": "E Taylor Stone", + "author_inst": "Saint Louis University" + }, + { + "author_name": "Mariah Hassert", + "author_inst": "Saint Louis University" + }, + { + "author_name": "Elizabeth Geerling", + "author_inst": "Saint Louis University" + }, + { + "author_name": "Brian T Grimberg", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Ana M Espino", + "author_inst": "University of Puerto Rico" + }, + { + "author_name": "Petraleigh Pantoja", + "author_inst": "University of Puerto Rico" + }, + { + "author_name": "Consuelo Climent", + "author_inst": "University of Puerto Rico" + }, + { + "author_name": "Daniel F Hoft", + "author_inst": "Saint Louis University" + }, + { + "author_name": "Sarah L George", + "author_inst": "Saint Louis University" + }, + { + "author_name": "Carlos A Sariol", + "author_inst": "University of Puerto Rico, Medical Sciences Campus" + }, + { + "author_name": "Amelia K Pinto", + "author_inst": "Saint Louis University" + }, + { + "author_name": "James D Brien", + "author_inst": "Saint Louis University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.08.19.20178087", "rel_title": "Pandemic Control in ECON-EPI Networks", @@ -1230738,117 +1234159,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.18.20176743", - "rel_title": "Breastmilk; a source of SARS-CoV-2 specific IgA antibodies", - "rel_date": "2020-08-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.18.20176743", - "rel_abs": "BackgroundSince the outbreak of COVID-19, many put their hopes in the rapid development of effective immunizations. For now patient isolation, physical distancing and good hygiene are the sole measures for prevention. Processed breast milk with antibodies against SaRS-CoV-2 may serve as additional protection. We aimed to determine the presence and neutralization capacity of antibodies against SaRS-CoV-2 in breastmilk of mothers who have recovered from COVID-19.\n\nMethodsThis prospective case control study included lactating mothers, recovered from (suspected) COVID-19 and healthy controls. Serum and breastmilk was collected. To assess the presence of antibodies in breastmilk and serum, we used multiple complementary assays, namely ELISA with the SARS-CoV-2 spike protein, SARS-CoV-2 receptor binding domain (RBD) and with the SARS-CoV-2 nucleocapsid (N) protein for IgG and bridging ELISA with the SARS-CoV-2 RBD and N protein for total Ig. To assess the effect of pasteurization breastmilk was exposed to Holder Pasteurization and High Pressure Pasteurization.\n\nResultsBreastmilk contained antibodies against SARS-CoV-2 using any of the assays in 24 out of 29 (83%) proven cases, in six out of nine (67%) suspected cases and in none of the 13 controls. In vitro neutralization of SARS-CoV-2 clinical isolate virus strain was successful in a subset of serum (13%) and milk samples (26%). Although after pasteurization of the milk SARS-CoV-2 antibodies were detected with both methods of pasteurization, virus neutralizing capacity of those antibodies was only retained with the HPP approach.\n\nConclusionBreastmilk of mothers who recovered from COVID-19 contains significant amounts of IgA against SARS-CoV-2, both before and after pasteurization.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSDoes breastmilk of mothers who have recovered from coronavirus disease 2019 (COVID-19) contain antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)?\n\nFindingsWe provide multiple lines of evidence on the presence of a variety of antibodies against SARS-CoV-2, with no such antibodies present in the controls. These antibodies are capable of neutralizing a clinical isolate of SARS-CoV-2 in vitro. We furthermore show that high pressure pasteurization hardly affects antibody levels and efficacy.\n\nMeaningBreastmilk, obtained from mothers who have recovered from COVID-19, may serve as a safe and widely applicable preventive strategy for vulnerable high risk populations", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Britt J van Keulen", - "author_inst": "Emma Children's Hospital" - }, - { - "author_name": "Michelle Romijn", - "author_inst": "Emma Children's Hospital" - }, - { - "author_name": "Albert Bondt", - "author_inst": "University of Utrecht" - }, - { - "author_name": "Kelly A Dingess", - "author_inst": "University of Utrecht" - }, - { - "author_name": "Eva Kontopodi", - "author_inst": "Wageningen University and Research" - }, - { - "author_name": "Karlijn van der Straten", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Maurits A den Boer", - "author_inst": "University of Utrecht" - }, - { - "author_name": "Berend J Bosch", - "author_inst": "University of Utrecht" - }, - { - "author_name": "Philip J.M. Brouwer", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Christianne J de Groot", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Max Hoek", - "author_inst": "University of Utrecht" - }, - { - "author_name": "Wentao Li", - "author_inst": "University of Utrecht" - }, - { - "author_name": "Dasja Pajkrt", - "author_inst": "Emma Children's Hospital" - }, - { - "author_name": "Roger W Sanders", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Anne Schoonderwoerd", - "author_inst": "Emma Children's Hospital" - }, - { - "author_name": "Sem Tamara", - "author_inst": "University of Utrecht" - }, - { - "author_name": "Rian A.H. Timmermans", - "author_inst": "Wageningen University and Research" - }, - { - "author_name": "Gestur Vidarsson", - "author_inst": "Sanquin Research" - }, - { - "author_name": "Koert J Stittelaar", - "author_inst": "Viroclinics" - }, - { - "author_name": "Theo T Rispens", - "author_inst": "Sanquin Research" - }, - { - "author_name": "Kasper A Hettinga", - "author_inst": "Wageningen University and Research" - }, - { - "author_name": "Marit J van Gils", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Albert J.R. Heck", - "author_inst": "University of Utrecht" - }, - { - "author_name": "Johannes B van Goudoever", - "author_inst": "Emma Children's Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.18.20174623", "rel_title": "Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom", @@ -1231169,6 +1234479,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.17.20176917", + "rel_title": "A DEEP LEARNING MODEL TO PREDICT THE NEED FOR MECHANICAL VENTILATION USING CHEST X-RAY IMAGES IN HOSPITALIZED COVID-19 PATIENTS", + "rel_date": "2020-08-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20176917", + "rel_abs": "PurposeEarly identification of a potentially deteriorating clinical course in hospitalized COVID-19 patients is critical since there exists a resource-demand gap for the ventilators.\n\nMaterialsWe aimed to develop and validate a deep learning-based approach to predict the need for mechanical ventilation as early as at the time of initial radiographic evaluation. We exploited the well-established DenseNet121 deep learning architecture for this purpose on 663 X-ray images derived from 528 hospitalized COVID-19 patients. Two Pulmonary and Critical Care experts blindly and independently evaluated the same X-ray images for purpose of validation.\n\nResultsWe found that our deep learning model predicted the need for ventilation with a high accuracy, sensitivity and specificity (90.06%, 86.34% and 84.38%, respectively). This prediction was done approximately three days ahead of the actual intubation event. Our model also outperformed two Pulmonary and Critical Care experts who evaluated the same X-ray images and provided an incremental accuracy of 7.24-13.25%.\n\nConclusionOur deep learning model accurately predicted the need for mechanical ventilation early during hospitalization of COVID-19 patients. Until effective preventive or treatment measures become widely available for COVID-19 patients, prognostic stratification as provided by our model is likely to be highly valuable.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Anoop R Kulkarni", + "author_inst": "Innotomy Consulting, Bengaluru, India" + }, + { + "author_name": "Ambarish M Athavale", + "author_inst": "Division of Nephrology, Department of Medicine, Cook County Health, Chicago, Illinois, USA" + }, + { + "author_name": "Ashima Sahni", + "author_inst": "Division of Pulmonary, Critical Care, Sleep, and Allergy, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, USA" + }, + { + "author_name": "Shashvat Sukhal", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Cook County Health, Chicago, Illinois, USA" + }, + { + "author_name": "Abhimanyu Sahni", + "author_inst": "Division of Cardiology, Department of Medicine, Cook County Health, Chicago, Illinois, USA" + }, + { + "author_name": "Matthew Itteera", + "author_inst": "Division of Nephrology, Department of Medicine, Cook County Health, Chicago, Illinois, USA" + }, + { + "author_name": "Sara Zhukovsky", + "author_inst": "Rush University Medical Center, Chicago, IL, USA" + }, + { + "author_name": "Jane Vernik", + "author_inst": "Division of Nephrology, Department of Medicine, Cook County Health, Chicago, Illinois, USA" + }, + { + "author_name": "Mohan Abraham", + "author_inst": "Division of Nephrology, Department of Medicine, Cook County Health, Chicago, Illinois, USA" + }, + { + "author_name": "Amit Joshi", + "author_inst": "Division of Nephrology, Department of Medicine, Cook County Health, Chicago, Illinois, USA" + }, + { + "author_name": "Amatur Amarah", + "author_inst": "Division of Nephrology, Department of Medicine, Cook County Health, Chicago, Illinois, USA" + }, + { + "author_name": "Juan Ruiz", + "author_inst": "Division of Nephrology, Department of Medicine, Cook County Health, Chicago, Illinois, USA" + }, + { + "author_name": "Peter Hart", + "author_inst": "Division of Nephrology, Department of Medicine, Cook County Health, Chicago, Illinois, USA" + }, + { + "author_name": "Hemant Kulkarni", + "author_inst": "M&H Research, LLC" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.08.17.20175158", "rel_title": "The ImmuneRACE Study: A Prospective Multicohort Study of Immune Response Action to COVID-19 Events with the ImmuneCODE\u2122 Open Access Database", @@ -1232376,81 +1235757,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.18.20168807", - "rel_title": "Laboratory biomarkers associated with COVID-19 severity and management.", - "rel_date": "2020-08-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.18.20168807", - "rel_abs": "The heterogeneous disease course of COVID-19 is unpredictable, ranging from mild self-limiting symptoms to cytokine storms, acute respiratory distress syndrome (ARDS), multi-organ failure and death. Identification of high-risk cases will enable appropriate intervention and escalation. This study investigates the routine laboratory tests and cytokines implicated in COVID-19 for their potential application as biomarkers of disease severity, respiratory failure and need of higher-level care.\n\nFrom analysis of 203 samples, CRP, IL-6, IL-10 and LDH were most strongly correlated with the WHO ordinal scale of illness severity, the fraction of inspired oxygen delivery, radiological evidence of ARDS and level of respiratory support (p[≤]0.001). IL-6 levels of [≥]3.27pg/ml provide a sensitivity of 0.87 and specificity of 0.64 for a requirement of ventilation, and a CRP of [≥]37mg/L of 0.91 and 0.66.\n\nReliable stratification of high-risk cases has significant implications on patient triage, resource management and potentially the initiation of novel therapies in severe patients.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Stephen Keddie", - "author_inst": "Neuroimmunology and CSF laboratory, University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - }, - { - "author_name": "Oliver J Ziff", - "author_inst": "University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - }, - { - "author_name": "Michael KL Chou", - "author_inst": "Neuroimmunology and CSF laboratory, University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - }, - { - "author_name": "Rachel L Taylor", - "author_inst": "Neuroimmunology and CSF laboratory, University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - }, - { - "author_name": "Amanda Heslegrave", - "author_inst": "UK Dementia Research Institute, University College London, London, UK" - }, - { - "author_name": "Edmund Garr", - "author_inst": "Neuroimmunology and CSF laboratory, University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - }, - { - "author_name": "Neghat Lakdawala", - "author_inst": "Neuroimmunology and CSF laboratory, University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - }, - { - "author_name": "Andrew Church", - "author_inst": "Neuroimmunology and CSF laboratory, University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - }, - { - "author_name": "Dalia Ludwig", - "author_inst": "Department of Rheumatology, University College London Hospitals NHS Trust, London, UK" - }, - { - "author_name": "Jessica Manson", - "author_inst": "Department of Rheumatology, University College London Hospitals NHS Trust, London, UK" - }, - { - "author_name": "Marie Scully", - "author_inst": "Department of Haematology, University College London Hospitals NHS Foundation Trust and Cardiometabolic Programme-NIHR UCLH/UC BRC London, UK" - }, - { - "author_name": "Eleni Nastouli", - "author_inst": "Infection control department, University College London Hospitals NHS Trust, London, UK" - }, - { - "author_name": "Miles D Chapman", - "author_inst": "Neuroimmunology and CSF laboratory, University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - }, - { - "author_name": "Melanie Hart", - "author_inst": "Neuroimmunology and CSF laboratory, University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - }, - { - "author_name": "Michael P Lunn", - "author_inst": "Neuroimmunology and CSF laboratory, University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2020.08.17.20177022", "rel_title": "Decontaminating N95 respirators during the Covid-19 pandemic: simple and practical approaches to increase decontamination capacity, speed, safety and ease of use.", @@ -1232671,6 +1235977,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2020.08.18.20177410", + "rel_title": "Inadequate preparedness for response to COVID-19 is associated with stress and burnout among healthcare workers in Ghana", + "rel_date": "2020-08-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.18.20177410", + "rel_abs": "IntroductionThe COVID-19 pandemic has compounded the global crisis of stress and burnout among healthcare workers (HCWs). But few studies have empirically examined the factors driving these outcomes. We examined the association between perceived preparedness to respond to the pandemic and HCW stress and burnout and identified potential mediating factors among HCWs in Ghana.\n\nMethodsData are from HCWs in Ghana who completed a cross-sectional self-administered online survey; 414 and 409 HCWs completed stress and burnout questions, respectively. Perceived preparedness, stress, and burnout were measured using validated psychosocial measures. We assessed associations using linear regressions with robust standard errors.\n\nResultsThe average score for preparedness was 24 (SD = 8.8), 16.3 (SD = 5.9) for stress, and 37.4 (SD = 15.5) for burnout. In multivariate analysis, HCWs who felt somewhat prepared and prepared had lower stress ({beta} = -1.89, 95%CI:-3.49 to -0.30 and {beta} = -2.66, 95%CI:-4.48 to -0.84) and burnout ({beta} = -7.74, 95%CI:-11.8 to -3.64 and {beta} = -9.25, 95%CI:-14.1 to -4.41) scores than those who did not feel prepared. Appreciation from management and family support were associated with lower stress and burnout, while fear of infection was associated with higher stress burnout. Fear of infection partially mediated the relationship between perceived preparedness and stress/burnout, accounting for about 16 to17% of the effect.\n\nConclusionLow perceived preparedness to respond to COVID-19 increases stress and burnout, and this is partly through fear of infection. Interventions to increase HCWs morale and capacity to respond to the pandemic are needed.\n\nStrengths and limitations of this studyO_LIOur study is among the first to report data on COVID-19 related stress and burnout among HCWs in Africa and to identify contributing factors, including HCWs perceived preparedness to respond to the pandemic.\nC_LIO_LIWe used validated psychosocial measures of stress and burnout, as well as a perceived preparedness for COVID-19 scale developed by our team, which has high validity and reliability; this scale can facilitate similar research in other settings.\nC_LIO_LIOur study shows that among healthcare workers in Ghana, low perceived preparedness to respond to the COVID-19 pandemic is associated with higher levels of stress and burnout and this association is partially mediated by fear of infection.\nC_LIO_LIPerceived appreciation from management and family support on the other hand are associated with lower stress and burnout.\nC_LIO_LIFindings are based on self-reported data from a cross-sectional online survey, thus, there may be social desirability bias; associations described are not causal; and the online survey may limit generalizability.\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Patience A Afulani", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Akua O. Gyamerah", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Jerry Nutor", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Amos Laar", + "author_inst": "University of Ghana School of Public Health" + }, + { + "author_name": "Raymond Aborigo", + "author_inst": "Navrongo Health Research Centre" + }, + { + "author_name": "Hawa Malechi", + "author_inst": "Tamale Teaching Hospital" + }, + { + "author_name": "Mona Sterling", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "John K. Awoonor-Williams", + "author_inst": "Ghana Health Service" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.18.20177196", "rel_title": "SARS-CoV-2 Serologic Assays in Control and Unknown Populations Demonstrate the Necessity of Virus Neutralization Testing.", @@ -1234238,89 +1237591,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.08.19.256800", - "rel_title": "Susceptibility of raccoon dogs for experimental SARS-CoV-2 infection", - "rel_date": "2020-08-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.19.256800", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in China at the end of 2019, and became pandemic. The zoonotic virus most likely originated from bats, but definite intermediate hosts have not yet been identified. Raccoon dogs (Nyctereutes procyonoides) are kept for fur production, in particular in China, and were suspected as potential intermediate host for both SARS-CoV6 and SARS-CoV2. Here we demonstrate susceptibility of raccoon dogs for SARS-CoV-2 infection after intranasal inoculation and transmission to direct contact animals. Rapid, high level virus shedding, in combination with minor clinical signs and pathohistological changes, seroconversion and absence of viral adaptation highlight the role of raccoon dogs as a potential intermediate host. The results are highly relevant for control strategies and emphasize the risk that raccoon dogs may represent a potential SARS-CoV-2 reservoir. Our results support the establishment of adequate surveillance and risk mitigation strategies for kept and wild raccoon dogs.\n\nArticle Summary LineRaccoon dogs are susceptible to and efficiently transmit SARS-CoV2 and may serve as intermediate host", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Conrad Martin Freuling", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Angele Breithaupt", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Thomas Mueller", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Julia Sehl", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Anne Balkema-Buschmann", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Melanie Rissmann", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Antonia Klein", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Claudia Wylezich", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Dirk Hoeper", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Kerstin Wernike", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Andrea Aebischer", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Donata Hoffmann", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Virginia Friedrichs", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Anca Dorhoi", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Martin Groschup", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Martin Beer", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Thomas C Mettenleiter", - "author_inst": "Friedrich-Loeffler-Institut" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.20.258772", "rel_title": "What if we perceive SARS-CoV-2 genomes as documents? Topic modelling using Latent Dirichlet Allocation to identify mutation signatures and classify SARS-CoV-2 genomes", @@ -1234665,6 +1237935,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.08.17.20176255", + "rel_title": "Effects of case- and population-based COVID-19 interventions in Taiwan", + "rel_date": "2020-08-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20176255", + "rel_abs": "In the first wave of the COVID-19 pandemic, broad usage of non-pharmaceutical interventions played a crucial role in controlling epidemics1-6. However, the substantial economic and societal costs of continuous use of border controls, travel restrictions, and physical distancing measures suggest that these measures may not be sustainable and that policymakers have to seek strategies to lift the restrictions. Taiwan was one of the few countries that demonstrated initial success in eliminating the COVID-19 outbreak without strict lockdown or school closure. To understand the key contributors to the successful control, we applied a stochastic branching model to empirical case data to evaluate and compare the effectiveness of more targeted case-based (including contact tracing and quarantine) and less targeted population-based interventions (including social distancing and face mask use) in Taiwan. We found that case-based interventions alone would not be sufficient to contain the epidemic, even in a setting where a highly efficient contact tracing program was in place. The voluntary population-based interventions have reduced the reproduction numbers by more than 60% and have likely played a critical role at the early stage of the outbreak. Our analysis of Taiwans success highlights that coordinated efforts from both the government and the citizens are indispensable in the fight against COVID-19 pandemic.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ta-Chou V Ng", + "author_inst": "Institute of Epidemiology and Preventive Medicine, National Taiwan University College of Public Health, Taipei, Taiwan" + }, + { + "author_name": "Hao-Yuan Cheng", + "author_inst": "Epidemic Intelligence Center, Taiwan Centers for Disease Control, Taipei, Taiwan" + }, + { + "author_name": "Hsiao-Han Chang", + "author_inst": "Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu City, Taipei" + }, + { + "author_name": "Cheng-Chieh Liu", + "author_inst": "Institute of Epidemiology and Preventive Medicine, National Taiwan University College of Public Health, Taipei, Taiwan" + }, + { + "author_name": "Chih-Chi Yang", + "author_inst": "Institute of Epidemiology and Preventive Medicine, National Taiwan University College of Public Health, Taipei, Taiwan" + }, + { + "author_name": "Shu-Wan Jian", + "author_inst": "Epidemic Intelligence Center, Taiwan Centers for Disease Control, Taipei, Taiwan" + }, + { + "author_name": "Ding-Ping Liu", + "author_inst": "Epidemic Intelligence Center, Taiwan Centers for Disease Control, Taipei, Taiwan" + }, + { + "author_name": "Ted Cohen", + "author_inst": "Department of Epidemiology of Microbial Diseases and the Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, USA" + }, + { + "author_name": "Hsien-Ho Lin", + "author_inst": "Institute of Epidemiology and Preventive Medicine, National Taiwan University College of Public Health, Taipei, Taiwan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.17.20176347", "rel_title": "The necessary cooperation between governments and public in the fight against COVID-19: why non-pharmaceutical interventions may be ineffective", @@ -1236076,37 +1239397,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.16.20035691", - "rel_title": "COVID-19 ICU and mechanical ventilation patient characteristics and outcomes - A systematic review and meta-analysis", - "rel_date": "2020-08-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.16.20035691", - "rel_abs": "BackgroundInsight into COVID-19 intensive care unit (ICU) patient characteristics, rates and risks of invasive mechanical ventilation (IMV) and associated outcomes as well as any regional discrepancies is critical in this pandemic for individual case management and overall resource planning.\n\nMethods and FindingsElectronic searches were performed for reports through May 1 2020 and reports on COVID-19 ICU admissions and outcomes were included using predefined search terms. Relevant data was subsequently extracted and pooled using fixed or random effects meta-analysis depending on heterogeneity. Study quality was assessed by the NIH tool and heterogeneity was assessed by I2 and Q tests. Baseline patient characteristics, ICU and IMV outcomes were pooled and meta-analyzed. Pooled odds ratios (pOR) were calculated for clinical features against ICU, IMV mortality. Subgroup analysis was carried out based on patient regions. A total of twenty-eight studies comprising 12,437 COVID-19 ICU admissions from seven countries were meta-analyzed. Pooled ICU admission rate was 21% [95% CI 0.12-0.34] and 69% of cases needed IMV [95% CI 0.61-0.75]. ICU and IMV mortality were 28.3% [95% CI 0.25-0.32], 43% [95% CI 0.29-0.58] and ICU, IMV duration was 7.78 [95% CI 6.99-8.63] and 10.12 [95% CI 7.08-13.16] days respectively. Besides confirming the significance of comorbidities and clinical findings of COVID-19 previously reported, we found the major correlates with ICU mortality were IMV [pOR 16.46, 95% CI 4.37-61.96], acute kidney injury (AKI) [pOR 12.47, 95% CI 1.52-102.7], and acute respiratory distress syndrome (ARDS) [pOR 6.52, 95% CI 2.66-16.01]. Subgroup analyses confirm significant regional discrepancies in outcomes.\n\nConclusionsThis is the most comprehensive systematic review and meta-analysis of COVID-19 ICU and IMV cases and associated outcomes to date and the only analysis to implicate IMVs associtaion with COVID-19 ICU mortality. The significant association of AKI, ARDS and IMV with mortality has implications for ICU resource planning for AKI and ARDS as well as research into optimal ventilation strategies for patients. Regional differences in outcome implies a need to develop region specific protocols for ventilatory support as well as overall treatment.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Raymond Chang", - "author_inst": "Institute of East West Medicine" - }, - { - "author_name": "Khaled Mossad Elhusseiny", - "author_inst": "Al-Azhar University" - }, - { - "author_name": "Yu-Chang Yeh", - "author_inst": "National Taiwan University Hospital" - }, - { - "author_name": "Wei-zen Sun", - "author_inst": "National Taiwan University Hospial" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.08.16.20176073", "rel_title": "Impacts on Surgery Resident Education at a first wave COVID-19 epicenter", @@ -1236379,6 +1239669,97 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.08.18.255877", + "rel_title": "Drug Repurposing Screen for Compounds Inhibiting the Cytopathic Effect of SARS-CoV-2", + "rel_date": "2020-08-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.18.255877", + "rel_abs": "Drug repurposing is a rapid approach to identifying therapeutics for the treatment of emerging infectious diseases such as COVID-19. To address the urgent need for treatment options, we carried out a quantitative high-throughput screen using a SARS-CoV-2 cytopathic assay with a compound collection of 8,810 approved and investigational drugs, mechanism-based bioactive compounds, and natural products. Three hundred and nineteen compounds with anti-SARS-CoV-2 activities were identified and confirmed, including 91 approved drug and 49 investigational drugs. Among these confirmed compounds, the anti-SARS-CoV-2 activities of 230 compounds, including 38 approved drugs, have not been previously reported. Chlorprothixene, methotrimeprazine, and piperacetazine were the three most potent FDA approved drugs with anti-SARS-CoV-2 activities. These three compounds have not been previously reported to have anti-SARS-CoV-2 activities, although their antiviral activities against SARS-CoV and Ebola virus have been reported. These results demonstrate that this comprehensive data set of drug repurposing screen for SARS-CoV-2 is useful for drug repurposing efforts including design of new drug combinations for clinical trials.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Catherine Z Chen", + "author_inst": "NCATS, NIH" + }, + { + "author_name": "Paul Shinn", + "author_inst": "NCATS, NIH" + }, + { + "author_name": "Zina Itkin", + "author_inst": "NCATS, NIH" + }, + { + "author_name": "Rich Eastman", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Robert Bostwick", + "author_inst": "Southern Research" + }, + { + "author_name": "Lynn Rasmussen", + "author_inst": "Southern Research" + }, + { + "author_name": "Ruili Huang", + "author_inst": "NCATS, NIH" + }, + { + "author_name": "Min Shen", + "author_inst": "NIH" + }, + { + "author_name": "Xin Hu", + "author_inst": "NCATS, NIH" + }, + { + "author_name": "Kelli M Wilson", + "author_inst": "NCATS, NIH" + }, + { + "author_name": "Brianna Brooks", + "author_inst": "NCATS, NIH" + }, + { + "author_name": "Hui Guo", + "author_inst": "NCATS, NIH" + }, + { + "author_name": "Tongan Zhao", + "author_inst": "NCATS, NIH" + }, + { + "author_name": "Carleen Klumpp-Thomas", + "author_inst": "NCATS, NIH" + }, + { + "author_name": "Anton Simeonov", + "author_inst": "NCATS, NIH" + }, + { + "author_name": "Samuel G. Michael", + "author_inst": "NCATS, NIH" + }, + { + "author_name": "Donald C Lo", + "author_inst": "NCATS, NIH" + }, + { + "author_name": "Matthew Hall", + "author_inst": "NCATS" + }, + { + "author_name": "Wei Zheng", + "author_inst": "NCATS, NIH" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.17.238444", "rel_title": "Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity", @@ -1237854,57 +1241235,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.15.20175562", - "rel_title": "Impact of COVID-19 on Primary Care Mental Health Services: A Descriptive, Cross-Sectional Timeseries of Electronic Healthcare Records", - "rel_date": "2020-08-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.15.20175562", - "rel_abs": "IntroductionThere are growing concerns about the impact of the COVID-19 pandemic on mental health. With government-imposed restrictions as well as a general burden on healthcare systems, the pandemic has the potential to disrupt the access to, and delivery of, mental healthcare. Ultimately, this could potentially lead to unmet needs of individuals requiring mental health support.\n\nMethodsElectronic healthcare records from primary care psychological therapy services (Improving Access to Psychological Therapy) in England were used to examine changes in access to mental health services and service delivery during early stages of the COVID-19 pandemic. A cross-sectional, descriptive timeseries was conducted using data from 1st January 2019 to 24th May 2020 across five NHS trusts to examine patterns in referrals to services (n = 171,823) and appointments taking place (n = 865,902).\n\nResultsThe number of patients accessing mental health services dropped by an average of 55% in the 9 weeks after lockdown was announced, reaching a maximum reduction of 74% in the initial 3 weeks after lockdown in the UK. As referrals began to increase again, there was a relatively faster increase in referrals from Black, Asian, and ethnic minority groups as well an increase in referrals from more densely populated areas. Despite a reduction in access, service providers adapted to infection control guidance by rapidly shifting to remote delivery of care.\n\nInterpretationServices were able to rapidly adapt to provide continuity of care in mental healthcare. However, patients accessing services reduced dramatically, potentially placing a future burden on service providers to treat a likely backlog of patients in addition to a possible excess of patients as the long-term consequences of the pandemic become more apparent. Despite the observational nature of the data, which should be noted, the present study can inform the planning of service provision and policy.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Clarissa M. M. Bauer-Staeb", - "author_inst": "University of Bath" - }, - { - "author_name": "Alice Davis", - "author_inst": "University of Bath; Mayden" - }, - { - "author_name": "Theresa R Smith", - "author_inst": "University of Bath" - }, - { - "author_name": "David Betts", - "author_inst": "Mayden" - }, - { - "author_name": "Wendy Wilsher", - "author_inst": "Mayden" - }, - { - "author_name": "Chris Eldridge", - "author_inst": "Mayden" - }, - { - "author_name": "Emma Griffith", - "author_inst": "University of Bath; Avon and Wiltshire Mental Health Partnership NHS Trust" - }, - { - "author_name": "Julian J Faraway", - "author_inst": "University of Bath" - }, - { - "author_name": "Katherine S Button", - "author_inst": "University of Bath" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.08.14.20170290", "rel_title": "Efficient Deep Network Architecture for COVID-19 Detection Using Computed Tomography Images", @@ -1238097,6 +1241427,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.14.20175356", + "rel_title": "SARS-Coronavirus-2 nucleocapsid protein measured in blood using a Simoa ultra-sensitive immunoassay differentiates COVID-19 infection with high clinical sensitivity.", + "rel_date": "2020-08-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.14.20175356", + "rel_abs": "The COVID-19 pandemic continues to have an unprecedented impact on societies and economies worldwide. Despite rapid advances in diagnostic test development and scale-up, there remains an ongoing need for SARS-CoV-2 tests which are highly sensitive, specific, minimally invasive, cost-effective and scalable for broad testing and surveillance. Here we report development of a highly sensitive single molecule array (Simoa) immunoassay on the automated HD-X platform for the detection of SARS-CoV-2 Nucleocapsid protein (N-protein) in venous and capillary blood (fingerstick). In pre-pandemic and clinical sample sets, the assay has 100% specificity and 97.4% sensitivity for serum / plasma samples. The limit of detection (LoD) estimated by titration of inactivated SARS-CoV-2 virus is 0.2 pg/ml, corresponding to 0.05 Median Tissue Culture Infectious Dose (TCID50) per ml, > 2000 times more sensitive than current EUA approved antigen tests. No cross-reactivity to other common respiratory viruses, including hCoV229E, hCoVOC43, hCoVNL63, Influenza A or Influenza B, was observed. We detected elevated N-protein concentrations in symptomatic, asymptomatic, and pre-symptomatic PCR+ individuals using capillary blood from a finger-stick collection device. The Simoa SARS-CoV-2 N-protein assay has the potential to detect COVID-19 infection via antigen in blood with performance characteristics similar to or better than molecular tests, while also enabling at home and point of care sample collection.\n\nOne Sentence SummarySARS-CoV-2 nucleocapsid protein (N-protein) measured in serum, plasma, and dried blood spots (DBS) via ultrasensitive immunoassay can be used to differentiate PCR+ from PCR- patients, even if asymptomatic.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Dandan Shan", + "author_inst": "Quanterix Corporation" + }, + { + "author_name": "Joseph M Johnson", + "author_inst": "Quanterix Corporation" + }, + { + "author_name": "Syrena C Fernandes", + "author_inst": "Quanterix Corporation" + }, + { + "author_name": "Muriel Mendes", + "author_inst": "Quanterix Corporation" + }, + { + "author_name": "Hannah Suib", + "author_inst": "Quanterix Corporation" + }, + { + "author_name": "Marcella Holdridge", + "author_inst": "Quanterix Corporation" + }, + { + "author_name": "Elaine M Burke", + "author_inst": "Quanterix Corporation" + }, + { + "author_name": "Katie G Beauregard", + "author_inst": "Quanterix Corporation" + }, + { + "author_name": "Ying Zhang", + "author_inst": "Quanterix Corporation" + }, + { + "author_name": "Megan Cleary", + "author_inst": "Quanterix Corporation" + }, + { + "author_name": "Samantha Xu", + "author_inst": "Quanterix Corporation" + }, + { + "author_name": "Xiao Yao", + "author_inst": "Quanterix Corporation" + }, + { + "author_name": "Purvish P Patel", + "author_inst": "Quanterix Corporation" + }, + { + "author_name": "Tatiana Plavina", + "author_inst": "Quanterix Corporation" + }, + { + "author_name": "David H Wilson", + "author_inst": "Quanterix Corporation" + }, + { + "author_name": "Lei Chang", + "author_inst": "Quanterix Corporation" + }, + { + "author_name": "Kim M Kaiser", + "author_inst": "Institute of Innate Immunity, University of Bonn" + }, + { + "author_name": "Jacob Natterman", + "author_inst": "Institute of Innate Immunity, University of Bonn, and German Center for Infection Research (DZIF)," + }, + { + "author_name": "Susanne V Schmidt", + "author_inst": "Department of Internal Medicine I, University of Bonn" + }, + { + "author_name": "Eicke Latz", + "author_inst": "Department of Internal Medicine I, University of Bonn and German Center for Neurodegenerative Diseases (DZNE)" + }, + { + "author_name": "Kevin Hrusovsky", + "author_inst": "Quanterix Corporation" + }, + { + "author_name": "Dawn Mattoon", + "author_inst": "Quanterix Corporation" + }, + { + "author_name": "Andrew J Ball", + "author_inst": "Quanterix Corporation" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.15.20175588", "rel_title": "A data-driven epidemiological model to explain the Covid-19 pandemic in multiple countries and help in choosing mitigation strategies", @@ -1239452,197 +1242889,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.08.15.252320", - "rel_title": "A SARS-CoV-2 neutralizing antibody protects from lung pathology in a COVID-19 hamster model", - "rel_date": "2020-08-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.15.252320", - "rel_abs": "The emergence of SARS-CoV-2 led to pandemic spread of coronavirus disease 2019 (COVID-19), manifesting with respiratory symptoms and multi-organ dysfunction. Detailed characterization of virus-neutralizing antibodies and target epitopes is needed to understand COVID-19 pathophysiology and guide immunization strategies. Among 598 human monoclonal antibodies (mAbs) from ten COVID-19 patients, we identified 40 strongly neutralizing mAbs. The most potent mAb CV07-209 neutralized authentic SARS-CoV-2 with IC50 of 3.1 ng/ml. Crystal structures of two mAbs in complex with the SARS-CoV-2 receptor-binding domain at 2.55 and 2.70 [A] revealed a direct block of ACE2 attachment. Interestingly, some of the near-germline SARS-CoV-2 neutralizing mAbs reacted with mammalian self-antigens. Prophylactic and therapeutic application of CV07-209 protected hamsters from SARS-CoV-2 infection, weight loss and lung pathology. Our results show that non-self-reactive virus-neutralizing mAbs elicited during SARS-CoV-2 infection are a promising therapeutic strategy.", - "rel_num_authors": 44, - "rel_authors": [ - { - "author_name": "Jakob Kreye", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "S Momsen Reincke", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "Hans-Christian Kornau", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "Elisa Sanchez-Sendin", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "Victor Max Corman", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Hejun Liu", - "author_inst": "The Scripps Research Institute, La Jolla, USA." - }, - { - "author_name": "Meng Yuan", - "author_inst": "The Scripps Research Institute, La Jolla, USA." - }, - { - "author_name": "Nicholas C Wu", - "author_inst": "The Scripps Research Institute, La Jolla, USA." - }, - { - "author_name": "Xueyong Zhu", - "author_inst": "The Scripps Research Institute, La Jolla, USA." - }, - { - "author_name": "Chang-Chun D Lee", - "author_inst": "The Scripps Research Institute, La Jolla, USA." - }, - { - "author_name": "Jakob Trimpert", - "author_inst": "Freie Universitaet Berlin, Berlin, Germany." - }, - { - "author_name": "Markus Hoeltje", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Kristina Dietert", - "author_inst": "Freie Universitaet Berlin, Berlin, Germany." - }, - { - "author_name": "Laura Stoeffler", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "Niels von Wardenburg", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "Scott van Hoof", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "Marie A Homeyer", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "Julius Hoffmann", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "Azza Abdelgawad", - "author_inst": "Freie Universitaet Berlin, Berlin, Germany." - }, - { - "author_name": "Achim D Gruber", - "author_inst": "Freie Universitaet Berlin, Berlin, Germany." - }, - { - "author_name": "Luca D Bertzbach", - "author_inst": "Freie Universitaet Berlin, Berlin, Germany." - }, - { - "author_name": "Daria Vladimirova", - "author_inst": "Freie Universitaet Berlin, Berlin, Germany." - }, - { - "author_name": "Lucie Y Li", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Paula Charlotte Barthel", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Karl Skriner", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Andreas C Hocke", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Stefan Hippenstiel", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Martin Witzenrath", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Norbert Suttorp", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Florian Kurth", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Christiana Franke", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Matthias Endres", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Dietmar Schmitz", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "Lara Maria Jeworowski", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Anja Richter", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Marie Luisa Schmidt", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Tatjana Schwarz", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Marcel Alexander Mueller", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Christian Drosten", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Daniel Wendisch", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Leif E Sander", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Nikolaus Osterrieder", - "author_inst": "Freie Universitaet Berlin, Berlin, Germany." - }, - { - "author_name": "Ian A Wilson", - "author_inst": "The Scripps Research Institute, La Jolla, USA." - }, - { - "author_name": "Harald Pruess", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.08.15.252395", "rel_title": "Susceptibility of swine cells and domestic pigs to SARS-CoV-2", @@ -1239891,6 +1243137,49 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.08.14.20174896", + "rel_title": "Modelling Suggests Limited Change in the Reproduction Number from Reopening Norwegian Kindergartens and Schools During the COVID-19 Pandemic", + "rel_date": "2020-08-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.14.20174896", + "rel_abs": "BackgroundTo suppress the COVID-19 outbreak, the Norwegian government closed all schools on March 13, 2020. The kindergartens reopened on April 20, and the schools on April 27 and May 11 of 2020. The effect of these measures is largely unknown since the role of children in the spread of the SARS-CoV-2 virus is still unclear. There are only a few studies of school closures as a separate intervention to other social distancing measures, and little research exists on the effect of school opening during a pandemic.\n\nObjectiveThis study aimed to model the effect of opening kindergartens and the schools in Norway in terms of a change in the reproduction number (R). A secondary objective was to assess if we can use the estimated R after school openings to infer the rates of transmission between children in schools.\n\nMethodsWe used an individual-based model (IBM) to assess the reopening of kindergartens and schools in two Norwegian cities, Oslo, the Norwegian capital, with a population of approximately 680 000, and Tromso, which is the largest city in Northern Norway, with a population of approximately 75 000. The model uses demographic information and detailed data about the schools in both cities. We carried out an ensemble study to obtain robust results in spite of the considerable uncertainty that remains about the transmission of SARS-CoV-2.\n\nResultsWe found that reopening of Norwegian kindergartens and schools are associated with a change in R of 0.10 (95%CI 0.04-0.16) and 0.14 (95%CI 0.01-0.25) in the two cities under investigation if the in-school transmission rates for the SARS-CoV-2 virus are equal to what Ferguson et al. have previously estimated for influenza pandemics [1].\n\nConclusionWe found only a limited effect of reopening schools on the reproduction number, and we expect the same to hold true in other countries where nonpharmaceutical interventions have suppressed the pandemic. Consequently, current R-estimates are insufficiently accurate for determining the transmission rates in schools. For countries that have not opened schools yet, planned interventions, such as the opening of selected schools, can be useful to infer general knowledge about children-to-children transmission of SARS-CoV-2.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Martin Rypdal", + "author_inst": "UiT The Arctic University of Norway" + }, + { + "author_name": "Veronika Gjertsen Rypdal", + "author_inst": "Department of Pediatrics, University Hospital of North Norway" + }, + { + "author_name": "Per Kirsten Jakobsen", + "author_inst": "UiT The Arctic University of Norway" + }, + { + "author_name": "Elinor Ytterstad", + "author_inst": "UiT The Arctic University of Norway" + }, + { + "author_name": "Ola Lovsletten", + "author_inst": "UiT The Arctic University of Norway" + }, + { + "author_name": "Claus Klingenberg", + "author_inst": "Department of Pediatrics, University Hospital of North Norway" + }, + { + "author_name": "Kristoffer Rypdal", + "author_inst": "UiT The Arctic University of Norway" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.14.20175059", "rel_title": "An Analysis of Self-reported Longcovid Symptoms on Twitter", @@ -1241410,33 +1244699,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.08.13.20174755", - "rel_title": "Dynamical balance between the transmission, intervention of COVID-19 and economic development", - "rel_date": "2020-08-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20174755", - "rel_abs": "The current explosive outbreak of coronavirus (COVID-19) is posing serious threats to public health and economy around the world. To clarify the coupling mechanism between this disease and economy, a new dynamical system is established. It is theoretically proved that the basic reproduction number is a nonlinear combination of parameters regarding disease transmission, intervention and economy effect, which totally determines the stability of the disease-free and endemic equilibria. Further results indicate the existence of interaction and mutual restraint among the transmission, intervention and economy, in which strong coupling of COVID-19 and economy would trigger disease outbreak and form poverty trap, while adaptive isolation of at-risk population could effectively reduce morbidity at the cost of least economic loss. Our findings can offer new insights to improve the intervention strategies against COVID-19.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Zhaowang Zhang", - "author_inst": "Guilin University of Electronic Technology" - }, - { - "author_name": "Hualiang Lin", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Guanghu Zhu", - "author_inst": "Guilin University of Electronic Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.13.249847", "rel_title": "Open Science Saves Lives: Lessons from the COVID-19 Pandemic", @@ -1241617,6 +1244879,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.13.249953", + "rel_title": "Immunoreactive peptide maps of SARS-CoV-2 and other human coronaviruses", + "rel_date": "2020-08-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.13.249953", + "rel_abs": "Serodiagnosis of SARS-CoV-2 infection is impeded by immunological cross-reactivity to the human coronaviruses (HCoV) SARS-CoV-2, SARS-CoV-1, MERS-CoV, OC43, 229E, HKU1, and NL63. Here we report the identification of humoral immune responses to SARS-CoV-2 and other HCoV peptides that can be used to detect asymptomatic, mild and, severe SARS-CoV-2 infections, and may enable the discovery of biomarkers for immunity following infection or vaccination.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Nischay Mishra", + "author_inst": "Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA" + }, + { + "author_name": "Xi Huang", + "author_inst": "Sun Yat-sen University, Guangzhou, Guangdong Province, China." + }, + { + "author_name": "Shreyas Joshi", + "author_inst": "Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA" + }, + { + "author_name": "Cheng Guo", + "author_inst": "Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA" + }, + { + "author_name": "James Ng", + "author_inst": "Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA" + }, + { + "author_name": "Riddhi Thakkar", + "author_inst": "Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA" + }, + { + "author_name": "Yongjian Wu", + "author_inst": "Sun Yat-sen University, Guangzhou, Guangdong Province, China" + }, + { + "author_name": "Xin Dong", + "author_inst": "Sun Yat-sen University, Guangzhou, Guangdong Province, China" + }, + { + "author_name": "Qianlin Li", + "author_inst": "Sun Yat-sen University, Guangzhou, Guangdong Province, China" + }, + { + "author_name": "Richard Pinapati", + "author_inst": "Nimble Therapeutics Inc, Madison, WI 53719, United States" + }, + { + "author_name": "Eric Sullivan", + "author_inst": "Nimble Therapeutics Inc, Madison, WI 53719, United States" + }, + { + "author_name": "Adrian Caciula", + "author_inst": "Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA" + }, + { + "author_name": "Rafal Tokarz", + "author_inst": "Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA" + }, + { + "author_name": "Thomas Briese", + "author_inst": "Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA" + }, + { + "author_name": "Jiahai Lu", + "author_inst": "Sun Yat-sen University, Guangzhou, Guangdong Province, China" + }, + { + "author_name": "W. Ian Lipkin", + "author_inst": "Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.13.20173161", "rel_title": "Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate", @@ -1242940,101 +1246281,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.08.11.20167353", - "rel_title": "Pharmacological inhibition of the kinin-kallikrein system in severe COVID-19 A proof-of-concept study", - "rel_date": "2020-08-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20167353", - "rel_abs": "Coronavirus disease-19 (COVID-19) can develop into a severe respiratory syndrome that results in up to 40% mortality. Acute lung inflammatory edema is a major pathological finding in autopsies explaining O2 diffusion failure and hypoxemia. Only dexamethasone has been shown to reduce mortality in severe cases, further supporting a role for inflammation in disease severity. SARS-CoV-2 enters cells employing angiotensin converting enzyme 2 (ACE2) as a receptor, which is highly expressed in lung alveolar cells. ACE2 is one of the components of the cellular machinery that inactivates the potent inflammatory agent bradykinin, and SARS-CoV-2 infection could interfere with the catalytic activity of ACE2, leading to accumulation of bradykinin. In this open-label, randomized clinical trial, we tested two pharmacological inhibitors of the kinin-kallikrein system that are currently approved for the treatment of hereditary angioedema, icatibant and inhibitor of C1 esterase/kallikrein, in a group of 30 patients with severe COVID-19. Neither icatibant nor inhibitor of C1 esterase/kallikrein resulted in significant changes in disease mortality and time to clinical improvement. However, both compounds promoted significant improvement of lung computed tomography scores and increased blood eosinophils, which has been reported as an indicator of disease recovery. In this small cohort, we found evidence for a beneficial role of pharmacological inhibition of the kinin-kallikrein system in two markers that indicate improved disease recovery.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Eli Mansour", - "author_inst": "University of Campinas" - }, - { - "author_name": "Andre C Palma", - "author_inst": "University of Campinas" - }, - { - "author_name": "Raisa G Ulaf", - "author_inst": "University of Campinas" - }, - { - "author_name": "Luciana C Ribeiro", - "author_inst": "University of Campinas" - }, - { - "author_name": "Ana Flavia Bernardes", - "author_inst": "University of Campinas" - }, - { - "author_name": "Thyago A Nunes", - "author_inst": "University of Campinas" - }, - { - "author_name": "Marcus V Agrela", - "author_inst": "University of Campinas" - }, - { - "author_name": "Bruna Bombassaro", - "author_inst": "University of Campinas" - }, - { - "author_name": "Milena Monfort-Pires", - "author_inst": "University of Campinas" - }, - { - "author_name": "Rafael L Camargo", - "author_inst": "University of Campinas" - }, - { - "author_name": "Eliana P Araujo", - "author_inst": "University of Campinas" - }, - { - "author_name": "Natalia S Brunetti", - "author_inst": "University of Campinas" - }, - { - "author_name": "Alessandro S Farias", - "author_inst": "University of Campinas" - }, - { - "author_name": "Antonio L Falcao", - "author_inst": "University of Campinas" - }, - { - "author_name": "Thiago M Santos", - "author_inst": "University of Campinas" - }, - { - "author_name": "Plinio Trabasso", - "author_inst": "University of Campinas" - }, - { - "author_name": "Rachel P Dertkigil", - "author_inst": "University of Campinas" - }, - { - "author_name": "Sergio S Dertkigil", - "author_inst": "University of Campinas" - }, - { - "author_name": "Maria Luiza Moretti", - "author_inst": "University of Campinas" - }, - { - "author_name": "Licio A Velloso", - "author_inst": "University of Campinas" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.11.20171843", "rel_title": "Functional SARS-CoV-2-specific immune memory persists after mild COVID-19", @@ -1243335,6 +1246581,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.12.20173856", + "rel_title": "Comparative Evaluation of SARS-CoV-2 IgG Assays in India", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.12.20173856", + "rel_abs": "IgG immunoassays have been developed and used widely for clinical samples and serosurveys for SARS-CoV-2. We compared the performance of three immunoassays, an in-house RBD assay, and two commercial assays, the Diasorin LIAISON SARS-CoV-2 IgG CLIA which detects antibodies against S1/S2 domains of the Spike protein and the Zydus Kavach assay based on inactivated virus using a well-characterized sera-panel. 379 sera/plasma samples from RT-PCR positive individuals >20 days of illness in symptomatic or RT-PCR positivity in asymptomatic individuals and 184 pre-pandemic samples were used. The sensitivity of the assays were 84.7, 82.6 and 75.7 respectively for RBD, LIAISON and Kavach. Kavach and the in-house RBD ELISA showed a specificity of 99.5% and 100%, respectively. The RBD and LIAISON (S1/S2) assays showed high agreement (94.7%;95%CI:92.0,96.6) and were able to correctly identify more positives than Kavach. All three assays are suitable for serosurveillance studies, but in low prevalence sites, estimation of exposure may require adjustment based on our findings.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "- DBT India Consortium for Covid-19 Research", + "author_inst": "" + }, + { + "author_name": "Shinjini Bhatnagar", + "author_inst": "Translational Health Science and Technology Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.13.20173757", "rel_title": "LAMP-BEAC: Detection of SARS-CoV-2 RNA Using RT-LAMP and Molecular Beacons", @@ -1244614,41 +1247883,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.10.20171819", - "rel_title": "Investigation of pooling strategies using clinical COVID-19 samples for more efficient diagnostic testing", - "rel_date": "2020-08-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20171819", - "rel_abs": "When testing large numbers of clinical COVID-19 samples for diagnostic purposes, pooling samples together for processing can offer significant reductions in the materials, reagents, time, and labor needed. We have evaluated two different strategies for pooling independent nasopharyngeal swab samples prior to testing with an EUA-approved SARS-CoV-2 RT-qPCR diagnostic assay. First, in the Dilution Study, we assessed the assay's ability to detect a single positive clinical sample diluted in multiple negative samples before the viral RNA extraction stage. We observed that positive samples with Ct values at ~30 can be reliably detected in pools of up to 30 independent samples, and positive samples with Ct values at ~35 can be detected in pools of 5 samples. Second, in the Reloading Study, we assessed the efficacy of reloading QIAamp viral RNA extraction columns numerous times using a single positive sample and multiple negative samples. We determined that one RNA extraction column can be reloaded with up to 20 clinical samples (1 positive and 19 negatives) sequentially without any loss of signal in the diagnostic assay. Furthermore, we found there was no significant difference in assay readout whether the positive sample was loaded first or last in a series of 20 samples. These results demonstrate that different pooling strategies can lead to increased process efficiencies for COVID-19 clinical diagnostic testing.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Samantha H Adikari", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Emily Z Alipio Lyon", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Attelia D Hollander", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Alina Deshpande", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Elizabeth Hong-Geller", - "author_inst": "Los Alamos National Laboratory" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.13.20173997", "rel_title": "Deep Learning for Automated Recognition of Covid-19 from Chest X-ray Images", @@ -1244833,6 +1248067,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.12.20173781", + "rel_title": "Analysis of the intestinal microbiota in COVID-19 patients and its correlation with the inflammatory factor IL-18 and SARS-CoV-2-specific IgA", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.12.20173781", + "rel_abs": "The current global COVID-19 pandemic is caused by beta coronavirus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which already infected over 10 million and caused 500 thousand deaths by June 2020. Overproduction of cytokines triggered by COVID-19 infection, known as \"cytokine storm\", is a highly risk factor associated with disease severity. However, how COVID-19 infection induce cytokine storm is still largely unknown. Accumulating in vitro and in vivo evidence suggests that gut is also susceptible to COVID19 infection: Human intestinal organoids, an in vitro model which mimic the specific cell type and spatial structure of the intestine, were susceptible to SARS-CoV2 infection; A significant fraction of patients reported gut symptoms; Viral RNA may persist for more than 30 days and infectious virus could be isolated in fecal samples. The gastrointestinal tract is the primary site of interaction between the host immune system with symbiotic and pathogenic microorganisms. The bacteria resident in our gastrointestinal tract, known as gut microbiota, is important to maintain the homeostasis of our immune system. While imbalance of gut microbiota, or dysbiosis, is associated with multiple inflammation diseases5. It's possible that SARS-CoV-2 infection may lead to alternation of gut microbiota thus worsen the host symptom. IL-18 is a proinflammatory cytokine produced multiple enteric cells, including intestinal epithelial cells (IECs), immune cells as well as enteric nervous system, and was shown to increase in the serum of COVID-19 patients. Immunoglobin A (IgA) is mainly produced in the mucosal surfaces, in humans 40-60mg kg-1 day-1 than all other immunoglobulin isotypes combined, and at least 80% of all plasma cells are located in the intestinal lamina propria. Recent study showed that SARS-CoV-2 specific IgA in the serum is positively correlate with the disease severity in COVID-19 patients11. Here we investigated the alterations of microbiota in COVID-19 patients, and its correlation with inflammatory factor IL-18 and SARS-CoV2 specific IgA.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Wanyin Tao", + "author_inst": "University of Science and Technology of China" + }, + { + "author_name": "Shu Zhu", + "author_inst": "University of Science and Technology of China" + }, + { + "author_name": "Guorong Zhang", + "author_inst": "University of Science and Technology of China" + }, + { + "author_name": "Xiaofang Wang", + "author_inst": "University of Science and Technology of China" + }, + { + "author_name": "Meng Guo", + "author_inst": "University of Science and Technology of China" + }, + { + "author_name": "Weihong Zeng", + "author_inst": "University of Science and Technology of China" + }, + { + "author_name": "Zihao Xu", + "author_inst": "University of Science and Technology of China" + }, + { + "author_name": "Lianxin Liu", + "author_inst": "University of Science and Technology of China" + }, + { + "author_name": "Kaiguang Zhang", + "author_inst": "University of Science and Technology of China" + }, + { + "author_name": "Yucai Wang", + "author_inst": "University of Science and Technology of China" + }, + { + "author_name": "Xiaoling Ma", + "author_inst": "University of Science and Technology of China" + }, + { + "author_name": "Zhengxu Chen", + "author_inst": "University of Science and Technology of China" + }, + { + "author_name": "Tengchuan Jin", + "author_inst": "University of Science and Technology of China" + }, + { + "author_name": "Jianping Weng", + "author_inst": "University of Science and Technology of China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.13.20167064", "rel_title": "Predicting the Impact of the COVID-19 Pandemic for the Low- and Middle-Income Countries", @@ -1246120,37 +1249425,6 @@ "type": "new results", "category": "ecology" }, - { - "rel_doi": "10.1101/2020.08.14.251538", - "rel_title": "Differential methylation as a mediator of COVID-19 susceptibility", - "rel_date": "2020-08-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.14.251538", - "rel_abs": "The COVID-19 outbreak shows a huge variation in prevalence and mortality on geographical level but also within populations1. The ACE2 gene, identified as the SARS-CoV2 receptor, has been shown to facilitate the viral invasion and people with higher ACE2 expression generally are more severely affected2, 3. As there is a lot of variability in ACE2 expression between individuals we hypothesized that differential DNA methylation profiles could be (one of) the confounding factors explaining this variability. Here we show that epigenetic profiling of host tissue, especially in the ACE2 promoter region and its homologue ACE1, may be important risk factors for COVID-19. Our results propose that variable methylation can explain (part of) the differential susceptibility, symptom severity and death rate for COVID-19. Our findings are a promising starting point to further evaluate the potential of ACE1/2 methylation and other candidates as a predictor for clinical outcome upon SARS-CoV2 infection.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Sandra Steyaert", - "author_inst": "doc.ai Inc. 636 Waverley Street, Palo Alto, CA 94301" - }, - { - "author_name": "Geert Trooskens", - "author_inst": "doc.ai Inc. 636 Waverley Street, Palo Alto, CA 94301" - }, - { - "author_name": "Joris R Delanghe", - "author_inst": "Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium" - }, - { - "author_name": "Wim Van Criekinge", - "author_inst": "Biobix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.08.13.250076", "rel_title": "In Silico Design of siRNAs Targeting Existing and Future Respiratory Viruses with VirusSi", @@ -1246435,6 +1249709,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.14.251090", + "rel_title": "Methylene Blue has a potent antiviral activity against SARS-CoV-2 in the absence of UV-activation in vitro", + "rel_date": "2020-08-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.14.251090", + "rel_abs": "Methylene blue is an FDA and EMA approved drug with an excellent safety profile. It displays broad-spectrum virucidal activity in the presence of UV light and has been shown to be effective in inactivating various viruses in blood products prior to transfusions. In addition, its use has been validated for methemoglobinemia and malaria treatment. Here we show the virucidal activity of methylene blue at low micromolar concentrations and in the absence of UV activation against SARS-CoV2.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Valeria Cagno", + "author_inst": "University of Geneva" + }, + { + "author_name": "Chiara Medaglia", + "author_inst": "University of Geneva" + }, + { + "author_name": "Andreas Cerny", + "author_inst": "Epatocentro Ticino, Lugano, Switzerland" + }, + { + "author_name": "Thomas Cerny", + "author_inst": "Kantonsspital St.Gallen, St.Gallen, Switzerland" + }, + { + "author_name": "Caroline Tapparel", + "author_inst": "University of Geneva" + }, + { + "author_name": "Erich Cerny", + "author_inst": "Omni Drugs SA, 13 Cours des Bastions, Geneva, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.13.248351", "rel_title": "Designed Variants of Recombinant ACE2-Fc that Decouple Anti-SARS-CoV-2 Activities from Unwanted Cardiovascular Effects", @@ -1247774,117 +1251087,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.10.20170894", - "rel_title": "Deciphering the state of immune silence in fatal COVID-19 patients", - "rel_date": "2020-08-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20170894", - "rel_abs": "Since the beginning of the SARS-CoV-2 pandemic, COVID-19 has appeared as a unique disease with unconventional tissue and systemic immune features. While COVID-19 severe forms share clinical and laboratory aspects with various pathologies such as hemophagocytic lymphohistiocytosis, sepsis or cytokine release syndrome, their exact nature remains unknown. This is severely impeding the ability to treat patients facing severe stages of the disease. To this aim, we performed an in-depth, single-cell RNA-seq analysis of more than 150.000 immune cells isolated from matched blood samples and broncho-alveolar lavage fluids of COVID-19 patients and healthy controls, and integrated it with clinical, immunological and functional ex vivo data. We unveiled an immune signature of disease severity that correlated with the accumulation of naive lymphoid cells in the lung and an expansion and activation of myeloid cells in the periphery. Moreover, we demonstrated that myeloid-driven immune suppression is a hallmark of COVID-19 evolution and arginase 1 expression is significantly associated with monocyte immune regulatory features. Noteworthy, we found monocyte and neutro-phil immune suppression loss associated with fatal clinical outcome in severe patients. Additionally, our analysis discovered that the strongest association of the patients clinical outcome and immune phenotype is the lung T cell response. We found that patients with a robust CXCR6+ effector memory T cell response have better outcomes. This result is line with the rs11385942 COVID-19 risk allel, which is in proximity to the CXCR6 gene and suggest effector memory T cell are a primary feature in COVID-19 patients. By systemically quantifying the viral landscape in the lung of severe patients, we indeed identified Herpes-Simplex-Virus 1 (HSV-1) as a potential opportunistic virus in COVID-19 patients. Lastly, we observed an unexpectedly high SARS-CoV-2 viral load in an immuno-compromised patient, allowing us to study the SARS-CoV-2 in-vivo life cycle. The development of myeloid dysfunctions and the impairment of lymphoid arm establish a condition of immune paralysis that supports secondary bacteria and virus infection and can progress to \"immune silence\" in patients facing death.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Pierre Bost", - "author_inst": "Department of Immunology, Weizmann Institute of Science, Rehovot, Israel, Systems Biology Group, Department of Computational Biology and USR 3756, Institut Past" - }, - { - "author_name": "Francesco De Sanctis", - "author_inst": "Immunology Section, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Stefania Cane", - "author_inst": "Immunology Section, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Stefano Ugel", - "author_inst": "Immunology Section, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Katia Donadello", - "author_inst": "Intensive Care Unit, Department of Surgery, Dentistry, Maternity and Infant, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Monica Castellucci", - "author_inst": "The Center for Technological Platforms, University of Verona, Verona, Italy" - }, - { - "author_name": "David Eyal", - "author_inst": "Department of Immunology, Weizmann Institute of Science, Rehovot, Israel" - }, - { - "author_name": "Alessandra Fiore", - "author_inst": "Immunology Section, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Cristina Anselmi", - "author_inst": "Immunology Section, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Roza Maria Barouni", - "author_inst": "Immunology Section, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Rosalinda Trovato", - "author_inst": "Immunology Section, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Simone Caligola", - "author_inst": "Immunology Section, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Alessia Lamolinara", - "author_inst": "CAST- Center for Advanced Studies and Technology, University of G. D Annunzio of Chieti-Pescara, Chieti, Italy" - }, - { - "author_name": "Manuela Iezzi", - "author_inst": "CAST- Center for Advanced Studies and Technology, University of G. D Annunzio of Chieti-Pescara, Chieti, Italy" - }, - { - "author_name": "Federica Facciotti", - "author_inst": "Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy" - }, - { - "author_name": "Anna Rita Mazzariol", - "author_inst": "Microbiology Unit, Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Davide Gibellini", - "author_inst": "Microbiology Unit, Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Pasquale De Nardo", - "author_inst": "Division of Infectious Diseases, Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Evelina Tacconelli", - "author_inst": "Division of Infectious Diseases, Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Leonardo Gottin", - "author_inst": "Intensive Care Unit, Department of Surgery, Dentistry, Maternity and Infant, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Enrico Polati", - "author_inst": "Intensive Care Unit, Department of Surgery, Dentistry, Maternity and Infant, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Benno Schwikowski", - "author_inst": "Systems Biology Group, Department of Computational Biology and USR 3756, Institut Pasteur and CNRS,Paris, France" - }, - { - "author_name": "Ido Amit", - "author_inst": "Department of Immunology, Weizmann Institute of Science, Rehovot, Israel." - }, - { - "author_name": "Vincenzo Bronte", - "author_inst": "Immunology Section, Department of Medicine, University and Hospital Trust of Verona, Verona , Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.10.20171629", "rel_title": "Risk of fomite-mediated transmission of SARS-CoV-2 in child daycares, schools, and offices: a modeling study", @@ -1248053,6 +1251255,61 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.08.12.246389", + "rel_title": "Maraviroc inhibits SARS-CoV-2 multiplication and s-protein mediated cell fusion in cell culture", + "rel_date": "2020-08-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.12.246389", + "rel_abs": "In an effort to identify therapeutic intervention strategies for the treatment of COVID-19, we have investigated a selection of FDA-approved small molecules and biologics that are commonly used to treat other human diseases. A investigation into 18 small molecules and 3 biologics was conducted in cell culture and the impact of treatment on viral titer was quantified by plaque assay. The investigation identified 4 FDA-approved small molecules, Maraviroc, FTY720 (Fingolimod), Atorvastatin and Nitazoxanide that were able to inhibit SARS-CoV-2 infection. Confocal microscopy with over expressed S-protein demonstrated that Maraviroc reduced the extent of S-protein mediated cell fusion as observed by fewer multinucleate cells in the context of drugtreatment. Mathematical modeling of drug-dependent viral multiplication dynamics revealed that prolonged drug treatment will exert an exponential decrease in viral load in a multicellular/tissue environment. Taken together, the data demonstrate that Maraviroc, Fingolimod, Atorvastatin and Nitazoxanide inhibit SARS-CoV-2 in cell culture.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Kenneth Risner", + "author_inst": "George Mason University" + }, + { + "author_name": "Katie V Tieu", + "author_inst": "Virginia Commonwealth University" + }, + { + "author_name": "Yafei Wang", + "author_inst": "Indiana University" + }, + { + "author_name": "Michael Getz", + "author_inst": "Indiana University" + }, + { + "author_name": "Allison Bakovic", + "author_inst": "George Mason University" + }, + { + "author_name": "Nishank Bhalla", + "author_inst": "George Mason University" + }, + { + "author_name": "Steven Nathan", + "author_inst": "INOVA Fairfax Hospital" + }, + { + "author_name": "Daniel E Conway", + "author_inst": "Virginia Commonwealth University" + }, + { + "author_name": "Paul Macklin", + "author_inst": "Indiana University" + }, + { + "author_name": "Aarthi Narayanan", + "author_inst": "George Mason University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.12.248823", "rel_title": "Attenuated influenza virions expressing the SARS- CoV-2 receptor-binding domain induce neutralizing antibodies in mice", @@ -1249416,45 +1252673,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.09.20149286", - "rel_title": "The effect of public health policies in the transmission of COVID-19 for South American countries", - "rel_date": "2020-08-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.09.20149286", - "rel_abs": "ObjectivesThe analysis of transmission dynamics is crucial to determine whether mitigation or suppression measures reduce the spread of Coronavirus disease 2019 (COVID-19). This study sought to estimate the basic (R0) and time-varying (Rt) reproduction number of COVID-19 and contrast the public health measures for ten South American countries.\n\nMethodsData was obtained from the European Centre for Disease Prevention and Control. Country-specific R0 estimates during the first two weeks of the outbreak and Rt estimates after 90 days were estimated.\n\nResultsCountries used a combination of isolation, physical distancing, quarantine, and community-wide containment measures to staunch the spread of COVID-19 at different points in time. R0 ranged from 1.52 (95% confidence interval: 1.13-1.99) in Venezuela to 3.83 (3.04-4.75) in Chile, whereas Rt after 90 days ranged from 0.71 (95% credible interval: 0.39-1.05) in Uruguay to 1.20 (1.19-1.20) in Brazil. Different R0 and Rt values may be related to the testing capacity of each country.\n\nConclusionR0 in the early phase of the outbreak varied across the South American countries. The public health measures adopted in the initial period of the pandemic appear to have reduced Rt over time in each country, albeit to different levels.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Bryan Valcarcel", - "author_inst": "Milken Institute School of Public Health" - }, - { - "author_name": "Jose L Avilez", - "author_inst": "University of Waterloo" - }, - { - "author_name": "J. Smith Torres-Roman", - "author_inst": "Universidad Cientifica del Sur" - }, - { - "author_name": "Julio A Poterico", - "author_inst": "Instituto Nacional de Salud del Nino San Borja" - }, - { - "author_name": "Janina Bazalar-Palacios", - "author_inst": "Instituto de Investigacion, Universidad Catolica Los Angeles de Chimbote" - }, - { - "author_name": "Carlo La Vecchia", - "author_inst": "Department of Clinical Sciences and Community Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.11.247395", "rel_title": "Elicitation of potent neutralizing antibody responses by designed protein nanoparticle vaccines for SARS-CoV-2", @@ -1249787,6 +1253005,45 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.08.12.247767", + "rel_title": "Suppression of MDA5-mediated antiviral immune responses by NSP8 of SARS-CoV-2", + "rel_date": "2020-08-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.12.247767", + "rel_abs": "Melanoma differentiation-associated gene-5 (MDA5) acts as a cytoplasmic RNA sensor to detect viral dsRNA and mediates type I interferon (IFN) signaling and antiviral innate immune responses to infection by RNA viruses. Upon recognition of viral dsRNA, MDA5 is activated with K63-linked polyubiquitination and then triggers the recruitment of MAVS and activation of TBK1 and IKK, subsequently leading to IRF3 and NF-{kappa}B phosphorylation. Great numbers of symptomatic and severe infections of SARS-CoV-2 are spreading worldwide, and the poor efficacy of treatment with type I interferon and antiviral agents indicates that SARS-CoV-2 escapes from antiviral immune responses via an unknown mechanism. Here, we report that SARS-CoV-2 nonstructural protein 8 (NSP8) acts as an innate immune suppressor and inhibits type I IFN signaling to promote infection of RNA viruses. It downregulates the expression of type I IFNs, IFN-stimulated genes and proinflammatory cytokines by binding to MDA5 and impairing its K63-linked polyubiquitination. Our findings reveal that NSP8 mediates innate immune evasion during SARS-CoV-2 infection and may serve as a potential target for future therapeutics for SARS-CoV-2 infectious diseases.\n\nImportanceThe large-scale spread of COVID-19 is causing mass casualties worldwide, and the failure of antiviral immune treatment suggests immune evasion. It has been reported that several nonstructural proteins of severe coronaviruses suppress antiviral immune responses; however, the immune suppression mechanism of SARS-CoV-2 remains unknown. Here, we revealed that NSP8 protein of SARS-CoV-2 directly blocks the activation of the cytosolic viral dsRNA sensor MDA5 and significantly downregulates antiviral immune responses. Our study contributes to our understanding of the direct immune evasion mechanism of SARS-CoV-2 by showing that NSP8 suppresses the most upstream sensor of innate immune responses involved in the recognition of viral dsRNA.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ziwei Yang", + "author_inst": "Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University" + }, + { + "author_name": "Xiaolin Zhang", + "author_inst": "Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University" + }, + { + "author_name": "Fan Wang", + "author_inst": "Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University" + }, + { + "author_name": "Peihui Wang", + "author_inst": "Advanced Medical Research Institute, Shandong University" + }, + { + "author_name": "Xiaojuan Li", + "author_inst": "Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University" + }, + { + "author_name": "Ersheng Kuang", + "author_inst": "Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.12.20169359", "rel_title": "Effect of Convalescent Plasma on Mortality among Hospitalized Patients with COVID-19: Initial Three-Month Experience", @@ -1251258,53 +1254515,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.07.20167957", - "rel_title": "Mask-associated de novo headache in healthcare workers during the Covid-19 pandemic.", - "rel_date": "2020-08-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20167957", - "rel_abs": "IntroductionThe pandemic caused by the new coronavirus (COVID-19) has led to changes in the development of health care activities by health professionals. We analysed whether there is an association between the appearance of \"de novo\" headache according to the type of mask used, the related factors, as well as the impact of the headache on health professionals.\n\nMethodcross-sectional study in a tertiary hospital in Extremadura, Spain. We administered an online questionnaire to healthcare workers during the period of maximum incidence of COVID-19 in our setting.\n\nResultsn=306, 244 women (79.7%), with an average age of 43 years (range 23-65). Of the total, 129 (42.2%) were physicians, 112 (36.6%) nurses and 65 (21.2%) other health workers. 208 (79.7%) used surgical masks and 53 (20.3%) used filtering masks. Of all those surveyed, 158 (51.6%) presented \"de novo\" headache. The occurrence of headache was independently associated with the use of a filtering mask, OR 2.14 (IC95% 1.07-4.32), being a nurse OR 2.09 (IC95% 1.18-3.72) or another health worker OR 6.94 (IC95% 3.01-16.04) or having a history of asthma OR 0.29 (IC95% 0.09-0.89). Depending on the type of mask used there were differences in headache intensity. And the impact of headache in the subjects who used a filtering mask was worse in the all aspects evaluated.\n\nConclusionsThe appearance of \"de novo\" headache is associated with the use of filtering masks and is more frequent in certain health care workers, causing a greater occupational, family, personal and social impact.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Jose M Ramirez-Moreno", - "author_inst": "Extremadura University. School of Medicine." - }, - { - "author_name": "David Ceberino", - "author_inst": "Hospital Universitario de Badajoz" - }, - { - "author_name": "Alberto Gonzalez", - "author_inst": "Hospital Universitario de Badajoz" - }, - { - "author_name": "Belen Rebollo", - "author_inst": "Hospital Universitario de Badajoz" - }, - { - "author_name": "Pablo Macias", - "author_inst": "Hospital Universitario de Badajoz" - }, - { - "author_name": "Roshan Hariramani", - "author_inst": "Hospital Universitario de Badajoz" - }, - { - "author_name": "Ana M Roa", - "author_inst": "Hospital Universitario de Badajoz" - }, - { - "author_name": "Ana B Constantino", - "author_inst": "Hospital Universitario de Badajoz" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.07.20170449", "rel_title": "Outcomes of COVID-19 related hospitalisation among people with HIV in the ISARIC WHO Clinical Characterisation Protocol UK Protocol: prospective observational study", @@ -1251589,6 +1254799,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.09.20171355", + "rel_title": "Sensitivity, specificity and predictive values of molecular and serological tests for COVID-19. A longitudinal study in emergency room.", + "rel_date": "2020-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.09.20171355", + "rel_abs": "Accuracy of diagnostic tests is essential for suspected cases of Coronavirus Disease 2019 (COVID-19). This study aimed to assess the sensitivity, specificity and positive and negative predictive value (PPV and NPV) of molecular and serological tests for the diagnosis of SARS-CoV-2 infection. A total of 346 consenting, adult patients were enrolled at the emergency room of IRCCS Sacro Cuore Don Calabria Hospital, Negrar, Italy. We evaluated three RT-PCR methods including six different gene targets; five serologic rapid diagnostic tests (RDT); one ELISA test. The final classification of infected/not infected patients was performed using Latent Class Analysis in combination with clinical re-assessment of incongruous cases and was the basis for the main analysis of accuracy.\n\nOf 346 patients consecutively enrolled, 85 (24.6%) were classified as infected. The molecular test with the highest sensitivity, specificity, PPV and NPV was RQ-SARS-nCoV-2 with 91.8% (C.I. 83.8-96.6), 100% (C.I. 98.6-100.0), 100.0% (C.I. 95.4-100.0) and 97.4% (C.I. 94.7-98.9) respectively, followed by CDC 2019-nCoV with 76.2% (C.I. 65.7-84.8), 99.6% (C.I. 97.9-100.0), 98.5% (C.I. 91.7-100.0) and 92.9% (C.I. 89.2-95.6) and by in-house test targeting E-RdRp with 61.2% (C.I. 50.0-71.6), 99.6% (C.I. 97.9-100.0), 98.1% (C.I. 89.9-100.0) and 88.7% (C.I. 84.6-92.1). The analyses on single gene targets found the highest sensitivity for S and RdRp of the RQ-SARS-nCoV-2 (both with sensitivity 94.1%, C.I. 86.8-98.1). The in-house RdRp had the lowest sensitivity (62.4%, C.I. 51.2-72.6). The specificity ranged from 99.2% (C.I. 97.3-99.9) for in-house RdRp and N2 to 95.0% (C.I. 91.6-97.3) for E. The PPV ranged from 97.1% (C.I. 89.8-99.6) of N2 to 85.4% (C.I. 76.3-92.00) of E, and the NPV from 98.1% (C.I. 95.5-99.4) of gene S to 89.0% (C.I. 84.8-92.4) of in-house RdRp. All serological tests had <50% sensitivity and low PPV and NPV. One RDT (VivaDiag IgM) had high specificity (98.5%, with PPV 84.0%), but poor sensitivity (24.7%). Molecular tests for SARS-CoV-2 infection showed excellent specificity, but significant differences in sensitivity. As expected, serological tests have limited utility in a clinical context.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Zeno Bisoffi", + "author_inst": "IRCCS Sacro Cuore Don Calabria Hospital" + }, + { + "author_name": "ELENA POMARI", + "author_inst": "IRCCS Sacro Cuore Don Calabria Hospital" + }, + { + "author_name": "Michela Deiana", + "author_inst": "IRCCS Sacro Cuore Don Calabria Hospital" + }, + { + "author_name": "Chiara Piubelli", + "author_inst": "IRCCS Sacro Cuore Don Calabria Hospital" + }, + { + "author_name": "Niccolo Ronzoni", + "author_inst": "IRCCS Sacro Cuore Don Calabria Hospital" + }, + { + "author_name": "Anna Beltrame", + "author_inst": "IRCCS Sacro Cuore Don Calabria Hospital" + }, + { + "author_name": "Giulia Bertoli", + "author_inst": "IRCCS Sacro Cuore Don Calabria Hospital" + }, + { + "author_name": "Niccolo Riccardi", + "author_inst": "IRCCS Sacro Cuore Don Calabria Hospital" + }, + { + "author_name": "Francesca Perandin", + "author_inst": "IRCCS Sacro Cuore Don Calabria Hospital" + }, + { + "author_name": "Fabio Formenti", + "author_inst": "IRCCS Sacro Cuore Don Calabria Hospital" + }, + { + "author_name": "Federico Gobbi", + "author_inst": "IRCCS Sacro Cuore Don Calabria Hospital" + }, + { + "author_name": "Dora Buonfrate", + "author_inst": "IRCCS Sacro Cuore Don Calabria Hospital" + }, + { + "author_name": "Ronaldo Silva", + "author_inst": "IRCCS Sacro Cuore Don Calabria Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.09.20171330", "rel_title": "A Systematic Review of the Cardiovascular Manifestations and Outcomes in the Setting of Coronavirus-19 Disease", @@ -1252936,61 +1256213,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.10.20172106", - "rel_title": "Mass molecular testing for COVID19 using NGS-based technology and a highly scalable workflow", - "rel_date": "2020-08-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20172106", - "rel_abs": "Since first reported case of the new coronavirus infection in Wuhan, China, researchers and governments have witnessed an unseen rise in the number of cases. Thanks to the rapid work of Chinese scientists, the pathogen now called SARS-CoV-2 has been identified and its whole genome has been deposited in public databases by early January 2020. The availability of the genome has allowed researchers to develop Reverse Transcription - Polymerase Chain Reaction (RT-PCR) assays, which are now the gold-standard for molecular diagnosis of the respiratory syndrome COVID19. Because of the rising number of cases and rapid spreading, the world has been facing a shortage of RT-PCR supplies, especially the ones involved in RNA extraction. This has been a major bottleneck to increase testing capacity in many countries that do not significantly manufacture these supplies (Brazil included). Additionally, RT-PCR scalability is highly dependent on equipment that usually perform testing of 96 samples at a time. In this work, we describe a cost-effective molecular NGS-based test for diagnosis of COVID19, which uses a single-step RNA extraction and presents high scalability and accuracy when compared to the gold-standard RT-PCR. A single run of the NGS-based test using the Illumina NextSeq 550 mid-end sequencing equipment is able to multiplex 1,536 patients samples, providing individual semi-qualitative results (detected, not detected). Detected results are provided with fragments per million (FPM) values, which was demonstrated to correlate with RT-PCR Cycle Threshold (CT) values. Besides, usage of the high-end Illumina Novaseq platform may yield diagnostic for up to 6,144 samples in a single run. Performance results when compared with RT-PCR show general accuracy of 96% (or 98% when only samples with CT values for gene N lower than 30 are considered). We have also developed an online platform, called VarsVID(R), a Varstation(R) feature, to help test executors to easily scale testing numbers. Sample registering, wet-lab worksheets, sample sheet for sequencing and results display are all features provided by VarsVID(R) on Varstation(R). Altogether, these results will contribute to control COVID19 pandemics.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Fernanda de Mello Malta", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Deyvid Emanuel Amgarten", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Felipe Camilo Val", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Rubia Anita Ferraz Santana", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Murilo Castro Cervato", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Bruna Mascaro Cordeiro de Azevedo", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Marcela de Souza Basqueira", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Camila Oliveira dos Santos Alves", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Maria Soares Nobrega", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Joao Renato Rebello Pinho", - "author_inst": "Hospital Israelita Albert Einstein" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.10.20171033", "rel_title": "Post-exertion oxygen saturation as a prognostic factor for adverse outcome in patients attending the emergency department with suspected COVID-19: Observational cohort study", @@ -1253355,6 +1256577,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.11.245993", + "rel_title": "Common low complexity regions for SARS-CoV-2 and human proteomes as potential multidirectional risk factor in vaccine development", + "rel_date": "2020-08-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.11.245993", + "rel_abs": "The rapid spread of the COVID-19 demands immediate response from the scientific communities. Appropriate countermeasures mean thoughtful and educated choice of viral targets (epitopes). There are several articles that discuss such choices in the SARS-CoV-2 proteome, other focus on phylogenetic traits and history of the Coronaviridae genome/proteome. However none consider viral protein low complexity regions (LCRs). Recently we created the first methods that are able to compare such fragments. We show that five low complexity regions (LCRs) in three proteins (nsp3, S and N) encoded by the SARS-CoV-2 genome are highly similar to regions from human proteome. As many as 21 predicted T-cell epitopes and 27 predicted B-cell epitopes overlap with the five SARS-CoV-2 LCRs similar to human proteins. Interestingly, replication proteins encoded in the central part of viral RNA are devoid of LCRs. Similarity of SARS-CoV-2 LCRs to human proteins may have implications on the ability of the virus to counteract immune defenses. The vaccine targeted LCRs may potentially be ineffective or alternatively lead to autoimmune diseases development. These findings are crucial to the process of selection of new epitopes for drugs or vaccines which should omit such regions.\n\nAuthor summaryThe outbreak of the COVID-19 disease affects humans all over the globe. More and more people get sick and many die because of the deadly SARS-CoV-2 virus. The whole machinery of this pathogen is enclosed in a short sequence of nucleotides, building blocks for both RNA and DNA strands. This RNA virus encodes less than 30 protein sequences that change the fate of our societies. Its proteins are composed of 20 amino acids (building bricks) that are usually used quite freely by proteins. However, there are fragments where only one or a few amino acids are used. We name those low complexity regions (LCRs). We invented the first programmes able to compare such LCRs. Using this new methodology we were able to show similarity of some viral proteins to human ones. This discovery has a serious implication when designing vaccines or drugs. It means that companies should not use these very LCRs as targets because it may trigger an autoimmune disease. On the other hand this specific similarity may suggest some kind of disguise of viral proteins into the machinery of human cells.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Aleksandra Gruca", + "author_inst": "Politechnika Slaska" + }, + { + "author_name": "Joanna Ziemska-Legiecka", + "author_inst": "Institute of Biochemistry and Biophysics" + }, + { + "author_name": "Patryk Jarnot", + "author_inst": "Politechnika Slaska" + }, + { + "author_name": "Elzbieta Sarnowska", + "author_inst": "Centrum Onkologii-Instytut im Marii Sklodowskiej-Curie w Warszawie" + }, + { + "author_name": "Tomasz Sarnowski", + "author_inst": "Polska Akademia Nauk Instytut Biochemii i Biofizyki" + }, + { + "author_name": "Marcin Grynberg", + "author_inst": "Institute of Biochemistry and Biophysics, Polish Academy of Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.08.11.246678", "rel_title": "Opposing activities of IFITM proteins in SARS-CoV-2 infection", @@ -1255126,25 +1258387,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dentistry and oral medicine" }, - { - "rel_doi": "10.1101/2020.08.06.20169896", - "rel_title": "Prediction of Covid-19 Infections Through December 2020 for 10 US States Using a Two Parameter Transmission Model Incorporating Outdoor Temperature and School Re-Opening Effects", - "rel_date": "2020-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20169896", - "rel_abs": "Covid-19 infection case predictions (total cases) are made for August through December 2020 for 10 US States (NY, WA, GA, IL, MN, FL, OH, MI, CA, and NC). A two-parameter model based on social distance index (SDI) and disease transmission efficiency (G) parameters is used to characterize SARS-CoV-2 disease spread. Current lack of coherent and coordinated US policy causes the US to follow a linear infection growth path with a limit cycle behavior that modulates the US between accelerating and decaying infection growth on either side of a linear growth path boundary.\n\nFour prediction cases are presented:\n\nO_LINo school re-openings; fall season temperature effect\nC_LIO_LINo school re-openings; no fall season temperature effect\nC_LIO_LISchool re-openings; fall season temperature effect\nC_LIO_LISchool re-openings; no fall season temperature effect\nC_LI\n\nFall outdoor temperatures, in contrast to the 1918 pandemic, are predicted to be beneficial for dampening SARS-CoV-2 transmission in States as they pass through \"swing season\" temperature range of 70F to 50F. Physical re-opening of schools in September are predicted to accelerate infections.\n\nStates with low current infectious case numbers (eg, NY) are predicted to be minimally impacted while States with high current infectious case numbers (eg, CA and FL) will be significantly impacted by school re-openings.\n\nUpdated infection predictions will be posted monthly (Sept, Oct, Nov, Dec) with adjustments based on actual trends in SDI and G. Assessments related to outdoor temperature impact, school re-openings, and other public gathering re-openings will be discussed in updated reports.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ty A Newell", - "author_inst": "University of Illinois" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.06.20155804", "rel_title": "Characterization of Israeli COVID-19 Outbreak Drivers and Forecasting Using a Versatile Web App", @@ -1255717,6 +1258959,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.08.06.20169276", + "rel_title": "The implementation of a rapid sample preparation method for the detection of SARS-CoV-2 in a diagnostic laboratory in South Africa", + "rel_date": "2020-08-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20169276", + "rel_abs": "The SARS-CoV-2 pandemic has resulted in shortages of both critical reagents for nucleic acid purification and highly trained staff as supply chains are strained by high demand, public health measures and frequent quarantining and isolation of staff. This created the need for alternate workflows with limited reliance on specialised reagents, equipment and staff. We present here the validation and implementation of such a workflow for preparing samples for downstream SARS-CoV-2 RT-PCR using liquid handling robots. The rapid sample preparation technique evaluated, which included sample centrifugation and heating prior to RT-PCR, showed a 97.37% (95% CI: 92.55-99.28%) positive percent agreement and 97.30% (95% CI: 90.67-99.52%) negative percent agreement compared to nucleic acid purification-based testing. This method was subsequently adopted as the primary sample preparation method in the Groote Schuur Hospital Virology Diagnostic Laboratory in Cape Town, South Africa.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Gert Johannes Kruger Marais", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Michelle Naidoo", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Nei-yuan Hsiao", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Ziyaad Valley-Omar", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Heidi Smuts", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Diana Ruth Hardie", + "author_inst": "University of Cape Town" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.06.20169367", "rel_title": "Dynamics of neutralizing antibody titers in the months after SARS-CoV-2 infection", @@ -1257148,29 +1260429,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.06.20169656", - "rel_title": "Obtaining prevalence estimates of COVID-19: A model to inform decision-making", - "rel_date": "2020-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20169656", - "rel_abs": "ObjectivesThe primary aim was to evaluate whether randomly sampling and testing a set number of individuals for active or past COVID-19 while adjusting for misclassification error captures a simulated prevalence. The secondary aim was to quantify the impact of misclassification error bias on publicly reported case data in Maryland.\n\nMethodsUsing a stratified random sampling approach, 50,000 individuals were selected from a simulated Maryland population to estimate the prevalence of active and past COVID-19. Data from the 2014-2018 and 2018 American Community Surveys were used. The simulated prevalence was 0.5% and 1.0% for active and past COVID-19, respectively. Bayesian models, informed by published validity estimates, were used to account for misclassification error when estimating the prevalence of active and past COVID-19.\n\nResultsFailure to account for misclassification error overestimated the simulated prevalence for active and past COVID-19. Adjustment for misclassification error decreased the point estimate for active and past COVID-19 prevalence by 55% and 29%, respectively. Adjustment for sampling method and misclassification error only captured the simulated past COVID-19 prevalence. The simulated active COVID-19 prevalence was only captured when set to 0.7% and above. Adjustment for misclassification error for publicly reported Maryland data increased the estimated average daily cases by 8%.\n\nConclusionsRandom sampling and testing of COVID-19 is needed but must be accompanied by adjustment for misclassification error to avoid over- or underestimating the prevalence. This approach bolsters disease control efforts. Implementing random testing for active COVID-19 may be best in a smaller geographic area with highly prevalent cases.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ida Sahlu", - "author_inst": "MITRE Corporation" - }, - { - "author_name": "Alexander B Whittaker", - "author_inst": "MITRE Corporation" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.06.20169722", "rel_title": "SARS-CoV-2 infection fatality risk in a nationwide seroepidemiological study", @@ -1257479,6 +1260737,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.06.20169870", + "rel_title": "BEHAVIORAL CHANGES DURING THE COVID-19 PANDEMIC: RESULTS OF A NATIONAL SURVEY IN SINGAPORE", + "rel_date": "2020-08-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20169870", + "rel_abs": "IntroductionAs part of infection control measures for COVID-19, individuals have been encouraged to adopt both preventive (e.g., handwashing) and avoidant behavioural changes (e.g., avoiding crowds). In this study, we examined whether demographics predicted the likelihood that a person would adopt these behaviours in Singapore.\n\nMaterials and Methods1145 participants responded to an online survey conducted between 7 March - 21 April 2020. As part of the survey, we collected demographic information and asked participants to report which of 17 behaviour changes they had undertaken because of the outbreak. We ran regression models to predict, using demographic information: (1) the total number of behavioural changes undertaken, (2) the number of preventive changes undertaken, and (3) the number of avoidant changes undertaken. Finally, we sought to identify predictors of persons who: (4) declared that they had not undertaken any of these measures following the outbreak.\n\nResultsFemales and those who were younger adopted more preventive behaviours: whereas females were more likely to increase handwashing frequency, younger individuals were more likely to wear face masks prior to legislation. Females and those who were married adopted more avoidant behaviours, with both groups avoiding crowded areas and staying home more than usual. Females also voluntarily reduced physical contact, whereas those who were married chose outdoor venues and relied on online shopping.\n\nConclusionOur characterisation of behavioural changes provides a baseline for public health advisories. Moving forward, local health authorities can focus their efforts to encourage segments of the population who do not readily adopt infection control measures against COVID-19.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Victoria JE Long", + "author_inst": "Duke-NUS Medical School" + }, + { + "author_name": "Jean CJ Liu", + "author_inst": "Yale-NUS College" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.06.239574", "rel_title": "Generation of tonsil organoids as an ex vivo model for SARS-CoV-2 infection", @@ -1258822,61 +1262103,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.05.20168971", - "rel_title": "Features and Functions of Systemic and Mucosal Humoral Immunity Among SARS-CoV-2 Convalescent Individuals", - "rel_date": "2020-08-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.05.20168971", - "rel_abs": "Understanding humoral immune responses to SARS-CoV-2 infection will play a critical role in the development of vaccines and antibody-based interventions. We report systemic and mucosal antibody responses in convalescent individuals who experienced varying disease severity. Robust antibody responses to diverse SARS-CoV-2 antigens and evidence of elevated responses to endemic CoV were observed among convalescent donors. SARS-CoV-2-specific IgA and IgG responses were often negatively correlated, particularly in mucosal samples, suggesting subject-intrinsic biases in isotype switching. Assessment of antibody-mediated effector functions revealed an inverse correlation between systemic and mucosal neutralization activity and site-dependent differences in the isotype of neutralizing antibodies. Serum neutralization correlated with systemic anti-SARS-CoV-2 IgG and IgM response magnitude, while mucosal neutralization was associated with nasal SARS-CoV-2-specific IgA. These findings begin to map how diverse Ab characteristics relate to Ab functions and outcomes of infection, informing public health assessment strategies and vaccine development efforts.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Savannah E Butler", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Andrew R Crowley", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Harini Natarajan", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Shiwei Xu", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Joshua A Weiner", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Jiwon Lee", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Wendy F Wieland-Alter", - "author_inst": "Dartmouth-Hitchcock Medical Center" - }, - { - "author_name": "Ruth I Connor", - "author_inst": "Dartmouth-Hitchcock Medical Center" - }, - { - "author_name": "Peter F Wright", - "author_inst": "Dartmouth-Hitchcock Medical Center" - }, - { - "author_name": "Margaret E Ackerman", - "author_inst": "Dartmouth College" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.05.20168948", "rel_title": "Development of mass spectrometry-based targeted assay for direct detection of novel SARS-CoV-2 coronavirus from clinical specimens", @@ -1259077,6 +1262303,185 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.04.20167874", + "rel_title": "Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing", + "rel_date": "2020-08-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.04.20167874", + "rel_abs": "The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission by individuals who are asymptomatic at the time of transmission1, 2. Frequent, widespread testing of the asymptomatic population for SARS-CoV-2 is essential to suppress viral transmission. Despite increases in testing capacity, multiple challenges remain in deploying traditional reverse transcription and quantitative PCR (RT-qPCR) tests at the scale required for population screening of asymptomatic individuals. We have developed SwabSeq, a high-throughput testing platform for SARS-CoV-2 that uses next-generation sequencing as a readout. SwabSeq employs sample-specific molecular barcodes to enable thousands of samples to be combined and simultaneously analyzed for the presence or absence of SARS-CoV-2 in a single run. Importantly, SwabSeq incorporates an in vitro RNA standard that mimics the viral amplicon, but can be distinguished by sequencing. This standard allows for end-point rather than quantitative PCR, improves quantitation, reduces requirements for automation and sample-to-sample normalization, enables purification-free detection, and gives better ability to call true negatives. After setting up SwabSeq in a high-complexity CLIA laboratory, we performed more than 80,000 tests for COVID-19 in less than two months, confirming in a real world setting that SwabSeq inexpensively delivers highly sensitive and specific results at scale, with a turn-around of less than 24 hours. Our clinical laboratory uses SwabSeq to test both nasal and saliva samples without RNA extraction, while maintaining analytical sensitivity comparable to or better than traditional RT-qPCR tests. Moving forward, SwabSeq can rapidly scale up testing to mitigate devastating spread of novel pathogens.", + "rel_num_authors": 41, + "rel_authors": [ + { + "author_name": "Joshua S. Bloom", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Laila Sathe", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Chetan Munugala", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Eric M. Jones", + "author_inst": "Octant Inc." + }, + { + "author_name": "Molly Gasperini", + "author_inst": "Octant Inc." + }, + { + "author_name": "Nathan B. Lubock", + "author_inst": "Octant Inc." + }, + { + "author_name": "Fauna Yarza", + "author_inst": "Octant Inc." + }, + { + "author_name": "Erin M. Thompson", + "author_inst": "Octant Inc." + }, + { + "author_name": "Kyle M. Kovary", + "author_inst": "Octant Inc." + }, + { + "author_name": "Jimin Park", + "author_inst": "Octant Inc." + }, + { + "author_name": "Dawn Marquette", + "author_inst": "UCLA" + }, + { + "author_name": "Stephania Kay", + "author_inst": "UCLA" + }, + { + "author_name": "Mark Lucas", + "author_inst": "UCLA" + }, + { + "author_name": "TreQuan Love", + "author_inst": "UCLA" + }, + { + "author_name": "A. Sina Booeshaghi", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Oliver F. Brandenberg", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Longhua Guo", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "James Boocock", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Myles Hochman", + "author_inst": "Octant Inc." + }, + { + "author_name": "Scott W. Simpkins", + "author_inst": "Octant Inc." + }, + { + "author_name": "Isabella Lin", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Nathan LaPierre", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Duke Hong", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Yi Zhang", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Gabriel Oland", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Bianca Judy Choe", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Sukantha Chandrasekaran", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Evann E. Hilt", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Manish J. Butte", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Robert Damoiseaux", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Clifford Kravit", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Aaron R. Cooper", + "author_inst": "Octant Inc." + }, + { + "author_name": "Yi Yin", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Lior Pachter", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Omai B. Garner", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Jonathan Flint", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Eleazar Eskin", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Chongyuan Luo", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Sriram Kosuri", + "author_inst": "Octant Inc." + }, + { + "author_name": "Leonid Kruglyak", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Valerie A. Arboleda", + "author_inst": "University of California, Los Angeles" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.04.20168450", "rel_title": "Social Behaviors Associated with a Positive COVID-19 Test Result", @@ -1260680,57 +1264085,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.08.05.237339", - "rel_title": "Evolutionary dynamics of SARS-CoV-2 nucleocapsid protein (N protein) and its consequences", - "rel_date": "2020-08-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.05.237339", - "rel_abs": "The emerging novel coronavirus SARS-CoV-2 has created a global confusing pandemic health crisis that warrants an accurate and detailed characterization of the rapidly evolving viral genome for understanding its epidemiology, pathogenesis and containment. We explored 61,485 sequences of the Nucleocapsid (N) protein, a potent diagnostic and prophylactic target, for identifying the mutations to review their roles in RT-PCR based diagnosis and observe consequent impacts. Compared to the Wuhan reference strain, a total of 1034 unique nucleotide mutations were identified in the mutant strains (49.15%, n=30,221) globally. Of these mutations, 367 occupy primer binding sites including 3-end mismatch to primer-pair of 11 well characterized primer sets. Noteworthy, CDC (USA) recommended N2 primer set contained lower mismatch than the other primer sets. Moreover, 684 amino acid (aa) substitutions located across 317 (75.66% of total aa) unique positions including 82, 21, and 83 of those in RNA binding N-terminal domain (NTD), SR-rich region, and C-terminal dimerization domain (CTD), respectively. Moreover, 11 in-frame deletions were revealed, mostly (n =10) within the highly flexible linker region, and the rest within the NTD region. Furthermore, we predicted the possible consequences of high-frequency mutations ([≥] 20) and deletions on the tertiary structure of the N protein. Remarkably, we observed that high frequency (67.94% of mutated sequences) coevolving mutations (R203K and G204R) destabilized and decreased overall structural flexibility. Despite being proposed as the alternate target to spike protein for vaccine and therapeutics, ongoing nonsynonymous evolution of the N protein may challenge the endeavors, thus need further immunoinformatics analyses. Therefore, continuous monitoring is required for tracing the ongoing evolution of the SARS-CoV-2 N protein in prophylactic and diagnostic interventions.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "M. Shaminur Rahman", - "author_inst": "Dhaka University" - }, - { - "author_name": "M. Rafiul Islam", - "author_inst": "Dhaka University" - }, - { - "author_name": "A. S. M. Rubayet Ul Alam", - "author_inst": "Jashore University of Science and Technology" - }, - { - "author_name": "Israt Islam", - "author_inst": "Dhaka University" - }, - { - "author_name": "M. Nazmul Hoque", - "author_inst": "Dhaka university" - }, - { - "author_name": "Salma Akter", - "author_inst": "Dhaka University" - }, - { - "author_name": "Md. Mizanur Rahaman", - "author_inst": "Dhaka University" - }, - { - "author_name": "Munawar Sultana", - "author_inst": "Dhaka University" - }, - { - "author_name": "M. Anwar Hossain", - "author_inst": "Dhaka University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2020.08.05.237404", "rel_title": "Analysis of single nucleotide polymorphisms between 2019-nCoV genomes and its impact on codon usage", @@ -1261079,6 +1264433,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.08.04.20165928", + "rel_title": "Testing for SARS-CoV-2 in care home staff and residents in English care homes: A service evaluation", + "rel_date": "2020-08-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.04.20165928", + "rel_abs": "BackgroundCOVID-19 has especially affected care home residents.\n\nAimTo evaluate a nurse-led Enhanced Care Home Team (ECHT) enhanced SARS-CoV-2 testing strategy.\n\nDesign and settingService evaluation in care homes in Norfolk UK.\n\nMethodResidents and staff received nose and throat swab tests (7 April to 29 June 2020). Resident test results were linked with symptoms on days 0-14 after test and mortality to 13 July 2020.\n\nResultsResidents (n=518) in 44 homes and staff (n=340) in 10 care homes were tested. SARS-CoV-2 positivity was identified in 103 residents in 14 homes and 49 staff in seven homes. Of 103 SARS-CoV-2+ residents, just 38 had typical symptom(s) at time of test (new cough and/or fever). Amongst 54 residents who were completely asymptomatic when tested, 12 (22%) developed symptoms within 14 days. Compared to SARS-CoV-2 negative residents, SARS-CoV-2+ residents were more likely to exhibit typical symptoms (new cough (n=26, p=0.001); fever (n=24, p=<0.001)) or as generally unwell (n=18, p=0.001). Of 38 resident deaths, 21 (55%) were initially attributed to SARS-CoV-2, all of whom tested SARS-CoV-2+. One death not initially attributed to SARS-CoV-2 also tested positive.\n\nConclusionTesting identified asymptomatic and pre-symptomatic SARS-CoV-2+ residents and staff. Being generally unwell was common amongst symptomatic residents and may indicate SARS-CoV-2 infection in older people in the absence of more typical symptoms. Where a resident appears generally unwell SARS-CoV-2-infection should be suspected. Protocols for testing involved integrated health and social care teams.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Emma Smith", + "author_inst": "NHS North Norfolk Primary Care" + }, + { + "author_name": "Clare F Aldus", + "author_inst": "University of East Anglia" + }, + { + "author_name": "Julii Brainard", + "author_inst": "University of East Anglia" + }, + { + "author_name": "Sharon Dunham", + "author_inst": "NHS North Norfolk Primary Care" + }, + { + "author_name": "Paul R Hunter", + "author_inst": "University of East Anglia" + }, + { + "author_name": "Nicholas Steel", + "author_inst": "University of East Anglia" + }, + { + "author_name": "Paul Everden", + "author_inst": "NHS North Norfolk Primary Care" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.08.05.238386", "rel_title": "Identification of SARS-CoV-2 recombinant genomes", @@ -1262838,137 +1266235,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.31.20165126", - "rel_title": "A longitudinal survey for genome-based identification of SARS-CoV-2 in sewage water in selected lockdown areas of Lahore city, Pakistan; a potential approach for future smart lockdown strategy", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.31.20165126", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections has affected more than 15 million people and, as of 22 July 2019, caused deaths of more than 0.6 million individuals globally. With the excretion of SARS-CoV-2 in the stool of symptomatic and asymptomatic COVID-19 patients, its genome detection in the sewage water can be used as a powerful epidemiological tool to predict the number of positive cases in a population. This study was conducted to detect SARS-CoV-2 genome in sewage water during the lockdown. Sewage samples, from 28 pre-selected sites, were collected on alternate days from 13-25 July, 2020 from two selected areas [Johar Town (n = 05) and Township (n = 23)], where smart lockdown were implemented by the government authorities on 9th July, 2020. Genomic RNA was extracted and the SARS-CoV-2 was detected and quantified using commercially available kit through Real-Time PCR. Out of 28, sixteen samples were positive on day one while 19, 17, 23, 17, 05 and 09 samples were positive on day 3, 5, 7, 9, 11, and 13, respectively. Results revealed a decreased positivity rate and SARS CoV-2 genome copies in sewage towards the end of lockdown however few sampling sites did not follow a clear pattern indicating the complexities in sewage water based surveillance i.e time of sampling etc. Hourly sampling from two sites for 24 hours also revealed the impact of sampling time on detection of SARS-CoV-2 genome in sewage. Results of current study insinuate a possible role of sewage-based COVID-19 surveillance in monitoring and execution of smart lockdowns.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Tahir Yaqub", - "author_inst": "University of Veterinary and Animal Sciences" - }, - { - "author_name": "Muhammad Nawaz", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Muhammad Zubair Shabbir", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Muhammad Asad Ali", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Imran Altaf", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Sohail Raza", - "author_inst": "University of Veterinary and Animal Sciences, Lahore" - }, - { - "author_name": "Muhammad Abu Bakr Shabbir", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Muhammad Adnan Ashraf", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Syed Zahid Aziz", - "author_inst": "Water and Sanitation Agency, Lahore-Pakistan" - }, - { - "author_name": "Sohail Qadir Cheema", - "author_inst": "Water and Sanitation Agency, Lahore-Pakistan" - }, - { - "author_name": "Muhammad Bilal Shah", - "author_inst": "Water and Sanitation Agency, Lahore-Pakistan" - }, - { - "author_name": "Sohail Hassan", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Saira Rafique", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Nageen Sardar", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Adnan Mehmood", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Muhammad Waqar Aziz", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Sehar Fazal", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Nadir Khan", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Muhammad Tahir Khan", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Muhammad Moavia Attique", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Ali Asif", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Muhammad Anwar", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Nabeel Ahmad Awan", - "author_inst": "Specialized Healthcare & Medical Education Department, Punjab, Pakistan" - }, - { - "author_name": "Muhammad Usman Younis", - "author_inst": "Primary and Secondary Healthcare Department, Punjab-Pakistan" - }, - { - "author_name": "Muhammad Ajmal Bhatti", - "author_inst": "Primary and Secondary Healthcare Department, Punjab-Pakistan" - }, - { - "author_name": "Zarfishan Tahir", - "author_inst": "Institute of Public Health, Lahore-Pakistan" - }, - { - "author_name": "Nadia Mukhtar", - "author_inst": "Institute of Public Health, Lahore-Pakistan" - }, - { - "author_name": "Huda Sarwar", - "author_inst": "Institute of Public Health, Lahore-Pakistan" - }, - { - "author_name": "Maaz Sohail Rana", - "author_inst": "Institute of Public Health, Lahore-Pakistan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.31.20165480", "rel_title": "Clinical course and severity outcome indicators among COVID 19 hospitalized patients in relation to comorbidities distribution Mexican cohort", @@ -1263153,6 +1266419,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.01.20166173", + "rel_title": "Comparison of media and standards for SARS-CoV-2 RT-qPCR without prior RNA preparation", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.01.20166173", + "rel_abs": "Since the emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, there have been demands on the testing infrastructure that have strained testing capacity. As a simplification of method, we confirm the efficacy of RNA extraction-free RT-qPCR and saline as an alternative patient sample storage buffer. In addition, amongst potential reagent shortages, it has sometimes been difficult to obtain inactivated viral particles. We have therefore also characterized armored SARS-CoV-2 RNA from Asuragen as an alternative diagnostic standard to ATCC genomic SARS-CoV-2 RNA and heat inactivated virions and provide guidelines for its use in RT-qPCR.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Katherine B Ragan", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Sanchita Bhadra", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Joon H Choi", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Dalton Towers", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Christopher S Sullivan", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Andrew D Ellington", + "author_inst": "University of Texas at Austin" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.31.20166249", "rel_title": "Reconciling epidemiological models with misclassified case-counts for SARS-CoV-2 with seroprevalence surveys: A case study in Delhi, India", @@ -1264376,33 +1267681,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.03.20167692", - "rel_title": "COVID-19 pandemic in Djibouti: epidemiology and the response strategy followed to contain the virus during the first two months, 17 March to 16 May 2020", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.03.20167692", - "rel_abs": "BackgroundFirst cases of COVID-19 were reported from Wuhan, China, in December 2019, and it progressed rapidly. On 30 January, WHO declared the new disease as a PHEIC, then as a Pandemic on 11 March. By mid-March, the virus spread widely; Djibouti was not spared and was hit by the pandemic with the first case detected on 17 March. Djibouti worked with WHO and other partners to develop a preparedness and response plan, and implemented a series of intervention measures. MoH together with its civilian and military partners, closely followed WHO recommended strategy based on four pillars: testing, isolating, early case management, and contact tracing. From 17 March to 16 May, Djibouti performed the highest per capita tests in Africa and isolated, treated and traced the contacts of each positive case, which allowed for a rapid control of the epidemic.\n\nMethodsCOVID-19 data included in this study was collected through MoH Djibouti during the period from 17 March to 16 May 2020.\n\nResultsA total of 1,401 confirmed cases of COVID-19 were included in the study with 4 related deaths (CFR: 0.3%) and an attack rate of 0.15%. Males represented (68.4%) of the cases, with the age group 31-45 years old (34.2%) as the most affected. Djibouti conducted 17,532 tests, and was considered as a champion for COVID-19 testing in Africa with 18.2 tests per 1000 habitant. All positive cases were isolated, treated and had their contacts traced, which led to early and proactive diagnosis of cases and in turn yielded up to 95-98% asymptomatic cases. Recoveries reached 69% of the infected cases with R0 (0.91). The virus was detected in 4 regions in the country, with the highest percentage in the capital (83%).\n\nConclusionDjibouti responded to COVID-19 pandemic following an efficient and effective strategy, using a strong collaboration between civilian and military health assets that increased the response capacities of the country. Partnership, coordination, solidarity, proactivity and commitment were the pillars to confront COVID-19 pandemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Mohamed Elhakim", - "author_inst": "World Health Organization" - }, - { - "author_name": "Saleh Banoita Tourab", - "author_inst": "Ministry of Health Djibouti" - }, - { - "author_name": "Ahmed Zouiten", - "author_inst": "World Health Organization" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.03.20167189", "rel_title": "Evaluating Data-Driven Forecasting Methods for Predicting SARS-CoV2 Cases: Evidence From 173 Countries", @@ -1264543,6 +1267821,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.03.20167361", + "rel_title": "Multisystem inflammatory syndrome in children (MIS-C) temporally associated with SARS-CoV-2 infection: a scoping review of the literature", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.03.20167361", + "rel_abs": "BackgroundWith the rise of the COVID-19 pandemic, a new severe life-threatening inflammatory syndrome has been reported in some pediatric populations. Global attention was shifted towards the syndrome termed multisystem inflammatory syndrome in children (MIS-C), with new case reports flooding in.\n\nObjectivesThe aim of this scoping review is to summarize the existing reports on MIS-C and focus on the demographics, diagnosis, clinical presentation, laboratory investigations, imaging studies, treatment, and patient outcomes.\n\nMethodsWe conducted a systemic search using LitCovid and MEDLINE electronic databases. We screened citations, titles and abstracts, then reviewed potentially relevant articles in full. After data extraction, we reported our final data under subheadings of demographics, diagnosis, clinical presentation, laboratory investigations, imaging studies, treatment, and patient outcomes.\n\nResultsOur search strategy yielded 42 original studies reporting 674 pediatric patients fitting the case definition of MIS-C. The studies included 21 case reports, 16 case series and 5 cohort studies. The most common reported symptom of MIS-C was fever (98%). Gastrointestinal symptoms were common (N=557, 83%). Interleukin-6 (IL-6) levels were measured in 125 patients and was elevated in 94 % (N=117). Echocardiography detected coronary artery lesions in 100 patients. Prophylactic and/or therapeutic heparin was required in 34% (N=227) of patients. The most commonly administered treatment modality targeting MIS-C was intravenous immunoglobulin (IVIG) (N=490). Corticosteroids (N=347) and aspirin (N=112) were also integral parts of the treatment regimens. Biologic therapy was integrated into the treatment regimen for 116 patients. Intensive care unit (ICU) admission was alarming (N=478, 71%). 9 fatalities were recorded due to MIS-C\n\nConclusionsWe believe MIS-C bears pathophysiological resemblance to the well-known Kawasaki disease but with some key differences highlighted. Understanding those differences will aid our management plan for such patients.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Mohmed Ali Sabbour", + "author_inst": "Faculty of Medicine, Ain Shams University" + }, + { + "author_name": "Seif Tarek El-Swaify", + "author_inst": "Faculty of Medicine, Ain Shams University, Cairo, Egypt" + }, + { + "author_name": "Nourhan Farrag", + "author_inst": "Faculty of Medicine, Ain Shams University, Cairo, Egypt" + }, + { + "author_name": "Menna Kamel", + "author_inst": "Faculty of Medicine, Ain Shams University, Cairo, Egypt" + }, + { + "author_name": "Sara H Ali", + "author_inst": "Faculty of Medicine, Ain Shams University, Cairo, Egypt" + }, + { + "author_name": "Abdelrahman Amir", + "author_inst": "Faculty of Medicine, Ain Shams University, Cairo, Egypt" + }, + { + "author_name": "Mazen A Refaat", + "author_inst": "Faculty of Medicine, Ain Shams University, Cairo, Egypt" + }, + { + "author_name": "Menatalla A Dyab", + "author_inst": "Faculty of Medicine, Ain Shams University, Cairo, Egypt" + }, + { + "author_name": "Ashraf Nabhan", + "author_inst": "Department of Obstetrics and Gynecology, Faculty of Medicine, Ain Shams University, Cairo, Egypt and Egyptian Center for Evidence Based Medicine, Cairo, Egypt" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.07.31.20166272", "rel_title": "Sooner than you think: a very early affective reaction to the COVID-19 pandemic and quarantine in Argentina", @@ -1265998,45 +1269327,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.03.20167262", - "rel_title": "Altitude as a protective factor from COVID-19", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.03.20167262", - "rel_abs": "The COVID-19 pandemic had a delayed onset in South America compared to Asia (outside of China), Europe or North America. In spite of the presumed time advantage for the implementation of preventive measures to help contain its spread, the pandemic in that region followed growth rates that paralleled, and currently exceed, those observed several weeks before in Europe. Indeed, in early August 2020, many countries in South and Central America presented among the highest rates in the world of COVID-19 confirmed cases and deaths per million inhabitants. Here, we have taken an ecological approach to describe the current state of the pandemic in Peru and its dynamics. Our analysis supports a protective effect of altitude from COVID-19 incidence and mortality. Further, we provide circumstantial evidence that internal migration through a specific land route is a significant factor progressively overriding the protection from COVID-19 afforded by high altitude. Finally, we show that protection by altitude is independent of poverty indexes and is inversely correlated with the prevalence in the population of risk factors associated with severe COVID-19, including hypertension and hypercholesterolemia. We discuss long-term multisystemic adaptive traits to hypobaric hypoxia as possible mechanisms that may explain the observed protective effect of high altitude from death due to COVID-19.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Timothy M Thomson", - "author_inst": "Institute for Molecular Biology, IBMB-CSIC" - }, - { - "author_name": "Fresia Casas", - "author_inst": "Universidad Peruana Cayetano Heredia" - }, - { - "author_name": "Harold Andre Guerrero", - "author_inst": "Universidad Peruana Cayetano Heredia" - }, - { - "author_name": "R\u00f3mulo Figueroa-Mujica", - "author_inst": "Universidad Peruana Cayetano Heredia" - }, - { - "author_name": "Francisco C Villafuerte", - "author_inst": "Universidad Peruana Cayetano Heredia" - }, - { - "author_name": "Claudia Machicado", - "author_inst": "Universidad Peruana Cayetano Heredia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.03.20167403", "rel_title": "The mental health and experiences of discrimination of LGBTQ+ people during the COVID-19 pandemic: Initial findings from the Queerantine Study", @@ -1266261,6 +1269551,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2020.08.04.20167940", + "rel_title": "SARS-CoV-2 antigens expressed in plants detect antibody responses in COVID-19 patients", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.04.20167940", + "rel_abs": "BackgroundThe SARS-CoV-2 pandemic has swept the world and poses a significant global threat to lives and livelihoods, with over 16 million confirmed cases and at least 650 000 deaths from COVID-19 in the first 7 months of the pandemic. Developing tools to measure seroprevalence and understand protective immunity to SARS-CoV-2 is a priority. We aimed to develop a serological assay using plant-derived recombinant viral proteins, which represent important tools in less-resourced settings.\n\nMethodsWe established an indirect enzyme-linked immunosorbent assay (ELISA) using the S1 and receptor-binding domain (RBD) portions of the spike protein from SARS-CoV-2, expressed in Nicotiana benthamiana. We measured antibody responses in sera from South African patients (n=77) who had tested positive by PCR for SARS-CoV-2. Samples were taken a median of six weeks after the diagnosis, and the majority of participants had mild and moderate COVID-19 disease. In addition, we tested the reactivity of pre-pandemic plasma (n=58) and compared the performance of our in-house ELISA with a commercial assay. We also determined whether our assay could detect SARS-CoV-2-specific IgG and IgA in saliva.\n\nResultsWe demonstrate that SARS-CoV-2-specific immunoglobulins are readily detectable using recombinant plant-derived viral proteins, in patients who tested positive for SARS-CoV-2 by PCR. Reactivity to S1 and RBD was detected in 51 (66%) and 48 (62%) of participants, respectively. Notably, we detected 100% of samples identified as having S1-specific antibodies by a validated, high sensitivity commercial ELISA, and OD values were strongly and significantly correlated between the two assays. For the pre-pandemic plasma, 1/58 (1.7%) of samples were positive, indicating a high specificity for SARS-CoV-2 in our ELISA. SARS-CoV-2-specific IgG correlated significantly with IgA and IgM responses. Endpoint titers of S1- and RBD-specific immunoglobulins ranged from 1:50 to 1:3200. S1-specific IgG and IgA were found in saliva samples from convalescent volunteers.\n\nConclusionsWe demonstrate that recombinant SARS-CoV-2 proteins produced in plants enable robust detection of SARS-CoV-2 humoral responses. This assay can be used for seroepidemiological studies and to measure the strength and durability of antibody responses to SARS-CoV-2 in infected patients in our setting.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Mohau S Makatsa", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Marius B Tincho", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Jerome M Wendoh", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Sherazaan D Ismail", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Rofhiwa Nesamari", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Francisco Pera", + "author_inst": "Cape Bio Pharms" + }, + { + "author_name": "Scott de Beer", + "author_inst": "Cape Bio Pharms" + }, + { + "author_name": "Anura David", + "author_inst": "University of Witwatersrand" + }, + { + "author_name": "Sarika Jugwanth", + "author_inst": "University of Witwatersrand" + }, + { + "author_name": "Maemu P Gededzha", + "author_inst": "University of Witwatersrand" + }, + { + "author_name": "Nakampe Mampeule", + "author_inst": "University of Witwatersrand" + }, + { + "author_name": "Ian Sanne", + "author_inst": "University of Witwatersrand" + }, + { + "author_name": "Wendy Stevens", + "author_inst": "University of Witwatersrand" + }, + { + "author_name": "Lesley Scott", + "author_inst": "University of Witwatersrand" + }, + { + "author_name": "Jonathan Blackburn", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Elizabeth S Mayne", + "author_inst": "University of Witwatersrand" + }, + { + "author_name": "Roanne S Keeton", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Wendy A Burgers", + "author_inst": "University of Cape Town" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2020.08.04.20167932", "rel_title": "Viral cultures for COVID-19 infectivity assessment. Systematic review", @@ -1267843,25 +1271220,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.30.20165035", - "rel_title": "Modified SIR-model applied to covid-19, similarity solutions and projections to further development", - "rel_date": "2020-08-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20165035", - "rel_abs": "The SIR-model is adapted to the covid-19 pandemic through a modification that consists in making the basic reproduction number variable. Independent of it, another reproduction number is introduced, which is defined similarly to the usual net reproduction number. Due to its simple analytic form, it enables a clear interpretation for all values. A further parameter, provisionally called acceleration parameter, is introduced and applied, which enables a more differentiated characterization of the infection number dynamics. By a variable transformation the 3 equations of the modified SIR-model can be reduced to 2. The latter are solved up to ordinary integrations. The solutions are evaluated for current situations, yielding a pretty good match with the data reported. Encouraged by this, a variety of possible future developments is examined, including linear and exponential growth of the infection numbers as well as sub- and super-exponential growth. In particular, the behavior of the two reproduction numbers and the acceleration parameter is studied, which in some cases leads to surprising results. With regard to the number of unreported infections it is shown, that from the solution for a special one solutions for others can be derived by similarity transformations.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Eckhard Rebhan", - "author_inst": "Heinrich Heine Universitaet Duesseldorf" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.02.233510", "rel_title": "Mechanism of duplex unwinding by coronavirus nsp13 helicases", @@ -1268206,6 +1271564,149 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.08.02.233064", + "rel_title": "Functional immune mapping with deep-learning enabled phenomics applied to immunomodulatory and COVID-19 drug discovery", + "rel_date": "2020-08-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.02.233064", + "rel_abs": "Development of accurate disease models and discovery of immune-modulating drugs is challenged by the immune systems highly interconnected and context-dependent nature. Here we apply deep-learning-driven analysis of cellular morphology to develop a scalable \"phenomics\" platform and demonstrate its ability to identify dose-dependent, high-dimensional relationships among and between immunomodulators, toxins, pathogens, genetic perturbations, and small and large molecules at scale. High-throughput screening on this platform demonstrates rapid identification and triage of hits for TGF-{beta}- and TNF--driven phenotypes. We deploy the platform to develop phenotypic models of active SARS-CoV-2 infection and of COVID-19-associated cytokine storm, surfacing compounds with demonstrated clinical benefit and identifying several new candidates for drug repurposing. The presented library of images, deep learning features, and compound screening data from immune profiling and COVID-19 screens serves as a deep resource for immune biology and cellular-model drug discovery with immediate impact on the COVID-19 pandemic.", + "rel_num_authors": 32, + "rel_authors": [ + { + "author_name": "Michael F Cuccarese", + "author_inst": "Recursion" + }, + { + "author_name": "Berton A Earnshaw", + "author_inst": "Recursion" + }, + { + "author_name": "Katie Heiser", + "author_inst": "Recursion" + }, + { + "author_name": "Ben Fogelson", + "author_inst": "Recursion" + }, + { + "author_name": "Chadwick T Davis", + "author_inst": "Recursion" + }, + { + "author_name": "Peter F McLean", + "author_inst": "Recursion" + }, + { + "author_name": "Hannah B Gordon", + "author_inst": "Recursion" + }, + { + "author_name": "Kathleen-Rose Skelly", + "author_inst": "Recursion" + }, + { + "author_name": "Fiona L Weathersby", + "author_inst": "Recursion" + }, + { + "author_name": "Vlad Rodic", + "author_inst": "Recursion" + }, + { + "author_name": "Ian K Quigley", + "author_inst": "Recursion" + }, + { + "author_name": "Elissa D Pastuzyn", + "author_inst": "Recursion" + }, + { + "author_name": "Brandon M Mendivil", + "author_inst": "Recursion" + }, + { + "author_name": "Nathan H Lazar", + "author_inst": "Recursion" + }, + { + "author_name": "Carl A Brooks", + "author_inst": "Recursion" + }, + { + "author_name": "Joseph Carpenter", + "author_inst": "Recursion" + }, + { + "author_name": "Brandon L Probst", + "author_inst": "Recursion" + }, + { + "author_name": "Pamela Jacobson", + "author_inst": "Recursion" + }, + { + "author_name": "Seth W Glazier", + "author_inst": "Recursion" + }, + { + "author_name": "Jes Ford", + "author_inst": "Recursion" + }, + { + "author_name": "James D Jensen", + "author_inst": "Recursion" + }, + { + "author_name": "Nicholas D Campbell", + "author_inst": "Recursion" + }, + { + "author_name": "Michael A Statnick", + "author_inst": "Recursion" + }, + { + "author_name": "Adeline S Low", + "author_inst": "Recursion" + }, + { + "author_name": "Kirk R Thomas", + "author_inst": "Recursion" + }, + { + "author_name": "Anne E Carpenter", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Sharath S Hegde", + "author_inst": "Recursion" + }, + { + "author_name": "Ronald W Alfa", + "author_inst": "Recursion" + }, + { + "author_name": "Mason L Victors", + "author_inst": "Recursion" + }, + { + "author_name": "Imran S Haque", + "author_inst": "Recursion" + }, + { + "author_name": "Yolanda T Chong", + "author_inst": "Recursion" + }, + { + "author_name": "Christopher C Gibson", + "author_inst": "Recursion" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.08.03.234559", "rel_title": "SARS-CoV-2 ORF6 disrupts nucleocytoplasmic transport through interactions with Rae1 and Nup98", @@ -1269861,81 +1273362,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.30.20165068", - "rel_title": "Outpatient screening of health status and lifestyle among post-bariatric patients during the Covid-19 pandemic in Sao Paulo, Brazil.", - "rel_date": "2020-08-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20165068", - "rel_abs": "Background/ObjectivesThis was an out-of-hospital screening of health status and lifestyle during the Covid-19 pandemic in post-operative bariatric patients from Sao Paulo, Brazil, prevented from face-to-face health care.\n\nSubjects/MethodsIn this cross-sectional study, 66 patients were remotely (via phone call) and in-person (by home visit) assessed for health status and lifestyle habits. Results: Mean age was 47.4 years. Patients were obese grade I (30.0%), II (22.0%), and III (30.0%), and 94.2% had above reference waist circumference values. Sixty-four percent displayed high blood pressure, whereas 24% showed CRP levels above normal range. Nineteen percent of patients reported irregular use of nutritional supplementation and 6.0% reported binge eating habits. Thirty-three exhibited symptoms of depression. Mild-to-moderate and moderate-to-severe anxiety symptoms were reported by 27.4% and 11.3% of the patients; 4.5% exhibited suicidal ideation and were referred to a specialist for healthcare. Of relevance, inactive patients (59.6%) had poorer global mental and physical health scores as compared to active peers (both p<0.05). Conclusion: This out-of-hospital screening revealed that the absence of face-to-face health care due to the Covid-19 pandemic is associated with suboptimal status of physical and mental health as well as lifestyle inadequacies among patients who have recently undergone bariatric surgery.\n\nKey pointsO_LIWe performed an out-of-hospital screening in post-operative bariatric patients prevented from face-to-face health care during the Covid-19 pandemic.\nC_LIO_LISixty-five percent displayed high blood pressure, whereas 24% showed C-reactive protein levels above normal range.\nC_LIO_LIAbout one third showed mild to severe symptoms of depression, whereas [~]40% showed mild to severe anxiety symptoms.\nC_LIO_LIInactive patients (59.6%) had poorer global mental and physical health scores as compared to active peers.\nC_LIO_LIThree patients exhibited suicidal ideation and were referred to a specialist for healthcare.\nC_LIO_LIDuring the Covid-19 pandemic, there are a considerable number of post-bariatric patients in need of direct health care.\nC_LI", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Karla Fabiana Goessler", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Carolina Ferreira Nicoletti", - "author_inst": "Univeristy of Sao Paulo" - }, - { - "author_name": "Diego Augusto Nunes Rezende", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Sofia Mendes Sieczkowska", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Gabriel Perri Esteves", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Rafael Genario", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Gersiel Nascimento Oliveira-Junior", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Kamila Meireles", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Ana Jessica Pinto", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Michele Nakahara-Melo", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Roberto Cleva", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Marco Aurelio Santo", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "John Kirwan", - "author_inst": "Pennington Biomedical Research Center" - }, - { - "author_name": "Hamilton Roschel", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Bruno Gualano", - "author_inst": "University of Sao Paulo" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "endocrinology" - }, { "rel_doi": "10.1101/2020.07.30.20165282", "rel_title": "A Compartmental Epidemic Model Incorporating Probable Cases to Model COVID-19 Outbreak in Regions with Limited Testing Capacity", @@ -1270176,6 +1273602,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.07.30.20164368", + "rel_title": "Persistence of anti-SARS-CoV-2 antibodies in non-hospitalized COVID-19 convalescent health care workers", + "rel_date": "2020-08-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20164368", + "rel_abs": "BackgroundCoronavirus disease-19 (COVID-19) is a respiratory illness caused by the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), a novel beta-coronavirus. Although antibody response to SARS-CoV-2 can be detected early during the infection, several outstanding questions remain to be addressed regarding magnitude and persistence of antibody titer against different viral proteins and their correlation with the strength of the immune response, as measured by serum levels of pro-inflammatory mediators.\n\nMethodsAn ELISA assay has been developed by expressing and purifying the recombinant SARS-CoV-2 Spike Receptor Binding Domain (RBD), Soluble Ectodomain (Spike), and full length nucleocapsid protein (N protein). Sera from healthcare workers affected by non-severe COVID-19 were longitudinally collected over four weeks, and compared to sera from patients hospitalized in Intensive Care Units (ICU) and SARS-CoV-2-negative subjects for the presence of IgM, IgG and IgA antibodies as well as soluble pro-inflammatory mediators in the sera.\n\nResultsSpecificity and sensitivity of the ELISA assays were high for anti-RBD IgG and IgA (92-97%) and slightly lower for IgM and the Spike and N proteins (70-85%). The ELISA allowed quantification of IgM, IgG and IgA antibody responses against all the viral antigens tested and showed a correlation between magnitude of the antibody response and disease severity. Non-hospitalized subjects showed lower antibody titers and blood pro-inflammatory cytokine profiles as compared to patients in Intensive Care Units (ICU), irrespective of the antibodies tested. Noteworthy, in non-severe COVID-19 infections, antibody titers against RBD and Spike, but not against the N protein, as well as pro-inflammatory cytokines decreased within a month after viral clearance.\n\nConclusionsRapid decline in antibody titers and in pro-inflammatory cytokines may be a common feature of non-severe SARS-CoV-2 infection, suggesting that antibody-mediated protection against re-infection with SARS-CoV-2 is of short duration. These results suggest caution in use serological testing to estimate the prevalence of SARS-CoV-2 infection in the general population.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Margherita Bruni", + "author_inst": "European Institute of Oncology IRCCS, Department of Experimental Oncology, 20139 Milan, Italy" + }, + { + "author_name": "Valentina Cecatiello", + "author_inst": "European Institute of Oncology IRCCS, Department of Experimental Oncology, 20139 Milan, Italy" + }, + { + "author_name": "Angelica Diaz-Basabe", + "author_inst": "1.European Institute of Oncology IRCCS, Department of Experimental Oncology, 20139 Milan, Italy, 2.University of Milan, Department of Oncology and Hemato-Oncolo" + }, + { + "author_name": "Georgia Lattanzi", + "author_inst": "1European Institute of Oncology IRCCS, Department of Experimental Oncology, 20139 Milan, Italy, 2University of Milan, Department of Oncology and Hemato-Oncology" + }, + { + "author_name": "Erika Mileti", + "author_inst": "European Institute of Oncology IRCCS, Department of Experimental Oncology, 20139 Milan, Italy" + }, + { + "author_name": "Silvia Monzani", + "author_inst": "European Institute of Oncology IRCCS, Department of Experimental Oncology, 20139 Milan, Italy" + }, + { + "author_name": "Laura Pirovano", + "author_inst": "European Institute of Oncology IRCCS, Department of Experimental Oncology, 20139 Milan, Italy" + }, + { + "author_name": "Francesca Rizzelli", + "author_inst": "European Institute of Oncology IRCCS, Department of Experimental Oncology, 20139 Milan, Italy" + }, + { + "author_name": "Clara Visintin", + "author_inst": "European Institute of Oncology IRCCS, Department of Experimental Oncology, 20139 Milan, Italy" + }, + { + "author_name": "Giuseppina Bonizzi", + "author_inst": "European Institute of Oncology IRCCS, 20139 Milan, Italy" + }, + { + "author_name": "Marco Giani", + "author_inst": "Department of Medicine and Surgery, University of Milan-Bicocca, 20126 Milan, Italy" + }, + { + "author_name": "Marialuisa Lavitrano", + "author_inst": "Department of Medicine and Surgery, University of Milan-Bicocca, 20126 Milan, Italy" + }, + { + "author_name": "Silvia Faravelli", + "author_inst": "The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy" + }, + { + "author_name": "Federico Forneris", + "author_inst": "The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy" + }, + { + "author_name": "Flavio Caprioli", + "author_inst": "1. Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, 20135 Milan, Italy, 2. Department of Pathophysiology and Tran" + }, + { + "author_name": "Pier Giuseppe Pelicci", + "author_inst": "1European Institute of Oncology IRCCS, Department of Experimental Oncology, 20139 Milan, Italy 2University of Milan, Department of Oncology and Hemato-Oncology," + }, + { + "author_name": "Gioacchino Natoli", + "author_inst": "European Institute of Oncology IRCCS, Department of Experimental Oncology, 20139 Milan, Italy" + }, + { + "author_name": "Sebastiano Pasqualato", + "author_inst": "European Institute of Oncology IRCCS, Department of Experimental Oncology, 20139 Milan, Italy" + }, + { + "author_name": "Marina Mapelli", + "author_inst": "European Institute of Oncology IRCCS, Department of Experimental Oncology, 20139 Milan, Italy" + }, + { + "author_name": "Federica Facciotti", + "author_inst": "European Institute of Oncology IRCCS, Department of Experimental Oncology, 20139 Milan, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.29.20164590", "rel_title": "Household transmission of SARS-CoV-2: a systematic review and meta-analysis of secondary attack rate", @@ -1271723,65 +1275244,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.30.20164327", - "rel_title": "Self-rated smell ability enables highly specific predictors of COVID-19 status: a case control study in Israel", - "rel_date": "2020-08-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20164327", - "rel_abs": "BackgroundClinical diagnosis of COVID-19 poses an enormous challenge to early detection and prevention of COVID-19, which is of crucial importance for pandemic containment. Cases of COVID-19 may be hard to distinguish clinically from other acute viral diseases, resulting in an overwhelming load of laboratory screening. Sudden onset of taste and smell loss emerge as hallmark of COVID-19. The optimal ways for including these symptoms in the screening of suspected COVID-19 patients should now be established.\n\nMethodsWe performed a case-control study on patients that were PCR-tested for COVID-19 (112 positive and 112 negative participants), recruited during the first wave (March 2020 - May 2020) of COVID-19 pandemic in Israel. Patients were interviewed by phone regarding their symptoms and medical history and were asked to rate their olfactory and gustatory ability before and during their illness on a 1-10 scale. Prevalence and degrees of symptoms were calculated, and odds ratios were estimated. Symptoms-based logistic-regression classifiers were constructed and evaluated on a hold-out set.\n\nResultsChanges in smell and taste occurred in 68% (95% CI 60%-76%) and 72% (64%-80%), of positive patients, with 24 (11-53 range) and 12 (6-23) respective odds ratios. The ability to smell was decreased by 0.5{+/-}1.5 in negatives, and by 4.5{+/-}3.6 in positives, and to taste by 0.4{+/-}1.5 and 4.9{+/-}3.8, respectively (mean {+/-} SD). A penalized logistic regression classifier based on 5 symptoms (degree of smell change, muscle ache, lack of appetite, fever, and a negatively contributing sore throat), has 66% sensitivity, 97% specificity and an area under the ROC curve of 0.83 (AUC) on a hold-out set. A classifier based on degree of smell change only is almost as good, with 66% sensitivity, 97% specificity and 0.81 AUC. Under the assumption of 8% positives among those tested, the predictive positive value (PPV) of this classifier is 0.68 and negative predictive value (NPV) is 0.97.\n\nConclusionsSelf-reported quantitative olfactory changes, either alone or combined with other symptoms, provide a specific and powerful tool for clinical diagnosis of COVID-19. The applicability of this tool for prioritizing COVID-19 laboratory testing is facilitated by a simple calculator presented here.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Noam Karni", - "author_inst": "Department of Medicine, Hadassah University Hospital, Mt. Scopus Campus, Jerusalem, Israel" - }, - { - "author_name": "Hadar Klein", - "author_inst": "The Institute of Biochemistry, Food and Nutrition, The Hebrew University, Rehovot, Israel" - }, - { - "author_name": "Kim Asseo", - "author_inst": "The Institute of Biochemistry, Food and Nutrition, The Hebrew University, Rehovot, Israel" - }, - { - "author_name": "Yuval Benjamini", - "author_inst": "Department of Statistics, The Hebrew University, Mt. Scopus Campus, Jerusalem, Israel" - }, - { - "author_name": "Sarah Israel", - "author_inst": "Department of Medicine, Hadassah University Hospital, Mt. Scopus Campus, Jerusalem, Israel" - }, - { - "author_name": "Musa Nimri", - "author_inst": "Department of Medicine, Hadassah University Hospital, Mt. Scopus Campus, Jerusalem, Israel" - }, - { - "author_name": "Keren Olstein", - "author_inst": "Department of Clinical Microbiology and Infectious Diseases Hadassah-Hebrew University medical center" - }, - { - "author_name": "Ran Nir-Paz", - "author_inst": "Department of Clinical Microbiology and Infectious Diseases Hadassah-Hebrew University medical center" - }, - { - "author_name": "Alon Hershko", - "author_inst": "Department of Medicine, Hadassah University Hospital, Mt. Scopus Campus, Jerusalem, Israel" - }, - { - "author_name": "Mordechai Muszkat", - "author_inst": "Department of Medicine, Hadassah University Hospital, Mt. Scopus Campus, Jerusalem, Israel" - }, - { - "author_name": "Masha Y Niv", - "author_inst": "The Institute of Biochemistry, Food and Nutrition, The Hebrew University, Rehovot, Israel" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.30.20165050", "rel_title": "Quantification of the association between predisposing health conditions, demographic, and behavioural factors with hospitalisation, intensive care unit admission, and death from COVID-19: a systematic review and meta-analysis", @@ -1271914,6 +1275376,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.30.20165043", + "rel_title": "A prospective study to identify rates of SARS-CoV-2 virus in the peritoneum and lower genital tract of patients having surgery", + "rel_date": "2020-08-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20165043", + "rel_abs": "IntroductionThe risks to surgeons of carrying out aerosol generating procedures during the COVID pandemic are unknown. To start to define these risks, in a systematic manner, we investigated the presence of SARS-CoV-2 virus in the abdominal fluid and lower genital tract of patients undergoing surgery.\n\nMethodsWe carried out a prospective cross sectional observational study of 113 patients undergoing abdominal surgery or instrumentation of the lower genital tract. We took COVID swabs from the peritoneal cavity and from the vagina from all eligible patients. Results were stratified by pre operative COVID status.\n\nResultsIn patients who were presumed COVID negative at the time of surgery SARS-CoV-2 virus RNA was detected in 0/102 peritoneal samples and 0/98 vaginal samples. Peritoneal and vaginal swabs were also negative in one patient who had a positive nasopharyngeal swab immediately prior to surgery.\n\nConclusionsThe presence of SARS-CoV-2 RNA in the abdominal fluid or lower genital tract of presumed negative patients is nil or extremely low. These data will inform surgeons of the risks of restarting laparoscopic surgery at a time when COVID19 is endemic in the population.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Dominique Jones", + "author_inst": "Manchester Foundation Trust" + }, + { + "author_name": "David Faluyi", + "author_inst": "Manchester Foundation Trust" + }, + { + "author_name": "Sarah Hamilton", + "author_inst": "Manchester Foundation Trust" + }, + { + "author_name": "Nicholas Stylianides", + "author_inst": "Manchester Foundation Trust" + }, + { + "author_name": "Kenneth Ma", + "author_inst": "Manchester Foundation Trust" + }, + { + "author_name": "Sarah Duff", + "author_inst": "Manchester Foundation Trust" + }, + { + "author_name": "Nicholas Machin", + "author_inst": "Manchester Foundation Trust" + }, + { + "author_name": "Richard Edmondson", + "author_inst": "University of Manchester" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "surgery" + }, { "rel_doi": "10.1101/2020.07.30.20165084", "rel_title": "The relative infectiousness of asymptomatic SARS-CoV-2 infected persons compared with symptomatic individuals: A rapid scoping review.", @@ -1273261,109 +1276770,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.07.29.20164285", - "rel_title": "Disease severity dictates SARS-CoV-2-specific neutralizing antibody responses in COVID-19", - "rel_date": "2020-07-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.29.20164285", - "rel_abs": "COVID-19 patients exhibit differential disease severity after SARS-CoV-2 infection. It is currently unknown as to the correlation between the magnitude of neutralizing antibody (NAb) responses and the disease severity in COVID-19 patients. In a cohort of 59 recovered patients with disease severity including severe, moderate, mild and asymptomatic, we observed the positive correlation between serum neutralizing capacity and disease severity, in particular, the highest NAb capacity in sera from the patients with severe disease, while a lack of ability of asymptomatic patients to mount competent NAbs. Furthermore, the compositions of NAb subtypes were also different between recovered patients with severe symptoms and with mild-to-moderate symptoms. These results reveal the tremendous heterogeneity of SARS-CoV-2-specific NAb responses and their correlations to disease severity, highlighting the needs of future vaccination in COVID-19 patients recovered from asymptomatic or mild illness.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Xiangyu Chen", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Zhiwei Pan", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Shuai Yue", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Fei Yu", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Junsong Zhang", - "author_inst": "Guangdong Academy of Medical Sciences" - }, - { - "author_name": "Yang Yang", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Ren Li", - "author_inst": "Chinese Academy of Agricultural Sciences" - }, - { - "author_name": "Bingfeng Liu", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Xiaofan Yang", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Leiqiong Gao", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Zhirong Li", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Yao Lin", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Qizhao Huang", - "author_inst": "The General Hospital of Western Theater Command" - }, - { - "author_name": "Lifan Xu", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Jianfang Tang", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Li Hu", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Jing Zhao", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Pinghuang Liu", - "author_inst": "China Agricultural University" - }, - { - "author_name": "Guozhong Zhang", - "author_inst": "China Agricultural University" - }, - { - "author_name": "Yaokai Chen", - "author_inst": "Chongqing Public Health Medical Center" - }, - { - "author_name": "Kai Deng", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Lilin Ye", - "author_inst": "Third Military Medical University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.29.20164293", "rel_title": "Persistent fatigue following SARS-CoV-2 infection is common and independent of severity of initial infection", @@ -1273604,6 +1277010,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dentistry and oral medicine" }, + { + "rel_doi": "10.1101/2020.07.29.20164269", + "rel_title": "The potential health and economic impact of dexamethasone treatment for patients with COVID-19", + "rel_date": "2020-07-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.29.20164269", + "rel_abs": "Dexamethasone has been shown to reduce mortality in hospitalised COVID-19 patients needing oxygen and ventilation by 18% and 36%, respectively. Here, we estimate the potential number of lives saved and life years gained if this treatment would be rolled out in the UK and globally, as well as its cost-effectiveness of implementing this intervention. We estimate that, for the UK, approximately 12,000 [4,250 - 27,000] lives could be saved by January 2021. Assuming that dexamethasone has a similar effect size in settings where access to oxygen therapies is limited, this would translate into approximately 650,000 [240,000 - 1,400,000] lives saved globally. If dexamethasone acts differently in these settings, the impact could be less than half of this value. To estimate the full potential of dexamethasone in the global fight against COVID-19, it is essential to perform clinical research in settings with limited access to oxygen and/or ventilators, e.g. in low and middle-income countries.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "RICARDO AGUAS", + "author_inst": "University of Oxford" + }, + { + "author_name": "Adam Mahdi", + "author_inst": "University of Oxford" + }, + { + "author_name": "RIMA SHRETTA", + "author_inst": "University of Oxford" + }, + { + "author_name": "Peter Horby", + "author_inst": "University of Oxford" + }, + { + "author_name": "Martin Landray", + "author_inst": "University of Oxford" + }, + { + "author_name": "Lisa J White", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.28.20163931", "rel_title": "Disparities in Case Frequency and Mortality of Coronavirus Disease 2019 (COVID-19) Among Various States in the United States", @@ -1274867,65 +1278312,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.07.24.20160101", - "rel_title": "Red blood cells injuries and hypersegmented neutrophils in COVID-19 peripheral blood film", - "rel_date": "2020-07-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.24.20160101", - "rel_abs": "In the current investigation, peripheral blood films of 15 COVID-19 patients (44.78{+/-}16.55 years), proven by computed tomographic imaging and RT-PCR for coronavirus SARS-CoV-2, were analyzed at the moment of hospital admission. Blood tests showed raised inflammatory markers (C-reactive protein 58.2{+/-}61.2 mg/L) with normal values for hemoglobin (126.2{+/-}2.6 g/L), WBC (6.8{+/-}18.74 109/L) RBC (4.55{+/-}0.99 1012/L) platelets (262.4{+/-}141.8, 109/L) MCV (79.84{+/-}8.2 fL) MCH (28{+/-}3.31 pg) and MCHC (350.3{+/-}1.15 g/L). The results revealed the presence of hypersegmented neutrophils in 66.66%% of the patients. The percentages of neutrophils with 4 and 5 lobes were 46.25 {+/-} 4.83% and 31.5 {+/-} 14.84%, respectively. Three major red blood cells morphological alteration were observed: (1) erythrocytes in \"rouleaux\" formation represented by linear erythrocytes aggregation, (2) spherocytes with the disappearance of the usual biconcave disk, and (3) echinocytes showing spiky projections. Apparent reorganization of hemoglobin is found in the majority of the analyzed erythrocytes. Rouleaux formation is observed in 33.33% of patients and spherocytes and echinocytes are present at variable levels in the all analyzed patients. The current results revealed erythrocytes injuries in COVID-19 peripheral blood, in association with hypersegmented neutrophils, alterations that could be involved in the respiratory syndrome.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Nordine Lakhdari", - "author_inst": "Department of Hematology, University Hospital Center, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Boualem Tabet", - "author_inst": "Department of Hematology, University Hospital Center, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Lila Boudraham", - "author_inst": "Department of Internal Medicine, University Hospital Center, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Malha Laoussati", - "author_inst": "Department of Internal Medicine, University Hospital Center, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Sofiane Aissanou", - "author_inst": "AME Laboratory, Faculty of Nature and Life Sciences, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Lamia Beddou", - "author_inst": "AME Laboratory, Faculty of Nature and Life Sciences, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Sihem Bensalem", - "author_inst": "AME Laboratory, Faculty of Nature and Life Sciences, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Yuva Bellik", - "author_inst": "AME Laboratory, Faculty of Nature and Life Sciences, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Lamine Bournine", - "author_inst": "AME Laboratory, Faculty of Nature and Life Sciences, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Sofiane Fatmi", - "author_inst": "AME Laboratory, Faculty of Nature and Life Sciences, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Mokrane Iguer-Ouada", - "author_inst": "AME Laboratory, Faculty of Nature and Life Sciences, Abderrahmane Mira University 06000 Bejaia, Algeria." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2020.07.29.20159442", "rel_title": "Early Clinical Factors Predicting the Development of Critical Disease in Japanese Patients with COVID-19: A Single-Center Retrospective, Observational Study", @@ -1275186,6 +1278572,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.28.20163626", + "rel_title": "Clinical validation of innovative, low cost, kit-free, RNA processing protocol for RT-PCR based COVID-19 testing.", + "rel_date": "2020-07-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.28.20163626", + "rel_abs": "The current gold-standard molecular diagnosis for COVID-19 is based on a multi-step assay involving RNA-extraction and RT-PCR analysis for the detection of SARS-CoV-2. RNA-extraction step has been a major rate-limiting step in implementing high-throughput screening for COVID-19 during this pandemic. Moreover, clinical laboratories are facing several challenges that include cost, reagents, instrumentation, turn-around time, trained personnel, and supply-chain constraints to efficiently implement and sustain testing. Cognizant of these limitations, we evaluated the extraction-free methods described in the literature and have developed an innovative, simplified and easy protocol employing limited reagents to extract RNA for subsequent RT-PCR analysis. Nasopharyngeal-swab samples were subjected to the following individual conditions: 65{degrees}C for 15 minutes; 80{degrees}C for 5 minutes; 90{degrees}C for 5 minutes or 80{degrees}C for 1 minute, and processed for direct RT-PCR. These groups were also compared with a supplemental protocol adding isopropanol-ethanol-water elution steps followed by RT-PCR assay. The direct RT-PCR assay did not detect SARS-CoV-2 within the various temperature incubation only groups, whereas, the 90{degrees}C for 5 minutes-isopropanol-ethanol-water method was found to be comparable to the FDA-EUA method. Evaluation of the performance metrics for 100 clinical samples demonstrated a sensitivity of 94.2% and a specificity of 100%. The limit of detection was ascertained to be [~]40 copies/ml by absolute-quantification. The protocol presented for this assay employs limited reagents and yields results with high sensitivity. Additionally, it presents a simplified methodology that would be easier to implement in laboratories in limited resource countries in order to meet the high current COVID-19 testing needs.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Nikhil Shri Sahajpal", + "author_inst": "Augusta University" + }, + { + "author_name": "Ashis K Mondal", + "author_inst": "Augusta University" + }, + { + "author_name": "Allan Njau", + "author_inst": "Aga Khan University Hospital" + }, + { + "author_name": "Sudha Ananth", + "author_inst": "Augusta University" + }, + { + "author_name": "Arvind Kothandaraman", + "author_inst": "PerkinElmer Inc." + }, + { + "author_name": "Madhuri Hegde", + "author_inst": "PerkinElmer Inc." + }, + { + "author_name": "Alka Chaubey", + "author_inst": "PerkinElmer" + }, + { + "author_name": "Sandeep Padala", + "author_inst": "Augusta University" + }, + { + "author_name": "Vamsi Kota", + "author_inst": "Augusta University" + }, + { + "author_name": "Kevin Caspary", + "author_inst": "Augusta University" + }, + { + "author_name": "Stephen Mark Tompkins", + "author_inst": "University of Georgia" + }, + { + "author_name": "Ted M. Ross", + "author_inst": "University of Georgia" + }, + { + "author_name": "Amyn M Rojiani", + "author_inst": "Augusta University" + }, + { + "author_name": "Ravindra Kolhe", + "author_inst": "Augusta University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.07.26.20157040", "rel_title": "Minimizing Population Health Loss in Times of Scarce Surgical Capacity", @@ -1276597,101 +1280054,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.26.20162248", - "rel_title": "ACE2 Expression is elevated in Airway Epithelial Cells from aged and male donors but reduced in asthma", - "rel_date": "2020-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.26.20162248", - "rel_abs": "RationaleCOVID-19 is complicated by acute lung injury, and death in some individuals. It is caused by SARS-CoV-2 that requires the ACE2 receptor and serine proteases to enter airway epithelial cells (AECs).\n\nObjectiveTo determine what factors are associated with ACE2 expression particularly in patients with asthma and chronic obstructive pulmonary disease (COPD).\n\nMethodsWe obtained upper and lower AECs from 145 people from two independent cohorts, aged 2-89, Newcastle (n=115), and from Perth (n= 30) Australia. The Newcastle cohort was enriched with people with asthma (n=37) and COPD (n=38). Gene expression for ACE2 and other genes potentially associated with SARS-CoV-2 cell entry were assessed by quantitative PCR, protein expression was confirmed with immunohistochemistry on endobronchial biopsies and cultured AECs.\n\nResultsIncreased gene expression of ACE2 was associated with older age (p=0.02) and male sex (p=0.03), but not pack-years smoked. When we compared gene expression between adults with asthma, COPD and healthy controls, mean ACE2 expression was lower in asthma (p=0.01). Gene expression of furin, a protease that facilitates viral endocytosis, was also lower in asthma (p=0.02), while ADAM-17, a disintegrin that cleaves ACE2 from the surface was increased (p=0.02). ACE2 protein levels were lower in endobronchial biopsies from asthma patients.\n\nConclusionsIncreased ACE2 expression occurs in older people and males. Asthma patients have reduced expression. Altered ACE2 expression in the lower airway may be an important factor in virus tropism and may in part explain susceptibility factors and why asthma patients are not over-represented in those with COVID-19 complications.\n\nImpactACE2 is the primary receptor for SARS-COV-2. We demonstrate that lower airway expression of ACE2 is increased in older adults and males. We also find that lower ACE2 expression in epithelial cells occurs in people with asthma and is associated with reduced Furin expression and increased ADAM-17 expression. This may explain at least in part the relative sparing of people with asthma from severe COVID-19 disease.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Peter Wark", - "author_inst": "University of Newcastle" - }, - { - "author_name": "Prabuddha Pathinyake", - "author_inst": "Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and School of Medicine and Public Health, University of Newcastle, Newcastle, New " - }, - { - "author_name": "Gerard Kaiko", - "author_inst": "Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle" - }, - { - "author_name": "Kristy Nichol", - "author_inst": "Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and School of Medicine and Public Health, University of Newcastle, Newcastle, New " - }, - { - "author_name": "Ayesha Ali", - "author_inst": "Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle" - }, - { - "author_name": "Ling Chen", - "author_inst": "Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle" - }, - { - "author_name": "Erika Suntanto", - "author_inst": "Telethon Kids Institute, University of Western Australia, Western Australia, Australia" - }, - { - "author_name": "Luke Garrat", - "author_inst": "Telethon Kids Institute, University of Western Australia, Western Australia, Australia" - }, - { - "author_name": "Sukhwinder S Sohal", - "author_inst": "Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, " - }, - { - "author_name": "Wenying Lu", - "author_inst": "Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, " - }, - { - "author_name": "Matthew Eapen", - "author_inst": "Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, " - }, - { - "author_name": "Christopher Oldmeadow", - "author_inst": "Hunter Medical Research Institute, Newcastle, New South Wales, Australia" - }, - { - "author_name": "Nathan Bartlett", - "author_inst": "Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle" - }, - { - "author_name": "Andrew Reid", - "author_inst": "Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle" - }, - { - "author_name": "Punnam Veerati", - "author_inst": "Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle" - }, - { - "author_name": "Alan Hsu", - "author_inst": "Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and School of Medicine and Public Health, University of Newcastle, Newcastle, New " - }, - { - "author_name": "Thomas Iosifides", - "author_inst": "Telethon Kids Institute, University of Western Australia, Western Australia, Australia" - }, - { - "author_name": "Stephen Stick", - "author_inst": "Telethon Kids Institute, University of Western Australia, Western Australia, Australia" - }, - { - "author_name": "Philip M Hansbro", - "author_inst": "Centre for Inflammation, Centenary Institute, and Faculty of Science, University of Technology Sydney, Sydney, New South Wales, Australia" - }, - { - "author_name": "Anthony Kicic", - "author_inst": "Telethon Kids Institute, University of Western Australia, Western Australia, Australia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.07.27.20162743", "rel_title": "How much reserve capacity is justifiable for hospital pandemic preparedness? A cost-effectiveness analysis for COVID-19 in Germany", @@ -1276908,6 +1280270,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.26.20162255", + "rel_title": "Magnetic bead-based ELISA allow inexpensive, rapid and quantitative detection of human antibodies against SARS-CoV-2", + "rel_date": "2020-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.26.20162255", + "rel_abs": "Here we describe a novel immunogenic method to detect COVID-19. The method is a chromogenic magnetic bead-based ELISA which allows inexpensive and quantitative detection of human IgG or IgM antibodies against SARS-CoV-2 in serum or whole blood samples in just 12 minutes. As a proof of concept, we compared the performance of our new method to classical ELISA. Person correlation between optical densities obtained using the two methods was 0.98, the color intensity observed in the novel method correlated with antibody titers determined by classical ELISA. The novel magnetic bead-based ELISA correctly classified all 6 positive COVID-19 samples tested and showed 100% specificity as judged by the analysis of a cohort of 26 negative samples. The magnetic bead-based ELISA performed better than classic ELISA to discriminate COVID-19 positive serum with low antibody titer. The chromogenic magnetic bead-based ELISA method described here can be applied to both point of care and high throughput analysis. The method is readily adaptable to be used with other protein and peptide-based antigens.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Luciano F Huergo", + "author_inst": "UFPR" + }, + { + "author_name": "Marcelo S Conzentino", + "author_inst": "UFPR" + }, + { + "author_name": "Edileusa C M Gerhardt", + "author_inst": "UFPR" + }, + { + "author_name": "Adrian R.S. Santos", + "author_inst": "UFPR" + }, + { + "author_name": "Fabio de Oliveira Pedrosa", + "author_inst": "Universidade Federal do Parana Setor de Ciencias Biologicas" + }, + { + "author_name": "Emanuel M Souza", + "author_inst": "UFPR" + }, + { + "author_name": "Meri B Nogueira", + "author_inst": "UFPR" + }, + { + "author_name": "Karl Forchhammer", + "author_inst": "Interfaculty Institute of Mikrobiologie and Infection Medicine" + }, + { + "author_name": "Fabiane G.M Rego", + "author_inst": "UFPR" + }, + { + "author_name": "Sonia M Raboni", + "author_inst": "UFPR" + }, + { + "author_name": "Rodrigo A Reis", + "author_inst": "UFPR" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.26.20159756", "rel_title": "Efficacy and tolerability of bevacizumab in patients with severe Covid -19", @@ -1278399,89 +1281820,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.28.20162941", - "rel_title": "Sensitive detection of SARS-CoV-2 seroconversion by flow cytometry reveals the presence of nucleoprotein-reactive antibodies in Covid-19-naive individuals", - "rel_date": "2020-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.28.20162941", - "rel_abs": "There is an ongoing need of developing sensitive and specific methods for the determination of SARS-CoV-2 seroconversion. For this purpose, we have developed a multiplexed flow cytometric bead array (C19BA) that allows the identification of IgG and IgM antibodies against three immunogenic proteins simultaneously: the spike receptor-binding domain (RBD), the spike protein subunit 1 (S1) and the nucleoprotein (N). Using different cohorts of samples collected before and after the pandemic, we show that this assay is more sensitive than ELISAs performed in our laboratory. The combination of three viral antigens allows for the interrogation of full seroconversion. Importantly, we have detected N-reactive antibodies in COVID-19-negative individuals. Here we present an immunoassay that can be easily implemented and has superior potential to detect low antibody titers compared to current gold standard serology methods.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Leire Egia-Mendikute", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Alexandre Bosch", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Endika Prieto-Fernandez", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "So Young Lee", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Borja Jimenez-Lasheras", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Ana Garcia del Rio", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Asier Antonana-Vildosola", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Chiara Bruzzone", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Maider Bizkarguenaga", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Nieves Embade", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Ruben Gil-Redondo", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Maria Luz Martinez-Chantar", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Marcos Lopez-Hoyos", - "author_inst": "Hospital Universitario Marques de Valdecilla-IDIVAL" - }, - { - "author_name": "Nicola G A Abrescia", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Jose M. Mato", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Oscar Millet", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Asis Palazon", - "author_inst": "CIC biogune" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2020.07.28.20163592", "rel_title": "Evaluation of a SARS-CoV-2 surrogate virus neutralization test for detection of antibody in human, canine, cat and hamster sera", @@ -1278682,6 +1282020,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.27.20163121", + "rel_title": "Impact Assessment of Full and Partial Stay-at-Home Orders, Face Mask Usage, and Contact Tracing: An Agent-Based Simulation Study of COVID-19 for an Urban Region", + "rel_date": "2020-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.27.20163121", + "rel_abs": "PurposeVarious social intervention strategies to mitigate COVID-19 are examined using a comprehensive agent-based simulation model. A case study is conducted using a large urban region, Miami-Dade County, Florida, USA. Results are intended to serve as a planning guide for public health decision makers.\n\nMethodsThe simulation model mimics daily social mixing behavior of the susceptible and infected generating the spread. Data representing demographics of the region, virus epidemiology, and social interventions shapes model behavior. Results include daily values of infected, reported, hospitalized, and dead.\n\nResultsStudy results show that stay-at-home order is quite effective in flattening and then reversing the case growth curve subsiding the pandemic with only 5.8% of the population infected. Whereas, following Floridas current Phase II reopening plan could end the pandemic via herd immunity with 75% people infected. Use of surgical variety face masks reduced infected by 20%. A further reduction of 66% was achieved through contact tracing.\n\nConclusionsFor Miami-Dade County, a strategy comprising mandatory use of face masks and aggressive contact tracing to identify 50% of the asymptomatic and pre-symptomatic, if adopted now, can potentially steer the COVID-19 pandemic to subside within next 3 months with approximately one fifth of the population infected.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Hanisha Tatapudi", + "author_inst": "Industrial and Management Systems Engineering, University of South Florida" + }, + { + "author_name": "Rachita Das", + "author_inst": "Miller School of Medicine, University of Miami, Miami, Florida" + }, + { + "author_name": "Tapas K. Das", + "author_inst": "Industrial and Management Systems Engineering, University of South Florida" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.27.20158105", "rel_title": "Comorbidities associated with regional variations in COVID-19 mortality revealed by population-level analysis", @@ -1280141,41 +1283506,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.25.20162156", - "rel_title": "30-day mortality and morbidity in COVID-19 versus influenza: A populationbased study", - "rel_date": "2020-07-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.25.20162156", - "rel_abs": "BackgroundAs of July 2020, COVID-19 has caused 500,000 deaths worldwide. However, large-scale studies of COVID-19 mortality and new-onset comorbidity compared to influenza and individuals tested negative for COVID-19 are lacking. We aimed to investigate COVID-19 30-day mortality and new-onset comorbidity compared to individuals with negative COVID-19 test results and individuals tested for influenza.\n\nMethods and findingsThis population-based cohort study utilized electronic health records covering roughly half (n=2,647,229) of Denmarks population, with nationwide linkage of microbiology test results and death records. All individuals [≥]18 years tested for COVID-19 and individuals tested for influenza were followed from November 1, 2017 to June 30, 2020. The main outcome was 30-day mortality after a test for either COVID-19 or influenza. Secondary outcomes were major comorbidity diagnoses 30-days after the test for either COVID-19 or influenza. In total, 224,639 individuals were tested for COVID-19. Among inpatients positive for COVID-19, 356 of 1657 (21%) died within 30 days, which was a 3.0 to 3.1-fold increased 30-day mortality rate, when compared to influenza and COVID-19-negative inpatients (all p<0.001). For outpatients, 128 of 6,263 (2%) COVID-19-positive patients died within 30 days, which was a 5.5 to 6.9-fold increased mortality rate compared to influenza and COVID-19-negative patients, respectively (all p<0.001). Compared to hospitalized patients with influenza, new-onset ischemic stroke, diabetes and nephropathy occurred more frequently in inpatients with COVID-19 (all p<0.05).\n\nConclusionsIn this population-based study comparing COVID-19 with influenza, COVID-19 was associated with increased rates of major systemic and vascular comorbidity and substantially higher mortality, which is likely even higher than the stated 3.0 to 5.5-fold increase owing to more extensive testing for COVID-19.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Vardan Nersesjan", - "author_inst": "Rigshospitalet" - }, - { - "author_name": "Moshgan Amiri", - "author_inst": "Rigshospitalet" - }, - { - "author_name": "Hanne Krarup Christensen", - "author_inst": "Bispebjerg Hospital" - }, - { - "author_name": "Michael E. Benros", - "author_inst": "Copenhagen Research Centre for Mental Health - CORE, Mental Health Centre Copenhagen, Copenhagen University Hospital, Hellerup, Denmark" - }, - { - "author_name": "Daniel Kondziella", - "author_inst": "Rigshospitalet, Copenhagen University Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.25.20162073", "rel_title": "Effectiveness and Safety of Chloroquine or Hydroxychloroquine as a mono-therapy or in combination with Azithromycin in the treatment of COVID-19 patients: Systematic Review and Meta-Analysis", @@ -1280356,6 +1283686,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.25.20161992", + "rel_title": "Modeling Control, Lockdown & Exit Strategies for COVID-19 Pandemic in India", + "rel_date": "2020-07-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.25.20161992", + "rel_abs": "COVID-19-a viral infectious disease-has quickly emerged as a global pandemic infecting millions of people with a significant number of deaths across the globe. The symptoms of this disease vary widely. Depending on the symptoms an infected person is broadly classified into two categories namely, asymptomatic and symptomatic. Asymptomatic individuals display mild or no symptoms but continue to transmit the infection to other-wise healthy individuals. This particular aspect of asymptomatic infection poses a major obstacle in managing and controlling the transmission of the infectious disease. In this paper, we attempt to mathematically model the spread of COVID-19 in India under various intervention strategies. We consider SEIR type epidemiological models, incorporated with India specific social contact matrix representing contact structures among different age groups of the population. Impact of various factors such as presence of asymptotic individuals, lockdown strategies, social distancing practices, quarantine, and hospitalization on the disease transmission is extensively studied. Numerical simulation of our model is matched with the real COVID-19 data of India till May 15, 2020 for the purpose of estimating the model parameters. Our model with zone-wise lockdown is seen to give a decent prediction for July 20, 2020.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Madhab Barman", + "author_inst": "IIITDM Kancheepuram" + }, + { + "author_name": "Snigdhashree Nayak", + "author_inst": "IIITDM Kancheepuram" + }, + { + "author_name": "Manoj Kumar Yadav", + "author_inst": "Mahindra University, Hyderabad" + }, + { + "author_name": "Soumyendu Raha", + "author_inst": "Indian Institute of Science, Bangalore, India" + }, + { + "author_name": "Nachiketa Mishra", + "author_inst": "IIITDM Kancheepuram, Chennai, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.26.20161570", "rel_title": "Magnitude, demographics and dynamics of the impact of the first phase of the Covid-19 pandemic on all-cause mortality in 17 industrialised countries", @@ -1281859,97 +1285224,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.24.20161653", - "rel_title": "COVID-19 Patients Form Memory CD8+ T Cells that Recognize a Small Set of Shared Immunodominant Epitopes in SARS-CoV-2", - "rel_date": "2020-07-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.24.20161653", - "rel_abs": "Development of effective strategies to detect, treat, or prevent COVID-19 requires a robust understanding of the natural immune response to SARS-CoV-2, including the cellular response mediated by T cells. We used an unbiased, genome-wide screening technology, termed T-Scan, to identify specific epitopes in SARS-CoV-2 that are recognized by the memory CD8+ T cells of 25 COVID-19 convalescent patients, focusing on epitopes presented by the six most prevalent HLA types: A*02:01, A*01:01, A*03:01, A*11:01, A*24:02, and B*07:02. For each HLA type, the patients T cells recognized 3-8 immunodominant epitopes that are broadly shared among patients. Remarkably, 94% of screened patients had T cells that recognized at least one of the three most dominant epitopes for a given HLA, and 53% of patients had T cells that recognized all three. Subsequent validation studies in 18 additional A*02:01 patients confirmed the presence of memory CD8+ T cells specific for the top six A*02:01 epitopes, and single-cell sequencing revealed that patients often have many different T cell clones targeting each epitope, but that the same T cell receptor V regions are predominantly used to recognize these epitopes, even across patients. In total, we identified 29 shared epitopes across the six HLA types studied. T cells that target most of these epitopes (27 of 29) do not cross-react with the endemic coronaviruses that cause the common cold, and the epitopes do not occur in regions with high mutational variation. Notably, only 3 of the 29 epitopes reside in the spike protein, highlighting the need to design new classes of vaccines that recapitulate natural CD8+ T cell responses to SARS-CoV-2.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Andrew P Ferretti", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Tomasz Kula", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Yifan Wang", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Dalena MV Nguyen", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Adam Weinheimer", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Garrett S Dunlap", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Qikai Xu", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Nancy Nabilsi", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Candace R Perullo", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Alexander W Cristofaro", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Holly J Whitton", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Amy Virbasius", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Kenneth J Olivier Jr.", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Lyndsey B Baiamonte", - "author_inst": "Ochsner Medical Center" - }, - { - "author_name": "Angela T Alistar", - "author_inst": "Atlantic Health System Cancer Care" - }, - { - "author_name": "Eric D Whitman", - "author_inst": "Atlantic Health System Cancer Care" - }, - { - "author_name": "Sarah A Bertino", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Shrikanta Chattopadhyay", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Gavin MacBeath", - "author_inst": "TScan Therapeutics" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.21.20153650", "rel_title": "Patient characteristics and predictors of mortality in 470 adults admitted to a district general hospital in England with Covid-19", @@ -1282214,6 +1285488,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.23.20160747", + "rel_title": "Associations of severe COVID-19 with polypharmacy in the REACT-SCOT case-control study", + "rel_date": "2020-07-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.23.20160747", + "rel_abs": "ObjectivesTo investigate the relation of severe COVID-19 to prior drug prescribing.\n\nDesignMatched case-control study (REACT-SCOT) based on record linkage to hospital discharges since June 2015 and dispensed prescriptions issued in primary care during the last 240 days.\n\nSettingScottish population.\n\nMain outcome measureSevere COVID-19, defined by entry to critical care or fatal outcome.\n\nParticipantsAll 4272 cases of severe COVID-19 in Scotland since the start of the epidemic, with 36948 controls matched for age, sex and primary care practice.\n\nResultsSevere COVID-19 was strongly associated with the number of non-cardiovascular drug classes dispensed. This association was strongest in those not resident in care homes, in whom the rate ratio (95% CI) associated with dispensing of 12 or more drug classes versus none was 10.8 (8.7, 13.2), and was not accounted for by treatment of conditions designated as conferring increased risk. Of 17 drug classes postulated at the start of the epidemic to be \"medications compromising COVID\", all were associated with increased risk of severe COVID-19. The largest effect was for antipsychotic agents: rate ratio 4.14 (3.39, 5.07). Other drug classes with large effects included proton pump inhibitors (rate rato 2.19 (1.70, 2.80) for >= 2 defined daily doses/day), opioids (3.62 (2.65, 4.94) for >= 50 mg morphine equivalent/day) and gabapentinoids. These associations persisted after adjusting for covariates, and were stronger with recent than with non-recent exposure.\n\nConclusionsSevere COVID-19 is associated with polypharmacy and with drugs that cause sedation, respiratory depression or dyskinesia, have anticholinergic effects or affect the gastrointestinal system. These associations are not easily explained by co-morbidity. Although the evidence for causality is not conclusive, these results support existing guidance on reducing overprescribing of these drug classes and limiting inappropriate polypharmacy as a potential means of reducing COVID-19 risk.\n\nRegistrationENCEPP number EUPAS35558\n\nWhat is already known on this topicTwo previous studies have examined the relationship of severe COVID-19 to drugs for the cardiovascular system. This is the first systematic study of the relationship of severe COVID-19 to prior drug prescribing.\n\nWhat this study addsSevere COVID-19 is associated with polypharmacy and with drugs that cause sedation, respiratory depression or dyskinesia, have anticholinergic effects or affect the gastrointestinal system. These associations are not easily explained by co-morbidity. These results support earlier warnings that these drug classes that these drugs might increase susceptibility to COVID-19, and reinforce existing guidance on reducing overprescribing of these drug classes.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Paul M McKeigue", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Sharon Kennedy", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "Amanda Weir", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "Jen Bishop", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "Stuart J McGurnaghan", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "David McAllister", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Chris Robertson", + "author_inst": "University of Strathclyde" + }, + { + "author_name": "Rachael Wood", + "author_inst": "NHS Information Services Division (Public Health Scotland)" + }, + { + "author_name": "Nazir Lone", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Janet Murray", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "Thomas M Caparrotta", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Alison Smith-Palmer", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "David Goldberg", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "Jim McMenamin", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "Colin Ramsay", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "Bruce Guthrie", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Sharon Hutchinson", + "author_inst": "Glasgow Caledonian University" + }, + { + "author_name": "Helen M Colhoun", + "author_inst": "University of Edinburgh" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.25.20161844", "rel_title": "Epidemiological investigation and prevention control analysis of longitudinal distribution of COVID-19 in Henan province, China", @@ -1283625,73 +1286986,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.26.222232", - "rel_title": "An alternative binding mode of IGHV3-53 antibodies to the SARS-CoV-2 receptor binding domain", - "rel_date": "2020-07-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.26.222232", - "rel_abs": "IGHV3-53-encoded neutralizing antibodies are commonly elicited during SARS-CoV-2 infection and target the receptor-binding domain (RBD) of the spike (S) protein. Such IGHV3-53 antibodies generally have a short CDR H3 due to structural constraints in binding the RBD (mode A). However, a small subset of IGHV3-53 antibodies to the RBD contain a longer CDR H3. Crystal structures of two IGHV3-53 neutralizing antibodies here demonstrate that a longer CDR H3 can be accommodated in a different binding mode (mode B). These two classes of IGHV3-53 antibodies both target the ACE2 receptor binding site, but with very different angles of approach and molecular interactions. Overall, these findings emphasize the versatility of IGHV3-53 in this common antibody response to SARS-CoV-2, where conserved IGHV3-53 germline-encoded features can be combined with very different CDR H3 lengths and light chains for SARS-CoV-2 RBD recognition and virus neutralization.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Nicholas C. Wu", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Meng Yuan", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Hejun Liu", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Chang-Chun D. Lee", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Xueyong Zhu", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Sandhya Bangaru", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Jonathan L. Torres", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Tom G. Caniels", - "author_inst": "University of Amsterdam" - }, - { - "author_name": "Philip J.M. Brouwer", - "author_inst": "University of Amsterdam" - }, - { - "author_name": "Marit J. van Gils", - "author_inst": "University of Amsterdam" - }, - { - "author_name": "Rogier W. Sanders", - "author_inst": "University of Amsterdam" - }, - { - "author_name": "Andrew B. Ward", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Ian A. Wilson", - "author_inst": "The Scripps Research Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.27.222901", "rel_title": "Evolution And Genetic Diversity Of SARSCoV-2 In Africa Using Whole Genome Sequences", @@ -1283908,6 +1287202,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.07.26.221572", + "rel_title": "COVID-19 and Rheumatoid Arthritis share myeloid pathogenic and resolving pathways", + "rel_date": "2020-07-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.26.221572", + "rel_abs": "BackgroundWe recently delineated the functional biology of pathogenic and inflammation resolving synovial tissue macrophage clusters in rheumatoid arthritis (RA). Whilst RA is not a viral respiratory syndrome, it represents a pro-inflammatory cytokine-driven chronic articular condition often accompanied by cardiovascular and lung pathologies. We hypothesised that functionally equivalent macrophage clusters in the lung might govern inflammation and resolution of COVID-19 pneumonitis.\n\nMethodsTo provide insight into the targetable functions of COVID-19 bronchoalveolar lavage (BALF) macrophage clusters, a comparative analysis of BALF macrophage single cell transcriptomics (scRNA-seq) with synovial tissue (ST) macrophage scRNA-seq and functional biology was performed. The function of shared BALF and ST MerTK inflammation-resolving pathway was confirmed with inhibitor in primary macrophage-synovial fibroblast co-cultures. Results. Distinct BALF FCNpos and FCNposSPP1pos macrophage clusters emerging in severe COVID-19 patients were closely related to ST CD48highS100A12pos and CD48posSPP1pos clusters driving synovitis in active RA. They shared transcriptomic profile and pathogenic mechanisms. Healthy lung resident alveolar FABP4pos macrophages shared a regulatory transcriptomic profile, including TAM (Tyro, Axl, MerTK) receptors pathway with synovial tissue TREM2pos macrophages that govern RA remission. This pathway was substantially altered in BALF macrophages of severe COVID-19. In vitro dexamethasone inhibited tissue inflammation via macrophages MerTK function.\n\nConclusionPathogenesis and resolution of COVID-19 pneumonitis and RA synovitis might be driven by similar macrophage clusters and pathways. The MerTK-dependent anti-inflammatory mechanisms of dexamethasone, and the homeostatic function of TAM pathways that maintain RA in remission advocate the therapeutic MerTK agonism to ameliorate the cytokine storm and pneumonitis of severe COVID-19.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Lucy MacDonald", + "author_inst": "Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), University of Glasgow, Glasgow, United Kingdom" + }, + { + "author_name": "Thomas Dan Otto", + "author_inst": "Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), University of Glasgow, Glasgow, United Kingdom" + }, + { + "author_name": "Aziza Elmesmari", + "author_inst": "Research into Inflammatory Arthritis Centre Versus Arthritis (RACE) ,University of Glasgow, Glasgow, United Kingdom" + }, + { + "author_name": "Barbara Tolusso", + "author_inst": "Division of Rheumatology, Universita Cattolica del Sacro Cuore, Rome, Italy" + }, + { + "author_name": "Domenico Somma", + "author_inst": "Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, United Kingdom." + }, + { + "author_name": "Charles McSharry", + "author_inst": "Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, United Kingdom." + }, + { + "author_name": "Elisa Gremese", + "author_inst": "Division of Rheumatology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy." + }, + { + "author_name": "Iain B McInnes", + "author_inst": "Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), University of Glasgow, Glasgow, United Kingdom." + }, + { + "author_name": "Stefano Alivernini", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS - Universita Cattolica del Sacro Cuore" + }, + { + "author_name": "Mariola Kurowska-Stolarska", + "author_inst": "Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), University of Glasgow, Glasgow, United Kingdom." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.07.24.220715", "rel_title": "CoVaccine HT\u2122 adjuvant potentiates robust immune responses to recombinant SARS-CoV-2 Spike S1 immunisation", @@ -1286131,25 +1289480,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.21.20131664", - "rel_title": "Covid19 2020 projection report: Germany, Israel, Italy and USA. Mid-July 2020", - "rel_date": "2020-07-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20131664", - "rel_abs": "A notion of implied susceptible population size ISPS was introduced in the context of the SIR differential equations in Epidemiology, in a companion paper. It is the potential target population size for which the solution to the SIR equations would yield the current number of new affected cases. This notion is applied to the analysis and projection of Covid19 2020, illustrated on the data of Germany, Israel, Italy and USA.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Isaac Meilijson", - "author_inst": "Tel Aviv University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.21.20125138", "rel_title": "Viral RNA level, serum antibody responses, and transmission risk in discharged COVID-19 patients with recurrent positive SARS-CoV-2 RNA test results: a population-based observational cohort study", @@ -1286414,6 +1289744,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.21.20136218", + "rel_title": "Covid-19 serology in nephrology health care workers", + "rel_date": "2020-07-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20136218", + "rel_abs": "BackgroundChronic kidney disease patients show a high mortality in case of a SARS-CoV-2 infection. Thus, to be informed on Nephrology personnels sero-status might be crucial for patient protection. However, limited information exists about the presence of SARS-CoV-2 antibodies in asymptomatic individuals.\n\nMethodsWe examined the seroprevalence of SARS-CoV-2 IgG and IgM antibodies among health care workers of a tertiary care kidney center during the peak phase of the Covid-19 crisis in Austria using an orthogonal test strategy and a total of 12 commercial nucleocapsid protein or spike glycoprotein based assays as well as Western blotting and a neutralization assay.\n\nResultsAt baseline 60 of 235 study participants (25.5%, 95% CI: 20.4-31.5) were judged to be borderline positive or positive for IgM or IgG using a high sensitivity/low specificity threshold in one test system. Follow-up analysis after about two weeks revealed IgG positivity in 12 (5.1%, 95% CI: 2.9-8.8) and IgM positivity in six (2.6%, 95% CI: 1.1-5.6) in at least one assay. 2.1% (95% CI: 0.8-5.0) of health care workers showed IgG nucleocapsid antibodies in at least two assays. By contrast, positive controls with proven Covid-19 showed antibody positivity among almost all test systems. Moreover, serum samples obtained from health care workers did not show SARS-CoV-2 neutralizing capacity, in contrast to positive controls.\n\nConclusionsUsing a broad spectrum of antibody tests the present study revealed inconsistent results for SARS-CoV-2 seroprevalence among asymptomatic individuals, while this was not the case among Covid-19 patients.\n\nTrial registration numberCONEC, ClinicalTrials.gov number NCT04347694", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Thomas Reiter", + "author_inst": "Medical University of Vienna, Department of Medicine III, Division of Nephrology and Dialysis" + }, + { + "author_name": "Sahra Pajenda", + "author_inst": "Medical University of Vienna, Department of Medicine III, Division of Nephrology and Dialysis" + }, + { + "author_name": "Ludwig Wagner", + "author_inst": "Medical University of Vienna, Department of Medicine III, Division of Nephrology and Dialysis" + }, + { + "author_name": "Martina Gaggl", + "author_inst": "Medical University of Vienna, Department of Medicine III, Division of Nephrology and Dialysis" + }, + { + "author_name": "Johanna Atamaniuk", + "author_inst": "Clinic Favoriten, Vienna Health Care Group, Institute of Laboratory Diagnostics, Vienna, Austria" + }, + { + "author_name": "Barbara Holzer", + "author_inst": "Austrian Agency for Health and Food Safety Ltd., Vienna, Austria" + }, + { + "author_name": "Irene Zimpernik", + "author_inst": "Austrian Agency for Health and Food Safety Ltd., Vienna, Austria" + }, + { + "author_name": "Daniela Gerges", + "author_inst": "Medical University of Vienna, Department of Medicine III, Division of Nephrology and Dialysis" + }, + { + "author_name": "Katharina Mayer", + "author_inst": "Medical University of Vienna, Department of Medicine III, Division of Nephrology and Dialysis" + }, + { + "author_name": "Christof Aigner", + "author_inst": "Medical University of Vienna, Department of Medicine III, Division of Nephrology and Dialysis" + }, + { + "author_name": "Robert Strassl", + "author_inst": "Medical University of Vienna, Clinical Institute of Laboratory Medicine, Division of Virology" + }, + { + "author_name": "Sonja Jansen-Skoupy", + "author_inst": "Clinic Favoriten, Vienna Health Care Group, Institute of Laboratory Diagnostics, Vienna, Austria" + }, + { + "author_name": "Manuela F\u00f6dinger", + "author_inst": "Clinic Favoriten, Vienna Health Care Group, Institute of Laboratory Diagnostics, Vienna, Austria" + }, + { + "author_name": "Gere Sunder-Plassmann", + "author_inst": "Medical University of Vienna, Department of Medicine III, Division of Nephrology and Dialysis" + }, + { + "author_name": "Alice Schmidt", + "author_inst": "Medical University of Vienna, Department of Medicine III, Division of Nephrology and Dialysis" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.24.20156240", "rel_title": "COVID-19 induces a hyperactive phenotype in circulating platelets", @@ -1287665,73 +1291070,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.22.20159400", - "rel_title": "Weak association of coinfection by SARS-CoV-2 and other respiratory viruses with severe cases and death", - "rel_date": "2020-07-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20159400", - "rel_abs": "BackgroundSARS-CoV-2 is a novel coronavirus described for the first time in China in December 2019. This virus can cause a disease that ranges in spectrum from asymptomatic to severe respiratory disease with multiorgan failure, and the most severe cases are associated with some comorbidities and patient age. However, there are patients who do not have those risk factors who still develop serious disease.\n\nMethodsIn this study, we identified the presence of other respiratory viruses in positive cases of COVID-19 in Mexico to determine if any coinfections were correlated with more severe manifestations of COVID-19. We analysed 103 confirmed cases of COVID-19 using RT-qPCR for the detection of 16 other respiratory viruses.\n\nResultsOf the cases analysed, 14 (13.6%) were cases of coinfection, and 92% of them never required hospitalization, even when comorbidities and advanced age were involved. There werent significant differences between the presence of comorbidities and the mean ages of the groups\n\nConclusionsThese results suggest that coinfection is not related to more severe COVID-19 and that, depending on the virus involved, it could even lead to a better prognosis. We believe that our findings may lay the groundwork for new studies aimed at determining the biological mechanism by which this phenomenon occurs and for proposing corresponding strategies to limit the progression to severe cases of COVID-19.\n\nCLINICAL TRIAL REGISTRATIONNot apply", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Larissa Fernandes-Matano", - "author_inst": "Divisi\u00f3n de Laboratorios de Vigilancia e Investigaci\u00f3n Epidemiol\u00f3gica. Instituto Mexicano del Seguro Social" - }, - { - "author_name": "Irma Eloisa Monroy-Mu\u00f1oz", - "author_inst": "Laboratorio de Gen\u00f3mica, Departamento de Gen\u00e9tica y Gen\u00f3mica Humana, Instituto Nacional de Perinatolog\u00eda, Isidro Espinosa de los Reyes" - }, - { - "author_name": "Luis Antonio Uribe-Noguez", - "author_inst": "Laboratorio Central de Epidemiolog\u00eda, Instituto Mexicano del Seguro Social." - }, - { - "author_name": "Mar\u00eda de los Angeles Hern\u00e1ndez-Cueto", - "author_inst": "Laboratorio Central de Epidemiolog\u00eda, Instituto Mexicano del Seguro Social" - }, - { - "author_name": "Brenda Sarquiz-Mart\u00ednez", - "author_inst": "Laboratorio Central de Epidemiolog\u00eda, Instituto Mexicano del Seguro Social" - }, - { - "author_name": "H\u00e9ctor Daniel Pardav\u00e9-Alejandre", - "author_inst": "Laboratorio Central de Epidemiolog\t\u00eda, Instituto Mexicano del Seguro Social" - }, - { - "author_name": "Andrea Santos Coy-Arechavaleta", - "author_inst": "Laboratorio Central de Epidemiolog\u00eda, Instituto Mexicano del Seguro Social" - }, - { - "author_name": "Julio Elias Alvarado-Yaah", - "author_inst": "Laboratorio Central de Epidemiolog\u00eda, Instituto Mexicano del Seguro Social" - }, - { - "author_name": "Teresita Rojas-Mendoza", - "author_inst": "Laboratorio Central de Epidemiolog\u00eda, Instituto Mexicano del Seguro Social" - }, - { - "author_name": "Clara Esperanza Santacruz-Tinoco", - "author_inst": "Divisi\u00f3n de Laboratorios de Vigilancia e Investigaci\u00f3n Epidemiol\u00f3gica. Instituto Mexicano del Seguro Social" - }, - { - "author_name": "Concepci\u00f3n Grajales-Mu\u00f1iz", - "author_inst": "Coordinaci\u00f3n de Control T\u00e9cnico de Insumos, Instituto Mexicano del Seguro Social" - }, - { - "author_name": "V\u00edctor Hugo Borja-Aburto", - "author_inst": "Direcci\u00f3n de Prestaciones M\u00e9dicas, Instituto Mexicano del Seguro Social" - }, - { - "author_name": "Jos\u00e9 Esteban Mu\u00f1oz-Medina", - "author_inst": "Divisi\u00f3n de Laboratorios de Vigilancia e Investigaci\u00f3n Epidemiol\u00f3gica. Instituto Mexicano del Seguro Social" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.21.20159053", "rel_title": "Prospective Observational Study of Screening Asymptomatic Healthcare Workers for SARS-CoV-2 at a Canadian Tertiary Care Center", @@ -1287968,6 +1291306,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.07.20.20158386", + "rel_title": "COVIDCare@Home: Lessons from a Family Medicine Led Remote Monitoring Program", + "rel_date": "2020-07-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.20.20158386", + "rel_abs": "BackgroundVirtual care for patients with COVID-19 allows providers to monitor COVID-19 positive patients with variable trajectories while reducing the risk of transmission to others and managing healthcare capacity in acute care facilities.\n\nObjectiveTo develop and test the feasibility of a family medicine-led remote monitoring model of care (COVIDCare@Home program) to manage patients with COVID-19 in the community.\n\nMethodsThis multi-faceted, family medicine-led, interprofessional team-based remote monitoring program was developed at Womens College Hospital in Toronto, Ontario. A cross-sectional chart review of the first cohort of patients was conducted and learnings from the implementation of CovidCare@Home are described.\n\nResultsDuring the study period, April 8 to May 11, 2020, there were 97 patients (average age 48.6, 62% female) with 424 recorded virtual visits with a median virtual length of stay of 8 days (IQR 5). 5.2% required escalation to an in-person visit with no patients requiring hospitalization. 16% of patients required support with mental and social health needs.\n\nInterpretationsA family medicine-led, team-based remote monitoring program can safely be used to manage outpatients diagnosed with COVID-19. Attention to mental and social health needs is critical for this population. Future efforts should consider how to design programs to best support populations disproportionately impacted by COVID-19, something which primary care is well-positioned to do. Further analysis will describe the effectiveness, impact, and satisfaction with the program among patients and providers.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Payal Agarwal", + "author_inst": "Womens College Hospital" + }, + { + "author_name": "Geetha Mukerji", + "author_inst": "Womens College Hospital" + }, + { + "author_name": "Celia Laur", + "author_inst": "Womens College Hospital" + }, + { + "author_name": "Shivani Chandra", + "author_inst": "Womens College Hospital" + }, + { + "author_name": "Nick Pimlott", + "author_inst": "Womens College Hospital" + }, + { + "author_name": "Ruth Heisey", + "author_inst": "Womens College Hospital" + }, + { + "author_name": "Rebecca Stovel", + "author_inst": "Womens College Hospital" + }, + { + "author_name": "Elaine Goulbourne", + "author_inst": "Womens College Hospital" + }, + { + "author_name": "Sacha Bhatia", + "author_inst": "Womens College Hospital" + }, + { + "author_name": "Onil Bhattacharyya", + "author_inst": "Womens College Hospital" + }, + { + "author_name": "Danielle Martin", + "author_inst": "Womens College Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.07.22.20158311", "rel_title": "Hospital Trainees Worries, Perceived Sufficiency of Information and Reported Psychological Health During The COVID-19 Pandemic", @@ -1289163,113 +1292560,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2020.07.21.20159376", - "rel_title": "Cerebral Microvascular Injury in Severe COVID-19", - "rel_date": "2020-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20159376", - "rel_abs": "Structured AbstractO_ST_ABSImportanceC_ST_ABSCerebral microvascular lesions are common in patients with severe COVID-19. Radiologic-pathologic correlation in one case suggests a combination of microvascular hemorrhagic and ischemic lesions that may reflect an underlying hypoxic mechanism of injury, which requires validation in larger studies.\n\nObjectiveTo determine the incidence, distribution, and clinical and histopathologic correlates of microvascular lesions in patients with severe COVID-19.\n\nDesignObservational, retrospective cohort study: March to May 2020.\n\nSettingSingle academic medical center.\n\nParticipantsConsecutive patients (n=16) admitted to the intensive care unit with severe COVID-19, undergoing brain MRI for evaluation of coma or focal neurologic deficits.\n\nExposuresNot applicable.\n\nMain Outcome and MeasuresHypointense microvascular lesions identified by a prototype ultrafast high-resolution susceptibility-weighted imaging (SWI) MRI sequence, counted by two neuroradiologists and categorized by neuroanatomic location. Clinical and laboratory data (most recent measurements before brain MRI). Brain autopsy and cerebrospinal fluid PCR for SARS-CoV-2 in one patient who died from severe COVID-19.\n\nResultsEleven of 16 patients (69%) had punctate and linear SWI lesions in the subcortical and deep white matter, and eight patients (50%) had >10 SWI lesions. In 4/16 patients (25%), lesions involved the corpus callosum. Brain autopsy in one patient revealed that SWI lesions corresponded to widespread microvascular injury, characterized by perivascular and parenchymal petechial hemorrhages and microscopic ischemic lesions.\n\nConclusions and RelevanceSWI lesions are common in patients with neurological manifestations of severe COVID-19 (coma and focal neurologic deficits). The distribution of lesions is similar to that seen in patients with hypoxic respiratory failure, sepsis, and disseminated intravascular coagulation. Collectively, these radiologic and histopathologic findings suggest that patients with severe COVID-19 are at risk for multifocal microvascular hemorrhagic and ischemic lesions in the subcortical and deep white matter.\n\nKey Points SectionO_ST_ABSQuestionC_ST_ABSWhat is the prevalence and pathophysiology of cerebral microvascular injury in patients with severe COVID-19?\n\nFindingsIn this retrospective cohort study of 16 patients undergoing MRI for neurologic complications of severe COVID-19, microvascular lesions were observed in 11 patients and showed an anatomic distribution similar to that seen in patients with hypoxic respiratory failure and sepsis. In one patient who died, brain autopsy revealed widespread microvascular injury, including perivascular microhemorrhages and microscopic ischemic lesions.\n\nMeaningMicrovascular injury is common in patients with severe COVID-19. Radiologic-pathologic correlation, though limited to a single case, provides insights into possible mechanisms of injury.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "John Conklin", - "author_inst": "Department of Radiology, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Matthew P. Frosch", - "author_inst": "C.S. Kubik Laboratory for Neuropathology, Massachusetts General Hospital" - }, - { - "author_name": "Shibani Mukerji", - "author_inst": "Department of Neurology, Massachusetts General Hospital" - }, - { - "author_name": "Otto Rapalino", - "author_inst": "Department of Radiology, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Mary Maher", - "author_inst": "Department of Radiology, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Pamela W. Schaefer", - "author_inst": "Department of Radiology, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Michael H. Lev", - "author_inst": "Department of Radiology, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Ramon G. Gonzalez", - "author_inst": "Department of Radiology, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Sudeshna Das", - "author_inst": "Department of Neurology, Massachusetts General Hospital" - }, - { - "author_name": "Samantha N. Champion", - "author_inst": "C.S. Kubik Laboratory for Neuropathology, Massachusetts General Hospital" - }, - { - "author_name": "Colin Magdamo", - "author_inst": "Department of Neurology, Massachusetts General Hospital" - }, - { - "author_name": "Pritha Sen", - "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "George Kyle Harrold", - "author_inst": "Department of Neurology, Massachusetts General Hospital" - }, - { - "author_name": "Haitham Alabsi", - "author_inst": "Department of Neurology, Massachusetts General Hospital" - }, - { - "author_name": "Erica Normandin", - "author_inst": "Broad Institute, Massachusetts Institute of Technology and Harvard University" - }, - { - "author_name": "Bennett Shaw", - "author_inst": "Department of Neurology, Massachusetts General Hospital" - }, - { - "author_name": "Jacob Lemieux", - "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Pardis Sabeti", - "author_inst": "Broad Institute, Massachusetts Institute of Technology and Harvard University" - }, - { - "author_name": "John A. Branda", - "author_inst": "Department of Pathology, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Emery N. Brown", - "author_inst": "Broad Institute, Massachusetts Institute of Technology and Harvard University" - }, - { - "author_name": "M. Brandon Westover", - "author_inst": "Department of Neurology, Massachusetts General Hospital" - }, - { - "author_name": "Susie Y. Huang", - "author_inst": "Department of Radiology, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Brian L Edlow", - "author_inst": "Center for Neurotechnology and Neurorecovery, Department of Neurology, Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2020.07.21.20159327", "rel_title": "COVID-19 Vulnerability of Transgender Women With and Without HIV Infection in the Eastern and Southern U.S.", @@ -1289586,6 +1292876,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.22.20159525", + "rel_title": "Comparative Evaluation of 19 Reverse Transcription Loop-Mediated Isothermal Amplification Assays for Detection of SARS-CoV-2", + "rel_date": "2020-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20159525", + "rel_abs": "Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has caused a global pandemics. To facilitate the detection of SARS-CoV-2 infection, various RT-LAMP assays using 19 sets of primers had been developed, but never been compared. We performed comparative evaluation of the 19 sets of primers using 4 RNA standards and 29 clinical samples from COVID-19 patients. Six of 15 sets of primers were firstly identified to have faster amplification when tested with four RNA standards, and were further subjected to parallel comparison with the remaining four primer sets using 29 clinical samples. Among these 10 primer sets, Set-4 had the highest positive detection rate of SARS-CoV-2 (82.8%), followed by Set-10, Set-11, Set-13 and Set-14 (75.9%), and Set-14 showed the fastest amplification speed (< 8.5 minutes), followed by Set-17 (< 12.5 minutes). Based on the overall detection performance, Set-4, Set-10, Set-11, Set-13, Set-14 and Set-17 that target Nsp3, S, S, E, N and N gene regions of SARS-CoV-2, respectively, are determined to be better than the other primer sets. Two RT-LAMP assays with the Set-14 primers in combination with any one of four other primer sets (Set-4, Set-10, Set-11, and Set-13) are recommended to be used in the COVID-19 surveillance.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Yajuan Dong", + "author_inst": "College of Life Sciences, Henan Normal University" + }, + { + "author_name": "Xiuming Wu", + "author_inst": "Pathogen Discovery and Evolution Unit, Institut Pasteur of Shanghai" + }, + { + "author_name": "Shenwei Li", + "author_inst": "Shanghai International Travel Healthcare Center" + }, + { + "author_name": "Renfei Lu", + "author_inst": "Clinical Laboratory, Nantong Third Hospital Affiliated to Nantong University" + }, + { + "author_name": "Zhenzhou Wan", + "author_inst": "Medical Laboratory of Taizhou Fourth People's Hospital" + }, + { + "author_name": "Jianru Qin", + "author_inst": "College of Life Sciences, Henan Normal University" + }, + { + "author_name": "Guoying Yu", + "author_inst": "College of Life Sciences, Henan Normal University" + }, + { + "author_name": "Xia Jin", + "author_inst": "Shanghai Public Health Clinical Center, Fudan University" + }, + { + "author_name": "Chiyu Zhang", + "author_inst": "Shanghai Public Health Clinical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.21.20159384", "rel_title": "Initial Experience in Predicting the Risk of Hospitalization of 496 Outpatients with COVID-19 Using a Telemedicine Risk Assessment Tool", @@ -1290669,29 +1294010,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.24.20161604", - "rel_title": "CCOFEE-GI Study: Colombian COVID19 First Experience in Gastroentrology. Characterization of digestive manifestations in patients diagnosed with COVID-19 at a highly complex institution in Bogota D.C., Colombia", - "rel_date": "2020-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.24.20161604", - "rel_abs": "The current pandemic caused by SARS-CoV-2 has posed an important threat to the human health, healthcare systems, economy, and structure of societies. In Colombia, the first case was diagnosed on March 6, 2020, with exponential progressive growth, and there were >200,000 confirmed cases as of July 20, 2020, in this cross-sectional, analytical, and observational study, we focused on the demographic, epidemiologic, and clinical characteristics of patients with confirmed SARS-CoV-2 infection at a highly complex institution in Latinamerica, with special emphasis on gastrointestinal symptoms. Methods: Demographic and clinical data were collected, results related to the outcomes such as hospitalization time, admission to ICU, need for orotracheal intubation, and death were also included. Statistical analyses were conducted using Stata software V.15.\n\nResultsWe included 72 patients RT-PCR positive for SARS-CoV-2 (34 women and 38 men) with age 47.5 {+/-} 17.7 years; 17 (23.6%) presented at least one of the gastrointestinal symptoms (nausea/vomiting, abdominal pain, and/or diarrhea). 13 (76.47%) presented with diarrhea, 29.41% with nausea/vomiting, and five (29.41%) with abdominal pain. Diarrhea in 18.06% of all those infected with SARS-CoV-2 at the time of consultation, which was the most common digestive symptom. No significant differences were observed in requirement for endotracheal intubation, hospitalization, ICU admission, and fatal outcome between the NGIS and GIS groups (p:0.671, 0.483, 1,000, and 1,000). Conclusion: In our study, patients with gastrointestinal symptoms had no significant differences in disease severity, admission to ICU or death compared to those who did not have such symptoms.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "ALEJANDRO CONCHA-MEJIA", - "author_inst": "FUNDACION CLINICA SHAIO" - }, - { - "author_name": "REINALDO ANDRES RINCON-SANCHEZ", - "author_inst": "FUNDACION CLINICA SHAIO" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2020.07.23.20160879", "rel_title": "Factors associated with psychological distress in health-care workers during an infectious disease outbreak: A rapid living systematic review", @@ -1290816,6 +1294134,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.07.24.20161596", + "rel_title": "The impact of COVID-19 on patients with asthma: A Big Data analysis", + "rel_date": "2020-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.24.20161596", + "rel_abs": "BackgroundFrom the onset of the COVID-19 pandemic, an association between the severity of COVID-19 and the presence of certain medical chronic conditions has been suggested. However, unlike influenza and other viruses, the burden of the disease in patients with asthma has been less evident.\n\nObjectiveThis study aims at a better understanding of the burden of COVID-19 in patients with asthma and the impact of asthma, its related comorbidities, and treatment on the prognosis of COVID-19.\n\nMethodsWe analyzed clinical data from patients with asthma from January 1st to May 10th, 2020 using big data analytics and artificial intelligence through the SAVANA Manager(R) clinical platform.\n\nResultsOut of 71,192 patients with asthma, 1,006 (1.41%) suffered from COVID-19. Compared to asthmatic individuals without COVID-19, patients with asthma and COVID-19 were significantly older (55 vs. 42 years), predominantly female (66% vs. 59%), had higher prevalence of hypertension, dyslipidemias, diabetes, and obesity, and smoked more frequently. Contrarily, allergy-related factors such as rhinitis and eczema were less frequent in asthmatic patients with COVID-19 (P < .001). Higher prevalence of hypertension, dyslipidemia, diabetes, and obesity was also confirmed in those patients with asthma and COVID-19 who required hospital admission. The percentage of individuals using inhaled corticosteroids (ICS) was lower in patients who required hospitalization due to COVID-19, as compared to non-hospitalized patients (48.3% vs. 61.5%; OR: 0.58: 95% CI 0.44 - 0.77). During the study period, 865 (1.21%) patients with asthma were being treated with biologics. Although these patients showed increased severity and more comorbidities at the ear, nose, and throat (ENT) level, their hospital admission rates due to COVID-19 were relatively low (0.23%). COVID-19 increased inpatient mortality in asthmatic patients (2.29% vs 0.54%; OR 2.29: 95% CI 4.35 - 6.66).\n\nConclusionOur results indicate that the number of COVID-19 cases in patients with asthma has been low, although higher than the observed in the general population. Patients with asthma and COVID-19 were older and were at increased risk due to comorbidity-related factors. ICS and biologics are generally safe and may be associated with a protective effect against severe COVID-19 infection.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jose Luis Izquierdo", + "author_inst": "Respiratory Medicine. University Hospital of Guadalajara, Guadalajara" + }, + { + "author_name": "Carlos Almonacid", + "author_inst": "Department of Medicine and Medical Specialties. University of Alcala, Madrid & Respiratory Medicine. University Hospital Ramon y Cajal, Madrid" + }, + { + "author_name": "Yolanda Gonzalez", + "author_inst": "Savana Medica" + }, + { + "author_name": "Carlos Del Rio-Bermudez", + "author_inst": "Savana Medica" + }, + { + "author_name": "Julio Ancochea", + "author_inst": "Respiratory Medicine. Hospital Universitario de La Princesa, Madrid; Universidad Autonoma de Madrid. Madrid; Respiratory Diseases Networking Biomedical Research" + }, + { + "author_name": "Remedios Cardenas", + "author_inst": "Allergy. University Hospital of Guadalajara, Guadalajara" + }, + { + "author_name": "Joan B Soriano", + "author_inst": "Respiratory Medicine. Hospital Universitario de La Princesa, Madrid; Universidad Autonoma de Madrid. Madrid; Respiratory Diseases Networking Biomedical Research" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.07.24.20161471", "rel_title": "Epidemiological and cohort study finds no association between COVID-19 and Guillain-Barre syndrome", @@ -1292103,41 +1295464,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.22.20160184", - "rel_title": "Forecasting hospitalizations due to COVID-19 in South Dakota, USA.", - "rel_date": "2020-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20160184", - "rel_abs": "1Anticipating the number of hospital beds needed for patients with COVID-19 remains a challenge. Early efforts to predict hospital bed needs focused on deriving predictions from SIR models, largely at the level of countries, provinces, or states. In the United States, these models rely on data reported by state health agencies. However, predictive disease and hospitalization dynamics at the state level are complicated by geographic variation in disease parameters. In addition it is difficult to make forecasts early in a pandemic due to minimal data. However, Bayesian approaches that allow models to be specified with informed prior information from areas that have already completed a disease curve can serve as prior estimates for areas that are beginning their curve. Here, a Bayesian non-linear regression (Weibull function) was used to forecast cumulative and active COVID-19 hospitalizations for South Dakota, USA. As expected, early forecasts were dominated by prior information, which was derived from New York City. Importantly, hospitalization trends also differed within South Dakota due to early peaks in an urban area, followed by later peaks in other rural areas of the state. Combining these trends led to altered forecasts with relevant policy implications.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jeff S Wesner", - "author_inst": "University of South Dakota" - }, - { - "author_name": "Dan Van Peursem", - "author_inst": "University of South Dakota" - }, - { - "author_name": "Jose Flores", - "author_inst": "University of South Dakota" - }, - { - "author_name": "Yuhlong Lio", - "author_inst": "University of South Dakota" - }, - { - "author_name": "Chelsea Wesner", - "author_inst": "University of South Dakota" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.22.20160283", "rel_title": "Heat-based Decontamination of N95 Masks Using a Commercial Laundry Dryer", @@ -1292398,6 +1295724,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.22.20159962", + "rel_title": "Mathematical model study of a pandemic: Graded lockdown approach", + "rel_date": "2020-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20159962", + "rel_abs": "A kinetic approach is developed, in a \"tutorial style\" to describe the evolution of an epidemic with spread taking place through contact. The \"infection - rate\" is calculated from the rate at which an infected person approaches an uninfected susceptible individual, i.e. a potential recipient of the disease, up to a distance p, where the value of p may lie between pmin[≤] p [≤] pmax. We consider a situation with a total population of N individuals, living in an area A, x(t) amongst them being infected while xd(t) = {beta}'x(t) is the number that have died in the course of transmission and evolution of the epidemic. The evolution is developed under the conditions (1) a faction (t) of the [N-x(t) - xd(t)] uninfected individuals and (2) a {beta}(t) fraction of the x(t) infected population are quarantined, while the \"source events\" that spread the infection are considered to occur with frequency{upsilon} 0. The processes of contact and transmission are considered to be Markovian. Transmission is assumed to be inhibited by several processes like the use of \"masks\", \"hand washing or use of sanitizers\" while \"physical distancing\" is described by p. The evolution equation for x(t) is a Riccati - type differential equation whose coefficients are time-dependent quantities, being determined by an interplay between the above parameters. A formal solution for x(t) is presented, for a \"graded lockdown\" with the parameters, 0[≤] (t), {beta}(t)[≤]1 reaching their respective saturation values in time scales,{tau} 1,{tau} 2 respectively, from their initial values (0)={beta}(0)=0. The growth is predicted for several BBMP wards in Bengaluru and in urban centers in Chikkaballapur district, as an illustrative case. Above selections serve as model cases for high, moderate and thin population densities. It is seen that the evolution of [x(t)/N] with time depends upon (a) the initial time scale of evolution, (b) the time scale of cure and (c) on the time dependence of the Lockdown function Q(t) = {[1-(t)]{middle dot}[1-{beta}(t)]}. The formulae are amenable to simple computations and show that in order to curb the spread one must ensure that Q({infty}) must be below a critical value and the vigilance has to be continued for a long time (at least 100 to 150 days) after the decay starts, to avoid all chances of the infection reappearing.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "S Chateerjee", + "author_inst": "Ongil, No. 4, Rajiv Gandhi Salai, Taramani, Chennai 600 113, India" + }, + { + "author_name": "V.C. Vani", + "author_inst": "Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore 560012, India" + }, + { + "author_name": "Ravinder Banyal", + "author_inst": "Indian Institute of Astrophysics, Bangalore, INDIA" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.22.20160127", "rel_title": "COVID-19 in-hospital mortality and mode of death in a dynamic and non-restricted tertiary care model in Germany", @@ -1293633,53 +1296986,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2020.07.22.212761", - "rel_title": "SARS-CoV-2-induced humoral immunity through B cell epitope analysis and neutralizing activity in COVID-19 infected individuals in Japan", - "rel_date": "2020-07-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.22.212761", - "rel_abs": "The aim of this study is to understand adaptive immunity to SARS-CoV-2 through the analysis of B cell epitope and neutralizing activity in coronavirus disease 2019 (COVID-19) patients. We obtained serum from thirteen COVID-19 patients. Most individuals revealed neutralizing activity against SARS-CoV-2 assessed by a pseudotype virus-neutralizing assay. The antibody production against the spike glycoprotein (S protein) or receptor-binding domain (RBD) of SARS-CoV-2 was elevated, with large individual differences, as assessed by ELISA. In the analysis of the predicted the linear B cell epitopes, two regions (671-690 aa. and 1146-1164 aa.), which were located in S1 and S2 but not in the RBD, were highly reactive with the sera from patients. In the further analysis of the B cell epitope within the S protein by utilizing a B cell epitope array, a hot spot in the N-terminal domain of the S protein but not the RBD was observed in individuals with neutralizing activity. Overall, the analysis of antibody production and B cell epitopes of the S protein from patient serum may provide a novel target for the vaccine development against SARS-CoV-2.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Shota Yoshida", - "author_inst": "Osaka University Graduate School of Medicine" - }, - { - "author_name": "Chikako Ono", - "author_inst": "Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Hiroki Hayashi", - "author_inst": "Osaka University Graduate School of Medicine" - }, - { - "author_name": "Satoshi Shiraishi", - "author_inst": "Juso Osaka City Hospital" - }, - { - "author_name": "Tomono Kazunori", - "author_inst": "Division of Infection Control and Prevention, Osaka University Hospital" - }, - { - "author_name": "Hisashi Arase", - "author_inst": "Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Yoshiharu Matsuura", - "author_inst": "Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Hironori Nakagami", - "author_inst": "Osaka University Graduate School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.07.23.212357", "rel_title": "Single-dose intranasal vaccination elicits systemic and mucosal immunity against SARS-CoV-2", @@ -1293944,6 +1297250,61 @@ "type": "new results", "category": "scientific communication and education" }, + { + "rel_doi": "10.1101/2020.07.23.217331", + "rel_title": "Development and validation of a clinical risk score to predict the risk of SARS-CoV-2 infection from administrative data: a population-based cohort study from Italy", + "rel_date": "2020-07-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.23.217331", + "rel_abs": "BackgroundThe novel coronavirus (SARS-CoV-2) pandemic spread rapidly worldwide increasing exponentially in Italy. To date, there is lack of studies describing clinical characteristics of the population most at risk of infection. Hence, we aimed to identify clinical predictors of SARS-CoV-2 infection risk and to develop and validate a score predicting SARS-CoV-2 infection risk comparing it with unspecific surrogates.\n\nMethodsRetrospective case/control study using administrative health-related database was carried out in Southern Italy (Campania region) among beneficiaries of Regional Health Service aged over than 30 years. For each subject with Covid-19 confirmed diagnosis (case), up to five controls were randomly matched for gender, age and municipality of residence. Odds ratios and 90% confidence intervals for associations between candidate predictors and risk of infection were estimated by means of conditional logistic regression. SARS-CoV-2 Infection Score (SIS), was developed by generating a total aggregate score obtained from assignment of a weight at each selected covariate using coefficients estimated from the model. Finally, the score was categorized by assigning increasing values from 1 to 4. SIS was validated by comparison with specific and unspecific predictors of SARS-CoV-2 infection.\n\nResultsSubjects suffering from diabetes, anaemias, Parkinsons disease, mental disorders, cardiovascular and inflammatory bowel and kidney diseases showed increased risk of SARS-CoV-2 infection. Similar estimates were recorded for men and women and younger and older than 65 years. Fifteen conditions significantly contributed to the SIS. As SIS value increases, risk progressively increases, being odds of SARS-CoV-2 infection among people with the highest SIS value (SIS=4), 1.74 times higher than those unaffected by any SIS contributing conditions (SIS=1).\n\nConclusionThis study identified conditions and diseases making individuals more vulnerable to SARS-CoV-2 infection. Our results are a decision-maker support tool for identifying population most at risk allowing adoption of preventive measures to minimize a potential new relapse damage.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Valentina Orlando", + "author_inst": "CIRFF Center of Drug utilization and Pharmacoeconomics" + }, + { + "author_name": "Federico Rea", + "author_inst": "Laboratoty of Healthcare Research and Pharmacoepidemiology, Unit of Biostatistics, Epidemiology and Public Health" + }, + { + "author_name": "Laura savar\u00e8", + "author_inst": "Laboratory of Halthcare Research and Pharmacoepidemiology, Unit of Biostatistics, Epidemiology and Public Health" + }, + { + "author_name": "Ilaria Guarino", + "author_inst": "CIRFF, Centre of Drug Utilization and Pharmacoeconomics" + }, + { + "author_name": "Sara Mucherino", + "author_inst": "CIRFF, Center of Drug Utilization and Pharmacoeconomics" + }, + { + "author_name": "Alessandro Perrella", + "author_inst": "Infectious Disease of Healthcare Direction" + }, + { + "author_name": "Ugo Trama", + "author_inst": "Regional Pharmaceeutical Unit" + }, + { + "author_name": "Enrico Coscioni", + "author_inst": "Division of Cardiac Surgery" + }, + { + "author_name": "Enrica Menditto", + "author_inst": "CIRFF, Center of Drug Utilization and Pharmacoeconomics" + }, + { + "author_name": "Giovanni Corrao", + "author_inst": "Laboratory of Healtcare Research and Pharmacoepidemiology, Unit of Biostatistics, Epidemiology and Public Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2020.07.21.20158956", "rel_title": "Impact of COVID-19 on Public Research Recruitment", @@ -1295483,37 +1298844,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.22.215731", - "rel_title": "Elucidation of Genome Polymorphisms in Emerging SARS-CoV-2", - "rel_date": "2020-07-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.22.215731", - "rel_abs": "The COVID-19 pandemic is having a devastating effect on the healthcare system and the economy of the world. The unavailability of a specific treatment regime and a candidate vaccine yet opens up scope for new approaches and discoveries of drugs for mitigation of the sufferings of humankind due to the disease. The present isolated whole-genome sequences of SARS-CoV-2 from 11 different nations subjected to evolutionary study and genome-wide association study through in silico approaches including multiple sequence alignment, phylogenetic study through MEGA7 and have been analyzed through DNAsp respectively. These investigations recognized the nucleotide varieties and single nucleotide mutations/polymorphisms on the genomic regions as well as protein-coding regions. The resulted mutations have diversified the genomic contents of SARS-CoV-2 according to the altered nucleotides found in 11 genome sequences. India and Nepal have found to have progressively more distinct species of SARS-CoV-2 with variations in Spike protein and Nucleocapsid protein-coding sites. These genomic variations might be the explanation behind the less case fatality rate of India and Nepal dependent on the populaces. The anticipated idea of this investigation upgrades the information about genomic medication and might be useful in the planning of antibodies against SARS-CoV-2.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Manisha Ray", - "author_inst": "All India Institute of Medical Sciences, Bhubaneswar" - }, - { - "author_name": "Saurav Sarkar", - "author_inst": "All India Institute of Medical Sciences, Bhubaneswar" - }, - { - "author_name": "Surya Narayan Rath", - "author_inst": "OUAT" - }, - { - "author_name": "Mukund Namdev Sable", - "author_inst": "All India Institute of Medical Sciences, Bhubaneswar" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.07.22.215590", "rel_title": "Inadequate level of knowledge, mixed outlook and poor adherence to COVID-19 prevention guideline among Ethiopians", @@ -1295634,6 +1298964,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.19.20157198", + "rel_title": "High Community SARS-CoV-2 Antibody Seroprevalence in a Ski Resort Community, Blaine County, Idaho, US. Preliminary Results", + "rel_date": "2020-07-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.19.20157198", + "rel_abs": "Community-level seroprevalence surveys are needed to determine the proportion of the population with previous SARS-CoV-2 infection, a necessary component of COVID-19 disease surveillance. In May, 2020, we conducted a cross-sectional seroprevalence study of IgG antibodies for nucleocapsid of SARS-CoV-2 among the residents of Blaine County, Idaho, a ski resort community with high COVID-19 attack rates in late March and Early April (2.9% for ages 18 and older). Participants were selected from volunteers who registered via a secure web link, using prestratification weighting to the population distribution by age and gender within each ZIP Code. Participants completed a survey reporting their demographics and symptoms; 88% of volunteers who were invited to participate completed data collection survey and had 10 ml of blood drawn. Serology was completed via the Abbott Architect SARS-CoV-2 IgG immunoassay. Primary analyses estimated seroprevalence and 95% credible intervals (CI) using a hierarchical Bayesian framework to account for diagnostic uncertainty. Stratified models were run by age, sex, ZIP Code, ethnicity, employment status, and a priori participant-reported COVID-19 status. Sensitivity analyses to estimate seroprevalence included base models with post-stratification for ethnicity, age, and sex, with or without adjustment for multi-participant households. IgG antibodies to the virus that causes COVID-19 were found among 22.7% (95% CI: 20.1%, 25.5%) of residents of Blaine County. Higher levels of antibodies were found among residents of the City of Ketchum 34.8% (95% CI 29.3%, 40.5%), compared to Hailey 16.8% (95%CI 13.7%, 20.3%) and Sun Valley 19.4% (95% 11.8%, 28.4%). People who self-identified as not believing they had COVID-19 had the lowest prevalence 4.8% (95% CI 2.3%, 8.2%). The range of seroprevalence after correction for potential selection bias was 21.9% to 24.2%. This study suggests more than 80% of SARS-CoV-2 infections were not reported. Although Blaine County had high levels of SARS-CoV-2 infection, the community is not yet near the herd immunity threshold.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Colleen McLaughlin", + "author_inst": "Albany College of Pharmacy and Health Sciences" + }, + { + "author_name": "Margaret K. Doll", + "author_inst": "Albany College of Pharmacy and Health Sciences" + }, + { + "author_name": "Kathryn T Morrison", + "author_inst": "Precision Analytics, Montreal, Quebec, Canada; McGill University, Montreal, Quebec, Canada" + }, + { + "author_name": "William L McLaughlin III", + "author_inst": "City of Ketchum Fire Department" + }, + { + "author_name": "Terry OConnor", + "author_inst": "Blaine County Ambulance District. University of Colorado School of Medicine, section Wilderness and Environmental Medicine. University of Washington Department " + }, + { + "author_name": "Anton M Sholukh", + "author_inst": "Vaccine and Infectious Diseases Division, Fred Hutch Cancer Research Center, Seattle WA" + }, + { + "author_name": "Emily L Bossard", + "author_inst": "Vaccine and Infectious Diseases Division, Fred Hutch Cancer Research Center, Seattle WA" + }, + { + "author_name": "Khamsone Phasouk", + "author_inst": "Vaccine and Infectious Diseases Division, Fred Hutch Cancer Research Center, Seattle WA" + }, + { + "author_name": "Emily S Ford", + "author_inst": "Vaccine and Infectious Diseases Division, Fred Hutch Cancer Research Center, Seattle WA; Division of Allergy and Infectious Diseases, Department of Medicine, Un" + }, + { + "author_name": "Kurt Diem", + "author_inst": "Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA" + }, + { + "author_name": "Alexis M Hlock", + "author_inst": "Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA" + }, + { + "author_name": "Keith R Jerome", + "author_inst": "Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA; Vaccine and Infectious Diseases Division, Fred Hutch Cancer Research Cent" + }, + { + "author_name": "Lawrence Corey", + "author_inst": "Vaccine and Infectious Diseases Division, Fred Hutch Cancer Research Center, Seattle WA; Division of Allergy and Infectious Diseases, Department of Medicine, Un" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.19.20157305", "rel_title": "Clinical Characteristics and Outcomes for 7,995 Patients with SARS-CoV-2 Infection", @@ -1296849,93 +1300246,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.16.20155663", - "rel_title": "Humoral Response Dynamics Following Infection with SARS-CoV-2", - "rel_date": "2020-07-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.16.20155663", - "rel_abs": "IntroductionSevere Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) specific antibodies have been shown to neutralize the virus in-vitro. Understanding antibody dynamics following SARS-CoV-2 infection is therefore crucial. Sensitive measurement of SARS-CoV-2 antibodies is also vital for large seroprevalence surveys which inform government policies and public health interventions. However, rapidly waning antibodies following SARS-CoV-2 infection could jeopardize the sensitivity of serological testing on which these surveys depend.\n\nMethodsThis prospective cohort study of SARS-CoV-2 humoral dynamics in a central London hospital analyzed 137 serial samples collected from 67 participants seropositive to SARS-CoV-2 by the Meso-Scale Discovery assay. Antibody titers were quantified to the SARS-CoV-2 nucleoprotein (N), spike (S-)protein and the receptor-binding-domain (RBD) of the S-protein. Titers were log-transformed and a multivariate log-linear model with time-since-infection and clinical variables was fitted by Bayesian methods.\n\nResultsThe mean estimated half-life of the N-antibody was 52 days (95% CI 42-65). The S- and RBD-antibody had significantly longer mean half-lives of 81 days (95% CI 61-111) and 83 days (95% CI 55-137) respectively. An ACE-2-receptor competition assay demonstrated significant correlation between the S and RBD-antibody titers and ACE2-receptor blocking in-vitro. The time-to-a-negative N-antibody test for 50% of the seropositive population was predicted to be 195 days (95% CI 163-236).\n\nDiscussionAfter SARS-CoV-2 infection, the predicted half-life of N-antibody was 52 days with 50% of seropositive participants becoming seronegative to this antibody at 195 days. Widely used serological tests that depend on the N-antibody will therefore significantly underestimate the prevalence of infection following the majority of infections.\n\nSignificance statementWe believe that our study has significant and urgent public health and translational impact. Firstly, our findings demonstrate that the half-life of the SARS-CoV-2 nucleoprotein antibody is only 52 days. This has immediate and important implications for large-scale seroprevalence surveys, government policy and mathematical modelling predictions which rely on serological tests that target this antibody. Secondly, the slower decay of the SARS-CoV-2 spike protein antibody identified in this study makes assays to the spike protein a more reliable target for serological assays in the longer term. We demonstrate a strong positive linear correlation between spike/RBD antibody and ACE-2 receptor binding in vitro. Our findings are therefore likely to reflect the time to loss of a functional antibody response in SARS-CoV-2.\n\nFundingGOSH charity, Wellcome Trust (201470/Z/16/Z and 220565/Z/20/Z). GOSH NIHR Funded Biomedical Research Centre.\n\nTrial registration numberNCT04380896.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Louis Grandjean", - "author_inst": "University College London, Institute of Child Health" - }, - { - "author_name": "Anja Saso", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Arturo Ortiz", - "author_inst": "Imperial College" - }, - { - "author_name": "Tanya Lam", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "James Hatcher", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Rosie Thistlethwaite", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Mark Harris", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Timothy Best", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Marina Johnson", - "author_inst": "University College London" - }, - { - "author_name": "Helen Wagstaffe", - "author_inst": "University College London" - }, - { - "author_name": "Elizabeth Ralph", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Annabelle Mai", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Caroline Colijn", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Judith Breuer", - "author_inst": "University College London" - }, - { - "author_name": "Matthew Buckland", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Kimberly Gilmour", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "David Goldblatt", - "author_inst": "University College London" - }, - { - "author_name": "- The Co-Stars Study Team", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.21.213777", "rel_title": "Cellular events of acute, resolving or progressive COVID-19 in SARS-CoV-2 infected non-human primates", @@ -1297184,6 +1300494,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "addiction medicine" }, + { + "rel_doi": "10.1101/2020.07.21.214049", + "rel_title": "Intranasal Immunization with a Lentiviral Vector Coding for SARS-CoV-2 Spike Protein Confers Vigorous Protection in Pre-Clinical Animal Models", + "rel_date": "2020-07-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.21.214049", + "rel_abs": "To develop a vaccine candidate against COVID-19, we generated a Lentiviral Vector (LV), eliciting neutralizing antibodies against the Spike glycoprotein of SARS-CoV-2. Systemic vaccination by this vector in mice, in which the expression of the SARS-CoV-2 receptor hACE2 has been induced by transduction of respiratory tract cells by an adenoviral vector, conferred only partial protection, despite an intense serum neutralizing activity. However, targeting the immune response to the respiratory tract through an intranasal boost with this LV resulted in > 3 log10 decrease in the lung viral loads and avoided local inflammation. Moreover, both integrative and non-integrative LV platforms displayed a strong vaccine efficacy and inhibited lung deleterious injury in golden hamsters, which are naturally permissive to SARS-CoV-2 replication and restitute the human COVID-19 physiopathology. Our results provide evidence of marked prophylactic effects of the LV-based vaccination against SARS-CoV-2 and designate the intranasal immunization as a powerful approach against COVID-19.\n\nHighlightsA lentiviral vector encoding for Spike predicts a promising COVID-19 vaccine\n\nTargeting the immune response to the upper respiratory tract is key to protection\n\nIntranasal vaccination induces protective mucosal immunity against SARS-CoV-2\n\nLung anti-Spike IgA responses correlate with protection and reduced inflammation", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Min-Wen Ku", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Maryline Bourgine", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Pierre Authie", + "author_inst": "Institut Pasteur - TheraVectys" + }, + { + "author_name": "Jodie Lopez", + "author_inst": "Institut Pasteur - TheraVectys" + }, + { + "author_name": "Kirill Nemirov", + "author_inst": "Institut Pasteur - TheraVectys" + }, + { + "author_name": "Fanny Moncoq", + "author_inst": "Institut Pasteur - TheraVectys" + }, + { + "author_name": "Amandine Noirat", + "author_inst": "Institut Pasteur - Theravectys" + }, + { + "author_name": "Benjamin Vesin", + "author_inst": "Institut Pasteur - TheraVectys" + }, + { + "author_name": "Fabien Nevo", + "author_inst": "Institut Pasteur - TheraVectys" + }, + { + "author_name": "Catherine Blanc", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Philippe Souque", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Houda Tabbal", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Emeline Simon", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Marine Le Dudal", + "author_inst": "IMMR" + }, + { + "author_name": "Francoise Guinet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Laurence Fiette", + "author_inst": "IMMR" + }, + { + "author_name": "Hugo Mouquet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Francois Anna", + "author_inst": "Institut Pasteur - TheraVectys" + }, + { + "author_name": "Annette Martin", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Nicolas Escriou", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Laleh Majlessi", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Pierre Charneau", + "author_inst": "Institut Pasteur - TheraVectys" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.07.21.214098", "rel_title": "Molecular mechanism of SARS-CoV-2 cell entry inhibition via TMPRSS2 by Camostat and Nafamostat mesylate", @@ -1298683,93 +1302096,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.19.20152322", - "rel_title": "Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy", - "rel_date": "2020-07-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.19.20152322", - "rel_abs": "From February to April, 2020, Lombardy (Italy) was the area who worldwide registered the highest numbers of SARS-CoV-2 infection. By extensively analyzing 346 whole SARS-CoV-2 genomes, we demonstrated the simultaneous circulation in Lombardy of two major viral lineages, likely derived from multiple introductions, occurring since the second half of January. Seven single nucleotide polymorphisms (five of them non-synonymous) characterized the SARS-CoV-2 sequences, none of them affecting N-glycosylation sites. These two lineages, and the presence of two well defined clusters inside Lineage 1, revealed that a sustained community transmission was ongoing way before the first COVID-19 case found in Lombardy.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Claudia Alteri", - "author_inst": "University of Milan" - }, - { - "author_name": "Valeria Cento", - "author_inst": "University of Milan" - }, - { - "author_name": "Antonio Piralla", - "author_inst": "Fondazione IRCCS Policlinico San Matteo" - }, - { - "author_name": "Valentino Costabile", - "author_inst": "University of Milan" - }, - { - "author_name": "Monica Tallarita", - "author_inst": "Fondazione IRCCS Policlinico San Matteo" - }, - { - "author_name": "Luna Colagrossi", - "author_inst": "Bambino Gesu Children's Hospital" - }, - { - "author_name": "Silvia Renica", - "author_inst": "University of Milan" - }, - { - "author_name": "Federica Giardina", - "author_inst": "Fondazione IRCCS Policlinico San Matteo" - }, - { - "author_name": "Federica Novazzi", - "author_inst": "Fondazione IRCCS Policlinico San Matteo" - }, - { - "author_name": "Stefano Gaiarsa", - "author_inst": "Fondazione IRCCS Policlinico San Matteo" - }, - { - "author_name": "Elisa Matarazzo", - "author_inst": "University of Milan" - }, - { - "author_name": "Maria Antonello", - "author_inst": "University of Milan" - }, - { - "author_name": "Chiara Vismara", - "author_inst": "ASST Grande Ospedale Metropolitano Niguarda" - }, - { - "author_name": "Roberto Fumagalli", - "author_inst": "ASST Grande Ospedale Metropolitano Niguarda" - }, - { - "author_name": "Oscar Massimiliano Epis", - "author_inst": "ASST Grande Ospedale Metropolitano Niguarda" - }, - { - "author_name": "Massimo Puoti", - "author_inst": "ASST Grande Ospedale Metropolitano Niguarda" - }, - { - "author_name": "Carlo Federico Perno", - "author_inst": "University of Milan" - }, - { - "author_name": "Fausto Baldanti", - "author_inst": "Fondazione IRCCS Policlinico San Matteo" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.18.210120", "rel_title": "High expression of angiotensin-converting enzyme-2 (ACE2) on tissue macrophages that may be targeted by virus SARS-CoV-2 in COVID-19 patients", @@ -1298954,6 +1302280,85 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.07.18.210013", + "rel_title": "The folate antagonist methotrexate diminishes replication of the coronavirus SARS-CoV-2 and enhances the antiviral efficacy of remdesivir in cell culture models", + "rel_date": "2020-07-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.18.210013", + "rel_abs": "The search for successful therapies of infections with the coronavirus SARS-CoV-2 is ongoing. We tested inhibition of host cell nucleotide synthesis as a promising strategy to decrease the replication of SARS-CoV-2-RNA, thus diminishing the formation of virus progeny. Methotrexate (MTX) is an established drug for cancer therapy and to induce immunosuppression. The drug inhibits dihydrofolate reductase and other enzymes required for the synthesis of nucleotides. Strikingly, the replication of SARS-CoV-2 was inhibited by MTX in therapeutic concentrations around 1 M, leading to more than 1000-fold reductions in virus progeny in Vero C1008 (Vero E6) as well as Calu-3 cells. Virus replication was more sensitive to equivalent concentrations of MTX than of the established antiviral agent remdesivir. MTX strongly diminished the synthesis of viral structural proteins and the amount of released virus RNA. Virus replication and protein synthesis were rescued by folinic acid (leucovorin) and also by inosine, indicating that purine depletion is the principal mechanism that allows MTX to reduce virus RNA synthesis. The combination of MTX with remdesivir led to synergistic impairment of virus replication, even at 300 nM MTX. The use of MTX in treating SARS-CoV-2 infections still awaits further evaluation regarding toxicity and efficacy in infected organisms, rather than cultured cells. Within the frame of these caveats, however, our results raise the perspective of a two-fold benefit from repurposing MTX for treating COVID-19. Firstly, its previously known ability to reduce aberrant inflammatory responses might dampen respiratory distress. In addition, its direct antiviral activity described here would limit the dissemination of the virus.\n\nSIGNIFICANCEO_LIMTX is one of the earliest cancer drugs to be developed, giving rise to seven decades of clinical experience. It is on the World Health Organizations List of Essential Medicines, can be administered orally or parenterally, and its costs are at single digit {euro} or $ amounts/day for standard treatment. In case of its successful further preclinical evaluation for treating SARS-CoV-2 infections, its repurposing to treat COVID-19 would thus be feasible, especially under low-resource conditions.\nC_LIO_LIAdditional drugs exist to interfere with the synthesis of nucleotides, e.g. additional folate antagonists, inhibitors of GMP synthetase, or inhibitors of dihydroorotate dehydrogenase (DHODH). Such inhibitors have been approved as drugs for different purposes and might represent further therapeutic options against infections with SARS-CoV-2\nC_LIO_LIRemdesivir is currently the most established drug for treating COVID-19. Our results argue that MTX and remdesivir, even at moderate concentrations, can act in a synergistic fashion to repress virus replication to a considerably greater extent than either drug alone.\nC_LIO_LICOVID-19, in its severe forms, is characterized by pneumonia and acute respiratory distress syndrome, and additional organ involvements. These manifestations are not necessarily a direct consequence of virus replication and cytopathic effects, but rather a result of an uncontrolled inflammatory and immune response. Anti-inflammatory drugs such as glucocorticoids are thus being evaluated for treating COVID-19. However, this bears the risk of re-activating virus spread by suppressing a sufficient and specific immune response. In this situation, it is tempting to speculate that MTX might suppress both excessive inflammation as well as virus replication at the same time, thus limiting both the pathogenesis of pneumonia and also the spread of virus within a patient.\nC_LI", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Kim M Stegmann", + "author_inst": "University Medical Center Goettingen" + }, + { + "author_name": "Antje Dickmanns", + "author_inst": "University Medical Center Goettingen" + }, + { + "author_name": "Sabrina Gerber", + "author_inst": "University Medical Center Goettingen" + }, + { + "author_name": "Vella Nikolova", + "author_inst": "University Medical Center Goettingen" + }, + { + "author_name": "Luisa Klemke", + "author_inst": "University Medical Center Goettingen" + }, + { + "author_name": "Valentina Manzini", + "author_inst": "University Medical Center Goettingen" + }, + { + "author_name": "Denise Schloesser", + "author_inst": "University Medical Center Goettingen" + }, + { + "author_name": "Cathrin Bierwirth", + "author_inst": "University Medical Center Goettingen" + }, + { + "author_name": "Julia Freund", + "author_inst": "University Medical Center Goettingen" + }, + { + "author_name": "Maren Sitte", + "author_inst": "University Medical Center Goettingen" + }, + { + "author_name": "Raimond Lugert", + "author_inst": "University Medical Center Goettingen" + }, + { + "author_name": "Gabriela Salinas", + "author_inst": "University Medical Center Goettingen" + }, + { + "author_name": "Dirk Goerlich", + "author_inst": "Max Planck Institute of Biophysical Chemistry" + }, + { + "author_name": "Bernd Wollnik", + "author_inst": "University Medical Center Goettingen" + }, + { + "author_name": "Uwe Gross", + "author_inst": "University Medical Center Goettingen" + }, + { + "author_name": "Matthias Dobbelstein", + "author_inst": "University Medical Center Goettingen" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.07.19.179101", "rel_title": "Haplotype Explorer: an infection cluster visualization tool for spatiotemporal dissection of the COVID-19 pandemic", @@ -1300085,33 +1303490,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.16.20155200", - "rel_title": "Gender and trust in government modify the association between mental health and stringency of social distancing related public health measures to reduce COVID-19: a global online survey", - "rel_date": "2020-07-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.16.20155200", - "rel_abs": "ObjectivesTo investigate the associations between stringency of COVID-19 social distancing policies and mental health outcomes, and the moderating effect of trust in government and gender.\n\nDesign and settingCross sectional study involving secondary analysis of publicly available data from a global online COVID-19 survey and the Oxford COVID-19 Government Response Tracker.\n\nParticipants106,497 participants from 58 countries.\n\nMain outcome measuresOutcomes were a worries index and a depression index. Predictors were stringency of policies, trust in government, and gender. Multivariable regression was conducted to determine the three-way interaction between the predictor variables for mental health outcomes, adjusting for age, income and education.\n\nResultsThe median age of participants (56.4% women) was 37 years (interquartile range 29 to 48 years). Women had higher worries and depression scores than men. 45.4% distrusted the government and 43.8% trusted the government to take care of its citizens. Among those who strongly trusted the government, an increase in the stringency of policies was associated with a significant increase in the worries index. Among men who distrusted the government, an increase in policy stringency was associated with an increase in the depression index but not the worries index. In women that strongly distrusted the government, there was an inversed U-shaped association between policy stringency and both the worries and depression indices.\n\nConclusionAs the stringency of public health measures increases, so too do depression and worries. The association is moderated by gender and trust in government. For safe and effective public health measures, governments should develop strategies to increase trust in their actions.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Lily O'Hara", - "author_inst": "Qatar University" - }, - { - "author_name": "Hanan F Abdul Rahim", - "author_inst": "Qatar University" - }, - { - "author_name": "Zumin Shi", - "author_inst": "Qatar University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.17.20155242", "rel_title": "Genetic inhibition of interleukin-6 receptor signaling and Covid-19", @@ -1300468,6 +1303846,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.07.16.20155747", + "rel_title": "Barriers to online learning in the time of COVID-19: A national survey of medical students in the Philippines", + "rel_date": "2020-07-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.16.20155747", + "rel_abs": "IntroductionIn March 2020, the coronavirus disease 2019 (COVID-19) pandemic forced medical schools in the Philippines to stop face-to-face learning activities and abruptly shift to an online curriculum. This study aimed to identify barriers to online learning from the perspective of medical students in a developing country.\n\nMethodsThe authors sent out an electronic survey to medical students in the Philippines from 11 to 24 May 2020. Using a combination of multiple choice, Likert scale, and open-ended questions, the following data were obtained: demographics, medical school information, access to technological resources, study habits, living conditions, self-assessment of capacity for and perceived barriers to online learning, and proposed interventions. Descriptive statistics were calculated. Responses were compared between student subgroups using nonparametric tests.\n\nResultsAmong 3,670 medical students, 3,421 (93%) owned a smartphone and 3,043 (83%) had a laptop or desktop computer. To access online resources, 2,916 (79%) had a postpaid internet subscription while 696 (19%) used prepaid mobile data. Under prevailing conditions, only 1,505 students (41%) considered themselves physically and mentally capable of engaging in online learning. Barriers were classified under five categories: technological, individual, domestic, institutional, and community barriers. Most frequently encountered were difficulty adjusting learning styles, having to perform responsibilities at home, and poor communication between educators and learners.\n\nDiscussionMedical students in the Philippines confronted several interrelated barriers as they tried to adapt to online learning. By implementing student-centered interventions, medical schools and educators play a significant role in addressing these challenges during the COVID-19 pandemic and beyond.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ronnie E Baticulon", + "author_inst": "Department of Anatomy, University of the Philippines College of Medicine" + }, + { + "author_name": "Nicole Rose I Alberto", + "author_inst": "University of the Philippines College of Medicine" + }, + { + "author_name": "Maria Beatriz C Baron", + "author_inst": "University of the Philippines College of Medicine" + }, + { + "author_name": "Robert Earl C Mabulay", + "author_inst": "University of the Philippines College of Medicine" + }, + { + "author_name": "Lloyd Gabriel T Rizada", + "author_inst": "University of the Philippines College of Medicine" + }, + { + "author_name": "Jinno Jenkin Sy", + "author_inst": "University of the Philippines College of Medicine" + }, + { + "author_name": "Christl Jan S Tiu", + "author_inst": "University of the Philippines College of Medicine" + }, + { + "author_name": "Charlie A Clarion", + "author_inst": "Section of Pulmonary Medicine, Department of Internal Medicine, Philippine General Hospital" + }, + { + "author_name": "John Carlo B Reyes", + "author_inst": "Department of Parasitology, University of the Philippines College of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "medical education" + }, { "rel_doi": "10.1101/2020.07.17.20155994", "rel_title": "Effect of corticosteroid treatment on 1376 hospitalized COVID-19 patients. A cohort study.", @@ -1301923,61 +1305352,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.16.206847", - "rel_title": "Longitudinal analysis of the humoral response to SARS-CoV-2 spike RBD in convalescent plasma donors", - "rel_date": "2020-07-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.16.206847", - "rel_abs": "Hema-Quebec, the blood supplier in the Province of Quebec, Canada, collects and tests convalescent plasma used in a clinical trial to determine the clinical efficacy of this product for the treatment of hospitalized COVID-19 patients. So far, we have collected 1159 plasma units from 282 COVID-19 convalescent donors. The presence of antibodies to the receptor binding domain (RBD) of SARS-CoV-2 spike protein in convalescent donors was established at the first donation. Seropositive donors were asked to donate additional plasma units every six days. Until now, 15 donors have donated at least four times and, in some cases, up to nine times. This allowed us to perform a longitudinal analysis of the persistence of SARS-CoV-2 RBD-specific antibodies in these repeat donors, with the first donation occurring 33-77 days after symptoms onset and donations up to 71-114 days after symptoms onset thereafter. In all donors, the level of antibodies remained relatively stable up to about 76 days after symptoms onset but then started to decrease more rapidly to reach, in some convalescent donors, a seronegative status within 100-110 days after symptoms onset. The decline in anti-RBD antibodies was not related to the number of donations but strongly correlated with the numbers of days after symptoms onset (r = 0.821). This suggests that de novo secretion of SARS-CoV-2 RBD antibodies by short-lived plasma cells stopped about 2-3 months after disease onset, an observation that has important implications for convalescent plasma collection and seroprevalence studies undertaken several months after the peak of infection.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Jos\u00e9e Perreault", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - }, - { - "author_name": "Tony Tremblay", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - }, - { - "author_name": "Marie-Jos\u00e9e Fournier", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - }, - { - "author_name": "Mathieu Drouin", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - }, - { - "author_name": "Guillaume Beaudoin-Bussi\u00e8res", - "author_inst": "CRCHUM" - }, - { - "author_name": "J\u00e9r\u00e9mie Pr\u00e9vost", - "author_inst": "CRCHUM / Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Antoine Lewin", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - }, - { - "author_name": "Philippe B\u00e9gin", - "author_inst": "CHU Ste-Justine" - }, - { - "author_name": "Andr\u00e9s Finzi", - "author_inst": "Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Ren\u00e9e Bazin", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.07.15.204339", "rel_title": "Mutational dynamics and transmission properties of SARS-CoV-2 superspreading events in Austria", @@ -1302286,6 +1305660,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.14.20153270", + "rel_title": "Dynamics and future of SARS-CoV-2 in the human host", + "rel_date": "2020-07-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.14.20153270", + "rel_abs": "Forecasting trends in COVID-19 infections is vital for the global economy, national governments and physical and mental well-being. Using the per capita number of new cases as a proxy for the abundance of the SARS-CoV-2 virus, and the number of deaths as a measure of virulence, the dynamics of the pandemic and the outcomes emerging from it are examined for three locations (England, Italy and New York State). The data are analysed with a new version of a population dynamics model that combines exponential/logistic growth with time-varying carrying capacity, allowing predictions of persistence or extinction of the virus. In agreement with coevolutionary theory, the model suggests a transition from exponential virus growth to low abundance, coupled with reduced virulence, during colonisation of the alternate human host. The structure of the model allows a straightforward assessment of key parameters, which can be contrasted with standard epidemiological models and interpreted with respect to ecological and evolutionary processes and isolation policies.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Michael Gillman", + "author_inst": "University of Lincoln" + }, + { + "author_name": "Nuno Crokidakis", + "author_inst": "Universidade Federal Fluminense" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.13.20152181", "rel_title": "Progressive worsening of the respiratory and gut microbiome in children during the first two months of COVID-19", @@ -1304161,89 +1307558,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.14.20151126", - "rel_title": "SARS-CoV-2 infection induces robust, neutralizing antibody responses that are stable for at least three months", - "rel_date": "2020-07-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.14.20151126", - "rel_abs": "SARS-CoV-2 has caused a global pandemic with millions infected and numerous fatalities. Questions regarding the robustness, functionality and longevity of the antibody response to the virus remain unanswered. Here we report that the vast majority of infected individuals with mild-to-moderate COVID-19 experience robust IgG antibody responses against the viral spike protein, based on a dataset of 19,860 individuals screened at Mount Sinai Health System in New York City. We also show that titers are stable for at least a period approximating three months, and that anti-spike binding titers significantly correlate with neutralization of authentic SARS-CoV-2. Our data suggests that more than 90% of seroconverters make detectible neutralizing antibody responses and that these titers are stable for at least the near-term future.\n\nOne Sentence SummaryAntibody responses induced by natural mild-to-moderate SARS-CoV-2 infection are robust, neutralizing and are stable for at least 3 months.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Ania Wajnberg", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Fatima Amanat", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Adolfo Firpo", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Deena Altman", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Mark Bailey", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Mayce Mansour", - "author_inst": "MOUNT SINAI HOSPITAL" - }, - { - "author_name": "Meagan McMahon", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Philip Meade", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Damodara Rao Mendu", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Kimberly Muellers", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Daniel Stadlbauer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Kimberly Stone", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Shirin Strohmeier", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Judith Aberg", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "David Reich", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Florian Krammer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Carlos Cordon-Cardo", - "author_inst": "Mount Sinai Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.15.20140095", "rel_title": "Preparedness, Perceived Impact and Concerns of health Care Workers in a Teaching Hospital during Coronavirus Disease 2019 (COVID-19)", @@ -1304372,6 +1307686,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pain medicine" }, + { + "rel_doi": "10.1101/2020.07.16.20150292", + "rel_title": "Continuity of services for patients with tuberculosis in China in the COVID-19 era", + "rel_date": "2020-07-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.16.20150292", + "rel_abs": "It is crucial to maintain continuity of essential services for people affected by tuberculosis (TB). Efforts to deliver these essential services in many global settings have been complicated by the emergence and global spread of SARS-CoV-2 and the pandemic of COVID-19. Understanding how the COVID-19 pandemic has impacted the availability of TB diagnostic and treatment services is critical for identifying policies that can mitigate disruptions of these essential services. China has a dual burden of TB and COVID-19. We conducted a survey and collected data from 13 provinces in China to evaluate the early impact of COVID-19 on TB services and to document interventions that were adopted to maintain the continuity services for TB patients during the pandemic. We use these data to identify additional opportunities which will improve the ability of TB programs to maintain essential services during this crisis. While health systems and underlying epidemiology differ between countries, we believe that sharing Chinas experience can inform the design of locally tailored strategies to maintain essential TB services during the COVID-19 pandemic.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Xin Shen", + "author_inst": "Division of TB and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China" + }, + { + "author_name": "Wei Sha", + "author_inst": "Department of Tuberculosis, Shanghai Pulmonary Hospital, Shanghai, China" + }, + { + "author_name": "Chongguang Yang", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA" + }, + { + "author_name": "Qichao Pan", + "author_inst": "Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China" + }, + { + "author_name": "Ted Cohen", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA" + }, + { + "author_name": "Shiming Chen", + "author_inst": "China Anti-tuberculosis Association, Beijing, China" + }, + { + "author_name": "Qingshan Cai", + "author_inst": "Division of Tuberculosis, Zhejiang Provincial Integrated Chinese and Western Medicine Hospital, Hangzhou, Zhejiang Province, China" + }, + { + "author_name": "Xiaohong Kan", + "author_inst": "Department of Scientific Research and Education, Anhui Chest Hospital, Hefei, Anhui Province, China" + }, + { + "author_name": "Peilan Zong", + "author_inst": "Division of Tuberculosis, Jiangxi Chest Hospital, Nanchang, Jiangxi Province, China" + }, + { + "author_name": "Zhong Zeng", + "author_inst": "Division of Tuberculosis, The Fifth People's Hospital, Ganzhou, Jiangxi Province, China" + }, + { + "author_name": "Shouyong Tan", + "author_inst": "Department of Tuberculosis, Guangzhou Chest Hospital. Guangzhou, Guangdong Province, China" + }, + { + "author_name": "Ruixia Liang", + "author_inst": "Department of Tuberculosis, Henan Provincial Chest Hospital, Zhengzhou, Henan Province, China" + }, + { + "author_name": "Liqiong Bai", + "author_inst": "Hunan Chest Hospital, Changsha, Hunan Province, China" + }, + { + "author_name": "Jia'An Xia", + "author_inst": "South Five Disease Zones, Wuhan Jinyintan Hospital, Wuhan, Hubei Province, China" + }, + { + "author_name": "Shucai Wu", + "author_inst": "Hebei Province Chest Hospital, Shijiazhuang, Hebei Province, China" + }, + { + "author_name": "Peng Sun", + "author_inst": "Tuberculosis Hospital of JiLin Province, Changchun, Jilin Province, China" + }, + { + "author_name": "Guihui Wu", + "author_inst": "Department of Tuberculosis, Public Health Clinical Center of Chengdu, Chengdu, Sichuan Province, China" + }, + { + "author_name": "Cui Cai", + "author_inst": "Tuberculosis Diagnosis and Treatment Quality Control Center, Guiyang Public Health Treatment Center, Zunyi Medical University, Zunyi, Guizhou Province, China" + }, + { + "author_name": "Xiaolin Wang", + "author_inst": "The Fourth People's Hospital of Ningxia Hui Autonomous Region, Yinchuan, Ningxia Hui Autonomous Region, China" + }, + { + "author_name": "Kaixing Ai", + "author_inst": "Shanghai Pulmonary Hospital, Shanghai, China" + }, + { + "author_name": "Jianjun Liu", + "author_inst": "Chinese Center for Diseases Control and Prevention, Beijing, China" + }, + { + "author_name": "Zheng'an Yuan", + "author_inst": "Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.07.17.20155986", "rel_title": "ABO polymorphism and SARS-CoV-2 infection - a meta-analysis", @@ -1306031,69 +1309448,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.17.20155929", - "rel_title": "Role of intermediate care unit admission and non-invasive respiratory support during the COVID-19 pandemic: a retrospective cohort study", - "rel_date": "2020-07-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20155929", - "rel_abs": "BackgroundThe COVID-19 pandemic has led to shortage of Intensive Care Unit (ICU) capacity. We developed a triage strategy including non-invasive respiratory support and admission to the intermediate care unit (IMCU). ICU admission was restricted to patients requiring invasive ventilation.\n\nObjectivesThe aim of this study is to describe the characteristics and outcomes of patients admitted to the intermediate care unit.\n\nMethodRetrospective cohort including consecutive patients admitted between March 28th and April 27th 2020. The primary outcome was the proportion of patients with severe hypoxemic respiratory failure avoiding ICU admission. Secondary outcomes included the rate of emergency intubation, 28-days mortality and predictors of ICU admission.\n\nResultsOne hundred fifty seven patients with COVID-19 associated pneumonia were admitted to the IMCU. Among the 85 patients admitted for worsening respiratory failure, 52/85 (61%) avoided ICU admission. In multivariate analysis, PaO2/FiO2 (OR 0.98; 95% CI 0.96 to 0.99) and Body Mass Index (OR 0.88; 95% CI 0.78 to 0.98) were significantly associated with ICU admission. No death or emergency intubation occurred in the intermediate care unit. Among the 72 patients transferred from the ICU, 60/72 (83%) presented neurological complications.\n\nConclusionsNon-invasive respiratory support including High-Flow Nasal Oxygen and continuous positive airway pressure prevents ICU admission for a large proportion of patients with COVID-19 hypoxemic respiratory failure. In the context of the COVID pandemic, intermediate care units may play an important role in preserving ICU capacity by avoiding ICU admission for patients with worsening respiratory failure and allowing early discharge of ICU patients.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Olivier Grosgurin", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Antonio Leidi", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Pauline Darbellay-Farhoumand", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Sebastian Carballo", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Jean-luc Reny", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Dan Adler", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Bernardo Bollen Pinto", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Anne Rossel", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Jacques Serratrice", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Thomas Agoritsas", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Jerome Stirnemann", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Christophe Marti", - "author_inst": "Geneva University Hospitals" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.07.17.20155937", "rel_title": "Disease-associated antibody phenotypes and probabilistic seroprevalence estimates during the emergence of SARS-CoV-2", @@ -1306450,6 +1309804,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.07.17.208371", + "rel_title": "Modeling the Impact of Lock-down on COVID-19 Spread in Malaysia", + "rel_date": "2020-07-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.17.208371", + "rel_abs": "After a breakdown notified in Wuhan, China in December 2019, COVID-19 is declared as pandemic diseases. To the date more than 13 million confirmed cases and more than half a million are dead around the world. This virus also attached Malaysia in its immature stage where 8718 cases were confirmed and 122 were declared as death. Malaysia responsibly controlled the spread by enforcing MCO. Hence, it is required to visualize the pattern of Covid-19 spread. Also, it is necessary to estimate the impact of the enforced prevention measures. In this paper, an infectious disease dynamic modeling (SEIR) is used to estimate the epidemic spread in Malaysia. The main assumption is to update the reproduction number Rt with respect to the implemented prevention measures. For a time-frame of five month, the Rt was assumed to vary between 2.9 and 0.3. Moreover, the manuscript includes two possible scenarios: the first will be the extension of the stricter measures all over the country, and the second will be the gradual lift of the lock-down. After implementing several stages of lock-down we have found that the estimated values of the Rt with respect to the strictness degree varies between 0.2 to 1.1. A continuous strict lock-down may reduce the Rt to 0.2 and accordingly the estimated active cases will be reduced to 20 by the beginning of September 2020. In contrast, the second scenario considers a gradual lift of the enforced prevention measures by the end of June 2020, here we have considered three possible outcomes according to the MCO relaxation. Thus, the estimated values of Rt = 0.7, 0.9, 1.1, which shows a rapid increase in the number of active cases. The implemented SEIR model shows a close resemblance with the actual data recorded from 10, March till 7, July 2020.\n\nAuthor summaryConceptualization, A.A.A; methodology, A.A.A, N.M; validation, A.A.A, N.M; formal analysis, A.A.A; investigation, N.M, A.A.A; resources, G.E.M.A, L.T; data collection, L.T, N.M; writing--original draft preparation, A.A.A, L.T, G.E.M.A, N.M; writing--review and editing, V.S.A, S.C.D, B.S.G, P.S, S.A.B.M.Z, N.M; visualization, N.M; supervision, V.S.A; project administration, V.S.A. All authors have read and agreed to the published version of the manuscript", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Altahir A. Altahir", + "author_inst": "Universiti Teknologi PETRONAS" + }, + { + "author_name": "Nirbhay Mathur", + "author_inst": "Universiti Teknologi Petronas" + }, + { + "author_name": "Loshini Thiruchelvam", + "author_inst": "Universiti Teknologi PETRONAS" + }, + { + "author_name": "Ghulam E. Mustafa Abro", + "author_inst": "Universiti Teknologi PETRONAS" + }, + { + "author_name": "Syaimaa S. M. Radzi", + "author_inst": "Universiti Teknologi PETRONAS" + }, + { + "author_name": "Sarat C Dass", + "author_inst": "Heriot-Watt University - Malaysia Campus" + }, + { + "author_name": "Balvinder Singh Gill", + "author_inst": "Kementerian Kesihatan Malaysia" + }, + { + "author_name": "Patrick Sebastian", + "author_inst": "Universiti Teknologi PETRONAS" + }, + { + "author_name": "Saiful A. Zulkifli", + "author_inst": "Universiti Teknologi PETRONAS" + }, + { + "author_name": "Vijanth S. Asirvadam", + "author_inst": "Universiti Teknologi PETRONAS" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.07.17.207019", "rel_title": "Identification of SARS-CoV-2 3CL Protease Inhibitors by a Quantitative High-throughput Screening", @@ -1307669,89 +1311078,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.15.20154765", - "rel_title": "Controlling COVID-19 via test-trace-quarantine", - "rel_date": "2020-07-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154765", - "rel_abs": "Initial COVID-19 containment in the United States focused on limiting mobility, including school and workplace closures. However, these interventions have had enormous societal and economic costs. Here we demonstrate the feasibility of an alternative control strategy, test-trace-quarantine: routine testing of primarily symptomatic individuals, tracing and testing their known contacts, and placing their contacts in quarantine. We performed this analysis using Covasim, an open-source agent-based model, which was calibrated to detailed demographic, mobility, and epidemiological data for the Seattle region from January through June 2020. With current levels of mask use and schools remaining closed, we found that high but achievable levels of testing and tracing are sufficient to maintain epidemic control even under a return to full workplace and community mobility and with low vaccine coverage. The easing of mobility restrictions in June 2020 and subsequent scale-up of testing and tracing programs through September provided real-world validation of our predictions. Although we show that test-trace-quarantine can control the epidemic in both theory and practice, its success is contingent on high testing and tracing rates, high quarantine compliance, relatively short testing and tracing delays, and moderate to high mask use. Thus, in order for test-trace-quarantine to control transmission with a return to high mobility, strong performance in all aspects of the program is required.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Cliff C Kerr", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Dina Mistry", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Robyn M Stuart", - "author_inst": "Department of Mathematical Sciences, University of Copenhagen" - }, - { - "author_name": "Katherine Rosenfeld", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Gregory R Hart", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Rafael C Nunez", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Jamie A Cohen", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Prashanth Selvaraj", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Romesh G Abeysuriya", - "author_inst": "Burnet Institute" - }, - { - "author_name": "Michal Jastrzebski", - "author_inst": "GitHub, Inc." - }, - { - "author_name": "Lauren George", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Brittany Hagedorn", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Jasmina Panovska-Griffiths", - "author_inst": "UCL" - }, - { - "author_name": "Meaghan Fagalde", - "author_inst": "Public Health - Seattle and King County" - }, - { - "author_name": "Jeffrey Duchin", - "author_inst": "Public Health - Seattle and King County" - }, - { - "author_name": "Michael Famulare", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Daniel J Klein", - "author_inst": "Institute for Disease Modeling" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.14.20153775", "rel_title": "Direct-to-Consumer Chat-Based Remote Care Before and During the COVID-19 Outbreak", @@ -1307864,6 +1311190,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.07.15.20154559", + "rel_title": "Moderate to vigorous physical activity and sedentary behavior change in self-isolating adults during the COVID-19 pandemic in Brazil: A cross-sectional survey exploring correlates", + "rel_date": "2020-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154559", + "rel_abs": "BackgroundSelf-distancing measures imposed major changes in daily life. This study aimed to (i) evaluate the changes (pre-versus during pandemic) in time spent in moderate to vigorous physical activity (MVPA) and sedentary behavior (SB) in self-isolating Brazilians during the COVID-19 pandemic, and (ii) to explore correlates of MVPA and SB.\n\nMethodsA cross-sectional self-report online survey, evaluating the time spent in MVPA and SB pre and during the COVID-19 pandemic. Sociodemographic, behavioral, clinical, variables, and time in self-isolation were also obtained. Changes in MVPA and SB and their correlates were explored using generalized estimating equations (GEE).\n\nResultsA total of 877 participants (72.7% women, 53.7% young adults [18-34 years]) were included. Overall, participants reported a 59.7% reduction (95%CI:35.6 to 82.2) in time spent on MVPA during the pandemic. Time spent in SB increased 42.0% (95%CI:31.7 to 52.5). Greater reductions in MVPA and/or increases in SB were seen in younger adults, those not married, those employed and those with a self-reported previous diagnosis of a mental disorder.\n\nConclusionsPeople in self-isolation significantly reduced MVPA levels and increased SB. Public health strategies should be implemented during epidemic times to mitigate the impact of self-isolation on MVPA and SB, particularly in vulnerable groups.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Felipe Schuch", + "author_inst": "Universidade Federal de Santa Maria" + }, + { + "author_name": "Rugero Bulzing", + "author_inst": "Universidade Federal de Santa Maria" + }, + { + "author_name": "Jacob Meyer", + "author_inst": "Iowa State University" + }, + { + "author_name": "Guillermo Lopez-Sanchez", + "author_inst": "University of Murcia" + }, + { + "author_name": "Igor Grabovac", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Peter Willeit", + "author_inst": "University of Innsbruck" + }, + { + "author_name": "Davy Vancampfort", + "author_inst": "KU Leuven" + }, + { + "author_name": "Cristina Caperchione", + "author_inst": "University of Technology Sydney" + }, + { + "author_name": "Kabir Sadarangani", + "author_inst": "Universidade Autonoma de Chile" + }, + { + "author_name": "Andre Werneck", + "author_inst": "Universidade de Sao Paulo" + }, + { + "author_name": "Philip Ward", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Mark Tully", + "author_inst": "Ulster University" + }, + { + "author_name": "Lee Smith", + "author_inst": "Anglia Ruskin University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "sports medicine" + }, { "rel_doi": "10.1101/2020.07.14.20153981", "rel_title": "Cell-based culture of SARS-CoV-2 informs infectivity and safe de-isolation assessments during COVID-19", @@ -1309203,41 +1312596,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.13.20153049", - "rel_title": "Mechanistic Transmission Modeling of COVID-19 on the Diamond Princess Cruise Ship Demonstrates the Importance of Aerosol Transmission", - "rel_date": "2020-07-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20153049", - "rel_abs": "BackgroundThe current prevailing position is that coronavirus disease 2019 (COVID-19) is transmitted primarily through large respiratory droplets within close proximity (i.e., 1-2 m) of infected individuals. However, quantitative information on the relative importance of specific transmission pathways of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (i.e., droplets, aerosols, and fomites across short- and long-range distances) remains limited.\n\nMethodsTo evaluate the relative importance of multiple transmission routes for SARS-CoV-2, we leveraged detailed information available from the Diamond Princess Cruise Ship outbreak that occurred in early 2020. We developed a framework that combines stochastic Markov chain and negative exponential dose-response modeling with available empirical data on mechanisms of SARS-CoV-2 dynamics and human behaviors, which informs a modified version of the Reed-Frost epidemic model to predict daily and cumulative daily case counts on the ship. We modeled 21,600 scenarios to generate a matrix of solutions across a full range of assumptions for eight unknown or uncertain epidemic and mechanistic transmission factors, including the magnitude of droplet and aerosol emissions from infected individuals, the infectious dose for deposition of droplets and aerosols to the upper and lower respiratory tracts, and others.\n\nFindingsA total of 132 model iterations met acceptability criteria (R2 > 0.95 for modeled vs. reported cumulative daily cases and R2 > 0 for daily cases). Analyzing only these successful model iterations yields insights into the likely values for uncertain parameters and quantifies the likely contributions of each defined mode of transmission. Mean estimates of the contributions of short-range, long-range, and fomite transmission modes to infected cases aboard the ship across the entire simulation time period were 35%, 35%, and 30%, respectively. Mean estimates of the contributions of large respiratory droplets and small respiratory aerosols were 41% and 59%. Short-range transmission was the dominant mode after passenger quarantine began, albeit due primarily to aerosol transmission, not droplets.\n\nInterpretationOur results demonstrate that aerosol inhalation was likely the dominant contributor to COVID-19 transmission among passengers aboard the Diamond Princess Cruise Ship. Moreover, close-range and long-range transmission likely contributed similarly to disease progression aboard the ship, with fomite transmission playing a smaller role. The passenger quarantine also affected the importance of each mode, demonstrating the impacts of the interventions. Although cruise ships represent unique built environments with high ventilation rates and no air recirculation, these findings underscore the importance of implementing public health measures that target the control of inhalation of aerosols in addition to ongoing measures targeting control of large droplet and fomite transmission, not only aboard cruise ships but in other indoor environments as well.\n\nFundingFunding information is not available.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Parham Azimi", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Zahra Keshavarz", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Jose Guillermo Cedeno Laurent", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Brent R. Stephens", - "author_inst": "Illinois Institute of Technology" - }, - { - "author_name": "Joseph G. Allen", - "author_inst": "Harvard T.H. Chan School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.14.20153304", "rel_title": "Post lockdown COVID-19 seroprevalence and circulation at the time of delivery, France", @@ -1309518,6 +1312876,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.13.20153056", + "rel_title": "Analysis of COVID-19 cases and associated ventilator requirement in Indian States", + "rel_date": "2020-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20153056", + "rel_abs": "Analysis of COVID-19 cases and prediction of quantity of associated ventilator requirement is very relevant during this pandemic. This paper presents a method for predictive estimation of ventilator requirement for COVID-19 patients in Indian states. It uses ARIMA (Autoregressive Integrated Moving Average) model for predicting the future cumulative cases and daily fatality. Taking cue from this, ventilator requirement is estimated for each state. State wise estimation of ventilator is important because public healthcare system in India is managed at state level. Dataset on Novel Corona Disease 2019 in India from Kaggle website is used in this work.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "V Dhanya", + "author_inst": "Defence Bio-Engineering and Electro Medical Laboratory, DRDO, C.V. Raman Nagar, Bangalore-560093, India" + }, + { + "author_name": "R Anitha", + "author_inst": "Defence Bio-Engineering and Electro Medical Laboratory, DRDO, C.V. Raman Nagar, Bangalore-560093, India" + }, + { + "author_name": "Ashwini Kumar Kishan", + "author_inst": "Defence Bio-Engineering and Electro Medical Laboratory, DRDO, C.V. Raman Nagar, Bangalore-560093, India" + }, + { + "author_name": "SR Sumathi", + "author_inst": "Defence Bio-Engineering and Electro Medical Laboratory, DRDO, C.V. Raman Nagar, Bangalore-560093, India" + }, + { + "author_name": "Amrit Roy", + "author_inst": "Defence Bio-Engineering and Electro Medical Laboratory, DRDO, C.V. Raman Nagar, Bangalore-560093, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.13.20152884", "rel_title": "AN AFFORDABLE ANTI-SARS-COV-2 SPIKE ELISA TEST FOR EARLY DETECTION OF IgG SEROCONVERSION SUITED FOR LARGE-SCALE SURVEILLANCE STUDIES IN LOW-INCOME COUNTRIES", @@ -1310945,77 +1314338,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.15.204404", - "rel_title": "A direct RNA-protein interaction atlas of the SARS-CoV-2 RNA in infected human cells", - "rel_date": "2020-07-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.15.204404", - "rel_abs": "SARS-CoV-2 infections pose a global threat to human health and an unprecedented research challenge. Among the most urgent tasks is obtaining a detailed understanding of the molecular interactions that facilitate viral replication or contribute to host defense mechanisms in infected cells. While SARS-CoV-2 co-opts cellular factors for viral translation and genome replication, a comprehensive map of the host cell proteome in direct contact with viral RNA has not been elucidated. Here, we use RNA antisense purification and mass spectrometry (RAP-MS) to obtain an unbiased and quantitative picture of the human proteome that directly binds the SARS-CoV-2 RNA in infected human cells. We discover known host factors required for coronavirus replication, regulators of RNA metabolism and host defense pathways, along with dozens of potential drug targets among direct SARS-CoV-2 binders. We further integrate the SARS-CoV-2 RNA interactome with proteome dynamics induced by viral infection, linking interactome proteins to the emerging biology of SARS-CoV-2 infections. Validating RAP-MS, we show that CNBP, a regulator of proinflammatory cytokines, directly engages the SARS-CoV-2 RNA. Supporting the functional relevance of identified interactors, we show that the interferon-induced protein RYDEN suppresses SARS-CoV-2 ribosomal frameshifting and demonstrate that inhibition of SARS-CoV-2-bound proteins is sufficient to manipulate viral replication. The SARS-CoV-2 RNA interactome provides an unprecedented molecular perspective on SARS-CoV-2 infections and enables the systematic dissection of host dependency factors and host defense strategies, a crucial prerequisite for designing novel therapeutic strategies.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Nora Schmidt", - "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg" - }, - { - "author_name": "Caleb A Lareau", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Hasmik Keshishian", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Randy Melanson", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Matthias Zimmer", - "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg" - }, - { - "author_name": "Luisa Kirschner", - "author_inst": "Institute for Virology and Immunobiology, Julius-Maximilians-University Wuerzburg" - }, - { - "author_name": "Jens Ade", - "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg" - }, - { - "author_name": "Simone Werner", - "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg" - }, - { - "author_name": "Neva Caliskan", - "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg" - }, - { - "author_name": "Eric S Lander", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Joerg Vogel", - "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg" - }, - { - "author_name": "Steven A Carr", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Jochen Bodem", - "author_inst": "Institute for Virology and Immunobiology, Julius-Maximilians-University Wuerzburg" - }, - { - "author_name": "Mathias Munschauer", - "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.15.205229", "rel_title": "The S1 protein of SARS-CoV-2 crosses the blood-brain barrier: Kinetics, distribution, mechanisms, and influence of ApoE genotype, sex, and inflammation", @@ -1311176,6 +1314498,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.12.20151936", + "rel_title": "Public Opinions towards COVID-19 in California and New York on Twitter", + "rel_date": "2020-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.12.20151936", + "rel_abs": "BackgroundWith the pandemic of COVID-19 and the release of related policies, discussions about the COVID-19 are widespread online. Social media becomes a reliable source for understanding public opinions toward this virus outbreak.\n\nObjectiveThis study aims to explore public opinions toward COVID-19 on social media by comparing the differences in sentiment changes and discussed topics between California and New York in the United States.\n\nMethodsA dataset with COVID-19-related Twitter posts was collected from March 5, 2020 to April 2, 2020 using Twitter streaming API. After removing any posts unrelated to COVID-19, as well as posts that contain promotion and commercial information, two individual datasets were created based on the geolocation tags with tweets, one containing tweets from California state and the other from New York state. Sentiment analysis was conducted to obtain the sentiment score for each COVID-19 tweet. Topic modeling was applied to identify top topics related to COVID-19.\n\nResultsWhile the number of COVID-19 cases increased more rapidly in New York than in California in March 2020, the number of tweets posted has a similar trend over time in both states. COVID-19 tweets from California had more negative sentiment scores than New York. There were some fluctuations in sentiment scores in both states over time, which might correlate with the policy changes and the severity of COVID-19 pandemic. The topic modeling results showed that the popular topics in both California and New York states are similar, with \"protective measures\" as the most prevalent topic associated with COVID-19 in both states.\n\nConclusionsTwitter users from California had more negative sentiment scores towards COVID-19 than Twitter users from New York. The prevalent topics about COVID-19 discussed in both states were similar with some slight differences.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Xueting Wang", + "author_inst": "Goergen Institute for Data Science, University of Rochester, Rochester, New York, USA" + }, + { + "author_name": "Canruo Zou", + "author_inst": "Department of Computer Science, University of Rochester, Rochester, New York, USA" + }, + { + "author_name": "Zidian Xie", + "author_inst": "University of Rochester Medical Center" + }, + { + "author_name": "Dongmei Li", + "author_inst": "University of Rochester Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.12.20151191", "rel_title": "COVID-19 scenarios for the United States", @@ -1312551,37 +1315904,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.05.20146043", - "rel_title": "Luminore CopperTouch\u2122 surface coating effectively inactivates SARS-CoV-2, Ebola and Marburg viruses in vitro", - "rel_date": "2020-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.05.20146043", - "rel_abs": "We investigated the ability of Luminore CopperTouch copper and copper-nickel surfaces to inactivate filoviruses and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For this purpose, we compared viral titers in Vero cells from viral droplets exposed to copper surfaces for 30 min. The copper and copper-nickel surfaces inactivated 99.9% of the viral titer of both Ebola and Marburg viruses. The copper surfaces also inactivated 99% of SARS-CoV-2 titers in 2 hours to close to the limit of detection. These data add Ebolavirus, Marburgvirus, and SARS-CoV-2 (COVID-19) to the list of pathogens that can be inactivated by exposure to copper ions, validating Luminore CopperTouch technology (currently the only Environmental Protection Agency-registered cold spray antimicrobial surface technology) as an efficacious, cost-friendly tool to improve infection control in hospitals, long-term care facilities, schools, hotels, buses, trains, airports, and other highly trafficked areas.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Emily Mantlo", - "author_inst": "University of Texas Medical Branch, Galveston" - }, - { - "author_name": "Slobodan Paessler", - "author_inst": "University of Texas Medical Branch, Galveston" - }, - { - "author_name": "Alexey V Seregin", - "author_inst": "University of Texas Medical Branch, Galveston" - }, - { - "author_name": "Alfred T Mitchell", - "author_inst": "Luminore CopperTouch" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.10.20150623", "rel_title": "Maternal and perinatal characteristics and outcomes of pregnancies complicated with COVID-19 in Kuwait", @@ -1312930,6 +1316252,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.11.20151308", + "rel_title": "'Trained immunity' from Mycobacterium spp. exposure or BCG vaccination and COVID-19 outcomes", + "rel_date": "2020-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.11.20151308", + "rel_abs": "Protective variables for COVID-19 are unknown. Trained immunity of the populace as a result of BCG immunization policy implementation and coverage had been suggested to be one of the factors responsible for the differential impact of COVID-19 on different countries. Several trials are underway to evaluate the potential protective role of BCG vaccination in COVID-19. However, the lack of clarity on the use of appropriate controls concerning the measures of trained immunity or the heterologous cell-mediated immunity conferred by BCG vaccination has been a cause of concern leading to more confusion as exemplified by a recently concluded trial in Israel that failed to find any protective correlation with regard to BCG vaccination. Whereas, when we analyze the COVID-19 data of European countries without any regard for BCG vaccination policy but with similar age distribution, comparable confounding variables, and the stage of the pandemic, the prevalence of tuberculin immunoreactivity - a measure of cell-mediated immunity persistence as a result of Mycobacterium spp. (including BCG vaccine) exposure of the populations, is found consistently negatively correlated with COVID-19 infections and mortality per million population, at all the time points evaluated. We propose that on-going and future studies evaluating the effect of BCG vaccination on COVID-19 outcomes may actively consider, if not already, the inclusion of controls for underlying trained immunity and heterologous cell-mediated immunity prevalence that may be pre-existing or resulting from the intervention (e.g., BCG vaccine) in such trials to arrive at more dependable conclusions concerning their potential benefit.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Samer Singh", + "author_inst": "Banaras Hindu University Institute of Medical Sciences" + }, + { + "author_name": "Rajendra P. Maurya", + "author_inst": "Banaras Hindu University Institute of Medical Sciences" + }, + { + "author_name": "Rakesh K. Singh", + "author_inst": "Banaras Hindu University Institute of Science" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.11.20151472", "rel_title": "The competing risk between in-hospital mortality and recovery: A pitfall in COVID-19 survival analysis research", @@ -1314333,25 +1317682,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.13.20152637", - "rel_title": "Modelling suggests blood group incompatibility may substantially reduce SARS-CoV-2 transmission", - "rel_date": "2020-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20152637", - "rel_abs": "Several independent datasets suggest blood type A is over-represented and type O under-represented among COVID-19 patients. Here, I model a scenario in which ABO transfusion incompatibility reduces the chance of a patient transmitting the virus to an incompatible recipient. Comparison of model outputs to published data on COVID-19 prevalence indicates that if this scenario holds true, ABO incompatibility may reduce virus transmissibility by 60% or more. Paradoxically, however, targeted vaccination of either high-susceptibility type A or \"super-spreader\" type O individuals is less effective than random vaccination at blocking community spread of the virus. Instead, the key is to maintain blood type diversity amongst the remaining susceptible individuals. I stress that these results illustrate a theoretical model of ABO blood group interaction with virus transmission and require confirmation by observation.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Peter James Ellis", - "author_inst": "University of Kent" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.13.20152330", "rel_title": "Discrete simulation analysis of COVID-19 and prediction of isolation bed numbers", @@ -1314516,6 +1317846,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.07.13.20144907", + "rel_title": "The National Early Warning Score (NEWS2) systematically underestimates the risk of in-hospital mortality in unplanned COVID-19 admissions to hospital.", + "rel_date": "2020-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20144907", + "rel_abs": "BackgroundAlthough the National Early Warning Score (NEWS) and its latest version NEWS2 are recommended for monitoring for deterioration in patients admitted to hospital, little is known about their performance in COVID-19 patients. We analysed the performance of National Early Warning Score (NEWS2) during the first phase of the COVID-19 pandemic.\n\nMethodsAdult non-elective admissions discharged between 11-March-2020 to 13-June-2020 with an index NEWS2 electronically recorded within {+/-}24 hours of admission are used to predict mortality at four time points (in-hospital, 24hours, 48hours, and 72hours) in COVID-19 versus non-COVID-19 admissions.\n\nResultsOut of 6480 non-elective admissions, 620 (9.6%) had a diagnosis of COVID-19. They were older (73.3 vs 67.7yrs), more often male (54.7% vs 50.1%), had higher index NEWS (4 vs 2.5) and NEWS2 (4.6 vs 2.8) scores and higher in-hospital mortality (32.1% vs 5.8%). The c-statistics for predicting in-hospital mortality in COVID-19 admissions was significantly lower using NEWS (0.64 vs 0.74) or NEWS2 (0.64 vs 0.74), however these differences reduced at 72hours (NEWS: 0.75 vs 0.81; NEWS2: 0.71 vs 0.81), 48 hours (NEWS: 0.78 vs 0.81; NEWS2: 0.76 vs 0.82) and 24hours (NEWS: 0.84 vs 0.84; NEWS2: 0.86 vs 0.84). Increasing NEWS2 values reflected increased mortality, but for any given value the absolute risk was on average 24% higher (e.g.NEWS2=5: 36% vs 9%).\n\nInterpretationNEWS2 is a valid predictor of the mortality risk but substantially underestimates the absolute mortality risk in COVID-19 patients. Clinical staff and escalation protocols based on NEWS2 need to make note of this finding.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Donald Richardson", + "author_inst": "York Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Muhammad Faisal", + "author_inst": "Faculty of Health Studies, University of Bradford, Bradford, UK; Bradford Institute for Health Research" + }, + { + "author_name": "Massimo Fiori", + "author_inst": "York Teaching Hospitals NHS Foundation Trust, England UK" + }, + { + "author_name": "Kevin Beatson", + "author_inst": "York Teaching Hospital NHS Foundation Trust" + }, + { + "author_name": "Mohammed A Mohammed", + "author_inst": "Faculty of Health Studies, University of Bradford, Bradford, UK;The Strategy Unit, NHS Midlands and Lancashire Commissioning Support Unit" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.13.20152587", "rel_title": "Linear epitope landscape of SARS-CoV-2 Spike protein constructed from 1,051 COVID-19 patients", @@ -1315999,33 +1319364,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.10.20150508", - "rel_title": "ICU admissions and in-hospital deaths linked to covid-19 in the Paris region are correlated with previously observed ambient temperature", - "rel_date": "2020-07-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20150508", - "rel_abs": "OBJECTIVETo study the effect of weather on severity indicators of coronavirus disease 2019 (covid-19).\n\nDESIGNEcological study.\n\nSETTINGParis region.\n\nPOPULATIONSeverely ill patients with covid-19.\n\nMAIN OUTCOME MEASURESDaily covid-19-related intensive care unit (ICU) admission and in-hospital deaths in the Paris region, and the daily weather characteristics of Paris midtown.\n\nRESULTSDaily ICU admissions and in-hospital deaths were strongly and negatively correlated to ambient temperatures, with a time lag. The highest Pearson correlation coefficients and statistically significant P values were found 8 days before occurrence of ICU admissions and 15 days before deaths.\n\nCONCLUSIONSThe study findings show a strong effect of previously observed ambient temperature that has an effect on severity indicators of covid-19.\n\nStrengths and limitations of this studyWe assessed the link between weather characteristics with a time lag and covid-19-related hospital severity indicators.\n\nThis is the first study, with reliable data, to find a strong negative correlation between previously observed ambient temperature with covid-19-related iCU admissions and in-hospital deaths.\n\nIt is compatible with the natural history (including hospitalisation) of covid-19 outbreak in a highly developed country.\n\nWe also report the duration after which iCU admissions and in-Hospital deaths occurs following temperature variation (respectively median of 8 and 15 days).\n\nOur analyses are mainly valid for temperate climate countries.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Mehdi Mejdoubi", - "author_inst": "Centre Hospitalier de Valenciennes" - }, - { - "author_name": "Xavier Kyndt", - "author_inst": "Centre Hospitalier de Valenciennes" - }, - { - "author_name": "Mehdi Djennaoui", - "author_inst": "Centre Hospitalier de Valenciennes" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.09.20150219", "rel_title": "Estimating the time-varying reproduction number of COVID-19 with a state-space method", @@ -1316114,6 +1319452,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.10.20150573", + "rel_title": "Eurofins Covid-19 Sentinel TM Wastewater Test Provide Early Warning of a potential COVID-19 outbreak", + "rel_date": "2020-07-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20150573", + "rel_abs": "The Eurofins Covid-19 Sentinel program was developed to monitor the evolution of the pandemic and for early detection of outbreaks. The study objective was to develop a wastewater testing method to analyze SARS-CoV-2 as an indicator of community infection rate as of resurgence of COVID-19 in well-defined sites such as production facilities, hospitals or nursing homes. Eurofins performed >700 tests on 78 unique samples from 18 sites in Denmark, France and Belgium. Ten variant test protocols were trialed. Protocol variations trialed included centrifugation, precipitation of the SARS-CoV-2 RNA, agitation prior to precipitation, cooling, and pasteurization of the samples. A method was succesfully developed and reliability was supported by stability, reproducibility, and dilution & linearity studies. Results obtained showed a direct link to number of RNA copies in the sample using a calibration curve with synthetic SARS-CoV-2. Analysis was performed on both the liquid phase and solid phase of wastewater samples, with virus RNA detected in both phases but more frequently in the liquid phase. The virus was present in a sample from a Danish community wastewater treatment plant collected on February 24, 3 days before the first COVID-19 case was officially reported in the country. The greatest concentration of virus detected corresponded to when the COVID-19 crisis was at its peak in Denmark. Based on studies carried out in a Danish hospital, the wastewater testing method is expected to be able to detect a community COVID-19 prevalence rate as low as a 0,02%-0,1% (i.e. between 2 virus shedders per 10000 persons and 1 virus shedder per 1000). The wastewater testing method was used to monitor a Danish Community after a COVID-19 outbreak and it was shown that the method can be used as a semi-quantitative method to monitor the development of an outbreak.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Alissa Udi Jorgensen", + "author_inst": "Eurofins Miljo A/S" + }, + { + "author_name": "Jesper Gamst", + "author_inst": "Eurofins Miljo A/S" + }, + { + "author_name": "Line Visby Hansen", + "author_inst": "Eurofins Miljo A/S" + }, + { + "author_name": "Ida Ingeborg Hogh Knudsen", + "author_inst": "Eurofins Miljo A/S" + }, + { + "author_name": "Soren Krohn Skovgaard Jensen", + "author_inst": "Eurofins Genomics" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.09.20150227", "rel_title": "A minimal model for household effects in epidemics", @@ -1317361,45 +1320734,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.10.20149013", - "rel_title": "The Age Pattern of the Male- to- Female Ratio in Mortality from COVID-19 Mirrors that of Cardiovascular Disease but not Cancer in the General Population", - "rel_date": "2020-07-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20149013", - "rel_abs": "BackgroundMales are at a higher risk of dying from COVID-19. Older age and cardiovascular disease are also associated with COVID-19 mortality. We compared the male-to-female (sex) ratios in mortality by age for COVID-19 with cardiovascular mortality and cancer mortality in the general population.\n\nMethodsWe obtained data from official government sources in the US and five European countries: Italy, Spain, France, Germany, and the Netherlands. We analyzed COVID-19 deaths by sex and age in these countries and similarly analyzed their deaths from cardiovascular disease (coronary heart disease or stroke) and cancer, the two leading age-related causes of death in middle-to-high income countries.\n\nFindingsIn both the US and European countries, the sex ratio of deaths from COVID-19 exceeded one throughout adult life. The sex ratio increased up to a peak in midlife, and then declined markedly in later life. This pattern was also observed for the sex ratio of deaths from cardiovascular disease, but not cancer, in the general populations of the US and European countries.\n\nInterpretationThe sex ratios of deaths from COVID-19 and from cardiovascular disease exhibit similar patterns across the adult life course. The underlying mechanisms are poorly understood, but could stem partially from sex-related biological differences that underlie the similar pattern for cardiovascular disease. These include, we propose, comparatively longer telomeres in females, ovarian hormones, and X chromosome mosaicism.\n\nFundingThe authors received no specific funding for this work.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSMortality from COVID-19 is higher in males and older persons. We searched PubMed.gov in June 2020, with no date restrictions, for articles published in English using the search terms \"COVID-19\", \"deaths\", \"mortality\", \"sex\", \"male\", \"female\", \"age\", \"disaggregated\", \"ratio\", and \"stratified\". We identified studies in several countries that stratified COVID-19 mortality data by age or by sex, but no study examined male-to-female (sex) ratios by age at a multi-national level.\n\nAdded value of this studyTo our knowledge, this is the first study to aggregate data on COVID-19 deaths at a multi-national level, and analyze how the sex ratio in deaths varies by age, taking into account the population at risk in each sex/age stratum. We found a distinctive pattern in sex ratio of deaths by age, illuminating the nature of the sex effect on death from COVID-19. Moreover, we found a similar pattern in sex ratio of deaths by age for cardiovascular disease, which is strongly associated with increased risk of dying from COVID-19. We did not find a similar age pattern for the sex ratio in deaths by cancer.\n\nImplications of all the available evidenceThe sex ratio in deaths from COVID-19 peaks in middle age and decreases at older ages, a pattern mirrored in deaths from cardiovascular disease. This intriguing similarity warrants research about whether sex-based differences in mortality from COVID-19 and from cardiovascular disease in general are partly due to common biological causes.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ila Nimgaonkar", - "author_inst": "Rutgers Robert Wood Johnson Medical School" - }, - { - "author_name": "Linda Valeri", - "author_inst": "Mailman School of Public Health, Columbia University" - }, - { - "author_name": "Ezra S. Susser", - "author_inst": "Mailman School of Public Health, Columbia University and New York State Psychiatric Institute" - }, - { - "author_name": "Sabiha Hussain", - "author_inst": "Rutgers Robert Wood Johnson Medical School" - }, - { - "author_name": "Jag Sunderram", - "author_inst": "Rutgers Robert Wood Johnson Medical School" - }, - { - "author_name": "Abraham Aviv", - "author_inst": "Rutgers New Jersey Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.09.20149534", "rel_title": "Saliva offers a sensitive, specific and non-invasive alternative to upper respiratory swabs for SARS-CoV-2 diagnosis.", @@ -1317588,6 +1320922,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.09.20149682", + "rel_title": "Undocumented infectives in the Covid-19 pandemic", + "rel_date": "2020-07-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.09.20149682", + "rel_abs": "BackgroundA crucial role in epidemics is played by the number of undetected infective individuals who continue to circulate and spread the disease. Epidemiological investigations and mathematical models have revealed that the rapid diffusion of Covid-19 can mostly be attributed to the large percentage of undocumented infective individuals who escape testing.\n\nMethodsThe dynamics of an infection can be described by the SIR model, which divides the population into susceptible (S), infective (I) and removed (R) subjects. In particular, we exploited the Kermack and McKendrick epidemic model which can be applied when the population is much larger than the fraction of infected subjects.\n\nResultsWe proved that the fraction of undocumented infectives, in comparison to the total number of infected subjects, is given by [Formula] where R0 is the basic reproduction number. Its mean value R0 = 2.10 (2.09 - 2.11) in three Italian regions for the Covid-19 epidemic yielded a percentage of undetected infectives of 52.4% (52.2% - 52.6%) compared to the total number of infectives.\n\nConclusionsOur results, straightforwardly obtained from the SIR model, highlight the role played by undetected carriers in the transmission and spread of the SARS-CoV-2 infection. Such evidence strongly recommends careful monitoring of the infective population and ongoing adjustment of preventive measures for disease control until a vaccine becomes available.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Maurizio Melis", + "author_inst": "AART (Association for the Advancement of Research on Transplantation), Cagliari, Italy" + }, + { + "author_name": "Roberto Littera", + "author_inst": "Complex Structure of Medical Genetics, R. Binaghi Hospital, ASSL Cagliari, ATS Sardegna, Italy" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.09.20149138", "rel_title": "Negative impact of the COVID-19 pandemic on sleep quantitative parameters, quality, and circadian alignment: Implications for psychological well-being and emotional regulation", @@ -1319119,117 +1322476,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.08.20148999", - "rel_title": "Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (ai-LAMP) for Rapid and Reliable Detection of SARS-CoV-2", - "rel_date": "2020-07-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.08.20148999", - "rel_abs": "Until vaccines and effective therapeutics become available, the practical way to transit safely out of the current lockdown may include the implementation of an effective testing, tracing and tracking system. However, this requires a reliable and clinically validated diagnostic platform for the sensitive and specific identification of SARS-CoV-2. Here, we report on the development of a de novo, high-resolution and comparative genomics guided reverse-transcribed loop-mediated isothermal amplification (LAMP) assay. To further enhance the assay performance and to remove any subjectivity associated with operator interpretation of result, we engineered a novel hand-held smart diagnostic device. The robust diagnostic device was further furnished with automated image acquisition and processing algorithms, and the collated data was processed through artificial intelligence (AI) pipelines to further reduce the assay run time and the subjectivity of the colorimetric LAMP detection. This advanced AI algorithm-implemented LAMP (ai-LAMP) assay, targeting the RNA-dependent RNA polymerase gene, showed high analytical sensitivity and specificity for SARS-CoV-2. A total of [~]200 coronavirus disease (CoVID-19)-suspected patient samples were tested using the platform and it was shown to be reliable, highly specific and significantly more sensitive than the current gold standard qRT-PCR. The system could provide an efficient and cost-effective platform to detect SARS-CoV-2 in resource-limited laboratories.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Mohammed A Rohaim", - "author_inst": "The Lancaster University" - }, - { - "author_name": "Emily Clayton", - "author_inst": "The Lancaster University" - }, - { - "author_name": "Irem Sahin", - "author_inst": "The Lancaster University" - }, - { - "author_name": "Julianne Vilela", - "author_inst": "The Lancaster University" - }, - { - "author_name": "Manar E Khalifa", - "author_inst": "The Lancaster University" - }, - { - "author_name": "Mohammed Q Al-Natour", - "author_inst": "The Lancaster University" - }, - { - "author_name": "Mahmoud Bayoumi", - "author_inst": "The Lancaster University" - }, - { - "author_name": "Aurore Poirier", - "author_inst": "The University of Surrey" - }, - { - "author_name": "Manoharanehru Branavan", - "author_inst": "Brunel University London" - }, - { - "author_name": "Mukunthan Tharmakulasingam", - "author_inst": "University of Surrey," - }, - { - "author_name": "Nouman S Chaudhry", - "author_inst": "The University of Surrey" - }, - { - "author_name": "Ravinder Sodi", - "author_inst": "Department of Biochemistry, Poole & Bournemouth Hospitals NHS Trust, Longfleet Road, Poole, UK BH15 2JB" - }, - { - "author_name": "Amy Brown", - "author_inst": "The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, UK" - }, - { - "author_name": "Peter Burkhart", - "author_inst": "The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, UK" - }, - { - "author_name": "Wendy Hacking", - "author_inst": "The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, UK" - }, - { - "author_name": "Judy Botham", - "author_inst": "The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, UK" - }, - { - "author_name": "Joe Boyce", - "author_inst": "The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, UK" - }, - { - "author_name": "Hayley Wilkinson", - "author_inst": "The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, UK" - }, - { - "author_name": "Craig Williams", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Michelle Bates", - "author_inst": "The Lancaster University" - }, - { - "author_name": "Roberto La Ragione", - "author_inst": "University of Surrey" - }, - { - "author_name": "Wamadeva Balachandran", - "author_inst": "College of Engineering, Design and Physical Sciences, Brunel University London, Kingston Lane, Uxbridge, UK" - }, - { - "author_name": "Anil Fernando", - "author_inst": "The University of Surrey" - }, - { - "author_name": "Muhammad Munir", - "author_inst": "Lancaster University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.07.20148478", "rel_title": "Natural killer cell activation related to clinical outcome of COVID-19", @@ -1319534,6 +1322780,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.09.20141762", + "rel_title": "Disentangling Increased Testing From Covid-19 Epidemic Spread", + "rel_date": "2020-07-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.09.20141762", + "rel_abs": "To design effective disease control strategies, it is critical to understand the incidence of diseases. In the Covid-19 epidemic in the United States (caused by outbreak of the SARS-CoV-2 virus), testing capacity was initially very limited and has been increasing at the same time as the virus has been spreading. When estimating the incidence, it can be difficult to distinguish whether increased numbers of positive tests stem from increases in the spread of the virus or increases in testing. This has made it very difficult to identify locations in which the epidemic poses the largest public health risks. Here, we use a probabilistic model to quantify beliefs about testing strategies and understand implications regarding incidence. We apply this model to estimate the incidence in each state of the United States, and find that: (1) the Covid-19 epidemic is likely to be more widespread than reported by limited testing, (2) the Covid-19 epidemic growth in the summer months is likely smaller than it was during the spring months, and (3) the regions which are at highest risk of Covid-19 epidemic outbreaks are not always those with the largest number of positive test results.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Benjamin J Lengerich", + "author_inst": "Carnegie Mellon University" + }, + { + "author_name": "Willie Neiswanger", + "author_inst": "Carnegie Mellon University" + }, + { + "author_name": "Eugene J. Lengerich", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Eric P. Xing", + "author_inst": "Carnegie Mellon University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.09.20149831", "rel_title": "ALeRT-COVID: Attentive Lockdown-awaRe Transfer Learning for Predicting COVID-19 Pandemics in Different Countries", @@ -1321001,89 +1324278,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.07.09.196188", - "rel_title": "SARS-CoV-2 infection in the lungs of human ACE2 transgenic mice causes severe inflammation, immune cell infiltration, and compromised respiratory function", - "rel_date": "2020-07-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.09.196188", - "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2) emerged in late 2019 and has spread worldwide resulting in the Coronavirus Disease 2019 (COVID-19) pandemic. Although animal models have been evaluated for SARS-CoV-2 infection, none have recapitulated the severe lung disease phenotypes seen in hospitalized human cases. Here, we evaluate heterozygous transgenic mice expressing the human ACE2 receptor driven by the epithelial cell cytokeratin-18 gene promoter (K18-hACE2) as a model of SARS-CoV-2 infection. Intranasal inoculation of SARS-CoV-2 in K18-hACE2 mice results in high levels of viral infection in lung tissues with additional spread to other organs. Remarkably, a decline in pulmonary function, as measured by static and dynamic tests of respiratory capacity, occurs 4 days after peak viral titer and correlates with an inflammatory response marked by infiltration into the lung of monocytes, neutrophils, and activated T cells resulting in pneumonia. Cytokine profiling and RNA sequencing analysis of SARS-CoV-2-infected lung tissues show a massively upregulated innate immune response with prominent signatures of NF-kB-dependent, type I and II interferon signaling, and leukocyte activation pathways. Thus, the K18-hACE2 model of SARS-CoV-2 infection recapitulates many features of severe COVID-19 infection in humans and can be used to define the mechanistic basis of lung disease and test immune and antiviral-based countermeasures.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Emma S Winkler", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Adam L Bailey", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Natasha M Kafai", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Sharmila Nair", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Broc T McCune", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Jinsheng Yu", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Julie M Fox", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Rita E Chen", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "James T Earnest", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Shamus P Keeler", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Jon H Ritter", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Liang-I Kang", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Sarah Dort", - "author_inst": "SCIREQ Scientific Respiratory Equipment Inc" - }, - { - "author_name": "Annette Robichaud", - "author_inst": "SCIREQ Scientific Respiratory Equipment Inc" - }, - { - "author_name": "Richard Head", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Michael J Holtzman", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Michael S Diamond", - "author_inst": "Washington University School of Medicine in St. Louis" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.07.09.194027", "rel_title": "Severely ill COVID-19 patients display augmented functional properties in SARS-CoV-2-reactive CD8+ T cells", @@ -1321356,6 +1324550,133 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.07.09.196519", + "rel_title": "Discriminating Mild from Critical COVID-19 by Innate and Adaptive Immune Single-cell Profiling of Bronchoalveolar Lavages", + "rel_date": "2020-07-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.09.196519", + "rel_abs": "How innate and adaptive lung immune responses to SARS-CoV-2 synchronize during COVID-19 pneumonitis and regulate disease severity is poorly established. To address this, we applied single-cell profiling to bronchoalveolar lavages from 44 patients with mild or critical COVID-19 versus non-COVID-19 pneumonia as control. Viral RNA-tracking delineated the infection phenotype to epithelial cells, but positioned mainly neutrophils at the forefront of viral clearance activity during COVID-19. In mild disease, neutrophils could execute their antiviral function in an immunologically controlled fashion, regulated by fully-differentiated T-helper-17 (TH17)-cells, as well as T-helper-1 (TH1)-cells, CD8+ resident-memory (TRM) and partially-exhausted (TEX) T-cells with good effector functions. This was paralleled by orderly phagocytic disposal of dead/stressed cells by fully-differentiated macrophages, otherwise characterized by anti-inflammatory and antigen-presenting characteristics, hence facilitating lung tissue repair. In critical disease, CD4+ TH1- and CD8+ TEX-cells were characterized by inflammation-associated stress and metabolic exhaustion, while CD4+ TH17- and CD8+ TRM-cells failed to differentiate. Consequently, T-cell effector function was largely impaired thereby possibly facilitating excessive neutrophil-based inflammation. This was accompanied by impaired monocyte-to-macrophage differentiation, with monocytes exhibiting an ATP-purinergic signalling-inflammasome footprint, thereby enabling COVID-19 associated fibrosis and worsening disease severity. Our work represents a major resource for understanding the lung-localised immunity and inflammation landscape during COVID-19.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Els Wauters", + "author_inst": "Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Belgium" + }, + { + "author_name": "Pierre Van Mol", + "author_inst": "VIB Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Belgium;" + }, + { + "author_name": "Abhishek D. Garg", + "author_inst": "Laboratory for Cell Stress & Immunity (CSI), Department of Cellular and Molecular Medicine (CMM), KU Leuven, Belgium" + }, + { + "author_name": "Sander Jansen", + "author_inst": "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Belgium" + }, + { + "author_name": "Yannick Van Herck", + "author_inst": "Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, Belgium" + }, + { + "author_name": "Lore Vanderbeke", + "author_inst": "Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Belgium" + }, + { + "author_name": "Ayse Bassez", + "author_inst": "Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium" + }, + { + "author_name": "Bram Boeckx", + "author_inst": "Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium" + }, + { + "author_name": "Bert Malengier-Devlies", + "author_inst": "Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Belgium" + }, + { + "author_name": "Anna Timmerman", + "author_inst": "Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium" + }, + { + "author_name": "Thomas Van Brussel", + "author_inst": "Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium" + }, + { + "author_name": "Tina Van Buyten", + "author_inst": "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Belgium" + }, + { + "author_name": "Rogier Schepers", + "author_inst": "Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium" + }, + { + "author_name": "Elisabeth Heylen", + "author_inst": "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Belgium" + }, + { + "author_name": "Dieter Dauwe", + "author_inst": "Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Belgium" + }, + { + "author_name": "Christophe Dooms", + "author_inst": "Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Belgium" + }, + { + "author_name": "Jan Gunst", + "author_inst": "Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Belgium" + }, + { + "author_name": "Greet Hermans", + "author_inst": "Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Belgium" + }, + { + "author_name": "Philippe Meersseman", + "author_inst": "Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology and Transplantation, KU Leuven, Belgium" + }, + { + "author_name": "Dries Testelmans", + "author_inst": "Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Belgium" + }, + { + "author_name": "Jonas Yserbyt", + "author_inst": "Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Belgium" + }, + { + "author_name": "Patrick Matthys", + "author_inst": "Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Belgium" + }, + { + "author_name": "Sabine Tejpar", + "author_inst": "Molecular Digestive Oncology, Department of Oncology, KU Leuven, Belgium" + }, + { + "author_name": "- CONTAGIOUS collaborators", + "author_inst": "-" + }, + { + "author_name": "Johan Neyts", + "author_inst": "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Belgium" + }, + { + "author_name": "Joost Wauters", + "author_inst": "Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology and Transplantation, KU Leuven, Belgium" + }, + { + "author_name": "Junbin Qian", + "author_inst": "Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium" + }, + { + "author_name": "Diether Lambrechts", + "author_inst": "Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.07.10.197095", "rel_title": "Genomic variations in SARS-CoV-2 genomes from Gujarat: Underlying role of variants in disease epidemiology", @@ -1323202,153 +1326523,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.08.193045", - "rel_title": "A single-dose live-attenuated YF17D-vectored SARS-CoV2 vaccine candidate", - "rel_date": "2020-07-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.08.193045", - "rel_abs": "The explosively expanding COVID-19 pandemic urges the development of safe, efficacious and fast-acting vaccines to quench the unrestrained spread of SARS-CoV-2. Several promising vaccine platforms, developed in recent years, are leveraged for a rapid emergency response to COVID-191. We employed the live-attenuated yellow fever 17D (YF17D) vaccine as a vector to express the prefusion form of the SARS-CoV-2 Spike antigen. In mice, the vaccine candidate, tentatively named YF-S0, induces high levels of SARS-CoV-2 neutralizing antibodies and a favorable Th1 cell-mediated immune response. In a stringent hamster SARS-CoV-2 challenge model2, vaccine candidate YF-S0 prevents infection with SARS-CoV-2. Moreover, a single dose confers protection from lung disease in most vaccinated animals even within 10 days. These results warrant further development of YF-S0 as a potent SARS-CoV-2 vaccine candidate.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Lorena Sanchez Felipe", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Thomas Vercruysse", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Sapna Sharma", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Ji Ma", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Viktor Lemmens", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Dominique van Looveren", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Mahadesh Prasad Arkalagud Javarappa", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Robbert Boudewijns", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Bert Malengier-Devlies", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Suzanne F. Kaptein", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Laurens Liesenborghs", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Carolien De Keyzer", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Lindsey Bervoets", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Madina Rasulova", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Laura Seldeslachts", - "author_inst": "KU Leuven" - }, - { - "author_name": "Sander Jansen", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Michael Bright Yakass", - "author_inst": "KU Leuven - Rega Institute, University of Ghana" - }, - { - "author_name": "Osbourne Quaye", - "author_inst": "University of Ghana" - }, - { - "author_name": "Li-Hsin Li", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Xin Zhang", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Sebastiaan ter Horst", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Niraj Mishra", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Lotte Coelmont", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Christopher Cawthorne", - "author_inst": "KU Leuven" - }, - { - "author_name": "Koen Van Laere", - "author_inst": "KU Leuven" - }, - { - "author_name": "Ghislain Opdenakker", - "author_inst": "KU Leuven" - }, - { - "author_name": "Greetje Van de Velde", - "author_inst": "KU Leuven" - }, - { - "author_name": "Birgit Weynand", - "author_inst": "KU Leuven" - }, - { - "author_name": "Dirk E. Teuwen", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Patrick Matthys", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Johan Neyts", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Hendrik Jan Thibaut", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Kai Dallmeier", - "author_inst": "KU Leuven - Rega Institute for Medical Research" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.09.195230", "rel_title": "Human angiotensin-converting enzyme 2 transgenic mice infected with SARS-CoV-2 develop severe and fatal respiratory disease", @@ -1323597,6 +1326771,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.06.20146712", + "rel_title": "Risk of Transmission of infection to Healthcare Workers delivering Supportive Care for Coronavirus Pneumonia;A Rapid GRADE Review", + "rel_date": "2020-07-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.06.20146712", + "rel_abs": "BackgroundAvenues of treatment currently implemented for Covid-19 pandemic are largely supportive in nature. Non-availability of an effective antiviral treatment makes supportive care for acute hypoxic respiratory failure is the most crucial intervention. Highly contagious nature of Covid-19 had created stress and confusion among front line Health Care Workers (HCWs) regarding infectious risk of supportive interventions and best preventive strategies.\n\nPurposeTo analyze and summarize key evidence from published literature exploring the risk of transmission of Covid-19 related to common supportive care interventions in hospitalized patients and effectiveness of currently used preventive measures in hospital setting.\n\nData SourcesCurated Covid-19 literature from NCBI Computational Biology Branch, Embase and Ovid till May 20,2020.Longitudinal and reference search till June 28,2020\n\nStudy SelectionStudies pertaining to risk of infection to HCWs providing standard supportive care of hospitalized Covid-19 mainly focusing on respiratory support interventions. Indirect studies from SARS,MERS or other ARDS pathology caused by infectious agents based on reference tracking and snow ball search. Clinical, Healthy volunteer and mechanistic studies were included. Two authors independently screened studies for traditional respiratory supportive-care (Hypoxia management, ventilatory support and pulmonary toileting) related transmission of viral or bacterial pneumonia to HCWs.\n\nData ExtractionTwo authors (TK and SP) independently screened articles and verified for consensus. Quality of studies and level of evidence was assessed using Oxford Center for Evidence Based Medicine (OCEBM), Newcastle - Ottawa quality assessment Scale for observational studies and Grading of Recommendations Assessment, Development and Evaluation (GRADE) system for grading evidence.\n\nData Synthesis22 studies were eligible for inclusion. In 11 mechanistic studies, 7 were manikin based,1 was in the setting of GNB pneumonia, 2 were healthy volunteer study and 1 was heterogenous setting.Out of 11 clinical studies, 5 were case controlled and 6 were cohort studies. Risk of corona virus transmission was significantly high in HCWs performing or assisting endotracheal intubation or contact with respiratory secretion.(Moderate certainty evidence, GRADE B) Safety of nebulization treatment in corona virus pneumonia patients are questionable(Low certainty evidence, GRADE C).Very low certainty evidence exist for risk of transmission with conventional HFNC (GRADE D) and NIV (GRADE D),CPR (GRADE D),Bag and mask ventilation(GRADE D).Moderate certainty evidence exist for protective effect of wearing a multilayered mask, gown, eye protection and formal training for PPE use (GRADE B).Low certainty evidence exist for transmission risk with bag and mask ventilation, suctioning before and after intubation and prolonged exposure (GRADE C).Certainty of evidence for wearing gloves,post exposure hand washing and wearing N 95 mask is low(GRADE C).\n\nLimitationsThis study was limited to articles with English abstract. Highly dynamic nature of body of literature related to Covid-19, frequent updates were necessary even during preparation of manuscript and longitudinal search was continued even after finalizing initial search. Due to the heterogeneity and broad nature of the search protocol, quantitative comparisons regarding the effectiveness of included management strategies could not be performed. Direct evidence was limited due to poor quality and non-comparative nature of available Covid-19 reporting.\n\nConclusionsMajor risk factors for transmission of corona virus infection were, performing or assisting endotracheal intubation and contact with respiratory secretion. Risk of transmission with HFNC or NIV can be significantly decreased by helmet interface, modified exhalation circuit or placing a properly fitting face mask over patient interface of HFNC. Evidence for risk of transmission with CPR, suctioning before or after intubation or bag and mask ventilation of very low certainty. Significant protective factors are Formal training for PPE use, consistently wearing mask, gown and eye protection.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "TK Luqman Arafath", + "author_inst": "Wake Forest School of Medicine" + }, + { + "author_name": "Sandeep S Jubbal", + "author_inst": "University of Massachusetts Medical School" + }, + { + "author_name": "Elakkat D Gireesh", + "author_inst": "Advent Health, Orlando, FL, USA." + }, + { + "author_name": "Jyothi Margapuri", + "author_inst": "University of Massachusetts Medical School" + }, + { + "author_name": "Hanumantha Rao Jogu", + "author_inst": "Wake Forest School of Mediicne" + }, + { + "author_name": "Hitesh Patni", + "author_inst": "Florida Nephrology PLC" + }, + { + "author_name": "Tyler Thompson", + "author_inst": "Wake Forest School of Medicine" + }, + { + "author_name": "Arsh Patel", + "author_inst": "Wake Forest School of Medicine" + }, + { + "author_name": "Amirahwaty Abdulla", + "author_inst": "Geisinger Medical Center" + }, + { + "author_name": "Suma Menon", + "author_inst": "Wake Forest School of Medicine" + }, + { + "author_name": "Sudheer Penupolu", + "author_inst": "Geisinger Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.06.20147470", "rel_title": "Chloroquine for treatment of COVID-19 - a pig in a poke?", @@ -1325112,41 +1328345,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.03.179028", - "rel_title": "Genes associated with liver damage signalling pathways may impact the severity of COVID-19 symptoms in Spanish and Italian populations", - "rel_date": "2020-07-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.03.179028", - "rel_abs": "AimThe novel SARS-CoV-2 virus, which causes the COVID-19 disease, has infected more than 10 million people and caused 500K deaths worldwide. In Europe, over 2 million confirmed cases have been reported, while nearly 200K people have died from the disease. Despite strict containment measures in Spain and Italy after the first reported COVID-19 patient, these two countries have remained in the top five European nations with the highest mortality rate for over two months. We hypothesised that a genetic mechanism could partially explain the poor survival outcome observed in these two countries.\n\nMethodsAn extensive literature search to identify human candidate genes linked to SARS-CoV infection, host immune evasion and disease aggressiveness was carried out. Pathway analysis (IPA) was performed to select the most significantly associated canonical signalling pathways with the genes of interest. The genetic variants at these genes with {+/-}1Mb flanking region was extracted (GRCh37/hg19 built). Over 80 million single nucleotide polymorphisms (SNPs) were analysed in genome-wide data of 2,504 individuals (1000 genomes, phase III, https://www.internationalgenome.org/). Principal component (PC) analysis was performed, ancestry by the whole genome was inferred and subsets of the regions of interest were extracted (PLINK v1.9b, http://pngu.mgh.harvard.edu/purcell/plink/). PC1 to PC20 values from five European ancestries, including the Spanish and Italian populations, were used for PC analysis. Gene function predictions were run with our genes of interest as a query to the GeneMANIA Cytoscape plugin (https://genemania.org/).\n\nResultsA total of 437 candidate genes associated with SARS were identified, including 21 correlated with COVID-19 aggressiveness. The two most significant pathways associated with all 437 genes (Caveolar-mediated Endocytosis and MSP-RON Signalling) did not show any segregation at the population level. However, the most significant canonical pathway associated with genes linked to COVID-19 aggressiveness, the Hepatic Fibrosis and Hepatic Stellate Cell Activation, showed population-specific segregation. Both the Spanish and Italian populations clustered together from the rest of Europe. This was also observed for the Finnish population but in the opposite direction. These results suggest some of the severe COVID-19 cases reported in Spain and Italy could be partially explained by a pre-existing liver condition (especially liver cancer) and/or may lead to further COVID-19 related liver complications.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Leire Moya", - "author_inst": "Queensland University of Technology, Translational Research Institute" - }, - { - "author_name": "Samaneh Farashi", - "author_inst": "Queensland University of Technology and Translational Research Institute" - }, - { - "author_name": "Prashanth Suravajhala", - "author_inst": "Birla Institute of Scientific Research" - }, - { - "author_name": "Panchadsaram Janaththani", - "author_inst": "Queensland University of Technology and Translational Research Institute" - }, - { - "author_name": "Jyotsna Batra", - "author_inst": "Queensland University of Technology, Translational Research Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.07.07.186122", "rel_title": "Towards the design of multiepitope-based peptide vaccine candidate against SARS-CoV-2", @@ -1325467,6 +1328665,73 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.07.07.192732", + "rel_title": "In vivo structural characterization of the whole SARS-CoV-2 RNA genome identifies host cell target proteins vulnerable to re-purposed drugs", + "rel_date": "2020-07-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.07.192732", + "rel_abs": "SUMMARYSARS-CoV-2 is an RNA virus of the Coronaviridae family that is the causal pathogen of the ongoing Coronavirus Disease 2019 pandemic. There are currently no antiviral drugs or vaccines to treat COVID-19, and the failure to identify effective interventions can be blamed on our incomplete understanding of the nature of this virus and its host cell infection process. Here, we experimentally determined structural maps of the SARS-CoV-2 RNA genome in infected human cells and also characterized in vitro refolded RNA structures for SARS-CoV-2 and 6 other coronaviruses. Our in vivo data confirms several structural elements predicted from theoretical analysis and goes much further in revealing many previously unknown structural features that functionally impact viral translation and discontinuous transcription in cells. Importantly, we harnessed our in vivo structure data alongside a deep-learning tool and accurately predicted several dozen functionally related host cell proteins that bind to the SARS-CoV-2 RNA genome, none of which were known previously. Thus, our in vivo structural study lays a foundation for coronavirus RNA biology and indicates promising directions for the rapid development of therapeutics to treat COVID-19.HIGHLIGHTSWe mapped the in vivo structure and built secondary structural models of the SARS-CoV-2 RNA genomeWe discovered functionally impactful structural features in the RNA genomes of multiple coronavirusesWe predicted and validated host cell proteins that bind to the SARS-CoV-2 RNA genome based on our in vivo RNA structural data using a deep-learning toolCompeting Interest StatementThe authors have declared no competing interest.View Full Text", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Lei Sun", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Pan Li", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Xiaohui Ju", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Jian Rao", + "author_inst": "Chinese Academy of Medical Sciences & Peking Union Medical College" + }, + { + "author_name": "Wenze Huang", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Shaojun Zhang", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Tuanlin Xiong", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Kui Xu", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Xiaolin Zhou", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Lili Ren", + "author_inst": "Chinese Academy of Medical Sciences & Peking Union Medical College" + }, + { + "author_name": "Qiang Ding", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Jianwei Wang", + "author_inst": "Chinese Academy of Medical Sciences & Peking Union Medical College" + }, + { + "author_name": "Qiangfeng Cliff Zhang", + "author_inst": "Tsinghua University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.07.08.193672", "rel_title": "Extracellular vesicles containing ACE2 efficiently prevent infection by SARS-CoV-2 Spike protein-containing virus", @@ -1326590,37 +1329855,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.07.05.20140467", - "rel_title": "Angiotensin-converting enzyme 2 (ACE2) expression increases with age in patients requiringmechanical ventilation.", - "rel_date": "2020-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.05.20140467", - "rel_abs": "Mortality due to Covid-19 is highly associated with advanced age, owing in large part to severe lower respiratory tract infection. SARS-CoV-2 utilizes the host ACE2 receptor for infection. Whether ACE2 abundance in the lung contributes to age-associated vulnerability is currently unknown. We set out to characterize the RNA and protein expression profiles of ACE2 in aging human lung in the context of phenotypic parameters likely to affect lung physiology. Examining publicly available RNA sequencing data, we discovered that mechanical ventilation is a critical variable affecting lung ACE2 levels. Therefore, we investigated ACE2 protein abundance in patients either requiring mechanical ventilation or spontaneously breathing. ACE2 distribution and expression were determined in archival lung samples by immunohistochemistry (IHC). Tissues were selected from the specimen inventory at a large teaching hospital collected between 2010-2020. Twelve samples were chosen from patients receiving mechanical ventilation for acute hypoxic respiratory failure (AHRF). Twenty samples were selected from patients not requiring ventilation. We compared samples across age, ranging from 40-83 years old in the ventilated cohort and 14-80 years old in the non-ventilated cohort. Within the alveolated parenchyma, ACE2 expression is predominantly observed in type II pneumocytes (or alveolar type II / AT2 cells) and alveolar macrophages. All 12 samples from our ventilated cohort showed histologic features of diffuse alveolar damage including reactive, proliferating AT2 cells. In these cases, ACE2 was strongly upregulated with age when normalized to lung area (p = 0.004) or cellularity (p = 0.003), associated with prominent expression in AT2 cells. In non-ventilated individuals, AT2 cell reactive changes were not observed and ACE2 expression did not change with age when normalized to lung area (p = 0.231) or cellularity (p = 0.349). Additionally, we observed prominent pulmonary endothelial ACE2 expression in 2 patients on either an angiotensin-converting enzyme inhibitor (ACEI) or angiotensin receptor blocker (ARB). In summary, ACE2 expression increases with age in the setting of alveolar damage observed in patients on mechanical ventilation, providing a potential mechanism for higher Covid-19 mortality in the elderly.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Steven A Baker", - "author_inst": "Stanford University" - }, - { - "author_name": "Shirley Kowk", - "author_inst": "Stanford University" - }, - { - "author_name": "Gerald J Berry", - "author_inst": "Stanford University" - }, - { - "author_name": "Thomas J Montine", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.07.05.20146878", "rel_title": "Effect of Systemic Inflammatory Response to SARS-CoV-2 on Lopinavir and Hydroxychloroquine Plasma Concentrations", @@ -1326821,6 +1330055,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2020.07.05.20146787", + "rel_title": "Racial segregation, testing sites access, and COVID-19 incidence rate in Massachusetts, USA", + "rel_date": "2020-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.05.20146787", + "rel_abs": "The U.S. has merely 4% of the world population but 25% of the worlds COVID-19 cases. Massachusetts has been in the leading position of total cases since the outbreak in the U.S. Racial residential segregation is a fundamental cause of racial disparities in health. Moreover, disparities of access to health care have a large impact on COVID-19 cases. Thus, this study estimates racial segregation and disparities in testing sites access and employs economic, demographic, and transportation variables at the city/town level in Massachusetts. Spatial regression models are applied to evaluate the relationships between COVID-19 incidence rate and related variables. This is the first study to apply spatial analysis methods across neighborhoods in the U.S. to examine the COVID-19 incidence rate. The findings are: 1) residential segregations of Hispanic and Non-Hispanic Black/African Americans have a significantly positive association with COVID-19 incidence rate, indicating the higher susceptibility of COIVD-19 infections among minority; 2) The Black has the shortest drive time to testing sites, followed by Hispanic, Asian, and Whites. The drive time to testing sites is significantly negatively associated with the COVID-19 incidence rate, implying the importance of testing location being accessed by all populations; 3) Poverty rate and road density are significant explanatory variables. Importantly, overcrowding represented by more than one person per room is a significant variable found to be positively associated with COVID-19 incidence rate, suggesting the effectiveness of social distancing for reducing infection; 4) Different from previous studies, elderly population rate is not statistically significant with incidence rate because the elderly population in Massachusetts is less distributed in the hot spot regions of COVID-19 infections. The findings in this study provide useful insights for policymakers to propose new strategies to contain the COVID-19 transmissions in Massachusetts.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Tao Hu", + "author_inst": "Center for Geographic Analysis, Harvard University" + }, + { + "author_name": "Han Yue", + "author_inst": "Geocomputation Center for Social Science, Wuhan University" + }, + { + "author_name": "Changzhen Wang", + "author_inst": "Department of Geography and Anthropology, Louisiana State University" + }, + { + "author_name": "Bing She", + "author_inst": "University of Michigan, Ann Arbor" + }, + { + "author_name": "Xinyue Ye", + "author_inst": "Department of Landscape Architecture and Urban Planning, Texas A&M University" + }, + { + "author_name": "Regina Liu", + "author_inst": "Department of Biology, Mercer University" + }, + { + "author_name": "Xinyan Zhu", + "author_inst": "State Key Laboratory of Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University" + }, + { + "author_name": "Shuming Bao", + "author_inst": "China Data Institute, Ann Arbor" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.07.06.20147009", "rel_title": "Impact of COVID-19 Attributable Deaths on Longevity, Premature Mortality and DALY: Estimates of USA, Italy, Sweden and Germany", @@ -1327860,37 +1331141,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.07.20140996", - "rel_title": "Modelling interventions to control COVID-19 outbreaks in a refugee camp", - "rel_date": "2020-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.07.20140996", - "rel_abs": "Refugee camp populations are expected to be vulnerable to COVID-19 due to overcrowding, unsanitary conditions, and inadequate medical facilities. Because there has been no COVID-19 outbreak in a refugee camp to date, the potential for nonpharmaceutical interventions to slow the spread of COVID-19 in refugee camps remains untested. We used an agent-based model to simulate COVID-19 outbreaks in the Moria refugee camp, and we studied the effects of feasible interventions. Subdividing the camp (sectoring) \"flattened the curve,\" reducing peak infection by up to 70% and delaying peak infection by up to several months. The use of face masks coupled with efficient isolation of infected individuals reduced the overall incidence of infection and sometimes averted epidemics altogether. These interventions must be implemented quickly to be effective. Lockdowns had little effect on COVID-19 dynamics. Our findings provide an evidence base for camp managers planning intervention strategies against COVID-19 or future epidemics.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "R Tucker Gilman", - "author_inst": "Centre for Crisis Studies and Mitigation, University of Manchester, Manchester, UK" - }, - { - "author_name": "Siyana Mahroof-Shaffi", - "author_inst": "Kitrinos Healthcare, Lesbos, Greece" - }, - { - "author_name": "Christian Harkensee", - "author_inst": "Department of Paediatrics, Queen Elizabeth Hospital Gateshead, Gateshead, UK" - }, - { - "author_name": "Andrew T Chamberlain", - "author_inst": "Department of Earth and Environmental Sciences, University of Manchester, Manchester, UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.05.20146837", "rel_title": "Change points in the spread of COVID-19 question the effectiveness of nonpharmaceutical interventions in Germany", @@ -1328007,6 +1331257,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.06.20141333", + "rel_title": "Passive Monitoring of Physiological Data and Self-reported Symptoms to Detect Clusters of People with COVID-19", + "rel_date": "2020-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.06.20141333", + "rel_abs": "Traditional screening for COVID-19 typically includes survey questions about symptoms, travel history, and sometimes temperature measurements. We explored whether longitudinal, personal sensor data can help identify subtle changes which may indicate an infection, such as COVID-19. To do this we developed an app that collects smartwatch and activity tracker data, as well as self-reported symptoms and diagnostic testing results from participants living in the US. We assessed whether symptoms and sensor data could differentiate COVID-19 positive versus negative cases in symptomatic individuals. Between March 25 and June 7, 2020, we enrolled 30,529 participants, of whom 3,811 reported symptoms, 54 reported testing positive for COVID-19, and 279 negative. We found that a combination of symptom and sensor data resulted in an AUC=0.80 [0.73 - 0.86] which was significantly better (p < 0.01) than a model which just considered symptoms alone (AUC=0.71 [0.63 - 0.79]) in the discrimination between symptomatic individuals positive or negative for COVID-19. Such orthogonal, continuous, passively captured data may be complementary to virus testing that is generally a one-off, or infrequent, sampling assay.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Giorgio Quer", + "author_inst": "Scripps Research Translational Institute" + }, + { + "author_name": "Jennifer M. Radin", + "author_inst": "Scripps Research Translational Institute" + }, + { + "author_name": "Matteo Gadaleta", + "author_inst": "Scripps Research Translational Institute" + }, + { + "author_name": "Katie Baca-Motes", + "author_inst": "Scripps Research Translational Institute" + }, + { + "author_name": "Lauren Ariniello", + "author_inst": "Scripps Research Translational Institute" + }, + { + "author_name": "Edward Ramos", + "author_inst": "CareEvolution" + }, + { + "author_name": "Vik Kheterpal", + "author_inst": "CareEvolution" + }, + { + "author_name": "Eric J. Topol", + "author_inst": "Scripps Research Translational Institute" + }, + { + "author_name": "Steven R. Steinhubl", + "author_inst": "Scripps Research Translational Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.07.05.20146894", "rel_title": "A topic analysis of traditional and social media news coverage of the early COVID-19 pandemic and implications for public health communication", @@ -1329242,41 +1332543,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.03.20145409", - "rel_title": "Split ventilation with pressure regulators for patient-specific tidal volumes", - "rel_date": "2020-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20145409", - "rel_abs": "As a measure of last resort during the COVID-19 pandemic, single mechanical ventilators have been repurposed to support multiple patients. In existing split-ventilator configurations using FDA-approved tubing adaptors, each patient receives the same inspiratory pressure, requiring careful matching of patients to avoid barotrauma. Progression of disease may cause tidal volumes to diverge from desired targets, and routine interventions (eg. suctioning) in one patient may adversely affect other patients. To overcome these limitations, we demonstrate a split-ventilator configuration that enables individualized patient management by incorporating a commonly available pressure regulator used for gas appliances. We validate this method by achieving various combinations of tidal volume in each of two synthetic lungs using a standard ventilator machine in combination with two gas flow analyzers. With further safety testing and instrumentation, pressure regulators may represent a viable path to substantially augment the capacity for ventilation in resource-constrained settings.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Lakshminarayan Srinivasan", - "author_inst": "Transcend Review, Inc." - }, - { - "author_name": "Chris A Rishel", - "author_inst": "Department of Anesthesia, Stanford University School of Medicine" - }, - { - "author_name": "Barrett J. Larson", - "author_inst": "Department of Anesthesia, Stanford University School of Medicine" - }, - { - "author_name": "Juhwan Yoo", - "author_inst": "Electrical Engineer" - }, - { - "author_name": "Ned Shelton", - "author_inst": "Mechanical Engineer" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.07.03.20145912", "rel_title": "Ultraviolet A Radiation and COVID-19 Deaths: A Multi Country Study", @@ -1329441,6 +1332707,33 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.07.06.190207", + "rel_title": "Conserved Genomic Terminals of SARS-CoV-2 as Co-evolving Functional Elements and Potential Therapeutic Targets", + "rel_date": "2020-07-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.06.190207", + "rel_abs": "ABSTRACTTo identify features in the genome of the SARS-CoV-2 pathogen responsible for the COVID-19 pandemic that may contribute to its viral replication, host pathogenicity, and vulnerabilities, we investigated how and to what extent the SARS-CoV-2 genome sequence differs from other well-characterized human and animal coronavirus genomes. Our analyses suggest the presence of unique sequence signatures in the 3\u2019-untranslated region (UTR) of betacoronavirus lineage B, which phylogenetically encompasses SARS-CoV-2, SARS-CoV, as well as multiple groups of bat and animal coronaviruses. In addition, we identified genome-wide patterns of variation across different SARS-CoV-2 strains that likely reflect the effects of selection. Finally, we provide evidence for a possible host microRNA-mediated interaction between the 3\u2019-UTR and human microRNA hsa-miR-1307-3p based on predicted, yet extensive, complementary base-pairings and similar interactions involving the Influenza A H1N1 virus. This interaction also suggests a possible survival mechanism, whereby a mutation in the SARS-CoV-2 3\u2019-UTR leads to a weakened host immune response. The potential roles of host microRNAs in SARS-CoV-2 replication and infection, and the exploitation of conserved features in the 3\u2019-UTR as therapeutic targets warrant further investigation.Competing Interest StatementThe authors have declared no competing interest.View Full Text", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Agnes P Chan", + "author_inst": "The Translational Genomics Research Institute (TGen), Phoenix, AZ" + }, + { + "author_name": "Yongwook Choi", + "author_inst": "The Translational Genomics Research Institute (TGen), Phoenix, AZ" + }, + { + "author_name": "Nicholas J Schork", + "author_inst": "The Translational Genomics Research Institute (TGen), Phoenix, AZ; Departments of Population Sciences and Molecular and Cell Biology, The City of Hope National " + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.07.06.189803", "rel_title": "Animal Model Prescreening: Pre-exposure to SARS-CoV-2 impacts responses in the NHP model", @@ -1330684,37 +1333977,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.03.20146134", - "rel_title": "Timing of PCR and Antibody Testing in Patients with COVID-19 associated dermatologic manifestations", - "rel_date": "2020-07-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20146134", - "rel_abs": "A recent study from Spain noted 40 patients with chilblain-like lesions in suspected COVID-19.1 None tested PCR positive for SARS-CoV-2, but 30% had detectable antibodies. The rapid increase in chilblain/pernio-like cases during the COVID-19 pandemic is likely SARS-CoV-2-associated. The relationship between skin symptom onset and COVID-19 PCR/antibody test timing, however, remains uncharacterized.\n\nWe established an international registry for cutaneous manifestations of COVID-19.2, 3 Providers reported time between dermatologic symptom onset and positive/negative COVID-19 laboratory results, when available.\n\nFrom 8 April-30 June, 2020, 906 laboratory-confirmed or suspected COVID-19 cases with dermatologic manifestations were reported, 534 of which were chilblains/pernio.3 Among PCR-tested patients, 57%(n=208) overall and 15%(n=23) of chilblains/pernio cases were PCR-positive. Antibody positivity was 37%(n=39) overall and 19%(n=15) for chilblains/pernio.\n\nWe evaluated 163 patients with timing information on PCR and/or antibody testing (Table 1). For patients with suspected COVID-19 and any cutaneous manifestation, PCR-positive testing occurred median 6 (IQR 1-14) days after dermatologic symptoms started while PCR-negative testing occurred median 14 (IQR 7-24) days later. For patients with pernio/chilblains, PCR-positivity was noted 8 (IQR 5-14) days after symptoms and negativity median 14 (IQR 7-28) days later. Antibody testing (IgM or IgG) was positive median 30 (IQR 19-39) days after symptom onset for all dermatologic manifestations and 27 (IQR 24-33) days after chilblains/pernio onset.\n\nLike Hubiche et al, our data highlight the low frequency of SARS-CoV-2 PCR+ testing in COVID-19 patients with cutaneous manifestations. Positive predictive values for COVID-19 PCR are influenced by viral shedding kinetics, which are difficult to assess in non-respiratory presentations.4 Our data reveal that early PCR testing is more likely to be positive than later testing, even when date-of-onset is defined by cutaneous manifestations rather than systemic symptoms.\n\nMost COVID-19 antibody data are from systemically-ill patients; the kinetics of antibody production in mild-to-moderate COVID-19 infections remain unclear.5 Here, positive antibodies resulted median 30 days from disease onset, beyond the frequently used 14-21 day testing window. In outpatients with true infection, many factors influence the likelihood of a positive antibody result: antibody production, test availability, assay sensitivity, and timing of care-seeking in relation to symptom-onset. These variables influence our interpretation of individual test results and our understanding of the association between pernio and COVID-19.\n\nMore population-level testing data is necessary to optimize diagnostic test timing. Positive identification of COVID-19 in minimally-symptomatic patients, including patients with skin findings, is critical to the public health effort.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Esther E Freeman", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Devon E McMahon", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Lindy P Fox", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Marlys S Fassett", - "author_inst": "University of California San Francisco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "dermatology" - }, { "rel_doi": "10.1101/2020.07.03.20145763", "rel_title": "Oxygen and mortality in COVID-19 pneumonia: a comparative analysis of supplemental oxygen policies and health outcomes across 26 countries.", @@ -1330835,6 +1334097,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.07.03.20145748", + "rel_title": "Are Our COVID Warriors Cared-for Enough?A Nationwide Survey on Stress Among Doctors During the COVID-19 Pandemic", + "rel_date": "2020-07-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20145748", + "rel_abs": "Limited and uneven accessibility to healthcare is a major impediment in the fight against the COVID-19 pandemic which continues on inexorably, across various parts of the globe. We conducted a nationwide survey of a large sample of Indian doctors to measure levels of perceived stress, identify risk factors for severe stress and assess their response to current issues related to safety and well-being of the HCP community. The survey found severely stressed doctors to be younger (<45years), of female gender working in the ICU setting and insecure regarding their finances. Concern regarding PPE shortages and ethical dilemmas of rationing care are factors inducing severe stress amongst doctors working in ICU settings. This is the first such survey done in the context of the COVID-19 pandemic from the Indian sub-continent. The findings have important implications on the International healthcare community, especially across Africa, Asia & South America where the contagion continues to wreak havoc. The survey has identified factors which adversely impact the mental health of doctors during this Pandemic. This can act as a valuable guide for governmental authorities, professional organisations and hospital managements to establish support systems at multiple levels for these \"COVID Warriors\".", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Amritha Nair", + "author_inst": "Dr.Rela Institute & Medical Centre" + }, + { + "author_name": "Jagadeesh Menon", + "author_inst": "Dr.Rela Institute & Medical Centre" + }, + { + "author_name": "Ashwin Rammohan", + "author_inst": "Dr.Rela Institute & Medical Centre" + }, + { + "author_name": "Abdul R Hakeem", + "author_inst": "Dr.Rela Institute & Medical Centre" + }, + { + "author_name": "Sathya D Cherukuri", + "author_inst": "Somerset NHS Foundation Trust" + }, + { + "author_name": "Naresh Shanmugam", + "author_inst": "Dr.Rela Institute & Medical Centre" + }, + { + "author_name": "Akila Rajakumar", + "author_inst": "Dr.Rela Institute & Medical Centre" + }, + { + "author_name": "Mettu Srinivas Reddy", + "author_inst": "Dr.Rela Institute & Medical Centre" + }, + { + "author_name": "Ilankumaran Kaliamoorthy", + "author_inst": "Dr.Rela Institute & Medical Centre" + }, + { + "author_name": "Mohamed Rela", + "author_inst": "Dr.Rela Institute & Medical Centre" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.07.02.20145532", "rel_title": "Impact of anxiety associated with COVID 19 on tinnitus", @@ -1331970,41 +1335287,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.03.20144931", - "rel_title": "Psychiatric symptoms, risk, and protective factors among university students in quarantine during the COVID-19 pandemic in China", - "rel_date": "2020-07-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20144931", - "rel_abs": "This study investigated psychiatric symptoms (depression, anxiety, and traumatic stress) during state-enforced quarantine among university students in China. We conducted a cross-sectional survey with 1,912 university students during March and April 2020. Psychiatric symptoms in the mild or higher range based on clinical cut-offs were alarmingly prevalent: 67.05% reported traumatic stress symptoms, 46.55% had depressive symptoms, and 34.73% reported anxiety symptoms. Further, 19.56% endorsed some degree of suicidal ideation. We explored factors that may contribute to poor psychological health as well as those that may function as protective factors. Risk and protective factors examined included demographic variables, two known protective factors for mental health (mindfulness, perceived social support), four COVID-specific factors (COVID-19 related efficacy, perceived COVID-19 threat, perceived COVID-19 societal stigma, COVID-19 prosocial behavior) and screen media usage. Across psychiatric symptom domains, mindfulness was associated with lower symptom severity, while COVID-19 related financial stress, perceived COVID-19 societal stigma, and perceived COVID-19 threat were associated with higher symptom severity. COVID-19 threat and COVID-19 stigma showed main and interactive effects in predicting all mental health outcomes, with their combination associated with highest symptom severity. Average screen media device usage was 6 hours and usage was positively associated with depression. Female gender and COVID-19 prosocial behavior were associated with higher anxiety, while COVID-19 self-efficacy associated with lower anxiety symptoms. Study limitations and implications for treatment and prevention of affective disorders during crisis are discussed.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Shufang Sun", - "author_inst": "Brown University" - }, - { - "author_name": "Simon B Goldberg", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Danhua Lin", - "author_inst": "Beijing Normal University" - }, - { - "author_name": "Shan Qiao", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Don Operario", - "author_inst": "Brown University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.07.02.20144899", "rel_title": "Curve-fitting approach for COVID-19 data and its physical background", @@ -1332261,6 +1335543,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.02.20144873", + "rel_title": "Clinical Characteristics of Recurrent-positive Coronavirus Disease 2019 after Curative Discharge: a retrospective analysis of 15 cases in Wuhan China", + "rel_date": "2020-07-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.02.20144873", + "rel_abs": "In China, the patients with previously negative RT-PCR results again test positive during the post-discharge isolation period. We aimed to determine the clinical characteristics of these \"recurrent-positive\" patients. We retrospectively reviewed the data of 15 recurrent-positive patients and 107 control patients with non-recurrent, moderate COVID-19 treated in Wuhan, China. Clinical data and laboratory results were comparatively analyzed. We found that recurrent-positive patients had moderate disease. The rate of recurrent-positive disease in our hospital was 1.87%. Recurrent-positive patients were significantly younger (43(35-54) years) than control patients (60(43-69) years) (P=0.011). The early LOS (length of stay in hospital before recurrence) was significantly longer in recurrent-positive patients (36(34-45) days) than in control patients (15(7-30) days) (P =0.001). The time required for the first conversion of RT-PCR results from positive to negative was significantly longer in recurrent-positive patients (14(10-17) days) than in control patients (6(3-9) days) (P =0.011). Serum COVID-19 antibody levels were significantly lower in recurrent-positive patients than in control patients (IgM: 13.69 {+/-} 4.38 vs. 68.10 {+/-} 20.85 AU/mL, P = 0.015; IgG: 78.53 {+/-} 9.30 vs. 147.85 {+/-} 13.33 AU/mL, P < 0.0001). Recurrent-positive patients were younger than control patients. The early LOS (length of stay in hospital before recurrence) was significantly longer in recurrent-positive group than that in control group. COVID-19 IgM/IgG antibody levels were significantly lower in recurrent-positive group than those in control group, which might explain why the virus RNA RT-PCR was positive after the initial \"clinical cure\"(with three times of virus RNA RT-PCR negative). The virus might not be fully eliminated because of the lower IgG level and their later replicating might result in recurrent-positive virus RNA RT-PCR.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Lan Chen", + "author_inst": "Zhongshan Hospital, Xiamen University" + }, + { + "author_name": "Zhen-Yu Zhang", + "author_inst": "Zhongshan Hospital, Xiamen University" + }, + { + "author_name": "Xiao-Bin Zhang", + "author_inst": "Zhongshan Hospital, Xiamen University" + }, + { + "author_name": "Su-Zhen Zhang", + "author_inst": "Zhongshan Hospital, Xiamen University" + }, + { + "author_name": "Qiu-Ying Han", + "author_inst": "Zhongshan Hospital, Xiamen University" + }, + { + "author_name": "Zhi-Peng Feng", + "author_inst": "Zhongshan Hospital, Xiamen University" + }, + { + "author_name": "Jian-Guo Fu", + "author_inst": "Zhongshan Hospital, Xiamen University" + }, + { + "author_name": "Xiong Xiao", + "author_inst": "Xiamen Branch of Zhongshan Hospital Affiliated to Fudan University" + }, + { + "author_name": "Hui-Min Chen", + "author_inst": "Xiamen Third Hospital" + }, + { + "author_name": "Li-Long Liu", + "author_inst": "Hongai Hospital, Xiamen" + }, + { + "author_name": "Xian-Li Chen", + "author_inst": "Xiang'an Hospital Affiliated to Xiamen University" + }, + { + "author_name": "Yu-Pei Lan", + "author_inst": "Xiamen Haicang Hospital" + }, + { + "author_name": "De-Jin Zhong", + "author_inst": "Xiamen Changgen Hospital" + }, + { + "author_name": "Lan Hu", + "author_inst": "Optics Valley Branch of Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan" + }, + { + "author_name": "Jun-Hui Wang", + "author_inst": "Optics Valley Branch of Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan" + }, + { + "author_name": "Zhen-Yu Yin", + "author_inst": "Zhongshan Hospital, Xiamen University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.02.20144865", "rel_title": "Highly predictive regression model of active cases of COVID-19 in a population by screening wastewater viral load", @@ -1333472,77 +1336833,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.02.20143206", - "rel_title": "Navigating hospitals safely through the COVID-19 epidemic tide: predicting case load for adjusting bed capacity", - "rel_date": "2020-07-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.02.20143206", - "rel_abs": "BackgroundThe pressures exerted by the pandemic of COVID-19 pose an unprecedented demand on health care services. Hospitals become rapidly overwhelmed when patients requiring life-saving support outpace available capacities. We here describe methods used by a university hospital to forecast caseloads and time to peak incidence.\n\nMethodsWe developed a set of models to forecast incidence among the hospital catchment population and describe the COVID-19 patient hospital care-path. The first forecast utilized data from antecedent allopatric epidemics and parameterized the care path model according to expert opinion (static model). Once sufficient local data were available, trends for the time dependent effective reproduction number were fitted and the care-path was parameterized using hazards for real patient admission, referrals, and discharge (dynamic model).\n\nResultsThe static model, deployed before the epidemic, exaggerated the bed occupancy (general wards 116 forecasted vs 66 observed, ICU 47 forecasted vs 34 observed) and predicted the peak too late (general ward forecast April 9, observed April 8, ICU forecast April 19, observed April 8). After April 5, the dynamic model could be run daily and precision improved with increasing availability of empirical local data.\n\nConclusionsThe models provided data-based guidance in the preparation and allocation of critical resources of a university hospital well in advance of the epidemic surge, despite overestimating the service demand. Overestimates should resolve when population contact pattern before and during restrictions can be taken into account, but for now they may provide an acceptable safety margin for preparing during times of uncertainty.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Tjibbe Donker", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Fabian B\u00fcrkin", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Martin Wolkewitz", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Christian Haverkamp", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Dominic Christoffel", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Oliver Kappert", - "author_inst": "Public Health Office, Public Health District Freiburg" - }, - { - "author_name": "Thorsten Hammer", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Hans-J\u00f6rg Busch", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Paul Biever", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Johannes Kalbhenn", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Hartmut B\u00fcrkle", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Winfried Kern", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Frederik Wenz", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Hajo Grundmann", - "author_inst": "UniversityMedical Center Freiburg" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.30.20143149", "rel_title": "Orthogonal Functions for Evaluating Social Distancing Impact on CoVID-19 Spread", @@ -1333667,6 +1336957,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.03.186296", + "rel_title": "The major genetic risk factor for severe COVID-19 is inherited from Neandertals", + "rel_date": "2020-07-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.03.186296", + "rel_abs": "A recent genetic association study (Ellinghaus et al. 2020) identified a gene cluster on chromosome 3 as a risk locus for respiratory failure in SARS-CoV-2. Recent data comprising 3,199 hospitalized COVID-19 patients and controls reproduce this and find that it is the major genetic risk factor for severe SARS-CoV-2 infection and hospitalization (COVID-19 Host Genetics Initiative). Here, we show that the risk is conferred by a genomic segment of ~50 kb that is inherited from Neandertals and occurs at a frequency of ~30% in south Asia and ~8% in Europe.Competing Interest StatementThe authors have declared no competing interest.View Full Text", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Hugo Zeberg", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Svante Paabo", + "author_inst": "Max-Planck-Inst, Leipzig" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.07.03.186304", "rel_title": "Robust and sensitive detection of SARS-CoV-2 using PCR based methods", @@ -1335126,29 +1338439,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.30.20143586", - "rel_title": "Does Lockdown Decrease the Protective Role of ultraviolet-B (UVB) Radiation in Reducing COVID-19 Deaths?", - "rel_date": "2020-07-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.30.20143586", - "rel_abs": "BackgroundNations are imposing unprecedented measures at large-scale to contain the spread of COVID-19 pandemic. Recent studies indicate that measures such as lockdowns may have slowed down the growth of COVID-19. However, in addition to substantial economic and social costs, these measures also limit the exposure to Ultraviolet-B radiation (UVB). Emerging observational evidence indicate the protective role of UVB and vitamin D in reducing the severity and mortality of COVID-19 deaths. In this observational study, we empirically outline the independent protective roles of lockdown and UVB exposure as measured by ultraviolet index (UVI), whilst also examining whether the severity of lockdown is associated with a reduction in the protective role.\n\nMethodsWe apply a log-linear fixed-effects model to a panel dataset of 162 countries over a period of 108 days (n=6049). We use the cumulative number of COVID-19 deaths as the dependent variable and isolate the mitigating influence of lockdown severity on the association between UVI and growth-rates of COVID-19 deaths from time-constant country-specific and time-varying country-specific potentially confounding factors.\n\nFindingsAfter controlling for time-constant and time-varying factors, we find that a unit increase in UVI and lockdown severity are independently associated with 17% [-1.8 percentage points] and 77% [-7.9 percentage points] decline in COVID-19 deaths growth rate, indicating their respective protective roles. However, the widely utilized and least severe lockdown (recommendation to not leave the house) already fully mitigates the protective role of UVI by 95% [1.8 percentage points] indicating its downside.\n\nInterpretationWe find that lockdown severity and UVI are independently associated with a slowdown in the daily growth rates of cumulative COVID-19 deaths. However, we find consistent evidence that increase in lockdown severity is associated with a significant reduction in the protective role of UVI in reducing COVID-19 deaths. Our results suggest that lockdowns in conjunction with adequate exposure to UVB radiation might have provided even more substantial health benefits, than lockdowns alone. For example, we estimate that there would be 21% fewer deaths on average with sufficient UVB exposure while people were recommended not to leave their house. Therefore, our study outlines the importance of considering UVB exposure, especially while implementing lockdowns and may support policy decision making in countries imposing such measures.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Rahul Kalippurayil Moozhipurath", - "author_inst": "Goethe University Frankfurt am Main" - }, - { - "author_name": "Lennart Kraft", - "author_inst": "Goethe University Frankfurt am Main" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.01.20144162", "rel_title": "Mass Screening for SARS-CoV-2 Infection among Residents and Staff in Twenty-eight Long-term Care Facilities in Fulton County, Georgia", @@ -1335321,6 +1338611,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.01.20144188", + "rel_title": "Differential COVID-19 case positivity in New York City neighborhoods: socioeconomic factors and mobility", + "rel_date": "2020-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.01.20144188", + "rel_abs": "New York City has been one of the hotspots of the COVID-19 pandemic and during the first two months of the outbreak considerable variability in case positivity was observed across the citys ZIP codes. In this study, we examined: a) the extent to which the variability in ZIP code level cases can be explained by aggregate markers of socioeconomic status and daily change in mobility; and b) the extent to which daily change in mobility independently predicts case positivity.\n\nOur analysis indicates that the markers considered together explained 56% of the variability in case positivity through April 1 and their explanatory power decreased to 18% by April 30. Our analysis also indicates that changes in mobility during this time period are not likely to be acting as a mediator of the relationship between ZIP-level SES and case positivity. During the middle of April, increases in mobility were independently associated with decreased case positivity. Together, these findings present evidence that heterogeneity in COVID-19 case positivity during the New York City spring outbreak was largely driven by residents socioeconomic status.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Matthew Raymond Lamb", + "author_inst": "Mailman School of Public Health, Columbia University" + }, + { + "author_name": "Sasikiran Kandula", + "author_inst": "Mailman School of Public Health, Columbia University" + }, + { + "author_name": "Jeffrey Shaman", + "author_inst": "Mailman School of Public Health, Columbia University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.01.20144394", "rel_title": "Temporary Immunity and Multiple Waves of COVID-19", @@ -1336780,133 +1340097,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.30.20142935", - "rel_title": "A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 within nasopharyngeal and oropharyngeal swabs at Hampshire Hospitals NHS Foundation Trust", - "rel_date": "2020-07-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.30.20142935", - "rel_abs": "The COVID-19 pandemic has illustrated the importance of rapid, accurate diagnostic testing for the effective triaging and cohorting of patients and timely tracking and tracing of cases. However, a surge in diagnostic testing quickly resulted in worldwide competition for the same sample preparation and real-time RT-PCR diagnostic reagents (rRT-PCR). Consequently, Hampshire Hospitals NHS Foundation Trust, UK sought to diversify their diagnostic portfolio by exploring alternative amplification chemistries including those that permit direct testing without RNA extraction. This study describes the validation of a SARS-CoV-2 RT-LAMP assay, which is an isothermal, autocycling, strand-displacement nucleic acid amplification technique which can be performed on extracted RNA (RNA RT-LAMP) or directly from swab (Direct RT-LAMP). Analytical specificity (ASp) of this new RT-LAMP assay was 100% and analytical sensitivity (ASe) was between 1[x]101 and 1[x]102 copies when using a synthetic DNA target. The overall diagnostic sensitivity (DSe) and specificity (DSp) of RNA RT-LAMP was 97% and 99% respectively, relative to the standard of care (SoC) rRT-PCR. When a CT cut-off of 33 was employed, above which increasingly evidence suggests there is a very low risk of patients shedding infectious virus, the diagnostic sensitivity was 100%. The DSe and DSp of Direct-RT-LAMP was 67% and 97%, respectively. When setting CT cut-offs of [≤]33 and [≤]25, the DSe increased to 75% and 100%, respectively. Time from swab-to-result for a strong positive sample (CT < 25) was < 15 minutes. We propose that RNA RT-LAMP could replace rRT-PCR where there is a need for increase in throughput, whereas Direct RT-LAMP could be used as a screening tool for triaging patients into appropriate hospitals wards, at GP surgeries and in care homes, or for population screening to identify super shedders. Direct RT-LAMP could also be used during times of high prevalence to save critical extraction and rRT-PCR reagents by screening out those strong positives from diagnostic pipelines.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Veronica L Fowler", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Bryony Armson", - "author_inst": "School of Biosciences and Medicine, University of Surrey" - }, - { - "author_name": "Jose L Gonzales", - "author_inst": "Wageningen Bioveterinary Research (WBVR)" - }, - { - "author_name": "Emma L Wise", - "author_inst": "School of Biosciences and Medicine, University of Surrey" - }, - { - "author_name": "Emma L. A. Howson", - "author_inst": "The Pirbright Institute" - }, - { - "author_name": "Zoe Vincent-Mistiaen", - "author_inst": "Gibraltar Health Authority" - }, - { - "author_name": "Sarah Fouch", - "author_inst": "School of Pharmacy and Biomedical Sciences, University of Portsmouth" - }, - { - "author_name": "Connor J Maltby", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Seden Grippon", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Simon Munro", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Lisa Jones", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Tom Holmes", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Claire Tillyer", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Joanne Elwell", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Amy Sowood", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Oliver de Peyer", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Sophie Dixon", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Thomas Hatcher", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Helen Knight", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Shailen Laxman", - "author_inst": "OptiSense Limited" - }, - { - "author_name": "Charlotte Walsh", - "author_inst": "GeneSys Biotech Limited" - }, - { - "author_name": "Michael Andreou", - "author_inst": "OptiSense Limited" - }, - { - "author_name": "Nick Morant", - "author_inst": "GeneSys Biotech Limited" - }, - { - "author_name": "Duncan Clark", - "author_inst": "GeneSys Biotech Limited" - }, - { - "author_name": "Rebecca Houghton", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Nathan Moore", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Nicholas Cortes", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Stephen P Kidd", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.30.20143255", "rel_title": "Handyfuge-LAMP: low-cost and electricity-free centrifugation forisothermal SARS-CoV-2 detection in saliva.", @@ -1337107,6 +1340297,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.29.20140111", + "rel_title": "Cost-effectiveness of public health strategies for COVID-19 epidemic control in South Africa", + "rel_date": "2020-07-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20140111", + "rel_abs": "BackgroundHealthcare resource constraints in low and middle-income countries necessitate selection of cost-effective public health interventions to address COVID-19.\n\nMethodsWe developed a dynamic COVID-19 microsimulation model to evaluate clinical and economic outcomes and cost-effectiveness of epidemic control strategies in KwaZulu-Natal, South Africa. Interventions assessed were Healthcare Testing (HT), where diagnostic testing is performed only for those presenting to healthcare centres; Contact Tracing (CT) in households of cases; Isolation Centres (IC), for cases not requiring hospitalisation; community health worker-led Mass Symptom Screening and diagnostic testing for symptomatic individuals (MS); and Quarantine Centres (QC), for contacts who test negative. Given uncertainties about epidemic dynamics in South Africa, we evaluated two main epidemic scenarios over 360 days, with effective reproduction numbers (Re) of 1{middle dot}5 and 1{middle dot}2. We compared HT, HT+CT, HT+CT+IC, HT+CT+IC+MS, HT+CT+IC+QC, and HT+CT+IC+MS+QC, considering strategies with incremental cost-effectiveness ratio (ICER) 8 million people worldwide with >2 million cases in the US (June 17th, 2020). There is an urgent need for vaccines and therapeutics to combat the spread of this coronavirus. Similarly, the development of diagnostic and research tools to determine infection and vaccine efficacy are critically needed. Molecular assays have been developed to determine viral genetic material present in patients. Serological assays have been developed to determine humoral responses to the spike protein or receptor binding domain (RBD). Detection of functional antibodies can be accomplished through neutralization of live SARS-CoV2 virus, but requires significant expertise, an infectible stable cell line, a specialized BioSafety Level 3 (BSL-3) facility. As large numbers of people return from quarantine, it is critical to have rapid diagnostics that can be widely adopted and employed to assess functional antibody levels in the returning workforce. This type of surrogate neutralization diagnostic can also be used to assess humoral immune responses induced in patients from the large number of vaccine and immunotherapy trials currently on-going. Here we describe a rapid serological diagnostic assay for determining antibody receptor blocking and demonstrate the broad utility of the assay by measuring the antibody functionality of sera from small animals and non-human primates immunized with an experimental SARS-CoV-2 vaccine and using sera from infected patients.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Daniel W Kulp", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Susanne Walker", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Neethu Chokkalingam", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Emma L Reuschel", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Mansi Purwar", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Ziyang Xu", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Ebony Y Gary", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Kevin Y. Kim", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Katherine Schultheis", + "author_inst": "Inovio Pharmaceuticals" + }, + { + "author_name": "Jewell Walters", + "author_inst": "Inovio Pharmaceuticals" + }, + { + "author_name": "Stephanie Ramos", + "author_inst": "Inovio Pharmaceuticals" + }, + { + "author_name": "Trevor R.F. Smith", + "author_inst": "Inovio Pharmaceuticals" + }, + { + "author_name": "Kate Broderick", + "author_inst": "Inovio Pharmaceuticals" + }, + { + "author_name": "Pablo Tebas", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ami Patel", + "author_inst": "The Wistar Instititue" + }, + { + "author_name": "David B Weiner", + "author_inst": "Wistar Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.06.20.161323", "rel_title": "The D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity and decreases neutralization sensitivity to individual convalescent sera", @@ -1360531,29 +1363628,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.18.20135053", - "rel_title": "Short-term Forecasting of Cumulative Confirmed Cases of Covid-19 Pandemic in Somalia", - "rel_date": "2020-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20135053", - "rel_abs": "Somalia has recorded the first confirmed Covid-19 case and first death case on March 16, and April 08, 2020, respectively. Since its arrival, it had infected 2,603 people and took the lives of 88 people while 577 patients were recovered as of 14 June, 2020. To fight this pandemic, the government requires to make the necessary plans accordingly. To plan effectively, the government needs to answer this question: what will be the effect of Covid-19 cases in the country? To answer this question accurately and objectively, forecasting the spread of confirmed Covid-19 cases will be vital. To this regard, this paper provides real times forecasts of Covid-19 cases employing Holts linear trend model without seasonality. Provided that the data employed is accurate and the past pattern of the disease will continue in the future, this model is powerful to produce real time forecasts in the future with some degree of uncertainty. With the help of these forecasts, the government can make evidence based decisions by utilizing the scarce resource available at its disposal.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Dahir Abdi Ali", - "author_inst": "SIMAD University" - }, - { - "author_name": "Habshah Midi", - "author_inst": "Universiti Putra Malaysia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.19.20135756", "rel_title": "Sensitivity of RT-PCR testing of upper respiratory tract samples for SARS-CoV-2 in hospitalised patients: a retrospective cohort study.", @@ -1360806,6 +1363880,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.06.19.20135475", + "rel_title": "Chloroquine, but not hydroxychlorquine, prolongs the QT interval in a primary care population", + "rel_date": "2020-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.19.20135475", + "rel_abs": "BackgroundChloroquine (CQ) and Hydroxychloroquine (HCQ) have recently been suggested as treatment for the current Corona Virus Disease 2019 (COVID-19) pandemic. However, despite their long-term use and only few case reports on adverse effects, CQ and HCQ are listed as a known risk of the lethal ventricular arrhythmia Torsade de Pointes and their cardiac safety profile is being questioned. Thus, we aimed to investigate the electrocardiographic and mortality effects of CQ and HCQ in a primary care population.\n\nMethodsWe used Danish health care registers and electrocardiograms (ECGs) from primary care to define three studies. 1) A paired study of subjects with ECGs before and during use of CQ/HCQ, 2) a matched ECG study of subjects taking CQ/HCQ compared to controls, and 3) a mortality study on people taking HCQ matched to control. In both matched studies, we adjusted for connective tissue diseases, use of QT-prolonging drugs, and cardiac disease. We used the QTc interval as the marker for electrocardiographic safety. In the mortality study, cases were followed from first claimed prescription until 300 days after estimated completion of the last prescription. 95% confidence intervals follow estimates in parenthesis.\n\nResultsUse of CQ was associated with a 5.5 (0.7;10) ms increase in QTc in the paired study (n=10). In the matched study (n=28, controls=280), QTc was insignificantly increased in subjects taking CQ by 4.7 (-3.4;13) ms. With a {Delta}QTc of 1.0 (-5.6;7.5), use of HCQ was not associated with an increased QTc in the paired study (n=32). In the matched study (n=172, controls=1,720), QTc also was not different between groups (p=0.5). In the mortality study (n=3,368), use of HCQ was associated with a hazard ratio of 0.67 (0.43;1.05).\n\nConclusionsIn subjects free of COVID-19, we found a small increase in QTc associated with use of chloroquine, but not hydroxychloroquine. We found no increased mortality associated with use of hydroxychloroquine.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jonas L Isaksen", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Anders Gaarsdal Holst", + "author_inst": "Acesion Pharma" + }, + { + "author_name": "Adrian Pietersen", + "author_inst": "Copenhagen General Practitioners' Laboratory" + }, + { + "author_name": "Jonas Bille Nielsen", + "author_inst": "University of Michigan" + }, + { + "author_name": "Claus Graff", + "author_inst": "Aalborg University" + }, + { + "author_name": "Jorgen K Kanters", + "author_inst": "University of Copenhagen" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.06.18.20134874", "rel_title": "Modelling for prediction of the spread and severity of COVID-19 and its association with socioeconomic factors and virus types", @@ -1361937,41 +1365050,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.06.17.20133595", - "rel_title": "Clozapine treatment and risk of COVID-19.", - "rel_date": "2020-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.17.20133595", - "rel_abs": "BackgroundClozapine, an antipsychotic with unique efficacy in treatment resistant psychosis, is associated with increased susceptibility to infection, including pneumonia.\n\nAimsTo investigate associations between clozapine treatment and increased risk of COVID-19 in patients with schizophrenia-spectrum disorders who are receiving antipsychotic medications, using electronic health records data, in a geographically defined population in London.\n\nMethodUsing information from South London and Maudsley NHS Foundation Trust (SLAM) clinical records, via the Clinical Record Interactive Search system, we identified 6,309 individuals who had an ICD-10 diagnosis of schizophrenia-spectrum disorders and were taking antipsychotics at the time on the COVID-19 pandemic onset in the UK. People who were on clozapine treatment were compared with those on any other antipsychotic treatment for risk of contracting COVID-19 between 1 March and 18 May 2020. We tested associations between clozapine treatment and COVID-19 infection, adjusting for gender, age, ethnicity, BMI, smoking status, and SLAM service use.\n\nResultsOf 6,309 patients, 102 tested positive for COVID-19. Individuals who were on clozapine had increased risk of COVID-19 compared with those who were on other antipsychotic medication (unadjusted HR = 2.62 (95% CI 1.73 - 3.96), which was attenuated after adjusting for potential confounders, including clinical contact (adjusted hazard ratio HR=1.76, 95% CI 1.14 - 2.72).\n\nConclusionsThese findings provide support for the hypothesis that clozapine treatment is associated with an increased risk of COVID-19. Further research will be needed in other samples to confirm this association. Potential clinical implications are discussed.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Risha Govind", - "author_inst": "King's College London" - }, - { - "author_name": "Daniela Fonesca de Freitas", - "author_inst": "King's College London" - }, - { - "author_name": "Megan R Pritchard", - "author_inst": "King's College London" - }, - { - "author_name": "Richard D Hayes", - "author_inst": "King's College London" - }, - { - "author_name": "James H MacCabe", - "author_inst": "King's College London" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.06.18.20134742", "rel_title": "Racial and ethnic determinants of Covid-19 risk", @@ -1362508,6 +1365586,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.06.18.20134353", + "rel_title": "IL-13 Predicts the Need for Mechanical Ventilation in COVID-19 Patients", + "rel_date": "2020-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20134353", + "rel_abs": "Immune dysregulation is characteristic of the more severe stages of SARS-CoV-2 infection. Understanding the mechanisms by which the immune system contributes to COVID-19 severity may open new avenues to treatment. Here we report that elevated interleukin-13 (IL-13) was associated with the need for mechanical ventilation in two independent patient cohorts. In addition, patients who acquired COVID-19 while prescribed Dupilumab had less severe disease. In SARS-CoV-2 infected mice, IL-13 neutralization reduced death and disease severity without affecting viral load, demonstrating an immunopathogenic role for this cytokine. Following anti-IL-13 treatment in infected mice, in the lung, hyaluronan synthase 1 (Has1) was the most downregulated gene and hyaluronan accumulation was decreased. Blockade of the hyaluronan receptor, CD44, reduced mortality in infected mice, supporting the importance of hyaluronan as a pathogenic mediator, and indicating a new role for IL-13 in lung disease. Understanding the role of IL-13 and hyaluronan has important implications for therapy of COVID-19 and potentially other pulmonary diseases.\n\nSummaryL-13 levels are elevated in patients with severe COVID-19. In a mouse model of disease, IL-13 neutralization results in reduced disease and lung hyaluronan deposition. Similarly, blockade of hyaluronans receptor, CD44, reduces disease, highlighting a novel mechanism for IL-13-mediated pathology.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Alexandra N Donlan", + "author_inst": "University of Virginia" + }, + { + "author_name": "Tara E Sutherland", + "author_inst": "University of Manchester" + }, + { + "author_name": "Chelsea Marie", + "author_inst": "University of Virginia" + }, + { + "author_name": "Saskia Preissner", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin" + }, + { + "author_name": "Ben T Bradley", + "author_inst": "University of Washington" + }, + { + "author_name": "Rebecca M Carpenter", + "author_inst": "University of Virginia" + }, + { + "author_name": "Jeffrey M Sturek", + "author_inst": "University of Virginia" + }, + { + "author_name": "Jennie Z Ma", + "author_inst": "University of Virginia" + }, + { + "author_name": "Brett Moreau", + "author_inst": "University of Virginia" + }, + { + "author_name": "Jeffrey R Donowitz", + "author_inst": "Virginia Commonwealth University" + }, + { + "author_name": "Gregory A Buck", + "author_inst": "Virginia Commonwealth University" + }, + { + "author_name": "Myrna G Serrano", + "author_inst": "Virginia Commonwealth University" + }, + { + "author_name": "Stacey L Burgess", + "author_inst": "University of Virginia" + }, + { + "author_name": "Mayuresh Abhyankar", + "author_inst": "University of Virginia" + }, + { + "author_name": "Cameron Mura", + "author_inst": "University of Virginia" + }, + { + "author_name": "Philip E. Bourne", + "author_inst": "University of Virginia" + }, + { + "author_name": "Robert Preissner", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin" + }, + { + "author_name": "Mary Young", + "author_inst": "University of Virginia" + }, + { + "author_name": "Genevieve R Lyons", + "author_inst": "University of Virginia" + }, + { + "author_name": "Johanna J Loomba", + "author_inst": "University of Virginia" + }, + { + "author_name": "Sarah J Ratcliffe", + "author_inst": "University of Virginia" + }, + { + "author_name": "Melinda D Poulter", + "author_inst": "University of Virginia" + }, + { + "author_name": "Amy J Mathers", + "author_inst": "University of Virginia" + }, + { + "author_name": "Anthony J Day", + "author_inst": "University of Manchester" + }, + { + "author_name": "Barbara J Mann", + "author_inst": "University of Virginia" + }, + { + "author_name": "Judith E Allen", + "author_inst": "University of Manchester" + }, + { + "author_name": "William A Petri Jr.", + "author_inst": "University of Virginia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.18.20133660", "rel_title": "SARS-CoV-2-specific antibody detection for sero-epidemiology: a multiplex analysis approach accounting for accurate seroprevalence", @@ -1364359,81 +1367560,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.17.158105", - "rel_title": "Dog Savior: Immediate Scent-Detection of SARS-COV-2 by Trained Dogs", - "rel_date": "2020-06-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.17.158105", - "rel_abs": "Molecular tests for viral diagnostics are essential to confront the COVID-19 pandemic, but their production and distribution cannot satisfy the current high demand. Early identification of infected people and their contacts is the key to being able to isolate them and prevent the dissemination of the pathogen; unfortunately, most countries are unable to do this due to the lack of diagnostic tools. Dogs can identify, with a high rate of precision, unique odors of volatile organic compounds generated during an infection; as a result, dogs can diagnose infectious agents by smelling specimens and, sometimes, the body of an infected individual. We trained six dogs of three different breeds to detect SARS-CoV-2 in respiratory secretions of infected patients and evaluated their performance experimentally, comparing it against the gold standard (rRT-PCR). Here we show that viral detection takes one second per specimen. After scent-interrogating 9,200 samples, our six dogs achieved independently and as a group very high sensitivity, specificity, predictive values, accuracy, and likelihood ratio, with very narrow confidence intervals. The highest metric was the negative predictive value, indicating that with a disease prevalence of 7.6%, 99.9% of the specimens indicated as negative by the dogs did not carry the virus. These findings demonstrate that dogs could be useful to track viral infection in humans, allowing COVID-19 free people to return to work safely.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Omar Vesga", - "author_inst": "Universidad de Antioquia" - }, - { - "author_name": "Andres Felipe Valencia", - "author_inst": "GRIPE, Universidad de Antioquia, Colombia; Colina K-9, La Ceja, Antioquia, Colombia." - }, - { - "author_name": "Alejandro Mira", - "author_inst": "GRIPE, Universidad de Antioquia, Medellin, Colombia; Colina K-9, La Ceja, Antioquia, Colombia" - }, - { - "author_name": "Felipe Ossa", - "author_inst": "GRIPE, Universidad de Antioquia, Medellin, Colombia; Colina K-9, La Ceja, Antioquia, Colombia" - }, - { - "author_name": "Esteban Ocampo", - "author_inst": "Colina K-9, La Ceja, Antioquia, Colombia" - }, - { - "author_name": "Maria Agudelo Perez", - "author_inst": "Hospital Universitario San Vicente Fundacion, Medellin, Colombia; GRIPE, Universidad de Antioquia, Medellin, Colombia." - }, - { - "author_name": "karl Ciouderis", - "author_inst": "Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia, Sede Medellin." - }, - { - "author_name": "Laura Perez", - "author_inst": "Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia, Sede Medellin." - }, - { - "author_name": "Andres Cardona", - "author_inst": "Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia, Sede Medellin." - }, - { - "author_name": "Yudy Aguilar Perez", - "author_inst": "GRIPE, Universidad de Antioquia, Medellin, Colombia." - }, - { - "author_name": "Javier Mauricio Gonzalez", - "author_inst": "GRIPE, Universidad de Antioquia, Medellin, Colombia" - }, - { - "author_name": "Juan Carlos Catano Correa", - "author_inst": "GRIPE, Universidad de Antioquia, Medellin, Colombia" - }, - { - "author_name": "Yuli Agudelo Berruecos", - "author_inst": "Hospital Universitario San Vicente Fundacion, Medellin, Colombia." - }, - { - "author_name": "Juan P. Hernandez-Ortiz", - "author_inst": "Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia, Sede Medellin; Departamento de Materiales y Minerales, Universidad Nacional de Colom" - }, - { - "author_name": "Jorge E. Osorio", - "author_inst": "Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia, Sede Medellin; Department of Pathobiology, School of Veterinary Medicine, University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.17.20133678", "rel_title": "FAR AWAY FROM HERD IMMUNITY TO SARS-CoV-2: results from a survey in healthy blood donors in South Eastern Italy", @@ -1364678,6 +1367804,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2020.06.16.20130914", + "rel_title": "A longitudinal study of immune cells in severe COVID-19 patients.", + "rel_date": "2020-06-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20130914", + "rel_abs": "Little is known about the time-dependent immune responses in severe COVID-19. Data of 15 consecutive patients were sequentially recorded from intensive care unit admission. Lymphocyte subsets and total monocyte and subsets counts were monitored as well as the expression of HLA-DR. For 5 patients, SARS-CoV-2-specific T-cell polyfunctionality was assessed against Spike and Nucleoprotein SARS-CoV-2 peptides. Non-specific inflammation markers were increased in all patients. Median monocyte HLA-DR expression was below the 8,000 AB/C threshold defining acquired immunodepression. A \"V\" trend curve for lymphopenia, monocyte numbers, and HLA-DR expression was observed with a nadir between days 11-14 after symptoms onset. Intermediate CD14++CD16+ monocytes increased early with a reduction in classic CD14++CD16- monocytes. Polyfunctional SARS-Cov-2-specific CD4 T-cells were present and functional, whereas virus-specific CD8 T-cells were less frequent and not efficient. We report a temporal variation of both innate and adaptive immunity in severe COVID-19 patients, helpful in guiding therapeutic decisions (e.g. anti-inflammatory vs. immunostimulatory ones). We describe a defect in virus-specific CD8 T-cells, a potential biomarker of clinical severity. These combined data also provide helpful knowledge for vaccine design.\n\nTrial registration numberNCT04386395", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Didier Payen", + "author_inst": "University Paris 7 Denis Diderot, UMR 1160 INSERM, Paris, France" + }, + { + "author_name": "Maxime Cravat", + "author_inst": "Universite de Lorraine, CHRU-Nancy, Laboratoire Immunologie" + }, + { + "author_name": "Hadil Maadadi", + "author_inst": "Universite de Lorraine, CHRU-Nancy, Departement Anesthesie Reanimation Brabois Adulte, Nancy, France" + }, + { + "author_name": "Carole Didelot", + "author_inst": "CHRU-Nancy, Plateforme de Cytometrie en Flux Diagnostique, Nancy, France" + }, + { + "author_name": "Lydia Prosic", + "author_inst": "CHRU-Nancy, Plateforme de Cytometrie en Flux Diagnostique, Nancy, France" + }, + { + "author_name": "Claire Dupuis", + "author_inst": "Medical Intensive Care Unit, Clermont-Ferrand University Hospital, Clermont-Ferrand, France" + }, + { + "author_name": "Marie-Reine Losser", + "author_inst": "CHRU Nancy and Universite de Lorraine, INSERM UMR 1116, Nancy, France" + }, + { + "author_name": "Marcelo De Carvalho Bittencourt", + "author_inst": "Universite de Lorraine, CHRU-Nancy, CNRS UMR 7365, IMoPA, Nancy, France" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.15.20038489", "rel_title": "On Identifying and Mitigating Bias in the Estimation of the COVID-19 Case Fatality Rate", @@ -1365733,49 +1368906,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.06.17.20106302", - "rel_title": "Standardized Testing Demonstrates Altered Odor Detection Sensitivity and Hedonics in Asymptomatic College Students as SARS-CoV-2 Emerged Locally", - "rel_date": "2020-06-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.17.20106302", - "rel_abs": "Aerosol droplets have emerged as the primary mode of SARS-Cov-2 transmission and can be spread by infectious asymptomatic/pre-symptomatic persons rendering indicators of latent viral infection essential. Olfactory impairment is now a recognized symptom of COVID-19 and is rapidly becoming one of the most reliable indicators of the disease. We compared olfaction data from asymptomatic students, who were assessed as SARS-CoV-2 was unknowingly spreading locally, to students tested prior to the arrival of the virus. This study was naturalistic by design as testing occurred in the context of four research studies, all of which used the same inclusion/exclusion criteria and the same protocol to objectively assess odor detection, identification, and hedonics with physiological tests. Data from students (Cohort II; N=22) with probable SARS-CoV-2 exposure were compared to students tested just prior to local virus transmission (Cohort I; N=25), and a normative sample of students assessed over the previous four years (N=272). Students in Cohort II demonstrated significantly reduced odor detection sensitivity compared to students in Cohort I (t=2.60; P=.01; d=0.77; CI, 0.17, 1.36), with a distribution skewed towards reduced detection sensitivity (D=0.38; P=.005). Categorically, the exposed group was significantly more likely to have hyposmia (OR=7.74; CI, 3.1, 19.40), particularly the subgroup assessed in the final week before campus closure (OR=13.61; CI, 3.40, 35.66;). The exposed cohort also rated odors as less unpleasant (P<.001, CLES=0.77). A limitation of our study is that participants were not tested for COVID-19 as testing was unavailable in the area. Objective measures of olfaction may detect olfactory impairment in asymptomatic persons who are otherwise unaware of smell loss. The development of cost-effective, objective olfaction tests that could be self-administered regularly could aid in early detection of SARS-CoV-2 exposure, which is vital to combatting this pandemic.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Julie Walsh-Messinger", - "author_inst": "University of Dayton" - }, - { - "author_name": "Sahar Kaouk", - "author_inst": "University of Dayton" - }, - { - "author_name": "Hannah Manis", - "author_inst": "University of Dayton" - }, - { - "author_name": "Rachel Kaye", - "author_inst": "Rutgers New Jersey Medical Center" - }, - { - "author_name": "Guillermo Cecchi", - "author_inst": "Thomas J. Watson Research Center" - }, - { - "author_name": "Pablo Meyer", - "author_inst": "Thomas J. Watson Research Center" - }, - { - "author_name": "Dolores Malaspina", - "author_inst": "Icahn School of Medicine at Mount Sinai" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.16.20133066", "rel_title": "Effect of hydroxychloroquine on SARS-CoV-2 viral load in patients with COVID-19", @@ -1365948,6 +1369078,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2020.06.17.20133587", + "rel_title": "Essential epidemiological parameters of COVID-19 for clinical and mathematical modeling purposes: a rapid review and meta-analysis", + "rel_date": "2020-06-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.17.20133587", + "rel_abs": "We present a literature review and meta-analysis of relevant epidemiological parameters (24 for adults, 7 for children) of COVID-19. Standardization of these parameters is key to performing valid clinical and mathematical modeling, as well as forecasts, helping us to improve our understanding about the characteristics and impact of the pandemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "EVA S. FONFRIA", + "author_inst": "UNIVERSIDAD DE ALICANTE, SPAIN" + }, + { + "author_name": "MARIA ISABEL VIGO", + "author_inst": "UNIVERSIDAD DE ALICANTE, SPAIN" + }, + { + "author_name": "DAVID GARCIA-GARCIA", + "author_inst": "UNIVERSIDAD DE ALICANTE, SPAIN" + }, + { + "author_name": "ZAIDA HERRADOR", + "author_inst": "INSTITUTO DE SALUD CARLOS III, SPAIN" + }, + { + "author_name": "MIRIAM NAVARRO", + "author_inst": "UNIVERSIDAD MIGUEL HERNANDEZ, SPAIN. UNIVERSIDAD DE ALICANTE, SPAIN." + }, + { + "author_name": "CESAR BORDEHORE", + "author_inst": "UNIVERSIDAD DE ALICANTE, SPAIN" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.17.20133884", "rel_title": "Hydroxychloroquine and mortality risk of patients with COVID-19: a systematic review and meta-analysis of human comparative studies", @@ -1367351,129 +1370520,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.16.20133157", - "rel_title": "Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease.", - "rel_date": "2020-06-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20133157", - "rel_abs": "BackgroundRapid COVID-19 diagnosis in hospital is essential for patient management and identification of infectious patients to limit the potential for nosocomial transmission. The diagnosis of infection is complicated by 30-50% of COVID-19 hospital admissions with nose/throat swabs testing negative for SARS-CoV-2 nucleic acid, frequently after the first week of illness when SARS-CoV-2 antibody responses become detectable. We assessed the diagnostic accuracy of combined rapid antibody point of care (POC) and nucleic acid assays for suspected COVID-19 disease in the emergency department.\n\nMethodsWe developed (i) an in vitro neutralization assay using a lentivirus expressing a genome encoding luciferase and pseudotyped with spike (S) protein and (ii) an ELISA test to detect IgG antibodies to nucleocapsid (N) and S proteins from SARS-CoV-2. We tested two lateral flow rapid fingerprick tests with bands for IgG and IgM. We then prospectively recruited participants with suspected moderate to severe COVID-19 and tested for SARS-CoV-2 nucleic acid in a combined nasal/throat swab using the standard laboratory RT-PCR and a validated rapid POC nucleic acid amplification (NAAT) test. Additionally, serum collected at admission was retrospectively tested by in vitro neutralisation, ELISA and the candidate POC antibody tests. We evaluated the performance of the individual and combined rapid POC diagnostic tests against a composite reference standard of neutralisation and standard laboratory based RT-PCR.\n\nResults45 participants had specimens tested for nucleic acid in nose/throat swabs as well as stored sera for antibodies. Using the composite reference standard, prevalence of COVID-19 disease was 53.3% (24/45). Median age was 73.5 (IQR 54.0-86.5) years in those with COVID-19 disease by our reference standard and 63.0 (IQR 41.0-72.0) years in those without disease. The overall detection rate by rapid NAAT was 79.2% (95CI 57.8-92.9%), decreasing from 100% (95% CI 65.3-98.6%) in days 1-4 to 50.0% (95% CI 11.8-88.2) for days 9-28 post symptom onset. Correct identification of COVID-19 with combined rapid POC diagnostic tests was 100% (95CI 85.8-100%) with a false positive rate of 5.3-14.3%, driven by POC LFA antibody tests.\n\nConclusionsCombined POC tests have the potential to transform our management of COVID-19, including inflammatory manifestations later in disease where nucleic acid test results are negative. A rapid combined approach will also aid recruitment into clinical trials and in prescribing therapeutics, particularly where potentially harmful immune modulators (including steroids) are used.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Petra Mlcochova", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Dami Collier", - "author_inst": "UCL" - }, - { - "author_name": "Allyson V Ritchie", - "author_inst": "Diagnostics for the Real World Europe Ltd" - }, - { - "author_name": "Sonny M Assennato", - "author_inst": "DRW" - }, - { - "author_name": "Myra Hosmillo", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Neha Goel", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Bo Meng", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Krishna Chatterji", - "author_inst": "NIHR Cambridge Clinical Research Facility" - }, - { - "author_name": "Vivien Mendoza", - "author_inst": "CUH NHS Trust" - }, - { - "author_name": "Nigel Temperton", - "author_inst": "University of Kent" - }, - { - "author_name": "Leo Kiss", - "author_inst": "Medical Research Council Laboratory of Molecular Biology, Cambridge" - }, - { - "author_name": "Katarzyna A Ciazyns", - "author_inst": "Medical Research Council Laboratory of Molecular Biology, Cambridge" - }, - { - "author_name": "Xiaoli Xiong", - "author_inst": "Medical Research Council Laboratory of Molecular Biology" - }, - { - "author_name": "John AG Briggs", - "author_inst": "Medical Research Council Laboratory of Molecular Biology" - }, - { - "author_name": "James Nathan", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Federica Mescia", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Hongyi Zhang", - "author_inst": "CUH NHS Trust" - }, - { - "author_name": "Petros Barmpounakis", - "author_inst": "Athens University of Economics and Business" - }, - { - "author_name": "Nikos Demeris", - "author_inst": "Cambridge Clinical Trials Unit-Cancer Theme" - }, - { - "author_name": "Richard Skells", - "author_inst": "Cambridge Clinical Trials Unit-Cancer Theme" - }, - { - "author_name": "Paul Lyons", - "author_inst": "University of Cambridge" - }, - { - "author_name": "John Bradley", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Stephen Baker", - "author_inst": "Cambridge University" - }, - { - "author_name": "Jean Pierre Allain", - "author_inst": "Diagnostics for the Real World EU Ltd" - }, - { - "author_name": "Kenneth GC Smith", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Ian Goodfellow", - "author_inst": "ig299@cam.ac.uk" - }, - { - "author_name": "Ravindra K Gupta", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.16.20133140", "rel_title": "COVID-19 outcomes, risk factors and associations by race: a comprehensive analysis using electronic health records data in Michigan Medicine", @@ -1367670,6 +1370716,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.16.20132746", + "rel_title": "Time Course of COVID-19 epidemic in Algeria: Retrospective estimate of the actual burden", + "rel_date": "2020-06-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20132746", + "rel_abs": "Since December 2019, the five continents have been incrementally invaded by SARS-CoV-2. Africa is the last and least affected to date. However, Algeria is among the first countries affected since February 25, 2020. In order to benefit from its experience in the least affected countries, this study aims to describe the epidemics current situation and then retrospectively estimate its real burden.\n\nAs a first part of the study, we described the epidemics indicators as; the cumulative and daily reported cases and deaths, and we computed the R0 evolution. Secondly, we used the New York City cases-fatality rate standardized by Algerian age structure, to retrospectively estimate the actual burden.\n\nWe found that reported cases are in a clear diminution, but, the epidemic epicentre is moving from Blida to other cities. We noted a clear peak in daily cases-fatality from March 30, to April 17, 2020, Fig. 3, due to underestimating the actual infections of the first 25 days. Since May 8, 2020, the daily R0 is around one, Fig. 4. Moreover, we noticed 31% reduction of its mean value from 1,41 to 0,97 between the last two months. The Algerian Age-Standardized Infection Fatality Rate we found is 0,88%. Based on that, we demonstrated that only 1,5% of actual infections were detected and reported before March 30, and 20% after March 31, Fig. 5. Therefore, the actual infections burden is currently five times higher than reported. At the end, we found that at least 0,2 % of the population have been infected until May 27. Consequently, the acquired herd immunity to date is therefore not sufficient to avoid a second wave.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC=\"FIGDIR/small/20132746v1_fig3.gif\" ALT=\"Figure 3\">\nView larger version (36K):\norg.highwire.dtl.DTLVardef@de2d68org.highwire.dtl.DTLVardef@7744d6org.highwire.dtl.DTLVardef@485fb1org.highwire.dtl.DTLVardef@1827013_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 3.C_FLOATNO Daily reported COVID-19 cases (blue), and cases-fatality (red) and cases-fatality shifted forwards 18 days as duration from onset of symptoms to death (green).\n\nC_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC=\"FIGDIR/small/20132746v1_fig4.gif\" ALT=\"Figure 4\">\nView larger version (26K):\norg.highwire.dtl.DTLVardef@8bf54corg.highwire.dtl.DTLVardef@956145org.highwire.dtl.DTLVardef@1251c30org.highwire.dtl.DTLVardef@15da971_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 4.C_FLOATNO Daily R0 evolution of COVID-19 epidemic in Algeria.\n\nC_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC=\"FIGDIR/small/20132746v1_fig5.gif\" ALT=\"Figure 5\">\nView larger version (20K):\norg.highwire.dtl.DTLVardef@1f429forg.highwire.dtl.DTLVardef@4ee325org.highwire.dtl.DTLVardef@122b739org.highwire.dtl.DTLVardef@2b1969_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 5.C_FLOATNO Fitting between COVID-19 daily reported cases (blue), and fatality-based retrospectively estimated infections (AS-IFR=0,88%)(red), taking into account 18 days as duration from onset of symptoms to death.\n\nC_FIG We believe that, the under estimation of the epidemics actual burden is probably due to the lack of testing capacities, however, all the indicators show that the situation is currently controlled. This requires more vigilance for the next weeks during the gradual easing of the preventive measures.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Mohamed HAMIDOUCHE Sr.", + "author_inst": "Pasteur Institute of Algeria/ Public Health school of Pasteur-CNAM of Paris" + }, + { + "author_name": "Nassira BELMESSABIH Sr.", + "author_inst": "Pasteur Institute of Algeria" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.16.20133199", "rel_title": "Epidemiological characteristics of patients with residual SARS-Cov-2 in Linyi, China", @@ -1369249,37 +1372318,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.15.20131516", - "rel_title": "National Early Warning Scores (NEWS / NEWS2) and COVID-19 deaths in care homes: a longitudinal ecological study", - "rel_date": "2020-06-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20131516", - "rel_abs": "ObjectivesTo investigate whether patterns of National Early Warning Scores (NEWS/NEWS2) in care homes during the COVID pandemic correspond with area-level COVID-19 death registrations from care homes.\n\nStudy designLongitudinal ecological study.\n\nSetting460 Care home units using the same software package to collect data on residents, from 46 local authority areas in England.\n\nParticipants6,464 care home residents with at least one NEWS recording.\n\nExposure measure29,656 anonymised person-level NEWS from 29/12/2019 to 20/05/2020 with component physiological measures: systolic blood pressure, respiratory rate, pulse rate, temperature, and oxygen saturation. Baseline values for each measure calculated using 80th and 20th centile scores before March 2020.\n\nOutcome measureTime series comparison with Office for National Statistics (ONS) weekly reported registered deaths of care home residents where COVID-19 was the underlying cause of death, and all other deaths (excluding COVID-19) up to 10/05/2020.\n\nResultsDeaths due to COVID-19 were registered from 23/03/2020 in the study geographical areas. Between 23/03/2020 and 10/05/2020, there were 5,753 deaths (1,532 involving COVID-19 and 4,221 other causes). The proportion of above-baseline NEWS increased from 16/03/2020 and closely followed the rise and fall in COVID-19 deaths over the study period. The proportion of above-baseline oxygen saturation, respiratory rate and temperature measurements also increased approximately two weeks before peaks in care home deaths in corresponding geographical areas.\n\nConclusionsNEWS may make a useful contribution to disease surveillance in care homes during the COVID-19 pandemic. Oxygen saturation, respiratory rate and temperature could be prioritised as they appear to signal rise in mortality almost as well as total NEWS. This study reinforces the need to collate data from care homes, to monitor and protect residents health. Further work using individual level outcome data is needed to evaluate the role of NEWS in the early detection of resident illness.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Daniel Stow", - "author_inst": "Newcastle University" - }, - { - "author_name": "Robert O Barker", - "author_inst": "Newcastle University" - }, - { - "author_name": "Fiona E Matthews", - "author_inst": "Newcastle University" - }, - { - "author_name": "Barbara Hanratty", - "author_inst": "Newcastle University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.12.20127498", "rel_title": "Reducing SARS-CoV-2 infectious spreading patterns by removing S and R compartments from SIR model equation", @@ -1369508,6 +1372546,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, + { + "rel_doi": "10.1101/2020.06.15.20131987", + "rel_title": "Can the protection be among us? Previous viral contacts and prevalent HLA alleles could be avoiding an even more disseminated COVID-19 pandemic.", + "rel_date": "2020-06-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20131987", + "rel_abs": "COVID-19 is bringing scenes of sci-fi movies into real life, and it seems to be far from over. Infected individuals exhibit variable severity, suggesting the involvement of the genetic constitution of populations and previous cross-reactive immune contacts in the individuals disease outcome. To investigate the participation of MHC alleles in COVID-19 severity, the combined use of HLA-B*07, HLA-B*44, HLA-DRB1*03, and HLA-DRB1*04 grouped affected countries presenting similar death rates, based only on their allele frequencies. To prospect T cell targets in SARS-CoV-2, we modeled 3D structures of HLA-A*02:01 complexed with immunogenic epitopes from SAR-CoV-1 and compared them with models containing the corresponding SARS-CoV-2 peptides. It reveals molecular conservation between SARS-CoV peptides, evidencing that the corresponding current sequences are putative T cell epitopes. These structures were also compared with other HCoVs sequences, and with a panel of epitopes from unrelated viruses, looking for the triggers of cross-protection in asymptomatic and uninfected individuals. 229E, OC43, and impressively, viruses involved in endemic human infections share fingerprints of immunogenicity with SARS-CoV peptides. Wide-scale HLA genotyping in COVID-19 patients shall improve prognosis prediction. Structural identification of previous triggers paves the way for herd immunity examination and wide spectrum vaccine development.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Eduardo Cheuiche Antonio", + "author_inst": "Universidade Federal do Rio Grande do Sul" + }, + { + "author_name": "Mariana Rost Meireles", + "author_inst": "Universidade Federal do Rio Grande do Sul" + }, + { + "author_name": "Marcelo A. S. Bragatte", + "author_inst": "Universidade Federal do Rio Grandedo Sul" + }, + { + "author_name": "Gustavo Fioravanti Vieira", + "author_inst": "Universidade La Salle Canoas" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.06.15.20132183", "rel_title": "Commercial Airline Protocol during Covid-19 Pandemic: An Experience of Thai Airways International", @@ -1370935,141 +1374004,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.06.17.156455", - "rel_title": "Multi-level proteomics reveals host-perturbation strategies of SARS-CoV-2 and SARS-CoV", - "rel_date": "2020-06-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.17.156455", - "rel_abs": "The global emergence of SARS-CoV-2 urgently requires an in-depth understanding of molecular functions of viral proteins and their interactions with the host proteome. Several individual omics studies have extended our knowledge of COVID-19 pathophysiology1-10. Integration of such datasets to obtain a holistic view of virus-host interactions and to define the pathogenic properties of SARS-CoV-2 is limited by the heterogeneity of the experimental systems. We therefore conducted a concurrent multi-omics study of SARS-CoV-2 and SARS-CoV. Using state-of-the-art proteomics, we profiled the interactome of both viruses, as well as their influence on transcriptome, proteome, ubiquitinome and phosphoproteome in a lung-derived human cell line. Projecting these data onto the global network of cellular interactions revealed crosstalk between the perturbations taking place upon SARS-CoV-2 and SARS-CoV infections at different layers and identified unique and common molecular mechanisms of these closely related coronaviruses. The TGF-{beta} pathway, known for its involvement in tissue fibrosis, was specifically dysregulated by SARS-CoV-2 ORF8 and autophagy by SARS-CoV-2 ORF3. The extensive dataset (available at https://covinet.innatelab.org) highlights many hotspots that can be targeted by existing drugs and it can guide rational design of virus- and host-directed therapies, which we exemplify by identifying kinase and MMPs inhibitors with potent antiviral effects against SARS-CoV-2.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Alexey Stukalov", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Virginie Girault", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Vincent Grass", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Ozge Karayel", - "author_inst": "Department of Proteomics and Signal transduction, Max-Planck Institute of Biochemistry, Martinsried/Munich, 82152, Germany" - }, - { - "author_name": "Valter Bergant", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Christian Urban", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Darya A. Haas", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Yiqi Huang", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Lila Oubraham", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Anqi Wang", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Sabri M. Hamad", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Antonio Piras", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Fynn M Hansen", - "author_inst": "Department of Proteomics and Signal transduction, Max-Planck Institute of Biochemistry, Martinsried/Munich, 82152, Germany" - }, - { - "author_name": "Maria Tanzer", - "author_inst": "Department of Proteomics and Signal transduction, Max-Planck Institute of Biochemistry, Martinsried/Munich, 82152, Germany" - }, - { - "author_name": "Igor Paron", - "author_inst": "Department of Proteomics and Signal transduction, Max-Planck Institute of Biochemistry, Martinsried/Munich, 82152, Germany" - }, - { - "author_name": "Luca Zinzula", - "author_inst": "Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Martinsried/Munich, 82152, Germany" - }, - { - "author_name": "Thomas Engleitner", - "author_inst": "Institute of Molecular Oncology and Functional Genomics and Department of Medicine II, School of Medicine, Technical University of Munich, 81675 Munich, Germany" - }, - { - "author_name": "Maria Reinecke", - "author_inst": "Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany" - }, - { - "author_name": "Teresa M. Lavacca", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Rosina Ehmann", - "author_inst": "Bundeswehr Institute of Microbiology, 80937 Munich, Germany" - }, - { - "author_name": "Roman W\u00f6lfel", - "author_inst": "Bundeswehr Institute of Microbiology, 80937 Munich, Germany" - }, - { - "author_name": "J\u00f6rg Jores", - "author_inst": "Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Bernhard K\u00fcster", - "author_inst": "Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany" - }, - { - "author_name": "Ulrike Protzer", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Roland Rad", - "author_inst": "Institute of Molecular Oncology and Functional Genomics and Department of Medicine II, School of Medicine, Technical University of Munich, 81675 Munich, Germany" - }, - { - "author_name": "John Ziebuhr", - "author_inst": "Justus Liebig University Giessen, Institute of Medical Virology, 35392 Giessen, Germany" - }, - { - "author_name": "Volker Thiel", - "author_inst": "Institute of Virology and Immunology (IVI), Bern, Switzerland & Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Pietro Scaturro", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Matthias Mann", - "author_inst": "Department of Proteomics and Signal transduction, Max-Planck Institute of Biochemistry, Martinsried/Munich, 82152, Germany" - }, - { - "author_name": "Andreas Pichlmair", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2020.06.17.156679", "rel_title": "Rapid assessment of ligand binding to the SARS-CoV-2 main protease by saturation transfer difference NMR spectroscopy", @@ -1371254,6 +1374188,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.14.20123315", + "rel_title": "Risk of death by age and gender from CoVID-19 in Peru, March-May, 2020", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.14.20123315", + "rel_abs": "Peru implemented strict social distancing measures during the early phase of the epidemic and is now experiencing one of the largest CoVID-19 epidemics in Latin America. Estimates of disease severity are an essential indicator to inform policy decisions about the intensity and duration of interventions needed to mitigate the outbreak. Here we derive delay-adjusted case fatality rates (aCFR) of CoVID-19 in a middle-income country in South America.\n\nWe used government-reported time series of CoVID-19 cases and deaths stratified by age group and gender.\n\nOur estimates as of May 25, 2020, of the aCFR for men and women are 10.8% (95%CrI: 10.5-11.1%) and 6.5% (95%CrI: 6.2-6.8%), respectively, and an overall aCFR of 9.1% (95%CrI: 8.9-9.3%). Our results show that senior individuals are the most severely affected by CoVID-19, particularly men, with aCFR of almost 60% for those aged 80-years. We found that men have a significantly higher cumulative morbidity ratio than women across most age groups (proportion test, p-value< 0.001), with the exception of those aged 0-9 years.\n\nThe COVID-19 epidemic is imposing a large mortality burden in Peru. Senior individuals, especially those who are older than 70 years of age, are being disproportionately affected by the COVID-19 pandemic.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Cesar Munayco", + "author_inst": "Centro Nacional de Epidemiologia, Prevencion y Control de Enfermedades, Peruvian Ministry of Health, Lima, Peru" + }, + { + "author_name": "Gerardo Chowell", + "author_inst": "Georgia State University School of Public Health" + }, + { + "author_name": "Amna Tariq", + "author_inst": "Georgia State University" + }, + { + "author_name": "Eduardo A Undurraga", + "author_inst": "Pontificia Universidad Catolica de Chile" + }, + { + "author_name": "Kenji Mizumoto", + "author_inst": "Kyoto University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.10.20126458", "rel_title": "The Impact of COVID-19 Pandemic on Cardiology Services", @@ -1372397,29 +1375366,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.14.20130518", - "rel_title": "An Extended Laboratory Validation Study and Comparative Performance Evaluation of the Abbott ID NOW COVID-19 Assay in a Coastal California Tertiary Care Medical Center", - "rel_date": "2020-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.14.20130518", - "rel_abs": "The Abbott ID NOW COVID-19 assay is a rapid molecular diagnostic test particularly designed for on-site, rapid turnaround point of care (POC) testing. The utilization of rapid diagnostic tests is integral to optimizing workflow within the hospital and/or procedural-based clinics. The capability to provide both rapid disposition and correct patient classification during this COVID-19 pandemic is critically important with broad infection control implications for both patients and healthcare staff. A tightly controlled, extended laboratory validation was performed at our medical center to determine the negative test agreement of the Abbott ID NOW compared with the BD MAX analyzer, a laboratory-based, two target, molecular analyzer with a sensitive cycle threshold (Ct) positive cutoff value of [≤] 42. There was strict adoption of the procedures listed in the Abbott ID NOW Instruction for Use (IFU)1 insert delineating preferred practices for \"optimal test performance.\" Under these conditions, our institution demonstrated a significant negative percent agreement with 116 out of 117 patients correlating, which equates to a 99.1% concordance similar to a recently reported correlation study2.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Stewart W. Comer", - "author_inst": "Santa Barbara Cottage Hospital" - }, - { - "author_name": "David Fisk", - "author_inst": "Santa Barbara Cottage Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.06.13.20130419", "rel_title": "Mental health service activity during COVID-19 lockdown: South London and Maudsley data on working age community and home treatment team services and mortality from February to mid-May 2020", @@ -1372604,6 +1375550,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.14.20130765", + "rel_title": "Risk factors for critical-ill events of patients with COVID-19 in Wuhan, China: a retrospective cohort study", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.14.20130765", + "rel_abs": "BackgroundLittle is known about the risk factors for critical-ill events (intensive care, invasive ventilation, or death) in patients with COVID-19.\n\nMethodsPatients with laboratory-confirmed COVID-19 admitted to the Wuhan Leishenshan Hospital from February 13 to March 14 was retrospectively analyzed. Demographic data, symptoms, laboratory values at baseline, comorbidities, treatments and clinical outcomes were extracted from electronic medical records and compared between patients with and without critical-ill events. The least absolute shrinkage and selection operator (LASSO) and multivariate logistic regression models were developed to explore the risk factors for critical-ill events. A risk nomogram was established to predict the probability for the critical-ill events. Survival analysis of patients with critical-ill events was performed by the Kaplan-Meier method.\n\nResults463 COVID-19 patients were included in this study, of whom 397 were non-critically ill and 66 were critically ill (all from the intensive care unit). The LASSO regression identified four variables (hypersensitive cardiac troponin I, blood urea nitrogen, haemoglobin, and interleukin-6) contributing to the critical-ill events. Multivariable regression showed increasing odds of in-hospital critical-ill events associated with hypersensitive cTnI greater than 0.04 ng/mL (OR 20.98,95% CI 3.51-125.31), blood urea nitrogen greater than 7.6 mmol/L (OR 5.22, 95% CI 1.52-17.81, decreased haemoglobin (OR 1.06, 95% CI 1.04-1.10), and higher interleukin-6 (OR 1.05, 95% CI 1.02-1.08) on admission.\n\nConclusionsHypersensitive cTnI greater than 0.04 ng/mL, blood urea nitrogen greater than 7.6 mmol/L, decreased haemoglobin, and high IL-6 were risk factors of critical-ill events in patients with COVID-19.\n\nMain pointHypersensitive cTnI greater than 0.04 ng/mL, BUN greater than 7.6 mmol/L, decreased haemoglobin, and high IL-6 were risk factors of critical-ill events (intensive care, invasive ventilation, or death) in patients with COVID-19.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Sen Yang", + "author_inst": "Department of General Practice, Yangpu Hospital, Tongji University School of Medicine, Shanghai, 200090, China" + }, + { + "author_name": "Le Ma", + "author_inst": "andyma2015@tongji.edu.cn" + }, + { + "author_name": "Yu-Lan Wang", + "author_inst": "Molecular Diagnostic Laboratory of Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China" + }, + { + "author_name": "Qian Wang", + "author_inst": "Department of Rheumatology and Immunology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200333, China" + }, + { + "author_name": "Qiang Tong", + "author_inst": "jasontong1985@163.com" + }, + { + "author_name": "Miao Chen", + "author_inst": "Department of Rheumatology and Immunology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200333, China" + }, + { + "author_name": "Hua Zhang", + "author_inst": "Department of Rheumatology and Immunology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200333, China" + }, + { + "author_name": "De-Hua Yu", + "author_inst": "Department of General Practice, Yangpu Hospital, Tongji University School of Medicine, Shanghai, 200090, China" + }, + { + "author_name": "Sheng-Ming Dai", + "author_inst": "Department of Rheumatology and Immunology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200333, China" + }, + { + "author_name": "Ran Cui", + "author_inst": "Shanghai Jiao Tong University Affiliated Sixth People's Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.13.20130484", "rel_title": "Double COVID-19 Confirmed Case Fatality Rate in Countries with High Elderly Female Vitamin D Deficiency Prevalence", @@ -1373767,33 +1376768,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.15.20131136", - "rel_title": "Modelling the Occurrence of the Novel Pandemic COVID-19 Outbreak; A Box and Jenkins Approach", - "rel_date": "2020-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20131136", - "rel_abs": "The corona virus disease 2019 (COVID-19) is a novel pandemic disease that spreads very fast and causes severe respiratory problem to its carrier and thereby results to death in some cases. In this research, we studied the trend, model Nigeria daily COVID-19 cases and forecast for the future occurrences in the country at large. We adopt the Box and Jenkins approach. The time plot showed that the cases of COVID-19 rises rapidly in recent time. KPSS test confirms the non-stationarity of the process (p < 0.05) before differencing. The test also confirmed the stationarity of the process (p > 0.05) after differencing. Various ARIMA (p,d,q) were examined with their respective AICs and Log-likelihood. ARIMA (1, 2, 1) was selected as the best model due to its least AIC (559.74) and highest log likelihood (-276.87). Both Shapiro-Wilk test and Box test performed confirm the fitness of the model (p > 0.05) for the series. Forecast for 30 days was then made for COVID-19 cases in Nigeria. Conclusively, the model obtained in this research can be used to model, monitor and forecast the daily occurrence of COVID-19 cases in Nigeria.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Nurudeen Ayobami Ajadi", - "author_inst": "Federal University of Agriculture Abeokuta" - }, - { - "author_name": "Isqeel Adesegun Ogunsola", - "author_inst": "Federal University of Agriculture Abeokuta" - }, - { - "author_name": "Saddam Adams Damisa", - "author_inst": "Ahmadu Bello University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.15.20130989", "rel_title": "Predictive accuracy of a hierarchical logistic model of cumulative SARS-CoV-2 case growth", @@ -1374006,6 +1376980,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2020.06.14.20125997", + "rel_title": "Impact of Chronic Comorbidities on Progression and Prognosis in Patients with COVID-19: A Retrospective Cohort Study in 1031 Hospitalized Cases in Wuhan, China", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.14.20125997", + "rel_abs": "ObjectivesThe main aim of our study is to observe clinical characteristics and effects of antihypertensive drugs in different hospitalized populations, and to further provide evidence to explore causes and specific clinical markers of the aggravation of COVID-19 in patients with underlying hypertension.\n\nDesignThis was a retrospective cohort study focusing on the clinical data of COVID-19 inpatients admitted at the early stage of pandemic.\n\nSettingA single center study conducted in Tongji Hospital, Tongji Medical College of Huazhong university of Science and Technology (Wuhan, China).\n\nParticipantsAll 1031 inpatients diagnosed with COVID-19 according to Prevention and control Scheme for Novel Coronavirus Pneumonia published by National Health Commission of the Peoples Republic of China and WHO interim guidance in Tongji hospital (Wuhan, China), from January 27, 2020, to March 8, 2020 with the cutoff date being March 30, 2020, were included in this study.\n\nMain outcome measuresDemographic data, medical history, clinical symptoms and signs, laboratory findings, chest computed tomography (CT), treatment, and clinical outcomes were extracted from electronic medical records.\n\nResults1031 COVID-19 inpatients were included in this study, of whom 866 were discharged and 165 were deceased in hospital. 73% of 165 deceased patients had chronic comorbidities. Patients with underlying diseases showed CFR 2.8 times as that of patients without. Senility and males were observed to be main risk factors for increased in-hospital case-fatality rate, with the odds ratio in multivariable regression being 2.94 (95%CI: 2.00 to 4.33; P <0.001) and 2.47 (95%CI: 1.65 to 3.70; P <0.001), respectively. The odds ratio of cases with composite endpoints for patients with simple hypertension was 1.53 (95%CI: 1.07 to 2.17; P=0.019). Senile patients with hypertension were proved to be at high risk early in the disease, which might be associated with the level of CRP, LDH, and eGFR. The odds ratio of case-fatality rate for patients with hypertension taking CCB group was 0.67 (95%CI: 0.37 to 1.20; P = 0.176). Among 271 severe cases without IKF, the odds ratio of case-fatality rate was 0.42 (95CI%: 0.18 to 0.99; P = 0.046) for patients in the CCB group after adjustment of age, sex, and underlying diseases.\n\nConclusionsHypertension is not just a chronic underlying comorbidity, but also a risk factor affecting the severity of COVID-19 and does play a critical role in worsening patients clinical outcomes. Therefore, hypertension management in patients with COVID-19 should be regarded as a major challenge in the diagnostic and therapeutic strategies.\n\nTrial registrationN.A.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Hesong Zeng", + "author_inst": "Department of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Tianlu Zhang", + "author_inst": "Medical Research Institute, Renmin Hospital of Wuhan University, Wuhan University" + }, + { + "author_name": "Xingwei He", + "author_inst": "Department of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Yuxin Du", + "author_inst": "Medical Research Institute, Renmin Hospital of Wuhan University, Wuhan University" + }, + { + "author_name": "Yan Tong", + "author_inst": "Medical Research Institute, Renmin Hospital of Wuhan University, Wuhan University" + }, + { + "author_name": "Xueli Wang", + "author_inst": "Institute of Central China Development, Wuhan University" + }, + { + "author_name": "Weizhong Zhang", + "author_inst": "Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiaotong University" + }, + { + "author_name": "Yin Shen", + "author_inst": "Medical Research Institute, Renmin Hospital of Wuhan University, Wuhan University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.06.14.20130922", "rel_title": "Clinical Characteristics and Outcomes of Venous Thromboembolism in Patients Hospitalized for COVID-19: Systematic Review and Meta-Analysis", @@ -1375517,41 +1378538,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.06.16.154591", - "rel_title": "Antigenic evolution on global scale reveals potential natural selection of SARS-CoV-2 by pre-existing cross-reactive T cell immunity", - "rel_date": "2020-06-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.16.154591", - "rel_abs": "The mutation pattern of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is constantly changing with the places of transmission, but the reason remains to be revealed. Here, we presented the study that comprehensively analyzed the potential selective pressure of immune system restriction, which can drive mutations in circulating SARS-CoV-2 isolates. The results showed that the most common mutation sites of SARS-CoV-2 proteins were located on the non-structural protein ORF1ab and the structural protein Spike. Further analysis revealed mutations in cross-reactive epitopes between SARS-CoV-2 and seasonal coronavirus may help SARS-CoV-2 to escape cellular immunity under the long-term and large-scale community transmission. Meanwhile, the mutations on Spike protein may enhance the ability of SARS-CoV-2 to enter the host cells and escape the recognition of B-cell immunity. This study will increase the understanding of the evolutionary direction and warn about the potential immune escape ability of SARS-CoV-2, which may provide important guidance for the potential vaccine design.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Chengdong Zhang", - "author_inst": "Shanghai Public Health Clinical Center, Fudan University" - }, - { - "author_name": "Xuanxuan Jin", - "author_inst": "Shanghai Public Health Clinical Center, Fudan University" - }, - { - "author_name": "Xianyang Chen", - "author_inst": "Guangzhou Medical University" - }, - { - "author_name": "Qibin Leng", - "author_inst": "Guangzhou Medical University" - }, - { - "author_name": "Tianyi Qiu", - "author_inst": "Fudan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.06.16.155267", "rel_title": "Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection.", @@ -1375784,6 +1378770,77 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.06.12.20128298", + "rel_title": "Self-reported taste and smell disorders in patients with COVID-19: distinct features in China", + "rel_date": "2020-06-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.12.20128298", + "rel_abs": "ObjectivesWe aimed to explore the frequencies of nasal symptoms in patients with COVID-19, including loss of smell and taste, as well as their presentation as the first symptom of the disease and their association with the severity of COVID-19.\n\nMethodsIn this retrospective study, 1,206 laboratory-confirmed COVID-19 patients were included and followed-up by telephone call one month after discharged from Tongji Hospital, Wuhan. Demographic data, laboratory values, comorbidities, symptoms, and numerical rating scale scores (0-10) of nasal symptoms were extracted from the hospital medical records, and confirmed or reevaluated by the telephone follow-up.\n\nResultsFrom COVID-19 patients (N = 1,172) completing follow-up, 199 (17%) subjects had severe COVID-19 and 342 (29.2%) reported nasal symptoms. The most common nasal symptom was loss of taste (20.6%, median score = 6), while 11.4% had loss of smell (median score = 5). The incidence of nasal symptom including loss of smell and loss of taste as the first onset symptom was <1% in COVID-19 patients. Loss of smell or taste scores showed no correlation with the scores of other nasal symptoms. Loss of taste scores, but not loss of smell scores, were significantly increased in severe vs. non-severe COVID-19 patients. Interleukin (IL)-6 and lactose dehydrogenase (LDH) serum levels positively correlated with loss of taste scores. About 80% of COVID-19 patients recovered from smell and taste dysfunction in 2 weeks.\n\nConclusionIn the Wuhan COVID-19 cohort, only 1 out of 10 hospital admitted patients had loss of smell while 1 out 5 reported loss of taste which was associated to severity of COVID-19. Most patients recovered smell and taste dysfunctions in 2 weeks.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Jia Song", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Yi-Ke Deng", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Hai Wang", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Zhi-Chao Wang", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Bo Liao", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Jin Ma", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Chao He", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Li Pan", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Yang Liu", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Isam Alobid", + "author_inst": "Hospital Clinic, IDIBAPS, Universitat de Barcelona, CIBERES" + }, + { + "author_name": "De-Yun Wang", + "author_inst": "Yong Loo Lin School of Medicine, National University of Singapore" + }, + { + "author_name": "Ming Zeng", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Joaquim Mullol", + "author_inst": "Hospital Clinic, IDIBAPS, Universitat de Barcelona, CIBERES" + }, + { + "author_name": "Zheng Liu", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "otolaryngology" + }, { "rel_doi": "10.1101/2020.06.12.20129981", "rel_title": "A discrete-time-evolution model to forecast progress of Covid-19 outbreak", @@ -1377267,37 +1380324,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.11.20129007", - "rel_title": "COVID-19 Deaths: Which Explanatory Variables Matter the Most?", - "rel_date": "2020-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20129007", - "rel_abs": "SO_SCPLOWUMMARYC_SCPLOWAs Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spreads around the World, many questions about the disease are being answered; however, many more remain poorly understood. Although the situation is rapidly evolving, with datasets being continually corrected or updated, it is crucial to understand what factors may be driving transmission through different populations. While studies are beginning to highlight specific parameters that may be playing a role, few have attempted to thoroughly estimate the relative importance of these disparate variables that likely include: climate, population demographics, and imposed state interventions. In this report, we compiled a database of more than 28 potentially explanatory variables for each of the 50 U.S. states through early May 2020. Using a combination of traditional statistical and modern machine learning approaches, we identified those variables that were the most statistically significant, and, those that were the most important. These variables were chosen to be fiduciaries of a range of possible drivers for COVID-19 deaths in the USA. We found that population-weighted density (PWD), some \"stay at home\" metrics, monthly temperature and precipitation, race/ethnicity, and chronic low-respiratory death rate, were all statistically significant. Of these, PWD and mobility metrics dominated. This suggests that the biggest impact on COVID-19 deaths was, at least initially, a function of where you lived, and not what you did. However, clearly, increasing social distancing has the net effect of (at least temporarily) reducing the effective PWD. Our results strongly support the idea that the loosening of \"lock-down\" orders should be tailored to the local PWD. In contrast to these variables, while still statistically significant, race/ethnicity, health, and climate effects could only account for a few percent of the variability in deaths. Where associations were anticipated but were not found, we discuss how limitations in the parameters chosen may mask a contribution that might otherwise be present.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Pete Riley", - "author_inst": "Predictive Science Inc." - }, - { - "author_name": "Allison Riley", - "author_inst": "Predictive Science Inc." - }, - { - "author_name": "James Turtle", - "author_inst": "Predictive Science Inc." - }, - { - "author_name": "Michal Ben-Nun", - "author_inst": "Predictive Science Inc." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.12.20129114", "rel_title": "How to better communicate exponential growth of infectious diseases", @@ -1377682,6 +1380708,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.14.150458", + "rel_title": "Calreticulin co-expression supports high level production of a recombinant SARS-CoV-2 spike mimetic in Nicotiana benthamiana", + "rel_date": "2020-06-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.14.150458", + "rel_abs": "An effective prophylactic vaccine is urgently needed to protect against SARS-CoV-2 infection. The viral spike, which mediates entry into cells by interacting with the host angiotensin-converting enzyme 2, is the primary target of most vaccines in development. These vaccines aim to elicit protective immunity against the glycoprotein by use of inactivated virus, vector-mediated delivery of the antigen in vivo, or by direct immunization with the purified antigen following expression in a heterologous system. These approaches are mostly dependent on the growth of mammalian or insect cells, which requires a sophisticated infrastructure that is not generally available in developing countries due to the incumbent costs which are prohibitive. Plant-based subunit vaccine production has long been considered as a cheaper alternative, although low expression yields and differences along the secretory pathway to mammalian cells have posed a challenge to producing certain viral glycoproteins. Recent advances that have enabled many of these constraints to be addressed include expressing the requisite human proteins in plants to support the maturation of the protein of interest. In this study we investigated these approaches to support the production of a soluble and putatively trimeric SARS-CoV-2 spike mimetic in Nicotiana benthamiana via transient Agrobacterium-mediated expression. The co-expression of human calreticulin dramatically improved the accumulation of the viral spike, which was barely detectable in the absence of the co-expressed accessory protein. The viral antigen was efficiently processed even in the absence of co-expressed furin, suggesting that processing may have occurred at the secondary cleavage site and was mediated by an endogenous plant protease. In contrast, the spike was not efficiently processed when expressed in mammalian cells as a control, although the co-expression of furin improved processing considerably. This study demonstrates the feasibility of molecular engineering to improve the production of viral glycoproteins in plants, and supports plant-based production of SARS-CoV-2 spike-based vaccines and reagents for serological assays.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Emmanuel Aubrey Margolin", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Matthew Verbeek", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Ann Meyers", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Rosamund Chapman", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Anna-Lise Williamson", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Edward Rybicki", + "author_inst": "University of Cape Town" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.06.14.150490", "rel_title": "The serotonin reuptake inhibitor Fluoxetine inhibits SARS-CoV-2", @@ -1378729,181 +1381794,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.06.12.148387", - "rel_title": "Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient", - "rel_date": "2020-06-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.12.148387", - "rel_abs": "The COVID-19 pandemic has had unprecedented health and economic impact, but currently there are no approved therapies. We have isolated an antibody, EY6A, from a late-stage COVID-19 patient and show it neutralises SARS-CoV-2 and cross-reacts with SARS-CoV-1. EY6A Fab binds tightly (KD of 2 nM) the receptor binding domain (RBD) of the viral Spike glycoprotein and a 2.6[A] crystal structure of an RBD/EY6A Fab complex identifies the highly conserved epitope, away from the ACE2 receptor binding site. Residues of this epitope are key to stabilising the pre-fusion Spike. Cryo-EM analyses of the pre-fusion Spike incubated with EY6A Fab reveal a complex of the intact trimer with three Fabs bound and two further multimeric forms comprising destabilized Spike attached to Fab. EY6A binds what is probably a major neutralising epitope, making it a candidate therapeutic for COVID-19.", - "rel_num_authors": 40, - "rel_authors": [ - { - "author_name": "Daming Zhou", - "author_inst": "University of Oxford" - }, - { - "author_name": "Helen M E Duyvesteyn", - "author_inst": "University of Oxford" - }, - { - "author_name": "Cheng-Pin Chen", - "author_inst": "Taoyuan General Hospital" - }, - { - "author_name": "Chung-Guei Huang", - "author_inst": "Chang Gung University" - }, - { - "author_name": "Ting-Hua Chen", - "author_inst": "Genomics Research Center, Academia Sinica, Taipei" - }, - { - "author_name": "Shin-Ru Shih", - "author_inst": "Chang Gung University" - }, - { - "author_name": "Yi-Chun Lin", - "author_inst": "Taoyuan General Hospital" - }, - { - "author_name": "Chien-Yu Cheng", - "author_inst": "Taoyuan General Hospital" - }, - { - "author_name": "Shu-Hsing Cheng", - "author_inst": "Taoyuan General Hospital" - }, - { - "author_name": "Yhu-Chering Huang", - "author_inst": "Chang Gung Memorial Hospital" - }, - { - "author_name": "Tzou-Yien Lin", - "author_inst": "Chang Gung Memorial Hospital" - }, - { - "author_name": "Che Ma", - "author_inst": "Genomics Research Center, Academia Sinica, Taipei" - }, - { - "author_name": "Jiandong Huo", - "author_inst": "University of Oxford" - }, - { - "author_name": "Loic Carrique", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tomas Malinauskas", - "author_inst": "University of Oxford" - }, - { - "author_name": "Reinis R Ruza", - "author_inst": "University of Oxford" - }, - { - "author_name": "Pranav Shah", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tiong Kit Tan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Pramila Rijal", - "author_inst": "University of Oxford" - }, - { - "author_name": "Robert F Donat", - "author_inst": "University of Oxford" - }, - { - "author_name": "Kerry Godwin", - "author_inst": "PHE, Porton Down" - }, - { - "author_name": "Karen Buttigieg", - "author_inst": "PHE Porton Down" - }, - { - "author_name": "Julia Tree", - "author_inst": "PHE Porton Down" - }, - { - "author_name": "Julika Radecke", - "author_inst": "Diamond Light Source" - }, - { - "author_name": "Neil G Paterson", - "author_inst": "Diamond Light Source" - }, - { - "author_name": "Piyasa Supasa", - "author_inst": "University of Oxford" - }, - { - "author_name": "Juthathip Mongkolsapaya", - "author_inst": "University of Oxford" - }, - { - "author_name": "Gavin R Screaton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Miles W Carroll", - "author_inst": "PHE Porton Down" - }, - { - "author_name": "Javier G Jaramillo", - "author_inst": "University of Oxford" - }, - { - "author_name": "MIchael Knight", - "author_inst": "University of Oxford" - }, - { - "author_name": "William S James", - "author_inst": "University of Oxford" - }, - { - "author_name": "Raymond J Owens", - "author_inst": "University of Oxford" - }, - { - "author_name": "James H Naismith", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alain Townsend", - "author_inst": "University of Oxford" - }, - { - "author_name": "Elizabeth E Fry", - "author_inst": "University of Oxford" - }, - { - "author_name": "Yuguang Zhao", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jingshan Ren", - "author_inst": "University of Oxford" - }, - { - "author_name": "David I Stuart", - "author_inst": "University of Oxford" - }, - { - "author_name": "Kuan-Ying A Huang", - "author_inst": "Chang Gung University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.13.149880", "rel_title": "Multi-epitope Based Peptide Vaccine Design Using Three Structural Proteins (S, E, and M) of SARS-CoV-2: An In Silico Approach", @@ -1379116,6 +1382006,45 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.06.12.148296", + "rel_title": "DeepEMhacer: a deep learning solution for cryo-EM volume post-processing", + "rel_date": "2020-06-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.12.148296", + "rel_abs": "Cryo-EM maps are valuable sources of information for protein structure modeling. However, due to the loss of contrast at high frequencies, they generally need to be post-processed to improve their interpretability. Most popular approaches, based on B-factor correction, suffer from limitations. For instance, they ignore the heterogeneity in the map local quality that reconstructions tend to exhibit. Aiming to overcome these problems, we present DeepEMhancer, a deep learning approach designed to perform automatic post-processing of cryo-EM maps. Trained on a dataset of pairs of experimental maps and maps sharpened using their respective atomic models, DeepEMhancer has learned how to post-process experimental maps performing masking-like and sharpening-like operations in a single step. DeepEMhancer was evaluated on a testing set of 20 different experimental maps, showing its ability to obtain much cleaner and more detailed versions of the experimental maps. Additionally, we illustrated the benefits of DeepEMhancer on the structure of the SARS-CoV-2 RNA polymerase.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ruben Sanchez Garcia", + "author_inst": "CNB-CSIC" + }, + { + "author_name": "Josue Gomez-Blanco", + "author_inst": "Departament of Anatomy and Cell Biology, McGill University" + }, + { + "author_name": "Ana Cuervo", + "author_inst": "CNB-CSIC" + }, + { + "author_name": "Jose Maria Carazo", + "author_inst": "CNB-CSIC" + }, + { + "author_name": "Carlos Oscar S Sorzano", + "author_inst": "National Center of Biotechnology (CSIC)" + }, + { + "author_name": "Javier Vargas", + "author_inst": "Universidad Complutense de Madrid" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.06.12.20129999", "rel_title": "Analysis of SARS-CoV-2 Genomes from Southern California Reveals Community Transmission Pathways in the Early Stage of the US COVID-19 Pandemic", @@ -1380179,33 +1383108,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.09.20123836", - "rel_title": "Point of care lung ultrasound is useful when screening for CoVid-19 in Emergency Department patients.", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20123836", - "rel_abs": "BackgroundCoVid-19 can be a life-threatening lung disease or a trivial upper respiratory infection depending on whether the alveoli are involved. Emergency department (ED) screening in symptomatic patients with normal vital signs is frequently limited to oro-nasopharyngeal swabs. We tested the null hypothesis that patients being screened for CoVid-19 in the ED with normal vital signs and without hypoxia would have a point-of-care lung ultrasound (LUS) consistent with CoVid-19 less than 2% of the time.\n\nMethodsO_ST_ABSSubjectsC_ST_ABSSubjects were identified from ED ultrasound logs.\n\nInclusion criteriaAge 14 years or older with symptoms prompting ED screening for CoVid-19.\n\nExclusion criteriaKnown congestive heart failure or other chronic lung condition likely to cause excessive B lines on LUS.\n\nInterventionStructured blinded ultrasound review and chart review\n\nAnalysisWe used a two-sided exact hypothesis test for binomial random variables. We also measured LUS diagnostic performance using computed tomography as the gold standard.\n\nResultsWe reviewed 77 charts; 49 met inclusion criteria. Vital signs were normal in 30/49 patients; 10 (33%) of these patients had LUS consistent with CoVid-19. We rejected the null hypothesis (p-value < 0.001). The treating physicians interpretation of their own point of care lung ultrasounds had a sensitivity of 100% (95% CI 75%, 100%) and specificity of 80% (95% CI 68%, 89%).\n\nConclusionLUS has a meaningful detection rate for CoVid-19 in symptomatic ED patients with normal vital signs. We recommend at least LUS be used in addition to PCR testing when screening symptomatic ED patients for CoVid-19.\n\nCapsule What is knownAuscultation and chest x-ray are insufficient to screen for lung involvement when SARS-CoV-2 infection is suspected. Point of care lung ultrasound is widely available, safer, and less resource intensive than CT imaging.\n\nWhat we foundIn symptomatic patients presenting to the ED even those with normal vital signs had point of care lung ultrasound evidence of alveolar level involvement 33%of patients. Point of care lung ultrasound was 100% sensitive and 80% specific compared to CT (reference standard) when evaluating patients for Covid-19.\n\nWhat this addsPoint of care lung ultrasound or similar imaging should performed when screening symptomatic patients in whom SARS-CoV-2 infection is suspected.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Andrea Hankins", - "author_inst": "Sutter Institute for Medical Research, 2801 L Street, Sacramento, CA 95816, United States of America" - }, - { - "author_name": "Heejung Bang", - "author_inst": "Division of Biostatistics, Department of Public Health Sciences, University of California Davis, Davis, California, United States of America" - }, - { - "author_name": "Paul Walsh", - "author_inst": "Pediatric Emergency Medicine, Sutter Medical Center Sacramento, 2825 Capitol Avenue, Sacramento, CA 95816" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2020.06.08.20123786", "rel_title": "Oscillations in USA COVID-19 Incidence and Mortality Data reflect societal factors", @@ -1380438,6 +1383340,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nutrition" }, + { + "rel_doi": "10.1101/2020.06.09.20124719", + "rel_title": "Kinetics of the humoral immune response to SARS-CoV-2: comparative analytical performance of seven commercial serology tests", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20124719", + "rel_abs": "BackgroundSARS-CoV-2 serology tests are clinically useful to document a prior SARS-CoV-2 infection in patients with no or inconclusive PCR results and suspected COVID-19 disease or sequelae. Data are urgently needed to select the assays with optimal sensitivity at acceptable specificity.\n\nMethodsA comparative analysis of analytical sensitivity was performed of seven commercial SARS-CoV-2 serology assays on 171 sera from 135 subjects with PCR-confirmed SARS-CoV-2 infection, composed of 71 patients hospitalized for COVID-19 pneumonia and 64 healthcare workers with paucisymptomatic infections. The kinetics of IgA/IgM/IgG seroconversion to viral N-and S-protein epitopes were studied from 0 to 54 days after symptom onset. Specificity was verified on 57 pre-pandemic samples.\n\nResultsWantai SARS-COV-2 Ab ELISA and Orient Gene COVID-19 IgG/IgM Rapid Test achieved a superior overall sensitivity. Elecsys Anti-SARS-CoV-2 assay and EUROIMMUN Anti-SARS-CoV-2 combined IgG/IgA also showed acceptable sensitivity (>95%) versus the consensus result of all assays from 10 days post symptom onset. Optimal specificity (>98%) was achieved only by Wantai SARS-COV-2 Ab ELISA, Elecsys Anti-SARS-CoV-2 assay and Innovita 2019-nCoV Ab rapid test. LIAISON SARS-CoV-2 S1/S2 IgG showed a significantly lower sensitivity as compared to all other assays. Lack of seroconversion by any test was seen in 1.4% of hospitalized and 4.7% of paucisymptomatic infections. Within 10 days from symptom onset, only the Wantai SARS-COV-2 Ab ELISA has acceptable sensitivity.\n\nConclusionsWantai SARS-COV-2 Ab ELISA and Elecsys Anti-SARS-CoV-2 assays are suitable for sensitive and specific screening of a SARS-CoV-2 infection from 10 days after symptom onset.\n\nBrief summaryThere is an urgent need for SARS-CoV-2 serology tests for the sensitive and specific detection of prior SARS-CoV-2 infection as a complementary diagnostic tool to molecular testing. Various commercial assays are becoming available but comparison of their relative performance is difficult unless they are head-to-head evaluated. Here we compared seven commercial assays on sera equally composed of mild and severe PCR-confirmed SARS-CoV-2 infections. Our analysis indicates a superior performance of the Wantai SARS-COV-2 ELISA for total antibodies to the S-RBD domain. Also, the Elecsys Anti-SARS-CoV-2 assay for total antibodies to the N-protein shows good performance for high-throughput screening.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Pauline H. Herroelen", + "author_inst": "AZ Delta Medical Laboratories, AZ Delta General Hospital" + }, + { + "author_name": "Geert Antoine Martens", + "author_inst": "AZ Delta Medical Laboratories, AZ Delta General Hospital (main), VUB Metabolomics Platform, Brussels Free University and Department of Biomolecular Medicine, Gh" + }, + { + "author_name": "Dieter De Smet", + "author_inst": "AZ Delta Medical Laboratories, AZ Delta General Hospital" + }, + { + "author_name": "Koen Swaerts", + "author_inst": "AZ Delta Medical Laboratories, AZ Delta General Hospital" + }, + { + "author_name": "An-Sofie Decavele", + "author_inst": "AZ Delta Medical Laboratories, AZ Delta General Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.11.20128058", "rel_title": "Power Laws in Superspreading Events: Evidence from Coronavirus Outbreaks and Implications for SIR Models", @@ -1381533,153 +1384470,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.11.20125849", - "rel_title": "Renin-angiotensin system blockers and susceptibility to COVID-19: a multinational open science cohort study", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20125849", - "rel_abs": "IntroductionAngiotensin converting enzyme inhibitors (ACEs) and angiotensin receptor blockers (ARBs) could influence infection risk of coronavirus disease (COVID-19). Observational studies to date lack pre-specification, transparency, rigorous ascertainment adjustment and international generalizability, with contradictory results.\n\nMethodsUsing electronic health records from Spain (SIDIAP) and the United States (Columbia University Irving Medical Center and Department of Veterans Affairs), we conducted a systematic cohort study with prevalent ACE, ARB, calcium channel blocker (CCB) and thiazide diuretic (THZ) users to determine relative risk of COVID-19 diagnosis and related hospitalization outcomes. The study addressed confounding through large-scale propensity score adjustment and negative control experiments.\n\nResultsFollowing over 1.1 million antihypertensive users identified between November 2019 and January 2020, we observed no significant difference in relative COVID-19 diagnosis risk comparing ACE/ARB vs CCB/THZ monotherapy (hazard ratio: 0.98; 95% CI 0.84 - 1.14), nor any difference for mono/combination use (1.01; 0.90 - 1.15). ACE alone and ARB alone similarly showed no relative risk difference when compared to CCB/THZ monotherapy or mono/combination use. Directly comparing ACE vs. ARB demonstrated a moderately lower risk with ACE, non-significant for monotherapy (0.85; 0.69 - 1.05) and marginally significant for mono/combination users (0.88; 0.79 - 0.99). We observed, however, no significant difference between drug-classes for COVID-19 hospitalization or pneumonia risk across all comparisons.\n\nConclusionThere is no clinically significant increased risk of COVID-19 diagnosis or hospitalization with ACE or ARB use. Users should not discontinue or change their treatment to avoid COVID-19.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Daniel R Morales", - "author_inst": "University of Dundee" - }, - { - "author_name": "Mitchell M Conover", - "author_inst": "Janssen Research and Development" - }, - { - "author_name": "Seng Chan You", - "author_inst": "Ajou University" - }, - { - "author_name": "Nicole Pratt", - "author_inst": "University of South Australia" - }, - { - "author_name": "Kristin Kostka", - "author_inst": "IQVIA" - }, - { - "author_name": "Talita Duarte Salles", - "author_inst": "IDIAPJGol" - }, - { - "author_name": "Sergio Fernandez Bertolin", - "author_inst": "IDIAPJGol" - }, - { - "author_name": "Maria Aragon", - "author_inst": "IDIAPJGol" - }, - { - "author_name": "Scott L. DuVall", - "author_inst": "Department of Veterans Affairs" - }, - { - "author_name": "Kristine Lynch", - "author_inst": "Department of Veterans Affairs" - }, - { - "author_name": "Thomas Falconer", - "author_inst": "Columbia University" - }, - { - "author_name": "Kees van Bochove", - "author_inst": "The Hyve" - }, - { - "author_name": "Cynthia Sung", - "author_inst": "Bill & Melinda Gates Medical Research Institute" - }, - { - "author_name": "Michael E. Matheny", - "author_inst": "Vanderbilt University" - }, - { - "author_name": "Christophe G. Lambert", - "author_inst": "University of New Mexico" - }, - { - "author_name": "Fredrik Nyberg", - "author_inst": "University of Gothenburg" - }, - { - "author_name": "Thamir M AlShammari", - "author_inst": "King Saud University" - }, - { - "author_name": "Andrew E. Williams", - "author_inst": "Tufts University" - }, - { - "author_name": "Rae Woong Park", - "author_inst": "Ajou University" - }, - { - "author_name": "James Weaver", - "author_inst": "Janssen Research and Development" - }, - { - "author_name": "Anthony G. Sena", - "author_inst": "Janssen Research and Development" - }, - { - "author_name": "Martijn J. Schuemie", - "author_inst": "Janssen Research and Development" - }, - { - "author_name": "Peter R. Rijnbeek", - "author_inst": "Erasmus University" - }, - { - "author_name": "Ross D. Williams", - "author_inst": "Erasmus University" - }, - { - "author_name": "Jennifer C.E Lane", - "author_inst": "University of Oxford" - }, - { - "author_name": "Albert Prats Uribe", - "author_inst": "University of Oxford" - }, - { - "author_name": "Lin Zhang", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Carlos Areia", - "author_inst": "University of Oxford" - }, - { - "author_name": "Harlan Krumholz", - "author_inst": "Yale University" - }, - { - "author_name": "Daniel Prieto Alhambra", - "author_inst": "University of Oxford" - }, - { - "author_name": "Patrick B Ryan", - "author_inst": "Janssen Research and Development" - }, - { - "author_name": "George Hripcsak", - "author_inst": "Columbia University" - }, - { - "author_name": "Marc A Suchard", - "author_inst": "University of California, Los Angeles" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.06.10.20127613", "rel_title": "On the interplay between mobility and hospitalization capacity during the COVID-19 pandemic: The SEIRHUD model", @@ -1381868,6 +1384658,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.10.20127530", + "rel_title": "State heterogeneity of human mobility and COVID-19 epidemics in the European Union", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127530", + "rel_abs": "Human mobility was associated with epidemic changes of coronavirus disease 2019 (COVID-19) in China, where strict public health interventions reduced human mobility and COVID-19 epidemics. But its association with COVID-19 epidemics in the European Union (EU) is unclear. In this quasi-experimental study, we modelled the temporal trends in human mobility and epidemics of COVID-19 in the 27 EU states between January 15 and May 9, 2020. COVID-19 and human mobility had 3 trend-segments, including an upward trend in COVID-19 daily incidence and a downward trend in most human mobilities in the middle segment. Compared with the EU states farther from Italy, the state-wide lockdown dates were more likely linked to turning points of human mobilities in the EU states closer to Italy, which were also more likely linked to second turning points of COVID-19 epidemics. Among the examined human mobilities, the second turning points in driving mobility and the first turning points in parks mobility were the best factors that connected lockdown dates and COVID-19 epidemics in the EU states closer to Italy. Our findings highlight the state- and mobility-heterogeneity in the associations of public health interventions and human mobility with changes of COVID-19 epidemics in the EU states.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Xiaoling Yuan", + "author_inst": "Department of Infectious Disease, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China" + }, + { + "author_name": "Kun Hu", + "author_inst": "Department of Pathology, University at Buffalo, Buffalo, NY, USA" + }, + { + "author_name": "Jie Xu", + "author_inst": "Department of Infectious Disease, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China" + }, + { + "author_name": "Xuchen Zhang", + "author_inst": "Department of Pathology, Yale University School of Medicine, New Haven, CT, USA" + }, + { + "author_name": "Wei Bao", + "author_inst": "Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, USA" + }, + { + "author_name": "Charles F Lynch", + "author_inst": "Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, USA" + }, + { + "author_name": "Lanjing Zhang", + "author_inst": "Princeton Medical Center/Rutgers University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.10.20127506", "rel_title": "Correlation between meteorological factors and COVID-19 infection in the Belem Metropolitan Region", @@ -1383059,61 +1385892,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, - { - "rel_doi": "10.1101/2020.06.11.20128934", - "rel_title": "SARS-CoV-2 Viral Load Predicts COVID-19 Mortality", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128934", - "rel_abs": "The need for reliable and widely available SARS-CoV-2 testing is well recognized, but it will be equally necessary to develop quantitative methods that determine viral load in order to guide patient triage and medical decision making. We are the first to report that SARS-CoV-2 viral load at the time of presentation is an independent predictor of COVID-19 mortality in a large patient cohort (n=1,145). Viral loads should be used to identify higher-risk patients that may require more aggressive care and should be included as a key biomarker in the development of predictive algorithms.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Elisabet Pujadas", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Fayzan Chaudhry", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Russell McBride", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Felix Richter", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Shan Zhao", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ania Wajnberg", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Girish Nadkarni", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Benjamin S Glicksberg", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Jane Houldsworth", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Carlos Cordon-Cardo", - "author_inst": "Icahn School of Medicine at Mount Sinai" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.11.20128900", "rel_title": "Associations between wearing masks, washing hands, and social distancing practices, and risk of COVID-19 infection in public: a cohort-based case-control study in Thailand", @@ -1383290,6 +1386068,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.11.20128710", + "rel_title": "Rotational Thromboelastometry predicts care level in Covid-19", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128710", + "rel_abs": "BackgroundHigh prevalence of thrombotic events in severely ill COVID-19 patients have been reported. Pulmonary embolism as well as microembolization of vital organs may in these individuals be direct causes of death. The identification of patients at high risk of developing thrombosis may lead to targeted, more effective prophylactic treatment.\n\nObjectivesTo test whether Rotational Thromboelastometry (ROTEM) indicates hypercoagulopathy in COVID-19 patients, and whether patients with severe disease have a more pronounced hypercoagulopathy compared with less severely ill patients.\n\nMethodsThe study was designed as a prospective observational study where COVID-19 patients over 18 years admitted to hospital were eligible for inclusion. Patients were divided into two groups depending on care level: 1) regular wards or 2) wards with specialized ventilation support. ROTEM was taken after admission and the data were compared with ROTEM in healthy controls.\n\nResultsThe ROTEM variables Maximum Clot Firmness (EXTEM-/FIBTEM-MCF) were higher in COVID-19 patients compared with healthy controls (p<0.001) and higher in severely ill patients compared with patients at regular wards (p<0.05). Coagulation Time (EXTEM-CT) was longer and Clot Formation Time (EXTEM-CFT) shorter in COVID-19 patients compared with healthy controls. Our results suggest that hypercoagulopathy is present in hospitalized patients with mild to severe COVID-19 pneumonia.\n\nConclusionROTEM variables were significantly different in COVID-19 patients early after admission compared with healthy controls. This pattern was more pronounced in patients with increased disease severity, suggesting that ROTEM-analysis may be useful to predict thromboembolic complications in these patients.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Lou Almskog", + "author_inst": "Department of Molecular Medicine and Surgery, Karolinska Institutet" + }, + { + "author_name": "Agneta Wikman", + "author_inst": "Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital and Department of CLINTEC, Karolinska Institutet" + }, + { + "author_name": "Jonas Svensson", + "author_inst": "Department of Clinical Neuroscience, Karolinska Institutet" + }, + { + "author_name": "Michael Wanecek", + "author_inst": "Department of Physiology and Pharmacology, Karolinska Institutet" + }, + { + "author_name": "Matteo Bottai", + "author_inst": "Unit of Biostatistics, Institute of Environmental Medicine, Karolinska Institutet" + }, + { + "author_name": "Jan van der Linden", + "author_inst": "Department of Molecular Medicine and Surgery, Karolinska Institutet" + }, + { + "author_name": "Anna Agren", + "author_inst": "Department of Clinical Sciences, Danderyd Hospital, Stockholm, Sweden" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.06.10.20127969", "rel_title": "Plasma levels of soluble ACE2 are associated with sex, Metabolic Syndrome, and its biomarkers in a large cohort, pointing to a possible mechanism for increased severity in COVID-19", @@ -1384413,65 +1387234,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.10.20127365", - "rel_title": "Spatial and temporal regularization to estimate COVID-19 Reproduction Number R(t): Promoting piecewise smoothness via convex optimization", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127365", - "rel_abs": "Among the different indicators that quantify the spread of an epidemic, such as the on-going COVID-19, stands first the reproduction number which measures how many people can be contaminated by an infected person. In order to permit the monitoring of the evolution of this number, a new estimation procedure is proposed here, assuming a well-accepted model for current incidence data, based on past observations. The novelty of the proposed approach is twofold: 1) the estimation of the reproduction number is achieved by convex optimization within a proximal-based inverse problem formulation, with constraints aimed at promoting piecewise smoothness; 2) the approach is developed in a multivariate setting, allowing for the simultaneous handling of multiple time series attached to different geographical regions, together with a spatial (graph-based) regularization of their evolutions in time. The effective-ness of the approach is first supported by simulations, and two main applications to real COVID-19 data are then discussed. The first one refers to the comparative evolution of the reproduction number for a number of countries, while the second one focuses on French counties and their joint analysis, leading to dynamic maps revealing the temporal co-evolution of their reproduction numbers.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "patrice abry", - "author_inst": "CNRS" - }, - { - "author_name": "nelly pustelnik", - "author_inst": "CNRS" - }, - { - "author_name": "stephane roux", - "author_inst": "ENS Lyon" - }, - { - "author_name": "pablo jensen", - "author_inst": "CNRS" - }, - { - "author_name": "Patrick Flandrin", - "author_inst": "CNRS" - }, - { - "author_name": "remi gribonval", - "author_inst": "INRIA" - }, - { - "author_name": "Charles G Lucas", - "author_inst": "ENS de Lyon" - }, - { - "author_name": "eric guichard", - "author_inst": "ENSSIB" - }, - { - "author_name": "Pierre Borgnat", - "author_inst": "CNRS" - }, - { - "author_name": "nicolas garnier", - "author_inst": "CNRS" - }, - { - "author_name": "benjamin audit", - "author_inst": "CNRS" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.11.20128801", "rel_title": "Early epidemic spread, percolation and Covid-19", @@ -1384612,6 +1387374,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2020.06.11.20128702", + "rel_title": "Emotional health concerns of oncology physicians in the United States: fallout during the COVID-19 pandemic", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128702", + "rel_abs": "IntroductionCancer care is significantly impacted by the Coronavirus Disease 2019 (COVID-19) pandemic. Our objective was to evaluate the effect of the pandemic on the emotional well-being of oncology providers across the United States and explore factors associated with anxiety and depression symptoms.\n\nMethods and MaterialsA cross-sectional survey was administered to United States cancer-care physicians recruited over a two-week period (3/27/2020 - 4/10/2020) using snowball-convenience sampling through social media. Symptoms of anxiety and depression were measured using the Patient Health Questionnaire (PHQ-4).\n\nResultsOf 486 participants, 374 (77.0%) completed the PHQ-4: mean age 45.7{+/-}9.6 years; 63.2% female; all oncologic specialties were represented. The rates of anxiety and depression symptoms were 62.0% and 23.5%, respectively. Demographic factors associated with anxiety included female sex, younger age, and less time in clinical practice. Perception of inadequate PPE (68.6% vs. 57.4%, p=0.03) and practicing in a state with more COVID-19 cases (65.8% vs. 51.1%, p=0.01) were associated with anxiety symptoms. Factors significantly associated with both anxiety and depression included: degree to which COVID-19 has interfered with the ability to provide treatment to cancer patients and concern that patients will not receive the level of care needed for non-COVID-19 illness (all p-values <0.01).\n\nConclusionThe prevalence of anxiety and depression symptoms among oncology physicians in the United States during the COVID-19 pandemic is high. Our findings highlight factors associated with and sources of psychological distress to be addressed to protect the well-being of oncology physicians.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Lauren Thomaier", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Deanna Teoh", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Patricia Jewett", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Heather Beckwith", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Helen Parsons", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Jianling Yuan", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Anne H. Blaes", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Emil Lou", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Jane Yuet Ching Hui", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Rachel I Vogel", + "author_inst": "University of Minnesota" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2020.06.11.20128686", "rel_title": "Sensitivity of commercial Anti-SARS-CoV-2 serological assays in a high-prevalence setting", @@ -1386535,61 +1389352,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.09.20127092", - "rel_title": "Antibody response to infectious diseases and other factors accurately predict COVID-19 infection and severity risk 10-14 years later: a retrospective UK Biobank cohort study", - "rel_date": "2020-06-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20127092", - "rel_abs": "BackgroundMany risk factors have emerged for novel 2019 coronavirus disease (COVID-19). It is relatively unknown how these factors collectively predict COVID-19 infection risk, as well as risk for a severe infection (i.e., hospitalization).\n\nMethodsAmong aged adults (69.3 {+/-} 8.6 years) in UK Biobank, COVID-19 data was downloaded for 4,510 participants with 7,539 test cases. We downloaded baseline data from 10-14 years ago, including demographics, biochemistry, body mass, and other factors, as well as antibody titers for 20 common to rare infectious diseases. Permutation-based linear discriminant analysis was used to predict COVID-19 risk and hospitalization risk. Probability and threshold metrics included receiver operating characteristic curves to derive area under the curve (AUC), specificity, sensitivity, and quadratic mean.\n\nResultsThe \"best-fit\" model for predicting COVID-19 risk achieved excellent discrimination (AUC=0.969, 95% CI=0.934-1.000). Factors included age, immune markers, lipids, and serology titers to common pathogens like human cytomegalovirus. The hospitalization \"best-fit\" model was more modest (AUC=0.803, 95% CI=0.663-0.943) and included only serology titers.\n\nConclusionsAccurate risk profiles can be created using standard self-report and biomedical data collected in public health and medical settings. It is also worthwhile to further investigate if prior host immunity predicts current host immunity to COVID-19.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Auriel A Willette", - "author_inst": "Iowa State University" - }, - { - "author_name": "Sara A Willette", - "author_inst": "Iowa State University" - }, - { - "author_name": "Qian Wang", - "author_inst": "Iowa State University" - }, - { - "author_name": "Colleen Pappas", - "author_inst": "Iowa State University" - }, - { - "author_name": "Brandon S Klinedinst", - "author_inst": "Iowa State University" - }, - { - "author_name": "Scott Le", - "author_inst": "Iowa State University" - }, - { - "author_name": "Brittany Larsen", - "author_inst": "Iowa State University" - }, - { - "author_name": "Amy Pollpeter", - "author_inst": "Iowa State University" - }, - { - "author_name": "Nicole Brenner", - "author_inst": "German Cancer Research Center (DKFZ)" - }, - { - "author_name": "Tim Waterboer", - "author_inst": "German Cancer Research Center (DKFZ)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.09.20127050", "rel_title": "Plasma from recovered COVID19 subjects inhibits spike protein binding to ACE2 in a microsphere-based inhibition assay", @@ -1386746,6 +1389508,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.09.20126805", + "rel_title": "What does and does not correlate with COVID-19 death rates", + "rel_date": "2020-06-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20126805", + "rel_abs": "We correlate county-level COVID-19 death rates with key variables using both linear regression and negative binomial mixed models, although we focus on linear regression models. We include four sets of variables: socio-economic variables, county-level health variables, modes of commuting, and climate and pollution patterns. Our analysis studies daily death rates from April 4, 2020 to May 27, 2020. We estimate correlation patterns both across states, as well as within states. For both models, we find higher shares of African American residents in the county are correlated with higher death rates. However, when we restrict ourselves to correlation patterns within a given state, the statistical significance of the correlation of death rates with the share of African Americans, while remaining positive, wanes. We find similar results for the share of elderly in the county. We find that higher amounts of commuting via public transportation, relative to telecommuting, is correlated with higher death rates. The correlation between driving into work, relative to telecommuting, and death rates is also positive across both models, but statistically significant only when we look across states and counties. We also find that a higher share of people not working, and thus not commuting either because they are elderly, children or unemployed, is correlated with higher death rates. Counties with higher home values, higher summer temperatures, and lower winter temperatures have higher death rates. Contrary to past work, we do not find a correlation between pollution and death rates. Also importantly, we do not find that death rates are correlated with obesity rates, ICU beds per capita, or poverty rates. Finally, our model that looks within states yields estimates of how a given states death rate compares to other states after controlling for the variables included in our model; this may be interpreted as a measure of how states are doing relative to others. We find that death rates in the Northeast are substantially higher compared to other states, even when we control for the four sets of variables above. Death rates are also statistically significantly higher in Michigan, Louisiana, Iowa, Indiana, and Colorado. Californias death rate is the lowest across all states.\n\nIt is important to understand that this research, and other observational analyses like it, only identify correlations: these relationships are not necessarily causal. However, these correlations may help policy makers identify variables that may potentially be causally related to COVID-19 death rates and adopt appropriate policies after understanding the causal relationship.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Christopher R Knittel", + "author_inst": "MIT" + }, + { + "author_name": "Bora Ozaltun", + "author_inst": "MIT" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.09.20126631", "rel_title": "Rapid characterization of the propagation of COVID-19 in different countries", @@ -1388249,61 +1391034,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2020.06.09.20076646", - "rel_title": "Prolonged SARS-CoV-2 Viral Shedding in Patients with COVID-19 was Associated with Delayed Initiation of Arbidol Treatment: a retrospective cohort study", - "rel_date": "2020-06-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20076646", - "rel_abs": "ObjectivesEvaluate the risk factors of prolonged SARS-CoV-2 virus shedding and the impact of arbidol treatment on SARS-CoV-2 virus shedding.\n\nMethodsData were retrospective collected from adults hospitalized with COVID-19 in Wuhan Union Hospital. We described the clinical features and SARS-CoV-2 RNA shedding of patients with COVID-19 and evaluated factors associated with prolonged virus shedding by multivariate regression analysis.\n\nResultsAmong 238 patients, the median age was 55.5 years, 57.1% were female, 92.9% (221/238) used arbidol, 58.4% (139/238) used arbidol combination with interferon. The median time from illness onset to start arbidol was 8 days (IQR, 5-14 days) and the median duration of SARS-CoV-2 virus shedding was 23 days (IQR, 17.8-30 days). SARS-CoV-2 RNA clearance was significantly delayed in patients who received arbidol >7 days after illness onset, compared with those in whom arbidol treatment was started[≤]7 days after illness onset (HR, 1.738 [95% CI, 1.339-2.257], P < .001). Multivariate regression analysis revealed that prolonged viral shedding was significantly associated with initiation arbidol more than seven days after symptom onset (OR 2.078, 95% CI [1.114-3.876], P .004), more than 7 days from onset of symptoms to first medical visitation (OR 3.321, 95% CI[1.559-7.073], P .002), illness onset before Jan.31, 2020 (OR 3.223, 95% CI[1.450-7.163], P .021). Arbidol combination with interferon was also significantly associated with shorter virus shedding (OR .402, 95% CI[.206-.787], P .008).\n\nConclusionsEarly initiation of arbidol and arbidol combination with interferon as well as consulting doctor timely after illness onset were helpful for SARS-CoV-2 clearance.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Yaya Zhou", - "author_inst": "Wuhan union hospital" - }, - { - "author_name": "Xinliang He", - "author_inst": "Wuhan union hospital" - }, - { - "author_name": "Jianchu Zhang", - "author_inst": "Wuhan union hospital" - }, - { - "author_name": "Yu e Xue", - "author_inst": "Wuhan union hospital" - }, - { - "author_name": "Mengyuan Liang", - "author_inst": "Wuhan union hospital" - }, - { - "author_name": "Bohan Yang", - "author_inst": "Wuhan union hospital" - }, - { - "author_name": "Wanli Ma", - "author_inst": "Wuhan union hospital" - }, - { - "author_name": "Qiong Zhou", - "author_inst": "Wuhan union hospital" - }, - { - "author_name": "Long Chen", - "author_inst": "Wuhan union hospital" - }, - { - "author_name": "Xiaorong Wang", - "author_inst": "Wuhan union hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.10.144196", "rel_title": "Evaluating the efficacy of RT-qPCR SARS-CoV-2 direct approaches in comparison to RNA extraction", @@ -1388560,6 +1391290,61 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.06.10.144188", + "rel_title": "Age-dependent progression of SARS-CoV-2 infection in Syrian hamsters", + "rel_date": "2020-06-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.10.144188", + "rel_abs": "In late 2019, an outbreak of a severe respiratory disease caused by an emerging coronavirus, SARS-CoV-2, resulted in high morbidity and mortality in infected humans1. Complete understanding of COVID-19, the multi-faceted disease caused by SARS-CoV-2, requires suitable small animal models, as does the development and evaluation of vaccines and antivirals2. Because age-dependent differences of COVID-19 were identified in humans3, we compared the course of SARS-CoV-2 infection in young and aged Syrian hamsters. We show that virus replication in the upper and lower respiratory tract was independent of the age of the animals. However, older hamsters exhibited more pronounced and consistent weight loss. In situ hybridization in the lungs identified viral RNA in bronchial epithelium, alveolar epithelial cells type I and II, and macrophages. Histopathology revealed clear age-dependent differences, with young hamsters launching earlier and stronger immune cell influx than aged hamsters. The latter developed conspicuous alveolar and perivascular edema, indicating vascular leakage. In contrast, we observed rapid lung recovery at day 14 after infection only in young hamsters. We propose that comparative assessment in young versus aged hamsters of SARS-CoV-2 vaccines and treatments may yield valuable information as this small-animal model appears to mirror age-dependent differences in human patients.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Nikolaus Osterrieder", + "author_inst": "Institute of Virology, Freie Universitaet Berlin, Germany" + }, + { + "author_name": "Luca D. Bertzbach", + "author_inst": "Institute of Virology, Freie Universitaet Berlin, Germany" + }, + { + "author_name": "Kristina Dietert", + "author_inst": "Institute of Veterinary Pathology, Freie Universitaet Berlin, Germany" + }, + { + "author_name": "Azza Abdelgawad", + "author_inst": "Institute of Virology, Freie Universitaet Berlin, Germany" + }, + { + "author_name": "Daria Vladimirova", + "author_inst": "Institute of Virology, Freie Universitaet Berlin, Germany" + }, + { + "author_name": "Dusan Kunec", + "author_inst": "Institute of Virology, Freie Universitaet Berlin, Germany" + }, + { + "author_name": "Donata Hoffmann", + "author_inst": "Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Germany" + }, + { + "author_name": "Martin Beer", + "author_inst": "Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Germany" + }, + { + "author_name": "Achim D. Gruber", + "author_inst": "Institute of Veterinary Pathology, Freie Universitaet Berlin, Germany" + }, + { + "author_name": "Jakob Trimpert", + "author_inst": "Institute of Virology, Freie Universitaet Berlin, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.10.144642", "rel_title": "Ultrastructural analysis of SARS-CoV-2 interactions with the host cell via high resolution scanning electron microscopy", @@ -1389703,41 +1392488,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.08.20125708", - "rel_title": "A web survey to assess the use efficacy of personnel protective materials among allied health care workers during COVID-19 pandemic at North-East India", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125708", - "rel_abs": "The rising pandemic is resulting in increased usage of personnel protective equipment in the hospital and community. The efficient and effective use of appropriate personal protective equipment will help assure its availability and healthcare provider safety. The purpose of this study was to assess the use efficacy of PPE among health care workers through a web based survey during the pandemic. the response rate of the survey was 66.75%. 35.2% gave a full rating on a point of 5 regarding the control measures taken by the hospital, 39% of respondents did not use the PPE, 90.6% used a surgical mask while 65.9% wore the disposable gloves and only 47.6% wore the goggles/face shield More than half the respondents did not wear the shoe-cover. 97.4% used the hand sanitizer and around 97% maintained hand hygiene practice.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Dr. Rahul P Kotian", - "author_inst": "Department of Medical Imaging, College of Allied Health Sciences, SRINIVAS UNIVERSITY" - }, - { - "author_name": "Manna Debnath", - "author_inst": "Department of Medical Imaging Technology, Charotar Institute of Paramedical Sciences, Charotar University of Science and Technology." - }, - { - "author_name": "Zosangliani", - "author_inst": "Department of Radiology, Faculty of Paramedical Sciences, Assam Downtown University, Assam, India." - }, - { - "author_name": "Brayal D'souza", - "author_inst": "Department of Health Innovation, PSPH, Manipal Academy of Higher Education, Manipal." - }, - { - "author_name": "Disha Faujdar", - "author_inst": "Department of Medical Imaging Technology, College of Allied Health Sciences, Srinivas University, Mukka." - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.06.08.20125872", "rel_title": "Cognitive impairment is a common comorbidity in COVID-19 deceased patients. A hospital-based retrospective cohort study.", @@ -1390114,6 +1392864,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.08.20125484", + "rel_title": "An analysis of SARS-CoV-2 viral load by patient age", + "rel_date": "2020-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125484", + "rel_abs": "As children are under-represented in current studies aiming to analyse transmission of SARS-coronavirus 2 (SARS-CoV-2), their contribution to transmission is unclear. Viral load, as measured by RT-PCR, can inform considerations regarding transmission, especially if existing knowledge of viral load in other respiratory diseases is taken into account. RT-PCR threshold cycle data from 3303 patients who tested positive for SARS-CoV-2 (out of 77,996 persons tested in total, drawn from across Germany) were analysed to examine the relationship between patient age and estimated viral load. Two PCR systems were used. In data from the PCR system predominantly used for community and cluster screening during the early phase of the epidemic (Roche LightCycler 480 II), when such screening was frequent practice, viral loads do not differ significantly in three comparisons between young and old age groups (differences in log10 viral loads between young and old estimated from raw viral load data and a Bayesian mixture model of gamma distributions collectively range between -0.11 and -0.43). Data from a second type of PCR system (Roche cobas 6800/8800), introduced into diagnostic testing on March 16, 2020 and used during the time when household and other contact testing was reduced, show a credible but small difference in the three comparisons between young and old age groups (differences, measured as above, collectively range between -0.43 and -0.83). This small difference may be due to differential patterns of PCR instrument utilization rather than to an actual difference in viral load. Considering household transmission data on influenza, which has a similar viral load kinetic to SARS-CoV-2, the viral load differences between age groups observed in this study are likely to be of limited relevance. Combined data from both PCR instruments show that viral loads of at least 250,000 copies, a threshold we previously established for the isolation of infectious virus in cell culture at more than 5% probability, were present across the study period in 29.0% of kindergarten-aged patients 0-6 years old (n=38), 37.3% of those aged 0-19 (n=150), and in 51.4% of those aged 20 and above (n=3153). The differences in these fractions may also be due to differences in test utilization. We conclude that a considerable percentage of infected people in all age groups, including those who are pre- or mild-symptomatic, carry viral loads likely to represent infectivity. Based on these results and uncertainty about the remaining incidence, we recommend caution and careful monitoring during gradual lifting of non-pharmaceutical interventions. In particular, there is little evidence from the present study to support suggestions that children may not be as infectious as adults.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Terry C Jones", + "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, University of Cambridge" + }, + { + "author_name": "Barbara M\u00fchlemann", + "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, DZIF" + }, + { + "author_name": "Talitha Veith", + "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, DZIF" + }, + { + "author_name": "Guido Biele", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Marta Zuchowski", + "author_inst": "Labor Berlin - Charit\u00e9 Vivantes GmbH" + }, + { + "author_name": "J\u00f6rg Hoffmann", + "author_inst": "Labor Berlin - Charit\u00e9 Vivantes GmbH" + }, + { + "author_name": "Angela Stein", + "author_inst": "Labor Berlin - Charit\u00e9 Vivantes GmbH" + }, + { + "author_name": "Anke Edelmann", + "author_inst": "Labor Berlin - Charit\u00e9 Vivantes GmbH" + }, + { + "author_name": "Victor Max Corman", + "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, DZIF" + }, + { + "author_name": "Christian Drosten", + "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, DZIF" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.09.20126045", "rel_title": "Worries and concerns among healthcare workers during the coronavirus 2019 pandemic: a web-based cross-sectional survey", @@ -1392008,53 +1394813,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.08.20119636", - "rel_title": "No Evidence for Reduced Hospital Admissions or Increased Deaths from Stroke or Heart Attack During COVID-19", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20119636", - "rel_abs": "Articles in the UK press have claimed that hospital admissions for heart attack and stroke have declined during the COVID-19 pandemic. However, data from the West Midlands Ambulance Service have not shown any reduction in call-outs for patients with stroke or ST-Elevation Myocardial Infarction. This study examined data from University Hospital Birmingham NHS Foundation Trust, comparing admissions from week 1 of 2016 to week 17 of 2019, with the same period in 2020, pre- and post-lockdown. The results showed that there was no evidence of a reduction in the overall mean number of admissions of patients with these conditions in the post-lockdown period.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Katharine Reeves", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Samuel I Watson", - "author_inst": "University of Warwick" - }, - { - "author_name": "Tanya Pankhurst", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Kamlesh Khunti", - "author_inst": "University of Leicester" - }, - { - "author_name": "Suzy Gallier", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Magdalena Skrybant", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Peter J Chilton", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Richard J Lilford", - "author_inst": "University of Birmingham" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.08.20122143", "rel_title": "Hydroxychloroquine inhibits trained immunity - implications for COVID-19", @@ -1392267,6 +1395025,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.08.140152", + "rel_title": "D936Y and Other Mutations in the Fusion Core of the SARS-Cov-2 Spike Protein Heptad Repeat 1 Undermine the Post-Fusion Assembly", + "rel_date": "2020-06-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.08.140152", + "rel_abs": "The iconic \"red crown\" of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is made of its spike (S) glycoprotein. The S protein is the Trojan horse of coronaviruses, mediating their entry into the host cells. While SARS-CoV-2 was becoming a global threat, scientists have been accumulating data on the virus at an impressive pace, both in terms of genomic sequences and of three-dimensional structures. On April 21st, the GISAID resource had collected 10,823 SARS-CoV-2 genomic sequences. We extracted from them all the complete S protein sequences and identified point mutations thereof. Six mutations were located on a 14-residue segment (929-943) in the \"fusion core\" of the heptad repeat 1 (HR1). Our modeling in the pre- and post-fusion S protein conformations revealed, for three of them, the loss of interactions stabilizing the post-fusion assembly. On May 29th, the SARS-CoV-2 genomic sequences in GISAID were 34,805. An analysis of the occurrences of the HR1 mutations in this updated dataset revealed a significant increase for the S929I and S939F mutations and a dramatic increase for the D936Y mutation, which was particularly widespread in Sweden and Wales/England. We notice that this is also the mutation causing the loss of a strong inter-monomer interaction, the D936-R1185 salt bridge, thus clearly weakening the post-fusion assembly.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Luigi Cavallo", + "author_inst": "King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division" + }, + { + "author_name": "Romina Oliva", + "author_inst": "University of Naples Parthenope, Department of Sciences and Technologies" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.06.07.20124693", "rel_title": "Changing patterns of mortality during the COVID-19 pandemic: population-based modelling to understand palliative care implications", @@ -1393654,49 +1396435,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.05.20123307", - "rel_title": "Reduced ICU demand with early CPAP and proning in COVID-19 at Bradford: a single centre cohort", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.05.20123307", - "rel_abs": "BackgroundGuidance in COVID-19 respiratory failure has favoured early intubation, with concerns over the use of CPAP. We adopted early CPAP and self-proning, and evaluated the safety and efficacy of this approach.\n\nMethodsThis retrospective observational study included all patients with a positive COVID-19 PCR, and others with high clinical suspicion. Our protocol advised early CPAP and self-proning for severe cases, aiming to prevent rather than respond to deterioration. CPAP was provided outside critical care by ward staff supported by physiotherapists and an intensive critical care outreach program. Data were analysed descriptively and compared against a large UK cohort (ISARIC).\n\nResults559 patients admitted before 1/May/20 were included. 376 were discharged alive, and 183 died. 165 patients (29.5%) received CPAP, 40 (7.2%) were admitted to critical care and 28 (5.0%) were ventilated. Hospital mortality was 32.7%, and 50% for critical care. Following CPAP, 62% of patients with S:F or P:F ratios indicating moderate or severe ARDS, who were candidates for escalation, avoided intubation. Figures for critical care admission, intubation and hospital mortality are lower than ISARIC, whilst critical care mortality is similar. Following ISARIC proportions we would have admitted 92 patients to critical care and intubated 55. Using the described protocol, we intubated 28 patients from 40 admissions, and remained within our expanded critical care capacity.\n\nConclusionBradfords protocol produced good results despite our population having high levels of co-morbidity and ethnicities associated with poor outcomes. In particular we avoided overloading critical care capacity. We advocate this approach as both effective and safe.\n\nSocial media summaryThe use of early CPAP and proning in COVID-19 was associated with lower critical care admissions, intubation, and mortality at Bradford compared to a large UK cohort (ISARIC WHO CCP-UK).", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Tom Lawton", - "author_inst": "Bradford Institute of Health Research & Bradford Teaching Hospitals NHS Trust" - }, - { - "author_name": "Kate M Wilkinson", - "author_inst": "Bradford Teaching Hospitals NHS Trust" - }, - { - "author_name": "Aaron Corp", - "author_inst": "Bradford Teaching Hospitals NHS Trust" - }, - { - "author_name": "Rabeia Javid", - "author_inst": "Bradford Teaching Hospitals NHS Trust" - }, - { - "author_name": "Laura MacNally", - "author_inst": "Bradford Teaching Hospitals NHS Trust" - }, - { - "author_name": "Michael McCooe", - "author_inst": "Bradford Institute of Health Research & Bradford Teaching Hospitals NHS Trust" - }, - { - "author_name": "Elizabeth Newton", - "author_inst": "Bradford Teaching Hospitals NHS Trust" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.06.07.20124933", "rel_title": "Who dies from COVID-19? Post-hoc explanations of mortality prediction models using coalitional game theory, surrogate trees, and partial dependence plots", @@ -1393813,6 +1396551,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2020.06.08.20124990", + "rel_title": "An Aberration Detection-Based Approach for Sentinel Syndromic Surveillance of COVID-19 and Other Novel Influenza-Like Illnesses", + "rel_date": "2020-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20124990", + "rel_abs": "Coronavirus Disease 2019 (COVID-19) has emerged as a significant global concern, triggering harsh public health restrictions in a successful bid to curb its exponential growth. As discussion shifts towards relaxation of these restrictions, there is significant concern of second-wave resurgence. The key to managing these outbreaks is early detection and intervention, and yet there is significant lag time associated with usage of laboratory confirmed cases for surveillance purposes. To address this, syndromic surveillance can be considered to provide a timelier alternative for first-line screening. Existing syndromic surveillance solutions are however typically focused around a known disease and have limited capability to distinguish between outbreaks of individual diseases sharing similar syndromes. This poses a challenge for surveillance of COVID-19 as its active periods are tend to overlap temporally with other influenza-like illnesses. In this study we explore performing sentinel syndromic surveillance for COVID-19 and other influenza-like illnesses using a deep learning-based approach. Our methods are based on aberration detection utilizing autoencoders that leverages symptom prevalence distributions to distinguish outbreaks of two ongoing diseases that share similar syndromes, even if they occur concurrently. We first demonstrate that this approach works for detection of outbreaks of influenza, which has known temporal boundaries. We then demonstrate that the autoencoder can be trained to not alert on known and well-managed influenza-like illnesses such as the common cold and influenza. Finally, we applied our approach to 2019-2020 data in the context of a COVID-19 syndromic surveillance task to demonstrate how implementation of such a system could have provided early warning of an outbreak of a novel influenza-like illness that did not match the symptom prevalence profile of influenza and other known influenza-like illnesses.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Andrew Wen", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Liwei Wang", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Huan He", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Sijia Liu", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Sunyang Fu", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Sunghwan Sohn", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Jacob A Kugel", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Vinod C Kaggal", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Ming Huang", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Yanshan Wang", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Feichen Shen", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Jungwei Fan", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Hongfang Liu", + "author_inst": "Mayo Clinic" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.06.08.20125518", "rel_title": "Indian Publications on SARS-CoV-2: A Bibliometric Study of WHO COVID-19 Database", @@ -1394992,53 +1397797,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.07.20124594", - "rel_title": "Early Detection of Coronavirus Cases Using Chest X-ray Images Employing Machine Learning and Deep Learning Approaches", - "rel_date": "2020-06-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.07.20124594", - "rel_abs": "This study aims to propose a deep learning model to detect COVID-19 positive cases more precisely utilizing chest X-ray images. We have collected and merged all the publicly available chest X-ray datasets of COVID-19 infected patients from Kaggle and Github, and pre-processed it using random sampling approach. Then, we proposed and applied an enhanced convolutional neural network (CNN) model to this dataset and obtained a 94.03% accuracy, 95.52% AUC and 94.03% f-measure for detecting COVID-19 positive patients. We have also performed a comparative performance between our proposed CNN model with several state-of-the-art machine learning classifiers including support vector machine, random forest, k-nearest neighbor, logistic regression, gaussian naive bayes, bernoulli naive bayes, decision tree, Xgboost, multilayer perceptron, nearest centroid and perceptron as well as deep learning and pre-trained models such as deep neural network, residual neural network, visual geometry group network 16, and inception network V3 were employed, where our model yielded outperforming results compared to all other models. While evaluating the performance of our models, we have emphasized on specificity along with accuracy to identify non-COVID-19 individuals more accurately, which may potentially facilitate the early detection of COVID-19 patients for their preliminary screening, especially in under-resourced health infrastructure with insufficient PCR testing systems and testing facilities. Moreover, this model could also be applicable to the cases of other lung infections.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Md. Shahriare Satu", - "author_inst": "Noakhali Science and Technology University Faculty of Business Administration" - }, - { - "author_name": "Khair Ahammed", - "author_inst": "Noakhali Science and Technology University" - }, - { - "author_name": "Mohammad Zoynul Abedin", - "author_inst": "Dailian Maritime University" - }, - { - "author_name": "Md. Auhidur Rahaman", - "author_inst": "Noakhali Science and Technology University" - }, - { - "author_name": "Shiekh Mohammed Shariful Islam", - "author_inst": "Deakin University" - }, - { - "author_name": "AKM Azad", - "author_inst": "University of Technology Sydney" - }, - { - "author_name": "Salem A. Alyami", - "author_inst": "Department of Mathematics and Statistics, Imam Mohammad Ibn Saud Islamic University, Saudi Arabia" - }, - { - "author_name": "Mohammad Ali Moni", - "author_inst": "University of New south Wales" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.06.20124123", "rel_title": "Clinical evaluation of self-collected saliva by RT-qPCR, direct RT-qPCR, RT-LAMP, and a rapid antigen test to diagnose COVID-19", @@ -1395295,6 +1398053,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.06.20124313", + "rel_title": "Closed form solution of the SIR model for the COVID-19 outbreak in Italy", + "rel_date": "2020-06-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.06.20124313", + "rel_abs": "The CODIV-19 outbreak in early 2020 generated a tremendous effort of epidemiologists and researchers to fit the experimental data with the solutions of the SIR model equations [1] or with more sophisticated models. In this paper we show that under same hypotheses, a closed form solution exists that reasonably fits the experimental data for Italy, and the results can be extended to any other area.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Riccardo Giubilei", + "author_inst": "Private" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.05.20123646", "rel_title": "A scaling approach to estimate the COVID-19 infection fatality ratio from incomplete data", @@ -1396810,49 +1399587,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.05.20123752", - "rel_title": "Changes in non-linear and time-domain heart rate variability indices between critically ill COVID-19 and all-cause sepsis patients -a retrospective study", - "rel_date": "2020-06-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.05.20123752", - "rel_abs": "ObjectiveTo measure heart rate variability metrics in critically ill COVID-19 patients with comparison to all-cause critically ill sepsis patients.\n\nDesign and patientsRetrospective analysis of COVID-19 patients admitted to an ICU for at least 24h at any of Emory Healthcare ICUs between March and April 2020. The comparison group was a cohort of all-cause sepsis patients prior to COVID-19 pandemic.\n\nInterventionsnone.\n\nMeasurementsContinuous waveforms were captured from the patient monitor. The EKG was then analyzed for each patient over a 300 second (s) observational window, that was shifted by 30s in each iteration from admission till discharge. A total of 23 HRV metrics were extracted in each iteration. We use the Kruskal-Wallis and Steel-Dwass tests (p < 0.05) for statistical analysis and interpretations of HRV multiple measures.\n\nResultsA total of 141 critically-ill COVID-19 patients met inclusion criteria, who were compared to 208 patients with all-cause sepsis. Demographic parameters were similar apart from a high proportion of African-Americans in the COVID-19 cohort. Three non-linear markers, including SD1:SD2, sample entropy, approximate entropy and four linear features mode of Beat-to-Beat interval (NN), Acceleration Capacity (AC), Deceleration Capacity (DC), and pNN50, were statistical significance between more than one binary combinations of the sub-groups (comparing survivors and non-survivors in both the COVID-19 and sepsis cohorts). The three nonlinear features and AC, DC, and NN (mode) were statistically significant across all four combinations. Temporal analysis of the main markers showed low variability across the 5 days of analysis, compared with sepsis patients.\n\nConclusionsHeart rate variability is broadly implicated across patients infected with SARSCoV-2, and admitted to the ICU for critical illness. Comparing these metrics to patients with all-cause sepsis suggests a unique set of expressions that differentiate this viral phenotype. This finding could be investigated further as a potential biomarker to predict poor outcome in this patient population, and could also be a starting point to measure potential autonomic dysfunction in COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Rishikesan Kamaleswaran", - "author_inst": "Emory University" - }, - { - "author_name": "Ofer Sadan", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Prem Kandiah", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Qiao Li", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "James M Blum", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Craig M Coopersmith", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Timothy G Buchman", - "author_inst": "Emory University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.06.05.20122903", "rel_title": "Impact of Governmental interventions on epidemic progression and workplace activity during the COVID-19 outbreak", @@ -1396965,6 +1399699,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.04.20122812", + "rel_title": "'Drawing on Wisdom to Cope with Adversity:' A Systematic Review Protocol of Older Adults' Mental and Psychosocial Health During Acute Respiratory Disease Propagated-Type Epidemics and Pandemics (COVID-19, SARS-CoV, MERS, and Influenza).", + "rel_date": "2020-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122812", + "rel_abs": "BackgroundMental health has become one of the fundamental priorities during the COVID-19 pandemic. Situations like physical distancing as well as being constantly tagged as the most vulnerable group could expose older adults to mental and psychosocial burdens. Nonetheless, there is little clarity about the impact of the COVID-19 pandemic or similar pandemics in the past on the mental illness, wellbeing, and psychosocial health of the older population compared to other age groups.\n\nObjectivesTo describe the patterns of older adults mental and psychosocial health related to acute respiratory disease propagated-type epidemics and pandemics and to evaluate the differences with how other age groups respond.\n\nEligibility criteriaquantitative and qualitative studies evaluating mental illness, wellbeing, or psychosocial health outcomes associated with respiratory propagated epidemics and pandemics exposure or periods (COVID-19, SARS-CoV, MERS, and Influenza) in people 65 years or older.\n\nData sourceOriginal articles published until June 1st, 2020, in any language searched in the electronic healthcare and social sciences database: MEDLINE, Embase, CINAHL, PsycINFO, Scopus, WHO Global literature on coronavirus disease database, China National Knowledge Infrastructure ( -CNKI). Furthermore, EPPI Centres COVID-19 living systematic map and the publicly available publication list of the COVID-19 living systematic review will be incorporated for preprints and recent COVID-19 publications.\n\nData extractionTwo independent reviewers will extract predefined parameters. The risk of bias will be assessed.\n\nData synthesisData synthesis will be performed according to study type and design, type of epidemic and pandemic, types of outcomes (mental health and psychosocial outcomes), and participant characteristics (e.g., sex, race, age, socioeconomic status, food security, presence of dependency in daily life activities independent/dependent older adults). Comparison between sex, race, and other age groups will be performed qualitatively, and quantitatively if enough data is available. The risk of bias and study heterogeneity will be reported for quantitative studies.\n\nConclusionThis study will provide information to take actions to address potential mental health difficulties during the COVID-19 pandemic in older adults and to understand responses on this age group. Furthermore, it will be useful to identify potential groups that are more vulnerable or resilient to the mental-health challenges of the current worldwide pandemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jose M Aravena", + "author_inst": "Department of Social & Behavioral Sciences, School of Public Health, Yale University." + }, + { + "author_name": "Cristopher Aceituno", + "author_inst": "Chilean-German Beneficence Corporation, Santiago, Chile." + }, + { + "author_name": "Kate Nyhan", + "author_inst": "Harvey Cushing / John Hay Whitney Medical Library, Environmental Health Sciences, Yale University." + }, + { + "author_name": "Kewei Shi", + "author_inst": "School of Public Health, Yale University." + }, + { + "author_name": "Sten Vermund", + "author_inst": "School of Public Health, School of Medicine, Yale University." + }, + { + "author_name": "Becca R Levy", + "author_inst": "Department of Social & Behavioral Sciences, School of Public Health, Yale University." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.06.05.20123042", "rel_title": "THE ERA OF CORONAVIRUS; KNOWLEDGE, ATTITUDE, PRACTICES, AND BARRIERS TO HAND HYGIENE AMONG MAKERERE UNIVERSITY STUDENTS AND KATANGA COMMUNITY RESIDENTS.", @@ -1398120,89 +1400893,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.05.137349", - "rel_title": "Synthetic Antibodies neutralize SARS-CoV-2 infection of mammalian cells", - "rel_date": "2020-06-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.05.137349", - "rel_abs": "Coronaviruses (CoV) are a large family of enveloped, RNA viruses that circulate in mammals and birds. Three highly pathogenic strains have caused zoonotic infections in humans that result in severe respiratory syndromes including the Middle East Respiratory Syndrome CoV (MERS), Severe Acute Respiratory Syndrome CoV (SARS), and the ongoing Coronavirus Disease 2019 (COVID-19) pandemic. Here, we describe a panel of synthetic monoclonal antibodies, built on a human IgG framework, that bind to the spike protein of SARS-CoV-2 (the causative agent of COVID-19), compete for ACE2 binding, and potently inhibit SARS-CoV-2. All antibodies that exhibited neutralization potencies at sub-nanomolar concentrations against SARS-CoV-2/USA/WA1 in Vero E6 cells, also bound to the receptor binding domain (RBD), suggesting competition for the host receptor ACE2. These antibodies represent strong immunotherapeutic candidates for treatment of COVID-19.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Shane Miersch", - "author_inst": "University of Toronto" - }, - { - "author_name": "Mart Ustav", - "author_inst": "University of Toronto" - }, - { - "author_name": "Zhijie Li", - "author_inst": "University of Toronto" - }, - { - "author_name": "James B. Case", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Safder Ganaie", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Giulia Matusali", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Francesca Colavita", - "author_inst": "National Institute for Infectious Diseases \"L. Spallanzani\" IRCCS" - }, - { - "author_name": "Daniele Lapa", - "author_inst": "National Institute for Infectious Diseases \"L. Spallanzani\" IRCCS" - }, - { - "author_name": "Maria R. Capobianchi", - "author_inst": "National Institute for Infectious Diseases \"L. Spallanzani\" IRCCS" - }, - { - "author_name": "Giuseppe Novelli", - "author_inst": "University of Rome" - }, - { - "author_name": "Jang B. Gupta", - "author_inst": "Intonation Research Laboratories" - }, - { - "author_name": "Suresh Jain", - "author_inst": "Intonation Research Laboratories" - }, - { - "author_name": "Pier Paolo Pandolfi", - "author_inst": "University of Turin" - }, - { - "author_name": "Michael S. Diamond", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Gaya Amarasinghe", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "James M. Rini", - "author_inst": "University of Toronto" - }, - { - "author_name": "Sachdev S. Sidhu", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.06.05.136887", "rel_title": "Protein covariance networks reveal interactions important to the emergence of SARS coronaviruses as human pathogens", @@ -1398407,6 +1401097,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.26.20114009", + "rel_title": "How Should Clinicians Interpret Imprecise Trials Assessing Drugs for COVID-19 Patients?", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20114009", + "rel_abs": "As the COVID-19 pandemic progresses, researchers are reporting findings of randomized trials comparing standard care with care augmented by experimental drugs. The trials have small sample sizes, so estimates of treatment effects are imprecise. Seeing imprecision, clinicians reading research articles may find it difficult to decide when to treat patients with experimental drugs. Whatever decision criterion one uses, there is always some probability that random variation in trial outcomes will lead to prescribing sub-optimal treatments. A conventional practice when comparing standard care and an innovation is to choose the innovation only if the estimated treatment effect is positive and statistically significant. This practice defers to standard care as the status quo. To evaluate decision criteria, we use the concept of near optimality, which jointly considers the probability and magnitude of decision errors. An appealing decision criterion from this perspective is the empirical success rule, which chooses the treatment with the highest observed average patient outcome in the trial. Considering the design of recent and ongoing COVID-19 trials, we show that the empirical success rule yields treatment results that are much closer to optimal than those generated by prevailing decision criteria based on hypothesis tests.\n\nWe have benefitted from the comments of Michael Gmeiner, Valentyn Litvin, Francesca Molinari, and John Mullahy. Tetenov has received funding from the Swiss National Science Foundation through grant number 100018-192580.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Charles F. Manski", + "author_inst": "Northwestern University" + }, + { + "author_name": "Aleksey Tetenov", + "author_inst": "University of Geneva" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.02.20106310", "rel_title": "Characteristics and Outcomes of Hospitalized Young Adults with Mild to Moderate Covid-19 at a University Hospital in India", @@ -1399970,33 +1402683,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2020.06.02.20116855", - "rel_title": "The attitudes, perceptions and experiences of medical school applicants following the closure of schools and cancellation of public examinations in 2020 due to the COVID-19 pandemic", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20116855", - "rel_abs": "ObjectiveTo describe medical applicants experiences of education and their views on changes to medical school admissions, including the awarding of calculated grades, following the 2020 closure of schools and universities, and the cancellation of public examinations in the United Kingdom due to the COVID-19/coronavirus pandemic. To understand how applicants from diverse social backgrounds might differ in these regards.\n\nDesignCross-sectional questionnaire study forming part of the longitudinal United Kingdom Medical Applicant Cohort Study (UKMACS).\n\nSettingUnited Kingdom medical school admissions.\n\nParticipants2887 participants (68% female; 64% with at least one degree-educated parent; 63% with at least one parent in the highest socioeconomic group) completed an online questionnaire between 8th and 22nd April 2020. To be invited to complete the questionnaire, participants had to have registered to take the University Clinical Admissions Test (UCAT) in 2019 and to have agreed to be invited to take part in the study, or they needed to have completed one or more previous UKMACS questionnaires. They also need to have been seriously considering applying to study medicine in the UK for entry in 2020 between May and October 2019, and be resident in the UK or Islands/Crown Dependencies.\n\nMain outcome measuresViews on calculated grades, views on potential changes to medical school admissions and teaching in 2020 and 2021, reported experiences of education following the closure of educational institutions in March 2020.\n\nResultsRespondents had concerns about the calculated grades that will replace A-level examinations, especially female applicants and applicants from Black Asian and Minority Ethnic (BAME) backgrounds who felt teachers would find it difficult to grade and rank students accurately, as well as those from non-selective state schools and those living in deprived areas who had some concerns about the grade standardisation process. Calculated grades were not considered fair enough by a majority to use in the acceptance or rejection of medical offer-holders, but several measures - including interview and aptitude test scores - were considered fair enough to use in combination. Respondents from non-selective state (public) schools reported less use of and less access to educational resources compared to their counterparts at private/selective schools. In particular they reported less online teaching in real time, and reported spending less time studying during the lockdown.\n\nConclusionsThe coronavirus pandemic will have significant and long term impacts on the selection, education and performance of our future medical workforce. It is important that the views and experiences of medical applicants from diverse backgrounds are taken into consideration in decisions affecting their futures and the future of the profession.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Katherine Woolf", - "author_inst": "University College London" - }, - { - "author_name": "Dave Harrison", - "author_inst": "University College London" - }, - { - "author_name": "I.C. McManus", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2020.06.02.20120642", "rel_title": "Estimating excess visual loss in people with neovascular age-related macular degeneration during the COVID-19 pandemic", @@ -1400169,6 +1402855,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.03.20120576", + "rel_title": "A RELAXATION VIEWPOINT TO COVID-19 INFECTION", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20120576", + "rel_abs": "One of the central tools to control the COVID-19 pandemics is the knowledge of its spreading dynamics. Here we develop a fractal model capable of describe this dynamics, in term of daily new cases, and provide quantitative criteria for some predictions. We propose a fractal dynamical model using conformed derivative and fractal time scale. A Burr-XII shaped solution of the fractal-like equation is obtained. The model is tested using data from several countries, showing that a single function is able to describe very different shapes of the outbreak. The diverse behavior of the outbreak on those countries is presented and discussed. Moreover, a criterion to determine the existence of the pandemic peak and a expression to find the time to reach herd immunity are also obtained.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Oscar Sotolongo-Costa", + "author_inst": "C\u00e1tedra \"Henri Poincar\u00e9\" de sistemas complejos. Universidad de La Habana. Cuba." + }, + { + "author_name": "Jos\u00e9 Weberszpil", + "author_inst": "Univ. Federal Rural do Rio de Janeiro-UFRRJ" + }, + { + "author_name": "Oscar Sotolongo-Grau", + "author_inst": "Alzheimer Research Center and Memory Clinic, Fundaci\u00f3n ACE, Institut Catal\u00e0 de Neurocin\u00e8ciens Aplicades. Spain." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.03.20119867", "rel_title": "The psychological effects of COVID-19 on frontline healthcare workers and how they are coping: a web-based, cross-sectional study from Pakistan", @@ -1401432,69 +1404145,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.03.20121392", - "rel_title": "Modulation of COVID-19 Epidemiology by UV-B and -A Photons from the Sun", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20121392", - "rel_abs": "Solar UV-C photons do not reach Earths surface, but are known to be endowed with germicidal properties that are also effective on viruses. The effect of softer UV-B and UV-A photons, which copiously reach the Earths surface, on viruses are instead little studied, particularly on single-stranded RNA viruses.\n\nHere we combine our measurements of the action spectrum of Covid-19 in response to UV light, Solar irradiation measurements on Earth during the SARS-CoV-2 pandemics, worldwide recorded Covid-19 mortality data and our \"Solar-Pump\" diffusive model of epidemics to show that (a) UV-B/A photons have a powerful virucidal effect on the single-stranded RNA virus Covid-19 and that (b) the Solar radiation that reaches temperate regions of the Earth at noon during summers, is sufficient to inactivate 63% of virions in open-space concentrations (1.5x103 TCID50/mL, higher than typical aerosol) in less than 2 minutes.\n\nWe conclude that the characteristic seasonality imprint displayed world-wide by the SARS-Cov-2 mortality time-series throughout the diffusion of the outbreak (with temperate regions showing clear seasonal trends and equatorial regions suffering, on average, a systematically lower mortality), might have been efficiently set by the different intensity of UV-B/A Solar radiation hitting different Earths locations at different times of the year.\n\nOur results suggest that Solar UV-B/A play an important role in planning strategies of confinement of the epidemics, which should be worked out and set up during spring/summer months and fully implemented during low-solar-irradiation periods.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Fabrizio Nicastro", - "author_inst": "INAF - Italian National Institute for Astrophysics" - }, - { - "author_name": "Giorgia Sironi", - "author_inst": "INAF - Italian National Institute for Astrophysics" - }, - { - "author_name": "Elio Antonello", - "author_inst": "INAF - Italian National Institute for Astrophysics" - }, - { - "author_name": "Andrea Bianco", - "author_inst": "INAF - Italian National Institute for Astrophysics" - }, - { - "author_name": "Mara Biasin", - "author_inst": "Department of Biomedical and Clinical Sciences L. Sacco, University of Milano, Milano, Italy" - }, - { - "author_name": "John R Brucato", - "author_inst": "INAF - Italian National Institute for Astrophysics" - }, - { - "author_name": "Ilaria Ermolli", - "author_inst": "INAF - Italian National Institute for Astrophysics" - }, - { - "author_name": "Giovanni Pareschi", - "author_inst": "INAF - Italian National Institute for Astrophysics" - }, - { - "author_name": "Marta Salvati", - "author_inst": "ARPA Lombardia" - }, - { - "author_name": "Paolo Tozzi", - "author_inst": "INAF - Italian National Institute for Astrophysics" - }, - { - "author_name": "Daria Trabattoni", - "author_inst": "Department of Biomedical and Clinical Sciences L. Sacco, University of Milano, Milano, Italy" - }, - { - "author_name": "Mario Clerici", - "author_inst": "Department of Pathophysiology and Transplantation, University of Milano and Don C. Gnocchi Foundation, IRCCS, Milano, Italy" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.03.20121442", "rel_title": "Reduction in preterm births during the COVID-19 lockdown in Ireland: a natural experiment allowing analysis of data from the prior two decades.", @@ -1401879,6 +1404529,69 @@ "type": "new results", "category": "animal behavior and cognition" }, + { + "rel_doi": "10.1101/2020.06.04.20121947", + "rel_title": "Extended use or re-use of single-use surgical masks and filtering facepiece respirators: A rapid evidence review", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20121947", + "rel_abs": "BackgroundThe COVID-19 pandemic has led to unprecedented demand for personal protective equipment. Shortages of surgical masks and filtering facepiece respirators has led to the extended use or re-use of single-use respirators and surgical masks by frontline healthcare workers. The evidence base underpinning such practices has been questioned.\n\nObjectivesTo summarise guidance and synthesise systematic review evidence on extended use, re-use or reprocessing of single-use surgical masks or filtering facepiece respirators.\n\nMethodsA targeted search of the World Health Organization, European Centre for Disease Prevention and Control, the US Centers for Disease Control and Prevention, and Public Health England websites was conducted to identify guidance. Four databases (Medline, Pubmed, Epistemonikos, Cochrane Database of Systematic Reviews) and three preprint repositories (Litcovid, MedRxiv and Open Science Framework) were searched for relevant systematic reviews. Record screening and data extraction was conducted by two reviewers. Quality of included systematic reviews was appraised using the AMSTAR-2 checklist. Findings were integrated and narratively synthesised to highlight the extent to which key claims in guidance documents were supported by research evidence.\n\nResultsSix guidance documents were identified. All note that extended use or re-use of single-use surgical masks and respirators (with or without reprocessing) should be considered only in situations of critical shortage. Extended use was generally favoured over re-use because of reduced risk of contact transmission. Four high-quality systematic reviews were included: three focused on reprocessing (decontamination) of N95 respirators and one focused on reprocessing of surgical masks. There was limited evidence on the impact of extended use on masks and respirators. Vaporised hydrogen peroxide and ultraviolet germicidal irradiation were highlighted as the most promising reprocessing methods, but evidence on the relative efficacy and safety of different methods was limited. We found no well-established methods for reprocessing respirators at scale.\n\nConclusionsThere is limited evidence on the impact of extended use and re-use of surgical masks and respirators. Where extended use or re-use is being practiced, healthcare organisations should ensure that policies and systems are in place to ensure these practices are carried out safely and in line with available guidance.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Elaine Toomey", + "author_inst": "University of Limerick" + }, + { + "author_name": "Yvonne Conway", + "author_inst": "National University of Ireland Galway" + }, + { + "author_name": "Christopher Burton", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Simon Smith", + "author_inst": "Canadian Standards Biological Aerosols Working Group" + }, + { + "author_name": "Michael Smalle", + "author_inst": "National University of Ireland Galway" + }, + { + "author_name": "Xin-Hui Chan", + "author_inst": "University of Oxford" + }, + { + "author_name": "Anil Adisesh", + "author_inst": "Unity Health Toronto" + }, + { + "author_name": "Sarah Tanveer", + "author_inst": "University of Maryland" + }, + { + "author_name": "Lawrence Ross", + "author_inst": "Children's Hospital of Los Angeles" + }, + { + "author_name": "Iain Thomson", + "author_inst": "Medecins Sans Frontieres/Doctors without Borders" + }, + { + "author_name": "Declan Devane", + "author_inst": "National University of Ireland Galway" + }, + { + "author_name": "Trish Greenhalgh", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.06.04.20122069", "rel_title": "Mechanical ventilation utilization in COVID-19: A systematic review and meta-analysis", @@ -1403469,61 +1406182,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.04.20122044", - "rel_title": "ACE2 levels are altered in comorbidities linked to severe outcome in COVID-19", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122044", - "rel_abs": "AimsSeverity of outcome in COVID-19 is disproportionately higher among the obese, males, smokers, those suffering from hypertension, kidney disease, coronary heart disease (CHD) and/or type 2 diabetes (T2D). We examined if serum levels of ACE2, the cellular entry point for the coronavirus SARS-CoV-2, were altered in these high-risk groups.\n\nMethodsAssociations of serum ACE2 levels to hypertension, T2D, obesity, CHD, smokers and males in a single center population-based study of 5457 Icelanders from the Age, Gene/Environment Susceptibility Reykjavik Study (AGES-RS) of the elderly (mean age 75{+/-}6 years).\n\nResultsSmokers, males, and individuals with T2D or obesity have altered serum levels of ACE2 that may influence productive infection of SARS-CoV-2 in these high-risk groups.\n\nConclusionACE2 levels are upregulated in some patient groups with comorbidities linked to COVID-19 and as such may have an emerging role as outcome in COVID-19. a circulating biomarker for severity of severity of outcome in COVID-19.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSSeverity of outcome in COVID-19 is disproportionately higher among the obese, males, smokers, those suffering from hypertension, kidney disease, coronary heart disease (CHD) and/or type 2 diabetes (T2D). Thus, we asked if the coronavirus SARS-CoV-2 receptor ACE2 was altered in the sera from these high-risk groups?\n\nFindingsIn a single center population-based study of 5457 Icelanders, the Age, Gene/Environment Susceptibility Reykjavik Study (AGES-RS), we find that ACE2 levels are significantly elevated in serum from smokers, obese and diabetic individuals, while reduced in males.\n\nMeaningThese results demonstrate that individuals with comorbidities associated with infection of SARS-CoV-2 in these individuals. severe outcome in COVID-19 have altered serum levels of ACE2 that may influence productive", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Valur Emilsson", - "author_inst": "Icelandic Heart Association" - }, - { - "author_name": "Elias F Gudmundsson", - "author_inst": "Icelandic Heart Association" - }, - { - "author_name": "Thor Aspelund", - "author_inst": "Icelandic Heart Association" - }, - { - "author_name": "Brynjolfur G Jonsson", - "author_inst": "Icelandic Heart Association" - }, - { - "author_name": "Alexander Gudjonsson", - "author_inst": "Icelandic Heart Association" - }, - { - "author_name": "Lenore J Launer", - "author_inst": "Laboratory of Epidemiology and Population Sciences, Intramural Research Program, National Institute on Aging, Bethesda, MD 20892-9205, USA" - }, - { - "author_name": "John R Lamb", - "author_inst": "GNF Novartis, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA" - }, - { - "author_name": "Valborg Gudmundsdottir", - "author_inst": "Icelandic Heart Association" - }, - { - "author_name": "Lori L Jennings", - "author_inst": "Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA 02139, USA" - }, - { - "author_name": "Vilmundur Gudnason", - "author_inst": "Icelandic Heart Association" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.06.04.20122176", "rel_title": "What variables can better predict the number of infections and deaths worldwide by SARS-CoV-2? Variation through time", @@ -1403660,6 +1406318,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.04.20122473", + "rel_title": "FAST: a Feasible, Accurate and Speedy Test Strategy for COVID-19", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122473", + "rel_abs": "Early detection of COVID-19 is critical in mitigating the spread of the virus. Commonly used tests include nucleic acid detection, antibodies detection via blood testing and CT imaging. Some tests are accurate but time-consuming, while others are cheaper but less accurate. Exactly which test to use is constrained by various considerations, such as availability, cost, accuracy and efficiency. In this paper, we propose a Flexible, Efficient and Accurate Test (FEAT). FEAT is based on group testing with simple but careful design by incorporating ideas such as close contact cliques and repeated tests. FEAT could dramatically improve the efficiency and/or accuracy for any existing test. For example, for accurate but slow test such as RT-PCR, FEAT can improve efficiency by multiple times without compromising accuracy. On the other hand, for fast but inaccurate tests, FEAT can sharply lower the false negative rates (FNR) and greatly increase efficiency. Theoretical justifications are provided. We point out some scenarios where the FEAT can be effectively employed.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Linjiajie Fang", + "author_inst": "Hong Kong University of Science and Technology" + }, + { + "author_name": "Shen Ling", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Bing-Yi Jing", + "author_inst": "Hong Kong University of Science and Technology" + }, + { + "author_name": "Qing Yang", + "author_inst": "Hong Kong University of Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.04.20122267", "rel_title": "Anemia and iron metabolism in COVID-19: A systematic review and meta-analysis", @@ -1405031,73 +1407720,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.06.02.20120808", - "rel_title": "The Relationship Between COVID-19 Infection and Risk Perception, Knowledge, Attitude As Well As Four Non-pharmaceutical Interventions (NPIs) During the Late Period Of The COVID-19 Epidemic In China An Online Cross-sectional Survey of 8158 Adults", - "rel_date": "2020-06-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20120808", - "rel_abs": "BackgroundSo far, there has been no published population study on the relationship between COVID-19 infection and publics risk perception, information source, knowledge, attitude and four non-pharmaceutical interventions(NPI: hand washing, proper coughing habits, social distancing and mask wearing) during the COVID-19 outbreak in China.\n\nMethodsAn online survey of 8158 Chinese adults between 22 February to 5 March 2020 was conducted. Bivariate associations between categorical variables were examined using Fisher exact test. We also explored the determinants of four NPIs as well as their association with COVID-19 infection using logistic regression.\n\nResultsOf 8158 adults included, 57 (0.73%) were infected with COVID-19. The overwhelming majority of respondents showed a positive attitude (99.2%), positive risk perception (99.9%) and high knowledge levels that were among the strongest predictors of four highly adopted NPIs (hand washing:96.8%; proper coughing: 93.1%; social distancing:87.1%; mask wearing:97.9%). There was an increased risk of COVID-19 infection for those who not washing hands (2.28% vs 0.65%; RR=3.53: 95%CI: 1.53-8.15; P<0.009); not practicing proper coughing (1.79% vs 0.73%; RR=2.44: 95%CI: 1.15-5.15;P=0.026); not practicing social distancing (1.52% vs 0.58%; RR=2.63:95%CI:1.48 - 4.67; P=0.002); and not wearing a mask (7.41% vs 0.6%; RR=12.38:95%CI:5.81-26.36; P<0.001). For those who did practice all other three NPIs, wearing mask was associated with significantly reduced risk of infection compared to those who did not wear a mask (0.6% vs 16.7%; p=0.035). Similarly, for those who did not practice all or part of the other three NPIs, wearing mask was also associated with significantly reduced risk of infection. In a penalised logistic regression model including all four NPIs, wearing a mask was the only significant predictor of COVID-19 infection among four NPIs (OR=7.20; 95%CI:2.24-23.11; p<0.001).\n\nConclusionsWe found high levels of risk perception, positive attitude, desirable knowledge as well as a high level of adopting four NPIs. The relevant knowledge, risk perception and attitude were strong predictors of adapting the four NPIs. Mask wearing, among four personal NPIs, was the most effective protective measure against COVID-19 infection with added preventive effect among those who practised all or part of the other three NPIs.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Hong Xu", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China" - }, - { - "author_name": "Yong Gan", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China" - }, - { - "author_name": "Daikun Zheng", - "author_inst": "Chongqing Three Gorges Medical College, Chongqing, China" - }, - { - "author_name": "Bo Wu", - "author_inst": "Wanzhou District Center for Disease Control and Prevention, Chongqing, China" - }, - { - "author_name": "Xian Zhu", - "author_inst": "School of Public Health and Management, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Chang Xu", - "author_inst": "School of Public Health and Management, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Chenglu Liu", - "author_inst": "School of Public Health and Management, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Zhou Tao", - "author_inst": "School of Public Health and Management, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Yaoyue Hu", - "author_inst": "School of Public Health and Management, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Min Chen", - "author_inst": "School of Public Health and Management, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Mingjiang Li", - "author_inst": "School of Public Health and Management, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Zuxun Lu", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China" - }, - { - "author_name": "Jack Chen", - "author_inst": "University of New South Wales" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.06.02.20120014", "rel_title": "Viral load dynamics in transmissible symptomatic patients with COVID-19", @@ -1405454,6 +1408076,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.02.20120865", + "rel_title": "Decreased plasma levels of the survival factor renalase are associated with worse outcomes in COVID-19", + "rel_date": "2020-06-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20120865", + "rel_abs": "IntroductionRenalase (RNLS), a novel secreted plasma flavoprotein, has anti-inflammatory effects in a variety of disease processes. Severe COVID-19 disease is associated with disordered inflammatory responses. We hypothesized that reduced plasma RNLS levels could be a marker of COVID-19 disease severity.\n\nMethodsPlasma was collected from 51 hospitalized COVID-19 patients and 15 uninfected non-hospitalized controls. Plasma RNLS and cytokine levels were measured and sociodemographic and clinical data were collected from chart review. Data were analyzed using nonparametric analyses and Kaplan Meir curve log rank analysis.\n\nResultsPlasma RNLs levels were negatively correlated with inflammatory markers, including IL-1{beta}, IL-6, and TNF (p = 0.04, p = 0.03, p = 0.01, respectively). Patients with COVID-19 disease had lower levels of RNLS than controls. Lower levels of RNLS were associated with more severe disease among COVID-19 patients. Low RNLS was also associated with worse survival among COVID-19 patients (HR = 4.54; 95% CI: 1.06-19.43; p = 0.005).\n\nConclusionLow plasma RNLS levels are associated with severe COVID-19 disease and may be a useful additional biomarker when identifying patients with severe COVID-19 disease. Given RNLS antiinflammatory properties and negative correlation with inflammatory markers, these findings also suggest evidence of a potential pathophysiological mechanism for severe COVID-19 disease.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Melinda Wang", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Xiaojia Guo", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Hyung J Chun", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Alfred Ian Lee", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Charles Cha", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Fred Gorelick", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Gary V Desir", + "author_inst": "Yale University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.03.20120881", "rel_title": "A prediction model based on machine learning for diagnosing the early COVID-19 patients", @@ -1406433,25 +1409098,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.31.20118760", - "rel_title": "Model Based Covid-19 Case Studies in the UK, the USA and India", - "rel_date": "2020-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.31.20118760", - "rel_abs": "Time dependent spread of Covid-19 among the population of the UK, the USA and India is analyzed using a recently developed mathematical model [1-3]. Results of model predictions of case growth in these countries during the next six weeks are also presented. The model is applicable to case studies and near term predictions for other countries and regions.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Santanu Basu", - "author_inst": "Sparkle Optics Corporation" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.31.20118455", "rel_title": "Hospital readmissions of discharged patients with COVID-19", @@ -1406720,6 +1409366,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.30.20117770", + "rel_title": "COVID-19 apparent reproductive number dropped during Spain's nationwide dropdown, then spiked at lower-incidence regions", + "rel_date": "2020-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20117770", + "rel_abs": "COVID-19 pandemic has rapidly spread worldwide. Spain has suffered one of the largest nationwide bursts, particularly in the highly populated areas of Madrid and Barcelona (two of the five largest conurbations in Europe). We used segmented regression analyses to identify shifts in the evolution of the apparent reproductive number (Rt) reported for 16 Spanish administrative regions. We associate these breaking points with a timeline of key containment measures taken by national and regional governments, applying time lags for the time from contagion to case detection, with their associated errors. Results show an early decrease of Rt that preceded the nationwide lockdown; a generalized, sharp decrease in Rt associated with such lockdown; a low impact of the strengthened lockdown, with a flattening of Rt evolution in high-incidence regions regions - but increases in Rt at low-incidence regions; and an increase in Rt, associated to the relaxation of the lockdown measures, in ten regions. These results evidence the importance of generalized lockdown measures to contain COVID-19 spread; and the limited effect of the subsequent application of a stricter lockdown (restrictions to all non-essential economic activities). Most importantly, they highlight the importance of maintaining strong social distancing measures and strengthening public health control during lockdown de-escalation.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Luis Santamaria", + "author_inst": "Donana Biological Station (EBD-CSIC)" + }, + { + "author_name": "Joaquin Hortal", + "author_inst": "Museo Nacional de Ciencias Naturales (MNCN-CSIC)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.30.20117556", "rel_title": "SIR-PID: A Proportional-Integral-Derivative Controller for COVID-19 Outbreak Containment", @@ -1407759,49 +1410428,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.30.20117283", - "rel_title": "Spreading of COVID-19 in Brazil: Impacts and uncertainties in social distancing strategies", - "rel_date": "2020-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20117283", - "rel_abs": "Brazils continental dimension poses a challenge to the control of the spread of COVID-19. Due to the country specific scenario of high social and demographic heterogeneity, combined with limited testing capacity, lack of reliable data, under-reporting of cases, and restricted testing policy, the focus of this study is twofold: (i) to develop a generalized SEIRD model that implicitly takes into account the quarantine measures, and (ii) to estimate the response of the COVID-19 spread dynamics to perturbations/uncertainties. By investigating the projections of cumulative numbers of confirmed and death cases, as well as the effective reproduction number, we show that the model parameter related to social distancing measures is one of the most influential along all stages of the disease spread and the most influential after the infection peak. Due to such importance in the outcomes, different relaxation strategies of social distancing measures are investigated in order to determine which strategies are viable and less hazardous to the population. The results highlight the need of keeping social distancing policies to control the disease spread. Specifically, the considered scenario of abrupt social distancing relaxation implemented after the occurrence of the peak of positively diagnosed cases can prolong the epidemic, with a significant increase of the projected numbers of confirmed and death cases. An even worse scenario could occur if the quarantine relaxation policy is implemented before evidence of the epidemiological control, indicating the importance of the proper choice of when to start relaxing social distancing measures.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Diego Tavares Volpatto", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Anna Claudia Mello Resende", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Lucas Anjos", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Joao Vitor Oliveira Silva", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Claudia Mazza Dias", - "author_inst": "Universidade Federal Rural do Rio de Janeiro" - }, - { - "author_name": "Regina Cerqueira Almeida", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Sandra Mara Cardoso Malta", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.28.122671", "rel_title": "Optimized pseudotyping conditions for the SARS-COV2 Spike glycoprotein", @@ -1407966,6 +1410592,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.06.01.20118869", + "rel_title": "It's the very time to learn a pandemic lesson: why have predictive techniques been ineffective when describing long-term events?", + "rel_date": "2020-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20118869", + "rel_abs": "We have detected a regular component of the monitoring error of officially registered total cases of the spread of the current pandemic. This regular error component explains the reason for the failure of a priori mathematical modelling of probable epidemic events in different countries of the world. Processing statistical data of countries that have reached an epidemic peak has shown that this regular monitoring obeys a simple analytical regularity which allows us to answer the question: is this or that country that has already passed the threshold of the epidemic close to its peak or is still far from it?", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Svetlana Nikitenkova", + "author_inst": "Lobachevsky Nizhny Novgorod State University" + }, + { + "author_name": "Dmitry Anatolyevich Kovriguine", + "author_inst": "Nizhny-Novgorod Technical State University n.a. R.E. Alekseev" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.06.01.20119123", "rel_title": "Testing for tracing or testing just for treating? A comparative analysis between strategies to face COVID-19 pandemic.", @@ -1408981,33 +1411630,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.01.20119172", - "rel_title": "SCALE19: A scalable and cost-efficient method for testing Covid-19 based on hierarchical group testing", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20119172", - "rel_abs": "Containment of Covid-19 requires an extensive testing of the affected population. Some propose global testing to effectively contain Covid-19. Current tests for Covid-19 are administered individually. These tests for Covid-19 are expensive and are limited due to the lack of resources and time. We propose a simple and efficient group testing method for Covid-19. We propose a group testing method where test subjects are grouped and tested. Depending on the result of the group test, subsequent sub groups are formed and tested recursively based on a quartery search algorithm. We designed and built an evaluation model that simulates test subject population, infected test subjects according to available Covid-19 statistics, and the group testing processes in SCALE19. We considered several population models including USA and the world. Our results show that we can significantly reduce the required number of tests up to 89% without sacrificing the accuracy of the individual test of the entire population. For USA, up to 280 million tests can be reduced from the total US population of 331 million and it would be equivalent saving of $28 billion assuming a cost of $100 per test. For the world, 6.96 billion tests can be reduced from the total population of 7.8 billion and it would be equivalent to saving $696 billion. We propose SCALE19 can significantly reduce the total required number of tests compared to individual tests of the entire population. We believe SCALE19 is efficient and simple to be deployed in containment of Covid-19.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jeremie S Kim", - "author_inst": "Carnegie Mellon University" - }, - { - "author_name": "Justine S Kim", - "author_inst": "UPMC" - }, - { - "author_name": "Hyong Kim", - "author_inst": "Carnegie Mellon Unviersity" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.25.20112623", "rel_title": "Serological surveys in Reunion Island of the first hospitalized patients revealed that long-lived immunoglobulin G antibodies specific against SARS-CoV2 virus are rapidly vanishing in severe cases", @@ -1409204,6 +1411826,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.30.20111393", + "rel_title": "Antibody profiling of COVID-19 patients in an urban low-incidence region in Northern Germany", + "rel_date": "2020-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20111393", + "rel_abs": "This explorative monocentric study shows IgA and IgG antibody profiles from 110 patients with self-reported mild to moderate, or no COVID-19 related symptoms after laboratory-confirmed infection with SARS-CoV-2. The study region is in an urban and well-defined environment in a low-incidence region in Northern Germany. We found that approx. 70 % of the patients developed sustainable antibodies 3 weeks or later after the infection. In about 30 % of the patients with mild to moderate symptoms, no significant antibodies could be detected in two consecutive analyses. Conversely, out of ten patients without symptoms, four were repeatedly positive. Expectedly, six had no specific antibodies. The data indicate that antibody-positivity is a useful indicator of a previous SARS-CoV-2 infection. Negative antibodies do not rule out SARS-CoV-2 infection. Future studies need to determine the functionality of the antibodies in terms of personal protection and ability to transmit the virus.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Werner Solbach", + "author_inst": "University of Luebeck, Center for Infection and Inflammation Research, Luebeck, Germany; Health Protection Authority, City of Luebeck, Luebeck, Germany" + }, + { + "author_name": "Julia Schiffner", + "author_inst": "Health Protection Authority, City of Luebeck, Luebeck, Germany" + }, + { + "author_name": "Insa Backhaus", + "author_inst": "Health Protection Authority, City of Luebeck, Luebeck, Germany; Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy" + }, + { + "author_name": "David Burger", + "author_inst": "Municipal Statistics Department, City of Luebeck, Luebeck, Germany" + }, + { + "author_name": "Ralf Staiger", + "author_inst": "Gemeinschaftspraxis Huextertor, Luebeck, Germany" + }, + { + "author_name": "Bettina Tiemer", + "author_inst": "Laboraerztliche Gemeinschaftspraxis Luebeck, Luebeck, Germany" + }, + { + "author_name": "Andreas Bobrowski", + "author_inst": "Laboraerztliche Gemeinschaftspraxis Luebeck, Luebeck, Germany" + }, + { + "author_name": "Timothy Hutchings", + "author_inst": "Municipal Statistics Department, City of Luebeck, Luebeck, Germany" + }, + { + "author_name": "Alexander Mischnik", + "author_inst": "Health Protection Authority, City of Luebeck, Luebeck, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.28.20110767", "rel_title": "The prevalence of antibodies to SARS-CoV-2 in asymptomatic healthcare workers with intensive exposure to COVID-19", @@ -1410651,25 +1413324,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.26.20113399", - "rel_title": "COVID-19 Trend and Forecast in India: A Joinpoint Regression Analysis", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20113399", - "rel_abs": "This paper analyses the trend in daily reported confirmed cases of COVID-19 in India using joinpoint regression analysis. The analysis reveals that there has been little impact of the nation-wide lockdown and subsequent extension on the progress of the COVID-19 pandemic in the country and there is no empirical evidence to suggest that relaxations under the third and the fourth phase of the lockdown have resulted in a spike in the reported confirmed cases. The analysis also suggests that if the current trend continues, in the immediate future, then the daily reported confirmed cases of COVID-19 in the country is likely to increase to 21 thousand by 15 June 2020 whereas the total number of confirmed cases of COVID-19 will increase to around 422 thousand. The analysis calls for a population-wide testing approach to check the increase in the reported confirmed cases of COVID-19.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Aalok Ranjan Chaurasia", - "author_inst": "MLC Foundation" - } - ], - "version": "1", - "license": "cc0_ng", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.05.27.20114512", "rel_title": "Diagnostic accuracy of a host response point-of-care test for identifying COVID-19", @@ -1410914,6 +1413568,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.01.20119602", + "rel_title": "High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay", + "rel_date": "2020-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20119602", + "rel_abs": "ObjectiveSerological testing is needed to investigate the extent of transmission of SARS-CoV-2 from front-line essential workers to their household members. However, the requirement for serum/plasma limits serological testing to clinical settings where it is feasible to collect and process venous blood. To address this problem we developed a serological test for SARS-CoV-2 IgG antibodies that requires only a single drop of finger stick capillary whole blood, collected in the home and dried on filter paper (dried blood spot, DBS).\n\nMethodsAn ELISA to the receptor binding domain of the SARS-CoV-2 spike protein was optimized to quantify IgG antibodies in DBS. Samples were self-collected from a community sample of 232 participants enriched with health care workers, including 30 known COVID-19 cases and their household members.\n\nResultsAmong 30 individuals sharing a household with a virus-confirmed case of COVID-19, 80% were seropositive. Of 202 community individuals without prior confirmed acute COVID-19 diagnoses, 36% were seropositive. Of documented convalescent COVID-19 cases from the community, 29 of 30 (97%) were seropositive for IgG antibodies to the receptor binding domain.\n\nConclusionDBS ELISA provides a minimally-invasive alternative to venous blood collection. Early analysis suggests a high rate of transmission among household members. High rates of seroconversion were also noted following recovery from infection. Serological testing for SARSCoV-2 IgG antibodies in DBS samples can facilitate seroprevalence assessment in community settings to address epidemiological questions, monitor duration of antibody responses, and assess if antibodies against the spike protein correlate with protection from reinfection.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Thomas W McDade", + "author_inst": "Northwestern University" + }, + { + "author_name": "Elizabeth McNally", + "author_inst": "Northwestern University" + }, + { + "author_name": "Aaron Zelikovich", + "author_inst": "Northwestern University" + }, + { + "author_name": "Richard D'Aquila", + "author_inst": "Northwestern University" + }, + { + "author_name": "Brian Mustanski", + "author_inst": "Northwestern University" + }, + { + "author_name": "Aaron Miller", + "author_inst": "Northwestern University" + }, + { + "author_name": "Lauren Vaught", + "author_inst": "Northwestern University" + }, + { + "author_name": "Nina Reiser", + "author_inst": "Northwestern University" + }, + { + "author_name": "Elena Bogdanovic", + "author_inst": "Northwestern University" + }, + { + "author_name": "Katherine Fallon", + "author_inst": "Northwestern University" + }, + { + "author_name": "Alexis Demonbreun", + "author_inst": "Northwestern University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.02.20119875", "rel_title": "Rapid and accurate detection of novel coronavirus SARS-CoV-2 using CRISPR-Cas3", @@ -1412765,29 +1415478,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.28.20115063", - "rel_title": "The Risk of Lifting COVID-19 Confinement in Mexico", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115063", - "rel_abs": "The novel coronavirus SARS-CoV-2 has paralysed our societies, leading to self isolation and quarantine for several days. As the 10th most populated country in the world, Mexico is on a major threat by COVID-19 due to the limitations of intensive care capacities, and a total of about 1.5 hospital beds for every 1000 citizens. In this paper, we projected different scenarios to evaluate sharp or gradual quarantine lifting strategies, however, even in the hypothetical scenario that Mexico would continue with full confinement, hospitals would be reaching the maximum capacity of hospital bed occupancy. Mexican government is planning to relax the strict social distancing regulations on 1 June 2020, however, epidemic rebound risks are latent.\n\nOur results suggest that lifting social confinement needs to be gradually sparse while maintaining a decentralized region strategy among the Mexican states. To substantially lower the number of infections, predictions highlight that the elderly should remain in social confinement (approximately 11.3% of the population); the confined working class (roughly 27% of the population) must gradually return in at least four parts in consecutive months; and to the last the return of students to schools (about 21.7%). As the epidemic progresses, de-confinement strategies need to be continuously re-adjusting with the new pandemic data. Assuming the most optimistic scenario by our predictions, the smallest number of new COVID-19 cases, Mexico would require at least a 3 fold increase in hospital capacities dedicated for COVID-19. Furthermore, to observe the real dimension of the epidemic, Mexico would need to increase to at least 18 samples per 1000 people, currently is only 0.6 per 1000.\n\nAll mathematical models, including ours, are only a possibility of many of the future, however, the different scenarios that were developed here highlight that a gradual decentralized region de-confinement with a significant increase in healthcare capacities is paramount to avoid a high death toll in Mexico.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Cristy Leonor Azanza Ricardo", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Esteban Abelardo Hernandez Vargas", - "author_inst": "Frankfurt Institute for Advanced Studies" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.28.20116046", "rel_title": "Immunochromatographic assays for COVID-19 epidemiological screening: our experience", @@ -1413044,6 +1415734,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.05.28.20116152", + "rel_title": "Early CPAP reduced mortality in covid-19 patients. Audit results from Wrightington, Wigan and Leigh Teaching Hospitals NHS Foundation Trust.", + "rel_date": "2020-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20116152", + "rel_abs": "COVID-19 infection typically causes pneumonia with bilateral changes on Chest radiograph. There is significant hypoxia and use of oxygen for patients admitted to hospital is standard. The use of Continuous Positive Airway Pressure (CPAP) in patients with COVID-19 has now become established as a common clinical practice based on recent experience. It is given as part of \"best endeavours\" treatment in the absence of sufficient evidence to guide best practice. The use of CPAP as a step up in clinical care is now common but has a poor evidence base.\n\nUsing routinely collected data, the use of CPAP as a supportive non-invasive ventilatory treatment is described in 35 patients with COVID infection. Patients given early CPAP and in particular within 48 hours of admission, are shown to have a better outcome (a significant probability of lower mortality) than patients who received late CPAP (more than 48 hours after admission).\n\nAlthough the analysis is affected by a small sample size, the results have shown good evidence that supports the early use of CPAP in patients with COVID-19 infection.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Abdul Ashish", + "author_inst": "Wrightington Wigan and Leigh NHS Teaching Hospitals Foundation Trust" + }, + { + "author_name": "Alison Unsworth", + "author_inst": "Wrightington Wigan and Leigh NHS Teaching Hospitals Foundation Trust" + }, + { + "author_name": "Jane Martindale", + "author_inst": "Wrightington Wigan and Leigh NHS Teaching Hospitals Foundation Trust" + }, + { + "author_name": "Ramachandran Sundar", + "author_inst": "Wrightington Wigan and Leigh NHS Teaching Hospitals Foundation Trust" + }, + { + "author_name": "Luigi Sedda", + "author_inst": "Lancaster University" + }, + { + "author_name": "Martin Farrier", + "author_inst": "Wrightington Wigan and Leigh NHS Trust" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.05.28.20116194", "rel_title": "Estimated Sp02/Fio2 ratio to predict mortality in patients with suspected COVID-19 in the Emergency Department: a prospective cohort study", @@ -1414419,37 +1417148,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.05.31.20118802", - "rel_title": "The Association Between Angiotensin-Converting Enzyme Inhibitors and Angiotensin Receptor Blockers and the Number of Covid-19 Confirmed Cases and Deaths in the United States: Geospatial Study", - "rel_date": "2020-06-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.31.20118802", - "rel_abs": "BackgroundThe novel coronavirus SARS-Cov2 uses the angiotensin-converting enzyme 2 (ACE2) receptor as an entry point to the cell. Cardiovascular disease (CVD) is a risk factor for the novel coronavirus disease (Covid-19) with poor outcomes. We hypothesized that the rate of ACE inhibitor (ACEI) and angiotensin receptor blocker (ARB) use is associated with the rate of Covid-19 confirmed cases and deaths.\n\nMethodsWe conducted a geospatial study using publicly available county-level data. The Medicare ACEI and ARB prescription rate was exposure. The Covid-19 confirmed case and death rates were outcomes. Spatial autoregression models were adjusted for the percentage of Black residents, children, residents with at least some college degree, median household income, air quality index, CVD hospitalization rate in Medicare beneficiaries, and CVD death rate in a total county population.\n\nFindingsAfter adjustment for confounders, the ACEI use rate did not associate with Covid-19 confirmed case rate (direct county-own effect +0.11 %; 95%CI -0.31 to 0.53; P=0.600, and indirect spillover effect -0.53 %; 95%CI -3.89 to 2.84; P=0.760). The ARB use rate was associated with increased Covid-19 confirmed case rate (direct county-owned effect +0.12 %; 95%CI 0.05-0.19; P=0.002, and indirect spillover effect -0.33 %; 95%CI -2.11 to 1.44; P=0.714). Sensitivity analysis indicated an absence of significant reverse causality bias for analyses with Covid-19 confirmed case rate, but not death rate outcome.\n\nInterpretationOur results highlight the safety of ACEI use for patients with clinical indications for ACEI use. However, an increase in ARB use by 1% was associated with a 0.12 % increase in Covid-19 confirmed cases. The use of ARB, due to known ACE2 upregulation, may facilitate SARS-CoV-2 entry into target cells and increase infectivity. Cluster-randomized controlled trial is warranted to answer the question of whether the replacement of ARB by ACEI may reduce the Covid-19 confirmed case rate.\n\nFundingLGT was supported in part by the National Institute of Health (HL118277).", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Kyle Johnson", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Maedeh Khayyat-Kholghi", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Blake Johnson", - "author_inst": "Flexport, San Francisco, CA" - }, - { - "author_name": "Larisa G Tereshchenko", - "author_inst": "Oregon Health & Science University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.05.31.20118695", "rel_title": "ON THE UNCERTAINTY ABOUT HERD IMMUNITY LEVELS REQUIRED TO STOP COVID-19 EPIDEMICS", @@ -1414594,6 +1417292,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.29.20102913", + "rel_title": "The Neutrophil Lymphocyte Ratio (NLR), Platelet Lymphocyte Ratio (PLR) and routine hematological parameters of COVID-19 Patient : A perspective of the Indian scenario from a frontline pilot study of 32 COVID-19 cases in a Tertiary Care Institute of North India", + "rel_date": "2020-06-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20102913", + "rel_abs": "IntroductionThe corona virus disease 2019(COVID-19) is caused by the virus SARS-CoV-2 and is declared as a global pandemic by World Health Organization (WHO). Various hematological parameters alteration has been documented in the Chinese literature in SARS-Cov-2 infection. However, there is a need for research to evaluate the pattern of the hematological parameters of COVID-19 patients in the Indian population.\n\nAims & ObjectivesThe objective of the study is to see the Neutrophil-Lymphocyte Ratio (NLR), Platelet Lymphocyte Ratio (PLR), and other hematological parameters alteration of COVID-19 patients along with their clinical course in the Indian scenario.\n\nMethodsA single-center prospective study of 32 patients with laboratory-confirmed COVID-19 admitted to Super Speciality Pediatric Hospital & Post Graduate Teaching Institute NOIDA, from March to April, were enrolled for the study. The demographic date, the clinical status of the patients during admission and follow up, baseline, and follow up hematological findings were recorded. Statistical analysis of the data was carried out, and relevant findings were presented.\n\nResultsDemographic characterization shows a mean age of 37.7 years, male (41.9%),female (58.1%)with majority patients are mildly symptomatic to asymptomatic(93%). The CBC values and NLR, PLR at baseline between the male and the female patients, are not showing any statistically significant difference as the 95% C.I. A statistically significant increment in the lab parameters is observed in follow-up visits.\n\nConclusionMajority of the patients are younger and have mild clinical presentation with female predominance. Pediatric cases have mild symptomology. Baseline CBC findings show mild neutrophilia, lymphopenia, eosinopenia and normal to mild thrombocytopenia. An increase in CBC parameters, NLR was noted in follow up cases. Anemia was not noted in baseline CBC and in follow up group. A onetime PLR is not indicative of disease progression.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Neema Tiwari", + "author_inst": "Super Speciality Pediatric Hospital and Post graduate Teaching Institute,NOIDA,India" + }, + { + "author_name": "Devajit Nath", + "author_inst": "Super Speciality Pediatric Hospital and Post Graduate Teaching Institute,NOIDA,India" + }, + { + "author_name": "Jyotsna Madan", + "author_inst": "Super Speciality Pediatric Hospital and Post Graduate Teaching Institute,NOIDA,India" + }, + { + "author_name": "Savitri Singh", + "author_inst": "Super Speciality Pediatric Hospital and Post Graduate Teaching Institute,NOIDA,India" + }, + { + "author_name": "Prashant Bajpai", + "author_inst": "University of Lucknow,Dept. of Biostatistics,Lucknow,India" + }, + { + "author_name": "Ujjwal Madan", + "author_inst": "University College of Medical Sciences,New-Delhi,India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.05.26.20102889", "rel_title": "Evaluation of COVID 19 infection in 279 cancer patients treated during a 90-day period in 2020 pandemic", @@ -1415732,73 +1418469,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.28.20115527", - "rel_title": "Analyzing Covid-19 Data using SIRD Models", - "rel_date": "2020-05-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115527", - "rel_abs": "The goal of this analysis is to estimate the effects of the diverse government intervention measures implemented to mitigate the spread of the Covid-19 epidemic. We use a process model based on a compartmental epidemiological framework Susceptible-Infected-Recovered-Dead (SIRD). Analysis of case data with such a mechanism-based model has advantages over purely phenomenological approaches because the parameters of the SIRD model can be calibrated using prior knowledge. This approach can be used to investigate how governmental interventions have affected the Covid-19-related transmission and mortality rate during the epidemic.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Abhijit Chakraborty", - "author_inst": "Complexity Science Hub Vienna, Josefstaedter Strasse 39, 1080 Vienna, Austria" - }, - { - "author_name": "Jiaying Chen", - "author_inst": "Section for Science of Complex Systems, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, 1090, Vienna, Austria" - }, - { - "author_name": "Amelie Desvars-Larrive", - "author_inst": "University of Veterinary Medicine Vienna" - }, - { - "author_name": "Peter Klimek", - "author_inst": "Section for Science of Complex Systems, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, 1090, Vienna, Austria" - }, - { - "author_name": "Erwin Flores Tames", - "author_inst": "Complexity Science Hub Vienna, Josefstaedter Strasse 39, 1080 Vienna, Austria" - }, - { - "author_name": "David Garcia", - "author_inst": "Section for Science of Complex Systems, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, 1090, Vienna, Austria" - }, - { - "author_name": "Leonhard Horstmeyer", - "author_inst": "Complexity Science Hub Vienna, Josefstaedter Strasse 39, 1080 Vienna, Austria" - }, - { - "author_name": "Michaela Kaleta", - "author_inst": "Section for Science of Complex Systems, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, 1090, Vienna, Austria" - }, - { - "author_name": "Jana Lasser", - "author_inst": "Complexity Science Hub Vienna, Josefstaedter Strasse 39, 1080 Vienna, Austria" - }, - { - "author_name": "Jenny Reddish", - "author_inst": "Complexity Science Hub Vienna, Josefstaedter Strasse 39, 1080 Vienna, Austria" - }, - { - "author_name": "Beate Pinior", - "author_inst": "Unit of Veterinary Public Health and Epidemiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, 12" - }, - { - "author_name": "Johannes Wachs", - "author_inst": "Vienna University of Economics and Business, Institute for Information Business. Welthandelsplatz 1, Vienna 1020, Austria" - }, - { - "author_name": "Peter Turchin", - "author_inst": "Complexity Science Hub Vienna, Josefstaedter Strasse 39, 1080 Vienna, Austria" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.29.124610", "rel_title": "COVID-3D: An online resource to explore the structural distribution of genetic variation in SARS-CoV-2 and its implication on therapeutic development", @@ -1416003,6 +1418673,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.05.29.124776", + "rel_title": "Validation and Performance Comparison of Three SARS-CoV-2 Antibody Assays", + "rel_date": "2020-05-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.29.124776", + "rel_abs": "Serology testing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly being used during the current pandemic of Coronavirus Disease 2019 (COVID-19). The clinical and epidemiologic utilities of antibody-based SARS-CoV-2 testing are under debate. Characterizing these assays helps to understand the disease and provides scientific basis for deciding how to best use these assays. The study assessed one chemiluminescent assay (Abbott COVID-2 IgG) and two lateral flow assays (STANDARD Q [SQ] IgM/IgG Duo and Wondfo Total Antibody Test). Validation included 113 blood samples from 71 PCR-confirmed COVID-19 patients and 1182 samples from negative controls with potential interferences/cross-reactions, including 1063 pre-pandemic samples. IgM antibodies against SARS-CoV-2 were detected as early as post-symptom onset days 3-4. IgG antibodies were first detected post-onset days 5-6 by SQ assays. The detection rates increased gradually, and SQ IgG, Abbott IgG and Wondfo Total detected antibodies from all the PCR-confirmed patients 14 days after symptom onset. Overall agreements between SQ IgM/IgG and Wondfo Total was 88.5% and between SQ IgG and Abbott IgG was 94.6% (Kappa = 0.75, 0.89). No cross-reaction with other endemic coronavirus infections were identified. Viral hepatitis and autoimmune samples were the main cross-reactions observed. However, the interferences/cross-reactions were low. The specificities were 100% for SQ IgG and Wondfo Total and 99.62% for Abbott IgG and 98.87% for SQ IgM. These findings demonstrate high sensitivity and specificity of appropriately validated antibody-based SARS-CoV-2 assays with implications for clinical use and epidemiological seroprevalence studies.View Full Text", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Shaolei Lu", + "author_inst": "Brown University" + }, + { + "author_name": "Kimberly J Paiva", + "author_inst": "Brown University" + }, + { + "author_name": "Ricky D Grisson", + "author_inst": "Brown University" + }, + { + "author_name": "Philip A Chan", + "author_inst": "Rhode Island Department of Health" + }, + { + "author_name": "John Lonks", + "author_inst": "The Miriam Hospital" + }, + { + "author_name": "Ewa King", + "author_inst": "Rhode Island Department of Health" + }, + { + "author_name": "Richard C Huard", + "author_inst": "Rhode Island Department of Health" + }, + { + "author_name": "Diane L Pytel-Parenteau", + "author_inst": "Brown University" + }, + { + "author_name": "Ga Hie Nam", + "author_inst": "Brown University" + }, + { + "author_name": "Evgeny Yakirevich", + "author_inst": "Brown University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.05.30.20117614", "rel_title": "Assessing the quality, readability and reliability of online information on COVID-19: aninfoveillance observational study", @@ -1417550,61 +1420275,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.28.20115964", - "rel_title": "Measuring COVID-19 and Influenza in the Real World via Person-Generated Health Data", - "rel_date": "2020-05-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115964", - "rel_abs": "BackgroundSince the beginning of the COVID-19 pandemic, data from smartphones and connected sensors have been used to better understand presentation and management outside the clinic walls. However, reports on the validity of such data are still sparse, especially when it comes to symptom progression and relevance of wearable sensors.\n\nObjectiveTo understand the relevance of Person-Generated Health Data (PGHD) as a means for early detection, monitoring, and management of COVID-19 in everyday life. This type of data include quantifying prevalence and progression of symptoms from self-reports as well as changes in activity and physiological parameters continuously measured from wearable sensors, and contextualizing findings for COVID-19 patients with those from cohorts of flu patients.\n\nDesign, Setting, and ParticipantsRetrospective digital cohort study of individuals with a self-reported positive SARS-CoV-2 or influenza test followed over the period 2019-12-02 to 2020-04-27. Three cohorts were derived: Patients who self-reported being diagnosed with flu prior to the SARS-CoV-2 pandemic (N=6270, of which 1226 also contributed sensor PGHD); Patients who reported being diagnosed with flu during the SARS-CoV-2 pandemic (N=426, of which 85 also shared sensor PGHD); and patients who reported being diagnosed with COVID-19 (N=230, of which sensor PGHD was available for 41). The cohorts were derived from a large-scale digital participatory surveillance study designed to track Influenza-like Illness (ILI) incidence and burden over time.\n\nExposuresSelf-reported demographic data, comorbidities, and symptoms experienced during a diagnosed ILI episode, including SARS-CoV-2. Physiological and behavioral parameters measured daily from commercial wearable sensors, including Resting Heart Rate (RHR), total step count, and nightly sleep hours.\n\nMain Outcomes and MeasuresWe investigated the percentage of individuals experiencing symptoms of a given type (e.g. shortness of breath) across demographic groups and over time. We examined illness duration, and care seeking behavior, and how RHR, step count, and nightly sleep hours deviated from expected behavior on healthy days over the course of the infection episode.\n\nResultsSelf-reported symptoms of COVID-19 present differently from flu. COVID-19 cases tended to last longer than flu (median of 12 vs. 9 days), are uniquely characterized by chest pain/pressure, shortness of breath, and anosmia. The fraction of elevated RHR measurements collected daily from commercial wearable devices rise significantly in the 2 days surrounding ILI symptoms onset, but does not appear to do so in a way specific to COVID-19. Steps lost due to COVID-19 persists for longer than for flu.\n\nConclusion and RelevancePGHD can be a valid source of longitudinal real world data to detect and monitor COVID-19-related symptoms and behaviors at population scale. PGHD may provide continuous, near real-time feedback to intervention effectiveness that otherwise requires waiting for symptoms to develop into contacts with the healthcare system. It has also the potential to increase pre-test probability of other downstream diagnostics. To effectively leverage PGHD for participatory surveillance it is crucial to invest in the creation of trusted, long-term communication channels with individuals through which data can be efficiently collected, consented, and contextualized, while protecting the privacy of individuals and ultimately facilitating the transition in and out of care.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Nikki Marinsek", - "author_inst": "Evidation Health" - }, - { - "author_name": "Allison Shapiro", - "author_inst": "Evidation Health" - }, - { - "author_name": "Ieuan Clay", - "author_inst": "Evidation Health" - }, - { - "author_name": "Ben Bradshaw", - "author_inst": "Evidation Health" - }, - { - "author_name": "Ernesto Ramirez", - "author_inst": "Evidation Health" - }, - { - "author_name": "Jae Min", - "author_inst": "Evidation Health" - }, - { - "author_name": "Andrew Trister", - "author_inst": "Bill and Melinda Gates Foundation" - }, - { - "author_name": "Yuedong Wang", - "author_inst": "Department of Statistics and Applied Probability, University of California, Santa Barbara" - }, - { - "author_name": "Tim Althoff", - "author_inst": "University of Washington" - }, - { - "author_name": "Luca Foschini", - "author_inst": "Evidation Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.28.20115980", "rel_title": "Restarting after COVID-19: A Data-driven Evaluation of Opening Scenarios", @@ -1417749,6 +1420419,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.28.20116095", + "rel_title": "Mortality rate and estimate of fraction of undiagnosed COVID-19 cases in the US in March and April 2020", + "rel_date": "2020-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20116095", + "rel_abs": "We use a simple model to derive a mortality probability distribution for a patient as a function of days since diagnosis (considering diagnoses made between 25 February and 29 March 2020). The peak of the mortality probability is the 13th day after diagnosis. The overall shape and peak location of this probability curve are similar to the onset-to-death probability distribution in a case study using Chinese data.\n\nThe total mortality probability of a COVID-19 patient in the US diagnosed between 25 February and 29 March is about 21%. We speculate that this high value is caused by severe under-testing of the population to identify all COVID-19 patients. With this probability, and an assumption that the true probability is 2.4%, we estimate that 89% of all SARS-CoV-2 infection cases were not diagnosed during this period.\n\nWhen the same method is applied to data extended to 25 April, we found that the total mortality probability of a patient diagnosed in the US after 1 April is about 6.4%, significantly lower than for the earlier period. We attribute this drop to increasingly available tests. Given the assumption that the true mortality probability is 2.4%, we estimate that 63% of all SARS-CoV-2 infection cases were not diagnosed during this period (1 - 25 April).", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "RuShan Gao", + "author_inst": "retired" + }, + { + "author_name": "Karen H. Rosenlof", + "author_inst": "n/a" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.27.119255", "rel_title": "Head-to-head comparison of four antigen-based rapid detection tests for the diagnosis of SARS-CoV-2 in respiratory samples", @@ -1418880,29 +1421573,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.27.20114868", - "rel_title": "A reductive analysis of a compartmental model for COVID-19: data assimilation andforecasting for the United Kingdom", - "rel_date": "2020-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20114868", - "rel_abs": "We introduce a deterministic model that partitions the total population into the susceptible, infected, quarantined, and those traced after exposure, the recovered and the deceased. We hypothesize accessible population for transmission of the disease to be a small fraction of the total population, for instance when interventions are in force. This hypothesis, together with the structure of the set of coupled nonlinear ordinary differential equations for the populations, allows us to decouple the equations into just two equations. This further reduces to a logistic type of equation for the total infected population. The equation can be solved analytically and therefore allows for a clear interpretation of the growth and inhibiting factors in terms of the parameters in the full model. The validity of the accessible population hypothesis and the efficacy of the reduced logistic model is demonstrated by the ease of fitting the United Kingdom data for the cumulative infected and daily new infected cases. The model can also be used to forecast further progression of the disease. In an effort to find optimized parameter values compatible with the United Kingdom coronavirus data, we first determine the relative importance of the various transition rates participating in the original model. Using this we show that the original model equations provide a very good fit with the United Kingdom data for the cumulative number of infections and the daily new cases. The fact that the model calculated daily new cases exhibits a turning point, suggests the beginning of a slow-down in the spread of infections. However, since the rate of slowing down beyond the turning point is small, the cumulative number of infections is likely to saturate to about 3.52 x 105 around late July, provided the lock-down conditions continue to prevail. Noting that the fit obtained from the reduced logistic equation is comparable to that with the full model equations, the underlying causes for the limited forecasting ability of the reduced logistic equation are elucidated. The model and the procedure adopted here are expected to be useful in fitting the data for other countries and in forecasting the progression of the disease.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Garani Ananthakrishna", - "author_inst": "Materials Research Centre, Indian Institute of Science, Bengaluru 560012, India" - }, - { - "author_name": "Jagadish Kumar", - "author_inst": "Utkal University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.27.20111955", "rel_title": "Age separation dramatically reduces COVID-19 mortality rate in a computational model of a large population", @@ -1419023,6 +1421693,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.28.20115477", + "rel_title": "Study of the Sudanese perceptions of COVID-19: Applying the Health Belief Model.", + "rel_date": "2020-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115477", + "rel_abs": "BackgroundCOVID-19 a pandemic declared by WHO, is the first in recent history pose challenges on public health. Health Belief Model is a psychosocial model explains and predicts health-related behaviours. This study aimed to explore the perceptions of the Sudanese on COVID-19-related preventive measures.\n\nMethodsA Cross-sectional study using online-questionnaire was conducted between 1st-16th April 2020 among Sudanese adults (aged [≥]18 years). We used a snowball sampling technique, starting from known professional and social media groups, and individuals and then was distributed on various internet platforms. The survey instrument was based on HBM constructs.\n\nResultsSome 877 individuals participated in the survey with a mean age 37.8 (SD{+/-}11.94) more males, mostly having a university education, employed and residing in Khartoum. More than half of the participants scored high in almost all Health Belief Model constructs, except for benefits of hand hygiene. The findings show that the HBM constructs are correlated to each others as well as to other socio-demographic factors. Self-efficacy correlated negatively with susceptibility (r -0.084), while positively with severity, benefits of and barriers to hand hygiene, benefits and barriers to social distancing (r 0.117, r 0.347, r 0.202, r 0.396, r 0.276), respectively.\n\nConclusionThe findings show that the HBM constructs are correlated to each others as well as to other socio-demographic factors. Self-efficacy must be taken into account as a strong changing factor to susceptibility and severity perceptions. Correlations found in this study might help drive behaviour-changing efforts.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Elwalid Fadul Nasir", + "author_inst": "King Faisal University" + }, + { + "author_name": "Hatim Almahdi Almahdi", + "author_inst": "King Faisal University" + }, + { + "author_name": "Ahmed Khalid alhag", + "author_inst": "King Faisal University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.27.20115113", "rel_title": "COVID-19 Lockdown in a Kenyan Informal Settlement: Impacts on Household Energy and Food Security", @@ -1420110,29 +1422807,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.05.25.20112797", - "rel_title": "Variation in Covid-19 Cases Across New York City", - "rel_date": "2020-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.25.20112797", - "rel_abs": "The number of confirmed COVID-19 cases, relative to population size, has varied greatly throughout the United States and even within the same city. In different zip codes in New York City, the epicentre of the epidemic, the number of cases per 100,000 residents has ranged from 437 to 4227, a 1:10 ratio. To guide policy decisions regarding containment and reopening of the economy, schools and other institutions, it is vital to identify the factors that drive this large variation.\n\nThis paper reports on a statistical study of incidence variation by zip code across New York City. Among many socio-economic and demographic measures considered, the average household size emerges as the single most important explanatory variable: an increase in average household size by one member increases the zip code incidence rate, in our final model specification, by at least 876 cases, 23% of the range of incidence rates, at a 95% confidence level.\n\nThe percentage of the population above the age of 65, the percentage below the poverty line, and their interaction term are also strongly positively associated with zip code incidence rates, In terms of ethnic/racial characteristics, the percentages of African Americans, Hispanics and Asians within the population, are significantly associated, but the magnitude of the impact is considerably smaller. (The proportion of Asians within a zip code has a negative association.)\n\nThese significant associations may be explained by comorbidities, known to be more (less) prevalent among the black and Hispanic (Asian) population segments. In turn, the increased prevalence of these comorbidities among the black and Hispanic population, is, in large part, the result of poorer dietary habits and more limited access to healthcare, themselves driven by lower incomes\n\nContrary to popular belief, population density, per se, does not have a significantly positive impact. Indeed, population density and zip code incidence rate are negatively correlated, with a -33% correlation coefficient.\n\nOur model specification is based on a well-established epidemiologic model that explains the effects of household sizes on R0, the basic reproductive number of an epidemic.\n\nOur findings support implemented and proposed policies to quarantine pre-acute and post-acute patients, as well as nursing home admission policies", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Awi Federgruen", - "author_inst": "Columbia University" - }, - { - "author_name": "Sherin R Naha", - "author_inst": "Columbia University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.05.27.20114652", "rel_title": "A SARS-CoV-2 serological assay to determine the presence of blocking antibodies that compete for human ACE2 binding", @@ -1420345,6 +1423019,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.26.20113167", + "rel_title": "A pilot study to investigate the fecal dissemination of SARS-CoV-2 virus genome in COVID-19 patients in Odisha, India", + "rel_date": "2020-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20113167", + "rel_abs": "In infectious diseases, the routes of transmission play major roles in determining the rate and extent of disease spread. Though fomites and aerosol droplets are major sources of SARS-CoV-2 human to human transmission, studies have also reported possible involvement of other routes of transmission like fecal-oral. Multiple studies around the world have reported shedding of the SARS-CoV-2 viral genome in certain COVID-19 patient fecal samples. Hence, the major objective of this study was to get the experimental evidence whether in Indian COVID-19 patients fecal dissemination of the SARS-CoV-2 genome occurs or not. Information obtained from twelve number of patients from a COVID-19 hospital of Odisha has demonstrated that both symptomatic and asymptomatic Indian patients could be positive for the SARS-CoV-2 genome in their fecal component. The findings have also established a protocol to collect and extract viral RNA for SARS-CoV-2 detection in fecal samples. Together, the study supports the hypothesis of possible fecal-oral transmission of SARS-CoV-2 virus and provides a rationale to extend this study in a larger cohort of patient samples and correlate the significance of the SARS-CoV-2 virus genome detection in fecal samples with disease severity and transmission.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Shantibhusan Senapati", + "author_inst": "Institute of Life Sciences, Bhubaneswar, Odisha, India" + }, + { + "author_name": "Jaya Singh Kshatri", + "author_inst": "Regional Medical Research Centre, Odisha, India" + }, + { + "author_name": "Punit Prasad", + "author_inst": "Institute of Life Sciences, Bhubaneswar, Odisha, India" + }, + { + "author_name": "Jyotirmayee Turuk", + "author_inst": "Regional Medical Research Centre, Odisha, India" + }, + { + "author_name": "Sanghamitra Pati", + "author_inst": "Regional Medical Research Centre, Odisha, India" + }, + { + "author_name": "Ajay Parida", + "author_inst": "Institute of Life Sciences, Bhubaneswar, Odisha, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.27.20114736", "rel_title": "Combining PCR and CT testing for COVID", @@ -1421408,37 +1424121,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2020.05.27.20111542", - "rel_title": "Ambient air pollutants, meteorological factors and their interactions affect confirmed cases of COVID-19 in 120 Chinese cities", - "rel_date": "2020-05-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20111542", - "rel_abs": "Emerging evidences have confirmed effects of meteorological factors on novel coronavirus disease 2019 (COVID-19). However, few studies verify the impact of air pollutants on this pandemic. This study aims to explore the association of ambient air pollutants, meteorological factors and their interactions effect confirmed case counts of COVID-19 in 120 Chinese cities. Here, we collected total confirmed cases of COVID-19 by combining with meteorological factors and air pollutants data from 15th January 2020 to 18th March 2020 in 120 Chinese cities. Spearman correlation analysis was employed to estimate the association between two variables; univariate and multivariate negative binomial regression analysis were applied to explore the effect of air pollutants and meteorological parameters on the COVID-19 confirmed cases. Positive associations were found between the confirmed cases of COVID-19 and carbon monoxide (CO), aerodynamic particulate matter with aerodynamic diameter [≤]2.5 m (PM2.5), relative humidity (RH) and air pressure (AP). And negative association was found for sulfur dioxide (SO2). In addition, multivariate negative binomial regression analysis suggested that confirmed cases of COVID-19 was positively correlated with ozone (O3) in lag 0 day while it was negatively associated with wind velocity (WV) in lag 14 days, and the pollutants-meteorological factors interactions also associate with COVID-19. In conclusions, air pollutants and meteorological factors and their interactions all associate with COVID-19.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jianli Zhou", - "author_inst": "Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern" - }, - { - "author_name": "Linyuan Qin", - "author_inst": "Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, 541001, P. R. China." - }, - { - "author_name": "Nan Liu", - "author_inst": "Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern" - }, - { - "author_name": "Xiaojing Meng", - "author_inst": "Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.05.26.20113886", "rel_title": "COVID-19 (SARS-CoV-2) Ventilator Resource Management Using a Network Optimization Model and Predictive System Demand", @@ -1421599,6 +1424281,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.26.20114124", + "rel_title": "Seroprevalence of SARS-CoV-2 among children visiting a hospital during the initial Seattle outbreak", + "rel_date": "2020-05-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20114124", + "rel_abs": "Children are strikingly underrepresented in COVID-19 case counts1-3. In the United States, children represent 22% of the population but only 1.7% of confirmed SARS-CoV-2 cases1. One possibility is that symptom-based viral testing is less likely to identify infected children, since they often experience milder disease than adults1,4-7. To better assess the frequency of pediatric SARS-CoV-2 infection, we serologically screened 1,775 residual samples from Seattle Children's Hospital collected from 1,076 children seeking medical care during March and April of 2020. Only one child was seropositive in March, but seven were seropositive in April for a period seroprevalence of {approx} 1%. Most seropositive children (6/8) were not suspected of having had COVID-19. The sera of seropositive children had neutralizing activity, including one that neutralized at a dilution >1:18,000. Therefore, an increasing number of children seeking medical care were infected by SARS-CoV-2 during the early Seattle outbreak despite few positive viral tests.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Adam S Dingens", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Katharine HD Crawford", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Amanda Adler", + "author_inst": "Seattle Children's Hospital" + }, + { + "author_name": "Sarah L Steele", + "author_inst": "Seattle Children's Hospital" + }, + { + "author_name": "Kirsten Lacombe", + "author_inst": "Seattle Children's Hospital" + }, + { + "author_name": "Rachel Eguia", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Fatima Amanat", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Alexandra C Walls", + "author_inst": "University of Washington" + }, + { + "author_name": "Caitlin R Wolf", + "author_inst": "University of Washingon" + }, + { + "author_name": "Michael Murphy", + "author_inst": "University of Washington" + }, + { + "author_name": "Deleah Pettie", + "author_inst": "University of Washington" + }, + { + "author_name": "Lauren Carter", + "author_inst": "University of Washington" + }, + { + "author_name": "Xuan Qin", + "author_inst": "Seattle Children's Hospital" + }, + { + "author_name": "Neil P King", + "author_inst": "University of Washington" + }, + { + "author_name": "David Veesler", + "author_inst": "University of Washington" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jane A Dickerson", + "author_inst": "Seattle Children's Hospital" + }, + { + "author_name": "Helen Y Chu", + "author_inst": "University of Washington" + }, + { + "author_name": "Janet A Englund", + "author_inst": "Seattle Children's Hospital" + }, + { + "author_name": "Jesse D Bloom", + "author_inst": "Fred Hutchinson Cancer Research Center" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.26.20113811", "rel_title": "Diabetes is associated with increased risk for in-hospital mortality in patients with COVID-19: a systematic review and meta-analysis comprising 18,506 patients", @@ -1422814,49 +1425591,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.25.20112805", - "rel_title": "The association of UV with rates of COVID-19 transmission and deaths in Mexico: the possible mediating role of vitamin D.", - "rel_date": "2020-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.25.20112805", - "rel_abs": "The first COVID-19 case in Mexico was confirmed on 26 February 2020 and by May 3 the number of registered cases had risen to 30,927. However the rate of transmission varied greatly from city to city. We used data on temperature, humidity and ultraviolet radiation (UV) from 45 cities all over the country to explore whether there was an association between these variables and rates of transmission and rates of accumulation of COVID-19 ascribed deaths. The advantage of an in-country study of this kind is that many of the variables that can confound international studies are held constant (e.g. public health policies, methods of reporting, cultural, behavioural and genetic factors). Although the official statistics undoubtedly greatly underestimate the situation in Mexico due to lack of testing, they are underestimated in all cities so this should not introduce bias across the sample. We found that temperature and humidity had no discernible association with transmission rates but that UV during the transmission period was negatively correlated with rates of transmission, suggesting a sterilizing effect. UV in the January preceding the epidemic had a slightly higher association with transmission rates than UV during the transmission period itself. We also found negative associations of UV in the transmission period and in January with rate of cumulative deaths, but at lower levels of statistical significance. We conclude that in addition to a sterilizing effect during the transmission period, UV may have a physiological effect in reducing transmission and deaths due to COVID-19, most likely through the medium of vitamin D production in the body. This follows the growing body of medical evidence that vitamin D deficiency is associated with severity of COVID-19. However, we also found a negative correlation between altitude and rates of COVID-19 transmission, distinct and independent of the UV effect, which may indicate that other physiological processes are also present. In a multiple regression, altitude and UV together accounted for 18% of the variation in transmission rates between cities.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Margaret Skutsch", - "author_inst": "Centro de Investigaciones en Geografia Ambiental, Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Carlos Dobler", - "author_inst": "Centro de Investigaciones en Geografia Ambiental, Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Matthew B.B. McCall", - "author_inst": "Radboud UMC, Nijmegen. the Netherlands" - }, - { - "author_name": "Adrian Ghilardi", - "author_inst": "Centro de Investigaciones en Geografia Ambiental, Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Miguel A. Salinas-Melgoza", - "author_inst": "Centro de Investigaciones en Geografia Ambiental, Universidad Naciona lAutonoma de Mexico" - }, - { - "author_name": "Michael K. McCall", - "author_inst": "Centro de Investigaciones en Geografia Ambiental, Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Gabriela Fenner-Sanchez", - "author_inst": "CESMECA-UNICACH, Geobrujas-comunidad de geografas y Grupo Estepa UNAL" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.26.20112680", "rel_title": "Fast initial Covid-19 response means greater caution may be needed later", @@ -1422973,6 +1425707,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.25.20112615", + "rel_title": "Thermal Disinfection Inactivates SARS-CoV-2 in N95 Respirators while Maintaining Their Protective Function", + "rel_date": "2020-05-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.25.20112615", + "rel_abs": "BackgroundThe unprecedented demand and consequent global shortage of N95 respirators during the COVID-19 pandemic have left frontline workers vulnerable to infection. To potentially expand the supply, we validated a rapidly applicable low-cost decontamination protocol in compliance with regulatory standards to enable the safe reuse of personalized, disposable N95-respirators.\n\nMethodsFour common models of N95-respirators were disinfected for 60 minutes at 70{degrees}C either at 0% or 50% relative humidity (RH). Effective inactivation of SARS-CoV-2 and E. coli was evaluated in inoculated masks. The N95 filter integrity was examined with scanning electron microscopy. The protective function of disinfected N95 respirators was tested against US NIOSH standards for particle filtration efficiency, breathing resistance and respirator fit.\n\nResultsA single heat treatment inactivated both SARS-CoV-2 (undetectable, detection limit: 100 TCID50/ml) and E. coli (0 colonies at 50%RH) in all four respirator models. Even N95-respirators that underwent ten decontamination cycles maintained their integrity and met US-governmental criteria for approval regarding fit, filtration efficiency and breathing resistance. Scanning electron microscopy demonstrated maintained N95 fiber diameter compared to baseline.\n\nInterpretationThermal disinfection enables large-scale, low cost decontamination of existing N95 respirators using commonly sourced equipment during the COVID-19 pandemic. This process could be used in hospitals and long term care facilities and also provides a feasible approach to expand the N95 supply in low- and middle-income regions.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Simeon C. Daeschler", + "author_inst": "SickKids Research Institute" + }, + { + "author_name": "Niclas Manson", + "author_inst": "The Hospital for Sick Children (SickKids) Occupational Health and Safety" + }, + { + "author_name": "Kariym Joachim", + "author_inst": "Division of Plastic and Reconstructive Surgery, The Hospital for Sick Children (SickKids) and University of Toronto" + }, + { + "author_name": "Alex W.H. Chin", + "author_inst": "School of Public Health, LKS Faculty of Medicine, The University of Hong Kong," + }, + { + "author_name": "Katelyn Chan", + "author_inst": "SickKids Research Institute; The Hospital for Sick Children (SickKids)" + }, + { + "author_name": "Paul Z Chen", + "author_inst": "Chemical Engineering & Applied Chemistry, University of Toronto" + }, + { + "author_name": "Kiana Tajdaran", + "author_inst": "SickKids Research Institute; The Hospital for Sick Children (SickKids)" + }, + { + "author_name": "Kaveh Mirmoeini", + "author_inst": "SickKids Research Institute; The Hospital for Sick Children (SickKids)" + }, + { + "author_name": "Jennifer J. Zhang", + "author_inst": "Division of Plastic and Reconstructive Surgery, The Hospital for Sick Children (SickKids) and University of Toronto" + }, + { + "author_name": "Jason T. Maynes", + "author_inst": "Department of Anaesthesiology, The Hospital for Sick Children" + }, + { + "author_name": "Michelle Science", + "author_inst": "Division of Infectious Disease, The Hospital for Sick Children" + }, + { + "author_name": "Ali Darbandi", + "author_inst": "SickKids Research Institute; The Hospital for Sick Children (SickKids)" + }, + { + "author_name": "Derek Stephens", + "author_inst": "Child Health Evaluative Sciences, The Hospital for Sick Children (SickKids)" + }, + { + "author_name": "Leo L.M. Poon", + "author_inst": "School of Public Health, LKS Faculty of Medicine, The University of Hong Kong," + }, + { + "author_name": "Frank Gu", + "author_inst": "Chemical Engineering & Applied Chemistry, University of Toronto" + }, + { + "author_name": "Gregory H. Borschel", + "author_inst": "Institute of Biomaterials and Biomedical Engineering and Division of Plastic and Reconstructive Surgery, The Hospital for Sick Children, University of Toronto" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.25.20112185", "rel_title": "Increased risk for COVID-19 among Migrants from Latin-America, Caribbean, and Sub-Saharan Africa living in Spain", @@ -1424480,25 +1427293,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.05.26.20113316", - "rel_title": "Scrutinising the COVID-19 data on 590.000 cases. A retrospective, population-based descriptive study for data quality surveillance and a review at 4.540.000 cases.", - "rel_date": "2020-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20113316", - "rel_abs": "BackgroundReports on the detected positive patients with COVID-19 are as per today the best estimation of a country spread of the pandemic. In order to evaluate the early indicators for true lethality and recovery time, the data where the model is built must be quality checked. Each country sets different procedures and criteria for fatality count due to COVID-19 and the health system is stressed by having insufficient testing, untracked patients and premature discharge. In this paper the dynamics behind such data quality issues are discussed throughout the disease course to support better modeling and decision-making processes in a stressed healthcare system.\n\nMethodsBased on data compiled and relayed by the Johns Hopkins University, tracking COVID-19 over 590.000 patients (march 27th, 2020), the data is clustered and compared with discrete regression. Regression parameters are restricted by a time interval of 1 day and must be meaningful for the diagnostic (i.e. a fatality cannot occur before the patient displays symptoms). Cumulative infection curves are taken and built. Infection baseline is based on the country official declaration. Infection synthetic curves are built from the Fatality count and the Recovered patient count. The adjusted parameters are {tau}=time to fatality (days), {delta}=time to discharge of recovered patients (days) and {varphi}=case fatality rate (CFR in per unit, P.U.). Therefore, the discharge rate (recovery rate) is forced to be (1-{varphi}).\n\nUsing forward or backward formulas have no other influence than the time reference. In both circumstances, time from Onset and Symptoms are neglected and shall be added if such dates are to be plot. There is a gap of two weeks since exposure to Hospital Admission to detection and the earlier the diagnose is done, the better the outcome.\n\nCumulative figures are used to smoothen the deviation and to provide the best estimator possible at the present time. The delay factor allows to compare figures belonging to the same date of detection.\n\nFast, daily models which can be used and integrated to a filtering stage on the parameter estimator in a complex approach are left out of scope. Continuous models can also be used and interpolation among the data points is another source of noise to be considered, especially when counting methods are suddenly changing as it is the case with COVID-19.\n\nCountries were grouped as found representative for methodology illustration purposes. Results are discussed and compared across the different groups and potential indicators of this behavior are drawn for further study.\n\nFindingsFrom 593.291 cases in the sample, and its 7 representative groups, the recovery time and the local CFR are negatively correlated, having the highest fatality rates (21%, Spain) the countries with shorter recovery time (11 days, Spain). Also, CFR can be an indicator of Infection inconsistencies (i.e. South Korea, CFR 1%, Time to recovery 25 days).\n\nAt the review part, focus is made on the inconsistencies detected in Germany and South Korea datasets as well as the potential misfits on China and Spain.\n\nOverall, the Time to Fatality ranges between 4 and 8 days, and the mean is of 6 days (South Korea, 7 days; Japan, 6days). Only Germany and France are detecting earlier than other countries and admit 10 days before fatality occurs.\n\nTo date, shortening hospital discharge times seem to lead to patient reinfections (COVID-19 positive), and studies are working on this line.\n\nInterpretationOne simple explanation for the local CFR and Recovery time correlation is to define such rate as a measure of the healthcare system overload. Anomalous CFR indexes point to a stressed healthcare system. The higher the overload, the more focus on critical cases and hence the higher local CFR.\n\nThe COVID-19 intrinsic CFR is unlikely to change by a factor of 10x from countries with similar lifestyle, GDP per capita and health services (i.e. the Mediterranean Basin, Northern Europe, etc.). Because of this fact, early CFR measured before Healthcare system overwhelming (COVID-19 free flow) are considered to be more accurate than the measured CFR while the outbreak is still ongoing,\n\nFinally, the synthetic Infection indexes may be a helpful indirect measure of the real population infection rate and also used for data quality audit. Any model built upon inconsistent data will be complex to explain and justify.\n\nFundingNo specific funding is raised.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Oriol Gallemi Rovira", - "author_inst": "Universitat Ramon Llull IQS" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.26.20113761", "rel_title": "Differentiating COVID-19 from other types of pneumonia with convolutional neural networks", @@ -1424651,6 +1427445,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.26.20113696", + "rel_title": "Application of pooled testing in screening and estimating the prevalence of Covid-19", + "rel_date": "2020-05-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20113696", + "rel_abs": "The recent emergence of the COVID-19 pandemic has posed an unprecedented healthcare challenge and catastrophic economic and social consequences to the countries across the world. The situation is even worse for emerging economies like India. WHO recommends mass scale testing as one of the most effective ways to contain its spread and fight the pandemic. But, due to the high cost and shortage of test kits, specifically in India, the testing is restricted to only those who are symptomatic. In this context, pooled testing is recommended by some experts as a partial solution to overcome this problem. In this article, we explain the basic statistical theory behind the pooled testing procedure for screening as well as prevalence estimation. In real world situations, the tests are imperfect, and lead to false positive and false negative results. We provide theoretical explanation of the impact of these diagnostic errors on the performances of individual testing and pooled testing procedures. Finally, we study the effect of misspecification of sensitivity and specificity of tests on the estimate of prevalence, an issue, which is debated a lot among the scientists in the context of COVID-19. Our theoretical investigations lead to some interesting and precise understanding of some of these issues.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Pritha Guha", + "author_inst": "XLRI-Xavier School of Management, Jamshedpur, Jharkhand-831001, India" + }, + { + "author_name": "Apratim Guha", + "author_inst": "XLRI-Xavier School of Management, Jamshedpur, Jharkhand-831001, India" + }, + { + "author_name": "Tathagata Bandyopadhyay", + "author_inst": "Indian Institute of Management, Ahmedabad, Gujarat-380015, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.26.20113431", "rel_title": "Detection of asymptomatic Leishmania infection in Bangladesh by novel antigen and antibody diagnostic tools shows strong association with PKDL patients", @@ -1425942,57 +1428763,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2020.05.20.20106633", - "rel_title": "Clinical and Radiological Evaluations of COVID-19 Patients with Anosmia: Preliminary Report.", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20106633", - "rel_abs": "ObjectiveTo investigate clinical and radiological features of olfactory clefts of patients with mild coronavirus disease 2019 (COVID-19).\n\nMethodsSixteen COVID-19 patients were recruited. The epidemiological and clinical data were extracted. Nasal complaints were assessed through the sino-nasal outcome test 22 (SNOT-22). Patients underwent psychophysical olfactory testing, olfactory cleft examination and CT-scan.\n\nResultsSixteen anosmic patients were included. The mean SniffinSticks score was 4.6{+/-}1.7. The majority of patients had no endoscopical abnormality, with a mean olfactory cleft endoscopy score of 0.6{+/-}0.9. The olfactory clefts were opacified in 3 patients on the CT-scan. The mean radiological olfactory cleft score was 0.7{+/-}0.8. There were no significant correlations between clinical, radiological and psychophysical olfactory testing.\n\nConclusionThe olfactory cleft of anosmic COVID-19 patients is free regarding endoscopic examination and imaging. The anosmia etiology would be not related to edema of the olfactory cleft.\n\nLevel of Evidence4", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jerome R Lechien", - "author_inst": "Department of Otorhinolaryngology and Head and Neck Surgery, CHU de Bruxelles, CHU Saint-Pierre, School of Medicine, Universite Libre de Bruxelles, Brussels, Be" - }, - { - "author_name": "Justin Michel", - "author_inst": "Aix Marseille University, APHM, IUSTI, La Conception University Hospital, Department of Oto-Rhino-Laryngology Head and Neck Surgery, Marseille, France" - }, - { - "author_name": "Thomas Radulesco", - "author_inst": "Aix Marseille University, APHM, IUSTI, La Conception University Hospital, Department of Oto-Rhino-Laryngology Head and Neck Surgery, Marseille, France" - }, - { - "author_name": "Carlos M Chiesa-Estomba", - "author_inst": "Hospital Universitario Donostia" - }, - { - "author_name": "Luigi A Vaira", - "author_inst": "Maxillofacial Surgery Unit, University Hospital of Sassari, Sassari, Italy." - }, - { - "author_name": "Giacomo De Riu", - "author_inst": "Maxillofacial Surgery Unit, University Hospital of Sassari, Sassari, Italy." - }, - { - "author_name": "Leigh J Sowerby", - "author_inst": "Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada" - }, - { - "author_name": "Claire Hopkins", - "author_inst": "Guy's and St Thomas's Hospitals" - }, - { - "author_name": "Sven Saussez", - "author_inst": "University of Mons" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "otolaryngology" - }, { "rel_doi": "10.1101/2020.05.19.20106575", "rel_title": "Mitigation Policies and Emergency Care Management in Europe's Ground Zero for COVID-19", @@ -1426117,6 +1428887,209 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.21.20105486", + "rel_title": "SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not associated with infectious virus", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20105486", + "rel_abs": "BackgroundLaboratory diagnosis of SARS-CoV-2 infection (the cause of COVID-19) uses PCR to detect viral RNA (vRNA) in respiratory samples. SARS-CoV-2 RNA has also been detected in other sample types, but there is limited understanding of the clinical or laboratory significance of its detection in blood.\n\nMethodsWe undertook a systematic literature review to assimilate the evidence for the frequency of vRNA in blood, and to identify associated clinical characteristics. We performed RT-PCR in serum samples from a UK clinical cohort of acute and convalescent COVID-19 cases (n=212), together with convalescent plasma samples collected by NHS Blood and Transplant (NHSBT) (n=111 additional samples). To determine whether PCR-positive blood samples could pose an infection risk, we attempted virus isolation from a subset of RNA-positive samples.\n\nResultsWe identified 28 relevant studies, reporting SARS-CoV-2 RNA in 0-76% of blood samples; pooled estimate 10% (95%CI 5-18%). Among serum samples from our clinical cohort, 27/212 (12.7%) had SARS-CoV-2 RNA detected by RT-PCR. RNA detection occurred in samples up to day 20 post symptom onset, and was associated with more severe disease (multivariable odds ratio 7.5). Across all samples collected [≥]28 days post symptom onset, 0/143 (0%, 95%CI 0.0-2.5%) had vRNA detected. Among our PCR-positive samples, cycle threshold (ct) values were high (range 33.5-44.8), suggesting low vRNA copy numbers. PCR-positive sera inoculated into cell culture did not produce any cytopathic effect or yield an increase in detectable SARS-CoV-2 RNA.\n\nConclusionsvRNA was detectable at low viral loads in a minority of serum samples collected in acute infection, but was not associated with infectious SARS-CoV-2 (within the limitations of the assays used). This work helps to inform biosafety precautions for handling blood products from patients with current or previous COVID-19.", + "rel_num_authors": 47, + "rel_authors": [ + { + "author_name": "Monique Andersson", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK" + }, + { + "author_name": "Carolina V Arancibia - Carcamo", + "author_inst": "Translational Gastroenterology Unit, University of Oxford, OX3 9DU, UK. Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre, University o" + }, + { + "author_name": "Kathryn Auckland", + "author_inst": "Nuffield Department of Medicine, University of Oxford, OX3 9DU, UK" + }, + { + "author_name": "J Kenneth Baillie", + "author_inst": "Roslin Institute, University of Edinburgh, EH25 9RJ, UK" + }, + { + "author_name": "Eleanor Barnes", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK. Nuffield Department of Medicine, University of Oxford, OX3 9DU, UK" + }, + { + "author_name": "Tom Beneke", + "author_inst": "Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, UK" + }, + { + "author_name": "Sagida Bibi", + "author_inst": "Dept of Paediatrics, University of Oxford, OX3 7LE, UK" + }, + { + "author_name": "Miles Carroll", + "author_inst": "Public Health England, Porton Down, SP4 0JG, UK" + }, + { + "author_name": "Derrick Crook", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK. Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre, University of" + }, + { + "author_name": "Kate Dingle", + "author_inst": "Nuffield Department of Medicine, University of Oxford, OX3 9DU, UK" + }, + { + "author_name": "Christina Dold", + "author_inst": "Dept of Paediatrics, University of Oxford, OX3 7LE, UK" + }, + { + "author_name": "Louise O Downs", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK" + }, + { + "author_name": "Laura Dunn", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK" + }, + { + "author_name": "David W Eyre", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK. Nuffield Department of Medicine, University of Oxford, OX3 9DU, UK" + }, + { + "author_name": "Javier Gilbert Jaramillo", + "author_inst": "Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, UK" + }, + { + "author_name": "Heli Harvala", + "author_inst": "NHS Blood and Transfusion, 26 Margaret St, Marylebone, London W1W 8NB" + }, + { + "author_name": "Sarah Hoosdally", + "author_inst": "Nuffield Department of Medicine, University of Oxford, OX3 9DU, UK" + }, + { + "author_name": "Samreen Ijaz", + "author_inst": "Public Health England, Porton Down, SP4 0JG, UK" + }, + { + "author_name": "Tim James", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK" + }, + { + "author_name": "William James", + "author_inst": "Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, UK" + }, + { + "author_name": "Katie Jeffery", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK" + }, + { + "author_name": "Anita Justice", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK" + }, + { + "author_name": "Paul Klenerman", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK. Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre, University of" + }, + { + "author_name": "Julian C Knight", + "author_inst": "Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre, University of Oxford, OX3 9DU, UK. Wellcome Centre for Human Genetics, OX3 7BN, UK" + }, + { + "author_name": "Michael Knight", + "author_inst": "Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, UK" + }, + { + "author_name": "Xu Liu", + "author_inst": "Key Laboratory of Human Disease Comparative Medicine, National Health Commission of P.R.C, Institute of Laboratory Animal Science, Chinese Academy of Medical Sc" + }, + { + "author_name": "Sheila F Lumley", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK. Nuffield Department of Medicine, University of Oxford, OX3 9DU, UK" + }, + { + "author_name": "Philippa C Matthews", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK. Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre, University of" + }, + { + "author_name": "Anna L McNaughton", + "author_inst": "Nuffield Department of Medicine, University of Oxford, OX3 9DU, UK" + }, + { + "author_name": "Alexander J Mentzer", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK. Nuffield Department of Medicine, University of Oxford, OX3 9DU, UK" + }, + { + "author_name": "Juthathip Mongkolsapaya", + "author_inst": "Nuffield Department of Medicine, University of Oxford, OX3 9DU, UK" + }, + { + "author_name": "Sarah Oakley", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK" + }, + { + "author_name": "Marta S Oliveira", + "author_inst": "NHSBT, Oxford" + }, + { + "author_name": "Timothy Peto", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK. Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre, University of" + }, + { + "author_name": "Rutger J Ploeg", + "author_inst": "NHSBT, Oxford" + }, + { + "author_name": "Jeremy Ratcliff", + "author_inst": "Nuffield Department of Medicine, University of Oxford, OX3 9DU, UK" + }, + { + "author_name": "David J Roberts", + "author_inst": "NHSBT, Oxford" + }, + { + "author_name": "Justine Rudkin", + "author_inst": "Nuffield Department of Population Health, University of Oxford, OX3 7LF, UK. Big Data Institute, University of Oxford, OX3 7LF, UK" + }, + { + "author_name": "Rebecca A Russell", + "author_inst": "University of Oxford" + }, + { + "author_name": "Gavin Screaton", + "author_inst": "Nuffield Department of Medicine, University of Oxford, OX3 9DU, UK" + }, + { + "author_name": "Malcolm G Semple", + "author_inst": "NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, L69 3BX, UK" + }, + { + "author_name": "Donal T Skelly", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK. Nuffield Department of Clinical Neurosciences, University of Oxford, OX3 9DU, UK" + }, + { + "author_name": "Peter Simmonds", + "author_inst": "Nuffield Department of Medicine, University of Oxford, OX3 9DU, UK" + }, + { + "author_name": "Nicole Stoesser", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK. Nuffield Department of Medicine, University of Oxford, OX3 9DU, UK" + }, + { + "author_name": "Lance Turtle", + "author_inst": "NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, L69 3BX, UK" + }, + { + "author_name": "Sue Wareing", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK" + }, + { + "author_name": "Maria Zambon", + "author_inst": "Public Health England, Colindale, London, NW9 5EQ, UK" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.22.20106724", "rel_title": "Emergence of Low-density Inflammatory Neutrophils Correlates with Hypercoagulable State and Disease Severity in COVID-19 Patients", @@ -1427344,53 +1430317,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.19.20107201", - "rel_title": "Computational Simulation to Assess Patient Safety of Uncompensated COVID-19 Two-patient Ventilator Sharing Using the Pulse Physiology Engine", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20107201", - "rel_abs": "BackgroundThe COVID-19 pandemic is stretching medical resources internationally, sometimes creating ventilator shortages that complicate clinical and ethical situations. The possibility of needing to ventilate multiple patients with a single ventilator raises patient health and safety concerns in addition to clinical conditions needing treatment.\n\nWherever ventilators are employed, additional tubing and splitting adaptors may be available. Adjustable flow-compensating resistance for differences in lung compliance on individual limbs may not be readily implementable.\n\nBy exploring a number and range of possible contributing factors using computational simulation without risk of patient harm, this paper attempts to define useful bounds for ventilation parameters when compensatory resistance in limbs of a shared breathing circuit is not possible. This desperate approach to shared ventilation support would be a last resort when alternatives have been exhausted.\n\nMethodsA whole-body computational physiology model (using lumped parameters) was used to simulate each patient being ventilated. The primary model of a single patient with a dedicated ventilator was augmented to model two patients sharing a single ventilator. In addition to lung mechanics or estimation of CO2 and pH expected for set ventilation parameters (considerations of lung physiology alone), full physiological simulation provides estimates of additional values for oxyhemoglobin saturation, arterial oxygen tension, and other patient parameters. A range of ventilator settings and patient characteristics were simulated for paired patients.\n\nFindingsTo be useful for clinicians, attention has been directed to clinically available parameters. These simulations show patient outcome during multi-patient ventilation is most closely correlated to lung compliance, oxygenation index, oxygen saturation index, and end-tidal carbon dioxide of individual patients. The simulated patient outcome metrics were satisfactory when the lung compliance difference between two patients was less than 12 mL/cmH2O, and the oxygen saturation index difference was less than 2 mmHg.\n\nInterpretationIn resource-limited regions of the world, the COVID-19 pandemic will result in equipment shortages. While single-patient ventilation is preferable, if that option is unavailable and ventilator sharing using limbs without flow resistance compensation is the only available alternative, these simulations provide a conceptual framework and guidelines for clinical patient selection.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Jeffrey B. Webb", - "author_inst": "Kitware, Inc." - }, - { - "author_name": "Aaron Bray", - "author_inst": "Kitware, Inc." - }, - { - "author_name": "Philip K. Asare", - "author_inst": "Bucknell University" - }, - { - "author_name": "Rachel B. Clipp", - "author_inst": "Kitware, Inc." - }, - { - "author_name": "Yatin B. Mehta", - "author_inst": "Geisinger" - }, - { - "author_name": "Sudheer Penupolu", - "author_inst": "Geisinger" - }, - { - "author_name": "Aalpen A. Patel", - "author_inst": "Geisinger" - }, - { - "author_name": "S. Mark Poler", - "author_inst": "Geisinger" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.05.21.20108522", "rel_title": "Expanding Covid-19 Testing: Mathematical Guidelines for the Optimal Sample Pool Size Given Positive Test Rate", @@ -1427535,6 +1430461,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.21.20108704", + "rel_title": "COVID-19 in Bangladesh: Measuring differences in individual precautionary behaviors among young adults", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20108704", + "rel_abs": "AimThe novel coronavirus disease 2019 (COVID-19) has already hit Bangladesh, and various control measures have been taken to flatten the epidemic curve. Due to the current demographic distribution in Bangladesh, young adults are vital to the demography of the country. Therefore, their precautionary behavior is very important to ensure the success of preventive policies. This exploratory study examined the differences in the adoption of precautionary behaviors among young adults, and estimated and compared the predictors of precautionary behavior adoption among young adults living in the capital city Dhaka and a nearby district, Tangail.\n\nSubject and MethodsA total of 350 respondents from each district participated in the study. ANOVA and two-sample t-tests were utilized to detect differences in precautionary behavior across demographic groups of young adults, and quantile regression modeling was used to find the predictors of adopting precautionary behaviors and to compare these predictors between the two districts.\n\nResultsIndividuals who had a postgraduate education and had good mental health tended to show better precautionary behaviors in Dhaka. Female respondents from Tangail who had no psychological distress took precautionary behaviors more often than their counterparts. However, no significant differences in the adoption of precautionary behaviors to prevent COVID-19 among young adults were found between the two districts. Better self-control ability, higher education and good mental health emerged as factors that significantly shaped the precautionary behaviors of young adults in this study.\n\nConclusionHaving better knowledge did not ensure better adoption of precautionary behaviors among the participants. In effect, the governments strong intervention to keep people at home and distant from each other and continued lockdown for several more days are probable immediate solutions. At the same time, the economic burden on lower-income people should be addressed.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Asif Imtiaz", + "author_inst": "University of Dhaka" + }, + { + "author_name": "Md. Akram Hossain", + "author_inst": "University of Dhaka" + }, + { + "author_name": "Noor Muhammad Khan", + "author_inst": "Mawlana Bhashani Science and Technology University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.23.20111526", "rel_title": "Hasty Reduction of COVID-19 Lockdown Measures Leads to the Second Wave of Infection", @@ -1428878,29 +1431831,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.05.24.20111625", - "rel_title": "Comparison of epidemic control strategies using agent-based simulations", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20111625", - "rel_abs": "A simulation of the dynamics of a small population is used to assess the impact of different confinement and testing strategies in the control of an epidemic. The simulation considers individuals as agents moving randomly across the habitat according to predefined urban patterns. Agents carry a simple tracing device that identifies signals emitted by other agents, recording the position and time of the encounter. The information of every device is propagated daily to an epidemic observatory based on an online graph database. Infections are simulated as stochastic processes depending on the proximity among individuals. Different epidemic control strategies are tested with and without the information of the tracing device under several scenarios. We observe that the success of the strategies strongly depends on the duration of the period of infectiousness before the presence of symptoms and the fraction of asymptomatic agents. If these values are high, strategies based on the presence of symptoms or on testing campaigns can hardly contain the epidemic. Strategies using massive confinement of the agents are able to control the epidemic at the cost of sending a large fraction of the population into quarantine. In cases with moderate and low values for these parameters, the tracing devices can provide a slightly better performance but only if a large fraction of the agents carry the device. Otherwise, the impact of these devices is found to be negligible in comparison with other strategies not using them. Finally, we provide a methodology allowing to use the information of the graph database to estimate basic parameters of the disease such as the infection probability.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Pablo Martinez Ruiz del Arbol", - "author_inst": "Instituto de Fisica de Cantabria" - }, - { - "author_name": "Lara Lloret Iglesias", - "author_inst": "Instituto de Fisica de Cantabria" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.25.20111047", "rel_title": "Characteristics of Ischemic Stroke in COVID-19: A Need for Early Detection and Management", @@ -1429193,6 +1432123,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.23.20110189", + "rel_title": "Explainable machine learning models to understand determinants of COVID-19 mortality in the United States", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20110189", + "rel_abs": "BackgroundCOVID-19 is now one of the leading causes of mortality amongst adults in the United States for the year 2020. Multiple epidemiological models have been built, often based on limited data, to understand the spread and impact of the pandemic. However, many geographic and local factors may have played an important role in higher morbidity and mortality in certain populations.\n\nObjectiveThe goal of this study was to develop machine learning models to understand the relative association of socioeconomic, demographic, travel, and health care characteristics of different states across the United States and COVID-19 mortality.\n\nMethodsUsing multiple public data sets, 24 variables linked to COVID-19 disease were chosen to build the models. Two independent machine learning models using CatBoost regression and random forest were developed. SHAP feature importance and a Boruta algorithm were used to elucidate the relative importance of features on COVID-19 mortality in the United States.\n\nResultsFeature importances from both the categorical models, i.e., CatBoost and random forest consistently showed that a high population density, number of nursing homes, number of nursing home beds and foreign travel were strongest predictors of COVID-19 mortality. Percentage of African American amongst the population was also found to be of high importance in prediction of COVID-19 mortality whereas racial majority (primarily, Caucasian) was not. Both models fitted the data well with a training R2 of 0.99 and 0.88 respectively. The effect of median age,median income, climate and disease mitigation measures on COVID-19 related mortality remained unclear.\n\nConclusionsCOVID-19 policy making will need to take population density, pre-existing medical care and state travel policies into account. Our models identified and quantified the relative importance of each of these for mortality predictions using machine learning.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Piyush Mathur", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Tavpritesh Sethi", + "author_inst": "IIIT-Delhi" + }, + { + "author_name": "Anya Mathur", + "author_inst": "Broadview-Brecksville Middle School" + }, + { + "author_name": "Ashish Kumar Khanna", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Kamal Maheshwari", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Jacek B Cywinski", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Simran Dua", + "author_inst": "Lambert High School" + }, + { + "author_name": "Frank Papay", + "author_inst": "Cleveland Clinic" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.05.24.20111872", "rel_title": "Predicting COVID-19 Pandemic in Saudi Arabia Using Modified Singular Spectrum Analysis", @@ -1430404,29 +1433381,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.24.20112128", - "rel_title": "Estimation and monitoring of COVID-19 transmissibility from publicly available data", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20112128", - "rel_abs": "The COVID-19 pandemic began in the city of Wuhan, China, at the end of 2019 and quickly spread worldwide. The disease is caused by contact with the SARS-CoV-2 virus, which probably jumped from an animal host to humans. SARS-CoV-2 infects various tissues in the body, notably the lungs, and patients usually die from respiratory complications. Mathematical models of the disease have been instrumental to guide the implementation of mitigation strategies aimed at slowing the spread of the disease. One of the key parameters of mathematical models is the basic reproduction ratio R0, which measures the degree of infectivity of affected individuals. The goal of mitigation is to reduce R0 as close or below 1 as possible, as it means that new infections are in decline. In the present work, we use the recursive least-squares algorithm to establish the stochastic variability of a time-varying R0(t) from eight different countries: Argentina, Belgium, Brazil, Germany, Italy, New Zealand, Spain, and the United States of America. The proposed system can be implemented as an online tracking application providing information about the dynamics of the pandemic to health officials and the public at large.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Antonio da Silva Silveira", - "author_inst": "Federal University of Para" - }, - { - "author_name": "Antonio Pereira Jr.", - "author_inst": "Federal University of Para" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.23.20110965", "rel_title": "Association of age, sex, comorbidities, and clinical symptoms with the severity and mortality of COVID-19 cases: a meta-analysis with 85 studies and 67299 cases", @@ -1430575,6 +1433529,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.23.20111435", + "rel_title": "Enveloped Virus Inactivation on Personal Protective Equipment by Exposure to Ozone", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20111435", + "rel_abs": "Ozone is a highly oxidizing gas easily generated from atmospheric oxygen with inexpensive equipment and is commonly used for the disinfection of municipal water, foods, and surfaces. We report tests of the ability of ozone to inactivate enveloped respiratory viruses (influenza A virus and respiratory syncytial virus), chosen as more easily handled surrogates for SARS-CoV-2, on N95 respirators and other personal protective equipment (PPE) commonly used in hospitals. At 20 ppm, an ozone concentration easily achieved by standard commercial equipment, the viruses were inactivated with high efficiency as long as the relative humidity was above a threshold value of approximately 50%. In the absence of humidity control, disinfection is more variable and requires considerably longer exposure under relatively dry conditions. This report extends the observations of a previous publication (http://doi.org/10.1080/01919510902747969) to hospital-relevant materials and provides additional details about the relationship of humidity to the antiviral activity of ozone. Home CPAP disinfection devices using ozone can provide effective results for individuals. Ozone did not appear to degrade any of the materials tested except for elastic bands if strained during treatment (such as by the pressure exerted by stapled attachment to N95 respirators). The filtration efficiency of N95 respirator material was not compromised. Overall, we recommend exposures of at least 40 minutes to 20 ppm ozone and >70% relative humidity at ambient temperatures (21-24{degrees}C) for 4-log (99.99%) reduction of viral infectivity on a variety of PPE, including gowns, face shields, and respirators. Shorter exposure times are likely to be effective under these conditions, but at the risk of some variability for different materials. Higher ozone concentrations and higher humidity levels promoted faster inactivation of viruses. Our work suggests that ozone exposure can be a widely accessible method for disinfecting PPE, permitting safer re-use for healthcare workers and patients alike in times of shortage.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Emmeline L. Blanchard", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Justin D. Lawrence", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Jeffery A. Noble", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Minghao Xu", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Taekyu Joo", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Nga Lee Ng", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Britney E. Schmidt", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Philip J. Santangelo", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "M.G. Finn", + "author_inst": "Georgia Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.26.20113357", "rel_title": "Excess mortality in England and Wales during the first wave of the COVID-19 pandemic", @@ -1431630,29 +1434635,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2020.05.23.20111039", - "rel_title": "Worldwide and Regional Forecasting of Coronavirus (Covid-19) Spread using a Deep Learning Model", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20111039", - "rel_abs": "In December 2019, Covid-19 epidemic was identified in Wuhan, China. Covid-19 may cause fatality especially among elderly, and people with chronic health problems. After human to human transmissions of the disease, it has rapidly spread throughout China, and then the outbreak has reached to neighboring countries in Asia. Now, the spread of the virus is accelerating in the world, and increasing number of new cases has been reported daily in Europe, Middle East, Africa and America regions. Recently, World Health Organization (WHO) also announced Covid-19 as a Pandemic. As of 3 April, worldwide around more than 1 million cases and around 60,000 fatalities are reported. Thus, forecasting regional and worldwide outbreak size of Covid-19 is important in order to take necessary actions regarding to preparedness plans and mitigation interventions. In this work, we design a deep learning model, which is an effective artificial intelligence method, to provide regional and worldwide forecasts. Particularly for worldwide, our approach predicts the cumulative number of cases, cumulative number of deaths and daily new cases. For Europe and Middle East regions, we predict the cumulative number of cases, and for Mainland China we predict daily new cases and the cumulative number of deaths. We predict the next 10 days based on the previously reported actual time series data of Covid-19. For worldwide forecasts, we use the data provided by Worldometers. For Europe and Middle East forecasts, we use the data provided by World Health Organization, and for China Mainland forecasts, the data is obtained from Chinese Centre for Disease Control and Prevention. This is the first time that a deep learning model has been employed for Covid-19 spread prediction, solely based on the known reported cases of Covid-19. The proposed deep learning architecture consists of Long Short Term Memory (LSTM) layer, dropout layer, and fully connected layers to predict regional and worldwide forecasts. We evaluate our approach with Root Mean Square Error (RMSE) metric. For forecasting, we use the network models that give the minimum RMSE on the last 3 days of actual data. Networks, which achieves the minimum RMSE on the last 3 days, are used to predict the next 10 days. Every day, the spread and situations are changing. Our approach can take into account these realtime changes; the deep learning model can be re-trained with new daily data and perform real-time forecasting. Results show that the proposed deep learning model is promising, it can predict possible scenarios regionally and globally for the spread of Covid-19.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Cem Direkoglu", - "author_inst": "Middle East Technical University - Northern Cyprus Campus" - }, - { - "author_name": "Melike Sah", - "author_inst": "Near East University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.05.26.116608", "rel_title": "Structure, function and variants analysis of the androgen-regulated TMPRSS2, a drug target candidate for COVID-19 infection", @@ -1431905,6 +1434887,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.26.116780", + "rel_title": "Study of cell to cell transmission of SARS CoV 2 virus particle using gene network from micro array data", + "rel_date": "2020-05-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.26.116780", + "rel_abs": "Microarray data from SARS CoV2 patients helps to construct a gene network relating to this disease. Analysis of these genes, present in network, highlights their biological functions and related cellular pathways. With the assistance of these information, a drug(s) can be identified to treat COVID-19. A detailed analysis of the human host response to SARS CoV 2 with expression profiling by high throughput sequencing has executed with primary human lung epithelium cell lines. Clustered genes annotation and gene network construction are performed with the help of String database. Among four cluster of genes from microarray data, cluster 1 is identified as basal cells with p= 1.37e-05 with 44 genes. Functional enrichment analysis of genes present in gene network has completed using String database, ToppFun online tool and NetworkAnalyst tool. For SARS CoV2 virus particles, keratin proteins, which are part of cytoskeleton structure of host cell, play a major role in cell to cell virus particle transmission. Among three types of cell- cell communication, only anchoring junction between basal cell membrane and basal lamina, is involved in this virus transmission. In this junction point, hemidesmosome structure play a vital role in virus spread from one cell to basal lamina in respiratory tract. In this protein complex structure, keratin, integrin and laminin proteins of host cell is used to promote the spread of virus infection into extracellular matrix. So, small molecular blockers of different anchoring junction proteins i.e. ITGA3, ITGA2 can provide efficient protection against this deadly virus disease. Understanding the human host response against this virus is very important to develop novel therapeutics for the treatment of SARS-CoV 2.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Anamika Basu", + "author_inst": "Gurudas College" + }, + { + "author_name": "Anasua Sarkar", + "author_inst": "Jadavpur University" + }, + { + "author_name": "Ujjwal Maulik", + "author_inst": "Jadavpur University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.23.20110999", "rel_title": "Modelling COVID-19 Transmission in the United States through Interstate and Foreign Travels and Evaluating Impact of Governmental Public Health Interventions", @@ -1433116,33 +1436125,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2020.05.22.20110163", - "rel_title": "Low Covid-19 hospitalisation in Dumfries and Galloway: comparison with other Scottish health boards", - "rel_date": "2020-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20110163", - "rel_abs": "BackgroundCovid-19 virus activity appears to have affected some parts of the United Kingdom more than others. Dumfries and Galloway (D&G) has seen fewer hospitalised cases than predicted. We wondered whether this might be related at least in part to population density.\n\nMethodsWe compared Covid-19 hospitalisation rates/100,000 population in D&G with those of the other 10 mainland Scottish health boards. We chose two time points: 19th April which was the peak of the pandemic in Scotland and 15th May, seven and a half weeks after lockdown. We used chi square and odds ratios with 95% confidence intervals to test for differences in hospitalisation rates and Pearsons correlation coefficient to examine the relation between hospitalisation rates and population density. Population density for each health board was provided by National Records of Scotland.\n\nResultsHospitalisation in D&G was 13.4/100,000 on 19th April, falling to 1.3/100,000 by 15th May. Corresponding hospitalisation rates in Greater Glasgow & Clyde (GGC) were 50.1/100,000 and 38.9/100,000. Compared to GGC, hospitalisation rates in D&G were 3 times lower at peak (OR 0.27, 95% CI 0.17, 0.42) and 30 times lower by 15th May (OR 0.03, 95% CI 0.01, 0.14). Hospitalisation rates for the other health boards lay in between values recorded for D&G and GGC and fell in 10 of the 11 boards between these two dates. There was a positive association between hospitalisation rate and population density (r=0.756, p=0.007 on 19th April and r=0.840, p<0.001 for 15th May).\n\nConclusionWe have confirmed there are large differences in Covid-19 hospitalisation rates across the 11 mainland Scottish health boards, that are in part related to population density. These data support a regional rather than one nation approach to easing Covid-19 restrictions.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Andrew Rideout", - "author_inst": "Department of Public Health, NHS Dumfries and Galloway." - }, - { - "author_name": "Calum Murray", - "author_inst": "Education Centre, Dumfries and Galloway Royal Infirmary, Dumfries DG2 8RX" - }, - { - "author_name": "Chris Isles", - "author_inst": "Dumfries Royal Infirmary" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2020.05.22.20109231", "rel_title": "Association of country-wide coronavirus mortality with demographics, testing, lockdowns, and public wearing of masks.", @@ -1433275,6 +1436257,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.21.20108910", + "rel_title": "Global Infodemiology of COVID-19: Focus on Google web searches and Instagram hashtags", + "rel_date": "2020-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20108910", + "rel_abs": "BackgroundThough infodemiological methods have been used in COVID-19 research, an examination of the extent of infodemic monikers (misinformation) use on the Internet remains limited.\n\nObjectiveTo investigate Internet search behavior related to COVID-19 and examine the circulation of infodemic monikers through two platforms--Google and Instagram--during the current global pandemic.\n\nMethodsUsing Google Trends and Instagram hashtags (#), we explored Internet search activities and behaviors related to the COVID-19 pandemic from February 20, 2020, to May 06, 2020. We investigated the names used to identify the virus, health and risk perception, life during the lockdown, and information related to the adoption of COVID-19 infodemic monikers. We computed the average peak volume (APC) with a 95% confidence interval (CI) during the study period for the monikers.\n\nResultsThe top five COVID-19-related terms in the Google searches were \"coronavirus\", \"corona\", \"COVID\", \"virus\", \"corona virus\", and \"COVID-19\". Countries with a higher number of COVID-19 cases had a higher number of COVID-19 queries on Google. The monikers \"coronavirus ozone\", \"coronavirus laboratory\", \"coronavirus 5G\", \"coronavirus conspiracy\" and \"coronavirus bill gates\" were widely circulated on the Internet. Searches about tips and cures for COVID-19 spiked in relation to the U.S. president speculating about a miracle cure and suggesting the injection of disinfectant to treat the virus. Around two-thirds (66.1%) of Instagram users used the hashtags \"COVID-19\", and \"coronavirus\" to disperse virus-related information.\n\nConclusionGlobally, there is a growing interest in COVID-19, and numerous infodemic monikers continue to circulate on the Internet. Based on our findings, we hope to encourage mass media regulators and health organizers to be vigilant and diminish the use and circulation of these infodemic monikers on the Internet, to decrease the spread of misinformation.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Alessandro Rovetta", + "author_inst": "Mensana srls" + }, + { + "author_name": "Akshaya Srikanth Bhagavathula", + "author_inst": "United Arab Emirates University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.21.20108233", "rel_title": "Performance and impact of disposable and reusable respirators for healthcare workers during pandemic respiratory disease: a rapid evidence review.", @@ -1434650,77 +1437655,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.05.24.113423", - "rel_title": "A comparative study of isothermal nucleic acid amplification methods for SARS-CoV-2 detection at point of care", - "rel_date": "2020-05-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.24.113423", - "rel_abs": "COVID-19, caused by the novel coronavirus SARS-CoV-2, has spread worldwide and put most of the world under lockdown. Despite that there have been emergently approved vaccines for SARS-CoV-2, COVID-19 cases, hospitalizations, and deaths have remained rising. Thus, rapid diagnosis and necessary public health measures are still key parts to contain the pandemic. In this study, the colorimetric isothermal nucleic acid amplification tests (iNAATs) for SARS-CoV-2 detection based on loop-mediated isothermal amplification (LAMP), cross-priming amplification (CPA), and polymerase spiral reaction (PSR) were designed and evaluated. The three methods showed the same limit of detection (LOD) value of 1 copy of the targeted gene per reaction. However, for the direct detection of SARS-CoV-2 genomic-RNA, LAMP outperformed both CPA and PSR, exhibiting the LOD value of roughly 43.14 genome copies/reaction. The results can be read with the naked eye within 45 minutes, without cross-reactivity to closely related coronaviruses. Moreover, the direct detection of SARS-CoV-2 RNA in simulated patient specimens by iNAATs was also successful. Finally, the ready-to-use lyophilized reagents for LAMP reactions were shown to maintain the sensitivity and LOD value of the liquid assays. The results indicate that the colorimetric lyophilized LAMP kit developed herein is highly suitable for detecting SARS-CoV-2 nucleic acids at point-of-care.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Diem Hong Tran", - "author_inst": "NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Quoc Cuong Hoang", - "author_inst": "Directorial Board, Pasteur Institute in Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Hau Thi Tran", - "author_inst": "NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Uyen Phuong Le", - "author_inst": "NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Hoang Dang Khoa Do", - "author_inst": "NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Le Minh Bui", - "author_inst": "NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Duc Hai Nguyen", - "author_inst": "Planning Division, Pasteur Institute in Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Thuy Linh Hoang", - "author_inst": "Medical Analysis Department, Pasteur Institute in Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Thi Thanh Thao Nguyen", - "author_inst": "Microbiology and Immunology Department, Pasteur Institute in Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Hoang Anh Nguyen", - "author_inst": "Microbiology and Immunology Department, Pasteur Institute in Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Trung Hieu Nguyen", - "author_inst": "Microbiology and Immunology Department, Pasteur Institute in Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Minh Thang Cao", - "author_inst": "Microbiology and Immunology Department, Pasteur Institute in Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Van Van Vu", - "author_inst": "NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Huong Thi Thu Phung", - "author_inst": "NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.05.24.113043", "rel_title": "Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein", @@ -1434881,6 +1437815,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.24.20112136", + "rel_title": "Spatiotemporal Analysis of Medical Resource Deficiencies in the U.S. under COVID-19 Pandemic", + "rel_date": "2020-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20112136", + "rel_abs": "A data-driven approach is developed to estimate medical resource deficiencies or medical burden at county level during the COVID-19 pandemic from February 15, 2020 to May 1, 2020 in the U.S. Multiple data sources were used to extract local population, hospital beds, critical care staff, COVID-19 confirmed case numbers, and hospitalization data at county level. We estimate the average length of stay from hospitalization data at state level, and calculate the hospitalized rate at both state and county level. Then we develop two medical resource deficiency indices that measure the local medical burden based on the number of accumulated active confirmed cases normalized by local maximum potential medical resources, and the number of hospitalized patients that can be supported per ICU beds per critical care staff, respectively. The medical resources data, and the two medical resource deficiency indices are illustrated in a dynamic spatiotemporal visualization platform based on ArcGIS Pro Dashboards. Our results provide new insights into the U.S. pandemic preparedness and local dynamics relating to medical burdens in response to the COVID-19 pandemic.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Dexuan Sha", + "author_inst": "NSF Spatiotemporal Innovation Center, George Mason University, Fairfax, VA 22030" + }, + { + "author_name": "Xin Miao", + "author_inst": "Department of Geography, Geology and Planning, Missouri State University" + }, + { + "author_name": "Hai Lan", + "author_inst": "Department of Geographical Sciences, University of Maryland" + }, + { + "author_name": "Kathleen Stewart", + "author_inst": "Department of Geographical Sciences, University of Maryland" + }, + { + "author_name": "Shiyang Ruan", + "author_inst": "Department of Geography and GeoInformation Science, George Mason University" + }, + { + "author_name": "Yifei Tian", + "author_inst": "NSF Spatiotemporal Innovation Center, George Mason University" + }, + { + "author_name": "Yuyang Tian", + "author_inst": "Mercy Clinic Family Medicine" + }, + { + "author_name": "Chaowei Yang", + "author_inst": "NSF Spatiotemporal Innovation Center, George Mason University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.19.20107458", "rel_title": "The IGNITE Trial: Participant Recruitment Lessons Prior to SARS-CoV-2", @@ -1436064,177 +1439045,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.23.20110916", - "rel_title": "A systems approach to inflammation identifies therapeutic targets in SARS-CoV-2 infection", - "rel_date": "2020-05-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20110916", - "rel_abs": "BackgroundInfection with SARS-CoV-2 manifests itself as a mild respiratory tract infection in the majority of individuals, which progresses to a severe pneumonia and acute respiratory distress syndrome (ARDS) in 10-15% of patients. Inflammation plays a crucial role in the pathogenesis of ARDS, with immune dysregulation in severe COVID-19 leading to a hyperinflammatory response. A comprehensive understanding of the inflammatory process in COVID-19 is lacking.\n\nMethodsIn this prospective, multicenter observational study, patients with PCR-proven or clinically presumed COVID-19 admitted to the intensive care unit (ICU) or clinical wards were included. Demographic and clinical data were obtained and plasma was serially collected. Concentrations of IL-6, TNF-, complement components C3a, C3c and the terminal complement complex (TCC) were determined in plasma by ELISA. Additionally, 269 circulating biomarkers were assessed using targeted proteomics. Results were compared between ICU and non ICU patients.\n\nFindingsA total of 119 (38 ICU and 91 non ICU) patients were included. IL-6 plasma concentrations were elevated in COVID-19 (ICU vs. non ICU, median 174.5 pg/ml [IQR 94.5-376.3] vs. 40.0 pg/ml [16.5-81.0]), whereas TNF- concentrations were relatively low and not different between ICU and non ICU patients (median 24.0 pg/ml [IQR 16.5-33.5] and 21.5 pg/ml [IQR 16.0-33.5], respectively). C3a and terminal complement complex (TCC) concentrations were significantly higher in ICU vs. non ICU patients (median 556.0 ng/ml [IQR 333.3-712.5]) vs. 266.5 ng/ml [IQR 191.5-384.0] for C3a and 4506 mAU/ml [IQR 3661-6595] vs. 3582 mAU/ml [IQR 2947-4300] for TCC) on the first day of blood sampling. Targeted proteomics demonstrated that IL-6 (logFC 2.2), several chemokines and hepatocyte growth factor (logFC 1.4) were significantly upregulated in ICU vs. non ICU patients. In contrast, stem cell factor was significantly downregulated (logFC -1.3) in ICU vs. non ICU patients, as were DPP4 (logFC -0.4) and protein C inhibitor (log FC -1.0), the latter two factors also being involved in the regulation of the kinin-kallikrein pathway. Unsupervised clustering pointed towards a homogeneous pathogenetic mechanism in the majority of patients infected with SARS-CoV-2, with patient clustering mainly based on disease severity.\n\nInterpretationWe identified important pathways involved in dysregulation of inflammation in patients with severe COVID-19, including the IL-6, complement system and kinin-kallikrein pathways. Our findings may aid the development of new approaches to host-directed therapy.\n\nFundingVidi grant (F.L.v.d.V.) and Spinoza grant (M.G.N.) from the Netherlands Organization for Scientific Research, and ERC Advanced Grant (#833247 to M.G.N.).", - "rel_num_authors": 39, - "rel_authors": [ - { - "author_name": "Frank L. van de Veerdonk", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Nico A.F. Janssen", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Inge Grondman", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Aline H. de Nooijer", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Valerie A.C.M. Koeken", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Vasiliki Matzaraki", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Collins K. Boahen", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Vinod Kumar", - "author_inst": "Radboud University Medical Center and University Medical Center Groningen" - }, - { - "author_name": "Matthijs Kox", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Hans J.P.M. Koenen", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Ruben L. Smeets", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Irma Joosten", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Roger J.M. Br\u00fcggemann", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Ilse J.E. Kouijzer", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Hans G. van der Hoeven", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Jeroen A. Schouten", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Tim Frenzel", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Monique Reijers", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Wouter Hoefsloot", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Anton S.M. Dofferhoff", - "author_inst": "Canisius Wilhelmina Hospital" - }, - { - "author_name": "Ang\u00e8le P.M. Kerckhoffs", - "author_inst": "Jeroen Bosch Hospital" - }, - { - "author_name": "Marc J.T. Blaauw", - "author_inst": "Bernhoven Hospital" - }, - { - "author_name": "Karin Veerman", - "author_inst": "Sint Maartenskliniek" - }, - { - "author_name": "Coen Maas", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Arjan H. Schoneveld", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Imo E. Hoefer", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Lennie P.G. Derde", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Loek Willems", - "author_inst": "Hycult Biotechnology" - }, - { - "author_name": "Erik Toonen", - "author_inst": "Hycult Biotechnology" - }, - { - "author_name": "Marcel van Deuren", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Jos W.M. van der Meer", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Reinout van Crevel", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Evangelos J. Giamarellos-Bourboulis", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Leo A.B. Joosten", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Michel M. van den Heuvel", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Jacobien Hoogerwerf", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Quirijn de Mast", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Peter Pickkers", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Mihai G. Netea", - "author_inst": "Radboud University Medical Center and University of Bonn" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.23.20110866", "rel_title": "Visualizing the COVID-19 pandemic in Bangladesh using coxcombs: A tribute to Florence Nightingale", @@ -1436443,6 +1439253,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.05.22.20110403", + "rel_title": "Why are most COVID-19 infection curves linear?", + "rel_date": "2020-05-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20110403", + "rel_abs": "Many countries have passed their first COVID-19 epidemic peak. Traditional epidemiological models describe this as a result of non-pharmaceutical interventions that pushed the growth rate below the recovery rate. In this new phase of the pandemic many countries show an almost linear growth of confirmed cases for extended time-periods. This new containment regime is hard to explain by traditional models where infection numbers either grow explosively until herd immunity is reached, or the epidemic is completely suppressed (zero new cases). Here we offer an explanation of this puzzling observation based on the structure of contact networks. We show that for any given transmission rate there exists a critical number of social contacts, Dc, below which linear growth and low infection prevalence must occur. Above Dc traditional epidemiological dynamics takes place, as e.g. in SIR-type models. When calibrating our corresponding model to empirical estimates of the transmission rate and the number of days being contagious, we find Dc ~ 7.2. Assuming realistic contact networks with a degree of about 5, and assuming that lockdown measures would reduce that to household-size (about 2.5), we reproduce actual infection curves with a remarkable precision, without fitting or fine-tuning of parameters. In particular we compare the US and Austria, as examples for one country that initially did not impose measures and one that responded with a severe lockdown early on. Our findings question the applicability of standard compartmental models to describe the COVID-19 containment phase. The probability to observe linear growth in these is practically zero.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Stefan Thurner", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Peter Klimek", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Rudolf Hanel", + "author_inst": "Medical University of Vienna" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.22.20110320", "rel_title": "Mortality of the COVID-19 outbreak in Sweden in relation to previous severe disease outbreaks", @@ -1437510,29 +1440347,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.21.20108860", - "rel_title": "Immunity after COVID-19: protection or sensitization ?", - "rel_date": "2020-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20108860", - "rel_abs": "Motivated by historical and present clinical observations, we discuss the possible unfavorable evolution of the immunity (similar to documented antibody-dependent enhancement scenarios) after a first infection with COVID-19. More precisely we ask the question of how the epidemic outcomes are affected if the initial infection does not provide immunity but rather sensitization to future challenges. We first provide background comparison with the 2003 SARS epidemic. Then we use a compartmental epidemic model structured by immunity level that we fit to available data; using several scenarios of the fragilization dynamics, we derive quantitative insights into the additional expected numbers of severe cases and deaths.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Antoine Danchin", - "author_inst": "Institut Cochin" - }, - { - "author_name": "Gabriel TURINICI", - "author_inst": "Universite Paris Dauphine - PSL" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.20.20108340", "rel_title": "The estimations of the COVID-19 incubation period: a systematic review of the literature", @@ -1437669,6 +1440483,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.21.20108639", + "rel_title": "Validation of the Kuwait Progression Indicator Score for predicting progression of severity in COVID19", + "rel_date": "2020-05-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20108639", + "rel_abs": "IntroductionIdentifying patients with COVID-19, at risk of having a severe clinical course during their hospitalization is important for appropriate allocation of clinical resources. We recently described the Kuwait Progression Indicator based on laboratory findings, in an initial training cohort derived from the first series of 1096 consecutive patients admitted to Jaber Al-Ahmad Al-Sabah Hospital in Kuwait. The aim of this study was to validate the KPI scoring system in an independent cohort of patients with COVID-19.\n\nMethodologyData was collected prospectively for consecutive patients admitted to Jaber Al-Ahmad Al-Sabah Hospital in Kuwait between 24th February - 28th April 2020. Patients were grouped according to the severity of their clinical course as their main outcome, based on clinical and radiological parameters, with ICU admission and death as secondary outcomes. Model discrimination was assessed through the area under the receiver operating characteristic curve (AUC) while model calibration was assessed through a calibration plot and measures of slope and calibration in the large (CITL).\n\nResultsOf 752 patients not used in model development previously, 414 met the criteria for inclusion in this validation study. The baseline characteristics for these 752 patients were similar to the patients that were included in our validation cohort. The area under the curve was equal to 0.904 (95% CI, 0.867-0.942), indicating good model discrimination. The calibration plot and CITL confirmed reasonably good model calibration. Sensitivity and specificity were above 90% for the low and high risk levels respectively.\n\nConclusionsWe were able to validate our previously described laboratory based prognostic scoring system for COVID-19 patients, to predict which patients progressed to a severe clinical course.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Sarah Al Youha", + "author_inst": "Jaber Al-Ahmad Al-Sabah Hospital" + }, + { + "author_name": "Suhail A. Doi", + "author_inst": "Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar" + }, + { + "author_name": "Mohammad H. Jamal", + "author_inst": "COVID-19 Research Group, Jaber Al-Ahmad Al-Sabah Hospital, Ministry of Health, Kuwait" + }, + { + "author_name": "Sulaiman Almazeedi", + "author_inst": "COVID-19 Research Group, Jaber Al-Ahmad Al-Sabah Hospital, Ministry of Health, Kuwait" + }, + { + "author_name": "Mohannad Al Haddad", + "author_inst": "COVID-19 Research Group, Jaber Al-Ahmad Al-Sabah Hospital, Ministry of Health, Kuwait" + }, + { + "author_name": "Mohammad AlSeaidan", + "author_inst": "Public Health Administration, Ministry of Health, Kuwait" + }, + { + "author_name": "Ali Y. Al-Muhaini", + "author_inst": "COVID-19 Research Group, Jaber Al-Ahmad Al-Sabah Hospital, Ministry of Health, Kuwait" + }, + { + "author_name": "Fahad Al-Ghimlas", + "author_inst": "Public Health Administration, Ministry of Health, Kuwait" + }, + { + "author_name": "Salman K. Al-Sabah", + "author_inst": "COVID-19 Research Group, Jaber Al-Ahmad Al-Sabah Hospital, Ministry of Health, Kuwait" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.21.20108985", "rel_title": "Congregate Shelter Characteristics and Prevalence of Asymptomatic SARS-CoV-2", @@ -1439164,41 +1442029,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "ophthalmology" }, - { - "rel_doi": "10.1101/2020.05.20.20108183", - "rel_title": "A Rapid Review of the Asymptomatic Proportion of PCR-Confirmed SARS-CoV-2 Infections in Community Settings", - "rel_date": "2020-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20108183", - "rel_abs": "BackgroundUp to 80% of active SARS-CoV-2 infections are proposed to be asymptomatic based on cross-sectional studies. However, accurate estimates of the asymptomatic proportion require systematic detection and follow-up to differentiate between truly asymptomatic and pre-symptomatic cases. We conducted a rapid review and meta-analysis of current evidence regarding the asymptomatic proportion of PCR-confirmed SARS-CoV-2 infections based on methodologically-appropriate studies in community settings.\n\nMethodsWe searched Medline and EMBASE for peer-reviewed articles, and BioRxiv and MedRxiv for pre-prints published prior to 05/05/2020. We included studies based in community settings that involved systematic PCR testing on participants and follow-up symptom monitoring regardless of symptom status. We extracted data on study characteristics, frequencies of PCR-confirmed infections by symptom status, and (if available) cycle threshold values and/or duration of viral shedding by symptom status. We computed estimates of the asymptomatic proportion and 95% confidence intervals for each study and overall using random effect meta-analysis.\n\nFindingsWe screened 270 studies and included 6. The pooled estimate for the asymptomatic proportion of SARS-CoV-2 infections was 11% (95% CI 4%-18%). Estimates of baseline viral load appeared to be similar for asymptomatic and symptomatic cases based on available data in three studies, though detailed reporting of cycle threshold values and natural history of viral shedding by symptom status was limited.\n\nInterpretationThe asymptomatic proportion of SARS-CoV-2 infections is relatively low when estimated from methodologically-appropriate studies. Further investigation into the degree and duration of infectiousness for asymptomatic infections is warranted.\n\nFundingMedical Research Council", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sarah Beale", - "author_inst": "University College London" - }, - { - "author_name": "Andrew Hayward", - "author_inst": "University College London" - }, - { - "author_name": "Laura Shallcross", - "author_inst": "University College London" - }, - { - "author_name": "Robert W Aldridge", - "author_inst": "University College London" - }, - { - "author_name": "Ellen Fragaszy", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.20.20108068", "rel_title": "Demographic and Clinical Characteristics of the Severe Covid-19 Infections: First Report from Mashhad University of Medical Sciences, Iran", @@ -1439403,6 +1442233,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.21.20109439", + "rel_title": "Longitudinal laboratory testing tied to PCR diagnostics in COVID-19 patients reveals temporal evolution of distinctive coagulopathy signatures", + "rel_date": "2020-05-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20109439", + "rel_abs": "Temporal inference from laboratory testing results and their triangulation with clinical outcomes as described in the associated unstructured text from the providers notes in the Electronic Health Record (EHR) is integral to advancing precision medicine. Here, we studied 181 COVIDpos and 7,775 COVIDneg patients subjected to 1.3 million laboratory tests across 194 assays during a two-month observation period centered around their SARS-CoV-2 PCR testing dates. We found that compared to COVIDneg at the time of clinical presentation and diagnostic testing, COVIDpos patients tended to have higher plasma fibrinogen levels and similarly low platelet counts, with approximately 25% of patients in both cohorts showing outright thrombocytopenia. However, these measures show opposite longitudinal trends as the infection evolves, with declining fibrinogen and increasing platelet counts to levels that are lower and higher compared to the COVIDneg cohort, respectively. Our EHR augmented curation efforts suggest a minority of patients develop thromboembolic events after the PCR testing date, including rare cases with disseminated intravascular coagulopathy (DIC), with most patients lacking the platelet reductions typically observed in consumptive coagulopathies. These temporal trends present, for the first time, fine-grained resolution of COVID-19 associated coagulopathy (CAC), via a digital framework that synthesizes longitudinal lab measurements with structured medication data and neural network-powered extraction of outcomes from the unstructured EHR. This study demonstrates how a precision medicine platform can help contextualize each patients specific coagulation profile over time, towards the goal of informing better personalization of thromboprophylaxis regimen.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Colin Pawlowski", + "author_inst": "nference" + }, + { + "author_name": "Tyler Wagner", + "author_inst": "nference" + }, + { + "author_name": "Arjun Puranik", + "author_inst": "nference" + }, + { + "author_name": "Karthik Murugadoss", + "author_inst": "nference" + }, + { + "author_name": "Liam Loscalzo", + "author_inst": "nference" + }, + { + "author_name": "AJ Venkatakrishnan", + "author_inst": "nference" + }, + { + "author_name": "Rajiv K Pruthi", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Damon E Houghton", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "John C O'Horo", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "William G Morice", + "author_inst": "Mayo Clinic Laboratories" + }, + { + "author_name": "John Halamka", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Andrew D Badley", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Elliot S Barnathan", + "author_inst": "Janssen pharmaceutical companies of Johnson & Johnson (J&J)" + }, + { + "author_name": "Hideo Makimura", + "author_inst": "Janssen pharmaceutical companies of Johnson & Johnson (J&J)" + }, + { + "author_name": "Najat Khan", + "author_inst": "Janssen pharmaceutical companies of Johnson & Johnson (J&J)" + }, + { + "author_name": "Venky Soundararajan", + "author_inst": "nference" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.20.20108415", "rel_title": "Underreporting of death by COVID-19 in Brazil's second most populous state", @@ -1440394,65 +1443303,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.18.20105841", - "rel_title": "An Interpretable Machine Learning Framework for Accurate Severe vs Non-severe COVID-19 Clinical Type Classification", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20105841", - "rel_abs": "Effectively and efficiently diagnosing COVID-19 patients with accurate clinical type is essential to achieve optimal outcomes for the patients as well as reducing the risk of overloading the healthcare system. Currently, severe and non-severe COVID-19 types are differentiated by only a few clinical features, which do not comprehensively characterize complicated pathological, physiological, and immunological responses to SARS-CoV-2 invasion in different types. In this study, we recruited 214 confirmed COVID-19 patients in non-severe and 148 in severe type, from Wuhan, China. The patients comorbidity and symptoms (26 features), and blood biochemistry (26 features) upon admission were acquired as two input modalities. Exploratory analyses demonstrated that these features differed substantially between two clinical types. Machine learning random forest (RF) models using features in each modality were developed and validated to classify COVID-19 clinical types. Using comorbidity/symptom and biochemistry as input independently, RF models achieved >90% and >95% predictive accuracy, respectively. Input features importance based on Gini impurity were further evaluated and top five features from each modality were identified (age, hypertension, cardiovascular disease, gender, diabetes; D-Dimer, hsTNI, neutrophil, IL-6, and LDH). Combining top 10 multimodal features, RF model achieved >99% predictive accuracy. These findings shed light on how the human body reacts to SARS-CoV-2 invasion as a unity and provide insights on effectively evaluating COVID-19 patients severity and developing treatment plans accordingly. We suggest that symptoms and comorbidities can be used as an initial screening tool for triaging, while biochemistry and features combined are applied when accuracy is the priority.\n\nOne Sentence SummaryWe trained and validated machine learning random forest (RF) models to predict COVID-19 severity based on 26 comorbidity/symptom features and 26 biochemistry features from a cohort of 214 non-severe and 148 severe type COVID-19 patients, identified top features from both feature modalities to differentiate clinical types, and achieved predictive accuracy of >90%, >95%, and >99% when comorbidity/symptom, biochemistry, and combined top features were used as input, respectively.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Yuanfang Chen", - "author_inst": "Institute of HIV/AIDS/STI Prevention and Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China" - }, - { - "author_name": "Liu Ouyang", - "author_inst": "Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China" - }, - { - "author_name": "Sheng Bao", - "author_inst": "Department of Computer Science, Iowa State University, USA" - }, - { - "author_name": "Qian Li", - "author_inst": "Department of Pediatrics, Affiliated Kunshan Hospital of Jiangsu University, Kunshan 215300, China" - }, - { - "author_name": "Lei Han", - "author_inst": "Department of Occupational Disease Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China" - }, - { - "author_name": "Hengdong Zhang", - "author_inst": "Department of Occupational Disease Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China" - }, - { - "author_name": "Baoli Zhu", - "author_inst": "Department of Occupational Disease Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China" - }, - { - "author_name": "Ming Xu", - "author_inst": "Department of Occupational Disease Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China" - }, - { - "author_name": "Jie Liu", - "author_inst": "Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China" - }, - { - "author_name": "Yaorong Ge", - "author_inst": "Department of Software and Information Systems, UNC Charlotte, Charlotte, NC 28223, USA" - }, - { - "author_name": "Shi Chen", - "author_inst": "Department of Public Health Sciences, College of Health and Human Services, University of North Carolina Charlotte, Charlotte, NC 28262, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.18.20105239", "rel_title": "Risks to Children under-five in India from COVID-19", @@ -1440681,6 +1443531,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.18.20106013", + "rel_title": "Exploring the spread dynamics of COVID-19 inMorocco", + "rel_date": "2020-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20106013", + "rel_abs": "Despite some similarities of the dynamic of COVID-19 spread in Morocco and other countries, the infection, recovery and death rates remain very variable. In this paper, we analyze the spread dynamics of COVID-19 in Morocco within a standard susceptible-exposed-infected-recovered-death (SEIRD) model. We have combined SEIRD model with a time-dependent infection rate function, to fit the real data of i) infection counts and ii) death rates due to COVID-19, for the period between March 2nd and Mai 15th 2020. By fitting the infection rate, SEIRD model placed the infection peak on 04/24/2020 and could reproduce it to a large extent on the expense of recovery and death rates. Fitting the SEIRD model to death rates gives rather satisfactory predictions with a maximum of infections on 04/06/2020. Regardless of the low peak position, the confirmed cases and transmission rate were well reproduced.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Mohamed NAJI", + "author_inst": "University of Sidi Mohamed Ben Abdellah" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.18.20106104", "rel_title": "Mathematical framework to model Covid-19 daily deaths", @@ -1442136,33 +1445005,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.19.20099317", - "rel_title": "Early antibody response to SARS-CoV-2", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20099317", - "rel_abs": "BackgroundThe role and significance of the immune response to SARS-CoV-2 infection is not yet well known.\n\nMethodsWe conducted a study on 46 symptomatic subjects with disease confirmed by laboratory tests, to evaluate the presence of IgG and IgM antibodies in these subjects in relation to the time elapsed since the onset of symptoms. The analytical performance of the method used in the study and the effect of two different serum and plasma matrices were also assessed.\n\nResultsIgG positivity was demonstrated in 100% of cases 15 days after the onset of the disease. IgM show lower concentrations and do not exceed 77% of cases after 15 days. The analytical performance of the method used (Maglumi 800, Snibe, China) was confirmed to be good in terms of imprecision, linearity and commutability in two sample matrix.\n\nConclusionThe serological study through the search for specific IgG for SARS-CoV-2 results to be sensitive and suitable for population research and evidences that this approach can also play an important role in diagnosis.\n\nThe diagnostic performance of specific IgMs are lower.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ruggero Dittadi", - "author_inst": "Laboratory Medicine, Ospedale dell'Angelo, ULSS3 Serenissima, Mestre, Venice, Italy" - }, - { - "author_name": "Haleh Afshar", - "author_inst": "Laboratory Medicine, Ospedale dell'Angelo, Mestre, Italy" - }, - { - "author_name": "Paolo Carraro", - "author_inst": "Laboratory Medicine, Ospedale dell'Angelo, Mestre, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.18.20086157", "rel_title": "COVID-19 in Great Britain: epidemiological and clinical characteristics of the first few hundred (FF100) cases: a descriptive case series and case control analysis", @@ -1442443,6 +1445285,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.05.17.20104562", + "rel_title": "COVID 19 in Bangladesh: Assumption of possible infection and death", + "rel_date": "2020-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20104562", + "rel_abs": "It is a painful job to predict the death of people. But sometimes it is important to predict the future and concern the government. A furious future is waiting for Bangladesh.\n\nObjectiveObjective of the study is to assume the number of positive case and death till 30th December, 2020 in Bangladesh.\n\nStudy designThis study was designed with systematic review and data analysis.\n\nMethodThe study was completed by analyzing data available on website. First COVID 19 case in Bangladesh was identified on 8th March. Analyzing the data increasing rate/common ratio of infection and death has been identified. Then this common ratio has been used in the formula of multiplication series (at decreasing rate). Data of China, Iran, Italy and the USA was also analyzed to assume how the death and case number increased. Social issues of Bangladesh were also analyzed. Considering all these the assumption was made.\n\nResultIt has been assumed that by the 43rd week (on 30th December, 2020) of first identification the total case can be 15640747 and total death can be 638769 by 30 December, 2020. As this is an assumption this can be true, partially true or false. But the base of assumption is strong enough so the possibility of being true or nearly true is higher.\n\nPolicy SuggestionGovernment should choose properly one between two options. Either government should declare curfew or let people lead normal life for the purpose of herd immunity. A very weak lockdown for a long time doesnt make any sense.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Sadik Hasan Shuvo", + "author_inst": "Jatiya Kabi Kazi Nazrul Islam University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.05.17.20104604", "rel_title": "Characterization of Patients Who Return to Hospital Following Discharge from Hospitalization For COVID-19", @@ -1443742,37 +1446603,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.05.17.20104927", - "rel_title": "Prevalence Threshold and Temporal Interpretation of Screening Tests: The Example of the SARS-CoV-2 (COVID-19) Pandemic", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20104927", - "rel_abs": "The curvilinear relationship between a screening tests positive predictive value (PPV) and its target disease prevalence is proportional. In consequence, there is an inflection point of maximum curvature in the screening curve defined as a function of the sensitivity (a) and specificity (b) beyond which the rate of change of a tests PPV declines sharply relative to disease prevalence ({phi}). Herein, we demonstrate a mathematical model exploring this phenomenon and define the prevalence threshold point ({phi}e) where this change occurs as:\n\nO_FD O_INLINEFIG[Formula]C_INLINEFIGC_FD\n\nUnderstanding where this prevalence point lies in the curve has important implications for the interpretation of test results, the administration of healthcare systems, the implementation of public health measures, and in cases of pandemics like SARS-CoV-2, the functioning of society at large. To illustrate the methods herein described, we provide the example of the screening strategies used in the SARS-CoV-2 (COVID-19) pandemic, and calculate the prevalence threshold statistic of different tests available today. This concept can help contextualize the validity of a screening test in real time, thereby enhancing our understanding of the dynamics of the current pandemic.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jacques Balayla", - "author_inst": "McGill University" - }, - { - "author_name": "Ariane Lasry", - "author_inst": "McGill University" - }, - { - "author_name": "Yaron Gil", - "author_inst": "McGill University" - }, - { - "author_name": "Alexander Volodarsky-Perel", - "author_inst": "McGill University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.17.20104612", "rel_title": "The correspondence between the structure of the terrestrial mobility network and the emergence of COVID-19 in Brazil", @@ -1443965,6 +1446795,45 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.05.21.108506", + "rel_title": "No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2", + "rel_date": "2020-05-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.21.108506", + "rel_abs": "The COVID-19 pandemic is caused by the coronavirus SARS-CoV-2, which jumped into the human population in late 2019 from a currently uncharacterised animal reservoir. Due to this extremely recent association with humans, SARS-CoV-2 may not yet be fully adapted to its human host. This has led to speculations that some lineages of SARS-CoV-2 may be evolving towards higher transmissibility. The most plausible candidate mutations under putative natural selection are those which have emerged repeatedly and independently (homoplasies). Here, we formally test whether any of the recurrent mutations that have been observed in SARS-CoV-2 are significantly associated with increased viral transmission. To do so, we develop a phylogenetic index to quantify the relative number of descendants in sister clades with and without a specific allele. We apply this index to a carefully curated set of recurrent mutations identified within a dataset of 46,723 SARS-CoV-2 genomes isolated from patients worldwide. We do not identify a single recurrent mutation in this set convincingly associated with increased viral transmission. Instead, recurrent SARS-CoV-2 mutations currently in circulation appear to be evolutionary neutral. Recurrent mutations also seem primarily induced by the human immune system via host RNA editing, rather than being signatures of adaptation to the novel human host. In conclusion, we find no evidence at this stage for the emergence of significantly more transmissible lineages of SARS-CoV-2 due to recurrent mutations.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Lucy van Dorp", + "author_inst": "UCL Genetics Institute, University College London, London WC1E 6BT, UK" + }, + { + "author_name": "Damien Richard", + "author_inst": "Cirad" + }, + { + "author_name": "Cedric CS Tan", + "author_inst": "UCL Genetics Institute, University College London, London WC1E 6BT, UK" + }, + { + "author_name": "Liam P. Shaw", + "author_inst": "Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK" + }, + { + "author_name": "Mislav Acman", + "author_inst": "UCL Genetics Institute, University College London, London WC1E 6BT, UK" + }, + { + "author_name": "Francois Balloux", + "author_inst": "UCL Genetics Institute, University College London, London WC1E 6BT, UK" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.05.18.20105569", "rel_title": "Who should we test for COVID-19?A triage model built from national symptom surveys", @@ -1445288,57 +1448157,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2020.05.17.20104901", - "rel_title": "Development of an interactive, agent-based local stochastic model of COVID-19 transmission and evaluation of mitigation strategies illustrated for the state of Massachusetts, USA", - "rel_date": "2020-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20104901", - "rel_abs": "Since its discovery in the Hubei province of China, the global spread of the novel coronavirus SARS-CoV-2 has resulted in millions of COVID-19 cases and hundreds of thousands of deaths. The spread throughout Asia, Europe, and the Americas has presented one of the greatest infectious disease threats in recent history and has tested the capacity of global health infrastructures. Since no effective vaccine is available, isolation techniques to prevent infection such as home quarantine and social distancing while in public have remained the cornerstone of public health interventions. While government and health officials were charged with implementing stay-at-home strategies, many of which had little guidance as to the consequences of how quickly to begin them. Moreover, as the local epidemic curves have been flattened, the same officials must wrestle with when to ease or cease such restrictions as to not impose economic turmoil. To evaluate the effects of quarantine strategies during the initial epidemic, an agent based modeling framework was created to take into account local spread based on geographic and population data with a corresponding interactive desktop and web-based application. Using the state of Massachusetts in the United States of America, we have illustrated the consequences of implementing quarantines at different time points after the initial seeding of the state with COVID-19 cases. Furthermore, we suggest that this application can be adapted to other states, small countries, or regions within a country to provide decision makers with critical information necessary to best protect human health.\n\nAuthor summaryIn this work we presented a local agent-based geographic model for the epidemic spread of COVID-19 with and without quarantine measures. The model is implemented as an interactive Microsoft Windows application, as a web tool online (summaries only), and the source code is freely available at GitHub. In this article, the model is presented for the state of Massachusetts (United States), but can be easily adopted to other administrative districts, areas and territories where the demographics and population characteristics of the reported cases are known. After calibration, the model predicts the morbidity and mortality of the epidemic as it spreads with different quarantine parameters, which lead to reduction of social contact probabilities between individuals. The model outputs for different quarantine start dates and durations are then summarized and compared to actual disease incidence. These summaries demonstrate the effectiveness of the early quarantine measures on the reduction of the number of new infections and deaths. The model framework can also be adopted for use in future decision making process for government and health officials as plans to cease or ease quarantines continue to evolve using the interactive application.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Alexander Kirpich", - "author_inst": "Georgia State University" - }, - { - "author_name": "Vladimir Koniukhovskii", - "author_inst": "EPAM Systems" - }, - { - "author_name": "Vladimir Shvartc", - "author_inst": "EPAM Systems" - }, - { - "author_name": "Pavel Skums", - "author_inst": "Georgia State University" - }, - { - "author_name": "Thomas A. Weppelmann", - "author_inst": "University of South Florida" - }, - { - "author_name": "Evgeny Imyanitov", - "author_inst": "N.N. Petrov Research Institute of Oncology" - }, - { - "author_name": "Semyon Semyonov", - "author_inst": "Quantori" - }, - { - "author_name": "Konstantin Barsukov", - "author_inst": "EPAM Systems" - }, - { - "author_name": "Yuriy Gankin", - "author_inst": "Quantori" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.16.099242", "rel_title": "Capillary Electrophoresis of PCR fragments with labelled primers for testing the SARS-Cov-2", @@ -1445515,6 +1448333,97 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2020.05.21.107565", + "rel_title": "Immunization with the receptor-binding domain of SARS-CoV-2 elicits antibodies cross-neutralizing SARS-CoV-2 and SARS-CoV without antibody-dependent enhancement", + "rel_date": "2020-05-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.21.107565", + "rel_abs": "Recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the pathogen responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic. Currently, there is no vaccine available for preventing SARS-CoV-2 infection. Like closely related severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2 also uses its receptor-binding domain (RBD) on the spike (S) protein to engage the host receptor, human angiotensin-converting enzyme 2 (ACE2), facilitating subsequent viral entry. Here we report the immunogenicity and vaccine potential of SARS-CoV-2 RBD (SARS2-RBD)-based recombinant proteins. Immunization with SARS2-RBD recombinant proteins potently induced a multi-functional antibody response in mice. The resulting antisera could efficiently block the interaction between SARS2-RBD and ACE2, inhibit S-mediated cell-cell fusion, and neutralize both SARS-CoV-2 pseudovirus entry and authentic SARS-CoV-2 infection. In addition, the anti-RBD sera also exhibited cross binding, ACE2-blockade, and neutralization effects towards SARS-CoV. More importantly, we found that the anti-RBD sera did not promote antibody-dependent enhancement of either SARS-CoV-2 pseudovirus entry or authentic virus infection of Fc receptor-bearing cells. These findings provide a solid foundation for developing RBD-based subunit vaccines for SARS-CoV2.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Jinkai Zang", + "author_inst": "Institut Pasteur of Shanghai" + }, + { + "author_name": "Chenjian Gu", + "author_inst": "Fudan University" + }, + { + "author_name": "Bingjie Zhou", + "author_inst": "Institut Pasteur of Shanghai" + }, + { + "author_name": "Chao Zhang", + "author_inst": "Institut Pasteur of Shanghai" + }, + { + "author_name": "Yong Yang", + "author_inst": "Institut Pasteur of Shanghai" + }, + { + "author_name": "Shiqi Xu", + "author_inst": "Institut Pasteur of Shanghai" + }, + { + "author_name": "Xueyang Zhang", + "author_inst": "Institut Pasteur of Shanghai" + }, + { + "author_name": "Yu Zhou", + "author_inst": "Institut Pasteur of Shanghai" + }, + { + "author_name": "Lulu Bai", + "author_inst": "Institut Pasteur of Shanghai" + }, + { + "author_name": "Yang Wu", + "author_inst": "Fudan University" + }, + { + "author_name": "Zhiping Sun", + "author_inst": "Fudan University" + }, + { + "author_name": "Rong Zhang", + "author_inst": "Fudan University" + }, + { + "author_name": "Qiang Deng", + "author_inst": "Fudan University" + }, + { + "author_name": "Zhenghong Yuan", + "author_inst": "Fudan University" + }, + { + "author_name": "Hong Tang", + "author_inst": "Institut Pasteur of Shanghai" + }, + { + "author_name": "Di Qu", + "author_inst": "Fudan University" + }, + { + "author_name": "Dimitri Lavillette", + "author_inst": "Institut Pasteur of Shanghai" + }, + { + "author_name": "Youhua Xie", + "author_inst": "Fudan University" + }, + { + "author_name": "Zhong Huang", + "author_inst": "Institut Pasteur of Shanghai" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.05.21.107870", "rel_title": "Unfractionated heparin potently inhibits the binding of SARS-CoV-2 spike protein to a human cell line", @@ -1446606,33 +1449515,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.16.20104133", - "rel_title": "Predicting the COVID-19 positive cases in India with concern to Lockdown by using Mathematical and Machine Learning based Models", - "rel_date": "2020-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.16.20104133", - "rel_abs": "In this study, we analyze the number of infected positive cases of COVID-19 outbreak with concern to lockdown in India in the time window of February 11th 2020 to Jun 30th 2020. The first case in India was reported in Kerala on January 30th 2020. To break the chain of spreading, Government announced a nationwide lockdown on March 24th 2020, which is increased two times. The Ongoing lockdown 3.0 is over on May 18th, 2020. We derived how the lockdown relaxation is going to impact on containment of the outbreak. Here the Exponential Growth Model has been used to derive the epidemic curve based on the data collected from February 11th 2020, to May 11th 2020, and the Machine Learning based Linear Regression model that gives the epidemic curve to predict the cases with the continuous flow of the lockdown. We estimate that if the lockdown is continuing with more relaxation, then the estimated infected cases reach up to 1.16 crores by June 30th 2020, and the lockdown would persist with current restriction, then the expected predicted infected cases are 5.69 lacs. The Exponential Growth Model and the Linear Regression Model are advantageous to predict the number of affected cases of COVID-19. These models can be used for forecasting in long term intervals. It shows from our result that lockdown with certain restriction has a vital role in preventing the spreading of this epidemic in this current situation.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ajit Kumar Pasayat", - "author_inst": "IIT Kharagpur" - }, - { - "author_name": "Satya Narayan Pati", - "author_inst": "Centurion University" - }, - { - "author_name": "Aashirbad Maharana", - "author_inst": "Centurion University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.16.20104489", "rel_title": "A Computer Simulation Study on novel Corona Virus Transmission among the People in a Queue", @@ -1446729,6 +1449611,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.16.20103747", + "rel_title": "Evaluate the timing of resumption of business for the states of New York, New Jersey and California via a pre-symptomatic and asymptomatic transmission model of COVID-19", + "rel_date": "2020-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.16.20103747", + "rel_abs": "The United States has the highest numbers of confirmed cases of COVID-19 in the world. The early hot spot states were New York, New Jersey, and Connecticut. The workforce in these states was required to work from home except for essential services. It was necessary to evaluate an appropriate date for resumption of business since the premature reopening of the economy would lead to a broader spread of COVID-19, while the opposite situation would cause greater loss of economy. To reflect the real-time risk of the spread of COVID-19, it was crucial to evaluate the population of infected individuals before or never being confirmed due to the pre-symptomatic and asymptomatic transmissions of COVID-19. To this end, we proposed an epidemic model and applied it to evaluate the real-time risk of epidemic for the states of New York, New Jersey, and Connecticut. We used California as the benchmark state because California began a phased reopening on May 8, 2020. The dates on which the estimated numbers of unidentified infectious individuals per 100,000 for states of New York, New Jersey, and Connecticut were close to those in California on May 8, 2020, were June 1, 22, and 22, 2020, respectively. By the practice in California, New York, New Jersey, and Connecticut might consider reopening their business. Meanwhile, according to our simulation models, to prevent resurgence of infections after reopening the economy, it would be crucial to maintain sufficient measures to limit the social distance after the resumption of businesses. This precaution turned out to be critical as the situation in California quickly deteriorated after our analysis was completed and its interventions after the reopening of business were not as effective as those in New York, New Jersey, and Connecticut.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ting Tian", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Jianbin Tan", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Yukang Jiang", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Xueqin Wang", + "author_inst": "University of Science and Technology of China" + }, + { + "author_name": "Heping Zhang", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.16.20103879", "rel_title": "The Effects of Stringent Interventions for Coronavirus Pandemic", @@ -1448160,49 +1451077,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.16.20102095", - "rel_title": "Systematic and Statistical Review of COVID19 Treatment Trials", - "rel_date": "2020-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.16.20102095", - "rel_abs": "ObjectiveThe following systematic review and meta-analysis compiles the current data regarding human controlled COVID-19 treatment trials.\n\nMethodsAn electronic search of the literature compiled studies pertaining to human controlled treatment trials with COVID-19. Medications assessed included lopinavir/ritonavir, arbidol, hydroxychloroquine, favipiravir, and heparin. Statistical analyzes were performed for common viral clearance endpoints whenever possible.\n\nResultsLopinavir/ritonavir showed no significant effect on viral clearance for COVID-19 cases (OR 0.95 [95% CI 0.50-1.83]). Hydroxychloroquine also showed no significant effect on COVID-19 viral clearance rates (OR 2.16 [95% CI 0.80-5.84]). Arbidol showed no seven-day (OR 1.63 [95% CI 0.76-3.50]) or 14-day viral (OR 5.37 [95% CI 0.35-83.30]) clearance difference compared to lopinavir/ritonavir. Review of literature showed no significant clinical improvement with lopinavir/ritonavir, arbidol, hydroxychloroquine, or remdesivir. Favipiravir showed quicker symptom improvement compared to lopinavir/ritonavir and arbidol. Heparin showed improvement with severe COVID-19 cases.\n\nConclusionCurrent medications do not show significant effect on COVID-19 viral clearance rates. Favipiravir shows favorable results compared to other tested medications. Heparin shows benefit for severe cases of COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Juan Arturo Siordia Jr.", - "author_inst": "Banner University Medical Center" - }, - { - "author_name": "Michael Bernaba", - "author_inst": "Banner University Medical Center" - }, - { - "author_name": "Kenji Yoshino", - "author_inst": "Banner University Medical Center" - }, - { - "author_name": "Abid Ulhaque", - "author_inst": "Banner University Medical Center" - }, - { - "author_name": "Sooraj Kumar", - "author_inst": "Banner University Medical Center" - }, - { - "author_name": "Mario Bernaba", - "author_inst": "Banner University Medical Center" - }, - { - "author_name": "Edward Bergin", - "author_inst": "Banner University Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.14.20102087", "rel_title": "Modeling the Effects of Non-PharmaceuticalInterventions on COVID-19 Spread in Kenya", @@ -1448343,6 +1451217,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.14.20102517", + "rel_title": "Assessment of dispersion of airborne particles of oral/nasal fluid by high flow nasal cannula therapy", + "rel_date": "2020-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20102517", + "rel_abs": "BackgroundNasal High Flow (NHF) therapy delivers flows of heated humidified gases up to 60 LPM (litres per minute) via a nasal cannula. Particles of oral/nasal fluid released by patients undergoing NHF therapy may pose a cross-infection risk, which is a potential concern for treating COVID-19 patients.\n\nMethodsLiquid particles within the exhaled breath of healthy participants were measured with two protocols: (1) high speed camera imaging and counting exhaled particles under high magnification (6 participants) and (2) measuring the deposition of a chemical marker (riboflavin-5-monophosphate) at a distance of 100 and 500 mm on filter papers through which air was drawn (10 participants). The filter papers were assayed with HPLC. Breathing conditions tested included quiet (resting) breathing and vigorous breathing (which here means nasal snorting, voluntary coughing and voluntary sneezing). Unsupported (natural) breathing and NHF at 30 and 60 LPM were compared.\n\nResultsO_LIImaging: During quiet breathing, no particles were recorded with unsupported breathing or 30 LPM NHF (detection limit for single particles 33 m). Particles were detected in 2 of 6 participants at 60 LPM quiet breathing at approximately 10% of the rate caused by unsupported vigorous breathing. Unsupported vigorous breathing released the greatest numbers of particles. Vigorous breathing with NHF at 60 LPM, released half the number of particles compared to vigorous breathing without NHF.\nC_LIO_LIChemical marker tests: No oral/nasal fluid was detected in quiet breathing without NHF (detection limit 0.28 L/m3). In quiet breathing with NHF at 60 LPM, small quantities were detected in 4 out of 29 quiet breathing tests, not exceeding 17 L/m3. Vigorous breathing released 200-1000 times more fluid than the quiet breathing with NHF. The quantities detected in vigorous breathing were similar whether using NHF or not.\nC_LI\n\nConclusionDuring quiet breathing, 60 LPM NHF therapy may cause oral/nasal fluid to be released as particles, at levels of tens of L per cubic metre of air.\n\nVigorous breathing (snort, cough or sneeze) releases 200 to 1000 times more oral/nasal fluid than quiet breathing. During vigorous breathing, 60 LPM NHF therapy caused no statistically significant difference in the quantity of oral/nasal fluid released compares to unsupported breathing.\n\nNHF use does not increase the risk of dispersing infectious aerosols above the risk of unsupported vigorous breathing. Standard infection prevention and control measures should apply when dealing with a patient who has an acute respiratory infection, independent of which, if any, respiratory support is being used.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Mark C Jermy", + "author_inst": "University of Canterbury" + }, + { + "author_name": "Callum JT Spence", + "author_inst": "Fisher and Paykel Healthcare" + }, + { + "author_name": "Robert Kirton", + "author_inst": "Fisher and Paykel Healthcare" + }, + { + "author_name": "Jane F O'Donnell", + "author_inst": "Fisher and Paykel Healthcare; School of Nursing, Massey University" + }, + { + "author_name": "Natalia Kabaliuk", + "author_inst": "University of Canterbury" + }, + { + "author_name": "Sally Gaw", + "author_inst": "University of Canterbury" + }, + { + "author_name": "Yannan Jiang", + "author_inst": "University of Auckland" + }, + { + "author_name": "Zulkhairi Zainol Abidin", + "author_inst": "Universiti Kebangsaan Malaysia" + }, + { + "author_name": "Ronald L Dougherty", + "author_inst": "University of Kansas" + }, + { + "author_name": "Philip Rowe", + "author_inst": "Fisher and Paykel Healthcare" + }, + { + "author_name": "Anjula Mahaliyana", + "author_inst": "University of Canterbury" + }, + { + "author_name": "Amelia Gibbs", + "author_inst": "Landcare Research" + }, + { + "author_name": "Sally Roberts", + "author_inst": "Auckland District Health Board" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.05.17.20097410", "rel_title": "COVID-19 death rates by age and sex and the resulting mortality vulnerability of countries and regions in the world", @@ -1449238,49 +1452179,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.15.20103051", - "rel_title": "Data-driven analysis on the simulations of the spread of COVID-19 under different interventions of China", - "rel_date": "2020-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.15.20103051", - "rel_abs": "Since February 2020, COVID-19 has spread rapidly to more than 200 countries in the world. During the pandemic, local governments in China have implemented different interventions to efficiently control the spread of the epidemic. Characterizing transmission of COVID-19 under some typical interventions is essential to help countries develop appropriate interventions. Based on the pre-symptomatic transmission patterns of COVID-19, we established a novel compartmental model: Baysian SIHR model with latent Markov structure, which treated the numbers of infected and infectious individuals without isolation to be the latent variables and allowed the effective reproduction number to change over time, thus the effects of policies could be reasonably estimated. By using the epidemic data of Wuhan, Wenzhou and Shenzhen, we migrated the corresponding estimated policy modes to South Korea, Italy, and the United States and simulated the potential outcomes for these countries when they adopted similar policy strategies of three cities in China. We found that the mild interventions implemented in Shenzhen were effective to control the epidemic in the early stage, while more stringent policies which were issued in Wuhan and Wenzhou were necessary if the epidemic was more severe and needed to be controlled in a short time.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ting Tian", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Jingwen Zhang", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Shiyun Lin", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Yukang Jiang", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Jianbin Tan", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Zhongfei Li", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Xueqin Wang", - "author_inst": "University of Science and Technology of China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.16.20103903", "rel_title": "Causal Modeling of Twitter Activity During COVID-19", @@ -1449481,6 +1452379,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.12.20098962", + "rel_title": "Experience of quantitative SARS-CoV-2 antibody screening of health-care workers in the southern part of Kyoto city during COVID-19 peri-pandemic period", + "rel_date": "2020-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20098962", + "rel_abs": "BackgroundPandemic of coronavirus disease-2019 (COVID-19) puts a heavy burden not only on patients physical and mental health but also on regional health care resource and economic activity across the world. Although we accumulate incidence rate and case fatality rate by the multidisciplinary approach, epidemiological data of prevalence of serum severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) antibody in health-care workers during COVID-19 peri-pandemic period is insufficient.\n\nMethodsWe prospectively recruited health-care workers from our hospital between April 10 and April 20, 2020. We collected serum samples from these participants and evaluated quantitative SARS-CoV-2 IgG antibody by enzyme-linked immunosorbent assay.\n\nResultsFive (5.4%), 15 (16.3%) and 72 (78.3%) participants showed positive, borderline and negative results of the serum SARS-CoV-2 IgG antibody, respectively. We found mean titer of the antibody levels of all, positive group, borderline group and negative group were clearly distinguished. Participants belonging to otolaryngology ward and/or having a history of seasonal common cold symptoms had significantly higher titer of SARS-CoV-2 IgG antibody (p=0.046, p=0.046, respectively).\n\nConclusionsFive (5.4%) and 15 (16.3%) participants showed positive and borderline SARS-CoV-2 IgG antibody during COVID-19 peri-pandemic period. These rates were much higher than the rates expected from situation reports of the government. Higher rates of positive and borderline antibody suggested that COVID-19 had already spread at early stage of pandemic in the southern part of Kyoto city.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Kohei Fujita", + "author_inst": "NHO Kyoto Medical Center" + }, + { + "author_name": "Shinpei Kada", + "author_inst": "NHO Kyoto Medical Center" + }, + { + "author_name": "Osamu Kanai", + "author_inst": "NHO Kyoto Medical Center" + }, + { + "author_name": "Hiroaki Hata", + "author_inst": "NHO Kyoto Medical Center" + }, + { + "author_name": "Takao Odagaki", + "author_inst": "NHO Kyoto Medical Center" + }, + { + "author_name": "Noriko Satoh-Asahara", + "author_inst": "NHO Kyoto Medical Center" + }, + { + "author_name": "Tetsuya Tagami", + "author_inst": "NHO Kyoto Medical Center" + }, + { + "author_name": "Akihiro Yasoda", + "author_inst": "NHO Kyoto Medical Center" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.15.20103119", "rel_title": "Survival of hospitalized COVID-19 patients in Northern Italy: a population-based cohort study by the ITA-COVID19 Network", @@ -1450792,73 +1453737,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.13.20100651", - "rel_title": "Efficacy of moist heat decontamination against various pathogens for the reuse of N95 respirators in the COVID-19 emergency", - "rel_date": "2020-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20100651", - "rel_abs": "Decontamination of N95 respirators has become critical to alleviate PPE shortages for healthcare workers in the current COVID-19 emergency. The factors that are considered for the effective reuse of these masks are the fit, filter efficiency and decontamination/disinfection level both for SARS-CoV2, which is the causative virus for COVID-19, and for other organisms of concern in the hospital environment such as Staphylococcus aureus or Clostridium difficile.\n\nThe efficacy of inactivation or eradication against various pathogens should be evaluated thoroughly to understand the level of afforded disinfection. Methods commonly used in the sterilization of medical devices such as ionizing radiation, vaporized hydrogen peroxide, and ethylene oxide can provide a high level of disinfection, defined as a 6 log10 reduction, against bacterial spores, considered the most resistant microorganisms. CDC guidance on the decontamination and reuse of N95s also includes the use of moist heat (60{degrees}C, 80% relative humidity, 15-30 min) as a possible recommendation based on literature showing preservation of fit efficiency and inactivation of H1N1 on spiked masks.\n\nHere, we explored the efficacy of using moist heat under these conditions as a decontamination method for an N95 respirator (3M 1860S, St. Paul, MN) against various pathogens with different resistance; enveloped RNA viruses, Gram (+/-) bacteria, and non-enveloped viruses.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Ebru Oral", - "author_inst": "Massachusetts General Hospital/Harvard Medical School" - }, - { - "author_name": "Keith K Wannomae", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Dmitry Gil", - "author_inst": "Massachusetts General Hospital/Harvard Medical School" - }, - { - "author_name": "Rachel L Connolly", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Joseph Gardecki", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Hui Min Leung", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Orhun K Muratoglu", - "author_inst": "Massachusetts General Hospital/Harvard Medical School" - }, - { - "author_name": "Amy Tsurumi", - "author_inst": "Massachusetts General Hospital/Harvard Medical School" - }, - { - "author_name": "Laurence G Rahme", - "author_inst": "Massachusetts General Hospital/Harvard Medical School" - }, - { - "author_name": "Tareq Jaber", - "author_inst": "Charles River Laboratories" - }, - { - "author_name": "Cassidy Collins", - "author_inst": "Charles River Laboratories" - }, - { - "author_name": "Amanda Budzilowicz", - "author_inst": "Charles River Laboratories" - }, - { - "author_name": "Julian Gjore", - "author_inst": "Charles River Laboratories" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.05.13.20100602", "rel_title": "Can we use these masks? Rapid Assessment of the Inhalation Resistance Performance of Uncertified Medical Face Masks in the Context of Restricted Resources Imposed during a Public Health Emergency", @@ -1451083,6 +1453961,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.14.20101378", + "rel_title": "COVID-19 FATALITY RISK: WHY IS AUSTRALIA LOWER THAN SOUTH KOREA?", + "rel_date": "2020-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20101378", + "rel_abs": "BackgroundAs the Covid-19 virus epidemic spreads, it is important to establish reliable estimates of fatality hazard rates. Australia and South Korea are ideal candidates for detailed consideration. Both have completed the first wave of the epidemic, they have extensive Covid-19 testing and tracking programs so that confirmed case load data are reliable, and neither country has had any significant case load stress in their hospital systems.\n\nMethodsFor each country, mortality hazard models were estimated using a parameterized distributed lag model where the number of daily deaths was dependent on the number of confirmed cases in each of the preceding six weeks. Age cohort CFRs were also examined.\n\nFindingsWe observed major difference in the mortality rates when comparing South Korea to Australia in both the simple age adjusted fatality rates and in the disease hazard curve. On a like-for-like basis, the CFR for South Korea appears to be close to double the Australian rate (aggregate; 2.4% vs 1.4%).\n\nInterpretationNeither differences in the time pattern of the peaking of the case load of confirmed cases, nor differences in the size of age cohorts of confirmed cases explain the difference in mortality observed. We discuss possible explanations that point the way for further investigation.\n\nFundingnil.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Peter John Collignon", + "author_inst": "Canberra Hospital" + }, + { + "author_name": "John Beggs", + "author_inst": "Monarch Institute, Melbourne" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.13.20101253", "rel_title": "The infection fatality rate of COVID-19 inferred from seroprevalence data", @@ -1451966,57 +1454867,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.06.20076687", - "rel_title": "COVID-19: disease pathways and gene expression changes predict methylprednisolone can improve outcome in severe cases", - "rel_date": "2020-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20076687", - "rel_abs": "BackgroundCurrent management efforts of COVID-19 include: early diagnosis, use of antivirals and immune modulation. After the initial viral phase of the illness, identification of the patients developing cytokine storm syndrome is critical. Treatment of this hyper-inflammation in these patients using existing, approved therapies with proven safety profiles could address the immediate need to reduce the rising mortality.\n\nMethodsUsing data from an A549 cell line, primary human bronchial epithelial (NBHE), as well as from COVID-19-infected lung, we compare the changes in the gene expression, pathways and mechanisms between SARS-CoV2, influenza A, and respiratory syncytial virus.\n\nResultsWe identified FDA-approved drugs that could be repurposed to help COVID-19 patients with severe symptoms related to hyper-inflammation. An important finding is that drugs in the same class will not achieve similar effects. For instance methylprednisolone and prednisolone were predicted to be effective in reverting many of the changes triggered by COVID-19, while other closely related steroids, such as prednisone or dexamethasone, were not. An independent clinical study evaluated 213 subjects, 81 (38%) and 132 (62%) in pre-and post-methylprednisolone groups, respectively. The composite end point was composed of escalation to intensive care units, need for mechanical ventilation, and death. The composite endpoint occurred at a significantly lower rate in post-methylprednisolone group compared to pre-methylprednisolone group (34.9% vs. 54.3%, p=0.005).\n\nConclusionClinical results confirmed the efficacy of the in silico prediction that indicated methylprednisolone could improve outcomes in severe COVID-19. These findings are important for any future pandemic regardless of the virus.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Sorin Draghici", - "author_inst": "Wayne State University" - }, - { - "author_name": "Tuan-Minh Nguyen", - "author_inst": "Wayne State University" - }, - { - "author_name": "Larry A Sonna", - "author_inst": "Bon Air Consulting" - }, - { - "author_name": "Cordelia Ziraldo", - "author_inst": "Advaita Bioinformatics" - }, - { - "author_name": "Radu L Vanciu", - "author_inst": "Advaita Bioinformatics" - }, - { - "author_name": "Raef Fadel", - "author_inst": "Henry Ford Health System" - }, - { - "author_name": "Austin Morrison", - "author_inst": "Henry Ford Health System" - }, - { - "author_name": "Mayur Ramesh", - "author_inst": "Henry Ford Health System" - }, - { - "author_name": "Gil Mor", - "author_inst": "Wayne State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.18.20105197", "rel_title": "SARS-CoV-2 seroconversion in health care workers", @@ -1452285,6 +1455135,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.05.19.100214", + "rel_title": "log(x+1)* and log(1+x)", + "rel_date": "2020-05-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.19.100214", + "rel_abs": "Single-cell RNA-seq technologies have been successfully employed over the past decade to generate many high resolution cell atlases. These have proved invaluable in recent efforts aimed at understanding the cell type specificity of host genes involved in SARS-CoV-2 infections. While single-cell atlases are based on well-sampled highly-expressed genes, many of the genes of interest for understanding SARS-CoV-2 can be expressed at very low levels. Common assumptions underlying standard single-cell analyses dont hold when examining low-expressed genes, with the result that standard workflows can produce misleading results.\n\nKey PointsLowly expressed genes in single-cell RNA-seq can be easliy misanalyzed.\nlog(1+x) count normalization introduces errors for lowly expressed genes\nThe average log(1+x) expression differs considerably from log(x) when x is small\nAn alternative approach is to use the fraction of cells with non-zero expression", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "A. Sina Booeshaghi", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Lior Pachter", + "author_inst": "California Institute of Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "contradictory results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.19.103630", "rel_title": "Transcriptional profiling of immune and inflammatory responses in the context of SARS-CoV-2 fungal superinfection in a human airway epithelial model", @@ -1453884,29 +1456757,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.12.20099366", - "rel_title": "A pitfall in estimating the effective reproductivenumber Rt for COVID-19", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20099366", - "rel_abs": "The effective reproductive number Rt of COVID-19 is determined indirectly from data that are only incompletely known. Approaches based on reconstructing these data by sampling time lags from suitable distributions introduce noise effects that can result in distorted estimates of Rt. This, in turn, may lead to misleading interpretations of the efficacy of the various measures taken to limit COVID-19 transmission. We discuss in some detail a study used for real time monitoring of the reproductive number in Switzerland; see https://ncs-tf.ch/en/situation-report.\n\nWe argue that the method used to derive the above curve is systematically flawed and leads to an underestimation of the efficacy of the lockdown. The method adopted by the Robert Koch Institute suffers from similar deficiencies, their impact is however smaller.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "daniel wyler", - "author_inst": "University of Zurich" - }, - { - "author_name": "markus petermann", - "author_inst": "Pud Consulting Zurich" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.11.20092692", "rel_title": "Household transmission of COVID-19, Shenzhen, January-February 2020", @@ -1454107,6 +1456957,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.05.13.20092510", + "rel_title": "A citizen science initiative for open data and visualization of COVID-19 outbreak in Kerala, India", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20092510", + "rel_abs": "ObjectiveIndia reported its first COVID-19 case in the state of Kerala and an outbreak initiated subsequently. The Department of Health Services, Government of Kerala, initially released daily updates through daily textual bulletins for public awareness to control the spread of the disease. However, this unstructured data limits upstream applications, such as visualization, and analysis, thus demanding refinement to generate open and reusable datasets.\n\nMaterials and MethodsThrough a citizen science initiative, we leveraged publicly available and crowd-verified data on COVID-19 outbreak in Kerala from the government bulletins and media outlets to generate reusable datasets. This was further visualized as a dashboard through a frontend web application and a JSON repository, which serves as an API for the frontend.\n\nResultsFrom the sourced data, we provided real-time analysis, and daily updates of COVID-19 cases in Kerala, through a user-friendly bilingual dashboard (https://covid19kerala.info/) for non-specialists. To ensure longevity and reusability, the dataset was deposited in an open-access public repository for future analysis. Finally, we provide outbreak trends and demographic characteristics of the individuals affected with COVID-19 in Kerala during the first 138 days of the outbreak.\n\nDiscussionWe anticipate that our dataset can form the basis for future studies, supplemented with clinical and epidemiological data from the individuals affected with COVID-19 in Kerala.\n\nConclusionWe reported a citizen science initiative on the COVID-19 outbreak in Kerala to collect and deposit data in a structured format, which was utilized for visualizing the outbreak trend and describing demographic characteristics of affected individuals.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Jijo Pulickiyil Ulahannan", + "author_inst": "Government College Kasaragod" + }, + { + "author_name": "Nikhil Narayanan", + "author_inst": "Open Data Researcher, Bengaluru, India" + }, + { + "author_name": "Nishad Thalhath", + "author_inst": "School of Library, Information and Media Studies., University of Tsukuba, Japan" + }, + { + "author_name": "Prem Prabhakaran", + "author_inst": "Department of Advanced Materials and Chemical Engineering, Hannam University, Daejeon, South Korea." + }, + { + "author_name": "Sreekanth Chaliyeduth", + "author_inst": "Centre for Cognitive and Brain Sciences, Indian Institute of Technology Gandhinagar, Gujarat, India" + }, + { + "author_name": "Sooraj P Suresh", + "author_inst": "Department of Humanities and Social Sciences, National Institute of Technology Tiruchirappalli, Tamil Nadu, India" + }, + { + "author_name": "Musfir Mohammed", + "author_inst": "Embedded Analytics, Machine Learning and Data Sciences, Experion Technologies, TechnoPark, Thiruvananthapuram, India." + }, + { + "author_name": "Rajeevan E", + "author_inst": "Department of Philosophy, Government Brennen College, Kannur University, Kerala, India" + }, + { + "author_name": "Sindhu Joseph", + "author_inst": "Department of Travel and Tourism Management, Govinda Pai Memorial Government College, Kannur University, Kerala, India" + }, + { + "author_name": "Akhil Balakrishnan", + "author_inst": "Crowcon - A Halma Company, ITPB, Whitefield, Bangalore" + }, + { + "author_name": "Jeevan Uthaman", + "author_inst": "Department of Marine Geophysics, Cochin University of Science and Technology, Kochi, Kerala, India" + }, + { + "author_name": "Manoj Karingamadathil", + "author_inst": "Swathanthra Malayalam Computing, Thrissur, Kerala, India" + }, + { + "author_name": "Sunil Thonikkuzhiyil Thomas", + "author_inst": "Department of Electronics, College of Engineering Attingal, APJ Abdul Kalam Technical University, Thiruvananthapuram, Kerala, India" + }, + { + "author_name": "Unnikrishnan Sureshkumar", + "author_inst": "Astronomical Observatory of the Jagiellonian University, Krakow, Malopolska, Poland" + }, + { + "author_name": "Shabeesh Balan", + "author_inst": "Laboratory for Molecular Psychiatry, RIKEN Center for Brain Science, Wakoshi, Saitama, Japan" + }, + { + "author_name": "Neetha Nanoth Vellichirammal", + "author_inst": "Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.05.14.20093633", "rel_title": "Evaluation of the US governors decision when to issue stay-at-home orders", @@ -1455702,77 +1458631,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.12.20073577", - "rel_title": "Feasibility of SARS-CoV-2 virus detection from consumer-grade cotton swabs", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20073577", - "rel_abs": "BackgroundDetermining the role of fomites in the transmission of SARS-CoV-2 is essential in the hospital setting and will likely be important outside of medical facilities as governments around the world make plans to ease COVID-19 public health restrictions and attempt to safely reopen economies. Expanding COVID-19 testing to include environmental surfaces would ideally be performed with inexpensive swabs that could be transported safely without concern of being a source of new infections. However, CDC-approved clinical-grade sampling supplies and techniques using a polyester swab are expensive, potentially expose laboratory workers to viable virus and prohibit analysis of the microbiome due to the presence of antibiotics in viral transport media (VTM). To this end, we performed a series of experiments comparing the diagnostic yield using five consumer-grade swabs (including plastic and wood shafts and various head materials including cotton, polyester, and foam) and one clinical grade swab for inhibition to RNA. For three of these swabs, we evaluated performance to detect SARS-CoV-2 in twenty intensive care unit (ICU) hospital rooms of patients with 16 COVID-19+. All swabs were placed in 95% ethanol and further evaluated in terms of RNase activity. SARS-CoV-2 was measured both directly from the swab and from the swab eluent.\n\nResultsCompared to samples collected in VTM, 95% ethanol demonstrated significant inhibition properties against RNases. When extracting directly from the swab head as opposed to the eluent, RNA recovery was approximately 2-4x higher from all six swab types tested as compared to the clinical standard of testing the eluent from a CDC-approved polyester swab. The limit of detection (LoD) of SARs-CoV-2 from floor samples collected using the CGp or TMI swabs was similar or better than the CDC standard, further suggesting that swab type does not impact RNA recovery as measured by SARs-CoV-2. The LoD for TMI was between 0-362.5 viral particles while PE and CGp were both between 725-1450 particles. Lastly microbiome analyses (16S rRNA) of paired samples (e.g., environment to host) collected using different swab types in triplicate indicated that microbial communities were not impacted by swab type but instead driven by the patient and sample type (floor or nasal).\n\nConclusionsCompared to using a clinical-grade polyester swab, detection of SARS-CoV-2 from environmental samples collected from ICU rooms of patients with COVID was similar using consumer grade swabs, stored in 95% ethanol. The yield was best from the swab head rather than the eluent and the low level of RNase activity in these samples makes it possible to perform concomitant microbiome analysis.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Jeremiah J Minich", - "author_inst": "Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA." - }, - { - "author_name": "Farhana Ali", - "author_inst": "Division of Gastroenterology, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA." - }, - { - "author_name": "Clarisse Marotz", - "author_inst": "Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA." - }, - { - "author_name": "Pedro Belda-Ferre", - "author_inst": "Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA." - }, - { - "author_name": "Leslie Chiang", - "author_inst": "Division of Infectious Diseases, Department of Pediatrics, University of California San Diego" - }, - { - "author_name": "Justin P. Shaffer", - "author_inst": "Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA." - }, - { - "author_name": "Carolina S. Carpenter", - "author_inst": "Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA." - }, - { - "author_name": "Daniel McDonald", - "author_inst": "Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA." - }, - { - "author_name": "Jack A Gilbert", - "author_inst": "Department of Pediatrics, School of Medicine; Scripps Institution of Oceanography; Center for Microbiome Innovation,University of California San Diego, La Jolla" - }, - { - "author_name": "Sarah M. Allard", - "author_inst": "Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA." - }, - { - "author_name": "Eric E Allen", - "author_inst": "Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego" - }, - { - "author_name": "Rob Knight", - "author_inst": "Departments of Pediatrics, Computer Science and Engineering, & Bioengineering, University of California San Diego, La Jolla, CA USA." - }, - { - "author_name": "Daniel A Sweeney", - "author_inst": "Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, University of California, San Diego, La Jolla, CA, USA." - }, - { - "author_name": "Austin D. Swafford", - "author_inst": "Center for Microbiome Innovation, University of California, San Diego" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.12.20094524", "rel_title": "Perceived versus proven SARS-CoV-2 specific immune responses in health care workers", @@ -1455937,6 +1458795,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.10.20096974", + "rel_title": "Study of Non-Pharmacological Interventions on COVID-19 Spread", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.10.20096974", + "rel_abs": "COVID-19 disease has emerged as one of the life threatening threat to the society. It is caused by a novel beta coronavirus. It began as unidentified pneumonia of unknown etiology in Wuhan City, Hubei province in China emerged in December 2019. No vaccine has been produced till now. Mathematical models are used to study impact of different measures used to decrease pandemic. Mathematical models have been designed to estimate the numbers of spreaders in different scenarios in the present manuscript. In the present manuscript, three different mathematical models have been proposed with different scenarios such as screening, quarantine and NPIs for estimating number of virus spreaders. The analysis shows that the numbers of COVID-19 patients will be more without screening the peoples coming from other countries. Since, every people suffering with COVID-19 disease are spreaders. The screening and quarantine with NPIs have been implemented to study their impact on the spreaders. It has been found that NPI measures are able to reduce number of spreaders. The NPI measures reduces the growth of the spread function and providing decision makers more time to prepare with in dealing of the disease.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Avaneesh Singh", + "author_inst": "Indian Institute of Information Technology, Design and Manufacturing, Jabalpur, India" + }, + { + "author_name": "Saroj Kumar Chandra", + "author_inst": "Indian Institute of Information Technology, Design and Manufacturing, Jabalpur, India" + }, + { + "author_name": "Manish Kumar Bajpai", + "author_inst": "Indian Institute of Information Technology, Design and Manufacturing, Jabalpur, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.11.20097865", "rel_title": "MODELING COVID19 IN INDIA (MAR 3 - MAY 7, 2020): HOW FLAT IS FLAT, AND OTHER HARD FACTS", @@ -1456912,61 +1459797,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.15.20102608", - "rel_title": "Fusing a Bayesian case velocity model with random forest for predicting COVID-19 in the U.S.", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.15.20102608", - "rel_abs": "Predictions of COVID-19 case growth and mortality are critical to the decisions of political leaders, businesses, and individuals grappling with the pandemic. This predictive task is challenging due to the novelty of the virus, limited data, and dynamic political and societal responses. We embed a Bayesian nonlinear mixed model and a random forest algorithm within an epidemiological compartmental model for empirically grounded COVID-19 predictions. The Bayesian case model fits a location-specific curve to the velocity (first derivative) of the transformed cumulative case count, borrowing strength across geographic locations and incorporating prior information to obtain a posterior distribution for case trajectory. The compartmental model uses this distribution and predicts deaths using a random forest algorithm trained on COVID-19 data and population-level characteristics, yielding daily projections and interval estimates for infections and deaths in U.S. states. We evaluate forecasting accuracy on a two-week holdout set, finding that the model predicts COVID-19 cases and deaths well, with a mean absolute scaled error of 0.40 for cases and 0.32 for deaths throughout the two-week evaluation period. The substantial variation in predicted trajectories and associated uncertainty between states is illustrated by comparing three unique locations: New York, Ohio, and Mississippi. The sophistication and accuracy of this COVID-19 model offer reliable predictions and uncertainty estimates for the current trajectory of the pandemic in the U.S. and provide a platform for future predictions as shifting political and societal responses alter its course.\n\nAuthor summaryCOVID-19 models can be roughly classified as mathematical models that simulate disease within a population, including epidemiological compartmental models, or statistical curve-fitting models that fit a function to observed data and extrapolate forward into the future. Bridging this divide, we combine the strengths of curve-fitting statistical models and the structure of epidemiological models, by embedding a Bayesian nonlinear mixed model for case velocity and a machine learning algorithm (random forest) into the framework of a compartmental model. Fusing these models together exploits the particular strengths of each to glean as much information as possible from the currently available data. We also identify the velocity of log cumulative cases as an excellent target for modeling and extrapolating COVID-19 case trajectories. We empirically evaluate the predictive performance of the model and provide predicted trajectories with credible intervals for cumulative confirmed case count, active confirmed infections and COVID-19 deaths for each of the 50 U.S. states. Combining sophisticated data analytic methods with proven epidemiological models offers an empirically grounded strategy for making realistic predictions and quantifying their uncertainty. These predictions indicate substantial variation in the COVID-19 trajectories of U.S. states.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Gregory L Watson", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Di Xiong", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Lu Zhang", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Joseph A Zoller", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "John Shamshoian", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Phillip Sundin", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Teresa Bufford", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Anne W Rimoin", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Marc A Suchard", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Christina M Ramirez", - "author_inst": "University of California Los Angeles" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.13.20098186", "rel_title": "Excess Out-Of-Hospital Mortality and Declining Oxygen Saturation Documented by EMS During the COVID-19 Crisis in Tijuana, Mexico", @@ -1457123,6 +1459953,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.11.20098517", + "rel_title": "An SEIARD epidemic model for COVID-19 in Mexico: mathematical analysis and state-level forecast", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20098517", + "rel_abs": "We propose an SEIARD mathematical model to investigate the current outbreak of coronavirus disease (COVID-19) in Mexico. Our model incorporates the asymptomatic infected individuals, who represent the majority of the infected population (with symptoms or not) and could play an important role in spreading the virus without any knowledge. We calculate the basic reproduction number (R0) via the next-generation matrix method and estimate the per day infection, death and recovery rates. The local stability of the disease free equilibrium is established in terms of R0. A sensibility analysis is performed to determine the relative importance of the model parameters to the disease transmission. We calibrate the parameters of the SEIARD model to the reported number of infected cases and fatalities for several states in Mexico by minimizing the sum of squared errors and attempt to forecast the evolution of the outbreak until August 2020.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ugo Avila-Ponce de Le\u00f3n", + "author_inst": "Universidad Nacional Autonoma de Mexico" + }, + { + "author_name": "\u00c1ngel G. C. P\u00e9rez", + "author_inst": "Universidad Autonoma de Yucatan" + }, + { + "author_name": "Eric Avila-Vales", + "author_inst": "Universidad Autonoma de Yucatan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.13.20098426", "rel_title": "Analytical performance of lateral flow immunoassay for SARS-CoV-2 exposure screening on venous and capillary blood samples", @@ -1458254,81 +1461111,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.05.17.100289", - "rel_title": "Establishment of an African green monkey model for COVID-19", - "rel_date": "2020-05-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.17.100289", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for an unprecedented global pandemic of COVID-19. Animal models are urgently needed to study the pathogenesis of COVID-19 and to screen candidate vaccines and treatments. Nonhuman primates (NHP) are considered the gold standard model for many infectious pathogens as they usually best reflect the human condition. Here, we show that African green monkeys support a high level of SARS-CoV-2 replication and develop pronounced respiratory disease that may be more substantial than reported for other NHP species including cynomolgus and rhesus macaques. In addition, SARS-CoV-2 was detected in mucosal samples of all animals including feces of several animals as late as 15 days after virus exposure. Importantly, we show that virus replication and respiratory disease can be produced in African green monkeys using a much lower and more natural dose of SARS-CoV-2 than has been employed in other NHP studies.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Courtney B. Woolsey", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA." - }, - { - "author_name": "Viktoriya Borisevich", - "author_inst": "1Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA." - }, - { - "author_name": "Abhishek N Prasad", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA." - }, - { - "author_name": "Krystle N. Agans", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA." - }, - { - "author_name": "Daniel J. Deer", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA." - }, - { - "author_name": "Natalie S. Dobias", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA." - }, - { - "author_name": "John C. Heymann", - "author_inst": "Department of Radiology, University of Texas Medical Branch, Galveston, TX 77555, USA." - }, - { - "author_name": "Stephanie L. Foster", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555" - }, - { - "author_name": "Corri B. Levine", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555" - }, - { - "author_name": "Liana Medina", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555" - }, - { - "author_name": "Kevin Melody", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555" - }, - { - "author_name": "Joan B. Geisbert", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555" - }, - { - "author_name": "Karla A. Fenton", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555" - }, - { - "author_name": "Thomas W. Geisbert", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555" - }, - { - "author_name": "Robert W. Cross", - "author_inst": "University of Texas Medical Branch-Galveston National Laboratory" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.16.099747", "rel_title": "REMBRANDT: A high-throughput barcoded sequencing approach for COVID-19 screening.", @@ -1458497,6 +1461279,37 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.05.17.100685", + "rel_title": "Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein", + "rel_date": "2020-05-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.17.100685", + "rel_abs": "The COVID-2019 pandemic is the most severe acute public health threat of the twenty-first century. To properly address this crisis with both robust testing and novel treatments, we require a deep understanding of the life cycle of the causative agent, the SARS-CoV-2 coronavirus. Here, we examine the architecture and self-assembly properties of the SARS-CoV-2 nucleocapsid protein, which packages viral RNA into new virions. We determined a 1.4 [A] resolution crystal structure of this proteins N2b domain, revealing a compact, intertwined dimer similar to that of related coronaviruses including SARS-CoV. While the N2b domain forms a dimer in solution, addition of the C-terminal spacer B/N3 domain mediates formation of a homotetramer. Using hydrogen-deuterium exchange mass spectrometry, we find evidence that at least part of this putatively disordered domain is structured, potentially forming an -helix that self-associates and cooperates with the N2b domain to mediate tetramer formation. Finally, we map the locations of amino acid substitutions in the N protein from over 38,000 SARS-CoV-2 genome sequences. We find that these substitutions are strongly clustered in the proteins N2a linker domain, and that substitutions within the N1b and N2b domains cluster away from their functional RNA binding and dimerization interfaces. Overall, this work reveals the architecture and self-assembly properties of a key protein in the SARS-CoV-2 life cycle, with implications for both drug design and antibody-based testing.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Qiaozhen Ye", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Alan M.V. West", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Steve Silletti", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Kevin D Corbett", + "author_inst": "University of California, San Diego" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.05.12.20099184", "rel_title": "Modelling and data-based analysis of COVID-19 outbreak in India : a study on impact of social distancing measures", @@ -1459512,53 +1462325,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.05.12.20099267", - "rel_title": "The impact of containment measures and air temperature on mitigating the transmission of COVID-19: a novel data-based comprehensive modeling analysis", - "rel_date": "2020-05-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20099267", - "rel_abs": "Early non-pharmaceutical interventions (NPIs) are crucial to prevent and control of COVID-19 pandemic. We established a stochastic non-classical SEIR NPIs model (ScEIQRsh) which can quantify the three kinds of NPIs measures simultaneously to mimic the clustered intra-family or intra-acquaintance spreading pattern of COVID-19 under the effective integrated NPIs in Mainland China. Model simulation demonstrated that measures to diminish contactable susceptible (Sc), such as home confinement, travel constraint, social distancing etc. and measures to avoid delay of diagnosis and hospitalized isolation ({eta}) were more effective but consumptive than contact tracing ({kappa}, {rho}). From fitted model by MCMC method, the proportion of asymptomatic infectors was 14.88% (IQR 8.17%, 25.37%). The association between air temperature and the fitted transmission rate ({beta}) of COVID-19 suggests that COVID-19 pandemic would be seasonal with the optimal temperature range of 5{degrees}C-14{degrees}C and peak of 10{degrees}C for spreading, and vaccine is indispensable to ultimate prevention COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Di Liu", - "author_inst": "Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, PR China" - }, - { - "author_name": "Qidong Tai", - "author_inst": "Shanghai Pulmonary Hospital, Tongji University School of Medicine" - }, - { - "author_name": "Yaping Wang", - "author_inst": "Public Health and Preventive Medicine, Tongji University School of Medicine" - }, - { - "author_name": "Miao Pu", - "author_inst": "Public Health and Preventive Medicine, Tongji University School of Medicine" - }, - { - "author_name": "Sikai Ge", - "author_inst": "Division of biostatistics, School of public health, University of Minnesota, Minneapolis" - }, - { - "author_name": "Tingting Ji", - "author_inst": "Department of Liver Disease, The Second Hospital of Nanjing Southeast University School of Medicine" - }, - { - "author_name": "Lei Zhang", - "author_inst": "Shanghai Pulmonary Hospital, Tongji University School of Medicine" - }, - { - "author_name": "Bo Su", - "author_inst": "Shanghai Pulmonary Hospital, Tongji University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.12.20099481", "rel_title": "The Evaluation of Deep Neural Networks and X-Ray as a Practical Alternative for Diagnosis and Management of COVID-19", @@ -1459687,6 +1462453,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.12.20099945", + "rel_title": "SARS pandemic exposure impaired early childhood development: A lesson for COVID-19", + "rel_date": "2020-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20099945", + "rel_abs": "Social and mental stressors associated with the COVID-19 pandemic may promote long-term effects on child development. However, reports aimed at identifying the relationship between pandemics and child health are limited. We conducted a retrospective study to evaluate the severe acute respiratory syndrome (SARS) pandemic in 2003 and its relationship to child development indicators using a representative sample across China. Our study involved longitudinal measurements of 14,647 children, 36% of whom (n = 5216) were born before or during the SARS pandemic. Cox models were utilized to examine the effects of SARS on preterm birth and four milestones of development: age to (1) walk independently, (2) say a complete sentence, (3) count from 0 to 10, and (4) undress him/herself for urination. Mixed effect models were utilized to associate SARS with birthweight, body weight and height. Our results show that experiencing SARS during early childhood was significantly associated with delayed milestones, with adjusted hazard ratios of 3.17 [95% confidence intervals (CI): 2.71, 3.70], 3.98 (3.50, 4.53), 4.96 (4.48, 5.49), or 5.57 (5.00, 6.20) for walking independently, saying a complete sentence, counting from 0 to 10, and undressing him/herself for urination, respectively. Experiencing SARS was also associated with reduced body weight. This effect was strongest for preschool children [a weight reduction of 4.86 (0.36, 9.35) kg, 5.48 (-0.56, 11.53) kg or 5.09 (-2.12, 12.30) kg for 2, 3, 4 year-olds, respectively]. We did not identify a significant effect of maternal SARS exposure on birthweight or gestational length. Collectively, our results showed that the SARS pandemic was associated with delayed child development and provided epidemiological evidence to support the association between infectious disease epidemics and impaired child health. These results provide a useful framework to investigate and mitigate relevant impacts from the COVID-19 pandemic.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Yunfei Fan", + "author_inst": "Peking University" + }, + { + "author_name": "Huiyu Wang", + "author_inst": "Peking University" + }, + { + "author_name": "Qiong Wu", + "author_inst": "Peking University" + }, + { + "author_name": "Xiang Zhou", + "author_inst": "Purdue University" + }, + { + "author_name": "Yubo Zhou", + "author_inst": "Peking University" + }, + { + "author_name": "Bin Wang", + "author_inst": "Peking University" + }, + { + "author_name": "Yiqun Han", + "author_inst": "Imperial College London" + }, + { + "author_name": "Tao xue", + "author_inst": "Peking University" + }, + { + "author_name": "Tong Zhu", + "author_inst": "Peking University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.13.20100677", "rel_title": "Number of International Arrivals Predicts Severity of the first Global Wave of the COVID-19 Pandemic", @@ -1461078,45 +1463895,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.05.14.095885", - "rel_title": "Predicting the Immunogenicity of T cell epitopes: From HIV to SARS-CoV-2", - "rel_date": "2020-05-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.095885", - "rel_abs": "We describe a physics-based learning model for predicting the immunogenicity of Cytotoxic T Lymphocyte (CTL) epitopes derived from diverse pathogens, given a Human Leukocyte Antigen (HLA) genotype. The model was trained and tested on experimental data on the relative immunodominance of CTL epitopes in Human Immunodeficiency Virus infection. The method is more accurate than publicly available models. Our model predicts that only a fraction of SARS-CoV-2 epitopes that have been predicted to bind to HLA molecules is immunogenic. The immunogenic CTL epitopes across all SARS-CoV-2 proteins are predicted to provide broad population coverage, but the immunogenic epitopes in the SARS-CoV-2 spike protein alone are unlikely to do so. Our model predicts that several immunogenic SARS-CoV-2 CTL epitopes are identical to those contained in low-pathogenicity coronaviruses circulating in the population. Thus, we suggest that some level of CTL immunity against COVID-19 may be present in some individuals prior to SARS-CoV-2 infection.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ang Gao", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Zhilin Chen", - "author_inst": "Ragon Insitute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard" - }, - { - "author_name": "Mary Carrington", - "author_inst": "Frederick National Laboratory for Cancer Research" - }, - { - "author_name": "Hendrik Streeck", - "author_inst": "Institute of Virology" - }, - { - "author_name": "Arup K. Chakraborty", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Boris Juelg", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.05.14.095620", "rel_title": "Unveiling diffusion pattern and structural impact of the most invasive SARS-CoV-2 spike mutation", @@ -1461245,6 +1464023,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nutrition" }, + { + "rel_doi": "10.1101/2020.05.11.20082396", + "rel_title": "Virtual health care for community management of patients with COVID-19.", + "rel_date": "2020-05-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20082396", + "rel_abs": "ObjectivesTo describe the implementation and early experience of virtual health care for community management of patients with COVID-19.\n\nDesignobservational cohort study.\n\nSettinglarge Australian metropolitan health service with established virtual health care program and remote patient monitoring capability.\n\nParticipantspatients with COVID-19 living within the health service who can self-isolate safely, do not require immediate admission to an inpatient setting, have no major active comorbid illness and can be managed at home or other suitable accommodation.\n\nMain outcome measurescare escalation rates, including hospital admission.\n\nResultsbetween 11-29 March 2020, 162/173 (93.6%) locally diagnosed patients with COVID-19 were accepted to the virtual health care program, median age 38y (range 11-79). For the 62 patients discharged during this period the median length of stay was 8 days (range 1-17). The peak of 100 prevalent patients equated to approximately 25 patients per Registered Nurse per shift. Patients were contacted a median of 16 times (range 1-30) during this period, with video consultations used 66.3% of the time; 132/162 (81.5%) patients were monitored remotely. Care escalation rates were low: ambulance attendance, 5 (3%); ED attendance, 4 (2.5%); hospital admission, 3 (1.9%). There were no deaths. Conclusions: community-based virtual health care is feasible for managing most patients with COVID-19 and can be rapidly implemented in an urban Australian context for pandemic management. Health services implementing virtual health care should anticipate challenges with rapid technology deployments and provide adequate support to resolve them including strategies supporting consumer use of health information technologies.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Owen Hutchings", + "author_inst": "Sydney Local Health District" + }, + { + "author_name": "Cassandra Dearing", + "author_inst": "Sydney Local Health District" + }, + { + "author_name": "Dianna Jagers", + "author_inst": "Sydney Local Health District" + }, + { + "author_name": "Miranda Shaw", + "author_inst": "Sydney Local Health District" + }, + { + "author_name": "Freya Raffan", + "author_inst": "Sydney Local Health District" + }, + { + "author_name": "Aaron Jones", + "author_inst": "Sydney Local Health District" + }, + { + "author_name": "Richard Taggart", + "author_inst": "Sydney Local Health District" + }, + { + "author_name": "Tim Sinclair", + "author_inst": "Sydney Local Health District" + }, + { + "author_name": "Teresa Anderson", + "author_inst": "Sydney Local Health District" + }, + { + "author_name": "Angus G Ritchie", + "author_inst": "Sydney Local Health District" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.05.10.20088369", "rel_title": "Medical overuse in the Iranian healthcare system: a systematic scoping review and practical recommendations for decreasing medical overuse during unexpected COVID-19 pandemic opportunity", @@ -1462635,53 +1465468,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.05.10.20096925", - "rel_title": "NON-WHITE ETHNICITY, MALE SEX, AND HIGHER BODY MASS INDEX, BUT NOT MEDICATIONS ACTING ON THE RENIN-ANGIOTENSIN SYSTEM ARE ASSOCIATED WITH CORONAVIRUS DISEASE 2019 (COVID-19) HOSPITALISATION: REVIEW OF THE FIRST 669 CASES FROM THE UK BIOBANK", - "rel_date": "2020-05-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.10.20096925", - "rel_abs": "BackgroundCardiometabolic morbidity and medications, specifically Angiotensin Converting Enzyme inhibitors (ACEi) and Angiotensin Receptor Blockers (ARBs), have been linked with adverse outcomes from coronavirus disease 2019 (COVID-19). This study aims to investigate factors associated with COVID-19 positivity for the first 669 UK Biobank participants; compared with individuals who tested negative, and with the untested, presumed negative, rest of the population.\n\nMethodsWe studied 1,474 participants from the UK Biobank who had been tested for COVID-19. Given UK testing policy, this implies a hospital setting, suggesting at least moderate to severe symptoms. We considered the following exposures: age, sex, ethnicity, body mass index (BMI), diabetes, hypertension, hypercholesterolaemia, ACEi/ARB use, prior myocardial infarction (MI), and smoking. We undertook comparisons between: 1) COVID-19 positive and COVID-19 tested negative participants; and 2) COVID-19 tested positive and the remaining participants (tested negative plus untested, n=501,837). Logistic regression models were used to investigate univariate and mutually adjusted associations.\n\nResultsAmong participants tested for COVID-19, non-white ethnicity, male sex, and greater BMI were independently associated with COVID-19 positive result. Non-white ethnicity, male sex, greater BMI, diabetes, hypertension, prior MI, and smoking were independently associated with COVID-19 positivity compared to the remining cohort (test negatives plus untested). However, similar associations were observed when comparing those who tested negative for COVID-19 with the untested cohort; suggesting that these factors associate with general hospitalisation rather than specifically with COVID-19.\n\nConclusionsAmong participants tested for COVID-19 with presumed moderate to severe symptoms in a hospital setting, non-white ethnicity, male sex, and higher BMI are associated with a positive result. Other cardiometabolic morbidities confer increased risk of hospitalisation, without specificity for COVID-19. Notably, ACE/ARB use did not associate with COVID-19 status.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Zahra Raisi-Estabragh", - "author_inst": "William Harvey Research Institute" - }, - { - "author_name": "Celeste McCracken", - "author_inst": "William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, London, UK" - }, - { - "author_name": "Maddalena Ardissino", - "author_inst": "Sir Alexander Fleming Building, Imperial College London, London, UK" - }, - { - "author_name": "Mae S Bethell", - "author_inst": "North West Anglia NHS Foundation Trust, Hinchingbrooke Hospital, Huntingdon, UK" - }, - { - "author_name": "Jackie Cooper", - "author_inst": "William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, London, UK" - }, - { - "author_name": "Cyrus Cooper", - "author_inst": "MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK" - }, - { - "author_name": "Nicholas C Harvey", - "author_inst": "MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK" - }, - { - "author_name": "Steffen E Petersen", - "author_inst": "William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, London, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.05.15.097741", "rel_title": "Analysis of SARS-CoV-2 RNA-Sequences by Interpretable Machine Learning Models", @@ -1462910,6 +1465696,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.10.20096446", + "rel_title": "Strategic release of lockdowns in a COVID infection model", + "rel_date": "2020-05-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.10.20096446", + "rel_abs": "The COVID-19 Pandemic has impacted the worlds socio-economic system, resulting in a serious health crisis and lockdowns around the world. As the growth of infection slows, decisions regarding easing of lockdown restrictions are required, keeping in view the capacity of the health-care system. In this paper, we quantify the impact of a multi-phased release of the population from lockdown. Using the SIR model for epidemic spread, we design and implement a method to determine the earliest time of release from lockdown restrictions, constrained by a specified threshold on the subsequent peaks of infection. Trade-offs between the threshold and the earliest times of removing lockdown restrictions are illustrated. Additionally, we consider alternative policy decisions where the population is released gradually from lockdown restrictions and illustrate the trade-offs between the rate of release of population and number of active infections.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Yi Zhang", + "author_inst": "Illinois Institute of Technology" + }, + { + "author_name": "Mohit Hota", + "author_inst": "Illinois Institute of Technology" + }, + { + "author_name": "Sanjiv Kapoor", + "author_inst": "Illinois Institute of Technology, Chicago, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.09.20096818", "rel_title": "Hemogram Data as a Tool for Decision-making in COVID-19 Management: Applications to Resource Scarcity Scenarios", @@ -1464453,61 +1467266,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.05.14.096016", - "rel_title": "Transcriptional profiling reveals TRPM5-expressing cells involved in viral infection in the olfactory epithelium", - "rel_date": "2020-05-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.096016", - "rel_abs": "BackgroundUnderstanding viral infection of the olfactory epithelium is essential because the olfactory nerve is an important route of entry for viruses to the central nervous system. Specialized chemosensory epithelial cells that express the transient receptor potential cation channel subfamily M member 5 (TRPM5) are found throughout the airways and intestinal epithelium and are involved in responses to viral infection.\n\nResultsHerein we performed deep transcriptional profiling of olfactory epithelial cells sorted by flow cytometry based on the expression of mCherry as a marker for olfactory sensory neurons and for eGFP in OMP-H2B::mCherry/TRPM5-eGFP transgenic mice (Mus musculus). We find profuse expression of transcripts involved in inflammation, immunity and viral infection in TRPM5-expressing microvillous cells.\n\nConclusionOur study provides new insights into a potential role for TRPM5-expressing microvillous cells in viral infection of the olfactory epithelium. We find that, as found for solitary chemosensory cells (SCCs) and brush cells in the airway epithelium, and for tuft cells in the intestine, the transcriptome of TRPM5-expressing microvillous cells indicates that they are likely involved in the inflammatory response elicited by viral infection of the olfactory epithelium.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Eric D Larson", - "author_inst": "University of Colorado" - }, - { - "author_name": "Laetitia Merle", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Paul Feinstein", - "author_inst": "Hunter College, CUNY" - }, - { - "author_name": "Arianna Gentile Polese", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Andrew N Bubak", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Christy S Niemeyer", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Douglas Shepherd", - "author_inst": "Arizona State University" - }, - { - "author_name": "Vijay R Ramakrishnan", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Maria A Nagel", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Diego Restrepo", - "author_inst": "Universtiy of Colorado Anschutz Medical Campus" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2020.05.15.096511", "rel_title": "Broad sarbecovirus neutralizing antibodies define a key site of vulnerability on the SARS-CoV-2 spike protein", @@ -1464884,6 +1467642,109 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.05.15.098616", + "rel_title": "SARS-CoV2 (COVID-19) Structural/Evolution Dynamicome: Insights into functional evolution and human genomics.", + "rel_date": "2020-05-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.15.098616", + "rel_abs": "The SARS-CoV-2 pandemic, starting in 2019, has challenged the speed at which labs perform science, ranging from discoveries of the viral composition to handling health outcomes in humans. The small ~30kb single-stranded RNA genome of Coronaviruses makes them adept at cross species spread and drift, increasing their probability to cause pandemics. However, this small genome also allows for a robust understanding of all proteins coded by the virus. We employed protein modeling, molecular dynamic simulations, evolutionary mapping, and 3D printing to gain a full proteome and dynamicome understanding of SARS-CoV-2. The Viral Integrated Structural Evolution Dynamic Database (VIStEDD) has been established (prokoplab.com/vistedd), opening future discoveries and educational usage. In this paper, we highlight VIStEDD usage for nsp6, Nucleocapsid (N), and Spike (S) surface glycoprotein. For both nsp6 and N we reveal highly conserved surface amino acids that likely drive protein-protein interactions. In characterizing viral S protein, we have developed a quantitative dynamics cross correlation matrix insight into interaction with the ACE2/SLC6A19 dimer complex. From this quantitative matrix, we elucidated 47 potential functional missense variants from population genomic databases within ACE2/SLC6A19/TMPRSS2, warranting genomic enrichment analyses in SARS-CoV-2 patients. Moreover, these variants have ultralow frequency, but can exist as hemizygous in males for ACE2, which falls on the X-chromosome. Two noncoding variants (rs4646118 and rs143185769) found in ~9% of African descent individuals for ACE2 may regulate expression and be related to increased susceptibility of African Americans to SARS-CoV-2. This powerful database of SARS-CoV-2 can aid in research progress in the ongoing pandemic.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Ruchir Gupta", + "author_inst": "Michigan State University" + }, + { + "author_name": "Jacob Charron", + "author_inst": "Michigan State University" + }, + { + "author_name": "Cynthia Stenger", + "author_inst": "University of North Alabama" + }, + { + "author_name": "Jared Painter", + "author_inst": "University of North Alabama" + }, + { + "author_name": "Hunter Steward", + "author_inst": "Michigan State University" + }, + { + "author_name": "Taylor Cook", + "author_inst": "Grand Rapids Community College" + }, + { + "author_name": "William Faber", + "author_inst": "Grand Rapids Community College" + }, + { + "author_name": "Austin Frisch", + "author_inst": "Michigan State University" + }, + { + "author_name": "Eric Lind", + "author_inst": "Michigan State University" + }, + { + "author_name": "Jacob Bauss", + "author_inst": "Michigan State University" + }, + { + "author_name": "Xiaopeng Li", + "author_inst": "Michigan State University" + }, + { + "author_name": "Olivia Sirpilla", + "author_inst": "Walsh University" + }, + { + "author_name": "Xavier Soehnlen", + "author_inst": "Walsh University" + }, + { + "author_name": "Adam Underwood", + "author_inst": "Walsh University" + }, + { + "author_name": "David Hinds", + "author_inst": "HudsonAlpha Institute for Biotechnology" + }, + { + "author_name": "Michele Morris", + "author_inst": "HudsonAlpha Institute for Biotechnology" + }, + { + "author_name": "Neil Lamb", + "author_inst": "HudsonAlpha Institute for Biotechnology" + }, + { + "author_name": "Joseph Carcillo", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Caleb Bupp", + "author_inst": "Spectrum Health" + }, + { + "author_name": "Bruce Uhal", + "author_inst": "Michigan State University" + }, + { + "author_name": "Surender Rajasekaran", + "author_inst": "Spectrum Health" + }, + { + "author_name": "Jeremy W Prokop", + "author_inst": "Michigan State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2020.05.14.097311", "rel_title": "Analytical and Clinical Comparison of Three Nucleic Acid Amplification Tests for SARS-CoV-2 Detection", @@ -1466131,37 +1468992,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.14.093757", - "rel_title": "Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome", - "rel_date": "2020-05-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.093757", - "rel_abs": "A novel coronavirus (SARS-CoV-2) emerged from China in late 2019 and rapidly spread across the globe, infecting millions of people and generating societal disruption on a level not seen since the 1918 influenza pandemic. A safe and effective vaccine is desperately needed to prevent the continued spread of SARS-CoV-2; yet, rational vaccine design efforts are currently hampered by the lack of knowledge regarding viral epitopes targeted during an immune response, and the need for more in-depth knowledge on betacoronavirus immunology. To that end, we developed a computational workflow using a series of open-source algorithms and webtools to analyze the proteome of SARS-CoV-2 and identify putative T cell and B cell epitopes. Using increasingly stringent selection criteria to select peptides with significant HLA promiscuity and predicted antigenicity, we identified 41 potential T cell epitopes (5 HLA class I, 36 HLA class II) and 6 potential B cell epitopes, respectively. Docking analysis and binding predictions demonstrated enrichment for peptide binding to HLA-B (class I) and HLA-DRB1 (class II) molecules. Overlays of predicted B cell epitopes with the structure of the viral spike (S) glycoprotein revealed that 4 of 6 epitopes were located in the receptor-binding domain of the S protein. To our knowledge, this is the first study to comprehensively analyze all 10 (structural, non-structural and accessory) proteins from SARS-CoV-2 using predictive algorithms to identify potential targets for vaccine development.\n\nSignificance StatementThe novel coronavirus SARS-CoV-2 recently emerged from China, rapidly spreading and ushering in a global pandemic. Despite intensive research efforts, our knowledge of SARS-CoV-2 immunology and the proteins targeted by the immune response remains relatively limited, making it difficult to rationally design candidate vaccines. We employed a suite of bioinformatic tools, computational algorithms, and structural modeling to comprehensively analyze the entire SARS-CoV-2 proteome for potential T cell and B cell epitopes. Utilizing a set of stringent selection criteria to filter peptide epitopes, we identified 41 T cell epitopes (5 HLA class I, 36 HLA class II) and 6 B cell epitopes that could serve as promising targets for peptide-based vaccine development against this emerging global pathogen.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Stephen N. Crooke", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Inna G. Ovsyannikova", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Richard B. Kennedy", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Gregory A. Poland", - "author_inst": "Mayo Clinic" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.05.13.093971", "rel_title": "Insights into molecular evolution recombination of pandemic SARS-CoV-2 using Saudi Arabian sequences", @@ -1466358,6 +1469188,53 @@ "type": "confirmatory results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.05.13.094490", + "rel_title": "A rapid, point of care red blood cell agglutination assay for detecting antibodies against SARS-CoV-2", + "rel_date": "2020-05-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.13.094490", + "rel_abs": "The COVID-19 pandemic has brought the world to a halt, with cases observed around the globe causing significant mortality. There is an urgent need for serological tests to detect antibodies against SARS-CoV-2, which could be used to assess the prevalence of infection, as well as ascertain individuals who may be protected from future infection. Current serological tests developed for SARS-CoV-2 rely on traditional technologies such as enzyme-linked immunosorbent assays (ELISA) and lateral flow assays, which may lack scalability to meet the demand of hundreds of millions of antibody tests in the coming year. Herein, we present an alternative method of antibody testing that just depends on one protein reagent being added to patient serum/plasma or whole blood and a short five-minute assay time. A novel fusion protein was designed that binds red blood cells (RBC) via a single-chain variable fragment (scFv) against the H antigen and displays the receptor-binding domain (RBD) of SARS-CoV-2 spike protein on the surface of RBCs. Upon mixing of the fusion protein, RBD-scFv with recovered COVID-19 patient serum and RBCs, we observed agglutination of RBCs, indicating the patient developed antibodies against SARS-CoV-2 RBD. Given that the test uses methods routinely used in hospital clinical labs across the world, we anticipate the test can be rapidly deployed with only the protein reagent required at projected manufacturing cost at U.S. cents per test. We anticipate our agglutination assay may find extensive use in low-resource settings for detecting SARS-CoV-2 antibodies.Competing Interest StatementR.L.K. is an inventor on a provisional patent application related to the work described in the manuscript. All other authors have no competing interests.View Full Text", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Robert L Kruse", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Yuting Huang", + "author_inst": "University of Maryland Medical Center - Midtown" + }, + { + "author_name": "Heather Smetana", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Eric A Gehrie", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Tim K Amukele", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Aaron AR Tobian", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Heba H Mostafa", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Zack Z Wang", + "author_inst": "Johns Hopkins University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.05.10.20097428", "rel_title": "Will an imperfect vaccine curtail the COVID-19 pandemic in the U.S.?", @@ -1467681,57 +1470558,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.09.20091454", - "rel_title": "Early Awake Prone and Lateral Position in Non-intubated Severe and Critical Patients with COVID-19 in Wuhan: A Respective Cohort Study", - "rel_date": "2020-05-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20091454", - "rel_abs": "BackgroundPrevious studies suggest applying prone position (PP) and lateral position (LP) in patients with severe acute respiratory distress syndrome (ARDS) for their efficacy in improving oxygenation and lung recruitment.This paper aims to share clinical experiences and outcome of using PP and LP in combination with oxygen therapy (OT) and Non-invasive ventilation (NIV) in severe and critical patients with COVID-19.\n\nMethodsClinical data of 48 severe and critical patients have been retrieved from medical records and reviewed. The primary outcome is the survival rate. Secondary outcome is the rate of patients requiring intubation.\n\nResultsIn total, 25 patients were finally included in the study. The mean respiratory rate of all 25 patients decreased from 28.4 breaths/min to 21.3 breaths/min. CT results showed increase in lung recruitment. All patients tolerated PP and LP well. No deterioration or severe adverse events associated with PP and LP occurred. All patients recovered and survived without intubation. Follow-up to date showed that all patients have been discharged except one with mild symptoms and positive RNA test.\n\nConclusionClinical outcomes of early application of PP and LP in combination with OT and NIV in severe and critical patients with COVID-19 indicated well tolerance of the therapy and resulted in improving patients oxygenation in a safe and effective manner. Therefore, this strategy can be explored as an early intervention in managing patients in early stage of disease development under the context of pandemic and limited medical resources.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Wei Dong", - "author_inst": "1.Critical Care Medicine Department, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Techno" - }, - { - "author_name": "Yiping Gong", - "author_inst": "1.\tDepartment of Infectious Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei, China" - }, - { - "author_name": "Juan Feng", - "author_inst": "1.\tDepartment of Infectious Disease, Renmin Hospital of Wuhan University,Wuhan,Hubei, China" - }, - { - "author_name": "Lang Bai", - "author_inst": "1.Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan, China; 2.Department of Infectious Disease, Renmin Hospital of Wuhan " - }, - { - "author_name": "Haomiao Qing", - "author_inst": "Radiology Department, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, " - }, - { - "author_name": "Peng Zhou", - "author_inst": "Radiology Department, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, " - }, - { - "author_name": "Yu Du", - "author_inst": "1.Emergency department and intensive care unit, West China School of Public Health, West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China; 2.D" - }, - { - "author_name": "Junchen Zhu", - "author_inst": "1.Intensive Care Unit, Affiliated Hospital of Chengdu University, Chengdu, Sichuan, China; 2.Department of Infectious Disease, Renmin Hospital of Wuhan Universi" - }, - { - "author_name": "Shanling Xu", - "author_inst": "1.Critical Care Medicine Department, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Techno" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.05.08.20095877", "rel_title": "Forecasting Transmission Dynamics of COVID-19 Epidemic in India under Various Containment Measures- A Time-Dependent State-Space SIR Approach", @@ -1467972,6 +1470798,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.05.08.20095745", + "rel_title": "On the Front (Phone) Lines: Results of a COVID-19 Hotline in Northeast Ohio", + "rel_date": "2020-05-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095745", + "rel_abs": "ImportanceSevere acute respiratory syndrome coronavirus (SARS-CoV-2) and the associated coronavirus disease of 2019 (COVID-19) have presented immense challenges for health care systems. Many regions have struggled to adapt to disruptions to health care practice and employ systems that effectively manage the demand for services.\n\nObjectiveTo examine the effectiveness of the first five weeks of a 24/7 physician-staffed COVID-19 hotline.\n\nDesignCohort study using electronic health records.\n\nSettingA single large health care system in Northeast Ohio.\n\nParticipantsDuring 5 weeks of operation, 10,112 patients called the hotline (callers) and were evaluated by a registered nurse (RN) using standardized protocols. Of these, 4,213 (42%) were referred for a physician telehealth visit (telehealth patients). The mean age of callers was 42 years. 67% were female, 51% white, and 46% were on Medicaid or uninsured.\n\nInterventionPhysician telehealth visits for COVID-19.\n\nMain Outcomes and MeasuresWe describe clinical diagnosis, patient characteristics (age, sex race/ethnicity, smoking status, insurance status), and visit disposition. We use logistic regression to evaluate associations between patient characteristics, visit disposition and subsequent emergency department use, hospitalization, and SARS-Cov-2 PCR testing.\n\nResultsCommon caller concerns included cough, fever, and shortness of breath. Most telehealth patients (79%) were advised to self-isolate at home, 14% were determined to be unlikely to have COVID-19, 3% were advised to seek emergency care, and 4% had miscellaneous other dispositions. A total of 287 (7%) patients had a subsequent ED visit, and 44 (1%) were hospitalized with a COVID-19 diagnosis. Of the callers, 482 (5%) had a COVID-19 test reported with 69 (14%) testing positive. Among patients advised to stay at home, 83% had no further face-to-face visits. In multivariable results, only a physician recommendation to seek emergency care was associated with emergency room use (OR=4.73, 95%CI 1.37-16.39, p=.014). Only older age was associated with having a positive test result.\n\nConclusions and RelevanceRobust, physician-directed telehealth services can meet a wide range of needs during the acute phase of a pandemic, conserving scarce resources such as personal protective equipment and testing supplies and preventing the spread of infections to patients and health care workers.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat is the feasibility and effectiveness of physician telehealth services during a pandemic?\n\nFindingsIn this cohort study of a COVID-19 telehealth hotline that included 10,112 callers and 4,213 physician telehealth visits, most patients (79%) were advised to self-isolate at home, 14% were found unlikely to have COVID-19, 4% dispositions (e.g. testing or office visit) and 3% were advised to immediately seek care emergency department. 83% of patients who were advised to stay home did not require in-person visits.\n\nMeaningPhysician-directed telehealth services conserve scarce resources and provide effective, equitable care during a pandemic without compromising patient safety.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "David Margolius", + "author_inst": "The MetroHealth System" + }, + { + "author_name": "Mary Hennekes", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Jimmy Yaho", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Douglas Einstadter", + "author_inst": "The MetroHealth System" + }, + { + "author_name": "Douglas Gunzler", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Nabil Chehade", + "author_inst": "The MetroHealth System" + }, + { + "author_name": "Ashwini R Sehgal", + "author_inst": "The MetroHealth System" + }, + { + "author_name": "Yasir Tarabichi", + "author_inst": "The MetroHealth System" + }, + { + "author_name": "Adam T Perzynski", + "author_inst": "The MetroHealth System" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, { "rel_doi": "10.1101/2020.05.08.20095604", "rel_title": "MIGRANTS IN TRANSIT AND ASYLUM SEEKERS IN MEXICO: AN EPIDEMIOLOGICAL ANALYSIS OF THE COVID-19 PANDEMIC", @@ -1468915,73 +1471792,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nutrition" }, - { - "rel_doi": "10.1101/2020.05.11.20092528", - "rel_title": "ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens", - "rel_date": "2020-05-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20092528", - "rel_abs": "Serologic assays are needed to determine SARS-CoV-2 seroprevalence, but poor specificity can overestimate exposures. Here, we built a pan-human coronavirus proteome-wide programmable phage display assay (VirScan) to profile coronavirus antigens specifically enriched by 20 COVID-19 patient serum IgG. With ReScan, a new diagnostic development workflow which combines the isolation of phage expressing the most immunogenic peptides with paper-based microarrays manufactured via acoustic liquid handling, we identified 9 candidate antigens from a library of 534 SARS-CoV-2 peptides. These arrays could form the basis of a multiplexed COVID-19 serologic assay with enhanced specificity. ReScan has broad applicability for serologic assay development.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Colin R. Zamecnik", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jayant V. Rajan", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Kevin A. Yamauchi", - "author_inst": "Chan Zuckerberg Biohub" - }, - { - "author_name": "Sabrina A. Mann", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Gavin M. Sowa", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Kelsey C. Zorn", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Bonny D. Alvarenga", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Mars Stone", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Philip J. Norris", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Wei Gu", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Charles Y Chiu", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Joseph L. DeRisi", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Michael R Wilson", - "author_inst": "University of California, San Francisco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.09.20096123", "rel_title": "Breaking the back of COVID-19: Is Bangladesh doing enough testing?", @@ -1469094,6 +1471904,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.09.20096636", + "rel_title": "The Coronavirus 2019 pandemic in Canada: the impact of public health interventions on the course of the outbreak in Alberta and other provinces", + "rel_date": "2020-05-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20096636", + "rel_abs": "Background:\n\nThe SARS-CoV-2 disease 2019 (COVID-19) pandemic has spread across the world with varying impact on health systems and outcomes. We assessed how the type and timing of public-health interventions impacted the course of the outbreak in Alberta and the other Canadian provinces.\n\nMethods:\n\nWe used publicly-available data to summarize rates of laboratory data and mortality in relation to measures implemented to contain the outbreak and testing strategy. We estimated the transmission potential of SARS-CoV-2 before the state of emergency declaration for each province (R0) and at the study end date (Rt).\n\nResults:\n\nThe first cases were confirmed in Ontario (January 25) and British Columbia (January 28). All provinces implemented the same health-policy measures between March 12 and March 30. Alberta had a higher percentage of the population tested (3.8%) and a lower mortality rate (3/100,000) than Ontario (2.6%; 11/100,000) or Quebec (3.1%; 31/100,000). British Columbia tested fewer people (1.7%) and had similar mortality as Alberta. Data on provincial testing strategies were insufficient to inform further analyses. Mortality rates increased with increasing rates of lab-confirmed cases in Ontario and Quebec, but not in Alberta. Ro was similar across all provinces, but varied widely from 2.6 (95% confidence intervals 1.9-3.4) to 6.4 (4.3-8.5), depending on the assumed time interval between onset of symptoms in a primary and a secondary case (serial interval). The outbreak is currently under control in Alberta, British Columbia and Nova Scotia (Rt <1).\n\nInterpretation:\n\nCOVID-19-related health outcomes varied by province despite rapid implementation of similar health-policy interventions across Canada. Insufficient information about provincial testing strategies and a lack of primary data on serial interval are major limitations of existing data on the Canadian COVID-19 outbreak.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Mohamed Mahsin", + "author_inst": "University of Calgary" + }, + { + "author_name": "Seungwon Lee", + "author_inst": "University of Calgary" + }, + { + "author_name": "David Vickers", + "author_inst": "University of Calgary" + }, + { + "author_name": "Alexis Guigue", + "author_inst": "University of Calgary" + }, + { + "author_name": "Tyler Williamson", + "author_inst": "University of Calgary" + }, + { + "author_name": "Hude Quan", + "author_inst": "University of Calgary" + }, + { + "author_name": "Robert Ross Quinn", + "author_inst": "University of Calgary" + }, + { + "author_name": "Pietro Ravani", + "author_inst": "University of Calgary" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.10.20096933", "rel_title": "Increased levels of anxiety among medical and non-medical university students during the COVID-19 pandemic in the United Arab Emirates.", @@ -1470517,25 +1473374,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.05.08.20092080", - "rel_title": "SELF-POLICING COVID-19 AND CIVIC RESPONSIBILITIES IN LAGOS METROPOLIS, NIGERIA", - "rel_date": "2020-05-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20092080", - "rel_abs": "This study investigated self-policing COVID-19 and civic responsibilities in Lagos Metropolis, Nigeria adopting an online qualitative interview due to the current lockdown that denied field (face to face) interview. Fifty out of the feedbacks from the online interview were picked randomly to arrive at the conclusion of this study. The feedbacks suggested that there is adequate awareness of the COVID-19 pandemic among the people living in Lagos Metropolis, Nigeria and that they are following the directives of federal and state governments in an effort to reduce the community transmission of the infectious diseases. However, the ban on public gatherings and movements has made it impossible for many homes to meet their basic needs especially feeding. The government provided palliatives have also been largely insufficient to cater for the vulnerable. There could be a crisis (such as hunger) and the breakdown of law and order if the government does not increase their capacity to mitigate the hardship which the ongoing lockdown has imposed on the people.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ayomide Ilori", - "author_inst": "University of Ibadan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.05.08.20095521", "rel_title": "Expected impact of reopening schools after lockdown on COVID-19 epidemic in Ile-de-France", @@ -1470716,6 +1473554,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.08.20095018", + "rel_title": "Clinical Course and Risk Factors for Recurrence of Positive SARS-CoV-2 RNA: A Retrospective Cohort Study from Wuhan, China", + "rel_date": "2020-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095018", + "rel_abs": "BackgroundCoronavirus Disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has developed into a full-blown global pandemic. It has been reported that patients with COVID-19 meeting the criteria for hospital discharge (including two consecutive negative RT-PCR results) have experienced recurrent PCR positivity. However, the clinical course and risk factors for these patients have not been well described.\n\nMethodsIn this retrospective cohort study, consecutive patients with COVID-19 confirmed by RT-PCR from the Guanggu Branch of Hubei Province Maternity and Childcare Hospital from February 24, 2020 to March 31, 2020 were enrolled. All patients received follow-up to April 15, 2020 from discharge. The epidemiological, radiographic, laboratory, treatment, and outcome data were extracted from medical records. Univariate and multivariable logistic regression methods were used to elucidate risk factors for patients with recurrence of positive SARS-CoV-2 RNA.\n\nResults1087 COVID-19 patients were included in this study. Of these, 20 (1.8%) died and 1067 (98.2%) were discharged from the hospital. Among the discharged cases, there were 81 (7.6%) patients found to develop a repeat positive SARS-Cov-2 RNA result. Older age was obviously associated with death. For patients with recurrent RT-PCR positivity, the median duration from illness onset to onset of complete RNA negative was 33.0 days (range, 6.0-82.0 days; IQR, 20.0-41.0 days), while that from illness onset to recurrence was 50.0 days (range, 21.0-95.0 days; IQR, 36.5-59.5 days). Multivariate regression analysis identified recurrence of positive SARS-Cov-2 RNA was associated with elevated IL-6 levels (P=0.004, OR=3.050; 95% CI, 1.432-6.499), increased lymphocyte count (P=0.038, OR=2.321; 95% CI, 1.048-5.138) and CT imaging features of lung consolidation (P=0.038, OR=1.641; 95% CI, 1.028-2.620) during hospitalization.\n\nConclusionElevated lymphocyte counts and IL-6 levels in blood, and consolidation features on CT imaging are useful risk factors for clinicians to identify patients at risk of developing recurrent positivity of SARS-CoV-2 RNA. This is speculated to be caused by a balance in immune regulation when fighting virus toxicity. For patients with a high risk of recurrent positivity, a prolonged observation and additional preventative measures should be implemented for at least 50 days after illness onset to prevent future outbreaks.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSHow is the clinical course of patients with recurrence of positive SARS-CoV-2 RNA and what clinical characteristics are associated with that?\n\nFindingsIn this cohort involving 1067 COVID-19 patients discharged from the hospital, 81 (7.6%) patients found to develop a repeat positive SARS-Cov-2 RNA result. For patients with recurrent RT-PCR positivity, the median duration from illness onset to onset of complete RNA negative was 3.30 days (range, 6.0-82.0 days; IQR, 20.0-41.0 days), while that from illness onset to recurrence was 50.0 days (range, 21.0-95.0 days; IQR, 36.5-59.5 days). Risk factors associated with recurrence of positive SARS-Cov-2 RNA included elevated IL-6 levels, increased lymphocyte count and CT imaging features of lung consolidation during hospitalization.\n\nMeaningThe recurrence of positive SARS-Cov-2 RNA is speculated to be caused by a balance in immune regulation when fighting virus toxicity. For patients with a high risk of recurrent positivity, a prolonged observation and additional preventative measures should be implemented for at least 50 days after illness onset to prevent future outbreaks.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Jie Chen", + "author_inst": "Naval Medical Center of PLA" + }, + { + "author_name": "Xiaoping Xu", + "author_inst": "Naval Medical Center of PLA" + }, + { + "author_name": "Jing Hu", + "author_inst": "Naval Medical Center of PLA" + }, + { + "author_name": "Qiangda Chen", + "author_inst": "Zhongshan Hospital, Fudan University" + }, + { + "author_name": "Fengfeng Xu", + "author_inst": "Naval Medical Center of PLA" + }, + { + "author_name": "Hui Liang", + "author_inst": "Naval Medical Center of PLA" + }, + { + "author_name": "Nanmei Liu", + "author_inst": "Naval Medical Center of PLA" + }, + { + "author_name": "Hengmei Zhu", + "author_inst": "Eastern Hepatobiliary Surgery Hospital, Naval Military Medical University" + }, + { + "author_name": "Jinlong Lan", + "author_inst": "Naval Medical Center of PLA" + }, + { + "author_name": "Lan Zhou", + "author_inst": "Naval Medical Center of PLA" + }, + { + "author_name": "Jiajun Xing", + "author_inst": "Naval Medical Center of PLA" + }, + { + "author_name": "Ning Pu", + "author_inst": "Zhongshan Hospital, Fudan University" + }, + { + "author_name": "Zhigang Cai", + "author_inst": "Naval Medical Center of PLA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.07.20094839", "rel_title": "Compassionate drug (mis)use during pandemics: lessons for COVID-19 from 2009.", @@ -1471959,153 +1474864,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.12.088716", - "rel_title": "Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability", - "rel_date": "2020-05-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.12.088716", - "rel_abs": "The rapid spread of SARS-CoV-2 has a significant impact on global health, travel and economy. Therefore, preventative and therapeutic measures are urgently needed. Here, we isolated neutralizing antibodies from convalescent COVID-19 patients using a SARS-CoV-2 stabilized prefusion spike protein. Several of these antibodies were able to potently inhibit live SARS-CoV-2 infection at concentrations as low as 0.007 {micro}g/mL, making them the most potent human SARS-CoV-2 antibodies described to date. Mapping studies revealed that the SARS-CoV-2 spike protein contained multiple distinct antigenic sites, including several receptor-binding domain (RBD) epitopes as well as previously undefined non-RBD epitopes. In addition to providing guidance for vaccine design, these mAbs are promising candidates for treatment and prevention of COVID-19.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Philip Brouwer", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Tom Caniels", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Karlijn van Straten", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Jonne Snitselaar", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Yoann Aldon", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Sandhya Bangaru", - "author_inst": "Scripps Research" - }, - { - "author_name": "Jonathan Torres", - "author_inst": "Scripps Research" - }, - { - "author_name": "Nisreen Okba", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Mathieu Claireaux", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Gius Kerster", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Arthur Bentlage", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Marlies van Haaren", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Denise Guerra", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Judith Burger", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Edith Schermer", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Kirsten Verheul", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Niels van der Velde", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Alex van der Kooi", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Jelle van Schooten", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Marielle van Breemen", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Tom Bijl", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Kwinten Sliepen", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Aafke Aartse", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Ronald Derking", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Ilja Bontjer", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Neeltje Kootstra", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Joost Wiersinga", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Gestur Vidarsson", - "author_inst": "Sanquin Research" - }, - { - "author_name": "Bart Haagmans", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Andrew Ward", - "author_inst": "Scripps Research" - }, - { - "author_name": "Godelieve de Bree", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Rogier Sanders", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Marit van Gils", - "author_inst": "Amsterdam UMC" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.12.091090", "rel_title": "Static All-Atom Energetic Mappings of the SARS-Cov-2 Spike Protein with Potential Latch Identification of the Down State Protomer", @@ -1472269,6 +1475027,37 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.05.12.090035", + "rel_title": "Comparative analysis of antiviral efficacy of FDA-approved drugs against SARS-CoV-2 in human lung cells: Nafamostat is the most potent antiviral drug candidate", + "rel_date": "2020-05-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.12.090035", + "rel_abs": "Drug repositioning represents an effective way to control the current COVID-19 pandemic. Previously, we identified 24 FDA-approved drugs which exhibited substantial antiviral effect against SARS-CoV-2 in Vero cells. Since antiviral efficacy could be altered in different cell lines, we developed an antiviral screening assay with human lung cells, which is more appropriate than Vero cell. Comparative analysis of antiviral activities revealed that nafamostat is the most potent drug in human lung cells (IC50 = 0.0022{micro}M).", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Meehyun Ko", + "author_inst": "Institut Pasteur Korea" + }, + { + "author_name": "Sangeun Jeon", + "author_inst": "Institut Pasteur Korea" + }, + { + "author_name": "Wang-Shick Ryu", + "author_inst": "Institut Pasteur Korea" + }, + { + "author_name": "Seungtaek Kim", + "author_inst": "Institut Pasteur Korea" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.05.11.088179", "rel_title": "SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is further increased by a naturally occurring elongation variant", @@ -1473448,129 +1476237,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.07.20073817", - "rel_title": "The majority of male patients with COVID-19 present low testosterone levels on admission to Intensive Care in Hamburg, Germany: a retrospective cohort study.", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20073817", - "rel_abs": "Males develop more severe SARS-CoV-2 infection related disease outcome than females. Herein, sex hormones were repeatedly proposed to play an important role in Covid-19 pathophysiology and immunity. However, it is yet unclear whether sex hormones are associated with Covid-19 outcome in males and females. In this study, we analyzed sex hormones, cytokine and chemokine responses as well as performed a large profile analysis of 600 metabolites in critically-ill male and female Covid-19 patients in comparison to healthy controls and patients with coronary heart diseases as a prime Covid-19 comorbidity. We here show that dysregulated sex hormones, IFN-{gamma} levels and unique metabolic signatures are associated with critical illness in Covid-19 patients. Both, male and female Covid-19 patients, present elevated estradiol levels which positively correlates with IFN-{gamma} levels. Male Covid-19 patients additionally display severe testosterone and triglyceride deficiencies as compared to female patients and healthy controls. Our results suggest that male Covid-19 patients suffer from multiple metabolic disorders, which may lead to higher risk for fatal outcome. These findings will help to understand molecular pathways involved in Covid-19 pathophysiology.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Maria Schroeder", - "author_inst": "Department for Intensive Care Medicine, University Hospital Hamburg-Eppendorf" - }, - { - "author_name": "Berfin Schaumburg", - "author_inst": "Department for Viral Zoonoses-One Health, Heinrich Pette Institute, Leibniz Institute for Experimental Virology" - }, - { - "author_name": "Zacharias Mueller", - "author_inst": "Department for Viral Zoonoses-One Health, Heinrich Pette Institute, Leibniz Institute for Experimental Virology" - }, - { - "author_name": "Ann Parplys", - "author_inst": "Department for Viral Zoonoses-One Health, Heinrich Pette Institute, Leibniz Institute for Experimental Virology" - }, - { - "author_name": "Dominik Jarczak", - "author_inst": "Department for Critical Care Medicine, University Hospital Hamburg Eppendorf" - }, - { - "author_name": "Axel Nierhaus", - "author_inst": "Department for Critical Care Medicine, University Hospital Hamburg Eppendorf" - }, - { - "author_name": "Andreas Kloetgen", - "author_inst": "Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig" - }, - { - "author_name": "Bettina Schneider", - "author_inst": "Department of Biometry, Epidemiology and Information Processing, University of Veterinary Medicine Hannover" - }, - { - "author_name": "Manuela Peschka", - "author_inst": "Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Fabian Stoll", - "author_inst": "Department for Viral Zonoses-One Health, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg" - }, - { - "author_name": "Tian Bai", - "author_inst": "Department for Viral Zoonoses-One Health, Heinrich Pette Institute, Leibniz Institute for EXperimental Virology" - }, - { - "author_name": "Henning Jacobsen", - "author_inst": "Department for Viral Zoonoses-One Health at the Heinrich Pette Institute, Leibniz Institute for Experimental Virology" - }, - { - "author_name": "Martin Zickler", - "author_inst": "Department for Viral Zoonoses-One Health at the Heinrich Pette Institute, Leibniz Institute for Experimental Virology" - }, - { - "author_name": "Stephanie Stanelle-Bertram", - "author_inst": "Department for Viral Zoonoses-One Health at the Heinrich Pette Institute, Leibniz Institute for Experimental Virology" - }, - { - "author_name": "Geraldine de Heer", - "author_inst": "Department for Intensive Care Medicine, University Hospital Hamburg-Eppendorf" - }, - { - "author_name": "Thomas Renne", - "author_inst": "Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Andreas Meinhardt", - "author_inst": "Institute of Anatomy and Cell Biology, Justus-Liebig University of Giessen, Germany" - }, - { - "author_name": "Joerg Heeren", - "author_inst": "Institute for Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Jens Aberle", - "author_inst": "Department of Endocrinology, University Hospital Hamburg Eppendorf" - }, - { - "author_name": "Alice C McHardy", - "author_inst": "Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig" - }, - { - "author_name": "Hartmut Schlueter", - "author_inst": "Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Jens Hiller", - "author_inst": "Institute for Transfusion Medicine, University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Sven Peine", - "author_inst": "Institute for Transfusion Medicine, University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Lothar Kreienbrock", - "author_inst": "Department of Biometry, Epidemiology and Information Processing, University of Veterinary Medicine Hannover" - }, - { - "author_name": "Karin Klingel", - "author_inst": "Institute for Pathology and Neuropathology, University Hospital Tuebingen" - }, - { - "author_name": "Stefan Kluge", - "author_inst": "Department for Intensive Care Medicine, University Hospital Hamburg Eppendorf" - }, - { - "author_name": "Guelsah Gabriel", - "author_inst": "Department for Viral Zoonoses-One Health at the Heinrich Pette Institute, Leibniz Institute for Experimental Virology; University for Veterinary Medicine, Hanno" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.06.20073742", "rel_title": "Evaluating transmission heterogeneity and super-spreading event of COVID-19 in a metropolis of China", @@ -1473795,6 +1476461,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.07.20084087", + "rel_title": "Concerns about disease management and psychological stress in SAPHO patients during the COVID-19 epidemic", + "rel_date": "2020-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20084087", + "rel_abs": "ObjectivesThe coronavirus disease 2019 (COVID-19) epidemic brings potentially impact on the care of patients with rheumatic diseases, including SAPHO syndrome. We aimed to investigate the disease status, concerns about management, and psychological stress in SAPHO patients during the COVID-19 epidemic.\n\nMethodA structured questionnaire was distributed online to patients with SAPHO syndrome enrolled in a Chinese cohort study on March 3rd, 2020. Patients were ask about the current treatments, disease status, and concerns about disease management during the epidemic. Psychologic stress (scored from 0 to 10 points) and psychological problems were reported by the patients.\n\nResultsA total of 157 patients (mean age 38.4 {+/-} 12.3 years, 66.9% females) were included in the study. None of the patients were diagnosed with COVID-19. Sixty-five (41.4%) patients worried about their disease conditions during the epidemic with concerns including medication shortage (73.8%), delay of consultation (46.2%), and disease aggravation (61.5%). Sixty-seven (42.7%) patients had medication withdrawal or dose reduction due to lack of drugs, irregular daily schedule or subjective reasons. The most common psychological problems reported was little interest or pleasure in doing things (66.2%). Patients with progressive disease condition were more distressed and disturbed by the epidemic. Patients with nail involvement felt more worried about their disease conditions than patients without (59.6% vs 31.0%, p =0. 001).\n\nConclusionsThe COVID-19 epidemic imposes a negative impact on the disease management and psychological stress in SAPHO patients. Patients access to specialty care and medication well as mental stress is of great concern.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Shuo Zhang", + "author_inst": "Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences" + }, + { + "author_name": "Xinyu Lu", + "author_inst": "Institute of Clinical Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College" + }, + { + "author_name": "Yihan Cao", + "author_inst": "Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences" + }, + { + "author_name": "Yueting Li", + "author_inst": "Institute of Clinical Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College" + }, + { + "author_name": "Chen Li", + "author_inst": "Department of Traditional Chinese Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences" + }, + { + "author_name": "Wen Zhang", + "author_inst": "Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "rheumatology" + }, { "rel_doi": "10.1101/2020.05.07.20090225", "rel_title": "Anxiety among the general population during Coronavirus-19 Disease in Saudi Arabia: Implications for a Mental Support Program", @@ -1475074,65 +1477779,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dentistry and oral medicine" }, - { - "rel_doi": "10.1101/2020.05.06.20093724", - "rel_title": "Variations in Personal Protective Equipment Preparedness in Intensive Care Units during the COVID-19 Pandemic: A Survey of Asia-Pacific Countries", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093724", - "rel_abs": "ObjectivesTo evaluate PPE-preparedness across intensive care units (ICUs) in 6 Asia-Pacific countries. PPE-preparedness was defined as the adherence to guidelines, training HCWs, procuring PPE stocks and responding appropriately to a suspected case (transportation and admission to hospital).\n\nDesignCross-sectional web-based survey.\n\nSettingICUs in Australia, New Zealand (NZ), Singapore, Hong Kong (HK), India and Philippines with a 24/7 Emergency/Casualty Department, and capable of mechanically ventilating patients for >24 hours.\n\nInterventionsQuestionnaire sent to intensivists in 633 Level ll/lll ICUs in 6 Asia-Pacific countries by email, WhatsApp and text messaging.\n\nMain outcome measures263 intensivists responded, of whom 231 were eligible for analysis. Response rates were 68%-100% in all countries except India, where it was 24%. 97% either conformed to or exceeded WHO recommendations for PPE-practice. 59% employed airborne precautions irrespective of aerosol-generation-procedures. There were variations in negative-pressure room use (highest in HK/Singapore), training (best in NZ), and PPE stock-awareness (best in HK/Singapore/NZ). High-flow-nasal-oxygenation and non-invasive ventilation were not options in most HK (66.7%, 83.3% respectively) and Singapore ICUs (50%, 80% respectively), but were considered in other countries to a greater extent. 38% reported not having specialized airway teams. Showering and \"buddy-systems\" were underutilized. Clinical waste disposal training was suboptimal (38%).\n\nConclusionsMost intensivists from six Asia-Pacific countries appeared to be aware of the WHO PPE-guidelines by either conforming to/exceeding the recommendations. Despite this, there were widespread variabilities across ICUs and countries in several domains, particularly related to PPE-training and preparedness. Standardising PPE guidelines may translate to better training, better compliance and policies that improve HCW safety. Adopting low-cost approaches such as buddy-systems should be encouraged. More importantly, better pandemic preparedness and building systems with deeply embedded culture of safety is essential to ensure the safety and well-being of HCWs during such pandemics.\n\nAuthor Contributorship\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@1f291aorg.highwire.dtl.DTLVardef@1c388ccorg.highwire.dtl.DTLVardef@4a1a65org.highwire.dtl.DTLVardef@10af39aorg.highwire.dtl.DTLVardef@1ff1eaa_HPS_FORMAT_FIGEXP M_TBL C_TBL Summary BoxO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIPersonal-protective equipment (PPE) is the cornerstone to preventing HCW- infections. A search was done on March 23, 2020 on PubMed, Embase or Google Scholar using the mesh terms \"personal protective equipment\", \"PPE\", \"preparedness OR practice OR training\". It revealed no previous studies on PPE preparedness in intensive care units (ICUs). No filters were used for the search.\nC_LIO_LISeveral guidelines/recommendations issued by health organisations on PPE practice exist\nC_LI\n\nWhat are the new findingsO_LIAs the first study to evaluate PPE-preparedness in ICUs, it demonstrated major concerns on PPE-preparedness across several ICUs, particularly in Australia, India and Philippines. There was suboptimal PPE-training, under-utilisation of low-cost interventions such as buddy-systems/team-training, and stock-awareness.\nC_LIO_LIThe guidelines by health organisations on PPE practice have several conflicting recommendations.\nC_LI\n\nHow might it impact on clinical practice in the foreseeable futureO_LIStandardising PPE guidelines by health organisations may translate to better training, better compliance and policies that improve HCW safety.\nC_LIO_LITo ensure the safety and well-being of HCWs, urgent measures are needed to improve PPE-preparedness and building systems with deeply embedded culture of safety. By helping ICUs evaluate and improve their current state of PPE preparedness, the study may help prevent healthcare worker infections and save lives.\nC_LI", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Arvind Rajamani", - "author_inst": "Nepean Clinical School University of Sydney" - }, - { - "author_name": "Ashwin SUBRAMANIAM", - "author_inst": "Frankston Hospital and Monash University, VIC" - }, - { - "author_name": "Kiran Shekar", - "author_inst": "The Prince Charles Hospital" - }, - { - "author_name": "Jumana Haji", - "author_inst": "ECMO program director, Consultant anesthesia and critical care 8.\tAster CMI hospital Bangalore" - }, - { - "author_name": "Jinghang Luo", - "author_inst": "Basic Physician Trainee 9.\tWestern Health, VIC" - }, - { - "author_name": "Shailesh BIHARI", - "author_inst": "Flinders university and Flinders Medical center, Bedford Park SA 5042" - }, - { - "author_name": "Wai Tat Wong", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Navya GULLAPALLI", - "author_inst": "Final Year Medical Student Monash University, Clayton VIC" - }, - { - "author_name": "Markus RENNER", - "author_inst": "Senior clinical lecturer Otago University, NZ." - }, - { - "author_name": "Claudia Maria ALCANCIA", - "author_inst": "Makati Medical Center, Philippines" - }, - { - "author_name": "Kollengode RAMANATHAN", - "author_inst": "National University Hospital, Singapore" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2020.05.07.20094094", "rel_title": "Epidemiology of CoVID-19 and predictors of recovery in the Republic of Korea", @@ -1475313,6 +1477959,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.08.20031666", + "rel_title": "Psychological morbidities and fatigue in patients with confirmed COVID-19 during disease outbreak: prevalence and associated biopsychosocial risk factors", + "rel_date": "2020-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20031666", + "rel_abs": "ObjectiveThe coronavirus disease 2019 (COVID-19) - a novel and highly infectious pneumonia - has now spread across China and beyond for over four months. However, its psychological impact on patients is unclear. We aim to examine the prevalence and associated risk factors for psychological morbidities and fatigue in patients with confirmed COVID-19 infection.\n\nMethodsAmidst the disease outbreak, 41 out of 105 COVID-19 patients in a local designated hospital in China were successfully assessed using a constellation of psychometric questionnaires to determine their psychological morbidities and fatigue. Several potential biopsychosocial risk factors (including pre-existing disabilities, CT severity score of pneumonia, social support, coping strategies) were assessed through multivariable logistic regression analyses to clarify their association with mental health in patients.\n\nResults43.9% of 41 patients presented with impaired general mental health, 12.2% had post-traumatic stress disorder (PTSD) symptoms, 26.8% had anxiety and/or depression symptoms, and 53.6% had fatigue. We did not find any association between pneumonia severity and psychological morbidities or fatigue in COVID-19 patients. However, high perceived stigmatization was associated with an increased risk of impaired general mental health and high perceived social support was associated with decreased risk. Besides, negative coping inclination was associated with an increased risk of PTSD symptoms; high perceived social support was associated with a decreased risk of anxiety and/or depression symptoms.\n\nConclusionsPsychological morbidities and chronic fatigue are common among COVID-19 patients. Negative coping inclination and being stigmatized are primary risk factors while perceived social support is the main protective factor.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Rongfeng Qi", + "author_inst": "Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University; Department of Radiology, Jinling Hospital, Southern Medical University." + }, + { + "author_name": "Wei Chen", + "author_inst": "Jinling Hospital, Southern Medical University, Nanjing, Jiangsu, China; The Second Affiliated Hospital and Yuying Children Hospital of Wenzhou Medical Universit" + }, + { + "author_name": "Saiduo Liu", + "author_inst": "Departments of Infectious Disease, Wenzhou Central Hospital, 32 West Jiangbin Road, Wenzhou, Zhejiang, China." + }, + { + "author_name": "Paul M Thompson", + "author_inst": "Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California" + }, + { + "author_name": "Long Jiang Zhang", + "author_inst": "Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University" + }, + { + "author_name": "Fei Xia", + "author_inst": "Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University" + }, + { + "author_name": "Fang Cheng", + "author_inst": "Departments of Infectious Disease, Wenzhou Central Hospital, 32 West Jiangbin Road, Wenzhou, Zhejiang" + }, + { + "author_name": "Ailing Hong", + "author_inst": "Departments of Infectious Disease, Wenzhou Central Hospital, 32 West Jiangbin Road, Wenzhou, Zhejiang" + }, + { + "author_name": "Wesley Surento", + "author_inst": "Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Marina del Rey, CA, 90292, USA." + }, + { + "author_name": "Song Luo", + "author_inst": "Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China" + }, + { + "author_name": "Zhi Yuan Sun", + "author_inst": "Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China" + }, + { + "author_name": "Chang Sheng Zhou", + "author_inst": "Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China" + }, + { + "author_name": "Lingjiang Li", + "author_inst": "Mental Health Institute, the Second Xiangya Hospital, National Technology Institute of Psychiatry, Key Laboratory of Psychiatry and Mental Health of Hunan Provi" + }, + { + "author_name": "Xiangao Jiang", + "author_inst": "Departments of Infectious Disease, Wenzhou Central Hospital, 32 West Jiangbin Road, Wenzhou, Zhejiang, China." + }, + { + "author_name": "Guang Ming Lu", + "author_inst": "Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.06.20093658", "rel_title": "Disinfection effect of pulsed xenon ultraviolet irradiation on SARS-CoV-2 and implications for environmental risk of COVID-19 transmission", @@ -1476672,61 +1479393,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.08.20095075", - "rel_title": "A rapid review of available evidence on the serial interval and generation time of COVID-19", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095075", - "rel_abs": "BackgroundThe serial interval is the time between symptom onsets in an infector-infectee pair. The generation time, also known as the generation interval, is the time between infection events in an infector-infectee pair. The serial interval and the generation time are key parameters for assessing the dynamics of a disease. A number of scientific papers reported information pertaining to the serial interval and/or generation time for COVID-19.\n\nObjectivesConduct a rapid review of available evidence to advise on appropriate parameter values for serial interval and generation time in national COVID-19 transmission models for Ireland and on methodological issues relating to those parameters.\n\nMethodsA review of scientific literature was conducted covering the period between December 1, 2019 and April 27, 2020. Nineteen scientific papers were evaluated in detail from 27 papers that contained information on the serial interval and/or generation time for COVID-19.\n\nResultsThe mean of the serial interval ranged from 3.1 to 7.5 days, based on 22 estimates, and the median from 1.9 to 6.0 days (based on 7 estimates). Only three estimates were provided for the mean of the generation time. These ranged from 3.9 to 5.2 days. One estimate of 5.0 days was provided for the median of the generation time.\n\nDiscussionThe values of the estimates for serial interval and generation time are heavily influenced by the contact rates between infectious and susceptible individuals. Mitigation measures that are introduced in a country or region are of paramount importance in this regard. The serial interval estimate of 6.6 days (95% confidence interval: 0.7 - 19.0) from the paper by Cereda et al.[10] is likely to be the most relevant to European countries. National estimates should be obtained as soon as possible.\n\nStrengths and limitations of this studyO_LIThe study provides timely information on serial interval and generation time for those involved in the development of models and in the implementation of control measures against COVID-19.\nC_LIO_LIThis is a rapid review of available evidence in the scientific literature between December 1, 2019 and April 27, 2020 on the serial interval and/or the generation time and it contains the usual limitations associated with such a review.\nC_LIO_LIEleven of the 19 papers reviewed in detail were pre-print articles.\nC_LIO_LIThe statistical methods used in the different papers were not analysed in detail.\nC_LI", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "John M Griffin", - "author_inst": "Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 W6F6, Ireland." - }, - { - "author_name": "Aine B Collins", - "author_inst": "Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 W6F6, Ireland." - }, - { - "author_name": "Kevin Hunt", - "author_inst": "School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, Ireland" - }, - { - "author_name": "David McEvoy", - "author_inst": "School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin 4, Ireland" - }, - { - "author_name": "Miriam Casey", - "author_inst": "Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 W6F6, Ireland." - }, - { - "author_name": "Andrew W Byrne", - "author_inst": "One Health Scientific Support Unit, Department of Agriculture, Food and the Marine (DAFM), Kildare Street, Dublin 2, Ireland" - }, - { - "author_name": "Conor G McAloon", - "author_inst": "Section of Herd Health and Animal Husbandry, UCD School of Veterinary Medicine, University College Dublin, Dublin D04 W6F6, Ireland" - }, - { - "author_name": "Ann Barber", - "author_inst": "Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 W6F6, Ireland." - }, - { - "author_name": "Elizabeth Ann Lane", - "author_inst": "Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 W6F6, Ireland." - }, - { - "author_name": "Simon J More", - "author_inst": "Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 W6F6, Ireland." - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.07.20094714", "rel_title": "DOUBLE POWER LAW FOR COVID-19: PREDICTION OF NEW CASES AND DEATH RATES IN ITALY AND SPAIN", @@ -1476899,6 +1479565,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.08.20095679", + "rel_title": "Negative nasopharyngeal SARS-CoV-2 PCR conversion in Response to different therapeutic interventions", + "rel_date": "2020-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095679", + "rel_abs": "BACKGROUNDDespite lack of convincing evidence of the efficacy of hydroxychloroquine, it has been suggested to be used for the treatment of SARS-CoV-2 to accelerate the negative virus conversion. We aimed to explore the association between negative nasopharyngeal SARS-CoV-2 PCR clearance and different therapeutic interventions.\n\nMETHODOLOGYThis was a retrospective cohort study of 93 patients who were admitted to medical ward with a PCR confirmed diagnosis of COVID-19 and met the inclusion criteria in a tertiary hospital in Mecca, Saudi Arabia. There were three interventional subgroups (group A (n=45): who received antimalarial drug only classified as (A1), combined with azithromycin (A2) or combined with antiviral drugs (A3)), and one supportive care group (group B) (n=48). The primary and secondary endpoints of the study were achieving negative SARS-CoV-2 nasopharyngeal PCR sample within five days or less from the start of the intervention and 12 days or less from the diagnose, respectively.\n\nRESULTSThe mean age of the patients was 43.9 years (SD:15.9). A median time of 3.00 days (IQR:2.00-6.50) needed from the time of starting the intervention/supportive care to the first negative PCR sample. There was no statistically significant difference neither between the percentage of patients in the interventional group and the supportive care group who achieved the primary or the secondary endpoint, nor in the median time needed to achieve the first negative PCR sample (p>0.05).\n\nCONCLUSIONPrescribing antimalarial medications was not shown to shorten the disease course nor to accelerate the negative PCR conversion rate.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Mohammed Hassan Shabrawishi", + "author_inst": "Pulmonology department, Al Noor Specialist Hospital, Mecca, Saudi Arabia." + }, + { + "author_name": "Abdallah Y Naser", + "author_inst": "Faculty of Pharmacy, Isra University, Amman, Jordan." + }, + { + "author_name": "Hassan Alwafi", + "author_inst": "Department of Clinical Pharmacology and Toxicology, Umm Alqura University, College of Medicine, Mecca, Saudi Arabia." + }, + { + "author_name": "Ahmad Mansoor Aldobyany", + "author_inst": "Pulmonology department, King Abdullah Medical City, Mecca, Saudi Arabia." + }, + { + "author_name": "Abdelfattah Ahmed Touman", + "author_inst": "Pulmonology department, King Abdullah Medical City, Mecca, Saudi Arabia." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.05.07.20094086", "rel_title": "Transmission in Latent Period Causes A Large Number of Infected People in the United States", @@ -1477986,49 +1480687,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.05.09.085613", - "rel_title": "Potential modes of COVID-19 transmission from human eye revealed by single-cell atlas", - "rel_date": "2020-05-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.09.085613", - "rel_abs": "There is a pressing urgency to understand the entry route of SARS-CoV-2 viruses into the human body. SARS-CoV-2 viruses enter through ACE2 receptors after the S proteins of the virus are primed by proteases such as TMPRSS2. Most studies focused on the airway epithelial and lung alveolar cells as the route of infection, while the mode of transmission through the ocular route is not well established. Here, we profiled the presence of SARS-CoV-2 receptors and receptor-associated enzymes at single-cell resolution of thirty-three human ocular cell types. We identified unique populations of corneal cells with high ACE2 expression, among which the conjunctival cells co-expressed both ACE2 and TMPRSS2, suggesting that they could serve as the entry points for the virus. Integrative analysis further models the signaling and transcription regulon networks involved in the infection of distinct corneal cells. Our work constitutes a unique resource for the development of new treatments and management of COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Kiyofumi Hamashima", - "author_inst": "Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, A*STAR Institute of Molecular and Cell Biology, Singapore 138673" - }, - { - "author_name": "Pradeep Gautam", - "author_inst": "Institute of Molecular and Cell Biology (IMCB)" - }, - { - "author_name": "Katherine Anne Lau", - "author_inst": "Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, A*STAR Institute of Molecular and Cell Biology, Singapore 138673" - }, - { - "author_name": "Chan Woon Khiong", - "author_inst": "Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore" - }, - { - "author_name": "Timothy A Blenkinsop", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA" - }, - { - "author_name": "Hu Li", - "author_inst": "Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA" - }, - { - "author_name": "Yuin Han Loh", - "author_inst": "Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, A*STAR Institute of Molecular and Cell Biology, Singapore 138673" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.05.09.086249", "rel_title": "Cholesterol and COVID19 lethality in elderly.", @@ -1478229,6 +1480887,121 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.05.06.20069872", + "rel_title": "Characterisation of Acute Kidney Injury in Critically Ill Patients with Severe Coronavirus Disease-2019 (COVID-19)", + "rel_date": "2020-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20069872", + "rel_abs": "BackgroundCOVID-19-associated acute kidney injury frequency, severity and characterisation in critically ill patients has not been reported.\n\nMethodsSingle-center cohort performed from March 3, 2020, to April 14, 2020 in 4 intensive care units in Bordeaux University Hospital, France. All patients with COVID19 and pulmonary severity criteria were included. AKI was defined using KDIGO criteria. A systematic urinary analysis was performed. The incidence, severity, clinical presentation, biological characterisation (transient vs. persistent acute kidney injury; proteinuria, hematuria and glycosuria), and short-term outcomes was evaluated.\n\nResults71 patients were included, with basal serum creatinine of 69 {+/-} 21 {micro}mol/L. At admission, AKI was present in 8/71 (11%) patients. Median follow-up was 17 [12-23] days. AKI developed in a total of 57/71 (80%) patients with 35% Stage 1, 35% Stage 2, and 30% Stage 3 acute kidney injury; 10/57 (18%) required renal replacement therapy. Transient AKI was present in only 4/55 (7%) patients and persistent AKI was observed in 51/55 (93%). Patients with persistent AKI developed a median urine protein/creatinine of 82 [54-140] (mg/mmol) with an albuminuria/proteinuria ratio of 0.23 {+/-} 20 indicating predominant tubulo-interstitial injury. Only 2 (4%) patients had glycosuria. At Day 7 onset of after AKI, six (11%) patients remained dependent on renal replacement therapy, nine (16%) had SCr > 200 {micro}mol/L, and four (7%) died. Day 7 and day 14 renal recovery occurred in 28% and 52 % respectively.\n\nConclusionCOVID-19-associated AKI is frequent, persistent severe and characterised by an almost exclusive tubulo-interstitial injury without glycosuria.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Sebastien RUBIN", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Arthur Orieux", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Renaud Prevel", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Antoine Garric", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Marie-Lise Bats", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Sandrine Dabernat", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Fabrice Camou", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Olivier Guisset", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Nahema Issa", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Gaelle Mourissoux", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Antoine Dewitte", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Olivier Joannes-boyau", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Catherine Fleureau", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Hadrien Roze", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Cedric Carrie", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Laurent Petit", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Benjamin Clouzeau", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Charline Sazio", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Hoang-Nam Bui", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Odile Pillet", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Claire Rigothier", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Frederic Vargas", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Christian Combe", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Didier Gruson", + "author_inst": "CHU de Bordeaux" + }, + { + "author_name": "Alexandre Boyer", + "author_inst": "CHU de Bordeaux" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2020.05.06.20093104", "rel_title": "How to Flatten the post-lockdown epidemic trajectory", @@ -1479732,53 +1482505,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.05.20088906", - "rel_title": "Predicting Disease Progression in COVID19: A Score Based On Lab Tests At Time Of Diagnosis", - "rel_date": "2020-05-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20088906", - "rel_abs": "BackgroundCOVID19 is worldwide pandemic that is mild in the majority of patients but can result in a pneumonia like illness with progression to acute respiratory distress syndrome and death. Predicting the disease severity at time of diagnosis can be helpful in prioritizing hospital admission and resources.\n\nMethodsWe prospectively recruited 1096 consecutive patients with COVID19 from the Jaber Hospital, a COVID19 facility in Kuwait, between 24 February and 20 April 2020. The primary endpoint of interest was disease severity defined algorithmically. Predefined risk variables were collected at the time of PCR based diagnosis of the infection. Prognostic model development used 5-fold cross-validated regularized logit regression. The cohort was divided into a training and validation cohort and all model development proceeded on the training cohort.\n\nResultsThere were 643 patients with clinical course data of whom 94 developed severe COVID19. In the final model, age, CRP, procalcitonin, lymphocyte and monocyte percentages and serum albumin were independent predictors of a more severe illness course. The final prognostic model demonstrated good discrimination, calibration and internal validity.\n\nConclusionWe developed and validated a simple score calculated at time of diagnosis that can predict patients with severe COVID19 disease.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Mohammad H. Jamal", - "author_inst": "Kuwait University School Of Medicine" - }, - { - "author_name": "Suhail Doi", - "author_inst": "Qatar University College of Medicine" - }, - { - "author_name": "Sarah Al Youha", - "author_inst": "Jaber Al-Ahmad Al-Sabah Hospital, Ministry of Health of Kuwait" - }, - { - "author_name": "Sulaiman AlMazeedi", - "author_inst": "Jaber Al-Ahmad Al-Sabah Hospital, Ministry of Health of Kuwait" - }, - { - "author_name": "Muhannad AlHaddad", - "author_inst": "Jaber Al-Ahmad Al-Sabah Hospital, Ministry of Health of Kuwait" - }, - { - "author_name": "Ali AlMuhaini", - "author_inst": "Jaber Al-Ahmad Al-Sabah Hospital, Ministry of Health of Kuwait" - }, - { - "author_name": "Fahad AlGhimlas", - "author_inst": "Public Health Administration, Ministry of Health of Kuwait" - }, - { - "author_name": "Salman K. AlSabah", - "author_inst": "Kuwait University,College of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.05.20091918", "rel_title": "Identification and Analysis of Shared Risk Factors in Sepsis and High Mortality Risk COVID-19 Patients", @@ -1479995,6 +1482721,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.05.20092288", + "rel_title": "Screening for SARS-CoV-2 infections with colorimetric RT-LAMP and LAMP sequencing", + "rel_date": "2020-05-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20092288", + "rel_abs": "The COVID-19 pandemic caused by the novel SARS-CoV-2 virus poses a significant public-health problem. In order to control the pandemic, rapid tests for detecting existing infections and assessing virus spread are critical.\n\nApproaches to detect viral RNA based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) hold outstanding promise towards greatly simplified and broadly applicable testing methods. RT-LAMP assays appear more robust than qPCR-based methods and only require incubation at a constant temperature, thus eliminating the need for sophisticated instrumentation.\n\nHere, we tested a two-color RT-LAMP protocol using clinical SARS-CoV-2 samples and also established a protocol that does not require prior RNA isolation (\"swab-to-RT-LAMP\"). Our study is based on several hundred clinical patient samples with a wide range of viral loads, thus allowing, for the first time, to accurately determine the sensitivity and specificity of the RT-LAMP assay for the detection of SARS-CoV-2 in patients. We found that RT-LAMP can reliably detect SARS-CoV-2 samples with a qPCR threshold cycle number (CT value) of up to 30 in the standard RT-qPCR assay. We used both, either purified RNA or direct pharyngeal swab specimens and showed that RT-LAMP assays have, despite a decreased sensitivity compared to RT-qPCR, excellent specificity. We also developed a multiplexed LAMP-sequencing protocol as a diagnostic and validation procedure to detect and record the outcome of RT-LAMP assays. LAMP-sequencing is fully scalable and can assess the results of thousands of LAMP reactions in parallel. Finally, we propose applications of RT-LAMP based assays for SARS-CoV-2 detection.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Viet Loan Dao Thi", + "author_inst": "Center of Infectious Diseases, Department of Virology, Heidelberg University Hospital" + }, + { + "author_name": "Konrad Herbst", + "author_inst": "Center for Molecular Biology (ZMBH), University of Heidelberg" + }, + { + "author_name": "Kathleen Boerner", + "author_inst": "Center of Infectious Diseases, Department of Virology, Heidelberg University Hospital" + }, + { + "author_name": "Matthias Meurer", + "author_inst": "Center for Molecular Biology (ZMBH), University of Heidelberg" + }, + { + "author_name": "Lukas P M Kremer", + "author_inst": "German Cancer Research Center (DKFZ)" + }, + { + "author_name": "Daniel Kirrmaier", + "author_inst": "Center for Molecular Biology (ZMBH), University of Heidelberg" + }, + { + "author_name": "Andrew Freistaedter", + "author_inst": "Center of Infectious Diseases, Department of Virology, Heidelberg University Hospital" + }, + { + "author_name": "Dimitrios Papagiannidis", + "author_inst": "Center for Molecular Biology (ZMBH), University of Heidelberg" + }, + { + "author_name": "Carla Galmozzi", + "author_inst": "Center for Molecular Biology (ZMBH), University of Heidelberg" + }, + { + "author_name": "Steffen Klein", + "author_inst": "Center of Infectious Diseases, Department of Virology, Heidelberg University Hospital" + }, + { + "author_name": "Petr Chandla", + "author_inst": "Center of Infectious Diseases, Department of Virology, Heidelberg University Hospital" + }, + { + "author_name": "Dina Khalid", + "author_inst": "Center of Infectious Diseases, Department of Virology, Heidelberg University Hospital" + }, + { + "author_name": "Isabel Barreto Miranda", + "author_inst": "Center of Infectious Diseases, Department of Virology, Heidelberg University Hospital" + }, + { + "author_name": "Paul Schnitzler", + "author_inst": "Center of Infectious Diseases, Department of Virology, Heidelberg University Hospital" + }, + { + "author_name": "Hans-Georg Kraeusslich", + "author_inst": "Center of Infectious Diseases, Department of Virology, Heidelberg University Hospital" + }, + { + "author_name": "Michael Knop", + "author_inst": "Center for Molecular Biology (ZMBH), University of Heidelberg" + }, + { + "author_name": "Simon Anders", + "author_inst": "Center for Molecular Biology (ZMBH), University of Heidelberg" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.05.20092346", "rel_title": "IKONOS: An intelligent tool to support diagnosis of Covid-19 by texture analysis of x-ray images", @@ -1481082,41 +1483891,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.02.20088013", - "rel_title": "Social distancing and movement constraint as the most likely factors for COVID-19 outbreak control in Brazil", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20088013", - "rel_abs": "As thousands of new cases of COVID-19 have been confirmed, there is an increasing demand to understand the factors underlying the spread of this disease. Using country-level data, we modeled the early growth in the number of cases for over 480 cities in all Brazilian states. As the main findings, we found that the percentage of people respecting social distancing protocols was the main explanatory factor for the observed growth rate of COVID-19. Those cities that presented the highest spread of the new coronavirus were also those that had lower averages of social distancing. We also underline that total population of cities and connectivity, represented by the city-level importance to the air transportation of people across the country, plays important roles in the dissemination of SARS-CoV-2. Climate and socioeconomic predictors had little contribution to the big-picture scenario. Our results show that different States had high variability in their growth rates, mostly due to quite different public health strategies to retain the outbreak of COVID-19. In spite of all limitations of such a large-scale approach, our results underline that climatic conditions are likely weak limiting factors for the spread of the new coronavirus, and the circulation of people in the city- and country-level are the most responsible factors for the early outbreak of COVID-19 in Brazil. Moreover, we reinforce that social distancing protocols are fundamental to avoid critical scenarios and the collapse of healthcare systems. We also predict that economic-induced decisions for relaxing social distancing might have catastrophic consequences, especially in large cities.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Matheus T Baumgartner", - "author_inst": "Universidade Estadual de Maringa" - }, - { - "author_name": "Fernando M Lansac-Toha", - "author_inst": "Universidade Estadual de Maringa" - }, - { - "author_name": "Marco Tulio P Coelho", - "author_inst": "Universidade Federal de Goias" - }, - { - "author_name": "Ricardo Dobrovolski", - "author_inst": "Universidade Federal da Bahia" - }, - { - "author_name": "Jose Alexandre F Diniz-Filho", - "author_inst": "Universidade Federal de Goias" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.02.20086314", "rel_title": "Testing lags and emerging COVID-19 outbreaks in federal penitentiaries in Canada", @@ -1481225,6 +1483999,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.05.20075275", + "rel_title": "Covid-19 prevalence estimation by random sampling in the wider population - Optimal sample pooling under varying assumptions about true prevalence", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20075275", + "rel_abs": "The number of confirmed Covid-19 cases in a population is used as a coarse measurement for the burden of disease. However, this number depends heavily on the sampling intensity and the various test criteria used in different jurisdictions. A wide range of sources indicate that a large fraction of cases go undetected. Estimates of the true prevalence of Covid-19 can be made by random sampling in the wider population. Here we use simulations to explore confidence intervals of prevalence estimates under different sampling intensities and degrees of sample pooling.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ola Brynildsrud", + "author_inst": "Norwegian Institute of Public Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.04.20090050", "rel_title": "Hospitalization and 30-day fatality in 121,263 COVID-19 outpatient cases", @@ -1482976,81 +1485769,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.04.20091231", - "rel_title": "Point-of-care testing for COVID-19 using SHERLOCK diagnostics", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20091231", - "rel_abs": "The recent outbreak of the novel coronavirus SARS-CoV-2, which causes COVID-19, can be diagnosed using RT-qPCR, but inadequate access to reagents and equipment has slowed disease detection and impeded efforts to mitigate viral spread. Alternative approaches based on combinations of isothermal amplification and CRISPR-mediated detection, such as the SHERLOCK (Specific High Sensitivity Enzymatic Reporter UnLOCKing) technique, offer reduced dependence on RT-qPCR equipment, but previously reported methods required multiple fluid handling steps, complicating their deployment outside clinical labs. Here we developed a simple test chemistry called STOP (SHERLOCK Testing in One Pot) for detecting SARS-CoV-2 in one hour that is suitable for point-of-care use. This simplified test, STOPCovid, provides sensitivity comparable to RT-qPCR-based SARS-CoV-2 tests and has a limit of detection of 100 copies of viral genome input in saliva or nasopharyngeal swabs per reaction. Using lateral flow readout, the test returns result in 70 minutes, and using fluorescence readout, the test returns result in 40 minutes. Moreover, we validated STOPCovid using nasopharyngeal swabs from COVID-19 patients and were able to correctly diagnose 12 positive and 5 negative patients out of 3 replicates. We envision that implementation of STOPCovid will significantly aid \"test-trace-isolate\" efforts, especially in low-resource settings, which will be critical for long-term public health safety and effective reopening of the society.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Julia Joung", - "author_inst": "Howard Hughes Medical Institute; Broad Institute of MIT and Harvard; McGovern Institute for Brain Research at MIT; Department of Biological Engineering at MIT" - }, - { - "author_name": "Alim Ladha", - "author_inst": "Howard Hughes Medical Institute; Broad Institute of MIT and Harvard; McGovern Institute for Brain Research at MIT; Department of Biological Engineering at MIT" - }, - { - "author_name": "Makoto Saito", - "author_inst": "Howard Hughes Medical Institute; Broad Institute of MIT and Harvard; McGovern Institute for Brain Research at MIT; Departments of Biological Engineering and Bra" - }, - { - "author_name": "Michael Segel", - "author_inst": "Howard Hughes Medical Institute; Broad Institute of MIT and Harvard; McGovern Institute for Brain Research at MIT; Departments of Biological Engineering and Bra" - }, - { - "author_name": "Robert Bruneau", - "author_inst": "University of Washington, Seattle" - }, - { - "author_name": "Meei-li W Huang", - "author_inst": "University of Washington, Seattle" - }, - { - "author_name": "Nam-Gyun Kim", - "author_inst": "University of Washington, Seattle" - }, - { - "author_name": "Xu Yu", - "author_inst": "Ragon Institute of MGH, MIT and Harvard; Massachusetts General Hospital; Massachusetts Consortium for Pathogen Readiness" - }, - { - "author_name": "Jonathan Li", - "author_inst": "Ragon Institute of MGH, MIT and Harvard; Brigham and Women's Hospital; Massachusetts Consortium for Pathogen Readiness" - }, - { - "author_name": "Bruce D. Walker", - "author_inst": "Howard Hughes Medical Institute; Massachusetts Consortium for Pathogen Readiness" - }, - { - "author_name": "Alexander L. Greninger", - "author_inst": "University of Washington, Seattle; Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Keith R. Jerome", - "author_inst": "University of Washington, Seattle; Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Jonathan S. Gootenberg", - "author_inst": "McGovern Institute for Brain Research at MIT; Massachusetts Consortium for Pathogen Readiness" - }, - { - "author_name": "Omar O. Abudayyeh", - "author_inst": "McGovern Institute for Brain Research at MIT; Massachusetts Consortium for Pathogen Readiness" - }, - { - "author_name": "Feng Zhang", - "author_inst": "Howard Hughes Medical Institute; Broad Institute of MIT and Harvard; McGovern Institute for Brain Research at MIT; Departments of Biological Engineering and Bra" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.04.20091132", "rel_title": "Phenomenological Modelling of COVID-19 epidemics in Sri Lanka, Italy and Hebei Province of China", @@ -1483663,6 +1486381,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.05.20091645", + "rel_title": "The First Wave of COVID-19 in Israel - Initial Analysis of Publicly Available Data", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20091645", + "rel_abs": "The first case of COVID-19 was confirmed in Israel on February 21, 2020. Within approximately 30 days, the total number of confirmed cases climbed up to 1,000, accompanied by a doubling period of less than 3 days. About one week later, after this number exceeded 4, 000 cases, and following some extreme lockdown measures taken by the Israeli government, the daily infection rate started a sharp decrease from the peak value of 1,131 down to slightly more than 100 new confirmed cases on April 30. Motivated by this encouraging data, similar to the trends observed in many other countries, along with the growing economic pressures, the Israeli government has quickly lifted most of its emergency regulations. Throughout May, the daily number of new cases stayed at a very low level of 20 - 40 until at the end of May it started a steady increase, exceeding 1, 000 by the end of June and 2,000 on July 22. As suggested by some experts and popular media, this disturbing trend may be even a part of a \"second wave\". This article attempts to analyze the currently available data on Israel, compared to three European countries (Greece, Italy, and Sweden), in order to understand the local dynamics of COVID-19, assess the effect of the implemented intervention measures, and discuss some plausible scenarios for the foreseeable future.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Mark Last", + "author_inst": "Ben-Gurion University of the Negev" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.05.20091553", "rel_title": "Health seeking behaviors of patients with acute respiratory infections during the outbreak of novel coronavirus disease 2019 in Wuhan, China", @@ -1484854,41 +1487591,6 @@ "type": "confirmatory results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.05.05.079400", - "rel_title": "Massive Multiplexing Can Deliver a $1 Test for COVID-19", - "rel_date": "2020-05-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.05.079400", - "rel_abs": "The severe acute respiratory syndrome virus, SARS-CoV-2 (hereafter COVID-19), rapidly achieved global pandemic status, provoking large-scale screening programs in many nations. Their activation makes it imperative to identify methods that can deliver a diagnostic result at low cost. This paper describes an approach which employs sequence variation in the gene coding for its envelope protein as the basis for a scalable, inexpensive test for COVID-19. It achieves this by coupling a simple RNA extraction protocol with low-volume RT-PCR, followed by E-Gel screening and sequencing on high-throughput platforms to analyze 10,000 samples in a run. Slight modifications to the protocol could support screening programs for other known viruses and for viral discovery. Just as the $1,000 genome is transforming medicine, a $1 diagnostic test for viral and bacterial pathogens would represent a major advance for public health.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Paul DN Hebert", - "author_inst": "Centre for Biodiversity Genomics, University of Guelph" - }, - { - "author_name": "Sean WJ Prosser", - "author_inst": "Centre for Biodiversity Genomics, University of Guelph" - }, - { - "author_name": "Natalia V Ivanova", - "author_inst": "Centre for Biodiversity Genomics, University of Guelph" - }, - { - "author_name": "Evgeny V. Zakharov", - "author_inst": "University of Guelph" - }, - { - "author_name": "Sujeevan Ratnasingham", - "author_inst": "Centre for Biodiversity Genomics, University of Guelph" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.05.03.20089755", "rel_title": "Who maintains a good mental health in a locked-down country? A French nationwide online survey of 11,391 participants", @@ -1485017,6 +1487719,37 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.05.03.20089508", + "rel_title": "A seven-day cycle in COVID-19 infection and mortality rates: Are inter-generational social interactions on the weekends killing susceptible people?", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20089508", + "rel_abs": "We observed a significant seven-day cycle in (i) reported COVID-19 new cases* (in 7/12 countries), and in (ii) reported COVID-19 deaths{yen} (in 7/12 countries), based on data from the 12 developed North-American and European countries that reported more than 1,000 deaths by April 28th (Spain*, Italy* and Switzerland*, Belgium{yen}, Canada{yen} and the USA{yen}, Germany*{yen}, Netherlands*{yen}, Sweden*{yen} and the UK*{yen}). Daily reported numbers (March 29th to April 28th) are based on Our World in Data database (derived from the European Center for Disease Control and Prevention, ECDC). In all seven countries, numbers of new cases peaked on Thursday-Friday, five days after the weekend, corresponding with a reported ~5-day lag between contact with an infected person and the manifestation of clinical symptoms. Death tolls peaked on Wednesday-Thursday in all seven countries, ~12-14 days following a weekend, corresponding with the reported median of 14-day hospitalization before death. One may suspect that the weekend restricts the availability of testing or reporting of new cases, that are eventually reported during the following week. However, to completely account for both observations, this artifact should occur uniformly in all the above-mentioned countries and consistently along the entire month studied. Moreover, deaths are defined events and seems less likely to be recorded or reported inaccurately, at least for the vast majority of cases. Thus, we hypothesize that an increase in inter-generational social interactions occurs during the weekend, which facilitates transfer of COVID-19 from younger people to older vulnerable individuals. These and additional infected older people account for most recognized COVID-19 cases and deaths, which may occur at regular time intervals, specifically in this vulnerable population. Additional explanations may include weekly rhythms in immune functions, hospital care quality, or other various health-related behaviors. Our hypotheses should be re-tested and refined based on databases that accurately report events times when these will become available.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Itay Ricon-Becker", + "author_inst": "Tel-Aviv University" + }, + { + "author_name": "Ricardo Tarrasch", + "author_inst": "Tel-Aviv University" + }, + { + "author_name": "Pablo Blinder", + "author_inst": "Tel-Aviv University" + }, + { + "author_name": "Shamgar Ben-Eliyahu", + "author_inst": "Tel-Aviv University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.06.050260", "rel_title": "SARS-CoV-2 proteins exploit host's genetic and epigenetic mediators for the annexation of key host signaling pathways that confers its immune evasion and disease pathophysiology", @@ -1486424,49 +1489157,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.03.20089342", - "rel_title": "Temperature and relative humidity are not major contributing factor on the occurrence of COVID-19 pandemic: An observational study in 57 countries", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20089342", - "rel_abs": "The world searching for hope has already experienced a huge loss of lives due to COVID-19 caused by SARS-CoV-2 started in Wuhan, China. There are speculations that climatic conditions can slowdown the transmission of COVID-19. Findings from the early outbreak indicated the possible association of air temperature and relative humidity in COVID-19 occurrence in China. Current study focused on whether climatic conditions (temperature and relative humidity) are having any influence in the occurrence of COVID-19 when the outbreak has been classified as pandemic. To determine the effect of daily average temperature and average relative humidity on log-transformed total daily cases of COVID-19, polynomial regression as a quadratic term and linear regression were done. Linear regression analysis was also carried out to explore the same effect on selected countries. Present study observed no correlation between the climatic conditions (the daily average temperature and relative humidity) and the number of cases of COVID-19. Similar result was found in relation between daily average temperature and average number of cases per day in country-wise analysis. However, about 93.5% cases of COVID-19 occurred between 1{degrees}C to 16{degrees}C and the average number of cases per day was lower in high temperature country than low temperature country with exceptions. The minimum effect of summer temperature may not be effective to control the pandemic rather need to apply the control measures of COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Md.Abdus Sobur", - "author_inst": "Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh." - }, - { - "author_name": "Md.Saiful Islam", - "author_inst": "Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh." - }, - { - "author_name": "Md.Emdadul Haque", - "author_inst": "Faculty of Fisheries, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh." - }, - { - "author_name": "AMM Taufiquer Rahman", - "author_inst": "Naogaon District Hospital, Naogaon, Bangladesh." - }, - { - "author_name": "Md.Taohidul Islam", - "author_inst": "Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh." - }, - { - "author_name": "Antonio Toniolo", - "author_inst": "Global Virus Network, University of Insubria, 21100 Varese, Italy." - }, - { - "author_name": "Md.Tanvir Rahman", - "author_inst": "Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.05.20092635", "rel_title": "Studies of Novel Coronavirus Disease 19 (COVID-19) Pandemic: A Global Analysis of Literature", @@ -1486687,6 +1489377,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.04.20088104", + "rel_title": "IDentif.AI: Artificial Intelligence Pinpoints Remdesivir in Combination with Ritonavir and Lopinavir as an Optimal Regimen Against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20088104", + "rel_abs": "The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease 2019 (COVID-19) has led to the rapid initiation of urgently needed clinical trials of repurposed drug combinations and monotherapies. These regimens were primarily relying on mechanism-of-action based selection of drugs, many of which have yielded positive in vitro but largely negative clinical outcomes. To overcome this challenge, we report the use of IDentif.AI, a platform that rapidly optimizes infectious disease (ID) combination therapy design using artificial intelligence (AI). In this study, IDentif.AI was implemented on a 12-drug candidate therapy search set representing over 530,000 possible drug combinations. IDentif.AI demonstrated that the optimal combination therapy against SARS-CoV-2 was comprised of remdesivir, ritonavir, and lopinavir, which mediated a 6.5-fold improvement in efficacy over remdesivir alone. Additionally, IDentif.AI showed hydroxychloroquine and azithromycin to be relatively ineffective. The identification of a clinically actionable optimal drug combination was completed within two weeks, with a 3-order of magnitude reduction in the number of tests typically needed. IDentif.AI analysis was also able to independently confirm clinical trial outcomes to date without requiring any data from these trials. The robustness of the IDentif.AI platform suggests that it may be applicable towards rapid development of optimal drug regimens to address current and future outbreaks.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Agata Blasiak", + "author_inst": "The N.1 Institute for Health (N.1), Institute for Digital Medicine (WisDM), and Department of Biomedical Engineering, National University of Singapore, Singapor" + }, + { + "author_name": "Jhin Jieh Lim", + "author_inst": "Cancer Science Institute, National University of Singapore, Singapore 117599" + }, + { + "author_name": "Shirley Gek Kheng Seah", + "author_inst": "Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore 117510 Singapore" + }, + { + "author_name": "Theodore Kee", + "author_inst": "The N.1 Institute for Health (N.1), Institute for Digital Medicine (WisDM), and Department of Biomedical Engineering, National University of Singapore, Singapor" + }, + { + "author_name": "Alexandria Remus", + "author_inst": "The N.1 Institute for Health (N.1), Institute for Digital Medicine (WisDM), and Department of Biomedical Engineering, National University of Singapore, Singapor" + }, + { + "author_name": "De Hoe Chye", + "author_inst": "Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore 117510 Singapore" + }, + { + "author_name": "Pui San Wong", + "author_inst": "Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore 117510 Singapore" + }, + { + "author_name": "Lissa Hooi", + "author_inst": "Cancer Science Institute, National University of Singapore, Singapore 117599" + }, + { + "author_name": "Anh T.L. Truong", + "author_inst": "The N.1 Institute for Health (N.1), Institute for Digital Medicine (WisDM), and Department of Biomedical Engineering, National University of Singapore, Singapor" + }, + { + "author_name": "Nguyen Le", + "author_inst": "The N.1 Institute for Health (N.1), Institute for Digital Medicine (WisDM), and Department of Biomedical Engineering, National University of Singapore, Singapor" + }, + { + "author_name": "Conrad E.Z. Chan", + "author_inst": "Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore 117510 Singapore" + }, + { + "author_name": "Rishi Desai", + "author_inst": "Osmosis (Knowledge Diffusion), Baltimore, Maryland 21224, United States" + }, + { + "author_name": "Xianting Ding", + "author_inst": "Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030 China" + }, + { + "author_name": "Brendon J. Hanson", + "author_inst": "Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore 117510 Singapore" + }, + { + "author_name": "Edward Kai-Hua Chow", + "author_inst": "Cancer Science Institute, National University of Singapore, Singapore 117599" + }, + { + "author_name": "Dean Ho", + "author_inst": "The N.1 Institute for Health (N.1), Institute for Digital Medicine (WisDM), and Department of Biomedical Engineering, National University of Singapore, Singapor" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.05.20084889", "rel_title": "Sensitivity of Nasopharyngeal, Nasal and Throat Swab for the Detection of SARS-CoV-2", @@ -1488074,53 +1490843,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.04.20090258", - "rel_title": "Safe Blues: A Method for Estimation and Control in the Fight Against COVID-19", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090258", - "rel_abs": "How do fine modifications to social distancing measures really affect COVID-19 spread? A major problem for health authorities is that we do not know.\n\nIn an imaginary world, we might develop a harmless biological virus that spreads just like COVID-19, but is traceable via a cheap and reliable diagnosis. By introducing such an imaginary virus into the population and observing how it spreads, we would have a way of learning about COVID-19 because the benign virus would respond to population behaviour and social distancing measures in a similar manner. Such a benign biological virus does not exist. Instead, we propose a safe and privacy-preserving digital alternative.\n\nOur solution is to mimic the benign virus by passing virtual tokens between electronic devices when they move into close proximity. As Bluetooth transmission is the most likely method used for such inter-device communication, and as our suggested \"virtual viruses\" do not harm individuals software or intrude on privacy, we call these Safe Blues.\n\nIn contrast to many app-based methods that inform individuals or governments about actual COVID-19 patients or hazards, Safe Blues does not provide information about individuals locations or contacts. Hence the privacy concerns associated with Safe Blues are much lower than other methods. However, from the point of view of data collection, Safe Blues has two major advantages:\n\nO_LIData about the spread of Safe Blues is uploaded to a central server in real time, which can give authorities a more up-to-date picture in comparison to actual COVID-19 data, which is only available retrospectively.\nC_LIO_LISampling of Safe Blues data is not biased by being applied only to people who have shown symptoms or who have come into contact with known positive cases.\nC_LI\n\nThese features mean that there would be real statistical value in introducing Safe Blues. In the medium term and end game of COVID-19, information from Safe Blues could aid health authorities to make informed decisions with respect to social distancing and other measures.\n\nIn this paper we outline the general principles of Safe Blues and we illustrate how Safe Blues data together with neural networks may be used to infer characteristics of the progress of the COVID-19 pandemic in real time. Further information is on the Safe Blues website: https://safeblues.org/.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Raj Abhijit Dandekar", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Shane G. Henderson", - "author_inst": "Cornell University" - }, - { - "author_name": "Marijn Jansen", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Sarat Moka", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Yoni Nazarathy", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Christopher Rackauckas", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Peter G. Taylor", - "author_inst": "The University of Melbourne" - }, - { - "author_name": "Aapeli Vuorinen", - "author_inst": "The University of Queensland and The University of Melbourne" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.04.20090324", "rel_title": "Estimating Excess Deaths in the United States Early in the COVID-19 Pandemic", @@ -1488245,6 +1490967,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.03.20089698", + "rel_title": "Social determinants of COVID-19 mortality at the county level", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20089698", + "rel_abs": "The United States is currently the global epicenter of the COVID-19 pandemic. Emerging data suggests that social determinants of health may be key drivers of the epidemic, and that minorities, migrants, and essential workers may bear a disproportionate degree of risk. We used publicly accessible datasets to build a series of spatial autoregressive models assessing county level associations between COVID- 19 mortality and (1) Percentage of Non-English speaking households, (2) percentage of individuals engaged in hired farm work, (3) percentage of uninsured individuals under the age of 65, and (3) percentage of individuals living at or below the poverty line. Across all counties (n=2940), counties with more farmworkers, more residents living in poverty, higher density, and more residents over the age of 65 had significantly higher levels of mortality. In urban counties (n=114), only county density was significantly associated with mortality. In non-urban counties (n=2826), counties with more non- English speaking households and more farm workers had significantly higher levels of mortality, as did counties with higher levels of poverty and more residents over the age of 65. More uninsured residents was significantly associated with decreased reported COVID-19 mortality. Individuals who do not speak English, individuals engaged in farm work, and individuals living in poverty may be at heightened risk for COVID-19 mortality in non-urban counties. Mortality among the uninsured may be being systematically undercounted in county and national level surveillance.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Rebecca K Fielding-Miller", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Maria E Sundaram", + "author_inst": "Emory University" + }, + { + "author_name": "Kimberly Brouwer", + "author_inst": "University of California, San Diego" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.03.20089623", "rel_title": "Risk of secondary infection waves of COVID-19 in an insular region: the case of the Balearic Islands, Spain", @@ -1489735,65 +1492484,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.04.20090746", - "rel_title": "Urban Air Pollution May Enhance COVID-19 Case-Fatality and Mortality Rates in the United States", - "rel_date": "2020-05-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090746", - "rel_abs": "BackgroundThe novel human coronavirus disease 2019 (COVID-19) pandemic has claimed more than 240,000 lives worldwide, causing tremendous public health, social, and economic damages. While the risk factors of COVID-19 are still under investigation, environmental factors, such as urban air pollution, may play an important role in increasing population susceptibility to COVID-19 pathogenesis.\n\nMethodsWe conducted a cross-sectional nationwide study using zero-inflated negative binomial models to estimate the association between long-term (2010-2016) county-level exposures to NO2, PM2.5 and O3 and county-level COVID-19 case-fatality and mortality rates in the US. We used both single and multipollutant models and controlled for spatial trends and a comprehensive set of potential confounders, including state-level test positive rate, county-level healthcare capacity, phase-of-epidemic, population mobility, sociodemographic, socioeconomic status, behavior risk factors, and meteorological factors.\n\nResults1,027,799 COVID-19 cases and 58,489 deaths were reported in 3,122 US counties from January 22, 2020 to April 29, 2020, with an overall observed case-fatality rate of 5.8%. Spatial variations were observed for both COVID-19 death outcomes and long-term ambient air pollutant levels. County-level average NO2 concentrations were positively associated with both COVID-19 case-fatality rate and mortality rate in single-, bi-, and tri-pollutant models (p-values<0.05). Per inter-quartile range (IQR) increase in NO2 (4.6 ppb), COVID-19 case-fatality rate and mortality rate were associated with an increase of 7.1% (95% CI 1.2% to 13.4%) and 11.2% (95% CI 3.4% to 19.5%), respectively. We did not observe significant associations between long-term exposures to PM2.5 or O3 and COVID-19 death outcomes (p-values>0.05), although per IQR increase in PM2.5 (3.4 ug/m3) was marginally associated with 10.8% (95% CI: -1.1% to 24.1%) increase in COVID-19 mortality rate.\n\nDiscussions and ConclusionsLong-term exposure to NO2, which largely arises from urban combustion sources such as traffic, may enhance susceptibility to severe COVID-19 outcomes, independent of longterm PM2.5 and O3 exposure. The results support targeted public health actions to protect residents from COVID-19 in heavily polluted regions with historically high NO2 levels. Moreover, continuation of current efforts to lower traffic emissions and ambient air pollution levels may be an important component of reducing population-level risk of COVID-19 deaths.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Donghai Liang", - "author_inst": "Emory University" - }, - { - "author_name": "Liuhua Shi", - "author_inst": "Emory University" - }, - { - "author_name": "Jingxuan Zhao", - "author_inst": "American Cancer Society" - }, - { - "author_name": "Pengfei Liu", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Joel Schwartz", - "author_inst": "Harvard University" - }, - { - "author_name": "Song Gao", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Jeremy A Sarnat", - "author_inst": "Emory University" - }, - { - "author_name": "Yang Liu", - "author_inst": "Emory University" - }, - { - "author_name": "Stefanie T Ebelt", - "author_inst": "Emory University" - }, - { - "author_name": "Noah C Scovronick", - "author_inst": "Emory University" - }, - { - "author_name": "Howard Chang", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.05.04.20090670", "rel_title": "Projection of COVID-19 Cases and Deaths in the US as Individual States Re-open May 4,2020", @@ -1489894,6 +1492584,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.01.20088021", + "rel_title": "COVID-19 in Children with Brain-Based Developmental Disabilities: A Rapid Review", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20088021", + "rel_abs": "BackgroundThe prevalence of symptomatic COVID-19 in children remains low to date. In just a few months, COVID-19 has affected millions of people worldwide, and as of the date of this publication, the pandemic continues. Based on the current available evidence, children do not appear to be at higher risk of contracting COVID-19 than adults. However, children with neurological and neuromuscular conditions are vulnerable to the respiratory complications of other viral infections.\n\nObjectivesTo assess whether children with brain-based developmental disabilities were more likely to develop COVID-19 and have complications or poorer outcomes following infection.\n\nMethodsWe conducted a two-week rapid review on studies with primary data regarding children aged between zero and 18 years old with brain-based developmental disabilities, or who were at risk of developing such disabilities, with confirmed or suspected COVID-19. We performed our literature searches on April 18, 2020.\n\nResultsOur search strategy identified 538 individual records, of which four were included in our review. Of the 50 COVID-19 pediatric patients reported in the included studies, a total of seven children were at risk of developing brain-based disabilities. Symptoms ranged in severity. However, generally, patients were discharged or saw improvements in their symptoms by the end of the study period. No deaths were reported.\n\nDiscussionOur study highlights a knowledge gap regarding the impact of COVID-19 in children with brain-based developmental disabilities.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Michele Dugas", + "author_inst": "VITAM Centre de recherche en sante durable, CIUSSS de la Capitale Nationale, Universite Laval, Quebec, Canada" + }, + { + "author_name": "Valerie Carnovale", + "author_inst": "VITAM Centre de recherche en sante durable, CIUSSS de la Capitale-Nationale, Universite Laval, Quebec, Canada" + }, + { + "author_name": "Andree-Anne Poirier", + "author_inst": "VITAM Centre de recherche en sante durable, CIUSSS de la Capitale-Nationale, Universite Laval, Quebec, Canada; Institut national d'excellence en sante et servic" + }, + { + "author_name": "Benoit Mailot", + "author_inst": "VITAM Centre de recherche en sante durable, CIUSSS de la Capitale-Nationale, Universite Laval, Quebec, Canada" + }, + { + "author_name": "Becky Skidmore", + "author_inst": "Independent Information Specialist, Ottawa, Canada" + }, + { + "author_name": "Lena Faust", + "author_inst": "Patient-partner (youth) with the CHILD-BRIGHT Network; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Canada" + }, + { + "author_name": "Carrie Costello", + "author_inst": "Patient-partner (caregiver) with the CHILD-BRIGHT Network" + }, + { + "author_name": "Donna Thomson", + "author_inst": "Patient-partner (caregiver) with the CHILD-BRIGHT Network" + }, + { + "author_name": "Annette Majnemer", + "author_inst": "School of Physical & Occupational Therapy, Faculty of Medicine, McGill University; Research Institute of the McGill University Health Centre, Montreal, Canada" + }, + { + "author_name": "Dan Goldowitz", + "author_inst": "Department of Medical Genetics, Centre of Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada" + }, + { + "author_name": "Steven Miller", + "author_inst": "Department of Paediatrics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada" + }, + { + "author_name": "Annie LeBlanc", + "author_inst": "VITAM Centre de recherche en sante durable, CIUSSS de la Capitale-Nationale, Universite Laval, Quebec, Canada" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.05.02.20088997", "rel_title": "Predictive Model with Analysis of the Initial Spread of COVID-19 in India", @@ -1490997,33 +1493750,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.05.03.20081380", - "rel_title": "FACTORS INFLUENCING MENTAL HEALTH DURING COVID-19 OUTBREAK: AN EXPLORATORY SURVEY AMONG INDIAN POPULATION", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20081380", - "rel_abs": "PurposeResearch on the impact of social distancing on mental health during epidemics is limited, especially in India. The purpose of this study is to scale the association between anxiety and socio-demographic factors during Covid19 lockdown among the general Indian population.\n\nDesign/methodology/approachA descriptive cross-sectional nationwide study was designed to enrol the general population. The inclusion criteria for this study were Indian citizens aged 18 years and above. The study was conducted from 29th March to 12th April 2020, using an online google questionnaire. The anxiety among respondents was detected and measured using a Generalised Anxiety Disorder Scale which consists of 7 questions (in English), i.e. GAD-7.\n\nFindingsRespondees were 392, and from these participants, the prevalence of anxiety was 25.3 per cent. Based on the bivariate logistic regression analysis, the predictors of anxiety were gender, religion, occupation as business/self-employed, marital status, family size, health status and sleep deprivation.\n\nConclusionThis study reports the prevalence of anxiety among Indian population who were grounded at their homes during lockdown due to coronavirus pandemic in the country.\n\nLimitations(1) The selection of participants through non-random sampling. (2) Because of the cross-sectional character of the study, causal conclusions cannot be drawn.\n\nOriginality/ValueThis paper fulfils an identified need to study the mental health status of the population under situations like lockdown, thereby helping fill a persistent gap in Indian research on this issue.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Absar Ahmad", - "author_inst": "Career Institute of Medical Sciences and Hospital, Lucknow, India" - }, - { - "author_name": "Ishrat Rahman", - "author_inst": "College of Dentistry, Princess Nourah Bint Abdulrahman University Riyadh, KSA" - }, - { - "author_name": "Maitri Agarwal", - "author_inst": "Career Institute of Medical Sciences & Hospital, Lucknow, India" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.05.01.20081034", "rel_title": "Evaluation of nCoV-QS (MiCo BioMed) for RT-qPCR detection of SARS-CoV-2 from nasopharyngeal samples using CDC FDA EUA qPCR kit as a gold standard: an example of the need of validation studies.", @@ -1492534,97 +1495260,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2020.05.01.20087080", - "rel_title": "Early phases of COVID-19 are characterized by a reduction of lymphocyte populations and the presence of atypical monocytes", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087080", - "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2 is a recently discovered pathogen responsible of coronavirus disease 2019 (COVID-19). The immunological changes associated with this infection are largely unknown.\n\nMethodsWe evaluated the peripheral blood mononuclear cells profile of 63 patients with COVID-19 at diagnosis and the presence of association with inflammatory biomarkers and 28-days mortality.\n\nResultsLymphocytopenia was present in 51 of 63 (80.9%) patients. This reduction was mirrored also on CD8+ lymphocytes (128 cells/L), natural killer cells (67 cells/L) and natural killer T cells (31 cells/L). Monocytes were preserved in total number but displayed a subpopulation composed mainly of cells with a reduced expression of both CD14 and HLA-DR. A direct correlation was found between serum values of IL-6 and the frequency of Th2 lymphocytes (R=0.17; p=0.04) but not with the monocytes count (R=0.01; p=0.60). Patients who died in the 28 days from admission (N=10, 15.9%), when compared to those who did not, displayed lower mean values of CD3+ (p=0.028) and CD4+ cells (p=0.042) and higher mean percentages of CD8+/CD38+/HLA-DR+ lymphocytes (p=0.026).\n\nConclusionsThe early phases of COVID-19 are characterized by lymphocytopenia, predominance of Th2 lymphocytes and less immunocompetent monocytes, which include atypical mononuclear cells.\n\neTOC-At diagnosis patients with COVID-19 have lymphocytopenia\n-Monocytes with both normal or altered scatter properties display a reduced expression of CD14 and HLA-DR in most of COVID-19 patients\n-Patients who die in the 28 days from admission have lower values of CD3+ and CD4+ cells and higher percentages of activated CTL cells compared to those who survive", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "ANDREA LOMBARDI", - "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" - }, - { - "author_name": "Elena Trombetta", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Alessandra Cattaneo", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Valeria Castelli", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Emanuele Palomba", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Mario Tirone", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Davide Mangioni", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Giuseppe Lamorte", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Maria Manunta", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Daniele Prati", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Ferruccio Ceriotti", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Roberta Gualtierotti", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Giorgio Costantino", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Stefano Aliberti", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Vittorio Scaravilli", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Giacomo Grasselli", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Andrea Gori", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Laura Porretti", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Alessandra Bandera", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.01.20087114", "rel_title": "Lung disease severity, Coronary Artery Calcium, Coronary inflammation and Mortality in Coronavirus Disease 2019.", @@ -1492838,6 +1495473,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.01.20087197", + "rel_title": "National and state wise estimate of time varying reproduction number for COVID-19 in India during the nationwide lockdown.", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087197", + "rel_abs": "To understand the effect of nationwide lockdown on transmissibilty of SARS-CoV-2 in India, time varying reproduction number during the first weeks of April, 2020 was estimated. The time varying reproduction number was estimated using EpiEstim package in R programming language. The reproduction number has come down significantly during the lockdown period both at national level and in most states but it wasnt reduced to less than 1. This calls for urgent need for more effective control measures in addition to lockdown to stop the epidemic spread of the virus.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Padmanaban Venkatesan", + "author_inst": "Christian Medical College" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.01.20087320", "rel_title": "Correlating Covid-19 mortality and infection levels", @@ -1493872,61 +1496526,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, - { - "rel_doi": "10.1101/2020.05.01.20087973", - "rel_title": "COVID-19 Utilization and Resource Visualization Engine (CURVE) to Forecast In-Hospital Resources", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087973", - "rel_abs": "BackgroundThe emergence of COVID-19 has created an urgent threat to public health worldwide. With rapidly evolving demands on healthcare resources, it is imperative that healthcare systems have the ability to access real-time local data to predict, plan, and effectively manage resources.\n\nObjectiveTo develop an interactive COVID-19 Utilization and Resource Visualization Engine (CURVE) as a data visualization tool to inform decision making and guide a large health systems proactive pandemic response.\n\nMethodsWe designed and implemented CURVE using R Shiny to display real-time parameters of healthcare utilization at Atrium Health with projections based upon locally derived models for the COVID-19 pandemic. We used the CURVE app to compare predictions from two of our models -one created before and one after the statewide stay-at-home and social distancing orders (denoted before- and after-SAH-order model). We established parameter settings for best-, moderate-, and worst-case scenarios for pandemic spread and resource use, leveraging two locally developed forecasting models to determine peak date trajectory, resource use, and root mean square error (RMSE) between observed and predicted results.\n\nResultsCURVE predicts and monitors utilization of hospital beds, ICU beds, and number of ventilators in the context of up-to-date local resources and provides Atrium Health leadership with timely, actionable insights to guide decision-making during the COVID-19 pandemic. The after-SAH-order model demonstrated the lowest RMSE in total bed, ICU bed, and patients on ventilators.\n\nConclusionsCURVE provides a powerful, interactive interface that provides locally relevant, dynamic, timely information to guide health system decision making and pandemic preparedness.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Shih-Hsiung Chou", - "author_inst": "Atrium Health" - }, - { - "author_name": "James T. Kearns", - "author_inst": "Atrium Health" - }, - { - "author_name": "Philip Turk", - "author_inst": "Atrium Health" - }, - { - "author_name": "Marc Kowalkowski", - "author_inst": "Atrium Health" - }, - { - "author_name": "Jason Roberge", - "author_inst": "Atrium Health" - }, - { - "author_name": "Jennifer S. Priem", - "author_inst": "Atrium Health" - }, - { - "author_name": "Yhenneko J Taylor", - "author_inst": "Atrium Health" - }, - { - "author_name": "Ryan Burns", - "author_inst": "Atrium Health" - }, - { - "author_name": "Pooja Palmer", - "author_inst": "Atrium Health" - }, - { - "author_name": "Andrew D. McWilliams", - "author_inst": "Atrium Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.05.01.20088179", "rel_title": "Impact of policy interventions and social distancing on SARS-CoV-2 transmission in the United States", @@ -1494088,6 +1496687,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.02.20087924", + "rel_title": "A strategy for finding people infected with SARS-CoV-2: optimizing pooled testing at low prevalence", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20087924", + "rel_abs": "Suppressing SARS-CoV-2 will likely require the rapid identification and isolation of infected individuals, on an ongoing basis. RT-PCR (reverse transcription polymerase chain reaction) tests are accurate but costly, making regular testing of every individual expensive. The costs are a challenge for all countries and particularly for developing countries. Cost reductions can be achieved by pooling (or combining) subsamples and testing them in groups. We propose an algorithm for pooling subsamples based on the geometry of a hypercube that, at low prevalence, uniquely identifies infected individuals in a small number of tests. We discuss the optimal group size and explain why, given the highly infectious nature of the disease, largely parallel searches are preferred. We report proof of concept experiments in which a positive subsample was detected even when diluted a hundred-fold with negative subsamples. Using these methods, the costs of mass testing could be reduced by a large factor. If infected individuals are quickly and effectively quarantined, the prevalence will fall and so will the cost of regular, mass testing. Such a strategy provides a possible pathway to the longterm elimination of SARS-CoV-2. Field trials of our approach are now under way in Rwanda.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Leon Mutesa", + "author_inst": "Centre for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda" + }, + { + "author_name": "Pacifique Ndishimye", + "author_inst": "African Institute for Mathematical Sciences, Kigali, Rwanda" + }, + { + "author_name": "Yvan Butera", + "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" + }, + { + "author_name": "Jacob Souopgui", + "author_inst": "Centre for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda" + }, + { + "author_name": "Annette Uwineza", + "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" + }, + { + "author_name": "Robert Rutayisire", + "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" + }, + { + "author_name": "Emile Musoni", + "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" + }, + { + "author_name": "Nadine Rujeni", + "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" + }, + { + "author_name": "Thierry Nyatanyi", + "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" + }, + { + "author_name": "Edouard Ntagwabira", + "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" + }, + { + "author_name": "Muhammed Semakula", + "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" + }, + { + "author_name": "Clarisse Musanabaganwa", + "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" + }, + { + "author_name": "Daniel Nyamwasa", + "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" + }, + { + "author_name": "Maurice Ndashimye", + "author_inst": "African Institute for Mathematical Sciences, Kigali, Rwanda" + }, + { + "author_name": "Eva Ujeneza", + "author_inst": "African Institute for Mathematical Sciences, Kigali, Rwanda" + }, + { + "author_name": "Ivan Emile Mwikarago", + "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" + }, + { + "author_name": "Claude Mambo Muvunyi", + "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" + }, + { + "author_name": "Jean Baptiste Mazarati", + "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" + }, + { + "author_name": "Sabin Nsanzimana", + "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" + }, + { + "author_name": "Neil Turok", + "author_inst": "Perimeter Institute for Theoretical Physics" + }, + { + "author_name": "Wilfred Ndifon", + "author_inst": "African Institute for Mathematical Sciences, Kigali, Rwanda" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.02.20086876", "rel_title": "Ultra-fast and onsite interrogation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in environmental specimens via surface enhanced Raman scattering (SERS)", @@ -1495438,29 +1498136,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, - { - "rel_doi": "10.1101/2020.04.29.20085787", - "rel_title": "A systematic review to evaluate the clinical outcomes in COVID -19 patients on angiotensin converting enzyme inhibitors or angiotensin receptor blockers", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20085787", - "rel_abs": "IntroductionAngiotensin converting enzyme inhibitors (ACEI) and angiotensin receptor blockers (ARB) share their target receptor site with the SARS-CoV-2 virus, that may cause ACE2 receptor upregulation which raised concerns regarding ACEI and ARB use in COVID-19 patients. However, many medical professional societies recommended their continued use given the paucity of clinical evidence but there is need for an updated systematic review of latest clinical studies.\n\nMethodsA search was conducted on PubMed, Google Scholar, EMBASE and various preprint servers for studies comparing clinical outcomes and mortality in COVID-19 patients on ACEI and/or ARB and a meta-analysis was performed.\n\nResultsA total of sixteen studies were included for review and meta-analysis. There were conflicting findings reported in several studies as Meng J. et al, Liu Y. et al, Feng Y. et al, Zhang P. et al, Mancia G. et al and Reynolds H.R. et al reported that patients on ACE inhibitors/ARB had lower rates of severe outcomes whereas Richardson S. et al reported higher rates of invasive ventilation and intensive care unit (ICU) admissions in patients on ACE inhibitors/ARB as compared to non-users. Similarly, there were conflicting results in the rate of mortality reported in the various studies. Meng J. et al, Li J. et al, Zhang P. et al, Yang G. et al, Zeng Z. et al and Andrew Ip et al reported lower rates of mortality in ACE inhibitors/ARB users versus non-users whereas Richardson S. et al and Guo T. et al reported higher rates of mortality. In a pooled analysis of 9 studies, there was a statistically significant reduction (OR = 0.86, 95% CI = 0.75-0.99, I2 = 53.25, p value = 0.03) in the odds of death in those on ACEI/ARB as compared to patients not on ACEI/ARB. In a pooled analysis of five studies, there was a statistically non-significant reduction (OR = 0.90, 95% CI: 0.63-1.23, I2=70.36) in the odds of developing severe disease in patients on ACEI/ARB versus non-users.\n\nConclusionIt is concluded that ACEI and ARB should be continued in COVID-19 patients. Additionally, the individual patient factors like ACE2 polymorphisms which might confer higher risk of adverse outcomes need to be evaluated further.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Abhinav Grover", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Mansi Oberoi", - "author_inst": "Internal Medicine, University of South Dakota, Sanford School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2020.04.29.20085563", "rel_title": "Public knowledge, attitudes and practices towards COVID-19: A cross-sectional study in Malaysia", @@ -1495634,6 +1498309,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.01.20086421", + "rel_title": "Characteristics of lymphocyte subsets and their predicting values for the severity of COVID-19 patients", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20086421", + "rel_abs": "Severe COVID-19 patients showed worse clinical outcomes compared to mild and moderate patients. However, effective indicators are still lacking to predict the severity of the disease. In the present study, we retrospectively analyzed the clinical and laboratory data of 16 COVID-19 patients and found that the absolute counts of three T-cells (CD3+, CD4+, and CD8+) were significantly lower in the moderate and severe patients than those in mild patients and were significantly lower in severe patients than in moderate patients on admission. With the recovery of the COVID-19, serum levels of inflammatory biomarkers (CRP, PCT, and IL6) of moderate and severe patients gradually decreased. In contrast, the counts of lymphocytes and their subsets including CD3+, CD4+, and CD8+ T cells gradually increased in severe patients, and eventually showed comparable levels with moderate patients. ROC analysis showed that the counts of CD3+, CD4+, and CD8+ T-cells with AUC > 0.9 have potential values for predicting the severity of COVID-19 patients. In conclusion, the reduction of CD3+, CD4+, and CD8+ T-cells is related to the severity of COVID-19 and dynamic detection of these T-lymphocyte subsets may help predict the outcome of the patients.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jingrong Wang", + "author_inst": "First People's Hospital of Yunnan Province" + }, + { + "author_name": "Xingqi Dong", + "author_inst": "Yunnan Provincial Hospital of Infectious Diseases" + }, + { + "author_name": "Boting Zhang", + "author_inst": "Yunnan Provincial Hospital of Infectious Diseases" + }, + { + "author_name": "Xinping Yang", + "author_inst": "Yunnan Provincial Hospital of Infectious Diseases" + }, + { + "author_name": "Zhi Li", + "author_inst": "First People's Hospital of Yunnan Province" + }, + { + "author_name": "Xicheng Wang", + "author_inst": "Yunnan Provincial Hospital of Infectious Diseases" + }, + { + "author_name": "Shuguang Zuo", + "author_inst": "Kaifeng Kangbien Medical Laboratory" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.30.20086082", "rel_title": "Probable causes and risk factors for positive SARS-CoV-2 test in recovered patients: Evidence from Brunei Darussalam", @@ -1496832,29 +1499550,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.30.20086181", - "rel_title": "A Simple Method for Estimating the Number of Unconfirmed COVID-19 Cases in a Local Area that Includes a Confidence Interval: A Case Study of Whatcom County, Washington", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20086181", - "rel_abs": "Along with many other data problems affecting the unfolding of the COVID-10 pandemic in the United States, virtually nothing is known about the number of positive, unconfirmed cases, especially in local areas. We show that it is possible to estimate the number of positive, unconfirmed COVID-19 cases using a simple, long-established method employed by demographers to estimate a population in the absence of a census count. We go on to show how a confidence interval can be constructed around an estimate of positive, unconfirmed COVID-19 cases constructed from this method, using Whatcom County, Washington as a case study.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "David A Swanson", - "author_inst": "University of California Riverside" - }, - { - "author_name": "Ronald E. Cossman", - "author_inst": "Social Science Research Center, Mississippi State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.30.20086652", "rel_title": "Perspectives of Cancer Patients and Their Health during the COVID-19 Pandemic", @@ -1497008,6 +1499703,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.30.20086496", + "rel_title": "Higher virulence of COVID-19 in the air-polluted regions of eight severely affected countries", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20086496", + "rel_abs": "COVID-19 has spread in all continents in a span of just over three months, escalating into a pandemic that poses several humanitarian as well as scientific challenges. We here investigated the geographical character of the infection and correlate it with several annual satellite and ground indexes of air quality in: China, the United States, Italy, Iran, France, Spain, Germany, and the United Kingdom. Controlling for population size, we found more viral infections in those areas afflicted by high PM 2.5 and Nitrogen Dioxide values. Higher mortality was also correlated with relatively poor air quality. In Italy, the correspondence between the Po valley pollution and SARS-CoV-2 infections and induced mortality was the starkest, originating right in the most polluted European area. Air pollution appears to be for this disease a risk factor similar to smoking. This suggests the detrimental impact climate change will have on the trajectory of future respiratory epidemics.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Riccardo Pansini", + "author_inst": "Yunnan University of Finance and Economics" + }, + { + "author_name": "Davide Fornacca", + "author_inst": "Dali University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.30.20086884", "rel_title": "Modeling the COVID-19 outbreak in the United States", @@ -1498098,61 +1500816,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.04.28.20083956", - "rel_title": "Sensitivity evaluation of 2019 novel coronavirus (SARS-CoV-2) RT-PCR detection kits and strategy to reduce false negative", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083956", - "rel_abs": "An ongoing outbreak of pneumonia associated with SARS-CoV-2 has now been confirmed globally. In absence of effective vaccines, infection prevention and control through diagnostic testing and quarantine is critical. Early detection and differential diagnosis of respiratory infections increases the chances for successful control of COVID-19 disease. The nucleic acid RT-PCR test is regarded as the current standard for molecular diagnosis with high sensitivity. However, the highest specificity confirmation target ORF1ab gene is considered to be less sensitive than other targets in clinical application. In addition, a large amount of recent evidence indicates that the initial missed diagnosis of asymptomatic patients with SARS-CoV-2 and discharged patients with \"re-examination positive\" may be due to low viral load, and the ability of rapid mutation of coronavirus also increases the rate of false negative results. We aimed to evaluate the sensitivity of different nucleic acid detection kits so as to make recommendations for the selection of validation kit, and amplify the suspicious result to be reportable positive by means of simple continuous amplification, which is of great significance for the prevention and control of the current epidemic and the discharge criteria of low viral load patients.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "yunying zhou", - "author_inst": "Jinan Central Hospital, Cheeloo College of Medicine, Shandong University" - }, - { - "author_name": "Fengyan Pei", - "author_inst": "Jinan Central Hospital Affiliated to Shandong University" - }, - { - "author_name": "Li Wang", - "author_inst": "inan Infectious Disease Hospital, Shandong University" - }, - { - "author_name": "Huailong Zhao", - "author_inst": "Jinan Center for Disease Control and Prevention" - }, - { - "author_name": "Huanjie Li", - "author_inst": "Jinan Central Hospital Affiliated to Shandong University" - }, - { - "author_name": "Mingyu Ji", - "author_inst": "Jinan Central Hospital Affiliated to Shandong University" - }, - { - "author_name": "Weihua Yang", - "author_inst": "Jinan Central Hospital Affiliated to Shandong University" - }, - { - "author_name": "Qingxi Wang", - "author_inst": "Jinan Central Hospital Affiliated to Shandong University" - }, - { - "author_name": "Qianqian Zhao", - "author_inst": "Jinan Central Hospital Affiliated to Shandong University" - }, - { - "author_name": "Yunshan Wang", - "author_inst": "Jinan Central Hospital Affiliated to Shandong University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.30.20082172", "rel_title": "Monitoring social distancing and SARS-CoV-2 transmission in Brazil using cell phone mobility data", @@ -1498454,6 +1501117,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "anesthesia" }, + { + "rel_doi": "10.1101/2020.04.29.20083485", + "rel_title": "Global prediction of unreported SARS-CoV2 infection from observed COVID-19 cases", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20083485", + "rel_abs": "Estimation of infectiousness and fatality of the SARS-CoV-2 virus in the COVID-19 global pandemic is complicated by ascertainment bias resulting from incomplete and non-representative samples of infected individuals. We developed a strategy for overcoming this bias to obtain more plausible estimates of the true values of key epidemiological variables. We fit mechanistic Bayesian latent-variable SIR models to confirmed COVID-19 cases, deaths, and recoveries, for all regions (countries and US states) independently. Bayesian averaging over models, we find that the raw infection incidence rate underestimates the true rate by a factor, the case ascertainment ratio CARt that depends upon region and time. At the regional onset of COVID-19, the predicted global median was 13 infections unreported for each case confirmed (CARt = 0.07 C.I. (0.02, 0.4)). As the infection spread, the median CARt rose to 9 unreported cases for every one diagnosed as of April 15, 2020 (CARt = 0.1 C.I. (0.02, 0.5)). We also estimate that the median global initial reproduction number R0 is 3.3 (C.I (1.5, 8.3)) and the total infection fatality rate near the onset is 0.17% (C.I. (0.05%, 0.9%)). However the time-dependent reproduction number Rt and infection fatality rate as of April 15 were 1.2 (C.I. (0.6, 2.5)) and 0.8% (C.I. (0.2%,4%)), respectively. We find that there is great variability between country- and state-level values. Our estimates are consistent with recent serological estimates of cumulative infections for the state of New York, but inconsistent with claims that very large fractions of the population have already been infected in most other regions. For most regions, our estimates imply a great deal of uncertainty about the current state and trajectory of the epidemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Carson C Chow", + "author_inst": "NIDDK, National Institutes of Health" + }, + { + "author_name": "Joshua C Chang", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Richard C Gerkin", + "author_inst": "Arizona State University" + }, + { + "author_name": "Shashaank Vattikuti", + "author_inst": "NIDDK, National Institutes of Healthj" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.28.20083782", "rel_title": "A Method to Identify the Missing COVID-19 Cases in the U.S. and Results for mid-April 2020", @@ -1499788,117 +1502482,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2020.05.02.20084673", - "rel_title": "Disruption of the CCL5/RANTES-CCR5 Pathway Restores Immune Homeostasis and Reduces Plasma Viral Load in Critical COVID-19", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20084673", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), is now pandemic with nearly three million cases reported to date1. Although the majority of COVID-19 patients experience only mild or moderate symptoms, a subset will progress to severe disease with pneumonia and acute respiratory distress syndrome (ARDS) requiring mechanical ventilation2. Emerging results indicate a dysregulated immune response characterized by runaway inflammation, including cytokine release syndrome (CRS), as the major driver of pathology in severe COVID-193,4. With no treatments currently approved for COVID-19, therapeutics to prevent or treat the excessive inflammation in severe disease caused by SARS-CoV-2 infection are urgently needed. Here, in 10 terminally-ill, critical COVID-19 patients we report profound elevation of plasma IL-6 and CCL5 (RANTES), decreased CD8+ T cell levels, and SARS-CoV-2 plasma viremia. Following compassionate care treatment with the CCR5 blocking antibody leronlimab, we observed complete CCR5 receptor occupancy on macrophage and T cells, rapid reduction of plasma IL-6, restoration of the CD4/CD8 ratio, and a significant decrease in SARS-CoV-2 plasma viremia. Consistent with reduction of plasma IL-6, single-cell RNA-sequencing revealed declines in transcriptomic myeloid cell clusters expressing IL-6 and interferon-related genes. These results demonstrate a novel approach to resolving unchecked inflammation, restoring immunologic deficiencies, and reducing SARS-CoV-2 plasma viral load via disruption of the CCL5-CCR5 axis, and support randomized clinical trials to assess clinical efficacy of leronlimab-mediated inhibition of CCR5 for COVID-19.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Bruce K Patterson", - "author_inst": "IncellDX" - }, - { - "author_name": "Harish Seethamraju", - "author_inst": "Montefiore Medical Center" - }, - { - "author_name": "Kush Dhody", - "author_inst": "Amarex Clinical Research, LLC" - }, - { - "author_name": "Michael J Corley", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Kazemm Kazempour", - "author_inst": "Amarex Clinical Research" - }, - { - "author_name": "Jay P Lalezari", - "author_inst": "Quest Clinical Research" - }, - { - "author_name": "Alina PS Pang", - "author_inst": "University of Hawaii" - }, - { - "author_name": "Christopher Sugai", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Edgar B Francisco", - "author_inst": "IncellDX" - }, - { - "author_name": "Amruta Pise", - "author_inst": "IncellDX" - }, - { - "author_name": "Hallison Rodrigues", - "author_inst": "IncellDX" - }, - { - "author_name": "Matthew Ryou", - "author_inst": "IncellDX" - }, - { - "author_name": "Helen L Wu", - "author_inst": "Oregon Health and Science University" - }, - { - "author_name": "Gabriela M Webb", - "author_inst": "Oregon Health and Science University" - }, - { - "author_name": "Byung S Park", - "author_inst": "Oregon Health and Science University" - }, - { - "author_name": "Scott Kelly", - "author_inst": "CytoDyn, Inc" - }, - { - "author_name": "Nadar Pourhassan", - "author_inst": "CytoDyn, Inc" - }, - { - "author_name": "Alena Lelic", - "author_inst": "Beckman Coulter" - }, - { - "author_name": "Lama Kdouh", - "author_inst": "Beckman Coulter" - }, - { - "author_name": "Monica Herrera", - "author_inst": "Bio-Rad, Inc" - }, - { - "author_name": "Eric Hall", - "author_inst": "Bio-Rad, Inc" - }, - { - "author_name": "Enver Aklin", - "author_inst": "Montefiore Medical Center" - }, - { - "author_name": "Lishomwa Ndhlovu", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Jonah B Sacha", - "author_inst": "Oregon Health and Science University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.29.20084533", "rel_title": "Pre-Existing Characteristics Associated with Covid-19 Illness Severity", @@ -1500072,6 +1502655,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.28.20075523", + "rel_title": "Detection of SARS-CoV-2 in Human Breast Milk", + "rel_date": "2020-05-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20075523", + "rel_abs": "SARS-CoV-2 (CoV-2) is mainly transmitted in the human population during close contact and respiratory droplets. It is currently unclear, however, whether CoV-2 is shed into milk and may also be transmitted from infected mothers to newborns trough breast feeding. Two recent reviews on the topic (1,2) did not find evidence for CoV-2 in human milk. However, the number of breast milk samples analyzed so far is small and samples were taken only once from each mother (2).", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "R\u00fcdiger Gro\u00df", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany" + }, + { + "author_name": "Carina Conzelmann", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany" + }, + { + "author_name": "Janis M\u00fcller", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany" + }, + { + "author_name": "Steffen Stenger", + "author_inst": "Institute for Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany" + }, + { + "author_name": "Karin Steinhart", + "author_inst": "Administrative District Heidenheim, Public Health Office, Heidenheim, Germany" + }, + { + "author_name": "Frank Kirchhoff", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany" + }, + { + "author_name": "Jan M\u00fcnch", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.28.20077602", "rel_title": "Commercial stocks of SARS-CoV-2 RNA may report low concentration values, leading to artificially increased apparent sensitivity of diagnostic assays", @@ -1501866,41 +1504492,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.05.03.075473", - "rel_title": "Computational analysis on the ACE2-derived peptides for neutralizing the ACE2 binding to the spike protein of SARS-CoV-2", - "rel_date": "2020-05-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.03.075473", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19, is spreading globally and has infected more than 3 million people. It has been discovered that SARS-CoV-2 initiates the entry into cells by binding to human angiotensin-converting enzyme 2 (hACE2) through the receptor binding domain (RBD) of its spike glycoprotein. Hence, drugs that can interfere the SARS-CoV-2-RBD binding to hACE2 potentially can inhibit SARS-CoV-2 from entering human cells. Here, based on the N-terminal helix 1 of human ACE2, we designed nine short peptides that have potential to inhibit SARS-CoV-2 binding. Molecular dynamics simulations of peptides in the their free and SARS-CoV-2 RBD-bound forms allow us to identify fragments that are stable in water and have strong binding affinity to the SARS-CoV-2 spike proteins. The important interactions between peptides and RBD are highlighted to provide guidance for the design of peptidomimetics against the SARS-CoV-2.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "cecylia s. lupala", - "author_inst": "beijing computational science research center" - }, - { - "author_name": "Vikash Kumar", - "author_inst": "Beijing computational science research center" - }, - { - "author_name": "xuanxuan li", - "author_inst": "tsinghua university" - }, - { - "author_name": "xiaodong su", - "author_inst": "peking university" - }, - { - "author_name": "haiguang liu", - "author_inst": "beijing computational science research center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.04.29.20084061", "rel_title": "Psychological Stress and Gender Differences during COVID-19 Pandemic in Chinese Population", @@ -1502010,6 +1504601,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.27.20081398", + "rel_title": "Estimation of SARS-CoV-2 emissions from non-symptomatic cases", + "rel_date": "2020-05-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081398", + "rel_abs": "ImportanceCases of the coronavirus disease 2019 (COVID-19) with no or mild symptoms were reported to frequently transmit the disease even without direct contact. The severe acute respiratory syndrome virus (SARS-COV-2) was found at very high concentrations in swab and sputum of such cases.\n\nObjectiveWe aimed to estimate in a mathematical modeling study the virus release from such cases into different aerosol sizes by normal breathing and coughing, and what exposure can result from this in a room shared with such as case.\n\nData Sources and ModelWe combined the size-distribution of exhaled breath microdroplets for coughing and normal breathing with viral sputum concentrations as approximation for lung lining liquid to obtain an estimate of emitted virus levels. The resulting emission data fed a single-compartment model of airborne concentrations in a room of 50 m3, the size of a small office or medical exam room.\n\nResultsThe estimated viral load in microdroplets emitted by simulated patients while breathing normally was on typical 0.0000049 copies/cm3 and could go up to 0.637 copies/cm3. The corresponding numbers for coughing simulated patients were 0.277 copies/cm3 and 36,030/cm3, respectively, per cough. The resulting concentrations in a room with a coughing emitter were always very high, up to 7.44 million copies/m3. However, also regular breathing microdroplets from high emitters was modelled to lead to 1248 copies/m3.\n\nConclusions and RelevanceIn this modelling study, breathing and coughing were estimated to release large numbers of viruses, ranging from thousands to millions of virus copies/m3 in a room with an emitter having a high viral load, depending on ventilation and microdroplet formation process. These findings suggest that strict respiratory protection may be needed when there is a chance to be in the same room with a patient - whether symptomatic or not - especially for a prolonged time.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSHow much SARS-CoV-2 virus is released from a case by breathing and coughing, and what is the resulting concentration in a room?\n\nFindingIn this mathematical modelling study, both, breathing and coughing were estimated to release large numbers of viruses, which can lead to millions of virus copies/m3 in a poorly ventilated room with a coughing emitter.\n\nMeaningThese results may explain the important rate of transmissions and implies the need for strict respiratory protection when people are in the same room with a case with COVID-19.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Michael Riediker", + "author_inst": "Swiss Centre for Occupational and Environmental Health" + }, + { + "author_name": "Dai-Hua Tsai", + "author_inst": "Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Zurich, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.04.27.20081372", "rel_title": "How Social Media and 3D Printing Tackles the PPE Shortage during Covid - 19 Pandemic", @@ -1503504,65 +1506118,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.27.20081711", - "rel_title": "Response strategies for COVID-19 epidemics in African settings: a mathematical modelling study", - "rel_date": "2020-05-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081711", - "rel_abs": "BackgroundThe health impact of COVID-19 may differ in African settings as compared to countries in Europe or China due to demographic, epidemiological, environmental and socio-economic factors. We evaluated strategies to reduce SARS-CoV-2 burden in African countries, so as to support decisions that balance minimising mortality, protecting health services and safeguarding livelihoods.\n\nMethodsWe used a Susceptible-Exposed-Infectious-Recovered mathematical model, stratified by age, to predict the evolution of COVID-19 epidemics in three countries representing a range of age distributions in Africa (from oldest to youngest average age: Mauritius, Nigeria and Niger), under various effectiveness assumptions for combinations of different non-pharmaceutical interventions: self-isolation of symptomatic people, physical distancing, and shielding (physical isolation) of the high-risk population. We adapted model parameters to better represent uncertainty about what might be expected in African populations, in particular by shifting the distribution of severity risk towards younger ages and increasing the case-fatality ratio.\n\nResultsWe predicted median clinical attack rates over the first 12 months of 17% (Niger) to 39% (Mauritius), peaking at 2-4 months, if epidemics were unmitigated. Self-isolation while symptomatic had a maximum impact of about 30% on reducing severe cases, while the impact of physical distancing varied widely depending on percent contact reduction and R0. The effect of shielding high-risk people, e.g. by rehousing them in physical isolation, was sensitive mainly to residual contact with low-risk people, and to a lesser extent to contact among shielded individuals. Response strategies incorporating self-isolation of symptomatic individuals, moderate physical distancing and high uptake of shielding reduced predicted peak bed demand by 46% to 54% and mortality by 60% to 75%. Lockdowns delayed epidemics by about 3 months. Estimates were sensitive to differences in age-specific social mixing patterns, as published in the literature.\n\nDiscussionIn African settings, as elsewhere, current evidence suggests large COVID-19 epidemics are expected. However, African countries have fewer means to suppress transmission and manage cases. We found that self-isolation of symptomatic persons and general physical distancing are unlikely to avert very large epidemics, unless distancing takes the form of stringent lockdown measures. However, both interventions help to mitigate the epidemic. Shielding of high-risk individuals can reduce health service demand and, even more markedly, mortality if it features high uptake and low contact of shielded and unshielded people, with no increase in contact among shielded people. Strategies combining self-isolation, moderate physical distancing and shielding will probably achieve substantial reductions in mortality in African countries. Temporary lockdowns, where socioeconomically acceptable, can help gain crucial time for planning and expanding health service capacity.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Kevin van Zandvoort", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Christopher I Jarvis", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Carl Pearson", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Nicholas G Davies", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "CMMID COVID-19 working group", - "author_inst": "" - }, - { - "author_name": "Timothy W Russell", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Adam J Kucharski", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Mark J Jit", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Stefan Flasche", - "author_inst": "LSHTM" - }, - { - "author_name": "Rosalind M Eggo", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Francesco Checchi", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.28.20083378", "rel_title": "Ocular toxicity and Hydroxychloroquine: A Rapid Meta-Analysis", @@ -1504040,6 +1506595,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.27.20081752", + "rel_title": "Variation among states in rate of coronavirus spread", + "rel_date": "2020-05-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081752", + "rel_abs": "The corona virus, COVID-19, has been spreading rapidly across the USA since early March, but at a decreasing rate, where the rate r is defined as the exponential increase. I modeled the way the rate of increase y = log(exp(r)-1) has declined through time in each of the 51 states with the goal of determining whether state-at-home orders correlate with reductions in the rate of spread of the virus. A piecewise linear regression was used, with a single break point. This model can identify whether there was a change in the rate of decline, when the change happened, and which states have shown the greatest improvement in reducing the spread of COVID-19. The piecewise model identified a significant breakpoint on 24 Mar for all states combined, and all states had nearly the same breakpoint. Prior to 24 Mar, the average change in y was -0.013 per day, meaning a reduction in the rate of spread from 23.5 pct. per day to 19.5 pct. per day; after 24 Mar, the average change in y was -0.070 per day, a reduction from 19.5 pct. per day to 7.5 pct. per day. Prior to 24 Mar there was no significant variation among states in the decline in y, but after 24 Mar there was substantial variation, and the date on which states issued stay at home orders correlated with that variation. Montana, Idaho, and Vermont showed the greatest improvement, while Nebraska, South Dakota, and Iowa the least. The improvement as measured by the reduction after 24 Mar did not correlate with case density in a state, nor state population.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Richard Condit", + "author_inst": "Retired" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.27.20081737", "rel_title": "COVID-19 spreading in Rio de Janeiro, Brazil: do the policies of social isolation really work?", @@ -1505318,77 +1507892,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2020.05.02.071811", - "rel_title": "Structural and Functional Implications of Non-synonymous Mutations in the Spike protein of 2,954 SARS-CoV-2 Genomes", - "rel_date": "2020-05-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.02.071811", - "rel_abs": "Protein-protein interactions between virus and host are crucial for infection. SARS-CoV-2, the causative agent of COVID-19 pandemic is an RNA virus prone to mutations. Formation of a stable binding interface between the Spike (S) protein Receptor Binding Domain (RBD) of SARS-CoV-2 and Angiotensin-Converting Enzyme 2 (ACE2) of host actuates viral entry. Yet, how this binding interface evolves as virus acquires mutations during pandemic remains elusive. Here, using a high fidelity bioinformatics pipeline, we analysed 31,403 SARS-CoV-2 genomes across the globe, and identified 444 non-synonymous mutations that cause 49 distinct amino acid substitutions in the RBD. Molecular phylogenetic analysis suggested independent emergence of these RBD mutants during pandemic. In silico structure modelling of interfaces induced by mutations on residues which directly engage ACE2 or lie in the near vicinity revealed molecular rearrangements and binding energies unique to each RBD mutant. Comparative structure analysis using binding interface from mouse that prevents SARS-CoV-2 entry uncovered minimal molecular determinants in RBD necessary for the formation of stable interface. We identified that interfacial interaction involving amino acid residues N487 and G496 on either ends of the binding scaffold are indispensable to anchor RBD and are well conserved in all SARS-like corona viruses. All other interactions appear to be required to locally remodel binding interface with varying affinities and thus may decide extent of viral transmission and disease outcome. Together, our findings propose the modalities and variations in RBD-ACE2 interface formation exploited by SARS-CoV-2 for endurance.\n\nImportanceCOVID-19, so far the worst hit pandemic to mankind, started in January 2020 and is still prevailing globally. Our study identified key molecular arrangements in RBD-ACE2 interface that help virus to tolerate mutations and prevail. In addition, RBD mutations identified in this study can serve as a molecular directory for experimental biologists to perform functional validation experiments. The minimal molecular requirements for the formation of RBD-ACE2 interface predicted using in silico structure models may help precisely design neutralizing antibodies, vaccines and therapeutics. Our study also proposes the significance of understanding evolution of protein interfaces during pandemic.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Shijulal Nelson-Sathi", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Perunthottathu K Umasankar", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Sreekumar Easwaran", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Radhakrishnan R Nair", - "author_inst": "Rajiv Gandhi Centre for Biotechnolgoy" - }, - { - "author_name": "Iype Joseph", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Sai Ravi Chandra Nori", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Jamiema Sara Philip", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Roshny Prasad", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Kolaparamba V Navyasree", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Shikha Ramesh", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Heera Pillai", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Sanu Gosh", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Santhosh Kumar TR", - "author_inst": "RajiV Gandhi Centre for Biotechnology" - }, - { - "author_name": "M Radhakrishna Pillai", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2020.05.01.071050", "rel_title": "CoV-Seq: SARS-CoV-2 Genome Analysis and Visualization", @@ -1505478,6 +1507981,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.04.28.20083667", + "rel_title": "Geographical identification of the vulnerable groups during COVID-19 crisis: the typhoon eye effect and its boundary conditions", + "rel_date": "2020-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083667", + "rel_abs": "AimAlthough some studies suggest the coronavirus disease (COVID-19) is associated with negative consequences on physical health, our knowledge about the detrimental effects of COVID-19 on peoples mental health is still nascent. This study uses typhoon eye theory to offer insights in helping clinical psychiatrists to screen people with well-being issues during COVID-19 outbreak.\n\nMethodsWe collected survey data from working adults across different geographical areas in China on 20 and 21 February 2020 during the outbreak of COVID-19. The sample contains 308 working adults, who were in various parts of China, with varying distance to the epicenter of Wuhan.\n\nResultsIndividual adults distance to the epicenter was negatively associated with life satisfaction ({beta} = -0.235, 95% CI -0.450 to -0.020, p = 0.032). This association between distance and life satisfaction was significant only for adults who were young or had smaller family sizes. For example, the negative relationship was strongest when the individuals were in the age bracket of 20 years old (15.7%; {beta} = -0.703, 95% CI -1.098 to -0.307; p = 0.001) and single (32.3%; {beta} = -0.767, 95% CI -1.125 to -0.408; p < 0.001).\n\nConclusionOur results that peoples well-being deteriorates by the distance from the epicenter for specific groups of people help guide mental healthcare providers towards the regions that are further away from the epicenter in the ongoing COVID-19 outbreak. Meanwhile, our results indicate the practitioners should be cautious of using typhoon eye effect for individuals who were older or had a larger family size.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Pok Man Tang", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Stephen X. Zhang", + "author_inst": "University of Adelaide" + }, + { + "author_name": "Chi Hon Li", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Feng Wei", + "author_inst": "Tongji University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.04.29.20084798", "rel_title": "Act early, save lives: managing COVID-19 in Greece", @@ -1506936,33 +1509470,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.26.20075937", - "rel_title": "Using the COVID-19 to influenza ratio to estimate the numbers of symptomatic COVID-19 cases in Wuhan prior to the lockdown", - "rel_date": "2020-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20075937", - "rel_abs": "A recent study tested 45 throat swabs taken from adults over age 30 who sought outpatient care at one of two central Wuhan hospitals for influenza-like-illness between December 30, 2019 and January 19, 2020. Although none were confirmed COVID-19 cases, nine retrospectively tested positive for the virus. Using the fact that Wuhan has 393 other hospitals, we extrapolate the total number of undetected cases of symptomatic COVID-19 in adults during this period. we estimate that there were 5,558 [95% CI: 2,761-9,864] adults with symptomatic COVID-19 infections in Wuhan between December 30th and January 19th, 2020.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Zhanwei Du", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Benjamin J Cowling", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Lauren Ancel Meyers", - "author_inst": "The University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.27.20080309", "rel_title": "Serial measurements in COVID-19-induced acute respiratory disease to unravel heterogeneity of the disease course: design of the Maastricht Intensive Care COVID cohort; MaastrICCht", @@ -1507224,6 +1509731,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.04.26.20073569", + "rel_title": "Regressing SARS-CoV-2 sewage measurements onto COVID-19 burden in the population: a proof-of-concept for quantitative environmental surveillance", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20073569", + "rel_abs": "SARS-CoV-2 is an RNA virus, a member of the coronavirus family of respiratory viruses that includes SARS-CoV-1 and MERS. COVID-19, the clinical syndrome caused by SARSCoV-2, has evolved into a global pandemic with more than 2,900,000 people infected. It has had an acute and dramatic impact on health care systems, economies, and societies of affected countries within these few months. Widespread testing and tracing efforts are employed in many countries in order to contain and mitigate this pandemic. Recent data has indicated that fecal shedding of SARS-CoV-2 is common, and that the virus can be detected in wastewater. This indicates that wastewater monitoring is a potentially efficient tool for epidemiological surveillance of SARS-CoV-2 infection in large populations at relevant scales. Collecting raw sewage data, representing specific districts, and crosslinking this data with the number of infected people from each location, will enable us to derive and provide quantitative surveillance tools. In particular, this will provide important means to (i) estimate the extent of outbreaks and their spatial distributions, based primarily on in-sewer measurements (ii) manage the early-warning system quantitatively and efficiently (and similarly, verify disease elimination). Here we report the development of a virus concentration method using PEG or alum, providing an important a tool for detection of SARS-CoV-2 RNA in sewage and relating it to the local populations and geographic information. This will provide a proof of concept for the use of sewage associated virus data as a reliable epidemiological tool.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Itay Bar Or", + "author_inst": "Central virology lab, Ministry of health, Sheba medical center, Israel" + }, + { + "author_name": "Karin Yaniv", + "author_inst": "Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel." + }, + { + "author_name": "Marilou Shagan", + "author_inst": "Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel." + }, + { + "author_name": "Eden Ozer", + "author_inst": "Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel" + }, + { + "author_name": "Oran Erster", + "author_inst": "Central virology lab, Ministry of health, Sheba medical center, Israel" + }, + { + "author_name": "Ella Mendelson", + "author_inst": "Central virology lab, Ministry of health, Sheba medical center, Israel and School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, " + }, + { + "author_name": "Batya Mannasse", + "author_inst": "Central virology lab, Ministry of health, Sheba medical center, Israel" + }, + { + "author_name": "Rachel Shirazi", + "author_inst": "Central virology lab, Ministry of health, Sheba medical center, Israel" + }, + { + "author_name": "Esti Kramarsky-Winter", + "author_inst": "Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel." + }, + { + "author_name": "Oded Nir", + "author_inst": "Zuckerberg Institute for Water Research (ZIWR), Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boker, 84990, Israel" + }, + { + "author_name": "Hala Abu-Ali", + "author_inst": "Zuckerberg Institute for Water Research (ZIWR), Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boker, 84990, Israel" + }, + { + "author_name": "Zeev Ronen", + "author_inst": "Zuckerberg Institute for Water Research (ZIWR), Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boker, 84990, Israel" + }, + { + "author_name": "Ehud Rinott", + "author_inst": "Faculty of Health Science, Ben-Gurion University of the Negev, Beer-Sheva, Israel" + }, + { + "author_name": "Yair E. Lewis", + "author_inst": "Faculty of Medicine, Technion-Israel Institute of Technology, Israel" + }, + { + "author_name": "Eran Friedler Friedler", + "author_inst": "Faculty of Civ. and Env. Eng., Technion-Israel Inst. of Technology; Haifa 32000, Israel" + }, + { + "author_name": "Yossi Paitan", + "author_inst": "Clinical Microbiology Laboratory, Meir Medical Center, 44282, Kfar Saba, Israel and Department of Clinical Microbiology and Immunology, Sackler Faculty of Medic" + }, + { + "author_name": "Eden Bitkover", + "author_inst": "Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel" + }, + { + "author_name": "Yakir Berchenko", + "author_inst": "Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel" + }, + { + "author_name": "Ariel Kushmaro", + "author_inst": "Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel and The Ilse Katz Center for M" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.27.20070466", "rel_title": "Correlation analysis of risk factors and GSI score of a medical team assisting Wuhan city during the epidemic of COVID-19 in China -A cohort study", @@ -1508406,33 +1511004,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.26.20080648", - "rel_title": "Risk assessment via layered mobile contact tracing for epidemiological intervention", - "rel_date": "2020-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20080648", - "rel_abs": "There is strong interest globally amidst the current COVID-19 pandemic in tracing contacts of infectious patients using mobile technologies, both as a warning system to individuals and as a targeted intervention strategy for governments. Several governments, including India, have introduced mobile apps for this purpose, which give a warning when the individuals phone establishes bluetooth contact with the phone of an infected person. We present a methodology to probabilistically evaluate risk of infection given the network of contacts that individuals are likely to encounter in real life. Instead of binary \"infected\" or \"uninfected\" statuses, an infection risk probability is maintained which can be efficiently calculated based on probabilities of recent contacts, and updated when a recent contact is diagnosed with a disease. We demonstrate on realistic networks that this method sharply outperforms a naive immediate-contact method even in an ideal circumstance that all infected persons are known to the naive method. We demonstrate robustness to missing contact information (such as when phones fail to make bluetooth contact or the app is not installed). We show, within our model, a strong flattening of the infectious peak when even a small fraction of cases are identified, tested and isolated. In the real world, where most known-infected persons are isolated or quarantined and where many individuals may not carry their mobiles in public, we believe the improvement offered by our method warrants consideration. Importantly, in view of widespread concerns on privacy and contact-tracing, our method relies mainly on direct contact data that can be stored locally on users phones, and uses limited communication via intermediary servers only upon testing, mitigating privacy concerns.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Vishwesha Guttal", - "author_inst": "Indian Institute of Science, Bengaluru, India" - }, - { - "author_name": "Sandeep Krishna", - "author_inst": "National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India" - }, - { - "author_name": "Rahul Siddharthan", - "author_inst": "The Institute of Mathematical Sciences, Chennai, India" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.26.20080655", "rel_title": "Preparedness and Mitigation by projecting the risk against COVID-19 transmission using Machine Learning Techniques", @@ -1508530,6 +1511101,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.28.20080671", + "rel_title": "Protective elements of mental health status during the COVID-19 outbreak in the Portuguese population", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20080671", + "rel_abs": "The outbreak of COVID-19 might produce dramatic psychological effects on the individuals life. In this study, we aimed to explore the elements that may reduce the negative effects on mental health of the quarantine period imposed by most governments during this worldwide crisis. We conducted an online survey to evaluate demographic, lifestyle and mental health variables in the Portuguese population. We observed that factors related with living conditions, maintaining the work either online or in the workplace, frequency of exercise and absence of a previous psychological or physic disorders are protective features of psychological well-being (anxiety, depression, stress and obsessive-compulsive symptoms). Finally, the individuals previously receiving psychotherapeutic support exhibited better psychological indicators if they did not interrupt the process as a consequence of the outbreak. Our results indicate that the practice of physical exercise, reduced consumption of COVID-19 information and the implementation of remote mental healthcare measures might prevent larger impacts on mental health during the COVID-19 outbreak.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Pedro Silva Moreira", + "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine - University of Minho. Psychological Neuroscience Lab, CIPsi, School of Psychology, Unive" + }, + { + "author_name": "Sonia Ferreira", + "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine - University of Minho" + }, + { + "author_name": "Beatriz Couto", + "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine - University of Minho" + }, + { + "author_name": "Mafalda Machado-Sousa", + "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine - University of Minho" + }, + { + "author_name": "Marcos Fernandez", + "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine - University of Minho" + }, + { + "author_name": "Catarina Raposo-Lima", + "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine - University of Minho" + }, + { + "author_name": "Nuno Sousa", + "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine - University of Minho" + }, + { + "author_name": "Maria Pico-Perez", + "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine - University of Minho" + }, + { + "author_name": "Pedro Morgado", + "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine - University of Minho" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.04.26.20080614", "rel_title": "Spread of virus during soccer matches", @@ -1509792,37 +1512414,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.05.01.067769", - "rel_title": "Heat inactivation of the Severe Acute Respiratory Syndrome Coronavirus 2", - "rel_date": "2020-05-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.01.067769", - "rel_abs": "Supernatants of cells infected with SARS-CoV-2, nasopharyngeal and sera samples containing SARS-CoV-2 were submitted to heat inactivation for various periods of time, ranging from 30 seconds to 60 minutes. Our results showed that SARS-CoV-2 could be inactivated in less than 30 minutes, 15 minutes and 3 minutes at 56{degrees}C, 65{degrees}C and 95{degrees}C respectively. These data could help laboratory workers to improve their protocols with handling of the virus in biosafety conditions.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Christophe Batejat", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Quentin Grassin", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Jean-Claude Manuguerra", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "India Leclercq", - "author_inst": "Universite de Paris" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.01.071654", "rel_title": "Mutational spectra of SARS-CoV-2 orf1ab polyprotein and Signature mutations in the United States of America", @@ -1509932,6 +1512523,25 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.05.01.072330", + "rel_title": "Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses - causes and consequences for their short and long evolutionary trajectories", + "rel_date": "2020-05-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.01.072330", + "rel_abs": "The pandemic of SARS coronavirus 2 (SARS-CoV-2) has motivated an intensive analysis of its molecular epidemiology following its worldwide spread. To understand the early evolutionary events following its emergence, a dataset of 985 complete SARS-CoV-2 sequences was assembled. Variants showed a mean 5.5-9.5 nucleotide differences from each other, commensurate with a mid-range coronavirus substitution rate of 3x10-4 substitutions/site/year. Almost half of sequence changes were C->U transitions with an 8-fold base frequency normalised directional asymmetry between C->U and U->C substitutions. Elevated ratios were observed in other recently emerged coronaviruses (SARS-CoV and MERS-CoV) and to a decreasing degree in other human coronaviruses (HCoV-NL63, -OC43, -229E and -HKU1) proportionate to their increasing divergence. C->U transitions underpinned almost half of the amino acid differences between SARS-CoV-2 variants, and occurred preferentially in both 5U/A and 3U/A flanking sequence contexts comparable to favoured motifs of human APOBEC3 proteins. Marked base asymmetries observed in non-pandemic human coronaviruses (U>>A>G>>C) and low G+C contents may represent long term effects of prolonged C->U hypermutation in their hosts.\n\nImportanceThe evidence that much of sequence change in SARS-CoV-2 and other coronaviruses may be driven by a host APOBEC-like editing process has profound implications for understanding their short and long term evolution. Repeated cycles of mutation and reversion in favoured mutational hotspots and the widespread occurrence of amino acid changes with no adaptive value for the virus represents a quite different paradigm of virus sequence change from neutral and Darwinian evolutionary frameworks that are typically used in molecular epidemiology investigations.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Peter Simmonds", + "author_inst": "Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK." + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.28.20083055", "rel_title": "A comparison of health care worker-collected foam and polyester nasal swabs in convalescent COVID-19 patients", @@ -1511146,29 +1513756,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.25.20079996", - "rel_title": "Public perceptions of COVID-19 in Australia: perceived risk, knowledge, health-protective behaviours, and vaccine intentions", - "rel_date": "2020-04-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20079996", - "rel_abs": "Widespread and sustained engagement with health-protective behaviours (i.e., hygiene and distancing) is critical to successfully managing the COVID-19 pandemic. Evidence from previous emerging infectious disease outbreaks points to the role of perceived risk, worry, media coverage, and knowledge in shaping engagement with health-protective behaviours as well as vaccination intentions. The current study examined these factors in 2,174 Australian residents. An online survey was completed between 2-9 March 2020, at an early stage of the COVID-19 outbreak in Australia. Results revealed that two thirds of respondents were at least moderately worried about a widespread COVID-19 outbreak in Australia (which subsequently occurred). Worry about the outbreak and closely following media coverage were consistent predictors of health-protective behaviours (both over the previous month, and intended behaviours in the case of a widespread outbreak) as well as vaccination intentions. Health-behaviour engagement over the previous month was lower in some demographic groups, including males and younger individuals (18-29 age group). These was a substantial mismatch between respondents expected symptoms of infection and emerging evidence that a meaningful proportion of people who contract the novel coronavirus will experience asymptomatic infection (i.e., they will not experience symptoms associated with COVID-19). Only 0.3% of those in the current study believed that they personally would not experience any symptoms if they were infected. Uncertainty and misconceptions about COVID-19 were common, including one third of respondents who reported being unsure whether people are likely have natural or existing immunity. There was also uncertainty around whether specific home remedies (e.g., vitamins, saline rinses) would offer protection, whether the virus could spread via the airborne route, and whether the virus was human made and deliberately released. Such misconceptions are likely to cause concern for members of the public. These results point to areas of uncertainty that could be usefully targeted by public education campaigns, as well as psychological and demographic factors associated with engagement with health-protective behaviours. These findings offer potential pathways for interventions to encourage health-protective behaviours to reduce the spread of COVID-19.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Kate Faasse", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Jill M Newby", - "author_inst": "UNSW" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.24.20077487", "rel_title": "SUCCESSFUL MANUFACTURING OF CLINICAL-GRADE SARS-CoV-2 SPECIFIC T CELLS FOR ADOPTIVE CELL THERAPY", @@ -1511334,6 +1513921,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.26.20079673", + "rel_title": "COVID-19 Control Strategies and Intervention Effects in Resource Limited Settings: A Modeling Study", + "rel_date": "2020-04-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20079673", + "rel_abs": "BackgroundMany countries with weaker health systems are struggling to put together a coherent strategy against the COVID-19 epidemic. We explored COVID-19 control strategies that could offer the greatest benefit in resource limited settings.\n\nMethodsUsing an age-structured SEIR model, we explored the effects of COVID-19 control interventions--a lockdown, physical distancing measures, and active case finding (testing and isolation, contact tracing and quarantine)-- implemented individually and in combination to control a hypothetical COVID-19 epidemic in Kathmandu (population 2.6 million), Nepal.\n\nResultsA month-long lockdown that is currently in place in Nepal will delay peak demand for hospital beds by 36 days, as compared to a base scenario of no interventions (peak demand at 108 days (Inter-Quartile Range IQR 97-119); a 2 month long lockdown will delay it by 74 days, without any difference in annual mortality, or healthcare demand volume. Year-long physical distancing measures will reduce peak demand to 36% (IQR 23%-46%) and annual morality to 67% (IQR 48%-77%) of base scenario. Following a month long lockdown with ongoing physical distancing measures and an active case finding intervention that detects 5% of the daily infection burden could reduce projected morality and peak demand by more than 99%.\n\nInterpretationLimited resources settings are best served by a combination of early and aggressive case finding with ongoing physical distancing measures to control the COVID-19 epidemic. A lockdown may be helpful until combination interventions can be put in place but is unlikely to reduce annual mortality or healthcare demand.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Kiran Raj Pandey", + "author_inst": "Hospital for Advanced Medicine and Surgery" + }, + { + "author_name": "Anup Subedee", + "author_inst": "Hospital for Advanced Medicine and Surgery" + }, + { + "author_name": "Bishesh Khanal", + "author_inst": "Nepal Applied Mathematics and Informatics Institute for Research" + }, + { + "author_name": "Bhagawan Koirala", + "author_inst": "Hospital for Advanced Medicine and Surgery" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.25.20079905", "rel_title": "Informative Ranking of Stand Out Collections of Symptoms: A New Data-Driven Approach to Identify the Strong Warning Signs of COVID 19", @@ -1512580,49 +1515198,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.28.20083998", - "rel_title": "Assessment of the outbreak risk, mapping and infestation behavior of COVID-19: Application of the autoregressive and moving average (ARMA) and polynomial models", - "rel_date": "2020-04-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083998", - "rel_abs": "Infectious disease outbreaks pose a significant threat to human health worldwide. The outbreak of pandemic coronavirus disease 2019 (COVID-2019) has caused a global health emergency. Identification of regions with high risk for COVID-19 outbreak is a major priority of the governmental organizations and epidemiologists worldwide. The aims of the present study were to analyze the risk factors of coronavirus outbreak and identify areas with a high risk of human infection with virus in Fars Province, Iran. A geographic information system (GIS)-based machine learning algorithm (MLA), support vector machine (SVM), was used for the assessment of the outbreak risk of COVID-19 in Fars Province, Iran. The daily observations of infected cases was tested in the third-degree polynomial and the autoregressive and moving average (ARMA) models to examine the patterns of virus infestation in the province and in Iran. The results of disease outbreak in Iran were compared with the data for Iran and the world. Sixteen effective factors including minimum temperature of coldest month (MTCM), maximum temperature of warmest month (MTWM), precipitation in wettest month (PWM), precipitation of driest month (PDM), distance from roads, distance from mosques, distance from hospitals, distance from fuel stations, human footprint, density of cities, distance from bus stations, distance from banks, distance from bakeries, distance from attraction sites, distance from automated teller machines (ATMs), and density of villages - were selected for spatial modelling. The predictive ability of an SVM model was assessed using the receiver operator characteristic - area under the curve (ROC-AUC) validation technique. The validation outcome reveals that SVM achieved an AUC value of 0.786 (March 20), 0.799 (March 29), and 86.6 (April 10) a good prediction of change detection. The growth rate (GR) average for active cases in Fars for a period of 41 days was 1.26, whilst it was 1.13 in country and the world. The results of the third-degree polynomial and ARMA models revealed an increasing trend for GR with an evidence of turning, demonstrating extensive quarantines has been effective. The general trends of virus infestation in Iran and Fars Province were similar, although an explosive growth of the infected cases is expected in the country. The results of this study might assist better programming COVID-19 disease prevention and control and gaining sorts of predictive capability would have wide-ranging benefits.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Hamid Reza Pourghasemi", - "author_inst": "Shiraz University" - }, - { - "author_name": "Soheila Pouyan", - "author_inst": "Yazd University" - }, - { - "author_name": "Zakariya Farajzadeh", - "author_inst": "Shiraz University" - }, - { - "author_name": "Nitheshnirmal Sadhasivam", - "author_inst": "Bharathidasan University" - }, - { - "author_name": "Bahram Heidari", - "author_inst": "Shiraz University" - }, - { - "author_name": "Sedigheh Babaei", - "author_inst": "Shiraz University" - }, - { - "author_name": "John P Tiefenbacher", - "author_inst": "Texas State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.28.20083873", "rel_title": "Bayesian Inference of COVID-19 Spreading Rates in South Africa", @@ -1512704,6 +1515279,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.24.20077966", + "rel_title": "Sequential informed pooling approach to detect SARS-CoV2 infection", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20077966", + "rel_abs": "The alarming spread of the pandemic coronavirus disease 2019 (COVID-19) caused by the SARS-CoV-2 virus is requiring several measures to reduce the risk of contagion. Every successful strategy in controlling SARS-CoV2 infection depends on the timely viral diagnosis which should include asymptomatic carriers. Consequently, strategies to increase the throughput for clinical laboratories to conduct large-scale diagnostic testing are urgently needed. Here we support the hypothesis that standard diagnostic protocol for SARS-CoV-2 virus could be conveniently applied to pooled samples obtained from different subjects. We suggest that a two-step sequential pooling procedure could identify positive subjects, ensuring at the same time significant benefits of costs and time. Simulation data are used to assess the efficiency, in terms of number of required tests, both for random assignment of the subjects to the pools and for situations when epidemiological and clinical data are used to create an \"informed\" version of the pooling. Different scenarios are examined in the simulations to measure the effect of different pool sizes and different values for the virus frequency. Our results allow to customize the pooling strategy according to the specific characteristics of the cohort to be tested.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Renato Millioni", + "author_inst": "University of Padova" + }, + { + "author_name": "Cinzia Mortarino", + "author_inst": "University of Padova" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.24.20077891", "rel_title": "COVID-19 in Africa -- outbreak despite interventions?", @@ -1513670,37 +1516268,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.04.24.20078923", - "rel_title": "Real-time time-series modelling for prediction of COVID-19 spread and intervention assessment", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078923", - "rel_abs": "Substantial amount of data about the COVID-19 pandemic is generated every day. Yet, data streaming, while considerably visualized, is not accompanied with advanced modelling techniques to provide real-time insights. This study introduces a unified platform which integrates visualization capabilities with advanced statistical methods for predicting the virus spread in the short run, using real-time data. The platform is backed up by advanced time series models to capture any possible non-linearity in the data which is enhanced by the capability of measuring the expected impact of preventive interventions such as social distancing and lockdowns. The platform enables lay users, and experts, to examine the data and develop several customized models with different restriction such as models developed for specific time window of the data. Our policy assessment of the case of Australia, shows that social distancing and travel ban restriction significantly affect the reduction of number of cases, as an effective policy.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Taha Hossein Rashidi", - "author_inst": "UNSW Sydney" - }, - { - "author_name": "Siroos Shahriari", - "author_inst": "UNSW Sudney" - }, - { - "author_name": "AKM Azad", - "author_inst": "UNSW Sydney" - }, - { - "author_name": "Fatemeh Vafaee", - "author_inst": "UNSW Sydney" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.04.25.20079830", "rel_title": "FIRST DETECTION OF SARS-COV-2 IN UNTREATED WASTEWATERS IN ITALY", @@ -1513798,6 +1516365,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.24.20079046", + "rel_title": "Gender-Based Disparities in COVID-19: Clinical Characteristics and Propensity-matched Analysis of Outcomes", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20079046", + "rel_abs": "COVID-19 epidemiological data show higher mortality among males as compared to females. However, it remains unclear if this disparity is due to gender differences in high-risk characteristics. Our study, including a large cohort of male and female patients, showed that males have a higher risk for mortality, hospitalization and mechanical ventilation even when compared to a matched cohort of females with similar age, high-risk behavior, and comorbidities. This gender-based risk of poor outcomes among COVID-19 patients is especially more pronounced in advanced age. High-risk characteristics only partially explain the gender disparity, and further research is needed to understand the causes of this disparity.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Shailendra Singh", + "author_inst": "Charleston Area Medical Center, Charleston WV" + }, + { + "author_name": "Monica Chowdhry", + "author_inst": "West Virginia University Health Sciences Center Charleston Division, Charleston, WV" + }, + { + "author_name": "Arka Chatterjee", + "author_inst": "Division of Cardiovascular Disease, University of Alabama at Birmingham" + }, + { + "author_name": "Ahmad Khan", + "author_inst": "Department of Medicine, West Virginia University Health Sciences Center Charleston Division, Charleston, WV" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.24.20078782", "rel_title": "Clinical Laboratory Parameters Associated with Severe or Critical Novel Coronavirus Disease 2019 (COVID-19): A Systematic Review and Meta-analysis", @@ -1515107,177 +1517705,146 @@ "category": "biochemistry" }, { - "rel_doi": "10.1101/2020.04.29.068890", - "rel_title": "Activity profiling of SARS-CoV-2-PLpro protease provides structural framework for anti-COVID-19 drug design", - "rel_date": "2020-04-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.29.068890", - "rel_abs": "In December 2019, the first cases of a novel coronavirus infection causing COVID-19 were diagnosed in Wuhan, China. Viral Papain-Like cysteine protease (PLpro, NSP3) is essential for SARS-CoV-2 replication and represents a promising target for the development of antiviral drugs. Here, we used a combinatorial substrate library containing natural and a wide variety of nonproteinogenic amino acids and performed comprehensive activity profiling of SARS-CoV-2-PLpro. On the scaffold of best hits from positional scanning we designed optimal fluorogenic substrates and irreversible inhibitors with a high degree of selectivity for SARS PLpro variants versus other proteases. We determined crystal structures of two of these inhibitors (VIR250 and VIR251) in complex with SARS-CoV-2-PLpro which reveals their inhibitory mechanisms and provides a structural basis for the observed substrate specificity profiles. Lastly, we demonstrate that SARS-CoV-2-PLpro harbors deISGylating activities similar to SARS-CoV-1-PLpro but its ability to hydrolyze K48-linked Ub chains is diminished, which our sequence and structure analysis provides a basis for. Altogether this work has revealed the molecular rules governing PLpro substrate specificity and provides a framework for development of inhibitors with potential therapeutic value or drug repositioning.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Wioletta Rut", - "author_inst": "Wroclaw University of Science and Technology" - }, - { - "author_name": "Zongyang Lv", - "author_inst": "Medical University of South Carolina" - }, - { - "author_name": "Mikolaj Zmudzinski", - "author_inst": "Wroclaw University of Science and Technology" - }, - { - "author_name": "Stephanie Patchett", - "author_inst": "New York University School of Medicine" - }, - { - "author_name": "Digant Nayak", - "author_inst": "Medical University of South Carolina" - }, - { - "author_name": "Scott J Snipas", - "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" - }, - { - "author_name": "Farid El Oualid", - "author_inst": "UbiQ Bio B.V." - }, - { - "author_name": "Miklos Bekes", - "author_inst": "Arvinas, Inc.," - }, - { - "author_name": "Tony T Huang", - "author_inst": "New York University School of Medicine" - }, - { - "author_name": "Marcin Drag", - "author_inst": "Wroclaw University of Science and Technology" - }, - { - "author_name": "Shaun K Olsen", - "author_inst": "Medical University of South Carolina" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, - { - "rel_doi": "10.1101/2020.04.29.068486", - "rel_title": "SARS-CoV-2 Spike S1 Receptor Binding Domain undergoes Conformational Change upon Interaction with Low Molecular Weight Heparins.", - "rel_date": "2020-04-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.29.068486", - "rel_abs": "The dependence of the host on the interaction of hundreds of extracellular proteins with the cell surface glycosaminoglycan heparan sulphate (HS) for the regulation of homeostasis is exploited by many microbial pathogens as a means of adherence and invasion. The closely related polysaccharide heparin, the widely used anticoagulant drug, which is structurally similar to HS and is a common experimental proxy, can be expected to mimic the properties of HS. Heparin prevents infection by a range of viruses when added exogenously, including S-associated coronavirus strain HSR1 and inhibits cellular invasion by SARS-CoV-2. We have previously demonstrated that unfractionated heparin binds to the Spike (S1) protein receptor binding domain, induces a conformational change and have reported the structural features of heparin on which this interaction depends. Furthermore, we have demonstrated that enoxaparin, a low molecular weight clinical anticoagulant, also binds the S1 RBD protein and induces conformational change. Here we expand upon these studies, to a wide range of low molecular weight heparins and demonstrate that they induce a variety of conformational changes in the SARS-CoV-2 RBD. These findings may have further implications for the rapid development of a first-line therapeutic by repurposing low molecular weight heparins, as well as for next-generation, tailor-made, GAG-based antiviral agents, against SARS-CoV-2 and other members of the Coronaviridae.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Courtney Mycroft-West", - "author_inst": "Keele University" - }, - { - "author_name": "Dunhao Su", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Yong Li", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Scott Guimond", - "author_inst": "Keele University" - }, - { - "author_name": "Timothy Rudd", - "author_inst": "National Institute for Biological Standards and Control" - }, - { - "author_name": "Stefano Elli", - "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" - }, - { - "author_name": "Gavin Miller", - "author_inst": "Keele University" - }, - { - "author_name": "Quentin Nunes", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Patricia Procter", - "author_inst": "Keele University" - }, - { - "author_name": "Antonella Bisio", - "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" - }, - { - "author_name": "Nicholas Forsyth", - "author_inst": "Keele University" - }, - { - "author_name": "Jeremy Turnbull", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Marco Guerrini", - "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" - }, - { - "author_name": "David Fernig", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Edwin Yates", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Marcelo Lima", - "author_inst": "Keele University" - }, - { - "author_name": "Mark Skidmore", - "author_inst": "Keele University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, - { - "rel_doi": "10.1101/2020.04.29.067728", - "rel_title": "An engineered stable mini-protein to plug SARS-Cov2 Spikes", + "rel_doi": "10.1101/2020.04.29.068890", + "rel_title": "Activity profiling of SARS-CoV-2-PLpro protease provides structural framework for anti-COVID-19 drug design", "rel_date": "2020-04-29", "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.29.067728", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe novel betacoronavirus SARS-CoV-2 is the etiological agent of the current pandemic COVID-19. Like other coronaviruses, this novel virus relies on the surface Spike glycoprotein to access the host cells, mainly through the interaction of its Receptor Binding Domain (RBD) with the human angiotensin-converting enzyme 2 (ACE2). Therefore, molecular entities able to interfere with binding of the SARS-CoV-2 Spike protein to ACE2 have a great potential to inhibit viral entry. Starting from the available structural data on the interaction between SARS-CoV-2 Spike protein and the host ACE2 receptor, we here engineered a mini-protein with the aim of creating a soluble and stable Spike interactor. This mini-protein, which was recombinantly produced in high yields, possesses a stable helical conformation and is able to interact with the RBD of glycosylated Spike protein from SARS-CoV-2 with nanomolar affinity, as measured by microscale thermophoresis. By plugging the Spike protein, our mini-protein constitutes a valid tool for the development of treatments against different types of coronavirus.", - "rel_num_authors": 4, + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.29.068890", + "rel_abs": "In December 2019, the first cases of a novel coronavirus infection causing COVID-19 were diagnosed in Wuhan, China. Viral Papain-Like cysteine protease (PLpro, NSP3) is essential for SARS-CoV-2 replication and represents a promising target for the development of antiviral drugs. Here, we used a combinatorial substrate library containing natural and a wide variety of nonproteinogenic amino acids and performed comprehensive activity profiling of SARS-CoV-2-PLpro. On the scaffold of best hits from positional scanning we designed optimal fluorogenic substrates and irreversible inhibitors with a high degree of selectivity for SARS PLpro variants versus other proteases. We determined crystal structures of two of these inhibitors (VIR250 and VIR251) in complex with SARS-CoV-2-PLpro which reveals their inhibitory mechanisms and provides a structural basis for the observed substrate specificity profiles. Lastly, we demonstrate that SARS-CoV-2-PLpro harbors deISGylating activities similar to SARS-CoV-1-PLpro but its ability to hydrolyze K48-linked Ub chains is diminished, which our sequence and structure analysis provides a basis for. Altogether this work has revealed the molecular rules governing PLpro substrate specificity and provides a framework for development of inhibitors with potential therapeutic value or drug repositioning.", + "rel_num_authors": 11, "rel_authors": [ { - "author_name": "Maria Romano", - "author_inst": "Institute of Biostructures and Bioimaging, CNR" + "author_name": "Wioletta Rut", + "author_inst": "Wroclaw University of Science and Technology" }, { - "author_name": "Alessia Ruggiero", - "author_inst": "Institute of Biostructures and Bioimaging, CNR" + "author_name": "Zongyang Lv", + "author_inst": "Medical University of South Carolina" + }, + { + "author_name": "Mikolaj Zmudzinski", + "author_inst": "Wroclaw University of Science and Technology" }, { - "author_name": "Flavia Squeglia", - "author_inst": "Institute of Biostructures and Bioimaging, CNR" + "author_name": "Stephanie Patchett", + "author_inst": "New York University School of Medicine" + }, + { + "author_name": "Digant Nayak", + "author_inst": "Medical University of South Carolina" + }, + { + "author_name": "Scott J Snipas", + "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" + }, + { + "author_name": "Farid El Oualid", + "author_inst": "UbiQ Bio B.V." + }, + { + "author_name": "Miklos Bekes", + "author_inst": "Arvinas, Inc.," }, { - "author_name": "Rita Berisio", - "author_inst": "CNR IBB" + "author_name": "Tony T Huang", + "author_inst": "New York University School of Medicine" + }, + { + "author_name": "Marcin Drag", + "author_inst": "Wroclaw University of Science and Technology" + }, + { + "author_name": "Shaun K Olsen", + "author_inst": "Medical University of South Carolina" } ], "version": "1", "license": "cc_no", "type": "new results", - "category": "biophysics" + "category": "biochemistry" + }, + { + "rel_doi": "10.1101/2020.04.29.068486", + "rel_title": "SARS-CoV-2 Spike S1 Receptor Binding Domain undergoes Conformational Change upon Interaction with Low Molecular Weight Heparins.", + "rel_date": "2020-04-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.29.068486", + "rel_abs": "The dependence of the host on the interaction of hundreds of extracellular proteins with the cell surface glycosaminoglycan heparan sulphate (HS) for the regulation of homeostasis is exploited by many microbial pathogens as a means of adherence and invasion. The closely related polysaccharide heparin, the widely used anticoagulant drug, which is structurally similar to HS and is a common experimental proxy, can be expected to mimic the properties of HS. Heparin prevents infection by a range of viruses when added exogenously, including S-associated coronavirus strain HSR1 and inhibits cellular invasion by SARS-CoV-2. We have previously demonstrated that unfractionated heparin binds to the Spike (S1) protein receptor binding domain, induces a conformational change and have reported the structural features of heparin on which this interaction depends. Furthermore, we have demonstrated that enoxaparin, a low molecular weight clinical anticoagulant, also binds the S1 RBD protein and induces conformational change. Here we expand upon these studies, to a wide range of low molecular weight heparins and demonstrate that they induce a variety of conformational changes in the SARS-CoV-2 RBD. These findings may have further implications for the rapid development of a first-line therapeutic by repurposing low molecular weight heparins, as well as for next-generation, tailor-made, GAG-based antiviral agents, against SARS-CoV-2 and other members of the Coronaviridae.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Courtney Mycroft-West", + "author_inst": "Keele University" + }, + { + "author_name": "Dunhao Su", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Yong Li", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Scott Guimond", + "author_inst": "Keele University" + }, + { + "author_name": "Timothy Rudd", + "author_inst": "National Institute for Biological Standards and Control" + }, + { + "author_name": "Stefano Elli", + "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" + }, + { + "author_name": "Gavin Miller", + "author_inst": "Keele University" + }, + { + "author_name": "Quentin Nunes", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Patricia Procter", + "author_inst": "Keele University" + }, + { + "author_name": "Antonella Bisio", + "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" + }, + { + "author_name": "Nicholas Forsyth", + "author_inst": "Keele University" + }, + { + "author_name": "Jeremy Turnbull", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Marco Guerrini", + "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" + }, + { + "author_name": "David Fernig", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Edwin Yates", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Marcelo Lima", + "author_inst": "Keele University" + }, + { + "author_name": "Mark Skidmore", + "author_inst": "Keele University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" }, { "rel_doi": "10.1101/2020.04.29.068098", @@ -1515420,6 +1517987,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.25.20079475", + "rel_title": "Genomics of Indian SARS-CoV-2: Implications in genetic diversity, possible origin and spread of virus", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20079475", + "rel_abs": "World Health Organization (WHO) declared COVID-19 as a pandemic disease on March 11, 2020. Comparison of genome sequences from diverse locations allows us to identify the genetic diversity among viruses which would help in ascertaining viral virulence, disease pathogenicity, origin and spread of the SARS-CoV-2 between countries. The aim of this study is to ascertain the genetic diversity among Indian SARS-CoV-2 isolates. Initial examination of the phylogenetic data of SARS-CoV-2 genomes (n=3123) from different continents deposited at GISAID (Global Initiative on Sharing All Influenza Data) revealed multiple origin for Indian isolates. An in-depth analysis of 449 viral genomes derived from samples representing countries from USA, Europe, China, East Asia, South Asia, Oceania, Middle East regions and India revealed that most Indian samples are divided into two clusters (A and B) with cluster A showing more similarity to samples from Oceania and Kuwait and the cluster B grouping with countries from Europe, Middle East and South Asia. Diversity analysis of viral clades, which are characterized by specific non-synonymous mutations in viral proteins, discovered that the cluster A Indian samples belong to I clade (V378I in ORF1ab), which is an Oceania clade with samples having Iran connections and the cluster B Indian samples belong to G clade (D614G in Spike protein), which is an European clade. Thus our study identifies that the Indian SARS-CoV-2 viruses belong to I and G clades with potential origin to be countries mainly from Oceania, Europe, Middle East and South Asia regions, which strongly implying the spread of virus through most travelled countries. The study also emphasizes the importance of pathogen genomics through phylogenetic analysis to discover viral genetic diversity and understand the viral transmission dynamics with eventual grasp on viral virulence and disease pathogenesis.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Kumaravel Somasundaram", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Mainak Mondal", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Ankita Lawarde", + "author_inst": "Indian Institute of Science" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.04.25.20079509", "rel_title": "Pregnancy and breastfeeding during COVID-19 pandemic: A systematic review of published pregnancy cases", @@ -1516878,37 +1519472,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.23.20077271", - "rel_title": "Enacting national social distancing policies corresponds with dramatic reduction in COVID19 infection rates", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20077271", - "rel_abs": "The outbreak the SARS-CoV-2 (CoV-2) virus has resulted in over 2.5 million cases of COVID19, greatly stressing global healthcare infrastructure. Lacking medical prophylactic measures to combat disease spread, many nations have adopted social distancing policies in order to mitigate transmission of CoV-2. While mathematical models have suggested the efficacy of social distancing to curb the spread of CoV-2, there is a lack of systematic studies to quantify the real-world efficacy of these approaches. Here, we quantify the spread rate of COVID19 before and after national social distancing measures were implemented in 26 nations and compare this to the changes in COVID19 spread rate over equivalent time periods in 27 nations that did not enact social distancing policies. We find that social distancing policies significantly reduced the COVID19 spread rate. Using mixed linear regression models we estimate that social distancing policies reduced the spread of COVID19 by 66%. These data suggest that social distancing policies may be a powerful tool to prevent spread of COVID19 in real-world scenarios.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Daniel J McGrail", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Jianli Dai", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Kathleen M McAndrews", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Raghu Kalluri", - "author_inst": "The University of Texas MD Anderson Cancer Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.23.20077446", "rel_title": "On the estimation of the total number of SARS-CoV-2 infections", @@ -1516990,6 +1519553,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.23.20077123", + "rel_title": "Significantly Improved COVID-19 Outcomes in Countries with Higher BCG Vaccination Coverage: A Multivariable Analysis", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20077123", + "rel_abs": "COVID-19 has spread to 210 countries within 3 months. We tested the hypothesis that the vaccination with BCG correlates with a better outcome for COVID-19 patients. Our analysis covers 55 countries, complying with predetermined thresholds on population size and deaths per million (DPM). We found a strong negative correlation between the years of BCG administration and a lower DPM along with the pandemic progression in time. The results from multivariable regression tests with 22 economical, demographic, and health-related quantitative properties for each country substantiate the dominant contribution of BCG administration years to the COVID-19 outcomes. Analyzing countries according to an age-group partition reveals that the strongest correlation is attributed to the coverage in BCG vaccination of the young population and mostly to recent years immunization. We propose that BCG immunization coverage, especially among the most recently vaccinated contributes to attenuation of the spread and severity of the COVID-19 pandemic.\n\nOne Sentence SummaryBCG vaccination regimes and COVID-19 outcomes", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Danielle Klinger", + "author_inst": "The Hebrew University of Jerusalem" + }, + { + "author_name": "Ido Blass", + "author_inst": "The Hebrew University of Jerusalem" + }, + { + "author_name": "Nadav Rappoport", + "author_inst": "Ben-Gurion University of the Negev" + }, + { + "author_name": "Michal Linial", + "author_inst": "The Hebrew University of Jerusalem" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.23.20077065", "rel_title": "Estimation of COVID-19 spread curves integrating global data and borrowing information", @@ -1518528,37 +1521122,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.24.20070649", - "rel_title": "Performance of temporal artery temperature measurement in ruling out fever: implications for COVID-19 screening.", - "rel_date": "2020-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20070649", - "rel_abs": "The use of non-invasive temperature testing methods like temporal artery thermometers (TATs) is growing exponentially in the face of the ongoing COVID-19 pandemic. We performed a retrospective analysis of over 1.8 million emergency department electronic health records to identify assess the performance of TAT measurement using patients with near-contemporaneous temperature measurements taken via rectal or oral approaches. Using over 17,000 matched measurements, we show poor fever sensitivity using TAT. We show that sensitivity is significantly improved by lowering the fever threshold and describe limits of agreement between methods of measurement. Our findings suggest that private, public, and healthcare delivery organizations may need to reconsider how we perform high-volume screening during this time of crisis and has implications for return-to-work protocols.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Adrian Haimovich", - "author_inst": "Yale University" - }, - { - "author_name": "Richard Andrew Taylor", - "author_inst": "Yale University" - }, - { - "author_name": "Harlan Krumholz", - "author_inst": "Yale University" - }, - { - "author_name": "Arjun K Venkatesh", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.24.20069633", "rel_title": "Lung injury in patients with or suspected COVID-19 : a comparison between lung ultrasound and chest CT-scanner severity assessments, an observational study", @@ -1518684,6 +1521247,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2020.04.22.20075697", + "rel_title": "Evaluation of WHO listed COVID-19 qPCR primers and probe in silico with 375 SERS-CoV-2 full genome sequences", + "rel_date": "2020-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20075697", + "rel_abs": "Quantitative reverse-transcription PCR (qRT-PCR) assays remains the gold standard for detection of the SARS-CoV-2 virus because of its sensitivity and specificity. However, successful design of qRT-PCR assays requires accurate viral genome sequences. With mutations accumulating as the virus is transmitted globally, we sought to compare current assays recommended by the World Health Organization with available SARS-CoV-2 genomic sequences in silico. While most sequences were conserved, there were notable mismatches, particularly in assays developed using early sequences when compared to more recent isolates. We recommend that any assay being evaluated for diagnostic tests be compared with prevalent sequence data from the region of proposed testing and that continued publicly accessible sequence information continue to be provided by the research community.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Derek Toms", + "author_inst": "University of Calgary" + }, + { + "author_name": "Julang Li", + "author_inst": "University of Guelph" + }, + { + "author_name": "Hugh Y Cai", + "author_inst": "University of Guelph" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.24.20075291", "rel_title": "Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors", @@ -1519914,25 +1522504,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.22.20076166", - "rel_title": "Early detection of superspreaders by mass group pool testing can mitigate COVID-19 pandemic", - "rel_date": "2020-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20076166", - "rel_abs": "BackgroundMost of epidemiological models applied for COVID-19 do not consider heterogeneity in infectiousness and impact of superspreaders, despite the broad viral loading distributions amongst COVID-19 positive people (1 - 106 per mL). Also, mass group testing is not used regardless to existing shortage of tests. I propose new strategy for early detection of superspreaders with reasonable number of RT-PCR tests, which can dramatically mitigate development COVID-19 pandemic and even turn it endemic.\n\nMethodsI used stochastic social-epidemiological SEIAR model, where S-suspected, E-exposed, I-infectious, A-admitted (confirmed COVID-19 positive, who are admitted to hospital or completely isolated), R-recovered. The model was applied to real COVID-19 dynamics in London, Moscow and New York City.\n\nFindingsViral loading data measured by RT-PCR were fitted by broad log-normal distribution, which governed high importance of superspreaders. The proposed full scale model of a metropolis shows that top 10% spreaders (100+ higher viral loading than median infector) transmit 45% of new cases. Rapid isolation of superspreaders leads to 4-8 fold mitigation of pandemic depending on applied quarantine strength and amount of currently infected people. High viral loading allows efficient group \"matrix\" pool testing of population focused on detection of the superspreaders requiring remarkably small amount of tests.\n\nInterpretationThe model and new testing strategy may prevent thousand or millions COVID-19 deaths requiring just about 5000 daily RT-PCR test for big 12 million city such as Moscow. Though applied to COVID-19 pandemic the results are universal and can be used for other infectious heterogenous epidemics.\n\nFundingNo funding", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Maxim B Gongalsky", - "author_inst": "Lomonosov Moscow State University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.21.20044594", "rel_title": "Smart Pooled sample Testing for COVID-19: A Possible Solution for Sparsity of Test Kits", @@ -1520074,6 +1522645,81 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2020.04.22.20072389", + "rel_title": "SARS-CoV-2 On-the-Spot Virus Detection Directly From Patients", + "rel_date": "2020-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20072389", + "rel_abs": "Many countries are currently in a lockdown state due to the SARS-CoV-2 pandemic. One key aspect to transition safely out of lockdown is to continuously test the population for infected subjects. Currently, detection is performed at points of care using quantitative reverse-transcription PCR (RT-qPCR), and requires dedicated professionals and equipment. Here, we developed a protocol based on Reverse Transcribed Loop-Mediated Isothermal Amplification (RT-LAMP) for detection of SARS-CoV-2. This protocol is applied directly on SARS-CoV-2 nose and throat swabs, with no RNA purification step required. We tested this protocol on over 180 suspected patients, and compared its results to the standard method. We further succeeded to apply the protocol on self-sampled saliva from confirmed cases. Since the proposed protocol provides results on-the-spot, and can detect SARS-CoV-2 from saliva, it can allow simple and continuous surveillance of the community.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Nadav Ben-Assa", + "author_inst": "Technion - Israel Institute of Technology" + }, + { + "author_name": "Rawi Naddaf", + "author_inst": "Technion-Israel Institute of Technology" + }, + { + "author_name": "Tal Gefen", + "author_inst": "Technion-Israel Institute of Technology" + }, + { + "author_name": "Tal Capucha", + "author_inst": "Technion-Israel Institute of Technology" + }, + { + "author_name": "Haitham Hajjo", + "author_inst": "Technion-Israel Institute of Technology" + }, + { + "author_name": "Noa Mandelbaum", + "author_inst": "Technion-Israel Institute of Technology" + }, + { + "author_name": "Lilach Elbaum", + "author_inst": "Technion-Israel Institute of Technology" + }, + { + "author_name": "Peter Rogov", + "author_inst": "311 cross st, Winchester MA 01890" + }, + { + "author_name": "Daniel A. King", + "author_inst": "Meir Medical Center" + }, + { + "author_name": "Shai Kaplan", + "author_inst": ". Robiotec ltd 9 Aharonwitz st. Rehovot, Israel, 7634709" + }, + { + "author_name": "Assaf Rotem", + "author_inst": "47 Bow Rd, Newton MA 02459" + }, + { + "author_name": "Michal Chowers", + "author_inst": "Tel-Aviv University" + }, + { + "author_name": "Moran Szwarcwort-Cohen", + "author_inst": "Rambam Health Care Campus" + }, + { + "author_name": "Mical Paul", + "author_inst": "Technion - Israel Institute of Technology" + }, + { + "author_name": "Naama Geva-Zatorsky", + "author_inst": "Technion - Israel Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.27.064774", "rel_title": "A SARS-CoV-2 vaccine candidate would likely match all currently circulating strains", @@ -1521300,37 +1523946,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.23.20076075", - "rel_title": "How fast does the SARS-Cov-2 virus really mutate in heterogeneous populations?", - "rel_date": "2020-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20076075", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe problem of estimating unknown features of viral species using a limited collection of observations is of great relevance in computational biology. We consider one such particular problem, concerned with determining the mutational support and distribution of the SARS-Cov-2 viral genome and its open reading frames (ORFs). The mutational support refers to the unknown number of sites that is expected to be eventually mutated in the SARS-Cov-2 genome. It may be used to assess the virulence of the virus or guide primer selection for real-time RT-PCR tests during the early stages of an outbreak. Estimating the unknown distribution of mutations in the genome of different subpopulations while accounting for the unseen may aid in discovering adaptation mechanisms used by the virus to evade the immune system. To estimate the mutational support in the small-sample regime, we use GISAID sequencing data and new state-of-the-art polynomial estimation techniques based on weighted and regularized Chebyshev approximations. For distribution estimation, we adapt the well-known Good-Turing estimator. We also perform a differential analysis of mutations and their sites across different populations. Our analysis reveals several findings: First, the mutational supports exhibit significant differences in the ORF6 and ORF7a regions (older vs younger patients), ORF1b and ORF10 regions (females vs males) and as may be expected, in almost all ORFs (for Asia versus Europe and North America). Second, despite the fact that the N region of SARS-Cov-2 has a predicted 10% mutational support, almost all observed mutations fall outside of the two regions of paired primers recommended for testing by the CDC.\n\nAuthor SummaryWe introduce the new problem of small-sample estimation of the number of mutations and the distribution of mutations in viral and bacterial genomes, and in particular, in the SARS-Cov-2 genome. The approach is of interest due to the fact that it aims to predict which regions in the genome will mutate in the future and with what frequency, given only a very limited number of complete viral sequences. This setting is usually encountered during the early stages of an outbreak when it is critical to assess the potential of the virus to gain mutations advantageous for its spreading. The results may also be used to guide the selection of genomic (primer) regions that are not subject to mutational pressure and can consequently be used as identifiers in the process of testing for the disease. They can also highlight differences in the mutation rates and locations of the SARS-Cov-2 virus affecting diverse subpopulations and therefore potentially suggest the role of certain mutations in evading the immune system. Our approach uses a new class of estimation methods that may find other applications in bioinformatics.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Vishal Rana", - "author_inst": "University of Illinois, Urbana-Champaign" - }, - { - "author_name": "Eli Chien", - "author_inst": "University of Illinois, Urbana-Champaign" - }, - { - "author_name": "Jianhao Peng", - "author_inst": "University of Illinois, Urbana-Champaign" - }, - { - "author_name": "Olgica Milenkovic", - "author_inst": "University of Illinois, Urbana-Champaign" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.22.20075861", "rel_title": "The Potential Impact of Interruptions to HIV Services: A Modelling Case Study for South Africa", @@ -1521404,6 +1524019,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.21.20068478", + "rel_title": "Bringing accountability to the peak of the pandemic using linear response theory", + "rel_date": "2020-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20068478", + "rel_abs": "The peak of the daily new infections in COVID-19 remained qualitative in description and elusive in arrival. Because of the lack of clarity in what to expect from the peak, apart from the hope that one day the peak will be reached, there has been no metric to describe the success of the implemented strategies. We propose a way of predicting the number of infections that can be expected after a lockdown, assuming they come from the asymptomatic cases prior to the lockdown and using linear response theory. These predictions for several western countries faithfully follow the observed infections for several weeks after the lockdown, suggesting universalities in the recovery pattern of several countries. At the same time, the gap between the quantitative predictions of the recovery patterns for New York and Milan and the observations is striking. These gaps which arise even while emulating the recovery patterns of other western countries raise the possibility of an audit of the success of the implemented strategies, and the potential newer sources of infection.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Meher K Prakash", + "author_inst": "Jawaharlal Nehru Centre for Advanced Scientific Research" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.22.20071043", "rel_title": "Contact Tracing: a game of big numbers in the time of COVID-19", @@ -1522326,37 +1524960,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.04.19.048991", - "rel_title": "CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2", - "rel_date": "2020-04-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.19.048991", - "rel_abs": "The ability to detect the SARS-CoV-2 in a widespread epidemic is crucial for screening of carriers and for the success of quarantine efforts. Methods based on real-time reverse transcription polymerase chain reaction (RT-qPCR) and sequencing are being used for virus detection and characterization. However, RNA viruses are known for their high genetic diversity which poses a challenge for the design of efficient nucleic acid-based assays. The first SARS-CoV-2 genomic sequences already showed novel mutations, which may affect the efficiency of available screening tests leading to false-negative diagnosis or inefficient therapeutics. Here we describe the CoV2ID (http://covid.portugene.com/), a free database built to facilitate the evaluation of molecular methods for detection of SARS-CoV-2 and treatment of COVID-19. The database evaluates the available oligonucleotide sequences (PCR primers, RT-qPCR probes, etc.) considering the genetic diversity of the virus. Updated sequences alignments are used to constantly verify the theoretical efficiency of available testing methods. Detailed information on available detection protocols are also available to help laboratories implementing SARS-CoV-2 testing.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jo\u00e3o Carneiro", - "author_inst": "Interdisciplinary Centre of Marine and Environmental Research (CIIMAR)" - }, - { - "author_name": "Catarina Gomes", - "author_inst": "IDENTIFICA University of Porto" - }, - { - "author_name": "Catia Couto", - "author_inst": "IDENTIFICA University of Porto" - }, - { - "author_name": "Filipe Pereira", - "author_inst": "IDENTIFICA genetic testing" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.04.25.060947", "rel_title": "MINERVA: A facile strategy for SARS-CoV-2 whole genome deep sequencing of clinical samples", @@ -1522590,6 +1525193,37 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.04.22.055327", + "rel_title": "Comparison of Cepheid Xpert Xpress and Abbott ID Now to Roche cobas for the Rapid Detection of SARS-CoV-2", + "rel_date": "2020-04-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.22.055327", + "rel_abs": "The SARS-CoV-2 pandemic has created an urgent and unprecedented need for rapid large-scale diagnostic testing to inform timely patient management. This study compared two recently-authorized rapid tests, Cepheid Xpert Xpress SARS-CoV-2 and Abbott ID Now SARS-CoV-2 to the Roche cobas SARS-CoV-2 assay. A total of 113 nasopharyngeal swabs were tested, including 88 positives spanning the full range of observed Ct values on the cobas assay. Compared to cobas, the overall positive agreement was 73.9% with ID Now and 98.9% with Xpert. Negative agreement was 100% and 92.0% for ID Now and Xpert, respectively. Both ID Now and Xpert showed 100% positive agreement for medium and high viral concentrations (Ct value <30). However, for Ct values >30, positive agreement was 34.3% for ID Now and 97.1% for Xpert. These findings highlight an important limitation of ID Now for specimens collected in viral or universal transport media with low viral concentrations. Further studies are needed to evaluate the performance of ID Now for direct swabs.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Marie C Smithgall", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Ioana Scherberkova", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Susan Whittier", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Daniel Green", + "author_inst": "Columbia University Irving Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.25.060350", "rel_title": "SARS-CoV-2 Productively Infects Human Gut Enterocytes", @@ -1523944,53 +1526578,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.21.20074435", - "rel_title": "The spatio-temporal epidemic dynamics of COVID-19 outbreak in Africa", - "rel_date": "2020-04-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20074435", - "rel_abs": "The novel coronavirus (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in the city of Wuhan, China in December 2019. Although, the disease appears on the African continent late, it has spread to virtually all the countries. We provide early spatio-temporal dynamics of COVID-19 within the first 62 days of the diseases appearance on the African continent. We used a two-parameter hurdle Poisson model to simultaneously analyze the zero counts and the frequency of occurrence. We investigate the effects of important healthcare capacities including hospital beds and number of medical doctors in the different countries. The results show that cases of the pandemic vary geographically across Africa with notable high incidence in neighboring countries particularly in West and North Africa. The burden of the disease (per 100,000) was most felt in Djibouti Tunisia, Morocco and Algeria. Temporally, during the first 4 weeks, the burden was highest in Senegal, Egypt and Mauritania, but by mid-April it shifted to Somalia, Chad, Guinea, Tanzania, Gabon, Sudan, and Zimbabwe. Currently, Namibia, Angola, South Sudan, Burundi and Uganda have the least burden. The findings could be useful in implementing epidemiological intervention and allocation of scarce resources based on heterogeneity of the disease patterns.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ezra Gayawan", - "author_inst": "Federal University of Technology, Akure, Nigeria" - }, - { - "author_name": "Olawale Awe", - "author_inst": "Anchor University, Lagos, Nigeria" - }, - { - "author_name": "Bamidele M Oseni", - "author_inst": "Federal University of Technology, Akure, Nigeria" - }, - { - "author_name": "Ikemefuna C Uzochukwu", - "author_inst": "Nnamdi Azikiwe University, Nigeria" - }, - { - "author_name": "Adeshina I Adekunle", - "author_inst": "James Cook University" - }, - { - "author_name": "Gemisola Samuel", - "author_inst": "covenant university, Nigeria" - }, - { - "author_name": "Damon Eisen", - "author_inst": "James Cook University" - }, - { - "author_name": "Oyelola Adegboye", - "author_inst": "James Cook University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.22.20074914", "rel_title": "Antibody tests in detecting SARS-CoV-2 infection: a meta-analysis", @@ -1524064,6 +1526651,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.22.20075440", + "rel_title": "Estimating the number of COVID-19-related infections, deaths and hospitalizations in Iran under different physical distancing and isolation scenarios: A compartmental mathematical modeling", + "rel_date": "2020-04-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20075440", + "rel_abs": "BackgroundIran is one of the countries that has been overwhelmed with COVID-19. We aimed to estimate the total number of COVID-19 related infections, deaths, and hospitalizations in Iran under different physical distancing and isolation scenarios.\n\nMethodsWe developed a Susceptible-Exposed-Infected-Removed (SEIR) model, parameterized to the COVID-19 pandemic in Iran. We used the model to quantify the magnitude of the outbreak in Iran and assess the effectiveness of isolation and physical distancing under five different scenarios (A: 0% isolation, through E: 40% isolation of all infected cases). We used Monte-Carlo simulation to calculate the 95% uncertainty intervals (UI).\n\nFindingsUnder scenario A, we estimated 5,196,000 (UI 1,753,000 - 10,220,000) infections to happen till mid-June with 966,000 (UI 467,800 - 1,702,000) hospitalizations and 111,000 (UI 53,400 - 200,000) deaths. Successful implantation of scenario E would reduce the number of infections by 90% (i.e. 550,000) and change the epidemic peak from 66,000 on June 9th to 9,400 on March 1st. Scenario E also reduces the hospitalizations by 92% (i.e. 74,500), and deaths by 93% (i.e. 7,800).\n\nInterpretationWith no approved vaccination or therapy, we found physical distancing and isolation that includes public awareness and case-finding/isolation of 40% of infected people can reduce the burden of COVID-19 in Iran by 90% by mid-June.\n\nFundingWe received no funding for this work.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSIran has been heavily impacted by the COVID-19 outbreak, and the virus has now spread to all of its provinces. Iran has been implementing different levels of partial physical distancing and isolation policies in the past few months. We searched PubMed and preprint archives for articles published up to April 15, 2020 that included information about control measures against COVID-19 in Iran using the following terms: (\"coronavirus\" OR \"2019-nCoV\" OR \"COVID-19\") AND \"Iran\" AND (\"intervention\" OR \"prevention\" OR \"physical distancing\" OR \"social distancing\"). We found no studies that had quantified the impact of policies in Iran.\n\nAdded value of this studyGiven the scarcity of evidence on the magnitude of the outbreak and the burden of COVID-19 in Iran, we used multiple sources of data to estimate the number of COVID-19 infections, hospitalizations, and deaths under different physical distancing and isolation scenarios until mid-June. We showed that implementing no control measures could lead to over five million infections in Iran; [~]19% of whom would be hospitalized, and [~]2% would die. However, under our most optimistic scenario, these estimates could be reduced by [~]90%.\n\nImplications of all the available evidenceWith no effective vaccination or treatment, advocating and enforcing physical distancing and isolation along with public education on prevention measures could significantly reduce the burden of COVID-19 in Iran. Nonetheless, even under the most optimistic scenario, the burden of COVID-19 would be substantial and well beyond the current capacity of the healthcare system in Iran.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Hamid Sharifi", + "author_inst": "HIV/STI Surveillance Research Center, and WHO Collaborating Center for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical S" + }, + { + "author_name": "Yunes Jahani", + "author_inst": "Modeling in Health Research Center, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran" + }, + { + "author_name": "Ali Mirzazadeh", + "author_inst": "Department of Epidemiology and Biostatistics, Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "Milad Ahmadi Gohari", + "author_inst": "Modeling in Health Research Center, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran" + }, + { + "author_name": "Mehran Nakhaeizadeh", + "author_inst": "Department of Biostatistics and Epidemiology, School of Public Health, Kerman University of Medical Sciences, Kerman, Iran" + }, + { + "author_name": "Mostafa Shokoohi", + "author_inst": "University of Toronto, Dalla Lana School of Public Health" + }, + { + "author_name": "Sana Eybpoosh", + "author_inst": "Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran" + }, + { + "author_name": "Hamid Reza Tohidinik", + "author_inst": "Department of Biostatistics and Epidemiology, School of Public Health, Kerman University of Medical Sciences, Kerman, Iran" + }, + { + "author_name": "Ehsan Mostafavi", + "author_inst": "Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran" + }, + { + "author_name": "Davood Khalili", + "author_inst": "Prevention of Metabolic Disorders Research Center, Research Institute for education Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Seyed Saeed Hashemi Nazari", + "author_inst": "Prevention of Cardiovascular Disease Research Center, Department of Epidemiology, School of Public Health and Safety, Shahid Beheshti University of Medical Scie" + }, + { + "author_name": "Mohammad Karamouzian", + "author_inst": "School of Population and Public Health, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada" + }, + { + "author_name": "Ali Akbar Haghdoost", + "author_inst": "Modeling in Health Research Center, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.22.20075572", "rel_title": "Forecast and interpretation of daily affected people during 21 days lockdown due to COVID 19 pandemic in India", @@ -1525526,77 +1528180,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2020.04.20.20065953", - "rel_title": "The production of antibodies for SARS-CoV-2 and its clinical implication", - "rel_date": "2020-04-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20065953", - "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2(SARS-CoV-2), a novel betacoronavirus, has caused an outburst of pneumonia cases in Wuhan, China. We report the production of specific IgM and IgG antibodies after the infection of SARS-CoV-2 and its implication for the diagnosis, pathology and the course of the disease as well as the recurrence of positive nucleic acid tests after discharge.\n\nMethodsTest results for SARS-CoV-2 IgM and IgG antibodies of 221 confirmed COVID-19 patients were retrospectively examined, and their clinical data were collected and analyzed based on various subgroups. SARS-CoV-2 IgM and IgG antibodies were determined with the chemiluminescence method.\n\nFindingsThe concentration (S/CO) of SARS-CoV-2 IgM and IgG antibodies peaked on day 19-21 after symptom onset, with a median of 17.38 (IQR 4.39-36.4) for IgM and 5.59 (IQR 0.73-13.65) for IgG. Detection rates reached highest on day 16-18 and day 19-21 for IgM and IgG, which were 73.6% and 98.6%, respectively, with significantly higher concentration of IgG in critically ill patients than in those with mild to moderate disease (P=0.027). The concentration of the antibodies on day 16-21 is not correlated with the course or outcome of the disease (Spearman r < 0.20, P > 0.05). Nasopharyngeal swabs revealed positive SARS-CoV-2 RNA in up to 52.7% of recovered patients after discharge, whose IgG proved to be significantly lower than that of those with negative RNA results (P = 0.009). IgG and IgM were tested twice within 14 days after discharge with a 7-day interval, and the second testing of these antibodies displayed a decrease in concentration of 21.2% (IQR, 11.2%,34.48%) for IgG and 23.05% (IQR, -27.96%,46.13%) for IgM, without statistical significance between the patients with re-detectable positive RNA results and those with negative RNA results after discharge. However, those with positive results experienced a count decrease in lymphocyte subsets.\n\nInterpretationThe concentration of SARS-CoV-2 IgM and IgG antibodies peaked on day 19-21 after symptom onset, and antibody testing on day 16-21 is associated with increased detection rates, but the antibody concentration does not affect the course and outcome of the infection. Recovering patients with re-detectable positive SARS-CoV-2 RNA displayed lower concentration of IgG, but the downward trend of IgG during recovery indicated its limited duration of protection, and the protective effect of IgG remains to be investigated.\n\nFundingChongqing Education Board, Chongqing Science and Technology Bureau, Famous teacher project of Chongqing talent plan", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Qianfang Hu", - "author_inst": "Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University" - }, - { - "author_name": "Xiaoping Cui", - "author_inst": "Department of Medical Laboratory, Chongqing Three Gorges Central Hospital" - }, - { - "author_name": "Xinzhu Liu", - "author_inst": "Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University" - }, - { - "author_name": "Bin Peng", - "author_inst": "Department of Health Statistics, School of Public Health and Management, Chongqing Medical University" - }, - { - "author_name": "Jinyue Jiang", - "author_inst": "Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University" - }, - { - "author_name": "Xiaohui Wang", - "author_inst": "Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University" - }, - { - "author_name": "Yan Li", - "author_inst": "Department of Health Management Centre, Chongqing Three Gorges Central Hospital," - }, - { - "author_name": "Wenhui Hu", - "author_inst": "Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University" - }, - { - "author_name": "Zhi Ao", - "author_inst": "Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University" - }, - { - "author_name": "Jun Duan", - "author_inst": "Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University" - }, - { - "author_name": "Xue Wang", - "author_inst": "Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University" - }, - { - "author_name": "Linxiao Zhu", - "author_inst": "Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University" - }, - { - "author_name": "Shuliang Guo", - "author_inst": "the First Affiliated Hospital of Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Guicheng Wu", - "author_inst": "Department of Hepatopathy, Chongqing Three Gorges Central Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2020.04.21.20066761", "rel_title": "Risk of drug-induced Long QT Syndrome associated with the use of repurposed COVID-19 drugs: a systematic review", @@ -1525718,6 +1528301,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.21.20073833", + "rel_title": "Collateral damage: the impact on cancer outcomes of the COVID-19pandemic", + "rel_date": "2020-04-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20073833", + "rel_abs": "BackgroundCancer diagnostics and surgery have been disrupted by the response of healthcare services to the COVID-19 pandemic. Progression of cancers during delay will impact on patient long-term survival.\n\nMethodsWe generated per-day hazard ratios of cancer progression from observational studies and applied these to age-specific, stage-specific cancer survival for England 2013-2017. We modelled per-patient delay of three months and six months and periods of disruption of one year and two years. Using healthcare resource costing, we contextualise attributable lives saved and life years gained from cancer surgery to equivalent volumes of COVID-19 hospitalisations.\n\nFindingsPer year, 94,912 resections for major cancers result in 80,406 long-term survivors and 1,717,051 life years gained. Per-patient delay of six months would cause attributable death of 10,555 of these individuals with loss of 205,024 life years. For cancer surgery, average life years gained (LYGs) per patient are 18{middle dot}1 under standard conditions and 15{middle dot}9 with a delay of six months (a loss of 2{middle dot}3 LYG per patient). Taking into account units of healthcare resource (HCRU), surgery results on average per patient in 2{middle dot}25 resource-adjusted life years gained (RALYGs) under standard conditions and 1{middle dot}98 RALYGs following delay of six months. For 94,912 hospital COVID-19 admissions, there are 474,505 LYGs requiring of 1,097,937 HCRUs. Hospitalisation of community-acquired COVID-19 patients yields on average per patient 5{middle dot}0 LYG and 0{middle dot}43 RALYGs.\n\nInterpretationDelay of six months in surgery for incident cancers would mitigate 43% of life years gained by hospitalisation of an equivalent volume of admissions for community acquired COVID-19. This rises to 62% when considering resource-adjusted life-years gained. To avoid a downstream public health crisis of avoidable cancer deaths, cancer diagnostic and surgical pathways must be maintained at normal throughput, with rapid attention to any backlog already accrued.\n\nFundingBreast Cancer Now, Cancer Research UK, Bobby Moore Fund for Cancer Research, National Institute for Health Research (NIHR)", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Amit Sud", + "author_inst": "Institute of Cancer Research" + }, + { + "author_name": "Michael E. Jones", + "author_inst": "Institute of Cancer Research" + }, + { + "author_name": "John Broggio", + "author_inst": "National Cancer Registration and Analysis Service, Public Health England" + }, + { + "author_name": "Chey Loveday", + "author_inst": "Institute of Cancer Research" + }, + { + "author_name": "Bethany Torr", + "author_inst": "Institute of Cancer Research" + }, + { + "author_name": "Alice Garrett", + "author_inst": "Institute of Cancer Research" + }, + { + "author_name": "David L. Nicol", + "author_inst": "Royal Marsden NHS Foundation Trust" + }, + { + "author_name": "Shaman Jhanji", + "author_inst": "Royal Marsden NHS Foundation Trust; Institute of Cancer Research" + }, + { + "author_name": "Stephen A. Boyce", + "author_inst": "Oxford University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Phillip Ward", + "author_inst": "Royal Marsden NHS Foundation Trust" + }, + { + "author_name": "Jonathan M. Handy", + "author_inst": "Royal Marsden NHS Foundation Trust" + }, + { + "author_name": "Nadia Yousaf", + "author_inst": "Royal Marsden NHS Foundation Trust" + }, + { + "author_name": "James Larkin", + "author_inst": "Royal Marsden NHS Foundation Trust; Institute of Cancer Research" + }, + { + "author_name": "Yae-Eun Suh", + "author_inst": "Royal Marsden NHS Foundation Trust" + }, + { + "author_name": "Stephen Scott", + "author_inst": "RM Partners, West London Cancer Alliance, Royal Marsden NHS Foundation Trust" + }, + { + "author_name": "Paul D.P. Pharoah", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Charles Swanton", + "author_inst": "The Francis Crick Institute; University College London Cancer Institute" + }, + { + "author_name": "Christopher Abbosh", + "author_inst": "The Francis Crick Institute; University College London Cancer Institute" + }, + { + "author_name": "Matthew Williams", + "author_inst": "Imperial College Healthcare NHS Trust; Imperial College London" + }, + { + "author_name": "Georgios Lyratzopoulos", + "author_inst": "National Cancer Registration and Analysis Service, Public Health England; University College London" + }, + { + "author_name": "Richard Houlston", + "author_inst": "Institute of Cancer Research" + }, + { + "author_name": "Clare Turnbull", + "author_inst": "Institute of Cancer Research" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2020.04.21.20063263", "rel_title": "A web-based Diagnostic Tool for COVID-19 Using Machine Learning on Chest Radiographs (CXR)", @@ -1527232,25 +1529918,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.19.20071761", - "rel_title": "Minimising lockdown periods for regional elimination of covid-19", - "rel_date": "2020-04-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071761", - "rel_abs": "There seems to be widespread pessimism regarding the ability of a nation to eliminate covid. One factor in this pessimism seems to be concern that covid might always be able to re-emerge because of the ongoing presence of unrecognised asymptomatic cases. However, it is shown here that it should be possible to eliminate covid more easily than anticipated, for a reason that at first glance seems paradoxical - the presence of superspreaders. If superspreaders are responsible for most of the spread, then, with the average number of secondary cases fixed at say R0 = 2.5, we have to conclude that superspreaders are relatively rare. When towards the end of an elimination program, there are very few infected people, whether symptomatic or asymptomatic, that small number of people may well not include any superspreaders. As a result, chance effects may make extinction likely. Nevertheless it is clear an attempt at elimination will require a rather onerous \"lockdown\". In this paper we use a branching processes model to look at the tradeoff between risk of disease re-emergence and the length of \"lockdown\" required after a program of elimination has dropped the number of symptomatic cases in a region to just one.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "David Abraham Kault", - "author_inst": "James Cook University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.20.20072470", "rel_title": "Prevalence of SARS-CoV-2 infection in previously undiagnosed health care workers at the onset of the U.S. COVID-19 epidemic", @@ -1527432,6 +1530099,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.21.20073114", + "rel_title": "Deaths from Covid-19: Who are the forgotten victims?", + "rel_date": "2020-04-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20073114", + "rel_abs": "BackgroundWith the global pandemic of coronavirus disease 2019 (Covid-19) there has been disruption to normal clinical activity in response to the increased demand on health services. There are reports of a reduction in non-Covid-19 emergency presentations. Consequentially, there are concerns that deaths from non-Covid-19 causes could increase. We examined recent reported population-based mortality rates, compared with expected rates, and compared any excess in deaths with the number of deaths attributed to Covid-19.\n\nMethodsNational agency and death registration reports were searched for numbers of deaths attributed to Covid-19 and overall mortality that had been publicly reported by 06 May 2020. Data on the number of deaths attributed to Covid-19, the total number of deaths registered in the population and the historical average over at least 3 years were collected. Data were available for 4 European countries (England & Wales, Scotland, Netherlands and Italy) and New York State, United States of America.\n\nResultsThere was an increase in observed, compared with expected, mortality in Scotland (+68%), England and Wales (+74%), the Netherlands (+58%), Italy (+39%) and New York state (+49%). Of these deaths, only 73% in Scotland, 71 % in England and Wales, 53% in the Netherlands, 54% in Italy and 79% in New York state were attributed to Covid-19 leaving a number of excess deaths not attributed to Covid-19. In the 5-week period of study, Scotland, 10% of the excess of deaths were attributed to dementia/Alzheimers disease and 7% to cardiovascular causes.\n\nConclusionA substantial proportion of excess deaths observed during the current COVID-19 pandemic are not attributed to COVID-19 and may represent unrecognised deaths due to Covid-19, an excess of deaths due to other causes, or both. The impact of Covid-19 on mortality and morbidity from other causes needs to be quantified and addressed in public health planning.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Kieran Docherty", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Jawad Butt", + "author_inst": "Rigshospitalet Copenhagen University Hospital" + }, + { + "author_name": "Rudolf de Boer", + "author_inst": "University of Groningen" + }, + { + "author_name": "Pooja Dewan", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Lars Koeber", + "author_inst": "Rigshospitalet Copenhagen University Hospital" + }, + { + "author_name": "Aldo Maggioni", + "author_inst": "Associazione Nazionale Medici Cardiologi Ospedalieri Research Center" + }, + { + "author_name": "John McMurray", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Scott Solomon", + "author_inst": "Division of Cardiovascular Medicine, Brigham and Women's Hospital" + }, + { + "author_name": "Pardeep Singh Jhund", + "author_inst": "University of Glasgow" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.20.20072918", "rel_title": "Clinical features of coronavirus disease 2019 (COVID-19) in a cohort of patients with disability due to spinal cord injury", @@ -1528938,6 +1531656,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.20.20073080", + "rel_title": "The risk of SARS-CoV-2 transmission in the healthcare setting and potential impact of cohorting strategies", + "rel_date": "2020-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20073080", + "rel_abs": "BackgroundSince its onset, the COVID-19 pandemic has caused significant morbidity and mortality worldwide, with particularly severe outcomes in healthcare institutions and congregate settings. To mitigate spread, healthcare systems have been cohorting patients to limit contacts between uninfected patients and potentially infected patients or healthcare workers (HCWs). A major challenge in managing the pandemic is the presence of currently asymptomatic individuals capable of transmitting the virus, who could introduce COVID-19 into uninfected cohorts. The optimal combination of personal protective equipment (PPE) and testing approaches to prevent these events is unclear, especially in light of ongoing limitations in access to both.\n\nMethodsUsing stochastic simulations with an SEIR model we quantified and compared the impacts of PPE use, patient and HCWs testing, and cohorting.\n\nFindingsIn the base case without testing or PPE, the healthcare system was rapidly overwhelmed, and became a net contributor to the force of infection. We found that effective use of PPE by both HCWs and patients could prevent this scenario, while random testing of apparently asymptomatic individuals on a weekly basis was less effective. We also found that even imperfect use of PPE could provide substantial protection by decreasing the force of infection, and that creation of smaller patient/HCW subcohorts can provide additional resilience to outbreak development.\n\nInterpretationThese findings reinforce the importance of ensuring adequate PPE supplies even in the absence of testing, and provide support for strict subcohorting regimens to reduce outbreak potential in healthcare institutions.\n\nFundingNational Institute of General Medical Sciences, National Institutes of Health.\n\nResearch in contextO_ST_ABSEvidence beforeC_ST_ABSPreserving healthcare from outbreaks of respiratory viruses is a longstanding concern, brought into sharp relief by the covid-19 pandemic. Early case series and numerous anecdotal reports suggest that health care workers (HCWs) and patients receiving treatment for conditions other than SARS-CoV-2 infection are at elevated risk of becoming infected, and the consequences of infections in long term care facilities are well known. In addition, the early stages of the pandemic have been marked by shortages of personal protective equipment (PPE) and diagnostic testing, but the most effective strategies for their use given the specific characteristics of SARS-CoV-2 transmission are unclear.\n\nValue addedOur research plainly shows the importance of presymptomatic transmission. Given reasonable estimates of this, random testing of currently asymptomatic staff and patients once a week is not able to prevent large outbreaks. We show that PPE is, as expected, the most effective intervention and moreover even suboptimal PPE use is highly beneficial. To further limit transmission, we show the benefit of sub-cohorting into smaller groups of HCWs and patients. When the force of infection in the community is low, this can entirely prevent the establishment of infection in a large fraction of healthcare.\n\nImplicationsPPE should be used throughout healthcare, on the assumption that any patient or HCWs is potentially infected. Further work should determine the most effective means of PPE for the non-COVID cohort. If PPE resources are limited, whether in general or due to a second surge, we recommend subcohorting to limit the impact of introductions from the community.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Joel C Miller", + "author_inst": "School of Engineering at Mathematical Sciences, La Trobe University, Bundoora, VIC" + }, + { + "author_name": "Xueting Qiu", + "author_inst": "Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University" + }, + { + "author_name": "Derek MacFadden", + "author_inst": "Ottawa Hospital Research Institute, Ottawa, Canada" + }, + { + "author_name": "William P Hanage", + "author_inst": "Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.20.20073023", "rel_title": "Estimated surge in hospitalization and intensive care due to the novel coronavirus pandemic in the Greater Toronto Area, Canada: a mathematical modeling study with application at two local area hospitals", @@ -1530305,61 +1533054,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.04.18.20071019", - "rel_title": "Distinguish Coronavirus Disease 2019 Patients in General Surgery Emergency by CIAAD Scale: Development and Validation of a Prediction Model Based on 822 Cases in China", - "rel_date": "2020-04-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.18.20071019", - "rel_abs": "ABATRACTO_ST_ABSIMPORTANCEC_ST_ABSIn the epidemic, surgeons cannot distinguish infectious acute abdomen patients suspected COVID-19 quickly and effectively.\n\nOBJECTIVETo develop and validate a predication model, presented as nomogram and scale, to distinguish infectious acute abdomen patients suspected coronavirus disease 2019 (COVID-19).\n\nDESIGNDiagnostic model based on retrospective case series.\n\nSETTINGTwo hospitals in Wuhan and Beijing, China.\n\nPTRTICIPANTS584 patients admitted to hospital with laboratory confirmed SARS-CoV-2 from 2 Jan 2020 to15 Feb 2020 and 238 infectious acute abdomen patients receiving emergency operation from 28 Feb 2019 to 3 Apr 2020.\n\nMETHODSLASSO regression and multivariable logistic regression analysis were conducted to develop the prediction model in training cohort. The performance of the nomogram was evaluated by calibration curves, receiver operating characteristic (ROC) curves, decision curve analysis (DCA) and clinical impact curves in training and validation cohort. A simplified screening scale and managing algorithm was generated according to the nomogram.\n\nRESULTSSix potential COVID-19 prediction variables were selected and the variable abdominal pain was excluded for overmuch weight. The five potential predictors, including fever, chest computed tomography (CT), leukocytes (white blood cells, WBC), C-reactive protein (CRP) and procalcitonin (PCT), were all independent predictors in multivariable logistic regression analysis (p [≤]0.001) and the nomogram, named COVID-19 Infectious Acute Abdomen Distinguishment (CIAAD) nomogram, was generated. The CIAAD nomogram showed good discrimination and calibration (C-index of 0.981 (95% CI, 0.963 to 0.999) and AUC of 0.970 (95% CI, 0.961 to 0.982)), which was validated in the validation cohort (C-index of 0.966 (95% CI, 0.960 to 0.972) and AUC of 0.966 (95% CI, 0.957 to 0.975)). Decision curve analysis revealed that the CIAAD nomogram was clinically useful. The nomogram was further simplified into the CIAAD scale.\n\nCONCLUSIONSWe established an easy and effective screening model and scale for surgeons in emergency department to distinguish COVID-19 patients from infectious acute abdomen patients. The algorithm based on CIAAD scale will help surgeons manage infectious acute abdomen patients suspected COVID-19 more efficiently.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Bangbo Zhao", - "author_inst": "Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Yingxin Wei", - "author_inst": "Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Wenwu Sun", - "author_inst": "Department of Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Sciences and Technology" - }, - { - "author_name": "Cheng Qin", - "author_inst": "Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Xingtong Zhou", - "author_inst": "Department of Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Zihao Wang", - "author_inst": "Department of Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Tianhao Li", - "author_inst": "Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Hongtao Cao", - "author_inst": "Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Weibin Wang", - "author_inst": "Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Yujun Wang", - "author_inst": "Department of Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Sciences and Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "surgery" - }, { "rel_doi": "10.1101/2020.04.17.20069930", "rel_title": "A single-cell atlas of the peripheral immune response to severe COVID-19", @@ -1530568,6 +1533262,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.18.20071142", + "rel_title": "Is there evidence that BCG vaccination has non-specific protective effects for COVID 19 infections or is it an illusion created by lack of testing?", + "rel_date": "2020-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.18.20071142", + "rel_abs": "The goal of this paper is to showcase that the COVID-19 disease pattern is evolving and to study the relationship between mandatory BCG policy and caseload/million or death/per million. We analyze seven recent publications on the impact of BCG vaccinations on the development of COVID19 illness and extend presented findings using the latest data from April 10, 2020. We analyze data from 98 countries and we extend existing models by adding the dimension of COVID-19-related testing conducted by the analyzed countries. Similarly to prior studies, we find that COVID-19 attributable case and death incidences across countries share a relationship with a countrys BCG vaccination inclusion in the national immunization program when testing is not taken into consideration. However, this relationship vanishes when we add the dimension of testing. We observe that case and death incidences conditional on testing do not get affected by the countries BCG vaccination inclusion in the national immunization program. Therefore, we show that there is no statistical evidence to support the assertion that inclusion of BCG vaccination in national immunization program (NIP) has any impact of COVID 19 infections (cases) or mortality.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Shivendu Shivendu", + "author_inst": "University fo South Florida" + }, + { + "author_name": "Saurav Chakraborty", + "author_inst": "University of Louisville" + }, + { + "author_name": "Agnieszka Onuchowska", + "author_inst": "University of South Florida" + }, + { + "author_name": "Arpit Srivastava", + "author_inst": "University of South Florida" + }, + { + "author_name": "Ankita Patidar", + "author_inst": "University of South Florida" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.18.20071134", "rel_title": "Cluster of COVID-19 in northern France: A retrospective closed cohort study", @@ -1532131,77 +1534860,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.17.20061242", - "rel_title": "Distinguishing COVID-19 from influenza pneumonia in the early stage through CT imaging and clinical features", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20061242", - "rel_abs": "PurposeTo identify differences in CT imaging and clinical features between COVID-19 and influenza pneumonia in the early stage, and to identify the most valuable features in the differential diagnosis.\n\nMaterials and MethodA consecutive cohort of 73 COVID-19 and 48 influenza pneumonia patients were retrospectively recruited from five independent institutions. The courses of both diseases were confirmed to be in the early stages (2.66 {+/-} 2.62 days for COVID-19 and 2.19 {+/-} 2.10 days for influenza pneumonia after onset). The chi-square test, students t-test, and Kruskal-Wallis H-test were performed to compare CT imaging and clinical features between the two groups. Spearman or Kendall correlation tests between feature metrics and diagnosis outcomes were also assessed. The diagnostic performance of each feature in differentiating COVID-19 from influenza pneumonia was evaluated with univariate analysis. The corresponding area under the curve (AUC), accuracy, specificity, sensitivity and threshold were reported.\n\nResultsThe ground-glass opacification (GGO) was the most common imaging feature in COVID-19, including pure-GGO (75.3%) and mixed-GGO (78.1%), mainly in peripheral distribution. For clinical features, most COVID-19 patients presented normal white blood cell (WBC) count (89.04%) and neutrophil count (84.93%). Twenty imaging features and 6 clinical features were identified to be significantly different between the two diseases. The diagnosis outcomes correlated significantly with the WBC count (r=-0.526, P<0.001) and neutrophil count (r=-0.500, P<0.001). Four CT imaging features had absolute correlations coefficients higher than 0.300 (P<0.001), including crazy-paving pattern, mixed-GGO in peripheral area, pleural effusions, and consolidation.\n\nConclusionsAmong a total of 1537 lesions and 62 imaging and clinical features, 26 features were demonstrated to be significantly different between COVID-19 and influenza pneumonia. The crazy-paving pattern was recognized as the most powerful imaging feature for the differential diagnosis in the early stage, while WBC count yielded the highest diagnostic efficacy in clinical manifestations.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Zhiqi Yang", - "author_inst": "Department of Radiology, Meizhou People`s Hospital, Guangdong, 514031, P. R. China." - }, - { - "author_name": "Daiying Lin", - "author_inst": "Department of Radiology, Shantou Central Hospital, Shantou, Guangdong, 515041, P. R. China." - }, - { - "author_name": "Xiaofeng Chen", - "author_inst": "Department of Radiology, Meizhou People`s Hospital, Guangdong, 514031, P. R. China" - }, - { - "author_name": "Jinming Qiu", - "author_inst": "Department of Radiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, 515000, P. R. China" - }, - { - "author_name": "Shengkai Li", - "author_inst": "Department of Radiology, Huizhou Municipal Central Hospital, Huizhou, Guangdong 516001, China." - }, - { - "author_name": "Ruibin Huang", - "author_inst": "Department of Radiology, First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, 515041, P. R. China." - }, - { - "author_name": "Hongfu Sun", - "author_inst": "School of Information Technology and Electrical Engineering, University of Queensland, Queensland, 4072, Australia." - }, - { - "author_name": "Yuting Liao", - "author_inst": "GE Healthcare, Guangzhou 510623, China." - }, - { - "author_name": "Jianning Xiao", - "author_inst": "Department of Radiology, Shantou Central Hospital, Shantou, Guangdong, 515041, P. R. China." - }, - { - "author_name": "Yanyan Tang", - "author_inst": "Department of Radiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, 515000, P. R. China" - }, - { - "author_name": "Guorui Liu", - "author_inst": "Department of Radiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, 515000, P. R. China" - }, - { - "author_name": "Renhua Wu", - "author_inst": "Department of Radiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, 515000, P. R. China" - }, - { - "author_name": "Xiangguang Chen", - "author_inst": "Department of Radiology, Meizhou People`s Hospital, Guangdong, 514031, P. R. China." - }, - { - "author_name": "Zhuozhi Dai", - "author_inst": "Second Affiliated Hospital of Shantou University Medical College" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.04.17.20064469", "rel_title": "Effectiveness and Safety of Glucocorticoids to Treat COVID-19: A Rapid Review and Meta-Analysis", @@ -1532390,6 +1535048,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.16.20067751", + "rel_title": "Estimates of COVID-19 case-fatality risk from individual-level data", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20067751", + "rel_abs": "When calculated from aggregate data on confirmed cases and deaths, the case-fatality risk (CFR) is a simple ratio between the former and the latter, which is prone to numerous biases. With individual-level data, the CFR can be estimated as a true measure of risk as the proportion of incidence for the disease. We present the first estimates of the CFR for COVID-19 by age and sex based on event history modelling of the risk of dying among confirmed positive individuals in the Canadian province of Ontario, which maintains one of the few individual-level datasets on COVID-19 in the world.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Simona Bignami", + "author_inst": "Universite de Montreal" + }, + { + "author_name": "Daniela Ghio", + "author_inst": "Joint Research Center European Commission" + }, + { + "author_name": "Ari Van Assche", + "author_inst": "HEC Montreal" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.16.20067587", "rel_title": "Impact of blood analysis and immune function on the prognosis of patients with COVID-19", @@ -1533669,65 +1536354,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.17.20068460", - "rel_title": "CAN-NPI: A Curated Open Dataset of Canadian Non-Pharmaceutical Interventions in Response to the Global COVID-19 Pandemic", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20068460", - "rel_abs": "Non-pharmaceutical interventions (NPIs) have been the primary tool used by governments and organizations to mitigate the spread of the ongoing pandemic of COVID-19. Natural experiments are currently being conducted on the impact of these interventions, but most of these occur at the subnational level - data not available in early global datasets. We describe the rapid development of the first comprehensive, labelled dataset of 1640 NPIs implemented at federal, provincial/territorial and municipal levels in Canada to guide COVID-19 research. For each intervention, we provide: a) information on timing to aid in longitudinal evaluation, b) location to allow for robust spatial analyses, and c) classification based on intervention type and target population, including classification aligned with a previously developed measure of government response stringency. This initial dataset release (v1.0) spans January 1st, and March 31st, 2020; bi-weekly data updates to continue for the duration of the pandemic. This novel dataset enables robust, inter-jurisdictional comparisons of pandemic response, can serve as a model for other jurisdictions and can be linked with other information about case counts, transmission dynamics, health care utilization, mobility data and economic indicators to derive important insights regarding NPI impact.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Liam G McCoy", - "author_inst": "Faculty of Medicine, University of Toronto; Institute of Health Policy, Management and Evaluation, University of Toronto" - }, - { - "author_name": "Jonathan Smith", - "author_inst": "Layer 6 AI" - }, - { - "author_name": "Kavya Anchuri", - "author_inst": "Cumming School of Medicine, University of Calgary" - }, - { - "author_name": "Isha Berry", - "author_inst": "Dalla Lana School of Public Health, University of Toronto" - }, - { - "author_name": "Joanna Pineda", - "author_inst": "Department of Computer Science, University of Toronto; Ontario Institute for Cancer Research" - }, - { - "author_name": "Vinyas Harish", - "author_inst": "Faculty of Medicine, University of Toronto; Institute of Health Policy, Management and Evaluation, University of Toronto" - }, - { - "author_name": "Andrew T Lam", - "author_inst": "Faculty of Medicine, University of Toronto" - }, - { - "author_name": "Seung Eun Yi", - "author_inst": "Layer 6 AI" - }, - { - "author_name": "Sophie Hu", - "author_inst": "Cumming School of Medicine, University of Calgary" - }, - { - "author_name": "Canadian Open Data Working Group: Non-Pharmaceutical Interventions", - "author_inst": "" - }, - { - "author_name": "Benjamin Fine", - "author_inst": "Institute for Better Health, Trillium Health Partners; Department of Medical Imaging, University of Toronto" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.17.20070052", "rel_title": "Surveying Tenants of Permanent Supportive Housing in Skid Row about COVID-19", @@ -1533856,6 +1536482,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2020.04.17.20070094", + "rel_title": "COVID-19 Outbreak Prediction with Machine Learning", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20070094", + "rel_abs": "Several outbreak prediction models for COVID-19 are being used by officials around the world to make informed-decisions and enforce relevant control measures. Among the standard models for COVID-19 global pandemic prediction, simple epidemiological and statistical models have received more attention by authorities, and they are popular in the media. Due to a high level of uncertainty and lack of essential data, standard models have shown low accuracy for long-term prediction. Although the literature includes several attempts to address this issue, the essential generalization and robustness abilities of existing models needs to be improved. This paper presents a comparative analysis of machine learning and soft computing models to predict the COVID-19 outbreak. Among a wide range of machine learning models investigated, two models showed promising results (i.e., multi-layered perceptron, MLP, and adaptive network-based fuzzy inference system, ANFIS). Based on the results reported here, and due to the highly complex nature of the COVID-19 outbreak and variation in its behavior from nation-to-nation, this study suggests machine learning as an effective tool to model the outbreak.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sina F. Ardabili", + "author_inst": "Thuringian Institute of Sustainability and Climate Protection, 07743 Jena, Germany" + }, + { + "author_name": "Amir MOSAVI", + "author_inst": "Obuda University" + }, + { + "author_name": "Pedram Ghamisi", + "author_inst": "Machine Learning Group, Exploration Division, Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden" + }, + { + "author_name": "Filip Ferdinand", + "author_inst": "Department of Mathematics and Informatics, J. Selye University, 94501 Komarno, Slovakia" + }, + { + "author_name": "Annamaria R. Varkonyi-Koczy", + "author_inst": "Department of Mathematics and Informatics, J. Selye University, 94501 Komarno, Slovakia" + }, + { + "author_name": "Uwe Reuter", + "author_inst": "Faculty of Civil Engineering, Technische University Dresden" + }, + { + "author_name": "Timon Rabczuk", + "author_inst": "Institute of Structural Mechanics (ISM), Bauhaus-University Weimar, 99423 Weimar, Germany" + }, + { + "author_name": "Peter M. Atkinson", + "author_inst": "Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.04.17.20070086", "rel_title": "Estimating the impact of COVID-19 control measures using a Bayesian model of physical distancing", @@ -1535095,117 +1537768,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.19.048751", - "rel_title": "REVEALING COVID-19 TRANSMISSION BY SARS-CoV-2 GENOME SEQUENCING AND AGENT BASED MODELLING", - "rel_date": "2020-04-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.19.048751", - "rel_abs": "Community transmission of the new coronavirus SARS-CoV-2 is a major public health concern that remains difficult to assess. We present a genomic survey of SARS-CoV-2 from a during the first 10 weeks of COVID-19 activity in New South Wales, Australia. Transmission events were monitored prospectively during the critical period of implementation of national control measures. SARS-CoV-2 genomes were sequenced from 209 patients diagnosed with COVID-19 infection between January and March 2020. Only a quarter of cases appeared to be locally acquired and genomic-based estimates of local transmission rates were concordant with predictions from a computational agent-based model. This convergent assessment indicates that genome sequencing provides key information to inform public health action and has improved our understanding of the COVID-19 evolution from outbreak to epidemic.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Rebecca J Rockett", - "author_inst": "University of Sydney" - }, - { - "author_name": "Alicia Arnott", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Connie Lam", - "author_inst": "Westmead Hospital" - }, - { - "author_name": "Rosemarie Sadsad", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Verlaine Timms", - "author_inst": "Westmead Hospital" - }, - { - "author_name": "Karen-Ann Gray", - "author_inst": "Westmead Hospital" - }, - { - "author_name": "John-Sebastian Eden", - "author_inst": "University of Sydney" - }, - { - "author_name": "Sheryl Le Chang", - "author_inst": "University of Sydney" - }, - { - "author_name": "Mailie Gall", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Jenny Draper", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Eby Sim", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Nathan L Bachmann", - "author_inst": "Westmead Hospital" - }, - { - "author_name": "Ian Carter", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Kerri Basile", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Roy Byun", - "author_inst": "NSW Ministry of Health" - }, - { - "author_name": "Matthew V O Sullivan", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Sharon C-A Chen", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Susan Maddocks", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Tania C Sorrell", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Dominic E Dwyer", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Edward C Holmes", - "author_inst": "University of Sydney" - }, - { - "author_name": "Jen Kok", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Mikhail Prokopenko", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Vitali Sintchenko", - "author_inst": "The University of Sydney" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.04.16.20067835", "rel_title": "Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs", @@ -1535558,6 +1538120,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.16.20068312", + "rel_title": "COVID-19 Outbreak Situations in Bangladesh: An Empirical Analysis", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20068312", + "rel_abs": "COVID-19 disease, as popularly known as Coronavirus 2019 disease, has been emerged from Wuhan, China in December 2019 and now is a pandemic for almost every nation in the earth. It affects every country without considering countrys race, nationality and economic status. This paper aims at analysing primarily the current situations of Bangladesh and predicting infections and deaths for moderated term intervals by a proposed projection technique called Infection Trajectory-Pathway Strategy (ITPS) and for short term intervals prediction for total infections, deaths along with total number of severe patients and Intensive Care Unit (ICU) patients by polynomial regression modeling approach. Since April 7, Bangladesh has started to face critical situations as the number of infections has accelerated very fast in the following days. However, the fatality rate decreases considerably from 15.7 on April 1 to 4.9 on April 14, which is still high among the south asian countries. Of the 1012 cases reported on April 14, almost 70% are the male, 42% are from the capital Dhaka. We have found that the potential pathway of infections for Bangldesh would be the similar pathways that are experienced by Austria, Netherlands, Israel, France and United Kingdom. These countries are ahead a number of weeks and days in terms of infection cases since their 100-th confirmed cases. Our proposed projection method ITPS suggests that by May 10, Bangladesh will cross 12000 incidences and 720 deaths which, by May 16 will be 27000 and 1644 respectively. On the other hand, the regression model suggests that by the end of April, total number of infections, deaths, severe patients and ICU patients will be 5780, 347, 775, and 694 respectively. This study will be favorable for the administrative units of Bangladesh to plan for the next few weeks and to consider various aspects related to the control of COVID-19 outspread in Bangladesh.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Md Hasinur Rahaman Khan", + "author_inst": "University of Dhaka, Bangladesh" + }, + { + "author_name": "Ahmed Hossain", + "author_inst": "North South University, Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.16.20068213", "rel_title": "Coronavirus Disease (COVID-19) Pandemic: An Overview of Systematic Reviews", @@ -1536669,53 +1539254,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.19.20071597", - "rel_title": "COVID-19 outbreak in Wuhan demonstrates the limitations of publicly available case numbers for epidemiological modelling.", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071597", - "rel_abs": "Epidemiological models are widely used to analyse the spread of diseases such as the global COVID-19 pandemic caused by SARS-CoV-2. However, all models are based on simplifying assumptions and on sparse data. This limits the reliability of parameter estimates and predictions.\n\nIn this manuscript, we demonstrate the relevance of these limitations by performing a study of the COVID-19 outbreak in Wuhan, China. We perform parameter estimation, uncertainty analysis and model selection for a range of established epidemiological models. Amongst others, we employ Markov chain Monte Carlo sampling, parameter and prediction profile calculation algorithms.\n\nOur results show that parameter estimates and predictions obtained for several established models on the basis of reported case numbers can be subject to substantial uncertainty. More importantly, estimates were often unrealistic and the confidence / credibility intervals did not cover plausible values of critical parameters obtained using different approaches. These findings suggest, amongst others, that several models are oversimplistic and that the reported case numbers provide often insufficient information.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Elba Raim\u00fandez", - "author_inst": "University of Bonn" - }, - { - "author_name": "Erika Dudkin", - "author_inst": "University of Bonn" - }, - { - "author_name": "Jakob Vanhoefer", - "author_inst": "University of Bonn" - }, - { - "author_name": "Emad Alamoudi", - "author_inst": "University of Bonn" - }, - { - "author_name": "Simon Merkt", - "author_inst": "University of Bonn" - }, - { - "author_name": "Lara Fuhrmann", - "author_inst": "University of Bonn" - }, - { - "author_name": "Fan Bai", - "author_inst": "University of Bonn" - }, - { - "author_name": "Jan Hasenauer", - "author_inst": "University of Bonn, Technische Universitaet Muenchen and Helmholtz Zentrum Muenchen" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.19.20071852", "rel_title": "A Bayesian analysis of the total number of cases of the COVID 19 when only a few data is available. A case study in the state of Goias, Brazil", @@ -1536844,6 +1539382,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.17.20070292", + "rel_title": "COVID-19 Epidemic Dynamics and Population Projections from Early Days of Case Reporting in a 40 million population from Southern India", + "rel_date": "2020-04-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20070292", + "rel_abs": "India reported its first COVID19 case on 30 January 2020. Since then the epidemic has taken different trajectories across different geographical locations in the country. This study explores the population aggregated trajectories of COVID19 susceptible, infected and recovered or dead cases in the south Indian state of Telangana with a population of approximately 40 million. Information on cases reported from March 2 to April 4 was collated from government records. The susceptible-infected-removed (SIR) model for the spread of an infectious disease was used. Transmission parameters were extracted from existing literature that has emerged over past weeks from other regions with similar population densities as Telangana. Optimisation algorithms were used to get basic reproduction rate for different phases of nonpharmaceutical interventions rolled by the government. Peak accumulation is projected towards end of July with 36% of the population being infected by August 2020 if the population lockdown or social distancing mechanism is not continued. The number of deaths assuming no intervention is projected to be 488000 (95% CI: (329400, 646600)). A draconian enforcement of population lockdown combined with hand and face hygiene adherence would reduce the transmission by at least 99.7% whereas partial social distancing and hygiene would reduce it by 51.2%. Transmission parameters reported should be interpreted with caution as they are population aggregated and do not consider unique characteristics of susceptibility among micro-clusters and vulnerable individuals. More data will need to be collected to optimize transmission parameters and evaluate the full complexity, to simulate real world scenarios in the models.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Rashmi Pant", + "author_inst": "Society for Health Allied Research and Education (SHARE-INDIA)" + }, + { + "author_name": "Lincoln Priyadarshi Choudhry", + "author_inst": "Krashapana consultancy private limited" + }, + { + "author_name": "Jammy Guru Rajesh", + "author_inst": "Society for Health Allied Research and Education (SHARE-INDIA)" + }, + { + "author_name": "Vijay V Yeldandi", + "author_inst": "Society for Health Allied Research and Education (SHARE-INDIA)" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.17.20070318", "rel_title": "Effects of medical resource capacities and intensities of public mitigation measures on outcomes of COVID-19 outbreaks", @@ -1538139,101 +1540708,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.16.20067231", - "rel_title": "Development and Multicenter Performance Evaluation of The First Fully Automated SARS-CoV-2 IgM and IgG Immunoassays", - "rel_date": "2020-04-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20067231", - "rel_abs": "BACKGROUNDThe outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread globally. The laboratory diagnosis of SARS-CoV-2 infection has relied on nucleic acid tests. However, there are many limitations of nucleic acid tests, including low throughput and high rates of false negatives. More sensitive and accurate tests to effectively identify infected patients are needed.\n\nMETHODSThis study has developed fully automated chemiluminescent immunoassays (CLIA) to determine IgM and IgG antibodies to SARS-CoV-2 in human serum. The assay performance has been evaluated at 10 hospitals. Clinical specificity was evaluated by measuring 972 hospitalized patients with diseases other than COVID-19, and 586 donors of a normal population. Clinical sensitivity was assessed on 503 confirmed cases of SARS-CoV-2 by RT-PCR and 52 suspected cases.\n\nRESULTSThe assays demonstrated satisfied assay precision with coefficient of variation (CV) of less than 4.45%. Inactivation of specimen does not affect assay measurement. SARS-CoV-2 IgM shows clinical specificity of 97.33% and 99.49% for hospitalized patients and normal population respectively. SARS-CoV-2 IgG shows clinical specificity of 97.43% and 99.15% for the hospitalized patients and the normal population respectively. SARS-CoV-2 IgM and IgG show clinical sensitivity of 85.88% and 96.62% respectively for confirmed SARS-Cov-2 infection with RT-PCR, of 73.08% and 86.54% respectively for suspected cases.\n\nCONCLUSIONSwe have developed fully automated immunoassays for detecting SARS-CoV-2 IgM and IgG antibodies in human serum. The assays demonstrated high clinical specificity and sensitivity, and add great value to nucleic acid testing in fighting against the global pandemic of the SARS-CoV-2 infection.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Chungen Qian", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Mi Zhou", - "author_inst": "Shenzhen YHLO Biotech Co., Ltd" - }, - { - "author_name": "Fangming Cheng", - "author_inst": "Shenzhen YHLO Biotech Co., Ltd" - }, - { - "author_name": "Xiaotao Lin", - "author_inst": "Shenzhen YHLO Biotech Co., Ltd" - }, - { - "author_name": "Yijun Gong", - "author_inst": "Shenzhen YHLO Biotech Co., Ltd" - }, - { - "author_name": "Xiaobing Xie", - "author_inst": "the First Affiliated Hospital of Hunan University of Chinese Medicine" - }, - { - "author_name": "Ping Li", - "author_inst": "the First Affiliated Hospital of Hunan University of Chinese Medicine" - }, - { - "author_name": "Zhiyong Li", - "author_inst": "the First Affiliated Hospital of Xiamen University" - }, - { - "author_name": "Pingan Zhang", - "author_inst": "Renmin Hospital of Wuhan University" - }, - { - "author_name": "Zejin Liu", - "author_inst": "Wuhan Asia General Hospital" - }, - { - "author_name": "Fang Hu", - "author_inst": "Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University)" - }, - { - "author_name": "Yun Wang", - "author_inst": "TongJi Hospital, TongJi Medical college, HUST" - }, - { - "author_name": "Quan Li", - "author_inst": "Changshou Peoples Hospital" - }, - { - "author_name": "Yan Zhu", - "author_inst": "Shenzhen Maternity & Child Healthcare Hospital" - }, - { - "author_name": "Guikai Duan", - "author_inst": "Shenzhen Maternity & Child Healthcare Hospital" - }, - { - "author_name": "Yinting Xing", - "author_inst": "The First Affiliated Hospital of Harbin Medical University" - }, - { - "author_name": "Huanyu Song", - "author_inst": "The First Affiliated Hospital of Harbin Medical University" - }, - { - "author_name": "Wenfang Xu", - "author_inst": "Affiliated Hospital of Shaoxing University" - }, - { - "author_name": "Bi-Feng Liu", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Fuzhen Xia", - "author_inst": "Reagent R&D Center, Shenzhen YHLO Biotech Co., Ltd" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.16.20066159", "rel_title": "Susceptibility and Sustainability of India against CoVid19: a multivariate approach", @@ -1538378,6 +1540852,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.17.20058545", + "rel_title": "Histopathology and Ultrastructural Findings of Fatal COVID-19 Infections", + "rel_date": "2020-04-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20058545", + "rel_abs": "BackgroundSARS-CoV-2 is the cause of an ongoing pandemic with a projected 100,000 to 240,000 U.S. deaths. To date, documentation of histopathologic features in fatal cases of COVID-19 has been limited due to small sample size and incomplete organ sampling.\n\nMethodsPost-mortem examinations were performed on 12 fatal COVID-19 cases in Washington State during February-March 2020. Clinical and laboratory data were reviewed. Tissue examination of all major organs was performed by light microscopy and electron microscopy. The presence of viral RNA in sampled tissues was tested by RT-PCR.\n\nResultsAll 12 patients were older with significant preexisting comorbidities. The major pulmonary finding was diffuse alveolar damage in the acute and/or organizing phases with virus identified in type I and II pneumocytes by electron microscopy. The kidney demonstrated viral particles in the tubular epithelium, endothelium, and podocytes without significant inflammation. Viral particles were also observed in the trachea and large intestines. SARS-CoV-2 RNA was detected in the cardiac tissue of a patient with lymphocytic myocarditis. RT-PCR also detected viral RNA in the subcarinal lymph nodes, liver, spleen, and large intestines.\n\nConclusionSARS-CoV-2 represents the third novel coronavirus to cause widespread human disease since 2002. Similar to SARS and MERS, the primary pathology was diffuse alveolar damage with virus located in the pneumocytes. However, other major organs including the heart and kidneys may be susceptible to viral replication and damage leading to increased mortality in those with disseminated disease. Understanding the pathology of SARS-CoV-2 will be essential to design effective therapies.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Benjamin T Bradley", + "author_inst": "University of Washington" + }, + { + "author_name": "Heather Maioli", + "author_inst": "University of Washington, Seattle, WA" + }, + { + "author_name": "Robert Johnston", + "author_inst": "King County Medical Examiner's Office, Seattle, WA" + }, + { + "author_name": "Irfan Chaudhry", + "author_inst": "King County Medical Examiner's Office, Seattle, WA" + }, + { + "author_name": "Susan L. Fink", + "author_inst": "University of Washington, Seattle, WA" + }, + { + "author_name": "Haodong Xu", + "author_inst": "University of Washington, Seattle, WA" + }, + { + "author_name": "Behzad Najafian", + "author_inst": "University of Washington, Seattle, WA" + }, + { + "author_name": "Desiree Marshall", + "author_inst": "University of Washington, Seattle, WA" + }, + { + "author_name": "J. Matthew Lacy", + "author_inst": "Snohomish County Medical Examiner's Office, Everett, WA" + }, + { + "author_name": "Timothy Williams", + "author_inst": "King County Medical Examiner's Office" + }, + { + "author_name": "Nicole Yarid", + "author_inst": "King County Medical Examiner's Office" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.04.15.20066266", "rel_title": "A Randomized, Single-blind, Group sequential, Active-controlled Study to evaluate the clinical efficacy and safety of \u03b1-Lipoic acid for critically ill patients with coronavirus disease 2019(COVID-19)", @@ -1540217,37 +1542750,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.04.15.20066894", - "rel_title": "Knowledge and practice of preventive measures against COVID-19 infection among pregnant women in a low-resource African setting", - "rel_date": "2020-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20066894", - "rel_abs": "BackgroundCoronavirus disease pandemic has resulted in death of thousands of people across several countries. Several preventive measures have been recommended to halt the spread of the disease and its associated mortality. However, the level knowledge and practice of these preventive measures against COVID-19 infection among pregnant women, which constitute vulnerable groups, are yet to be evaluated.\n\nAimTo determine the knowledge and practice of preventive measures against COVID-19 infection among pregnant women in Abakaliki.\n\nMaterials and MethodsThis was a self-administered questionnaire-based cross-sectional study conducted from February 1, 2020 to March 31, 2020 among 284 antenatal clinic attendees at Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State. A pretested and validated questionnaire was used to collect the data. Data analysis was done using SPSS version 22.\n\nResultsOf 284 participants, 60.9% (n=173) had adequate knowledge of the preventive measures against COVID-19 infection. However, the overall practice of these preventive measures among the participants were poor as 69.7% of the participants were not practicing the preventive measures against the coronavirus. The determinants of poor practice of the preventive measures among the participants were being in age group 31-40 years (AOR=2.04, 95%CI: 1.26 - 5.37, p=0.022), married (AOR=2.99, 95%CI: 1.40 - 6.33, p=0.035) grandmultiparous (AOR=3.11, 95%CI: 1.32 - 6.56, p=0.021), residing in rural area (AOR=2.08, 95%CI: 1.32 - 4.05, p=0.031), and having no formal education (AOR=6.73, 95%CI: 2.66 - 18.34, p=0.002).\n\nConclusionThe study showed that most of the participants had adequate knowledge of preventive measures against COVID-19 infection but the practice of these preventive measures were poor among the participants.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Johnbosco Ifunanya Nwafor", - "author_inst": "Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria" - }, - { - "author_name": "Joseph Kenechi Aniukwu", - "author_inst": "Emergency Department, Qatif Central Hospital, Kingdom of Saudi Arabia" - }, - { - "author_name": "Bonaventure Okechukwu Anozie", - "author_inst": "Department of Obstetrics and Gynaecology, Alex Ekwueme Federal University Teaching Hospital, Abakaliki" - }, - { - "author_name": "Arinze Chidiebere Ikeotuonye", - "author_inst": "Department of Obstetrics and Gynaecology, Alex Ekwueme Federal University Teaching Hospital, Abakaliki." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2020.04.15.20067066", "rel_title": "Estimating SARS-CoV-2 seroprevalence and epidemiological parameters with uncertainty from serological surveys", @@ -1540648,6 +1543150,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.15.20066712", + "rel_title": "COVID-19 outbreak in Greece has passed its rising inflection point and stepping into its peak", + "rel_date": "2020-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20066712", + "rel_abs": "Since the beginning of 2020, COVID-19 is the most urgent and challenging task for the international scientific community, in order to identify its behaviour, track its progress and plan effective mitigation policies. In this study, Greece is the main focus for assessing the national outbreak and estimating the general trends and outlook of it. Multiple data analytics procedures, spectral decomposition and curve-fitting formulations are developed based on the data available at hand. Standard SIEQRDP epidemic modelling is applied for Greece and for the general region around it, providing hints for the outbreak progression in the mid- and long-term, for various infections under-reporting rates. The overall short-term outlook for Greece seems to be towards positive, with a downward trend in infections rate daily increase (i.e., now beyond the exponential growth rate), a possible peak within a few days beyond April 14th, as well as the high availability level of ICU w.r.t. expected demand at peak. On the negative side, the fade-out period seems to be in the order of several months, with high probability of recurrent surges of the outbreak. The mitigation policies for the next day should be focused on close tracking of the epidemic via large-scale tests, strict border checking in international travelling and an adaptive plan for selective activation of mitigation measures when deemed necessary.\n\nSignificance StatementThis study focuses on the COVID-19 outbreak in Greece and provides data-driven epidemic modelling and experimental results regarding the current state. Based on these results, the overall short-term outlook for Greece seems to be towards positive, having recently passed the rising inflection point and approaching the peak of the infections, and most probably capable of covering the projected ICU demand peak by a large margin. On the downside, the fade-out period seems to be in the order of several months, with high probability of recurrent surges of the outbreak. The next day mitigation policies need to be carefully planned, highly adaptive and based on close tracking of the outbreak via large-scale testing in the general population.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Harris V Georgiou", + "author_inst": "University of Piraeus" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.15.20064980", "rel_title": "Crowding and the epidemic intensity of COVID-19 transmission", @@ -1541923,97 +1544444,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.16.045302", - "rel_title": "Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates", - "rel_date": "2020-04-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.16.045302", - "rel_abs": "The novel coronavirus SARS-CoV-2 is the cause of Coronavirus Disease-2019 (COVID-19). The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of 410 vertebrates, including 252 mammals, to study cross-species conservation of ACE2 and its likelihood to function as a SARS-CoV-2 receptor. We designed a five-category ranking score based on the conservation properties of 25 amino acids important for the binding between receptor and virus, classifying all species from very high to very low. Only mammals fell into the medium to very high categories, and only catarrhine primates in the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 binding, and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (<0.1%) variants in 10/25 binding sites. In addition, we observed evidence of positive selection in ACE2 in multiple species, including bats. Utilized appropriately, our results may lead to the identification of intermediate host species for SARS-CoV-2, justify the selection of animal models of COVID-19, and assist the conservation of animals both in native habitats and in human care.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Joana Damas", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Graham M. Hughes", - "author_inst": "University College Dublin, Ireland" - }, - { - "author_name": "Kathleen C. Keough", - "author_inst": "University of California San Francisco, USA; Gladstone Institute of Data Science and Biotechnology, USA" - }, - { - "author_name": "Corrie A. Painter", - "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA" - }, - { - "author_name": "Nicole S. Persky", - "author_inst": "Broad Institute of MIT and Harvard, USA" - }, - { - "author_name": "Marco Corbo", - "author_inst": "University of California Davis, USA" - }, - { - "author_name": "Michael Hiller", - "author_inst": "Max Planck Institute of Molecular Cell Biology and Genetics, Germany; Max Planck Institute for the Physics of Complex Systems, Germany; Center for Systems Biolo" - }, - { - "author_name": "Klaus-Peter Koepfli", - "author_inst": "Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, USA" - }, - { - "author_name": "Andreas R. Pfenning", - "author_inst": "Carnegie Mellon University, USA" - }, - { - "author_name": "Huabin Zhao", - "author_inst": "Wuhan University, China" - }, - { - "author_name": "Diane P. Genereux", - "author_inst": "Broad Institute of MIT and Harvard, USA" - }, - { - "author_name": "Ross Swofford", - "author_inst": "Broad Institute of MIT and Harvard, USA" - }, - { - "author_name": "Katherine S. Pollard", - "author_inst": "University of California San Francisco, USA; Gladstone Institute of Data Science and Biotechnology, USA; Chan Zuckerberg Biohub, USA" - }, - { - "author_name": "Oliver A. Ryder", - "author_inst": "San Diego Zoo Institute for Conservation Research, USA; University of California San Diego, USA" - }, - { - "author_name": "Martin T. Nweeia", - "author_inst": "Harvard School of Dental Medicine, USA; Case Western Reserve University School of Dental Medicine, USA; Smithsonian Institution, USA" - }, - { - "author_name": "Kerstin Lindblad-Toh", - "author_inst": "Broad Institute of MIT and Harvard, USA; Uppsala University, Sweden" - }, - { - "author_name": "Emma C. Teeling", - "author_inst": "University College Dublin, Ireland" - }, - { - "author_name": "Elinor K. Karlsson", - "author_inst": "Broad Institute of MIT and Harvard, USA; University of Massachusetts Medical School, USA" - }, - { - "author_name": "Harris A. Lewin", - "author_inst": "University of California Davis, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.04.16.045419", "rel_title": "Synthetic nanobodies targeting the SARS-CoV-2 receptor-binding domain", @@ -1542246,6 +1544676,53 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2020.04.17.045161", + "rel_title": "An in silico map of the SARS-CoV-2 RNA Structurome", + "rel_date": "2020-04-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.17.045161", + "rel_abs": "SARS-CoV-2 is a positive-sense single-stranded RNA virus that has exploded throughout the global human population. This pandemic coronavirus strain has taken scientists and public health researchers by surprise and knowledge of its basic biology (e.g. structure/function relationships in its genomic, messenger and template RNAs) and modes for therapeutic intervention lag behind that of other human pathogens. In this report we used a recently-developed bioinformatics approach, ScanFold, to deduce the RNA structural landscape of the SARS-CoV-2 transcriptome. We recapitulate known elements of RNA structure and provide a model for the folding of an essential frameshift signal. Our results find that the SARS-CoV-2 is greatly enriched in unusually stable and likely evolutionarily ordered RNA structure, which provides a huge reservoir of potential drug targets for RNA-binding small molecules. Our results also predict regions that are accessible for intermolecular interactions, which can aid in the design of antisense therapeutics. All results are made available via a public database (the RNAStructuromeDB) where they may hopefully drive drug discovery efforts to inhibit SARS-CoV-2 pathogenesis.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Ryan J Andrews", + "author_inst": "Iowa State University" + }, + { + "author_name": "Jake M Peterson", + "author_inst": "Iowa State University" + }, + { + "author_name": "Hafeez F Haniff", + "author_inst": "Scripps Florida" + }, + { + "author_name": "Jonathan Chen", + "author_inst": "Scripps Florida" + }, + { + "author_name": "Cristopher Williams", + "author_inst": "Scripps Florida" + }, + { + "author_name": "Maison Greffe", + "author_inst": "Scripps Florida" + }, + { + "author_name": "Matthew D Disney", + "author_inst": "Scripps Florida" + }, + { + "author_name": "Walter N Moss", + "author_inst": "Iowa State University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.04.17.047548", "rel_title": "Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets", @@ -1543781,53 +1546258,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.04.15.20065623", - "rel_title": "Neutralizing Antibodies Responses to SARS-CoV-2 in COVID-19 Inpatients and Convalescent Patients", - "rel_date": "2020-04-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20065623", - "rel_abs": "BackgroundCOVID-19 is a pandemic with no specific antiviral treatments or vaccines. The urgent needs for exploring the neutralizing antibodies from patients with different clinical characteristics are emerging.\n\nMethodsA total of 117 blood samples were collected from 70 COVID-19 inpatients and convalescent patients. The presence of neutralizing antibody was determined with a modified cytopathogenic assay based on live SARS-CoV-2. The dynamics of neutralizing antibody levels at different with different clinical characteristics were analyzed.\n\nResultsThe seropositivity rate reached up to 100.0% within 20 days since onset, and remained 100.0% till day 41-53. The total GMT was 1:163.7 (95% CI, 128.5 to 208.6), and the antibody level was highest during day 31-40 since onset, and then decreased slightly. Individual differences in changes of antibody levels were observed among 8 representative convalescent patients. In multivariate GEE analysis, patients at age of 31-60 and 61-84 had a higher antibody level than those at age of 16-30 ({beta}=1.0518, P=0.0152; {beta}=1.3718, P=0.0020). Patients with a worse clinical classification had a higher antibody titer ({beta}=0.4639, P=0.0227).\n\nConclusionsThe neutralizing antibodies were detected even at the early stage of disease, and a significant response showed in convalescent patients. Moreover, changes on antibody levels ware individual specific.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Xiaoli Wang", - "author_inst": "Beijing Center for Disease Prevention and Control, Beijing, China;School of Public Health, Capital Medical University, Beijing, China" - }, - { - "author_name": "Xianghua Guo", - "author_inst": "Beijing YouAn hospital, Capital Medical University, Beijing, China" - }, - { - "author_name": "Qianqian Xin", - "author_inst": "Sinovac Biotech Co., Ltd., Beijing, China" - }, - { - "author_name": "Yang Pan", - "author_inst": "Beijing Center for Disease Prevention and Control, Beijing, China;School of Public Health, Capital Medical University, Beijing, China" - }, - { - "author_name": "Jing Li", - "author_inst": "Sinovac Biotech Co., Ltd., Beijing, China" - }, - { - "author_name": "Yanhui Chu", - "author_inst": "Xicheng District Center for Disease Prevention and Control, Beijing, China" - }, - { - "author_name": "Yingmei Feng", - "author_inst": "Beijing YouAn hospital, Capital Medical University, Beijing, China" - }, - { - "author_name": "Quanyi Wang", - "author_inst": "Beijing Center for Disease Prevention and Control, Beijing, China;School of Public Health, Capital Medical University, Beijing, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.15.20065425", "rel_title": "A consideration of publication-derived immune-related associations in Coronavirus and related lung damaging diseases", @@ -1543992,6 +1546422,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.15.20066548", + "rel_title": "Social Isolation as a predictor for mortality: Implications for COVID-19 prognosis", + "rel_date": "2020-04-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20066548", + "rel_abs": "The health benefits of social support have been widely documented. However, the social distancing practices from the COVID-19 pandemic is causing social disruption on a grand scale, potentially causing poor health outcomes. Through Google Trends analysis, we found a COVID-19-related surge in interest surrounding \"loneliness.\" We assessed if social isolation and loneliness increase the risk for all-cause and cardiovascular disease (CVD) mortality (ICD-10: I00-I99) and used the data to create a conceptual framework. Using the 10-year overall and cardiovascular mortality follow-up data (n = 12,019) from the National Health and Nutrition Examination Survey (1999-2008), we conducted survival analyses and found that individuals who experience social isolation or loneliness have a significantly higher likelihood of overall and CVD mortality than those without support. These effects generally remained strong with further adjustment for NHANES-detected health and demographic differences showing the need to address COVID-19 related loneliness through increasing social nearing.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Sri Banerjee", + "author_inst": "Walden University School of Health Sciences" + }, + { + "author_name": "Gary Burkholder", + "author_inst": "Walden University School of Psychology" + }, + { + "author_name": "Beyan Sana", + "author_inst": "Johns Hopkins University COVID-19 team" + }, + { + "author_name": "Mihalyi Szirony", + "author_inst": "Walden University School of Counseling" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.15.20066480", "rel_title": "Mathematical assessment of the impact of non-pharmaceutical interventions on curtailing the 2019 novel Coronavirus", @@ -1545403,37 +1547864,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.14.20064956", - "rel_title": "Multinational modeling of SARS-CoV-2 spreading dynamics: Insights on the heterogeneity of COVID-19 transmission and its potential healthcare burden", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20064956", - "rel_abs": "BackgroundModelling and projections of COVID-19 using a single set of transmission parameters can be an elaborated because the application of different levels of containment measures at different stages of the worldwide COVID-19 outbreak.\n\nMethodsWe developed a piecewise fitting SEIR methodology to fit the progress of the COVID-19 that can be applied on any of the 185 countries listed in John Hopkins Coronavirus Resource Center. The contagious contact rate, the rate of removal and the initially exposed population were obtained at three different stages of the pandemic for a set of 18 countries, and globally for the total number of cases worldwide. The active number of infections and the removed populations were fitted simultaneously to validate the SEIR model against the available time series reports on the number of confirmed infections, recoveries and deaths. We evaluate the effect of a reduction of contagious contact rate on the level of burden put on local healthcare infrastructure considering different levels of intervention. As a guideline for future public health interventions, we also estimated the maximum number of future cases and its potential peak date.\n\nFindingsWe project that the peak in the number of infections worldwide will take place after the third quarter of 2020 with a decline rate that might extend beyond 2020. For 12 out of the 18 countries analyzed, we observe that, following the trend at the date of this study, the number of severe infections will surpass their healthcare capacity. For a 90% reduction scenario of the contagious contact rate, four out of the 18 countries analyzed will undergo a significant delay in the peak of infection, extending the course of the epidemic further than our simulation window (365 days).\n\nInterpretationWe identify three stages for the COVID-19 transmission dynamics, which suggest that it is highly heterogeneous between countries and its contagious contact rate, is currently affected by both local responses of the public health interventions and to the populations adherence to the measures.\n\nFundingNo funding received.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Erick R Martinez-Loran", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "J Jesus Naveja", - "author_inst": "UNAM" - }, - { - "author_name": "Omar Yaxmehen Bello-Chavolla", - "author_inst": "National Institute of Geriatrics" - }, - { - "author_name": "Flavio Fernando Contreras-Torres", - "author_inst": "Tecnologico de Monterrey" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.13.20063412", "rel_title": "Analysis of COVID-19 spread in South Korea using the SIR model with time-dependent parameters and deep learning", @@ -1545570,6 +1548000,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.13.20064360", + "rel_title": "Supportive Care for Patient with Respiratory Diseases: An Umbrella Review", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20064360", + "rel_abs": "BackgroundSupportive treatment is an important and effective part of the management for patients with life-threatening diseases. This study aims to identify and evaluate the forms of supportive care for patients with respiratory diseases.\n\nMethodsAn umbrella review of supportive care for patient respiratory diseases was undertaken. We comprehensively searched the following databases: Medline, EMBASE, Web of Science, CNKI (China National Knowledge Infrastructure), Wanfang Data and CBM (SinoMed) from their inception to 31 March 2020, and other sources to identify systematic reviews and meta-analyses related to supportive treatments for patient with respiratory diseases including COVID-19, SARS, MERS and influenza. We assessed the methodological quality using the AMSTAR score and the quality of the evidence for the primary outcomes of each included systematic review and meta-analysis.\n\nResultsWe included 18 systematic reviews and meta-analyses in this study. Most studies focused on the respiratory and circulatory support. Ten studies were of high methodological quality, five studies of medium quality, and three studies of low quality. According to four studies extracorporeal membrane oxygenation did not reduce mortality in adults (OR/RR ranging from 0.71 to 1.28), but two studies reported significantly lower mortality in patients receiving venovenous extracorporeal membrane oxygenation than in the control group (OR/RR ranging from 0.38 to 0.73). Besides, monitoring of vital signs and increasing the number of medical staff may also reduce the mortality in patients with respiratory diseases.\n\nConclusionsOur overview suggests that supportive care may reduce the mortality of patients with respiratory diseases to some extent. However, the quality of evidence for the primary outcomes in the included studies was low to moderate. Further systematic reviews and meta-analyses are needed to address the evidence gap regarding the supportive care for SARS, MERS and COVID-19.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Xufei Luo Sr.", + "author_inst": "School of Public Health, Lanzhou University" + }, + { + "author_name": "Meng Lv Jr.", + "author_inst": "School of Public Health, Lanzhou University" + }, + { + "author_name": "Xiaoqing Wang Jr.", + "author_inst": "Children's Hospital of Chongqing Medical University" + }, + { + "author_name": "Xin Long Jr.", + "author_inst": "Children's Hospital of Chongqing Medical University" + }, + { + "author_name": "Mengjuan Ren Jr.", + "author_inst": "School of Public Health, Lanzhou University" + }, + { + "author_name": "Xianzhuo Zhang Sr.", + "author_inst": "The First School of Clinical Medicine, Lanzhou University" + }, + { + "author_name": "Yunlan Liu Jr.", + "author_inst": "School of Public Health, Lanzhou University" + }, + { + "author_name": "Weiguo Li Sr.", + "author_inst": "Chongqing Key Laboratory of Pediatrics" + }, + { + "author_name": "Qi Zhou Jr.", + "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University" + }, + { + "author_name": "Yanfang Ma Jr.", + "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University" + }, + { + "author_name": "Toshio Fukuoka Sr.", + "author_inst": "Emergency and Critical Care Center, the Department of General Medicine, Department of Research and Medical Education at Kurashiki Central Hospital" + }, + { + "author_name": "Hyeong Sik Ahn Jr.", + "author_inst": "Department of Preventive Medicine, Korea University College of Medicine" + }, + { + "author_name": "Myeong Soo Lee Sr.", + "author_inst": "Korea Cochrane Centre, Korea" + }, + { + "author_name": "Zhengxiu Luo Sr.", + "author_inst": "Department of Respiratory Medicine, Childrens Hospital of Chongqing Medical University" + }, + { + "author_name": "Enmei Liu Sr.", + "author_inst": "Department of Respiratory Medicine, Childrens Hospital of Chongqing Medical University" + }, + { + "author_name": "Xiaohui Wang Jr.", + "author_inst": "School of Public Health, Lanzhou University" + }, + { + "author_name": "Yaolong Chen Sr.", + "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.04.14.20065094", "rel_title": "Rapid Open Development and Clinical Validation of Multiple New 3D-Printed Nasopharyngeal Swabs in Response to the COVID-19 Pandemic", @@ -1546709,25 +1549222,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.14.20065268", - "rel_title": "Countries should aim to lower the reproduction number R close to 1.0 for the short-term mitigation of COVID-19 outbreaks", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20065268", - "rel_abs": "The COVID-19 pandemic is still in its early stages and given the speed and magnitude of local outbreaks it is urgent to understand how mitigation measures translate into changes in key epidemiological and clinical outcomes. Here, we employ a mathematical model to explore the short-term consequences of lowering the reproduction number [R]0 and delaying measures on total infections and fatalities. The positive implications of mitigation generally accrue as these measures are adopted early, with the most striking effects seen when the reproductive number is lowered to a level [R]C{approx}1.0. As the delay in adopting measures exceeds approximately the half-way point to the peak of an outbreak, the effects of lowering [R]0 markedly decrease. Aiming for reproduction numbers close to 1.0 can substantially reduce fatality probabilities over short time scales, particularly for larger populations. We conclude that research is urgently needed on how mitigation measures impact [R]0 and how these can be optimized so as to achieve [R]C{approx}1.0 whilst supporting individual freedoms, society and the economy.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Michael E. Hochberg", - "author_inst": "University of Montpellier, France; Santa Fe Institute, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.14.20065300", "rel_title": "The Easter and Passover Blip in New York City", @@ -1546824,6 +1549318,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.15.20065532", + "rel_title": "Estimation of Tunisia COVID-19 infected cases based on mortality rate", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20065532", + "rel_abs": "Estimating the number of people affected by COVID-19 is crucial in deciding which public health policies to follow. The authorities in different countries carry out mortality counts. We propose that the mortality reported in each country can be used to create an index of the number of actual cases at a given time. The specificity of whether or not deaths are rapid or not by COVID-19 also affects the number of actual cases. The number of days between the declaration of illness and death varies between 12 and 18 days. For a delay of 18 days, and using an estimated mortality rate of 2%, the number of cases in April 2020 in Tunisia would be 5 580 people. The pessimistic scenario predicts 22 320 infected people, and the most optimistic predicts 744 (which is the number of reported cases on April 12, 2020). Modeling the occurrence of COVID-19 cases is critical to assess the impact of policies to prevent the spread of the virus.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ines Abdeljaoued-Tej", + "author_inst": "BIMS Laboratory, LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar, Tunisia" + }, + { + "author_name": "Marc Dhenain", + "author_inst": "CNRS" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.12.20062679", "rel_title": "Time course quantitative detection of SARS-CoV-2 in Parisian wastewaters correlates with COVID-19 confirmed cases", @@ -1547855,73 +1550372,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.14.20059501", - "rel_title": "A High Through-put Assay for Circulating Antibodies Directed against the S Protein of Severe Acute Respiratory Syndrome Corona virus 2", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20059501", - "rel_abs": "BackgroundMore than one million infections with the severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) have been confirmed. While PCR-based assays are used for diagnosis, high through-put serologic methods are needed to detect antibodies for seroserveillance and for identification of seroconversion, potential plasma donors, and the nature of the immune response to this pathogen.\n\nMethodsA Luminex binding assay was used to assess the presence of antibodies in human sera from COVID-19-infected and -uninfected individuals specific for two recombinant proteins of SARS-CoV-2.\n\nFindingsFluorochrome-labeled beads were coated with a recombinant soluble stabilized trimeric SARS-CoV-2 S protein ectodomain or its central portion, the receptor binding domain (RBD). Coated beads were incubated with sera, followed by incubation with biotinylated anti-human total Ig antibodies and phycoerythrin (PE)-labeled streptavidin. Readout using a Luminex analyzer clearly differentiated between sera of the infected and uninfected subjects, delineating a wide range of serum antibody levels in infected subjects.\n\nInterpretationAntibody assays of sera can identify individuals who are infected with SARS-CoV-2 and have seroconverted, as well as subjects who have been infected and recovered. The use of the Luminex binding Ab assay has the advantage that it can be run in approximately 2.5 hours, uses very little antigen, and permits a high through-put of samples/day.\n\nFundingNIAID contracts and grants, Department of Veterans Affairs grants, the Microbiology Laboratory Clinical Services, Translational Science Hub, and Personalized Virology Initiative, and Department of Medicine of Mount Sinai Health System and Icahn School of Medicine at Mount Sinai.\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSThe outbreak of infections with SARS-CoV-2 began in late 2019. Specimens from nasopharyngeal swabs are being used in PCR-based assays to test for the presence of the virus. Until the first week in April, 2020 there were no licensed tests for the presence of serum antibodies against proteins of the virus. The first approved tests are now becoming available, but none use a format that can be scaled up for mass screening which is now needed for implementing various public health measures. As per a recent Pubmed search, less than 10 studies using serologic assays have been published and none are high through-put.\n\nAdded value of this studyHigh through-put antibody tests are needed in order to identify seroconversion, to perform serosurveys, identify potential donors for plasma therapy, assess the prevalence of infection in populations, identify healthcare workers who may be immune to SARS-CoV-2, and to study the nature of the immune response to this pathogen. The method described for detecting antibodies in SARS-CoV-2-infected patients can be applied in hospital and reference labs, allowing the assessment of present and past infection in a much higher number of donors per unit of time than assays described heretofore.\n\nImplications of all the available evidenceThis study shows that a test in which magnetic beads are coated with soluble forms of the spike protein of SARS-CoV-2 can be used to test for the presence of antibodies targeting this pathogen. The platform allows for the efficient testing of multiple specimens simultaneously using as little as 5 nanograms of antigen per test. This test affords the possibility of large scale, economical and efficient antibody testing.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Svenja Weiss", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Jeromine Klingler", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Catarina Hioe", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Fatima Amanat", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ian Baine", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Erna Milunka Kojic", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Mount Sinai West and Moriningside, NY, USA" - }, - { - "author_name": "Jonathan Stoever", - "author_inst": "Pulmonary and Critical Care Medicine, Mount Sinai West, NY, USA" - }, - { - "author_name": "Sean Liu", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Denise Jurczyszak", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Maria Bermudez-Gonzalez", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Viviana Simon", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Florian Krammer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Susan Zolla-Pazner", - "author_inst": "Icahn School of Medicine at Mount Sinai" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.14.20059733", "rel_title": "Distinct early IgA profile may determine severity of COVID-19 symptoms: an immunological case series", @@ -1548062,6 +1550512,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.12.20062919", + "rel_title": "Analysis of the SARS-Cov-2 epidemic in Lombardy (Italy) in its early phase. Are we going in the right direction?", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.12.20062919", + "rel_abs": "BACKGROUNDWe described the epidemiological features of the codiv-19 outbreak, and evaluated the impact of interventions measures on the epidemic in the Lombardy region, Italy.\n\nMETHODSLaboratory-confirmed covid-19 cases reported through the beginning of April were extracted from the Italian Civil Protection database. Based on key events and interventions, we divided the epidemic into three periods: before February 21, from February 22 to early March, after early March. We compared epidemiological characteristics across periods and developed a modified susceptible-exposed-infectious-recovered model to study the epidemic and evaluate the impact of interventions. We explicitly took into account for unascertained cases (positive cases with no symptoms or mild symptoms that have not been accounted for in official statistics).\n\nRESULTSCurrently, the number of positive active cases has increased to around 30,000 in the Lombardy region. Due to restriction measures, the effective reproduction number dropped from 3.33 (95% CI: 2.03-3.69) during the first period, to 2.36 (95% CI: 2.21-2.70) during the second period. In the third period, the effective reproduction number is estimated to have dropped to 1.49 (95% CI: 1.35-1.62). The model estimates a great proportion of unascertained cases, about 90% of infected people has not been accounted for in official statistics.\n\nCONCLUSIONSConsiderable countermeasures have slowed down the covid-19 outbreak in the Lombardy region. However, notwithstanding the long-lasting lockdown period, the epidemic is still not under control. The effective reproduction number, according to the model used in this work, is still greater than 1.0. Estimation of unascertained cases has important implications on continuing surveillance and interventions.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Angelo Riccio", + "author_inst": "Universita' Parthenope di Napoli" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.12.20062588", "rel_title": "An SEIR Model for Assessment of Current COVID-19 Pandemic Situation in the UK", @@ -1549057,29 +1551526,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.15.20062752", - "rel_title": "Analysis of the COVID-19 epidemic in french overseas department Mayotte based on a modified deterministic and stochastic SEIR model", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20062752", - "rel_abs": "In order to anticipate a future trends in the development of the novel coronavirus COVID-19 epidemic started early at march 13, in the french overseas department Mayotte, we consider in this paper a modified deterministic and stochastic epidemic model. The model divides the total population into several possible states or compartment: susceptible (S), exposed (E) infected and being under an incubation period, infected (I) being infectious, simple or mild removed RM, severe removed (including hospitalized) RS and death cases (D). The adding of the two new compartment RM and RS are driven by data which together replace the original R compartment in the classical SEIR model.\n\nWe first fit the constant transmission rate parameter to the epidemic data in Mayotte during an early exponential growth phase using an algorithm with a package of the software R and based on a Maximum Likewood estimator. This allows us to predict the epidemic without any control in order to understand how the control measure and public policies designed are having the desired impact of controlling the epidemic. To do this, we introduce a temporally varying decreasing transmission rate parameter with a control or quarantine parameter q. Then we pointed out some values of q to maintain control which is critical in Mayotte given the fragility of its health infrastructure and the significant fraction of the population without access to water.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Solym MANOU-ABI", - "author_inst": "IMAG-Montpellier" - }, - { - "author_name": "Julien BALICCHI", - "author_inst": "French National Health Agency of Mayotte" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.12.20062927", "rel_title": "MARKOVIAN RANDOM WALK MODELING AND VISUALIZATION OF THE EPIDEMIC SPREAD OF COVID-19", @@ -1549276,6 +1551722,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.14.20063636", + "rel_title": "Automated and semi-automated contact tracing: Protocol for a rapid review of available evidence and current challenges to inform the control of COVID-19", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20063636", + "rel_abs": "IntroductionTraditional approaches to case-finding, case isolation, and contact tracing methods have so far proved insufficient on their own to prevent the development of local epidemics of COVID-19 in many high-income countries despite relatively advanced public health systems. As a result, many governments have resorted to widespread social distancing measures and mass quarantines ( lock-downs) to reduce transmission and to prevent healthcare systems from being overwhelmed. However, such measures impose heavy human and societal costs. Automated or semi-automated digital contact tracing, in conjunction with scaled-up community testing, has been proposed as a key part of exit strategies from lockdowns. However, the effectiveness of these approaches to contact tracing is unclear, and to be effective, trusted, and widely adopted such technology must overcome several challenges.\n\nMethods and analysisWe will perform a rapid systematic review to assess the effectiveness of automated and semi-automated digital tools for contact tracing, and identify key considerations for successful implementation, to inform the control of COVID-19. We will search PubMed, EMBASE, EBSCO Medical COVID information portal, OVID Global Health, Cochrane Library, medRxiv, BioRxiv, and arXiv for peer-reviewed and pre-print papers on automated or semi-automated digital tools for contact tracing of COVID-19, another respiratory disease with pandemic potential (limited to SARS, MERS, or pandemic influenza), or Ebola, in human populations. Studies will be eligible if published in English between 1 January 2000 and 14 April 2020. We will synthesise study findings narratively and will consider meta-analysis if [≥] 3 suitable studies with comparable interventions and outcomes are available.\n\nEthics and disseminationEthical approval is not required for this review. We plan to disseminate findings via pre-print, journal publication, through social media and web-based platforms and through direct stakeholder engagement.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Isobel Braithwaite", + "author_inst": "Institute of Health Informatics, University College London" + }, + { + "author_name": "Tom Callender", + "author_inst": "Department of Applied Health Research, University College London" + }, + { + "author_name": "Miriam Bullock", + "author_inst": "UCL Collaborative Centre for Inclusion Health, University College London" + }, + { + "author_name": "Rob Aldridge", + "author_inst": "Institute of Health Informatics, University College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.11.20061713", "rel_title": "The Potential role of Particulate Matter in the Spreading of COVID-19 in Northern Italy: First Evidence-based Research Hypotheses", @@ -1550131,29 +1552608,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.10.20061051", - "rel_title": "A Mathematical prediction of the time evolution of the Covid-19 pandemic in some countries of the European Union using Monte Carlo simulations", - "rel_date": "2020-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20061051", - "rel_abs": "In this paper we study the statistical evolution in time of the Covid-19 pandemic in Spain, Italy, Germany, Belgium, The Netherlands, Austria and Portugal, i.e., the countries of the European Union (EU) that have a number of positive cases higher than 12 thousand at April 7, 2020. France is the third country of the EU for number of cases but a jump in the data on April 3, 2020 does not allow, at least for the moment, to have a reliable prediction curve. The analysis is based on the use of a function of the type of a Gauss Error Function, with four parameters, as a Cumulative Distribution Function (CDF). A Monte Carlo analysis is used to estimate the uncertainty. The approach used in this paper is mathematical and statistical and thus does not explicitly consider a number of relevant issues, including number of nasopharyngeal swabs, mitigation measures, social distancing, virologic, epidemiological and models of contamination diffusion.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ignazio Ciufolini", - "author_inst": "University of Salento" - }, - { - "author_name": "Antonio Paolozzi", - "author_inst": "Sapienza University of Rome" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.12.20062943", "rel_title": "Incidence, clinical outcomes, and transmission dynamics of hospitalized 2019 coronavirus disease among 9,596,321 individuals residing in California and Washington, United States: a prospective cohort study", @@ -1550354,6 +1552808,57 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.04.11.20059170", + "rel_title": "Delayed-Phase Thrombocytopenia in Patients of Coronavirus Disease 2019 (COVID-19)", + "rel_date": "2020-04-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20059170", + "rel_abs": "The pandemic COVID-19 pneumonia has engulfed the entire world. Hematopoietic system can also be affected by COVID-19. Thrombocytopenia at admission was prevalent, while late-phase or delayed-phase thrombocytopenia is obscure. This retrospective single-center case series analyzed patients with COVID-19 at the Union Hospital, Wuhan, China, from January 25th to March 9th, 2020. Analysis began on March 11th, 2020. COVID-19 associated delayed-phase thrombocytopenia was occurred in 11.8% percent of enrolled patients. The delayed-phase thrombocytopenia in COVID-19 is prone to develop in elderly patients or patients with low lymphocyte count on admission. The delayed-phase thrombocytopenia is significantly associated with increased length of hospital stay and higher ICU admission rate. Delayed-phase nadir platelet counts demonstrated a high and significantly negative linear correlation with B cell percentages and serum IL-6 levels. We also presented bone marrow aspiration pathology of three patients with delayed-phase thrombocytopenia, showing impaired maturation of megakaryocytes. We speculated that the delayed-phase platelet destruction might be mediated by antibodies, and suggest immunoregulatory treatment in severe patients to improve outcomes. Besides, clinicians need to pay attention to the delayed-phase thrombocytopenia especially at 3-4 weeks after symptom onset.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Hao Zhou", + "author_inst": "Institute of Hematology, Union Hospital, Tongji Medial College, Huazhong University of Science and Technology" + }, + { + "author_name": "Wanxin Chen", + "author_inst": "Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Ziping Li", + "author_inst": "Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Bohan Yang", + "author_inst": "Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Qiong Zhou", + "author_inst": "Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Ping Wang", + "author_inst": "Department of Clinical Laboratory, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Jianhua Zhu", + "author_inst": "Laboratory of Clinical Immunology, Wuhan No. 1 Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Xuexing Chen", + "author_inst": "Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Peng Yang", + "author_inst": "Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2020.04.11.20062018", "rel_title": "Assessment of N95 respirator decontamination and re-use for SARS-CoV-2", @@ -1551452,29 +1553957,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.10.20060822", - "rel_title": "Estimate of the Maximum Limit of Total Cases of Infected Patients COVID-19", - "rel_date": "2020-04-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20060822", - "rel_abs": "In this work, we present a method to estimate the maximum limit of total cases COVID-19 cases considering that the time in which the maximum number of new daily cases occurs corresponds to the inflection point of the curve described by the total number of cases that assumed to have a growth according to a logistical function in which the number of total cases at the inflection point will correspond to half of the maximum limit of total cases COVID-19. We estimate this maximum limit for China and South Korea, obtaining results compatible with the observations. And we also estimate for Italy, Germany, United Kingdom, United States and Spain.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Carlos Maximiliano Dutra Sr.", - "author_inst": "Universidade Federal do Pampa - UNIPAMPA" - }, - { - "author_name": "Carlos Augusto Riella de Melo Sr.", - "author_inst": "Universidade Federal do Pampa - UNIPAMPA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.11.20061465", "rel_title": "Hospitalization time and outcome in patients with Coronavirus Disease 2019 (COVID-19): analysis data from China", @@ -1551687,6 +1554169,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.10.20060525", + "rel_title": "When Resources Are Scarce - Feasibility of Emergency Ventilation of Two Patients With One Ventilator", + "rel_date": "2020-04-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20060525", + "rel_abs": "A potential shortage of intensive care ventilators has led to the idea to ventilate more than one patient with a single ventilator. Besides other problems, this is associated with the lack of knowledge concerning distribution of tidal volume and the patients individual respiratory system mechanics.\n\nIn this study we used two simple hand-manufactured adaptors to connect physical models of two adult respiratory systems to one ventilator. The artificial lungs were ventilated in the pressure-controlled mode and we investigated if disconnecting one lung from the ventilation circuit for several breaths would allow to determine reliably the other lungs tidal volume and compliance.\n\nCompliances and volumes were measured both with the ventilator and external sensors corresponded well. However, tidal volumes measured via the ventilator were smaller compared to the tidal volumes measured via the external sensors with an absolute error of 5.3 {+/-} 2.5%. The tidal volumes of the individual artificial lungs were distributed in proportion to the compliances and did not differ relevantly when both artificial lungs were connected to when one was disconnected.\n\nWe conclude that in case of emergency, ventilation of two patients with one ventilator requires two simple hand-crafted tubes as adaptors and available standard breathing circuit components. In such a setting, respiratory system mechanics and tidal volume of each individual patient can be reliably measured during short term clamping of the tracheal tube of the respective other patient.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Peter C. Reinacher", + "author_inst": "Department of Stereotactic and Functional Neurosurgery, Medical Center, University of Freiburg, Germany and Fraunhofer Institute for Laser Technology, Aachen, " + }, + { + "author_name": "Thomas E. Schlaepfer", + "author_inst": "Department of Interventional Biological Psychiatry, University of Freiburg, Germany and The Johns Hopkins University, Baltimore, MD, USA" + }, + { + "author_name": "Martin A. Schick", + "author_inst": "Department of Anesthesiology and Critical Care, Medical Center, University of Freiburg, Germany" + }, + { + "author_name": "Juergen Beck", + "author_inst": "Department of Neurosurgery, Medical Center, University of Freiburg, Germany" + }, + { + "author_name": "Hartmut Buerkle", + "author_inst": "Department of Anesthesiology and Critical Care, Medical Center, University of Freiburg, Germany" + }, + { + "author_name": "Stefan Schumann", + "author_inst": "Department of Anesthesiology and Critical Care, Medical Center, University of Freiburg, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.04.12.20059972", "rel_title": "Challenges in control of Covid-19: short doubling time and long delay to effect of interventions", @@ -1553018,33 +1555539,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.04.09.20059550", - "rel_title": "Diminishing Marginal Benefit of Social Distancing in Balancing COVID-19 Medical Demand-to-Supply", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20059550", - "rel_abs": "Social distancing has been adopted as a non-pharmaceutical intervention to prevent the COVID-19 pandemic from overwhelming the medical resources across the United States (US). The catastrophic socio-economic impacts of this intervention could outweigh its benefits if the timing and duration of implementation are left uncontrolled and ill-strategized. Here we investigate the dynamics of social distancing on age-stratified US population and benchmark its effectiveness in reducing the burden on hospital and ICU beds. Our findings highlight the diminishing marginal benefit of social distancing, characterized by a linear decrease in medical demands against an exponentially increasing social distancing duration. We determine an optimal intermittent social-to-no-distancing ratio of 5:1 corresponding to [~]80% reduction in healthcare demands - beyond this ratio, benefit of social distancing diminishes to a negligible level.\n\nCOVID-19 Medical Demand Forecasthttps://eece.wustl.edu/chakrabarty-group/covid/", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Pai Liu", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Payton Beeler", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Rajan K Chakrabarty", - "author_inst": "Washington University in Saint Louis" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.09.20059113", "rel_title": "Transmission routes of Covid-19 virus in the Diamond Princess Cruise ship", @@ -1553193,6 +1555687,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.09.20059659", + "rel_title": "How do environmental, economic and health factors influence regional vulnerability to COVID-19?", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20059659", + "rel_abs": "We have studied the correlations between twelve environmental, economic and health variables, by carrying out a statistical analysis of the fatality rate of COVID-19 in 14 countries. Our statistical analysis indicates that, among the 12 variables, the diabetes percentage of the total population and the extent of the population ages 65 and older in each country are correlated most strongly with the total number of deaths in them. Although the strength of the correlations between the variables and the total ND may change as the ongoing pandemic evolves, the study highlights the importance of integrating regional-specific variables in the modelling efforts aimed at projecting how the spread of the virus may influence different parts of the world.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Pejman Tahmasebi", + "author_inst": "University of Wyoming" + }, + { + "author_name": "Salome M.S. Shokri-Kuehni", + "author_inst": "Imperial College London" + }, + { + "author_name": "Muhammad Sahimi", + "author_inst": "University of Southern California" + }, + { + "author_name": "Nima Shokri", + "author_inst": "The University of Manchester" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.09.20059683", "rel_title": "Case- fatality rate in COVID- 19 patients: A meta-analysis of publicly accessible database", @@ -1554156,89 +1556681,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.07.20054767", - "rel_title": "Pulmonary radiological change of COVID-19 patients with 99mTc-MDP treatment", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20054767", - "rel_abs": "BackgroundAs increasing cases of COVID-19 around world, urgent need for effective COVID-19-specific therapeutic drugs is necessary; therefore, we conducted a pilot randomized-controlled study to evaluate the efficacy of 99mTc-MDP for COVID-19 therapeutic treatment.\n\nMethodsA total of 21 mild patients with COVID-19 were enrolled in this pilot RCT from February 2020 through March 2020, and then were assigned, in a 1:1 ratio, into control (11 patients) and 99mTc-MDP group (10 patients). Patients in the control group received routine treatment and patients assigned to the 99mTc-MDP group received a combination of routine treatment and an administration of 99mTc-MDP injection of 5ml/day. Both of the patients in the control and 99mTc-MDP groups were treated for 7 days with the primary end point of CT-based radiological pulmonary changes during 7-day follow-up.\n\nFindingsFrom baseline to the day 7, 8 (80%) of 10 mild patients in the 99mTc-MDP group had a significant radiological improvement in lung and a decline in inflammatory infiltration, whereas only 1 (9.1%) of 11 patients in the control group had a radiological improvement in lung. None of the patients in the 99mTc-MDP group had disease progression from mild to severe, as well as an inflammatory cytokine storm, and 2 mild patients (18.2%) in the control group developed severe. During days 7 through 14, the number of patients with radiological improvement in the 99mTc-MDP group remained consistent, and only 1 additional case (22%) in the control group were reported.\n\nConclusionIn this randomized pilot study, 99mTc-MDP had an effective inhibitory effect on the inflammatory disease progression for the therapy of COVID-19, and it can accelerate the absorption of pulmonary inflammation in a short period of time during the process of treatment.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Xiaolin Yuan", - "author_inst": "Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Wanrong Yi", - "author_inst": "Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Baoyi Liu", - "author_inst": "Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Simiao Tian", - "author_inst": "Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Fang Cao", - "author_inst": "Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Ruoyu Wang", - "author_inst": "Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Baiwen Qi", - "author_inst": "Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Faqiang Lu", - "author_inst": "Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Meiyun Fang", - "author_inst": "Department of Rheumotology, Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Fuyang Pei", - "author_inst": "Department of Respiratory Medicine, Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Ming Chen", - "author_inst": "Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Lichuan Zhang", - "author_inst": "Department of Respiratory Medicine, Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Yong Zhang", - "author_inst": "Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Xiuzhi Zhang", - "author_inst": "Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Zhenyu Pan", - "author_inst": "Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Dewei Zhao", - "author_inst": "Affiliated Zhongshan hospital of Dalian University" - }, - { - "author_name": "Aixi Yu", - "author_inst": "Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.10.20059121", "rel_title": "ACE inhibition and cardiometabolic risk factors, lung ACE2 and TMPRSS2 gene expression, and plasma ACE2 levels: a Mendelian randomization study", @@ -1554499,6 +1556941,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.09.20059881", + "rel_title": "Next weeks of SARS-CoV-2: Projection model to predict time evolution scenarios of accumulated cases in Spain", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20059881", + "rel_abs": "Background and objectivesSARS-CoV-2 is a new type of coronavirus that can affect people and causes respiratory disease, COVID-19. It is affecting the entire planet and we focus in Spain, where the first case was detected at the end of January 2020 and in recent weeks it has increased in many cases. We need predictive models in order to be efficient and take actions. The general goal of this work is present a new model of SARS-CoV-2 to predict different scenarios of accumulated cases in Spain.\n\nMaterial and methodsIn this short report is used a model proposed previously, based on a parametric model Weibull and in a the library BDSbiost3 developed in R to infer and predict different scenarios of the evolution of SARS-CoV-2 for the accumulated cases in Spain after the spread that affects Spain detected at the end of January of this year.\n\nResultsIn the analyses presented, projective curves have been generated for the evolution of accumulated cases in which they reach about 4,000 cases or about 15,000 cases, for which the lines of the day in which the value for 90 will be reached can be seen vertically 90, 95 and 99% of the asymptote (maximum number of cases, from that day they will begin to descend or remain the same), that is why the vertical lines would indicate the brake of the disease. For the worst-case scenario, it takes 118, 126 or 142 days to reach the maximum number of cases (n = 15,000) to reach 90, 95 and 99% of the asymptote (maximum number of cases), respectively. This means translated in a time scale that in the worst case the virus will not stop its progress, in Spain, until summer 2020, hopefully before.\n\nComments and conclusionsThis model could be used to plan the resources and see if the policies or means dedicated to the virus are slowing the progress of the virus or it is necessary to implement others that are more effective, and can also validate a method for future outbreaks of diseases such as these.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "TONI MONLEON-GETINO Sr.", + "author_inst": "UNIVERSITY OF BARCELONA" + }, + { + "author_name": "Jaume Canela-Soler", + "author_inst": "University of Barcelona" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.08.20058842", "rel_title": "The Epidemiological Implications of Incarceration Dynamics in Jails for Community, Corrections Officer, and Incarcerated Population Risks from COVID-19", @@ -1555722,29 +1558187,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2020.04.10.20060319", - "rel_title": "Analysing recovery from pandemics by Learning Theory: the case of CoVid-19", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20060319", - "rel_abs": "We present a method for predicting the recovery time from infectious diseases outbreaks such as the recent CoVid-19 virus. The approach is based on the theory of learning from errors, specifically adapted to the control of the virus spread by reducing infection rates using countermeasures such as medical treatment, isolation, social distancing etc. When these are effective, the infection rate, after reaching a peak, declines following a given recovery rate curve. We use presently available data from China, South Korea and others to make actual predictions of the time needed for securing minimum infection rates in the future.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Romney B. Duffey", - "author_inst": "Idaho Falls" - }, - { - "author_name": "Enrico Zio", - "author_inst": "Politecnico di Milano" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.13.039263", "rel_title": "Comparative in vitro transcriptomic analyses of COVID-19 candidate therapy hydroxychloroquine suggest limited immunomodulatory evidence of SARS-CoV-2 host response genes.", @@ -1555933,6 +1558375,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.10.20061176", + "rel_title": "Multi-Stage Group Testing Optimizes COVID-19 Mass Population Testing", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20061176", + "rel_abs": "BackgroundSARS-CoV-2 test kits are in critical shortage in many countries. This limits large-scale population testing and hinders the effort to identify and isolate infected individuals.\n\nObjectivesHerein, we developed and evaluated multi-stage group testing schemes that test samples in groups of various pool sizes in multiple stages. Through this approach, groups of negative samples can be eliminated with a single test, avoiding the need for individual testing and achieving considerable savings of resources.\n\nStudy designWe designed and parameterized various multi-stage testing schemes and compared their efficiency at different prevalence rates using computer simulations.\n\nResultsWe found that three-stage testing schemes with pool sizes of maximum 16 samples can test up to three and seven times as many individuals with the same number of test kits for prevalence rates of around 5% and 1%, respectively. We propose an adaptive approach, where the optimal testing scheme is selected based on the expected prevalence rate.\n\nConclusionThese group testing schemes could lead to a major reduction in the number of testing kits required and help improve large-scale population testing in general and in the context of the current COVID-19 pandemic.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Jens Niklas Eberhardt", + "author_inst": "Max Planck Institute for Mathematics, Bonn" + }, + { + "author_name": "Nikolas Peter Breuckmann", + "author_inst": "University College London" + }, + { + "author_name": "Christiane Sigrid Eberhardt", + "author_inst": "Center for Vaccinology and Department of Pediatrics, University Hospitals of Geneva" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.10.20060293", "rel_title": "A SIMPLE COLORIMETRIC MOLECULAR DETECTION OF NOVEL CORONAVIRUS (COVID-19), AN ESSENTIAL DIAGNOSTIC TOOL FOR PANDEMIC SCREENING", @@ -1557180,61 +1559649,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.12.025577", - "rel_title": "Mechanistic modeling of the SARS-CoV-2 disease map", - "rel_date": "2020-04-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.12.025577", - "rel_abs": "Here we present a web interface that implements a comprehensive mechanistic model of the SARS-CoV-2 disease map in which the detailed activity of the human signaling circuits related to the viral infection and the different antiviral responses, including immune and inflammatory activities, can be inferred from gene expression experiments. Moreover, given to the mechanistic properties of the model, the effect of potential interventions, such as knock-downs, over-expression or drug effects (currently the system models the effect of more than 8000 DrugBank drugs) can be studied in specific conditions. By providing a holistic, systems biology approach to the understanding of the complexities of the viral infection process, this tool will become an important asset in the search for efficient antiviral treatments.\n\nThe tool is freely available at: http://hipathia.babelomics.org/covid19/", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Kinza Rian", - "author_inst": "Fundacion Progreso y Salud" - }, - { - "author_name": "Marina Esteban-Medina", - "author_inst": "Fundacion Progreso y Salud" - }, - { - "author_name": "Marta R Hidalgo", - "author_inst": "Centro de Investigacion Principe Felipe" - }, - { - "author_name": "Cankut Cubuk", - "author_inst": "Fundacion Progreso y Salud" - }, - { - "author_name": "Matias M Falco", - "author_inst": "Fundacion Progreso y Salud" - }, - { - "author_name": "Carlos Loucera", - "author_inst": "Fundacion Progreso y Salud" - }, - { - "author_name": "Devrim Gunyel", - "author_inst": "University of Luxembourg" - }, - { - "author_name": "Marek Ostaszewski", - "author_inst": "University of Luxembourg" - }, - { - "author_name": "Maria Pena-Chilet", - "author_inst": "Fundacion Progreso y Salud" - }, - { - "author_name": "Joaquin Dopazo", - "author_inst": "Fundacion Progreso y Salud" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2020.04.10.036335", "rel_title": "A Computational Approach to Design Potential siRNA Molecules as a Prospective Tool for Silencing Nucleocapsid Phosphoprotein and Surface Glycoprotein Gene of SARS-CoV-2", @@ -1557419,6 +1559833,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.08.20058248", + "rel_title": "U.S. county-level characteristics to inform equitable COVID-19 response", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20058248", + "rel_abs": "BackgroundThe spread of Coronavirus Disease 2019 (COVID-19) across the United States confirms that not all Americans are equally at risk of infection, severe disease, or mortality. A range of intersecting biological, demographic, and socioeconomic factors are likely to determine an individuals susceptibility to COVID-19. These factors vary significantly across counties in the United States, and often reflect the structural inequities in our society. Recognizing this vast inter-county variation in risks will be critical to mounting an adequate response strategy.\n\nMethods and FindingsUsing publicly available county-specific data we identified key biological, demographic, and socioeconomic factors influencing susceptibility to COVID-19, guided by international experiences and consideration of epidemiological parameters of importance. We created bivariate county-level maps to summarize examples of key relationships across these categories, grouping age and poverty; comorbidities and lack of health insurance; proximity, density and bed capacity; and race and ethnicity, and premature death. We have also made available an interactive online tool that allows public health officials to query risk factors most relevant to their local context.\n\nOur data demonstrate significant inter-county variation in key epidemiological risk factors, with a clustering of counties in certain states, which will result in an increased demand on their public health system. While the East and West coast cities are particularly vulnerable owing to their densities (and travel routes), a large number of counties in the Southeastern states have a high proportion of at-risk populations, with high levels of poverty, comorbidities, and premature death at baseline, and low levels of health insurance coverage.\n\nThe list of variables we have examined is by no means comprehensive, and several of them are interrelated and magnify underlying vulnerabilities. The online tool allows readers to explore additional combinations of risk factors, set categorical thresholds for each covariate, and filter counties above different population thresholds.\n\nConclusionCOVID-19 responses and decision making in the United States remain decentralized. Both the federal and state governments will benefit from recognizing high intra-state, inter-county variation in population risks and response capacity. Many of the factors that are likely to exacerbate the burden of COVID-19 and the demand on healthcare systems are the compounded result of long-standing structural inequalities in US society. Strategies to protect those in the most vulnerable counties will require urgent measures to better support communities attempts at social distancing and to accelerate cooperation across jurisdictions to supply personnel and equipment to counties that will experience high demand.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Taylor Chin", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Rebecca Kahn", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Ruoran Li", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Jarvis T. Chen", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Nancy Krieger", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Caroline O. Buckee", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Satchit Balsari", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Mathew V. Kiang", + "author_inst": "Stanford University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.06.20054114", "rel_title": "A streamlined approach to rapidly detect SARS-CoV-2 infection, avoiding RNA extraction", @@ -1558358,73 +1560819,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.04.06.20054890", - "rel_title": "Key to successful treatment of COVID-19: accurate identification of severe risks and early intervention of disease progression", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20054890", - "rel_abs": "BackgroundCOVID-19 is a new and highly contagious respiratory disease that has caused global spread, high case fatality rate in severe patients, and a huge medical burden due to invasive mechanical ventilation. The current diagnosis and treatment guidelines are still need to be improved, and more excellent clinical experience is needed to provide reference.\n\nMethodsWe analyzed and summarized clinical data of 97 confirmed COVID-19 adult patients (including 26 severe cases) admitted to the Fifth Affiliated Hospital of Sun Yat-sen University from January 17, 2020 to March 10, 2020, included laboratory examination results, imaging findings, treatment effect, prognosis, etc, in order to put forward prediction index of severe COVID-19 patients, principles of early intervention and methylprednisolone usages in COVID-19 patients.\n\nResultsO_LIHypoxemia, hyperlactic acid, hypoproteinemia, and hypokalemia were prevalent in COVID-19 patients. The significant low lymphocyte count, hypoproteinemia, hypokalemia, the persistent or worsen high CRP, high D-dimer, and high BNP, and the occurrence of hemoptysis and novel coronavirus (SARS-CoV-2) viremia were important indicators for early diagnosis and prediction of severe disease progression.\nC_LIO_LICharacteristic images of lung CT had a clear change in COVID-19, Ground-glass opacity (GGO) and high-density linear combinations may indicate different pathological changes. Rapid lobular progression of GGO suggests the possibility of severe disease.\nC_LIO_LIBasic principles of early intervention treatment of COVID-19: on the premise of no effective antiviral drugs, treatment is based on supportive and symptomatic therapy (albumin supplementation, supplement of potassium, supplement blood plasma, etc.) in order to maintain the stability of the intracellular environment and adequately reactivate body immunity to clean up SARS-CoV-2.\nC_LIO_LIAccording to severity, oxygenation index, body weight, age, underlying diseases, appropriate amount methylprednisolone application on severe/critical COVID-19 patients on demand, improved blood oxygen and reduced the utilization rate of invasive mechanical ventilation, case fatality rate and medical burden significantly. The most common indications for invasive mechanical ventilation should be strictly control in critical COVID-19 patients.\nC_LI\n\nConclusionsO_LIAccurate and timely identification of clinical features in severe risks, and early and appropriate intervention can block disease progression. 2. Appropriate dose of methylprednisolone can effectively avoid invasive mechanical ventilation and reduce case fatality rate in critical COVID-19 patients.\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "meizhu chen", - "author_inst": "hospital" - }, - { - "author_name": "changli tu", - "author_inst": "hospital" - }, - { - "author_name": "Cuiyan Tan", - "author_inst": "hospital" - }, - { - "author_name": "Xiaobin Zheng", - "author_inst": "hospital" - }, - { - "author_name": "xiaohua wang", - "author_inst": "hospital" - }, - { - "author_name": "jian wu", - "author_inst": "hospital" - }, - { - "author_name": "Yiying Huang", - "author_inst": "hospital" - }, - { - "author_name": "zhenguo wang", - "author_inst": "hospital" - }, - { - "author_name": "yan yan", - "author_inst": "hospital" - }, - { - "author_name": "zhonghe li", - "author_inst": "hospital" - }, - { - "author_name": "hong shan", - "author_inst": "hospital" - }, - { - "author_name": "Jing Liu", - "author_inst": "Fifth Affiliated Hospital of Sun Yan-sen University" - }, - { - "author_name": "jin huang", - "author_inst": "hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.04.07.20056390", "rel_title": "Adjuvant corticosteroid therapy for critically ill patients with COVID-19", @@ -1558565,6 +1560959,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2020.04.07.20056440", + "rel_title": "Convalescent Plasma to Treat COVID-19: Chinese Strategy and Experiences", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20056440", + "rel_abs": "The COVID-19 is currently spreading around the world, which has posed significant threats to global health and economy. Convalescent plasma is confirmed effective against the novel corona virus in preliminary studies. In this paper, we first described the therapeutic schedule, antibody detection method, indications, contraindications of the convalescent plasmas, and reported the operability of the treatment by case study.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Shiyao Pei", + "author_inst": "Department of Dermatology, Hunan Engineering Research Center of Skin Heath and Disease, Xiangya Hospital, Central South University, Changsha, Hunan Province, Ch" + }, + { + "author_name": "Xi Yuan", + "author_inst": "Department of Blood Transfusion of Xiangya Hospital, Central South University, Changsha, Hunan Province, China" + }, + { + "author_name": "Zhimin Zhimin Zhang", + "author_inst": "Department of Blood Transfusion of Xiangya Hospital, Central South University, Changsha, Hunan Province, China" + }, + { + "author_name": "Run Run Yao", + "author_inst": "Department of Blood Transfusion of Xiangya Hospital, Central South University, Changsha, Hunan Province, China" + }, + { + "author_name": "Yubin Xie", + "author_inst": "Department of Blood Transfusion Laboratory of Changsha Blood Center, 509 Wanjiali North Road, Changsha 410001, Hunan Province, China" + }, + { + "author_name": "Minxue Minxue Shen", + "author_inst": "Department of Dermatology, Hunan Engineering Research Center of Skin Heath and Disease, Xiangya Hospital, Central South University, Changsha, Hunan Province, Ch" + }, + { + "author_name": "Bijuan Bijuan Li", + "author_inst": "Department of Blood Transfusion of Xiangya Hospital, Central South University, Changsha, Hunan Province, China" + }, + { + "author_name": "Xiang Chen", + "author_inst": "Department of Dermatology, Hunan Engineering Research Center of Skin Heath and Disease, Xiangya Hospital, Central South University, Changsha, Hunan Province, Ch" + }, + { + "author_name": "Mingzhu Yin", + "author_inst": "Xiangya Hospital, Central South University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.06.20055392", "rel_title": "A study of SARS-CoV-2 evolution in Italy: from early days to secondary effects after social distancing", @@ -1559664,69 +1562109,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.04.10.032342", - "rel_title": "Potential host range of multiple SARS-like coronaviruses and an improved ACE2-Fc variant that is potent against both SARS-CoV-2 and SARS-CoV-1", - "rel_date": "2020-04-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.10.032342", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a currently uncontrolled pandemic and the etiological agent of coronavirus disease 2019 (COVID-19). It is important to study the host range of SARS-CoV-2 because some domestic species might harbor the virus and transmit it back to humans. In addition, insight into the ability of SARS-CoV-2 and SARS-like viruses to utilize animal orthologs of the SARS-CoV-2 receptor ACE2 might provide structural insight into improving ACE2-based viral entry inhibitors. Here we show that ACE2 orthologs of a wide range of domestic and wild animals support entry of SARS-CoV-2, as well as that of SARS-CoV-1, bat coronavirus RaTG13, and a coronavirus isolated from pangolins. Some of these species, including camels, cattle, horses, goats, sheep, pigs, cats, and rabbits may serve as potential intermediate hosts for new human transmission, and rabbits in particular may serve as a useful experimental model of COVID-19. We show that SARS-CoV-2 and SARS-CoV-1 entry could be potently blocked by recombinant IgG Fc-fusion proteins of viral spike protein receptor-binding domains (RBD-Fc) and soluble ACE2 (ACE2-Fc). Moreover, an ACE2-Fc variant, which carries a D30E mutation and has ACE2 truncated at its residue 740 but not 615, outperforms all the other ACE2-Fc variants on blocking entry of both viruses. Our data suggest that RBD-Fc and ACE2-Fc could be used to treat and prevent infection of SARS-CoV-2 and any new viral variants that emerge over the course of the pandemic.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Yujun Li", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Haimin Wang", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Xiaojuan Tang", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Danting Ma", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Chengzhi Du", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Yifei Wang", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Hong Pan", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Qing Zou", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Jie Zheng", - "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences" - }, - { - "author_name": "Liangde Xu", - "author_inst": "School of Biomedical Engineering and Eye Hospital, Wenzhou Medical University" - }, - { - "author_name": "Michael Farzan", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute" - }, - { - "author_name": "Guocai Zhong", - "author_inst": "Shenzhen Bay Laboratory" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.04.08.20057919", "rel_title": "Burden and prevalence of prognostic factors for severe covid-19 disease in Sweden", @@ -1559887,6 +1562269,49 @@ "type": "confirmatory results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.04.08.20058214", + "rel_title": "Characterizing key attributes of the epidemiology of COVID-19 in China: Model-based estimations", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20058214", + "rel_abs": "BackgroundA novel coronavirus strain, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in China in late 2019. The resulting disease, Coronavirus Disease 2019 (COVID-2019), soon became a pandemic. This study aims to characterize key attributes of the epidemiology of this infection in China.\n\nMethodsAn age-stratified mathematical model was constructed to describe the transmission dynamics and estimate the age-specific differences in the biological susceptibility to the infection, age-assortativeness in transmission mixing, case fatality rate (CFR), and transition in rate of infectious contacts (and reproduction number R0) following introduction of mass interventions.\n\nResultsThe model estimated the infectious contact rate in early epidemic at 0.59 contacts per day (95% uncertainty interval (UI)=0.48-0.71). Relative to those 60-69 years of age, susceptibility to the infection was only 0.06 in those [≤]19 years, 0.34 in 20-29 years, 0.57 in 30-39 years, 0.69 in 40-49 years, 0.79 in 50-59 years, 0.94 in 70-79 years, and 0.88 in [≥]80 years. The assortativeness in transmission mixing by age was very limited at 0.004 (95% UI=0.002-0.008). Final CFR was 5.1% (95% UI=4.8-5.4%). R0 rapidly declined from 2.1 (95% UI=1.8-2.4) to 0.06 (95% UI=0.05-0.07) following onset of interventions.\n\nConclusionAge appears to be a principal factor in explaining the patterns of COVID-19 transmission dynamics in China. The biological susceptibility to the infection seems limited among children, intermediate among young to mid-age adults, but high among those >50 years of age. There was no evidence for differential contact mixing by age, consistent with most transmission occurring in households rather than in schools or workplaces.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Houssein H Ayoub", + "author_inst": "Department of Mathematics, Statistics, and Physics, Qatar University, Doha, Qatar" + }, + { + "author_name": "Hiam Chemaitelly", + "author_inst": "Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar" + }, + { + "author_name": "Ghina R Mumtaz", + "author_inst": "Department of Epidemiology and population Health, American University of Beirut, Beirut, Lebanon" + }, + { + "author_name": "Shaheen Seedat", + "author_inst": "Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar" + }, + { + "author_name": "Susanne F Awad", + "author_inst": "Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar" + }, + { + "author_name": "Monia Makhoul", + "author_inst": "Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar" + }, + { + "author_name": "Laith J Abu-Raddad", + "author_inst": "Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.09.031252", "rel_title": "In-depth Bioinformatic Analyses of Human SARS-CoV-2, SARS-CoV, MERS-CoV, and Other Nidovirales Suggest Important Roles of Noncanonical Nucleic Acid Structures in Their Lifecycles", @@ -1560945,61 +1563370,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.09.20057901", - "rel_title": "Self-collection: an appropriate alternative during the SARS-CoV-2 pandemic", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20057901", - "rel_abs": "BACKGROUNDSwabs for SARS-CoV-2 are routinely collected by health care workers, putting them at risk of infection and requiring use of personal protective equipment (PPE). Self-collected swabs offer many advantages provided detection rate of SARS-CoV-2 and other respiratory viruses is not compromised.\n\nMETHODSIn a prospective study, patients attending dedicated COVID-19 collection clinics were offered the option to first self-collect (SC) nasal and throat swabs prior to health worker collection (HC). Two different laboratory services participated, with HC at Site 1 collecting nasal and throat swabs and at Site 2 nasopharyngeal (NP) and throat swabs. Samples were analysed for SARS-CoV-2 as well as common respiratory viruses. Concordance of results between methods was assessed using Cohens kappa ({kappa}).\n\nRESULTSOf 236 patients sampled by HC and SC, 25 had COVID-19 (24 by HC and 25 by SC) and 63 had other respiratory viruses (56 by HC and 58 by SC). SC was highly concordant with HC ({kappa} = 0.890) for all viruses including SARS-CoV-2 and more concordant than HC to positive results by any method ({kappa} = 0.959 vs 0.933).\n\nCONCLUSIONSSelf-collection of throat and nasal swabs offers a reliable alternative to health worker collection for the diagnosis of SARS-CoV-2 and other common respiratory viruses. High viral load of SARS-CoV-2 throughout the respiratory tract and sensitive molecular methods may explain these findings. Self-collection also provides patients with easier access to testing, reduces the exposure of the community and health workers to those undergoing testing and reduces the requirement for PPE.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Michael C Wehrhahn", - "author_inst": "Douglass Hanly Moir Pathology" - }, - { - "author_name": "Jennifer Robson", - "author_inst": "Sullivan Nicolaides Pathology" - }, - { - "author_name": "Suzanne Brown", - "author_inst": "Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital" - }, - { - "author_name": "Evan Bursle", - "author_inst": "Sullivan Nicolaides Pathology" - }, - { - "author_name": "Shane Byrne", - "author_inst": "Sullivan Nicolaides Pathology" - }, - { - "author_name": "David New", - "author_inst": "Clinipath Pathology" - }, - { - "author_name": "Smathi Chong", - "author_inst": "Clinipath Pathology" - }, - { - "author_name": "James P Newcombe", - "author_inst": "Douglass Hanly Moir Pathology" - }, - { - "author_name": "Terri Sivertsen", - "author_inst": "Douglass Hanly Moir Pathology" - }, - { - "author_name": "Narelle Hadlow", - "author_inst": "Clinipath Pathology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.08.20057794", "rel_title": "Factors associated with hospitalization and critical illness among 4,103 patients with COVID-19 disease in New York City", @@ -1561132,6 +1563502,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.07.20056937", + "rel_title": "Modeling the COVID-19 pandemic - parameter identification and reliability of predictions", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20056937", + "rel_abs": "In this paper, we try to identify the parameters for two elementary epidemic models, the so-called SI- and SIS-models, via non-linear regression using data of the COVID-19 pandemic. This is done based on the data for the number of daily infections. Studying the history of predictions made, we attempt to estimate their reliability concerning the future course of the epidemic. We validate this procedure using data for the case numbers in China and South Korea. Then we apply it in order to find predictions for Germany, Italy and the United States. The results are encouraging, but no final judgment on the validity of the procedure can yet be made.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Klaus Hackl", + "author_inst": "Ruhr-Universitaet Bochum" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.06.20053934", "rel_title": "Estimation of the percentages of asymptomatic patients and undiagnosed patients of the novel coronavirus (SARS-CoV-2) infection in Hokkaido, Japan by using birth-death process with recursive full tracing", @@ -1562083,33 +1564472,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.06.20053561", - "rel_title": "Probability of current COVID-19 outbreaks in all US counties", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20053561", - "rel_abs": "For each US county, we calculated the probability of an ongoing COVID-19 epidemic that may not yet be apparent. Based on confirmed cases as of April 15, 2020, COVID-19 is likely spreading in 86% of counties containing 97% of US population. Proactive measures before two cases are confirmed are prudent.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Emily M. Javan", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Spencer J. Fox", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Lauren Ancel Meyers", - "author_inst": "University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.09.20058974", "rel_title": "Predicting the number of reported and unreported cases for the COVID-19 epidemics in China, South Korea, Italy, France, Germany and United Kingdom", @@ -1562274,6 +1564636,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.06.20050575", + "rel_title": "Pulmonary and Cardiac Pathology in Covid-19: The First Autopsy Series from New Orleans", + "rel_date": "2020-04-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20050575", + "rel_abs": "SARS-CoV-2 has rapidly spread across the United States, causing extensive morbidity and mortality, though the histopathologic basis of severe disease cases has yet to be studied in detail. Over the past century, autopsy has contributed significantly to our understanding of numerous disease processes, but for several reasons, autopsy reports following deaths related to SARS- CoV-2 have thus far been limited across the globe. We report on the relevant cardiopulmonary findings in the first series of autopsies in the United States, with the cause of death being due to SARS-CoV-2 infection. These cases identify key pathologic states potentially contributing to severe disease and decompensation in these patients.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sharon E. Fox", + "author_inst": "LSU Health Sciences Center - New Orleans/ Southeast Louisiana Veterans Healthcare System" + }, + { + "author_name": "Aibek Akmatbekov", + "author_inst": "LSU Health Sciences Center - New Orleans" + }, + { + "author_name": "Jack L. Harbert", + "author_inst": "LSU Health Sciences Center - New Orleans" + }, + { + "author_name": "Guang Li", + "author_inst": "Tulane University" + }, + { + "author_name": "J. Quincy Brown", + "author_inst": "Tulane University" + }, + { + "author_name": "Richard S. Vander Heide", + "author_inst": "LSU Health Sciences Center - New Orleans" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.04.07.20045617", "rel_title": "Textile Masks and Surface Covers - A 'Universal Droplet Reduction Model'Against Respiratory Pandemics", @@ -1563293,41 +1565694,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.04.03.024885", - "rel_title": "Rapid in silico design of antibodies targeting SARS-CoV-2 using machine learning and supercomputing", - "rel_date": "2020-04-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.03.024885", - "rel_abs": "Rapidly responding to novel pathogens, such as SARS-CoV-2, represents an extremely challenging and complex endeavor. Numerous promising therapeutic and vaccine research efforts to mitigate the catastrophic effects of COVID-19 pandemic are underway, yet an efficacious countermeasure is still not available. To support these global research efforts, we have used a novel computational pipeline combining machine learning, bioinformatics, and supercomputing to predict antibody structures capable of targeting the SARS-CoV-2 receptor binding domain (RBD). In 22 days, using just the SARS-CoV-2 sequence and previously published neutralizing antibody structures for SARS-CoV-1, we generated 20 initial antibody sequences predicted to target the SARS-CoV-2 RBD. As a first step in this process, we predicted (and publicly released) structures of the SARS-CoV-2 spike protein using homology-based structural modeling. The predicted structures proved to be accurate within the targeted RBD region when compared to experimentally derived structures published weeks later. Next we used our in silico design platform to iteratively propose mutations to SARS-CoV-1 neutralizing antibodies (known not to bind SARS-Cov-2) to enable and optimize binding within the RBD of SARS-CoV-2. Starting from a calculated baseline free energy of -48.1 kcal/mol ({+/-} 8.3), our 20 selected first round antibody structures are predicted to have improved interaction with the SARS-CoV-2 RBD with free energies as low as -82.0 kcal/mole. The baseline SARS-CoV-1 antibody in complex with the SARS-CoV-1 RBD has a calculated interaction energy of -52.2 kcal/mole and neutralizes the virus by preventing it from binding and entering the human ACE2 receptor. These results suggest that our predicted antibody mutants may bind the SARS-CoV-2 RBD and potentially neutralize the virus. Additionally, our selected antibody mutants score well according to multiple antibody developability metrics. These antibody designs are being expressed and experimentally tested for binding to COVID-19 viral proteins, which will provide invaluable feedback to further improve the machine learning-driven designs. This technical report is a high-level description of that effort; the Supplementary Materials includes the homology-based structural models we developed and 178,856 in silico free energy calculations for 89,263 mutant antibodies derived from known SARS-CoV-1 neutralizing antibodies.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Thomas Desautels", - "author_inst": "Lawrence Livermore National Laboratory" - }, - { - "author_name": "Adam Zemla", - "author_inst": "Lawrence Livermore National Laboratory" - }, - { - "author_name": "Edmond Lau", - "author_inst": "Lawrence Livermore National Laboratory" - }, - { - "author_name": "Magdalena Franco", - "author_inst": "Lawrence Livermore National Laboratory" - }, - { - "author_name": "Daniel Faissol", - "author_inst": "Lawrence Livermore National Laboratory" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.04.07.20057356", "rel_title": "The Immediate Effect of COVID-19 Policies on Social Distancing Behavior in the United States", @@ -1563420,6 +1565786,25 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.04.08.20057489", + "rel_title": "Signature of State measures on the COVID-19 Pandemic in China, Italy, and USA", + "rel_date": "2020-04-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20057489", + "rel_abs": "We show the dynamics of COVID-19 outbreak in Italy and USA, in comparison with China, and the early response of the countries. Our mathematical techniques makes it possible to calculate the rate of growth of the cases efficiently, and provides a good understanding of future trends in Italy and USA. The evolution of the real time data makes it possible to analyse the suitability of steps taken to eradicate the pandemic by the countries. We compare the day to day development of the coronavirus cases in Italy and USA, that keeping in view the population pyramid and the population density, leads us to understand possible difference in the number of effected population.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Farhan Saif", + "author_inst": "Quaid-i-Azam University, Islamabad" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.06.028522", "rel_title": "Systemic analysis of tissue cells potentially vulnerable to SARS-CoV-2 infection by the protein-proofed single-cell RNA profiling of ACE2, TMPRSS2 and Furin proteases", @@ -1565143,117 +1567528,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.04.08.029769", - "rel_title": "Tocilizumab treatment in severe COVID-19 patients attenuates the inflammatory storm incited by monocyte centric immune interactions revealed by single-cell analysis", - "rel_date": "2020-04-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.08.029769", - "rel_abs": "ABSTRACTDespite the current devastation of the COVID-19 pandemic, several recent studies have suggested that the immunosuppressive drug Tocilizumab can powerfully treating inflammatory responses that occur in this disease. Here, by employing single-cell analysis of the immune cell composition of severe-stage COVID-19 patients and these same patients in post Tocilizumab-treatment remission, we have identified a monocyte subpopulation specific to severe disease that contributes to inflammatory storms in COVID-19 patients. Although Tocilizumab treatment attenuated the strong inflammatory immune response, we found that immune cells including plasma B cells and CD8+ T cells still exhibited an intense humoral and cell-mediated anti-virus immune response in COVID-19 patients after Tocilizumab treatment. Thus, in addition to providing a rich, very high-resolution data resource about the immune cell distribution at multiple stages of the COVID-19 disease, our work both helps explain Tocilizumab\u2019s powerful therapeutic effects and defines a large number of potential new drug targets related to inflammatory storms.Competing Interest StatementJingwen Fang is the executive officer of HanGen BiotechView Full Text", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Chuang Guo", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Bin Li", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Huan Ma", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Xiaofang Wang", - "author_inst": "Department of Hepatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of Chin" - }, - { - "author_name": "Pengfei Cai", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Qiaoni Yu", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Lin Zhu", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Liying Jin", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Chen Jiang", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Jingwen Fang", - "author_inst": "HanGene Biotech, Xiaoshan Innovation Polis, Hangzhou, Zhejiang, China" - }, - { - "author_name": "Qian Liu", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Dandan Zong", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Wen Zhang", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Yichen Lu", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Kun Li", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Xuyuan Gao", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Binqing Fu", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Lianxin Liu", - "author_inst": "Department of Hepatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of Chin" - }, - { - "author_name": "Xiaoling Ma", - "author_inst": "Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China," - }, - { - "author_name": "Jianping Weng", - "author_inst": "Department of Endocrinology and Metabolism, The First Affiliated Hospital of USTC, Division of Life Sciences of Medicine, University of Science and Technology o" - }, - { - "author_name": "Haiming Wei", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Tengchuan Jin", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Jun Lin", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Kun Qu", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.04.07.030742", "rel_title": "Gene expression and in situ protein profiling of candidate SARS-CoV-2 receptors in human airway epithelial cells and lung tissue", @@ -1565502,6 +1567776,105 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.04.09.033233", + "rel_title": "Structural basis for the inhibition of COVID-19 virus main protease by carmofur, an antineoplastic drug", + "rel_date": "2020-04-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.09.033233", + "rel_abs": "The antineoplastic drug Carmofur was shown to inhibit SARS-CoV-2 main protease (Mpro). Here the X-ray crystal structure of Mpro in complex with Carmofur reveals that the carbonyl reactive group of Carmofur is covalently bound to catalytic Cys145, whereas its fatty acid tail occupies the hydrophobic S2 subsite. Carmofur inhibits viral replication in cells (EC50 = 24.30 M) and it is a promising lead compound to develop new antiviral treatment for COVID-19.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Zhenming Jin", + "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" + }, + { + "author_name": "Yao Zhao", + "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" + }, + { + "author_name": "Yuan Sun", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China." + }, + { + "author_name": "Bing Zhang", + "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" + }, + { + "author_name": "Haofeng Wang", + "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" + }, + { + "author_name": "Yan Wu", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China." + }, + { + "author_name": "Yan Zhu", + "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" + }, + { + "author_name": "Chen Zhu", + "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" + }, + { + "author_name": "Tianyu Hu", + "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" + }, + { + "author_name": "Xiaoyu Du", + "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" + }, + { + "author_name": "Yinkai Duan", + "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" + }, + { + "author_name": "Jing Yu", + "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" + }, + { + "author_name": "Xiaobao Yang", + "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" + }, + { + "author_name": "Xiuna Yang", + "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" + }, + { + "author_name": "Kailin Yang", + "author_inst": "Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA" + }, + { + "author_name": "Xiang Liu", + "author_inst": "State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, College of Pharmacy, Nankai University" + }, + { + "author_name": "Luke W. Guddat", + "author_inst": "School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia" + }, + { + "author_name": "Gengfu Xiao", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China" + }, + { + "author_name": "Leike Zhang", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China" + }, + { + "author_name": "Haitao Yang", + "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" + }, + { + "author_name": "Zihe Rao", + "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.04.08.033001", "rel_title": "Relative Abundance of SARS-CoV-2 Entry Genes in the Enterocytes of the Lower Gastrointestinal Tract", @@ -1566624,33 +1568997,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.04.03.20052563", - "rel_title": "Interaction between malarial transmission and BCG vaccination with COVID-19 incidence in the world map: A changing landscape human immune system?", - "rel_date": "2020-04-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.03.20052563", - "rel_abs": "BackgroundCOVID-19 (Corona virus Disease-2019) is a new public health emergency and is a pandemic currently. Incidence and mortality of COVID-19 vary in different geographical areas. In this study we aimed to analyse the relationship between malaria transmission and BCG vaccination with COVID-19 incidence in the world map.\n\nMaterials and methodsWe collected malaria cases data (World Health Organisation (WHO), 2018), worldwide COVID-19 cases and mortality data (European Centre for Disease Prevention and Control) and data on BCG vaccination. COVID-19 incidence and mortality was compared.\n\nFindingsData on 5316978938 persons from 166 countries were analysed. Malaria incidence rate was negatively correlated with COVID-19 incidence rate (correlation coefficient = -0.513, p<0.001). Malaria free countries had significantly higher number of COVID-19 cases compared to malaria endemic countries. In Europe and Americas, countries, which have higher BCG vaccination coverage, had significantly less mortality per thousand population compared to those with low BCG coverage (median 0.0002 (0-0.0005) vs 0.0029 (0.0002-0.0177), p=0.017). The case fatality ratio of COVID-19 was related nonlinearly to the malaria incidence.\n\nConclusionsThe results suggest the changing human immune system as we progress to eliminate parasitic diseases with time. Chloroquine exposure in malaria endemic zones might have a protective effect.\n\nSummary boxO_ST_ABS\"What is already known on this subject?\"C_ST_ABSTo the best of the authors no similar evidence, of the effect of malarial transmission on the COVID-19 global distribution is known. The effect of the Bacille Calmette Guerin (BCG) vaccine on modifying the human immune system has been reported before and is postulated to protective against certain viral infections like Influenza A (H1N1) and herpes virus.\n\n\"What this study adds?\"This study finds that COVID-19 incidence, worldwide is less in countries, which are malaria-endemic. In the European and American countries, increased BCG coverage may have some mortality advantage against COVID-19. The case fatality rate was related to malaria incidence, however, in a complex way. This could be a window into the changing landscape of human immune system as we progress to eliminate parasitic disease with time or this could be due to long-term protective body level of anti-malarials like chloroquine or hydroxychloroquine in countries with higher malaria incidence rate.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Rudra Prosad Goswami", - "author_inst": "All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Dheeraj K Mittal", - "author_inst": "AIIMS, New Delhi, India" - }, - { - "author_name": "Rama Prosad Goswami", - "author_inst": "School of Tropical Medicine, Kolkata, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.06.026765", "rel_title": "Noisy Pooled PCR for Virus Testing", @@ -1567929,73 +1570275,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.05.20046433", - "rel_title": "The phenotypic changes of \u03b3\u03b4 T cells in COVID-19 patients", - "rel_date": "2020-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.05.20046433", - "rel_abs": "A novel pneumonia-associated respiratory syndrome named coronavirus disease-2019 (COVID-19), which caused by SARS-CoV-2 and broken in Wuhan, China in the end of 2019. Unfortunately, there is no specific antiviral agent or vaccine available to treat SARS-CoV-2 infections. Also, information regarding the immunological characteristics in COVID-19 patients remains limited. Here we collected the blood samples from 18 healthy donors (HD) and 38 COVID-19 patients to analyze changes in {gamma}{delta} T cells. In comparison to HD, the {gamma}{delta} T cells percentage was decreased. {gamma}{delta} T cells are able to immediately respond to SARS-CoV-2 infection and upregulate the activation marker CD25. In addition, the increased expression of CD4 in {gamma}{delta} T cells may serve as a biomarker for the assessment of SARS-CoV-2 infection.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Lei Lei", - "author_inst": "Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center" - }, - { - "author_name": "Hongbo Qian", - "author_inst": "Department of Clinical Laboratory, The 8th hospital of Xi'an" - }, - { - "author_name": "Xiaofeng Yang", - "author_inst": "Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center" - }, - { - "author_name": "Xiaobo Zhou", - "author_inst": "Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center" - }, - { - "author_name": "Xingzhe Zhang", - "author_inst": "Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center" - }, - { - "author_name": "Dan Zhang", - "author_inst": "Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center" - }, - { - "author_name": "Tongxin Dai", - "author_inst": "Department of Clinical Laboratory, The 8th hospital of Xi'an" - }, - { - "author_name": "Rui Guo", - "author_inst": "Department of Clinical Laboratory, The 8th hospital of Xi'an" - }, - { - "author_name": "Lin Shi", - "author_inst": "Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center" - }, - { - "author_name": "Yanbin Cheng", - "author_inst": "Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center" - }, - { - "author_name": "Baojun Zhang", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Jinsong Hu Hu", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Yaling Guo", - "author_inst": "Department of Clinical Laboratory, The 8th hospital of Xi'an" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2020.04.03.20051649", "rel_title": "Efficacy of face mask in preventing respiratory virus transmission: a systematic review and meta-analysis", @@ -1568081,6 +1570360,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.05.20048421", + "rel_title": "Loss of smell and taste in combination with other symptoms is a strong predictor of COVID-19 infection", + "rel_date": "2020-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.05.20048421", + "rel_abs": "ImportanceA strategy for preventing further spread of the ongoing COVID-19 epidemic is to detect infections and isolate infected individuals without the need of extensive bio-specimen testing.\n\nObjectivesHere we investigate the prevalence of loss of smell and taste among COVID-19 diagnosed individuals and we identify the combination of symptoms, besides loss of smell and taste, most likely to correspond to a positive COVID-19 diagnosis in non-severe cases.\n\nDesignCommunity survey.\n\nSetting and ParticipantsSubscribers of RADAR COVID-19, an app that was launched for use among the UK general population asking about COVID-19 symptoms.\n\nMain ExposureLoss of smell and taste.\n\nMain Outcome MeasuresCOVID-19.\n\nResultsBetween 24 and 29 March 2020, 1,573,103 individuals reported their symptoms via the app; 26% reported suffering from one or more symptoms of COVID-19. Of those, n=1702 reported having had a RT-PCR COVID-19 test and gave full report on symptoms including loss of smell and taste; 579 were positive and 1123 negative. In this subset, we find that loss of smell and taste were present in 59% of COVID-19 positive individuals compared to 18% of those negative to the test, yielding an odds ratio (OR) of COVID-19 diagnosis of OR[95%CI]=6.59[5.25; 8.27], P= 1.90x10-59. We also find that a combination of loss of smell and taste, fever, persistent cough, fatigue, diarrhoea, abdominal pain and loss of appetite is predictive of COVID-19 positive test with sensitivity 0.54[0.44; 0.63], specificity 0.86[0.80; 0.90], ROC-AUC 0.77[0.72; 0.82] in the test set, and cross-validation ROC-AUC 0.75[0.72; 0.77]. When applied to the 410,598 individuals reporting symptoms but not formally tested, our model predicted that 13.06%[12.97%;13.15] of these might have been already infected by the virus.\n\nConclusions and RelevanceOur study suggests that loss of taste and smell is a strong predictor of having been infected by the COVID-19 virus. Also, the combination of symptoms that could be used to identify and isolate individuals includes anosmia, fever, persistent cough, diarrhoea, fatigue, abdominal pain and loss of appetite. This is particularly relevant to healthcare and other key workers in constant contact with the public who have not yet been tested for COVID-19.\n\nKey pointsO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIThe spread of COVID-19 can be reduced by identifying and isolating infected individuals but it is not possible to test everyone and priority has been given in most countries to individuals presenting symptoms of the disease.\nC_LIO_LICOVID-19 symptoms, such as fever, cough, aches, fatigue are common in many other viral infections\nC_LIO_LIThere is therefore a need to identify symptom combinations that can rightly pinpoint to infected individuals\nC_LI\n\nWhat this study addsO_LIAmong individuals showing symptoms severe enough to be given a COVID-19 RT-PCR test in the UK the prevalence of loss of smell (anosmia) was 3-fold higher (59%) in those positive to the test than among those negative to the test (18%).\nC_LIO_LIWe developed a mathematical model combining symptoms to predict individuals likely to be COVID-19 positive and applied this to over 400,000 individuals in the general population presenting some of the COVID-19 symptoms.\nC_LIO_LIWe find that [~]13% of those presenting symptoms are likely to have or have had a COVID-19 infection. The proportion was slightly higher in women than in men but is comparable in all age groups, and corresponds to 3.4% of those who filled the app report.\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Cristina Menni", + "author_inst": "King's College London" + }, + { + "author_name": "Ana Valdes", + "author_inst": "NIHR Nottingham Biomedical Research Centre, School of Medicine, University of Nottingham" + }, + { + "author_name": "Maxim B Freydin", + "author_inst": "King's College London" + }, + { + "author_name": "Sajaysurya Ganesh", + "author_inst": "Zoe Global limited" + }, + { + "author_name": "Julia El-Sayed Moustafa", + "author_inst": "King's College London" + }, + { + "author_name": "Alessia Visconti", + "author_inst": "King's College London" + }, + { + "author_name": "Pirro Hysi", + "author_inst": "King's College London" + }, + { + "author_name": "Ruth C E Bowyer", + "author_inst": "King's College London" + }, + { + "author_name": "Massimo Mangino", + "author_inst": "King's College London" + }, + { + "author_name": "Mario Falchi", + "author_inst": "King's College London" + }, + { + "author_name": "Jonathan Wolf", + "author_inst": "Zoe Global Limited" + }, + { + "author_name": "Claire Steves", + "author_inst": "King's College London" + }, + { + "author_name": "Tim Spector", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.06.20052159", "rel_title": "Efficient and Practical Sample Pooling High-Throughput PCR Diagnosis of COVID-19", @@ -1569139,49 +1571485,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.05.20053769", - "rel_title": "Validation of reported risk factors for disease classification and prognosis in COVID-19: a descriptive and retrospective study", - "rel_date": "2020-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.05.20053769", - "rel_abs": "Risk indicators viral load (ORF1ab Ct), lymphocyte percentage (LYM%), C-reactive protein (CRP), interleukin-6 (IL-6), procalcitonin (PCT) and lactic acid (LA) in COVID-19 patients have been proposed in recent studies. However, the predictive effects of those indicators on disease classification and prognosis remains largely unknown. We dynamically measured those reported indicators in 132 cases of COVID-19 patients including the moderate-cured (moderated and cured), severe-cured (severe and cured) and critically ill (died). Our data showed that CRP, PCT, IL-6, LYM%, lactic acid and viral load could predict prognosis and guide classification of COVID-19 patients in different degrees. CRP, IL-6 and LYM% were more effective than other three factors in predicting prognosis. For disease classification, CRP and LYM% were sensitive in identifying the types between critically ill and severe (or moderate). Notably, among the investigated factors, LYM% was the only one that could distinguish between the severe and moderate types. Collectively, we concluded that LYM% was the most sensitive and reliable predictor for disease typing and prognosis. During the COVID-19 pandemic, the precise classification and prognosis prediction are critical for saving the insufficient medical resources, stratified treatment and improving the survival rate of critically ill patients. We recommend that LYM% be used independently or in combination with other indicators in the management of COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Li Tan", - "author_inst": "General Hospital of Central Theater Command of PLA, Wuhan, Hubei, China" - }, - { - "author_name": "Xia Kang", - "author_inst": "Third Military Medical University (Army Medical University)" - }, - { - "author_name": "Xinran Ji", - "author_inst": "Chinese People's Liberation Army General Hospital (301 Hospital)" - }, - { - "author_name": "Qi Wang", - "author_inst": "General hospital of Central Threater Command,PRC" - }, - { - "author_name": "Yongsheng li", - "author_inst": "Third Military Medical University (Army Medical University)" - }, - { - "author_name": "Qiongshu Wang", - "author_inst": "General Hospital of Central Theater Command of PLA, Wuhan, Hubei, China" - }, - { - "author_name": "Hongming Miao", - "author_inst": "Third Military Medical University (Army Medical University)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.03.20052878", "rel_title": "Search for trends of Covid-19 infection in India, China, Denmark, Brazil, France. Germany and the USA on the basis of power law scaling", @@ -1569295,6 +1571598,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.04.20053017", + "rel_title": "A mechanistic population balance model to evaluate the impact of interventions on infectious disease outbreaks: Case for COVID19", + "rel_date": "2020-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.04.20053017", + "rel_abs": "Infectious diseases can be devastating, especially when new and highly contagious, producing epidemic outbreaks that can become pandemics. Such is the case of COVID-19, the worst pandemic the world has seen in more than 100 years. Predicting the course and outcomes of such a pandemic in relation to possible interventions is crucial for societal and healthcare planning and forecasting of resource needs. In this work a deterministic model was developed, using elements from the SIR-type models, that describes individuals in a population in compartments by infection stage and age group. The model assumes a close well-mixed community with no migrations. Infection rates and clinical and epidemiological information govern the transitions between stages of the disease. The present model provides a platform to build upon and its current low complexity retains accessibility to both experts and non-experts as well as policy makers to comprehend the variables and phenomena at play.\n\nThe impact of several possible interventions that have been or may be applied to slow the spread of the COVID-19 outbreak is evaluated. Key findings in our model simulation results indicate that (i) universal social isolation measures may be effective in reducing total fatalities only if they are strict and the average number of daily social interactions is reduced to very low numbers; (ii) selective isolation of only the age groups most vulnerable to the disease (i.e. older than 60) appears almost as effective in reducing total fatalities but at a much lower economic damage; (iii) the use of protective equipment (PPE) appears capable of very significantly reducing total fatalities if implemented extensively and to a high degree; (iv) extensive random testing of the population leading to infection recognition and subsequent immediate (self) isolation of the infected individuals, appears to be an ineffective intervention due to the required (unreachable with existing test sensitivities) high percentage of infection detections and the incapability to be sustained over time; (v) an increase in the number of critical care beds to directly save significant numbers of lives with a direct reduction in total final fatalities per each extra available critical care bed unit.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jorge Rodriguez", + "author_inst": "Khalifa University" + }, + { + "author_name": "Mauricio Paton", + "author_inst": "Khalifa University" + }, + { + "author_name": "Joao M Uratani", + "author_inst": "Khalifa University" + }, + { + "author_name": "Juan M Acuna", + "author_inst": "Khalifa University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.04.20053579", "rel_title": "Adaptive cyclic exit strategies from lockdown to suppress COVID-19 and allow economic activity", @@ -1570589,45 +1572923,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.02.20051441", - "rel_title": "Chaos theory applied to the outbreak of Covid-19: an ancillary approach to decision-making in pandemic context", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20051441", - "rel_abs": "Predicting the course of an epidemic is difficult, predicting the course of a pandemic from an emerging virus even more so. The validity of most predictive models relies on numerous parameters, involving biological and social characteristics often unknown or highly uncertain. Data of the COVID-19 epidemics in China, Japan, South Korea and Italy were used to build up deterministic models without strong hypothesis. These models were then applied to other countries to identify the closest scenarios in order to foresee their coming behaviour. The models enabled to predict situations that were confirmed little by little, proving that these tools can be efficient and useful for decision-making in a quickly evolving operational context.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sylvain Mangiarotti", - "author_inst": "Centre d'Etudes Spatiales de la Biosphere" - }, - { - "author_name": "Marisa Peyre", - "author_inst": "ASTRE" - }, - { - "author_name": "Yan Zhang", - "author_inst": "CESBIO" - }, - { - "author_name": "Mireille Huc", - "author_inst": "CESBIO" - }, - { - "author_name": "Francois Roger", - "author_inst": "ASTRE" - }, - { - "author_name": "Yann Kerr", - "author_inst": "CESBIO" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.02.20051466", "rel_title": "Predictions for COVID-19 outbreak in India using Epidemiological models", @@ -1570705,6 +1573000,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.01.20047225", + "rel_title": "Using curvature to infer COVID-19 fractal epidemic network fragility and systemic risk", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.01.20047225", + "rel_abs": "The damage of the novel Coronavirus disease (COVID-19) is reaching unprecedented scales. There are numerous classical epidemiology models trying to quantify epidemiology metrics. Usually, to forecast epidemics, classical approaches need parameter estimations, such as the contagion rate or the basic reproduction number. Here, we propose a data-driven, parameter-free, geometric approach to access the emergence of a pandemic state by studying the Forman-Ricci and Ollivier-Ricci network curvatures. Discrete Ollivier-Ricci curvature has been used successfully to forecast risk in financial networks and we suggest that those results can provide analogous results for COVID-19 epidemic time-series. We first compute both curvatures in a toy-model of epidemic time-series with delays, which allows us to create epidemic networks. By doing so, we are able to verify that the Ollivier-Ricci and Forman-Ricci curvatures can be a parameter-free estimate for identifying a pandemic state in the simulated epidemic. On this basis, we then compute both Forman-Ricci and Ollivier-Ricci curvatures for real epidemic networks built from COVID-19 epidemic time-series available at the World Health Organization (WHO). Both curvatures allow us to detect early warning signs of the emergence of the pandemic. The advantage of our method lies in providing an early geometrical data marker for the pandemic state, regardless of parameter estimation and stochastic modelling. This work opens the possibility of using discrete geometry to study epidemic networks.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Danillo Barros de Souza", + "author_inst": "Departamento de Matematica, Universidade Federal de Pernambuco, Recife-Brazil" + }, + { + "author_name": "Jonatas T. S. da Cunha", + "author_inst": "Departamento de Matematica, Universidade Federal de Pernambuco, Recife-PE Brazil" + }, + { + "author_name": "Everlon Figueiroa", + "author_inst": "Laboratorio de Imunopatologia Keizo Asami (LIKA) - Universidade de Federal de Pernambuco, Recife-Brazil" + }, + { + "author_name": "Jailson B Correia", + "author_inst": "Laboratorio de Imunopatologia Keizo Asami (LIKA) - Universidade de Federal de Pernambuco, Recife-Brazil" + }, + { + "author_name": "Hernande P da Silva", + "author_inst": "Laboratorio de Imunopatologia Keizo Asami (LIKA) - Universidade de Federal de Pernambuco, Recife-Brazil" + }, + { + "author_name": "Jose Luiz de Lima Filho", + "author_inst": "Laboratorio de Imunopatologia Keizo Asami (LIKA) - Universidade de Federal de Pernambuco (UFPE), Recife-Brazil" + }, + { + "author_name": "Jones Albuquerque", + "author_inst": "Instituto para Reducao de Riscos e Disastres de Pernambuco - Universidade Federal Rural de Pernambuco (IRRD-PE) and Laboratorio de Imunopatologia Keizo Asami " + }, + { + "author_name": "Fernando A N Santos", + "author_inst": "Vrije Universiteit Amsterdam Medical Center, Amsterdam - The Netherlands and Departamento de Matematica, Universidade Federal de Pernambuco, Recife-Brazil" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.03.20052084", "rel_title": "Quantifying the effect of quarantine control in Covid-19 infectious spread using machine learning", @@ -1571763,45 +1574105,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.03.20050195", - "rel_title": "Assessment of Specimen Pooling to Conserve SARS CoV-2 Testing Resources", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.03.20050195", - "rel_abs": "ObjectivesTo establish the optimal parameters for group testing of pooled specimens for the detection of SARS-CoV-2.\n\nMethodsThe most efficient pool size was determined to be 5 specimens using a web-based application. From this analysis, 25 experimental pools were created using 50 microliter from one SARS-CoV-2 positive nasopharyngeal specimen mixed with 4 negative patient specimens (50 microliter each) for a total volume of 250 microliter l. Viral RNA was subsequently extracted from each pool and tested using the CDC SARS-CoV-2 RT-PCR assay. Positive pools were consequently split into individual specimens and tested by extraction and PCR. This method was also tested on an unselected group of 60 nasopharyngeal specimens grouped into 12-pools.\n\nResultsAll 25 pools were positive with Cycle threshold (Ct) values within 0 and 5.03 Ct of the original individual specimens. The analysis of 60 specimens determined that two pools were positive followed by identification of two individual specimens among the 60 tested. This testing was accomplished while using 22 extractions/PCR tests, a savings of 38 reactions.\n\nConclusionsWhen the incidence rate of SARS-CoV-2 infection is 10% or less, group testing will result in the saving of reagents and personnel time with an overall increase in testing capability of at least 69%.\n\nKey PointsSARS CoV-2, COVID-19, Group testing", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Baha Abdalhamid", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Christopher R Bilder", - "author_inst": "University of Nebraska-Lincoln" - }, - { - "author_name": "Emily L McCutchen", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Steven H Hinrichs", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Scott A Koepsell", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Peter C Iwen", - "author_inst": "Nebraska Public Health Laboratory, University of Nebraska Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.02.20050997", "rel_title": "Acute liver injury and its association with death risk of patients with COVID-19: a hospital-based prospective case-cohort study", @@ -1571939,6 +1574242,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.01.20050229", + "rel_title": "A Contribution to the Mathematical Modeling of the Corona/COVID-19 Pandemic", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.01.20050229", + "rel_abs": "The responsible estimation of parameters is a main issue of mathematical pandemic models. Especially a good choice of {beta} as the number of others that one infected person encounters per unit time (per day) influences the adequateness of the results of the model. For the example of the actual COVID-19 pandemic some aspects of the parameter choice will be discussed. Because of the incompatibility of the data of the Johns-Hopkins-University [3] to the data of the German Robert-Koch-Institut we use the COVID-19 data of the European Centre for Disease Prevention and Control [2] (ECDC) as a base for the parameter estimation. Two different mathematical methods for the data analysis will be discussed in this paper and possible sources of trouble will be shown.\n\nParameters for several countries like UK, USA, Italy, Spain, Germany and China will be estimated and used in W. O. Kermack and A. G. McKendricks SIR model[1]. Strategies for the commencing and ending of social and economic shutdown measures are discussed.\n\nThe numerical solution of the ordinary differential equation system of the modified SIR model is being done with a Runge-Kutta integration method of fourth order [4].\n\nAt the end the applicability of the SIR model could be shown. Suggestions about appropriate points in time at which to commence with lockdown measures based on the acceleration rate of infections conclude the paper. This paper is an improved sequel of [5].", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Guenter K.F. Baerwolff", + "author_inst": "Technical University of Berlin" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.01.20049908", "rel_title": "The effect of non-pharmaceutical interventions on COVID-19 cases, deaths and demand for hospital services in the UK: a modelling study", @@ -1572929,33 +1575251,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.04.02.20051490", - "rel_title": "Forecast of the COVID-19 outbreak, collapse of medical facilities, and lockdown effects in Tokyo, Japan", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20051490", - "rel_abs": "BackgroundThe number of patients of COVID-19 in Tokyo has been increasing gradually through the end of March, 2020.\n\nObjectSupport for policymaking requires forecasting of the entire course and outcome of the outbreak if a self-restraint in going out is not initiated. Moreover, the effects of a self-restraint in going out must be considered when choosing to initiate one. Method: Data of Tokyo patients with symptoms during January 14 - March 28, 2020 were used to formulate a susceptible-infected-recovered (SIR) model using three age classes and to estimate the basic reproduction number (R0). Based on the estimated R0, We inferred outbreak outcomes and medical burden if a self-restraint in going out were not enacted. Then we estimate the self-restraint in going out effects.\n\nResultsResults suggest R0 as 2.86, with a 95% confidence interval of [2.73, 2.97]. Exhaustion of medical resources can be expected to occur on April 26 if no self-restraint in going out occurs. If a self-restraint in going out were enacted from April 6, and if more than 60% of trips outside the home were restricted voluntarily, then medical care service could be maintained.\n\nDiscussion and ConclusionThe estimated R0 was similar to that found from other studies conducted in China and Japan. Results demonstrate that a self-restraint in going out with reasonable cooperation of residents is required to maintain medical care.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Junko Kurita", - "author_inst": "Department of Nursig, Tokiwa University, Ibaraki, Japan" - }, - { - "author_name": "Tamie Sugawara", - "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" - }, - { - "author_name": "Yasushi Ohkusa", - "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.01.20047373", "rel_title": "Frequency of testing for COVID 19 infection and the presence of higher number of available beds per country predict outcomes with the infection, not the GDP of the country - A descriptive statistical analysis", @@ -1573185,6 +1575480,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2020.04.03.20047530", + "rel_title": "Estimating Impact of Austerity policies in COVID-19 fatality rates:Examining the dynamics of economic policy and Case Fatality Rates (CFR) of COVID-19 in OCED countries", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.03.20047530", + "rel_abs": "The paper will attempt to estimate factors which determine the variability of case fatality rates of COVID-19 across OECD countries in the recent time. The objective of the paper is to estimate the impact of government health policies on fatality rates (Case fatality rates) of COVID-19 in_OECD countries while controlling for other demographic and economic characteristics. The analysis is done using non-parametric regression method, i.e. Quantile regression. The result from quantile regression analysis shows that a policy of Austerity (health expenditure cuts) significantly increases the mortality rates of COVID-19 in OECD countries. The policy implication of the study is the need for a robust public-funded health system with wider accessibility to deal with major public health crisis like COVID-19 pandemic.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Dawa Sherpa", + "author_inst": "Jawaharlal Nehru University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2020.04.02.20051177", "rel_title": "Could SARS-CoV-2 be transmitted via speech droplets?", @@ -1574351,45 +1576665,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.03.31.018556", - "rel_title": "Fatal toxicity of chloroquine or hydroxychloroquine with metformin in mice", - "rel_date": "2020-04-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.31.018556", - "rel_abs": "Guided by the principle of primum non nocere (first do no harm), we report a cautionary note on the potential fatal toxicity of chloroquine (CQ) or hydroxychloroquine (HCQ) in combination with anti-diabetic drug metformin. We observed that the combination of CQ or HCQ and metformin, which were used in our studies as potential anti-cancer drugs, killed 30-40% of mice. While our observations in mice may not translate to toxicity in humans, the reports that CQ or HCQ has anti-COVID-19 activity, the use of CQ resulting in toxicity and at least one death, and the recent Emergency Use Authorization (EUA) for CQ and HCQ by the US Food and Drug Administration (FDA) prompted our report. Here we report the lethality of CQ or HCQ in combination with metformin as a warning of its potential serious clinical toxicity. We hope that our report will be helpful to stimulate pharmacovigilance and monitoring of adverse drug reactions with the use of CQ or HCQ, particularly in combination with metformin.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "N.V Rajeshkumar", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Shinichi Yabuuchi", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Shweta G Pai", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Anirban Maitra", - "author_inst": "UT MD Anderson Cancer Center" - }, - { - "author_name": "Manuel Hidalgo", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Chi V Dang", - "author_inst": "Ludwig Institute for Cancer Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.03.31.20038935", "rel_title": "Angiotensin II Receptor Blockers and Angiotensin-Converting Enzyme Inhibitors Usage is Associated with Improved Inflammatory Status and Clinical Outcomes in COVID-19 Patients With Hypertension", @@ -1574527,6 +1576802,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2020.04.01.20047381", + "rel_title": "Level of IL-6 predicts respiratory failure in hospitalized symptomatic COVID-19 patients", + "rel_date": "2020-04-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.01.20047381", + "rel_abs": "The pandemic Coronavirus-disease 19 (COVID-19) is characterized by a heterogeneous clinical course. While most patients experience only mild symptoms, a relevant proportion develop severe disease progression with increasing hypoxia up to acute respiratory distress syndrome. The substantial number of patients with severe disease have strained intensive care capacities to an unprecedented level. Owing to the highly variable course and lack of reliable predictors for deterioration, we aimed to identify variables that allow the prediction of patients with a high risk of respiratory failure and need of mechanical ventilation Patients with PCR proven symptomatic COVID-19 infection hospitalized at our institution from 29th February to 27th March 2020 (n=40) were analyzed for baseline clinical and laboratory findings. Patients requiring mechanical ventilation 13/40 (32.5%) did not differ in age, comorbidities, radiological findings, respiratory rate or qSofa score. However, elevated interleukin-6 (IL-6) was strongly associated with the need for mechanical ventilation (p=1.2.10-5). In addition, the maximal IL-6 level (cutoff 80 pg/ml) for each patient during disease predicted respiratory failure with high accuracy (p=1.7.10-8, AUC=0.98). The risk of respiratory failure for patients with IL-6 levels of >; 80 pg/ml was 22 times higher compared to patients with lower IL-6 levels. In the current situation with overwhelmed intensive care units and overcrowded emergency rooms, correct triage of patients in need of intensive care is crucial. Our study shows that IL-6 is an effective marker that might be able to predict upcoming respiratory failure with high accuracy and help physicians correctly allocate patients at an early stage.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Tobias Herold", + "author_inst": "University Hospital, LMU Munich" + }, + { + "author_name": "Vindi Jurinovic", + "author_inst": "Institute for Medical Information Processing, Biometry and Epidemiology, LMU Munich, Munich, Germany" + }, + { + "author_name": "Chiara Arnreich", + "author_inst": "Department of Medicine III, University Hospital, LMU Munich, Munich, Germany" + }, + { + "author_name": "Johannes C Hellmuth", + "author_inst": "Department of Medicine III, University Hospital, LMU Munich, Munich, Germany" + }, + { + "author_name": "Michael von Bergwelt-Baildon", + "author_inst": "Department of Medicine III, University Hospital, LMU Munich, Munich, Germany" + }, + { + "author_name": "Matthias Klein", + "author_inst": "Department of Neurology, University Hospital, LMU Munich, Munich, Germany" + }, + { + "author_name": "Tobias Weinberger", + "author_inst": "Department of Medicine I, University Hospital, LMU Munich, Munich, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.01.20047357", "rel_title": "Detecting SARS-CoV-2 at point of care: Preliminary data comparing Loop-mediated isothermal amplification (LAMP) to PCR", @@ -1575677,53 +1577995,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2020.03.31.20049023", - "rel_title": "Quantifying the impact of physical distance measures on the transmission of COVID-19 in the UK", - "rel_date": "2020-04-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20049023", - "rel_abs": "BackgroundTo mitigate and slow the spread of COVID-19, many countries have adopted unprecedented physical distancing policies, including the UK. We evaluate whether these measures might be sufficient to control the epidemic by estimating their impact on the reproduction number (R0, the average number of secondary cases generated per case).\n\nMethodsWe asked a representative sample of UK adults about their contact patterns on the previous day. The questionnaire documents the age and location of contacts and as well as a measure of their intimacy (whether physical contact was made or not). In addition, we asked about adherence to different physical distancing measures. The first surveys were sent on Tuesday 24th March, one day after a \" lockdown\" was implemented across the UK. We compared measured contact patterns during the \" lockdown\" to patterns of social contact made during a non-epidemic period. By comparing these, we estimated the change in reproduction number as a consequence of the physical distancing measures imposed. We used a meta-analysis of published estimates to inform our estimates of the reproduction number before interventions were put in place.\n\nFindingsWe found a 73% reduction in the average daily number of contacts observed per participant (from 10.2 to 2.9). This would be sufficient to reduce R0 from 2.6 prior to lockdown to 0.62 (95% confidence interval [CI] 0.37 - 0.89) after the lockdown, based on all types of contact and 0.37 (95% CI = 0.22 - 0.53) for physical contacts only.\n\nInterpretationThe physical distancing measures adopted by the UK public have substantially reduced contact levels and will likely lead to a substantial impact and a decline in cases in the coming weeks. However, this projected decline in incidence will not occur immediately as there are significant delays between infection, the onset of symptomatic disease and hospitalisation, as well as further delays to these events being reported. Tracking behavioural change can give a more rapid assessment of the impact of physical distancing measures than routine epidemiological surveillance.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSMany governments have adopted physical distancing measures to mitigate the impact of the COVID-19 pandemic. However, it is unclear to what extent these measures reduce the number of contacts and therefore transmission. We searched PubMed and medRxiv on March 28, 2020, with the terms \" (coronavirus OR COVID-19 OR influenza) AND ((school OR work) AND (closure OR holiday)) AND (contact OR mixing)\" and identified 59 and 17 results, respectively. Only one study conducted in China during the COVID-19 pandemic reported a reduction in daily contacts outside the home during the period of \" lockdown\". We found no other published articles that empirically quantify the impact of these measures on age- and location-specific mixing patterns.\n\nAdded value of this studyBy surveying adults behaviour in the UK during a period of stringent physical distancing (\" lockdown\") and comparing the results to previously collected data, we found a large reduction in daily contacts particularly outside the home, resulting in a marked reduction in the estimated reproduction number from 2.6 to 0.62 (95% bootstrapped confidence interval [CI] 0.37 - 0.89). This method allows for rapid assessment of changes in the reproduction number that is unaffected by reporting delays.\n\nImplications of all the available evidenceChanges in human contact behaviour drive respiratory infection rates. Understanding these changes at different stages of the COVID-19 pandemic allows us to rapidly quantify the impact of physical distancing measures on the transmission of pathogens.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Christopher I Jarvis", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel " - }, - { - "author_name": "Kevin Van Zandvoort", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel " - }, - { - "author_name": "Amy Gimma", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel " - }, - { - "author_name": "Kiesha Prem", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel " - }, - { - "author_name": "- CMMID COVID-19 working group", - "author_inst": "" - }, - { - "author_name": "Petra Klepac", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel " - }, - { - "author_name": "G James Rubin", - "author_inst": "Department of Psychological Medicine, King's College London, Denmark Hill, London United Kingdom" - }, - { - "author_name": "W John Edmunds", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel " - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.31.20049312", "rel_title": "Projected ICU and Mortuary load due to COVID-19 in Sydney", @@ -1575837,6 +1578108,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.31.20049130", + "rel_title": "Modelling the COVID-19 epidemics in Brasil: Parametric identification and public health measures influence", + "rel_date": "2020-04-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20049130", + "rel_abs": "A SIRU-type epidemic model is employed for the prediction of the COVID-19 epidemy evolution in Brazil, and analyse the influence of public health measures on simulating the control of this infectious disease. Since the reported cases are typically only a fraction of the total number of the symptomatic infectious individuals, the model accounts for both reported and unreported cases. Also, the model allows for a time variable functional form of both the transmission rate and the fraction of asymptomatic infectious that become reported symptomatic individuals, so as to reflect public health interventions, towards its control, along the course of the epidemic evolution. An analytical exponential behaviour for the accumulated reported cases evolution is assumed at the onset of the epidemy, for explicitly estimating initial conditions, while a Bayesian inference approach is adopted for parametric estimations employing the present direct problem model with the data from the known portion of the epidemics evolution, represented by the time series for the reported cases of infected individuals. The direct-inverse problem analysis is then employed with the actual data from China, with the initial phase of the data been employed for the parametric estimation and the remaining data being used for validation of the predictive capability of the proposed approach. The full dataset for China is then employed in another parameter identification, aimed at refining the values for the average times that asymptomatic infectious individuals and that symptomatic individuals remain infectious. Following this validation, the available data on reported cases in Brazil from February 15th till March 29th, 2020, is used for estimating parameters and then predict the epidemy evolution from these initial conditions. As for the China analysis, the data for the reported cases in Brazil from March 30th till April 23rd are reserved for validation of the model. Finally, public health interventions are simulated, aimed at evaluating the effects on the disease spreading, by acting on both the transmission rate and the fraction of the total number of the symptomatic infectious individuals, considering time variable exponential behaviours for these two parameters, usually assumed constant in epidemic evolutions without intervention. It is demonstrated that a combination of actions to affect both parameters can have a more effective result in the control of the epidemy dynamics.\n\nNOMENCLATURE\n\n\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@7023org.highwire.dtl.DTLVardef@c21831org.highwire.dtl.DTLVardef@c26a97org.highwire.dtl.DTLVardef@1e41435org.highwire.dtl.DTLVardef@ead7d5_HPS_FORMAT_FIGEXP M_TBL C_TBL\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@12a8org.highwire.dtl.DTLVardef@c901c1org.highwire.dtl.DTLVardef@92440dorg.highwire.dtl.DTLVardef@b1e409org.highwire.dtl.DTLVardef@f244ac_HPS_FORMAT_FIGEXP M_TBL C_TBL", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Renato Machado Cotta", + "author_inst": "Federal University of Rio de Janeiro" + }, + { + "author_name": "Carolina Palma Naveira-Cotta", + "author_inst": "Federal University of Rio de Janeiro" + }, + { + "author_name": "pierre magal", + "author_inst": "University of Bordeaux" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.31.20049155", "rel_title": "Parametric analysis of early data on COVID-19 expansion in selected European countries", @@ -1576763,89 +1579061,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.03.31.015941", - "rel_title": "Identification of a common deletion in the spike protein of SARS-CoV-2", - "rel_date": "2020-04-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.31.015941", - "rel_abs": "Two notable features have been identified in the SARS-CoV-2 genome: (1) the receptor binding domain of SARS-CoV-2; (2) a unique insertion of twelve nucleotide or four amino acids (PRRA) at the S1 and S2 boundary. For the first feature, the similar RBD identified in SARs-like virus from pangolin suggests the RBD in SARS-CoV-2 may already exist in animal host(s) before it transmitted into human. The left puzzle is the history and function of the insertion at S1/S2 boundary, which is uniquely identified in SARS-CoV-2. In this study, we identified two variants from the first Guangdong SARS-CoV-2 cell strain, with deletion mutations on polybasic cleavage site (PRRAR) and its flank sites. More extensive screening indicates the deletion at the flank sites of PRRAR could be detected in 3 of 68 clinical samples and half of 22 in vitro isolated viral strains. These data indicate (1) the deletion of QTQTN, at the flank of polybasic cleavage site, is likely benefit the SARS-CoV-2 replication or infection in vitro but under strong purification selection in vivo since it is rarely identified in clinical samples; (2) there could be a very efficient mechanism for deleting this region from viral genome as the variants losing 23585-23599 is commonly detected after two rounds of cell passage. The mechanistic explanation for this in vitro adaptation and in vivo purification processes (or reverse) that led to such genomic changes in SARS-CoV-2 requires further work. Nonetheless, this study has provided valuable clues to aid further investigation of spike protein function and virus evolution. The deletion mutation identified in vitro isolation should be also noted for current vaccine development.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Zhe Liu", - "author_inst": "Guangdong Provincial Institution of Public Health, Guangzhou, China" - }, - { - "author_name": "Huanying Zheng", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Runyu Yuan", - "author_inst": "Guangdong Provincial Institution of Public Health, Guangzhou" - }, - { - "author_name": "Mingyue Li", - "author_inst": "The Third Affilated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Huifang Lin", - "author_inst": "Guangdong Provincial Institution of Public Health" - }, - { - "author_name": "Jingju Peng", - "author_inst": "Guangdong Provincial Institution of Public Health" - }, - { - "author_name": "Qianlin Xiong", - "author_inst": "Guangdong Provincial Institution of Public Health" - }, - { - "author_name": "Jiufeng Sun", - "author_inst": "Guangdong Provincial Institution of Public Health" - }, - { - "author_name": "Baisheng Li", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Jie Wu", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Changwen Ke", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Ruben J.G. Hulswit", - "author_inst": "University of Oxford, Oxford, UK" - }, - { - "author_name": "Thomas A. Bowden", - "author_inst": "University of Oxford, Oxford, UK" - }, - { - "author_name": "Andrew Rambaut", - "author_inst": "University of Edinburgh, UK" - }, - { - "author_name": "Oliver G Pybus", - "author_inst": "University of Oxford, Oxford, UK" - }, - { - "author_name": "Nick Loman", - "author_inst": "Institute of Microbiology and Infection, University of Birmingham, UK" - }, - { - "author_name": "Jing Lu", - "author_inst": "Guangdong Provincial Center for Diseases Control and prevention" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.03.31.017889", "rel_title": "Characterization and treatment of SARS-CoV-2 in nasal and bronchial human airway epithelia", @@ -1577067,6 +1579282,37 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2020.03.30.014555", + "rel_title": "deepMINE - Natural Language Processing based Automatic Literature Mining and Research Summarization for Early Stage Comprehension in Pandemic Situations specifically for COVID-19", + "rel_date": "2020-04-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.30.014555", + "rel_abs": "The recent pandemic created due to Novel Coronavirus (nCOV-2019) from Wuhan, China demanding a large scale of a general health emergency. This demands novel research on the vaccine to fight against this pandemic situation, re-purposing of the existing drugs, phylogenetic analysis to identify the origin and determine the similarity with other known viruses, etc. The very preliminary task from the research community is to analyze the wide verities of existing related research articles, which is very much time-consuming in such situations where each minute counts for saving hundreds of human lives. The entire manual processing is even lower down the efficiency in mining the information. We have developed a complete automatic literature mining system that delivers efficient and fast mining from existing biomedical literature databases. With the help of modern-day deep learning algorithms, our system also delivers a summarization of important research articles that provides ease and fast comprehension of critical research articles. The system is currently scanning nearly 1,46,115,136 English words from 29,315 research articles in not greater than 1.5 seconds with multiple search keywords. Our research article presents the criticality of literature mining, especially in pandemic situations with the implementation and online deployment of the system.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Bhrugesh Pravinchandra Joshi", + "author_inst": "Uka Tarsadia University" + }, + { + "author_name": "Vishvajit D Bakrola", + "author_inst": "Uka Tarsadia University" + }, + { + "author_name": "Parth Shah", + "author_inst": "Uka Tarsadia University" + }, + { + "author_name": "Ramar Krishnamurthy", + "author_inst": "Uka Tarsadia University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.04.01.019463", "rel_title": "Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations", @@ -1578053,33 +1580299,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2020.03.29.20046649", - "rel_title": "COVID-19, City Lockdown, and Air Pollution: Evidence from China", - "rel_date": "2020-04-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.29.20046649", - "rel_abs": "The rapid spread of COVID-19 is a global public health challenge. To prevent the escalation of its transmission, China locked down one-third of its cities and strictly restricted personal mobility and economic activities. Using timely and comprehensive air quality data in China, we show that these counter-COVID-19 measures led to a remarkable improvement in air quality. Within weeks, the Air Quality Index and PM2.5 concentrations were brought down by 25%. The effects are larger in colder, richer, and more industrialized cities. We estimate that such improvement would avert 24,000 to 36,000 premature deaths from air pollution on a monthly basis.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Guojun He", - "author_inst": "Division of Social Science, Division of Environment and Sustainability, and Department of Economics, Hong Kong University of Science and Technology" - }, - { - "author_name": "Yuhang Pan", - "author_inst": "Division of Environment and Sustainability, Hong Kong University of Science and Technology" - }, - { - "author_name": "Takanao Tanaka", - "author_inst": "Division of Social Science, Hong Kong University of Science and Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.03.30.20047308", "rel_title": "Predicting Mortality Risk in Patients with COVID-19 Using Artificial Intelligence to Help Medical Decision-Making", @@ -1578141,6 +1580360,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.30.20047274", + "rel_title": "Patterns of the COVID19 epidemic spread around the world: exponential vs power laws", + "rel_date": "2020-04-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20047274", + "rel_abs": "We have analyzed the COVID19 epidemic data of more than 174 countries (excluding China) in the period between January 22 and March 28, 2020. We found that some countries (such as the US, the UK, and Canada) follow an exponential epidemic growth, while others (like Italy and several other European countries) show a power law like growth. At the same time, regardless of the best fitting law, most countries can be shown to follow a trajectory similar to that of Italy, but with varying degrees of delay. We found that countries with \"younger\" epidemics tend to exhibit more exponential like behavior, while countries that are closer behind Italy tend to follow a power law growth. We hypothesize that there is a universal growth pattern of this infection that starts off as exponential and subsequently becomes more power law like. Although it cannot be excluded that this growth pattern is a consequence of social distancing measures, an alternative explanation is that it is an intrinsic epidemic growth law, dictated by a spatially distributed community structure, where the growth in individual highly mixed communities is exponential but the longer term, local geographical spread (in the absence of global mixing) results in a power-law. This is supported by computer simulations of a metapopulation model that gives rise to predictions about the growth dynamics that are consistent with correlations found in the epidemiological data. Therefore, seeing a deviation from straight exponential growth may not be a consequence of working non-pharmaceutical interventions (except for, perhaps, restricting the air travel). Instead, this is a normal course of raging infection spread. On the practical side, this cautions us against overly optimistic interpretations of the countries epidemic development and emphasizes the need to continue improving the compliance with social distancing behavior recommendations.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Natalia L. Komarova", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Luis M. Schang", + "author_inst": "Cornell University" + }, + { + "author_name": "Dominik Wodarz", + "author_inst": "University of California Irvine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.29.20047159", "rel_title": "SARS-CoV-2 infection in health care workers: a retrospective analysis and a model study", @@ -1579275,20 +1581521,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.29.20046706", - "rel_title": "No Evidence for Temperature-Dependence of the COVID-19 Epidemic", - "rel_date": "2020-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.29.20046706", - "rel_abs": "1.The pandemic of the COVID-19 disease extended from China across the north-temperate zone, and more recently to the tropics and southern hemisphere. We find no evidence that spread rates decline with temperatures above 20 {degrees}C, suggesting that the COVID-19 disease is unlikely to behave as a seasonal respiratory virus.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.28.013672", "rel_title": "Cigarette smoke triggers the expansion of a subpopulation of respiratory epithelial cells that express the SARS-CoV-2 receptor ACE2", @@ -1579382,6 +1581614,49 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.03.30.015008", + "rel_title": "Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic", + "rel_date": "2020-03-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.30.015008", + "rel_abs": "There are outstanding evolutionary questions on the recent emergence of coronavirus SARS-CoV-2/hCoV-19 in Hubei province that caused the COVID-19 pandemic, including (1) the relationship of the new virus to the SARS-related coronaviruses, (2) the role of bats as a reservoir species, (3) the potential role of other mammals in the emergence event, and (4) the role of recombination in viral emergence. Here, we address these questions and find that the sarbecoviruses - the viral subgenus responsible for the emergence of SARS-CoV and SARS-CoV-2 - exhibit frequent recombination, but the SARS-CoV-2 lineage itself is not a recombinant of any viruses detected to date. In order to employ phylogenetic methods to date the divergence events between SARS-CoV-2 and the bat sarbecovirus reservoir, recombinant regions of a 68-genome sarbecovirus alignment were removed with three independent methods. Bayesian evolutionary rate and divergence date estimates were consistent for all three recombination-free alignments and robust to two different prior specifications based on HCoV-OC43 and MERS-CoV evolutionary rates. Divergence dates between SARS-CoV-2 and the bat sarbecovirus reservoir were estimated as 1948 (95% HPD: 1879-1999), 1969 (95% HPD: 1930-2000), and 1982 (95% HPD: 1948-2009). Despite intensified characterization of sarbecoviruses since SARS, the lineage giving rise to SARS-CoV-2 has been circulating unnoticed for decades in bats and been transmitted to other hosts such as pangolins. The occurrence of a third significant coronavirus emergence in 17 years together with the high prevalence and virus diversity in bats implies that these viruses are likely to cross species boundaries again.\n\nIn BriefThe Betacoronavirus SARS-CoV-2 is a member of the sarbecovirus subgenus which shows frequent recombination in its evolutionary history. We characterize the extent of this genetic exchange and identify non-recombining regions of the sarbecovirus genome using three independent methods to remove the effects of recombination. Using these non-recombining genome regions and prior information on coronavirus evolutionary rates, we obtain estimates from three approaches that the most likely divergence date of SARS-CoV-2 from its most closely related available bat sequences ranges from 1948 to 1982.\n\nKey PointsO_LIRaTG13 is the closest available bat virus to SARS-CoV-2; a sub-lineage of these bat viruses is able to infect humans. Two sister lineages of the RaTG13/SARS-CoV-2 lineage infect Malayan pangolins.\nC_LIO_LIThe sarbecoviruses show a pattern of deep recombination events, indicating that there are high levels of co-infection in horseshoe bats and that the viral pool can generate novel allele combinations and substantial genetic diversity; the sarbecoviruses are efficient explorers of phenotype space.\nC_LIO_LIThe SARS-CoV-2 lineage is not a recent recombinant, at least not involving any of the bat or pangolin viruses sampled to date.\nC_LIO_LINon-recombinant regions of the sarbecoviruses can be identified, allowing for phylogenetic inference and dating to be performed. We constructed three such regions using different methods.\nC_LIO_LIWe estimate that RaTG13 and SARS-CoV-2 diverged 40 to 70 years ago. There is a diverse unsampled reservoir of generalist viruses established in horseshoe bats.\nC_LIO_LIWhile an intermediate host responsible for the zoonotic event cannot be ruled out, the relevant evolution for spillover to humans very likely occurred in horseshoe bats.\nC_LI", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Maciej F Boni", + "author_inst": "Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA" + }, + { + "author_name": "Philippe Lemey", + "author_inst": "Katholieke University, Leuven, Belgium" + }, + { + "author_name": "Tommy Tsan-Yuk Lam", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China" + }, + { + "author_name": "Blair Perry", + "author_inst": "Department of Biology, University of Texas Arlington, Arlington, TX, USA" + }, + { + "author_name": "Todd Castoe", + "author_inst": "Department of Biology, University of Texas Arlington, Arlington, TX, USA" + }, + { + "author_name": "Andrew Rambaut", + "author_inst": "Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "David L Robertson", + "author_inst": "MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, UK" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.03.29.008631", "rel_title": "Azithromycin and ciprofloxacin have a chloroquine-like effect on respiratory epithelial cells", @@ -1580872,29 +1583147,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.27.20043752", - "rel_title": "Forecasting COVID-19 impact on hospital bed-days, ICU-days, ventilator-days and deaths by US state in the next 4 months", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20043752", - "rel_abs": "ImportanceThis study presents the first set of estimates of predicted health service utilization and deaths due to COVID-19 by day for the next 4 months for each state in the US.\n\nObjectiveTo determine the extent and timing of deaths and excess demand for hospital services due to COVID-19 in the US.\n\nDesign, Setting, and ParticipantsThis study used data on confirmed COVID-19 deaths by day from WHO websites and local and national governments; data on hospital capacity and utilization for US states; and observed COVID-19 utilization data from select locations to develop a statistical model forecasting deaths and hospital utilization against capacity by state for the US over the next 4 months.\n\nExposure(s)COVID-19.\n\nMain outcome(s) and measure(s)Deaths, bed and ICU occupancy, and ventilator use.\n\nResultsCompared to licensed capacity and average annual occupancy rates, excess demand from COVID-19 at the peak of the pandemic in the second week of April is predicted to be 64,175 (95% UI 7,977 to 251,059) total beds and 17,380 (95% UI 2,432 to 57,955) ICU beds. At the peak of the pandemic, ventilator use is predicted to be 19,481 (95% UI 9,767 to 39,674). The date of peak excess demand by state varies from the second week of April through May. We estimate that there will be a total of 81,114 (95% UI 38,242 to 162,106) deaths from COVID-19 over the next 4 months in the US. Deaths from COVID-19 are estimated to drop below 10 deaths per day between May 31 and June 6.\n\nConclusions and RelevanceIn addition to a large number of deaths from COVID-19, the epidemic in the US will place a load well beyond the current capacity of hospitals to manage, especially for ICU care. These estimates can help inform the development and implementation of strategies to mitigate this gap, including reducing non-COVID-19 demand for services and temporarily increasing system capacity. These are urgently needed given that peak volumes are estimated to be only three weeks away. The estimated excess demand on hospital systems is predicated on the enactment of social distancing measures in all states that have not done so already within the next week and maintenance of these measures throughout the epidemic, emphasizing the importance of implementing, enforcing, and maintaining these measures to mitigate hospital system overload and prevent deaths.\n\nData availability statementA full list of data citations are available by contacting the corresponding author.\n\nFunding StatementBill & Melinda Gates Foundation and the State of Washington\n\nKey PointsO_ST_ABSQuestionC_ST_ABSAssuming social distancing measures are maintained, what are the forecasted gaps in available health service resources and number of deaths from the COVID-19 pandemic for each state in the United States?\n\nFindingsUsing a statistical model, we predict excess demand will be 64,175 (95% UI 7,977 to 251,059) total beds and 17,380 (95% UI 2,432 to 57,955) ICU beds at the peak of COVID-19. Peak ventilator use is predicted to be 19,481 (95% UI 9,767 to 39,674) ventilators. Peak demand will be in the second week of April. We estimate 81,114 (95% UI 38,242 to 162,106) deaths in the United States from COVID-19 over the next 4 months.\n\nMeaningEven with social distancing measures enacted and sustained, the peak demand for hospital services due to the COVID-19 pandemic is likely going to exceed capacity substantially. Alongside the implementation and enforcement of social distancing measures, there is an urgent need to develop and implement plans to reduce non-COVID-19 demand for and temporarily increase capacity of health facilities.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "IHME COVID-19 health service utilization forecasting team", - "author_inst": "" - }, - { - "author_name": "Christopher JL Murray", - "author_inst": "Institute for Health Metrics and Evaluation" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.27.20045807", "rel_title": "The psychological distress and coping styles in the early stages of the 2019 coronavirus disease (COVID-19) epidemic in the general mainland Chinese population: a web-based survey", @@ -1581068,6 +1583320,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2020.03.27.20045138", + "rel_title": "When will the Covid-19 epidemic fade out?", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20045138", + "rel_abs": "A discrete-time deterministic epidemic model is proposed with the aim of reproducing the behaviour observed in the incidence of real infectious diseases. For this purpose, we analyse a SIRS model under the framework of a small world network formulation. Using this model, we make predictions about the peak of the Covid-19 epidemic in Italy. A Gaussian fit is also performed, to make a similar prediction.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ilaria Renna", + "author_inst": "ISEP, institut superieur d'electronique de paris" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.27.20045153", "rel_title": "Evaluations of serological test in the diagnosis of 2019 novel coronavirus (SARS-CoV-2) infections during the COVID-19 outbreak", @@ -1582078,37 +1584349,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.26.20041426", - "rel_title": "Clinical features and outcomes of 197 adult discharged patients with COIVD-19 in Yichang, Hubei", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20041426", - "rel_abs": "PurposeTo investigate the epidemiology and clinical features of discharged adult patients with coronavirus infection disease 2019 (COVID-19) in Yichang.\n\nMethodThe retrospective study recruited 197 cases of COVID-19 discharged from Yichang Central Peoples Hospital and Yichang Third Peoples Hospital from Jan 17 to Feb 26, 2020. All cases were confirmed by real-time RT-PCR or chest computer tomography (CT). The survivors were followed up until March 4,2020. Clinical data, including demographic characteristic, presentation, underlying illness, exposure history, laboratory examination, radiology and prognosis were enrolled and analyzed by SPSS 19.0 software.\n\nResultsThere were 197 adult discharged patients with COVID-19 in this study. Statistical analysis indicated that the average age was 55.94 years, and female patients were 99(50.3%).Those patients mainly resided in urban with exposure history in 2 weeks, while 7 medical staffs were infected. Fever (77.6%%), cough (43.6%) and weakness (14.7%) were the common symptoms. Leukocytes were mainly normal or decreased in 185 patients (92.9%), both lymphocytes and eosinophils were below normal range, the ratios were 56.9% and 50.3%, respectively. On the contrary, lactate dehydrogenases raised in 65 patients. C-reactive protein (72.4%) elevated in the most of patients. The sensitivity of RT-PCR was 63.5%. Chest CT indicated that bilateral patchy shadows (69.0%) were the most common imaging manifestations.169(85.8%) patients recovered and transferred to a designated hospital for observation, and the others (14.2%) turned worst and died of acute respiratory failure.\n\nConclusionCOVID-19 infection with highly contagious have become a life-threaten public healthy problem, the sensitivity of RT-PCR was limited. Chest CT scan was recommended for the suspected patients. Furthermore, lymphocytopenia and eosinophils declining without leukocytes increasing may be considered as a useful evidence for the diagnosis.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Fating Zhou", - "author_inst": "Yichang Central people's hospital" - }, - { - "author_name": "Xiaogang Yu", - "author_inst": "Yichang Central people's hospital" - }, - { - "author_name": "Xiaowei Tong", - "author_inst": "Yichang Third people's hospital" - }, - { - "author_name": "Rong Zhang", - "author_inst": "Yichang Central people's hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.27.20045302", "rel_title": "Mobility traces and spreading of COVID-19", @@ -1582202,6 +1584442,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.27.20045104", + "rel_title": "Prediction of the time evolution of the Covid-19 Pandemic in Italy by a Gauss Error Function and Monte Carlo simulations", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20045104", + "rel_abs": "In this paper are presented predictions on the evolution in time of the number of positive cases in Italy of the Covid-19 pandemic based on official data and on the use of a function of the type of a Gauss Error Function as a Cumulative Distribution Function (CDF). We have analyzed the available data for China and Italy. The evolution in time of the number of cumulative diagnosed positive cases of Covid-19 in China very well approximates a distribution of the type of the Error Function, that is, the integral of a normal, Gaussian distribution. We have then used such a function to study the potential evolution in time of the number of positive cases in Italy by performing a number of fits of the official data so far available. We then found a statistical prediction for the day in which the peak of the number of daily positive cases in Italy occurs, corresponding to the flex of the fit, i.e., to the change in sign of its second derivative (that is the change from acceleration to deceleration) as well as of the day in which a substantial attenuation of such number of daily cases is reached. We have then performed 150 Monte Carlo simulations in the attempt to have a more robust prediction of the day of the above-mentioned peak and of the day of the substantial decrease of the number of daily positive cases. Although, official data have been used, these predictions are obtained with a heuristic approach, since those predictions are based on statistical approach and do not take into account either a number of relevant issues (such as medical, social distancing, virologic, epidemiological, etc.) or models of contamination diffusion.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ignazio Ciufolini", + "author_inst": "University of Salento" + }, + { + "author_name": "Antonio Paolozzi", + "author_inst": "Sapienza University of Rome" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.27.20044891", "rel_title": "Evaluating the effectiveness of social distancing interventions against COVID-19", @@ -1583432,29 +1585695,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.03.26.20044420", - "rel_title": "Causal empirical estimates suggest COVID-19 transmission rates are highly seasonal", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044420", - "rel_abs": "Nearly every country is now combating the 2019 novel coronavirus (COVID-19). It has been hypothesized that if COVID-19 exhibits seasonality, changing temperatures in the coming months will shift transmission patterns around the world. Such projections, however, require an estimate of the relationship between COVID-19 and temperature at a global scale, and one that isolates the role of temperature from confounding factors, such as public health capacity. This paper provides the first plausibly causal estimates of the relationship between COVID-19 transmission and local temperature using a global sample comprising of 166,686 confirmed new COVID-19 cases from 134 countries from January 22, 2020 to March 15, 2020. We find robust statistical evidence that a 1{degrees}C increase in local temperature reduces transmission by 13% [-21%, -4%, 95%CI]. In contrast, we do not find that specific humidity or precipitation influence transmission. Our statistical approach separates effects of climate variation on COVID-19 transmission from other potentially correlated factors, such as differences in public health responses across countries and heterogeneous population densities. Using constructions of expected seasonal temperatures, we project that changing temperatures between March 2020 and July 2020 will cause COVID-19 transmission to fall by 43% on average for Northern Hemisphere countries and to rise by 71% on average for Southern Hemisphere countries. However, these patterns reverse as the boreal winter approaches, with seasonal temperatures in January 2021 increasing average COVID-19 transmission by 59% relative to March 2020 in northern countries and lowering transmission by 2% in southern countries. These findings suggest that Southern Hemisphere countries should expect greater transmission in the coming months. Moreover, Northern Hemisphere countries face a crucial window of opportunity: if contagion-containing policy interventions can dramatically reduce COVID-19 cases with the aid of the approaching warmer months, it may be possible to avoid a second wave of COVID-19 next winter.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Tamma Carleton", - "author_inst": "University of Chicago" - }, - { - "author_name": "Kyle C. Meng", - "author_inst": "University of California, Santa Barbara" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.29.014209", "rel_title": "Orthogonal genome-wide screenings in bat cells identify MTHFD1 as a target of broad antiviral therapy", @@ -1583648,6 +1585888,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.03.26.20044750", + "rel_title": "Symptom-Based Isolation Policies: Evidence from a Mathematical Model of Outbreaks of Influenza and COVID-19", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044750", + "rel_abs": "BackgroundNon-pharmaceutical interventions such as social distancing, school closures and travel restrictions are often implemented to control outbreaks of infectious diseases. For influenza in schools, the Center of Disease Control (CDC) recommends that febrile students remain isolated at home until they have been fever-free for at least one day and a related policy is recommended for SARS-CoV2 (COVID-19). Other authors proposed using a school week of four or fewer days of in-person instruction for all students to reduce transmission. However, there is limited evidence supporting the effectiveness of these interventions.\n\nMethodsWe introduced a mathematical model of school outbreaks that considers both intervention methods. Our model accounts for the school structure and schedule, as well as the time-progression of fever symptoms and viral shedding. The model was validated on outbreaks of seasonal and pandemic influenza and COVID-19 in schools. It was then used to estimate the outbreak curves and the proportion of the population infected (attack rate) under the proposed interventions.\n\nResultsFor influenza, the CDC-recommended one day of post-fever isolation can reduce the attack rate by a median (interquartile range) of 29 (13 - 59)%. With two days of post-fever isolation the attack rate could be reduced by 70 (55 - 85)%. Alternatively, shortening the school week to four and three days reduces the attack rate by 73 (64 - 88)% and 93 (91 - 97)%, respectively. For COVID-19, application of post-fever isolation policy was found to be less effective and reduced the attack rate by 10 (5 - 17)% for a two-day isolation policy and by 14 (5 - 26)% for 14 days. A four-day school week would reduce the median attack rate in a COVID-19 outbreak by 57 (52 - 64)%, while a three-day school week would reduce it by 81 (79 - 83)%. In both infections, shortening the school week significantly reduced the duration of outbreaks.\n\nConclusionsShortening the school week could be an important tool for controlling influenza and COVID-19 in schools and similar settings. Additionally, the CDC-recommended post-fever isolation policy for influenza could be enhanced by requiring two days of isolation instead of one.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Adam Burns", + "author_inst": "Loyola University of Chicago" + }, + { + "author_name": "Alexander Gutfraind", + "author_inst": "Loyola University Medical Center; University of Illinois at Chicago" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.28.013920", "rel_title": "Crystal structure of the SARS-CoV-2 non-structural protein 9, Nsp9", @@ -1584738,69 +1587001,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.03.26.20044198", - "rel_title": "No SARS-CoV-2 in expressed prostatic secretion of patients with coronavirus disease 2019: a descriptive multicentre study in China", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044198", - "rel_abs": "PurposeThe aim of the present study was to assess whether SARS-CoV-2 can be detected in the expressed prostatic secretion (EPS) of patients with corona virus disease 2019 (COVID-19).\n\nMethods18 cases of COVID-19, and 5 suspected cases, were selected from three medical centers to detect the RNA expression of SARS-CoV-2 in their EPS with RT-PCR.\n\nResultsResults were negative in all EPS samples for SARS-CoV-2 of suspected and confirmed patients.\n\nConclusionsNo SARS-CoV-2 was expressed in EPS of patients with COVID-19.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "weihe quan", - "author_inst": "Shenzhen Hospital of Southern Medical University" - }, - { - "author_name": "qingyou zheng", - "author_inst": "Shenzhen Hospital of Southern Medical University" - }, - { - "author_name": "jinfei tian", - "author_inst": "Shenzhen Hospital of Southern Medical University" - }, - { - "author_name": "jun chen", - "author_inst": "Xiangyang Central Hospital" - }, - { - "author_name": "zhigang liu", - "author_inst": "Wuhan Third Hospital (Hospital-Tongren) of Wuhan University Wuhan" - }, - { - "author_name": "xiangqiu chen", - "author_inst": "Shenzhen Hospital of Southern Medical University" - }, - { - "author_name": "tao wu", - "author_inst": "Shenzhen Hospital of Southern Medical University" - }, - { - "author_name": "ziliang ji", - "author_inst": "Shenzhen Hospital of Southern Medical University" - }, - { - "author_name": "jinqi tang", - "author_inst": "Shenzhen Hospital of Southern Medical University" - }, - { - "author_name": "hao chu", - "author_inst": "Wuhan Third Hospital (Hospital-Tongren) of Wuhan University Wuhan" - }, - { - "author_name": "haijia xu", - "author_inst": "Wuhan Third Hospital (Hospital-Tongren) of Wuhan University Wuhan" - }, - { - "author_name": "yong zhao", - "author_inst": "Wuhan Third Hospital (Hospital-Tongren) of Wuhan University Wuhan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "urology" - }, { "rel_doi": "10.1101/2020.03.28.20043471", "rel_title": "Disposable N95 Masks Pass Qualitative Fit-Test But Have Decreased Filtration Efficiency after Cobalt-60 Gamma Irradiation", @@ -1584906,6 +1587106,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.03.26.20044412", + "rel_title": "Public events and delayed flight restrictions were the turning point of the COVID-19 mitigation policy of Israel", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044412", + "rel_abs": "BackgroundThe impact of COVID-19 has been profound, and the public health challenge seem to be the most serious regarding respiratory viruses since the 1918 H1N1 influenza pandemic. In the absence of effective vaccine or biomedical treatment, the basic rules of public health measures have not changed, namely public distancing.\n\nMethodsWe analyzed epidemiological investigation reports during the first month of the outbreak in Israel. In addition, we present a deterministic compartment model and simulations of several scenarios emphasizing quarantine and isolation policies given their efficiency.\n\nResultsWe identify an abrupt change from controlled epidemic regime to an exponential growth (R0 = 2.19) in light of the actual policy-makers decisions and public behavior in Israel. Our analysis show that before the abrupt change, the new cases trend was due to returning citizens infected abroad. The abrupt change followed a holiday in which social distancing was clearly inefficient and many public gatherings were held. We further discuss three different modeled scenarios of quarantine efficiency: high-, medium-, and low-efficiency.\n\nConclusionsIsrael early lessons show that there is no allowance to compromise with the directive of social distancing. Even before the onset of the pandemic in Israel, fine-tuned but determined early decisions were taken by policy makers to monitor flight arrivals from Covid-19 affected regions and to limit public gatherings. Our analysis show that one particular holiday has shifted the occurrence curve from controlled regime to exponential growth. Therefore, even a short lapse in public responsiveness can have a dramatic effect.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Ziv Klausner", + "author_inst": "Israel Institute for Biological Research, Ness-Ziona, Israel" + }, + { + "author_name": "Eyal Fattal", + "author_inst": "Israeli Institute for Biological Research" + }, + { + "author_name": "Eitan Hirsch", + "author_inst": "Israel Institute for Biological Research, Ness-Ziona, Israel" + }, + { + "author_name": "Shmuel C Shapira", + "author_inst": "Israel Institute for Biological Research, Ness-Ziona, Israel" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.30.20044099", "rel_title": "COVID-19 transmission in Mainland China is associated with temperature and humidity: a time-series analysis", @@ -1586100,45 +1588331,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2020.03.24.20041095", - "rel_title": "Modeling for Corona Virus Outbreak in IRAN", - "rel_date": "2020-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20041095", - "rel_abs": "BackgroundAs the outbreak of coronavirus disease 2019 (COVID-19) is a worldwide pandemic, it is rapidly expanding in Iran, real-time analyses of epidemiological data are needed to increase situational awareness and inform interventions. In this study, we built a predictive model based on the cumulative trend of new cases and deaths for the top five provinces. we will also look at modeling the trends for confirmed cases, deaths and recovered for the whole country.\n\nMethodIn this study, we have chosen to apply the exponential smoothing model to iteratively forecast future values of a regular time seires from weighted averages of past daily values of the series. This method is exponential because the value of each level is influenced by every preceeding actual value to an exponentially decreasing degree - more recent values are given a greater weight. The available data is too small to identify seasonal patterns and make predictable variation in value, such as annual fluctuation in temperature relative to the season. Trend is a tendency in the data to increase or decrease over time.\n\nResultsIf no control measures are put in place, it is expected that over 40,000 would be infected in Tehran around the middle of June. However, if control measures were implemented with a high degree of success, one would expect the spread of the COV-19 virus would peak at the start of April with a downward trend dropping off by the end of May (70 days). In the scenario, that no further measures are implemented, one would expect the spread of COVID-19 to continue on a gentle incline, reaching 21,000 by mid-June. The same process has been applied to review the confirmed, deaths and recovered dataset. The forecast has been carried out for the next 30 days, a shorter timeframe has been selected as there is a high probability that the Iranian New Years celebration, Farvardin, first month of Spring (30th March in Western calendar) will have an impact on the infection rate following the event.\n\nThe best predictive model predicts the confirmed cases to be in the range of 35,000-70,000, with the number of reported COVDI-19 deaths to be between 3,000 - 5,000 and 5,000 - 30,000 of recovered cases.\n\nConclusionsModeling outbreak ofCovid-19 shows that the number of patients and deaths is still increasing. Contagious diseases follow an exponential model and the same be Haves this one. This is because, the virus can spread to others and finally each person turns into a carrier of the virus and transmit it to another person. Disease control depends on disconnection and social distancing. In addition, many factors are effective in stopping the disease. These include citizens participation in the prevention process, health education, the effectiveness of instructive traditions, environmental conditions, and so on.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Maryam Moghadami", - "author_inst": "Tehran university" - }, - { - "author_name": "Maryam Moghadami", - "author_inst": "Tehran University" - }, - { - "author_name": "Mohammad Hassanzadeh", - "author_inst": "Tarbiat Modare University" - }, - { - "author_name": "ka wa", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Aziz Hedayati", - "author_inst": "Shahid Madani Azarbayjan University" - }, - { - "author_name": "Mila Malekolkalami", - "author_inst": "Tarbiat Modares University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.03.24.20041087", "rel_title": "Hydrogen Peroxide Vapor sterilization of N95 respirators for reuse", @@ -1586296,6 +1588488,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.22.20041137", + "rel_title": "Is scaling-up COVID-19 testing cost-saving?", + "rel_date": "2020-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.22.20041137", + "rel_abs": "The World Health Organization currently recommends that governments scale up testing for COVID-19 infection. We performed health economic analyses projecting whether the additional costs from screening would be offset by the avoided costs with hospitalizations. We analysed Portuguese COVID-19 data up until the 22nd March 2020, and estimated the additional number of cases that would be detected if different testing rates and frequencies of positive results would have been observed. We projected that, in most scenarios, the costs with scaling up COVID-19 tests would be lower than savings with hospitalization costs, rendering large scale testing cost-saving.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Bernardo Sousa-Pinto", + "author_inst": "Faculty of Medicine, University of Porto" + }, + { + "author_name": "Joao Almeida Fonseca", + "author_inst": "Department of Community Medicine, Information and Health Decision Sciences - Faculty of Medicine, University of Porto, Porto, Portugal" + }, + { + "author_name": "Altamiro Costa-Pereira", + "author_inst": "Department of Community Medicine, Information and Health Decision Sciences - Faculty of Medicine, University of Porto, Porto, Portugal" + }, + { + "author_name": "Francisco Nuno Rocha-Goncalves", + "author_inst": "Department of Community Medicine, Information and Health Decision Sciences - Faculty of Medicine, University of Porto, Porto, Portugal" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.22.20041285", "rel_title": "Elevated serum IgM levels indicate poor outcome in patients with coronavirus disease 2019 pneumonia: A retrospective case-control study", @@ -1587698,113 +1589921,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.03.25.009084", - "rel_title": "Non-neural expression of SARS-CoV-2 entry genes in the olfactory epithelium suggests mechanisms underlying anosmia in COVID-19 patients", - "rel_date": "2020-03-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.25.009084", - "rel_abs": "Altered olfactory function is a common symptom of COVID-19, but its etiology is unknown. A key question is whether SARS-CoV-2 (CoV-2) - the causal agent in COVID-19 - affects olfaction directly by infecting olfactory sensory neurons or their targets in the olfactory bulb, or indirectly, through perturbation of supporting cells. Here we identify cell types in the olfactory epithelium and olfactory bulb that express SARS-CoV-2 cell entry molecules. Bulk sequencing revealed that mouse, non-human primate and human olfactory mucosa expresses two key genes involved in CoV-2 entry, ACE2 and TMPRSS2. However, single cell sequencing and immunostaining demonstrated ACE2 expression in support cells, stem cells, and perivascular cells; in contrast, neurons in both the olfactory epithelium and bulb did not express ACE2 message or protein. These findings suggest that CoV-2 infection of non-neuronal cell types leads to anosmia and related disturbances in odor perception in COVID-19 patients.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "David Brann", - "author_inst": "Harvard Medical School Department of Neurobiology" - }, - { - "author_name": "Tatsuya Tsukahara", - "author_inst": "Harvard Medical School Department of Neurobiology" - }, - { - "author_name": "Caleb Weinreb", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Koen Van den Berge", - "author_inst": "Department of Statistics, University of California, Berkeley; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgi" - }, - { - "author_name": "Boying Gong", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Rebecca Chance", - "author_inst": "Department of Molecular and Cell Biology, University of California," - }, - { - "author_name": "Iain C Macaulay", - "author_inst": "Earlham Institute" - }, - { - "author_name": "Hsin-jung Chou", - "author_inst": "Department of Molecular and Cell Biology, University of California, Berkeley" - }, - { - "author_name": "Russell Fletcher", - "author_inst": "Department of Molecular and Cell Biology, University of California," - }, - { - "author_name": "Diya Das", - "author_inst": "Department of Molecular and Cell Biology, University of California, Berkeley" - }, - { - "author_name": "Kelly Street", - "author_inst": "Department of Data Sciences, Dana-Farber Cancer Institute; Department of Biostatistics, Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Hector Roux de Bezieux", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Yoon-Gi Choi", - "author_inst": "QB3 Functional Genomics Laboratory, University of California, Berkeley" - }, - { - "author_name": "Davide Risso", - "author_inst": "Department of Statistical Sciences, University of Padova" - }, - { - "author_name": "Sandrine Dudoit", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Elizabeth Purdom", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Jonathan C Mill", - "author_inst": "University of Exeter" - }, - { - "author_name": "Ralph Abi Hachem", - "author_inst": "Duke University" - }, - { - "author_name": "Hiroaki Matsunami", - "author_inst": "Duke University" - }, - { - "author_name": "Darren W. Logan", - "author_inst": "Waltham Petcare Science Institute, Leicestershire LE14 4RT, UK" - }, - { - "author_name": "Bradley Goldstein", - "author_inst": "Duke University" - }, - { - "author_name": "John Ngai", - "author_inst": "Department of Molecular and Cell Biology, University of California, Berkeley; Helen Wills Neuroscience Institute; QB3 Functional Genomics Laboratory" - }, - { - "author_name": "Sandeep Robert Datta", - "author_inst": "Harvard Medical School" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2020.03.25.20043893", "rel_title": "A Simple Mathematical Model for Estimating the Inflection Points of COVID-19 Outbreaks", @@ -1587938,6 +1590054,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.24.20036285", + "rel_title": "Transmission dynamics of SARS-COV-2 in China: impact of public health interventions", + "rel_date": "2020-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20036285", + "rel_abs": "COVID-19 has become a global pandemic. However, the impact of the public health interventions in China needs to be evaluated. We established a SEIRD model to simulate the transmission trend of China. In addition, the reduction of the reproductive number was estimated under the current forty public health interventions policies. Furthermore, the infection curve, daily transmission replication curve, and the trend of cumulative confirmed cases were used to evaluate the effects of the public health interventions. Our results showed that the SEIRD curve model we established had a good fit and the basic reproductive number is 3.38 (95% CI, 3.25-3.48). The SEIRD curve show a small difference between the simulated number of cases and the actual number; the correlation index (H2) is 0.934, and the reproductive number (R) has been reduced from 3.38 to 0.5 under the current forty public health interventions policies of China. The actual growth curve of new cases, the virus infection curve, and the daily transmission replication curve were significantly going down under the current public health interventions. Our results suggest that the current public health interventions of China are effective and should be maintained until COVID-19 is no longer considered a global threat.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Wang Wenbao", + "author_inst": "Department of Engineering Managment, College of Civil Engineering, Yango University, Fuzhou, Fujian, China" + }, + { + "author_name": "Chen Yiqin", + "author_inst": "Fujian Province Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian, China" + }, + { + "author_name": "Wang Qi", + "author_inst": "Fujian Province Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian, China" + }, + { + "author_name": "Cai Ping", + "author_inst": "Department of Health Inspection and Quarantine, School of Public Health, Fujian Medical University, Fuzhou, Fujian, China" + }, + { + "author_name": "He Ye", + "author_inst": "Department of Health Inspection and Quarantine, School of Public Health, Fujian Medical University, Fuzhou, Fujian, China" + }, + { + "author_name": "Hu Shanwen", + "author_inst": "Department of Health Inspection and Quarantine, School of Public Health, Fujian Medical University, Fuzhou, Fujian, China" + }, + { + "author_name": "Wu Yan", + "author_inst": "Department of Health Inspection and Quarantine, School of Public Health, Fujian Medical University, Fuzhou, Fujian, China" + }, + { + "author_name": "Huang Zuxiong", + "author_inst": "Department of Hepatology, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, Fujian Province, China" + }, + { + "author_name": "Wang Wenxiang", + "author_inst": "Fujian Medical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.26.20044370", "rel_title": "Severe airport sanitarian control could slow down the spreading of COVID-19 pandemics in Brazil", @@ -1589152,125 +1591319,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.26.20042184", - "rel_title": "Serological diagnostic kit of SARS-CoV-2 antibodies using CHO-expressed full-length SARS-CoV-2 S1 proteins", - "rel_date": "2020-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20042184", - "rel_abs": "WHO has declared COVID-19 a pandemic with more than 300,000 confirmed cases and more than 14,000 deaths. There is urgent need for accurate and rapid diagnostic kits. Here we report the development and validation of a COVID-19/SARS-CoV-2 S1 serology ELISA kit for the detection of total anti-virus antibody (IgG+IgM) titers in sera from either the general population or patients suspected to be infected. For indirect ELISA, CHO-expressed recombinant full length SARS-CoV-2-S1 protein with 6* His tag was used as the coating antigen to capture the SARS-CoV-2-S1 antibodies specifically. The specificity of the ELISA kit was determined to be 97.5%, as examined against total 412 normal human sera including 257 samples collected prior to the outbreak and 155 collected during the outbreak. The sensitivity of the ELISA kit was determined to be 97.5% by testing against 69 samples from hospitalized and/or recovered COVID-19 patients. The overall accuracy rate reached 97.3%. Most importantly, in one case study, the ELISA test kit was able to identify an infected person who had previously been quarantined for 14 days after coming into contact with a confirmed COVID-19 patient, and discharged after testing negative twice by nucleic acid test. With the assays developed here, we can screen millions of medical staffs in the hospitals and people in residential complex, schools, public transportations, and business parks in the epidemic centers of the outbreaks to fish out the \"innocent viral spreaders\", and help to stop the further spreading of the virus.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Rongqing Zhao", - "author_inst": "AnyGo Technology Co., Ltd" - }, - { - "author_name": "Maohua Li", - "author_inst": "AbMax Biotechnology Co., LTD" - }, - { - "author_name": "Hao Song", - "author_inst": "Research Network of Immunity and Health (RNIH)" - }, - { - "author_name": "Jianxin Chen", - "author_inst": "Zhenge Biotechnology Co., LTD" - }, - { - "author_name": "Wenlin Ren", - "author_inst": "AbMax Biotechnology Co., LTD" - }, - { - "author_name": "Yingmei Feng", - "author_inst": "Beijing You an Hospital, Capital Medical University" - }, - { - "author_name": "Jin-Wen Song", - "author_inst": "The Fifth Medical Center of PLA General Hospital" - }, - { - "author_name": "Ya Peng", - "author_inst": "Research Network of Immunity and Health (RNIH)" - }, - { - "author_name": "Bin Su", - "author_inst": "Beijing You an Hospital, Capital Medical University" - }, - { - "author_name": "Xianghua Guo", - "author_inst": "Beijing You an Hospital, Capital Medical University" - }, - { - "author_name": "Yanjun Wang", - "author_inst": "Beijing Institute of Hepatology" - }, - { - "author_name": "Jingong Chen", - "author_inst": "Zhenge Biotechnology Co., LTD" - }, - { - "author_name": "Jianli Li", - "author_inst": "AbMax Biotechnology Co., LTD" - }, - { - "author_name": "Hunter Sun", - "author_inst": "AnyGo Technology Co., Ltd" - }, - { - "author_name": "Zhonghu Bai", - "author_inst": "School of Biotechnology, Jiangnan University" - }, - { - "author_name": "Wen Jing Cao", - "author_inst": "Bengbu Medical University" - }, - { - "author_name": "Jin Zhu", - "author_inst": "Quzhou People's Hospital" - }, - { - "author_name": "Qinlu Zhang", - "author_inst": "ShaanXi Provincial Engineering Research Center for Nano-BioMedical Detection" - }, - { - "author_name": "Yufei Sun", - "author_inst": "AnyGo Technology Co., Ltd" - }, - { - "author_name": "Sean Sun", - "author_inst": "AnyGo Technology Co., Ltd" - }, - { - "author_name": "Xinkun Mao", - "author_inst": "AnyGo Technology Co., Ltd" - }, - { - "author_name": "Junchi Su", - "author_inst": "AnyGo Technology Co., Ltd" - }, - { - "author_name": "Hui Chen", - "author_inst": "School of Biotechnology, Jiangnan Univ" - }, - { - "author_name": "Ailiang He", - "author_inst": "Zhenge Biotechnology Co., LTD" - }, - { - "author_name": "Ronghua Jin", - "author_inst": "Beijing You an Hospital, Capital Medical University" - }, - { - "author_name": "Le Sun", - "author_inst": "AbMax Biotechnology Co., LTD" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.22.20040642", "rel_title": "The Effect of Large-Scale Anti-Contagion Policies on the Coronavirus (COVID-19) Pandemic", @@ -1589424,6 +1591472,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.23.20040493", + "rel_title": "Modelling SARS-CoV-2 Dynamics: Implications for Therapy", + "rel_date": "2020-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.23.20040493", + "rel_abs": "The scientific community is focussed on developing antiviral therapies to mitigate the impacts of the ongoing novel coronavirus disease (COVID-19) outbreak. This will be facilitated by improved understanding of viral dynamics within infected hosts. Here, using a mathematical model in combination with published viral load data collected from the same specimen (throat / nasal swabs or nasopharyngeal / sputum / tracheal aspirate), we compare within-host dynamics for patients infected in the current outbreak with analogous dynamics for MERS-CoV and SARS-CoV infections. Our quantitative analyses revealed that SARS-CoV-2 infection dynamics are more severe than those for mild cases of MERS-CoV, but are similar to severe cases, and that the viral dynamics of SARS-CoV infection are similar to those of MERS-CoV in mild cases but not in severe case. Consequently, SARS-CoV-2 generates infection dynamics that are more severe than SARS-CoV. Furthermore, we used our viral dynamics model to predict the effectiveness of unlicensed drugs that have different methods of action. The effectiveness was measured by AUC of viral load. Our results indicated that therapies that block de novo infections or virus production are most likely to be effective if initiated before the peak viral load (which occurs around three days after symptom onset on average), but therapies that promote cytotoxicity are likely to have only limited effects. Our unique mathematical approach provides insights into the pathogenesis of SARS-CoV-2 in humans, which are useful for development of antiviral therapies.\n\nSignificance StatementAntiviral agents with different mechanisms of action have different curative effects depending on precisely when therapy is initiated. Based on a model of viral dynamics, parameterised using viral load data from SARS-CoV-2 infected patients reported by Zou et al. (1), computer simulations were performed. We propose that effective treatment of SARS-CoV-2 infection requires an appropriate choice of class-specific drugs and initiation timing as reported for treatment of other viral infections (2); otherwise, antivirals do not have a significant effect on the within-host viral dynamics of SARS-CoV-2 and are wasted.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Kwang Su Kim", + "author_inst": "Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan" + }, + { + "author_name": "Keisuke Ejima", + "author_inst": "Indiana University" + }, + { + "author_name": "Yusuke Ito", + "author_inst": "Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan" + }, + { + "author_name": "Shoya Iwanami", + "author_inst": "Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan" + }, + { + "author_name": "Hirofumi Ohashi", + "author_inst": "Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan" + }, + { + "author_name": "Yoshiki Koizumi", + "author_inst": "National Center for Global Health and Medicine, Tokyo, Japan" + }, + { + "author_name": "Yusuke Asai", + "author_inst": "National Center for Global Health and Medicine, Tokyo, Japan" + }, + { + "author_name": "Shinji Nakaoka", + "author_inst": "Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan" + }, + { + "author_name": "Koichi Watashi", + "author_inst": "Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan" + }, + { + "author_name": "Robin N Thompson", + "author_inst": "University of Oxford" + }, + { + "author_name": "Shingo Iwami", + "author_inst": "Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.23.20040501", "rel_title": "Climate affects global patterns of COVID-19 early outbreak dynamics", @@ -1590790,65 +1592897,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "urology" }, - { - "rel_doi": "10.1101/2020.03.21.20037127", - "rel_title": "A Multicentre Study of 2019 Novel Coronavirus Disease Outcomes of Cancer Patients in Wuhan, China", - "rel_date": "2020-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.21.20037127", - "rel_abs": "BackgroundAt present, there is a global pandemic of coronavirus disease 2019 (COVID-19) pneumonia. For COVID-19 patients, cancer is a coexisting disease that should not be Here, we conducted a multicenter retrospective study to show the clinical information and outcomes of cancer patients infected with COVID-19.\n\nMeasurementsMedical records of COVID-19 patients with cancer admitted to hospitals from Jan 5, 2020 to Feb 18, 2020 were collected.\n\nResultsOf the 67 patients (median age: 66 years), the median age of patients with severe illness was older than that of patients with mild symptoms (P<0.001). The proportion of severe patients had co-morbidities was higher than patients with mild disease (P=0.004). During the treatment of COVID-19 pneumonia, tumor progression and recurrence was not observed for those patients still at the anticancer treatment phase. Lymphocytopenia was the main laboratory finding accompanying increased C-reactive protein and procalcitonin in cancer patients, especially in severe cases. By Mar 10, 2020, 18 (26.9%) patients died from COVID-19. The median age of survivors was younger than that of deaths (P=0.014). Lung cancer (n=15, 22.4%) was the most common cancer type and accounted for the highest proportion COVID-19 resulted deaths (33.3%, 5/15). We observed a tendency that patients at the follow-up phase had a better prognosis than that at anticancer treatment phase (P=0.095).\n\nConclusionThis study showed COVID-19 patients with cancer seem to have a higher proportion of severe cases and poorer prognosis. We should pay more intensive attentions to cancer patients infected with COVID-19.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Hong-Yan Zhang", - "author_inst": "Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Lin-Wei Wang", - "author_inst": "Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Yuan-Yuan Chen", - "author_inst": "Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Xiao-Kun Shen", - "author_inst": "Convalife (Shanghai) Co., Ltd." - }, - { - "author_name": "Qun Wang", - "author_inst": "the Fifth Hospital of Wuhan" - }, - { - "author_name": "You-Qin Yan", - "author_inst": "the Seventh Hospital of Wuhan" - }, - { - "author_name": "Yi Yu", - "author_inst": "Han Kou Hospital of Wuhan" - }, - { - "author_name": "Qiuji Wu", - "author_inst": "Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Ya-Hua Zhong", - "author_inst": "Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Melvin Chua Lee Kiang", - "author_inst": "National Cancer Centre Singapore" - }, - { - "author_name": "Cong-Hua Xie", - "author_inst": "Zhongnan Hospital of Wuhan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2020.03.22.20040600", "rel_title": "Human leukocyte antigen susceptibility map for SARS-CoV-2", @@ -1591066,6 +1593114,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.24.20042606", + "rel_title": "Modes of contact and risk of transmission in COVID-19 among close contacts", + "rel_date": "2020-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20042606", + "rel_abs": "BackgroundRapid spread of SARS-CoV-2 in Wuhan prompted heightened surveillance in Guangzhou and elsewhere in China. Modes of contact and risk of transmission among close contacts have not been well estimated.\n\nMethodsWe included 4950 closes contacts from Guangzhou, and extracted data including modes of contact, laboratory testing, clinical characteristics of confirmed cases and source cases. We used logistic regression analysis to explore the risk factors associated with infection of close contacts.\n\nResultsAmong 4950 closes contacts, the median age was 38.0 years, and males accounted for 50.2% (2484). During quarantine period, 129 cases (2.6%) were diagnosed, with 8 asymptomatic (6.2%), 49 mild (38.0%), and 5 (3.9%) severe to critical cases. The sensitivity of throat swab was 71.32% and 92.19% at first to second PCR test. Among different modes of contact, household contacts were the most dangerous in catching with infection of COVID-19, with an incidence of 10.2%. As the increase of age for close contacts and severity of source cases, the incidence of COVID-19 presented an increasing trend from 1.8% (0-17 years) to 4.2% (60 or over years), and from 0.33% for asymptomatic, 3.3% for mild, to 6.2% for severe and critical source cases, respectively. Manifestation of expectoration in source cases was also highly associated with an increased risk of infection in their close contacts (13.6%). Secondary cases were in general clinically milder and were less likely to have common symptoms than those of source cases.\n\nConclusionsIn conclusion, the proportion of asymptomatic and mild infections account for almost half of the confirmed cases among close contacts. The household contacts were the main transmission mode, and clinically more severe cases were more likely to pass the infection to their close contacts. Generally, the secondary cases were clinically milder than those of source cases.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Lei Luo", + "author_inst": "Guangzhou Center for Disease Control and Prevention" + }, + { + "author_name": "Dan Liu", + "author_inst": "Department of Epidemiology, School of Public Health, Southern Medical University" + }, + { + "author_name": "Xin-long Liao", + "author_inst": "Guangzhou Center for Disease Control and Prevention" + }, + { + "author_name": "Xian-bo Wu", + "author_inst": "Department of Epidemiology, School of Public Health, Southern Medical University" + }, + { + "author_name": "Qin-long Jing", + "author_inst": "Guangzhou Center for Disease Control and Prevention" + }, + { + "author_name": "Jia-zhen Zheng", + "author_inst": "Department of Epidemiology, School of Public Health, Southern Medical University" + }, + { + "author_name": "Fang-hua Liu", + "author_inst": "Guangzhou Center for Disease Control and Prevention" + }, + { + "author_name": "Shi-gui Yang", + "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The" + }, + { + "author_name": "Bi Bi", + "author_inst": "Guangzhou Center for Disease Control and Prevention" + }, + { + "author_name": "Zhi-hao Li", + "author_inst": "Department of Epidemiology, School of Public Health, Southern Medical University" + }, + { + "author_name": "Jian-ping Liu", + "author_inst": "Department of Epidemiology, School of Public Health, Southern Medical University" + }, + { + "author_name": "Wei-qi Song", + "author_inst": "Department of Epidemiology, School of Public Health, Southern Medical University" + }, + { + "author_name": "Wei Zhu", + "author_inst": "Guangzhou Center for Disease Control and Prevention" + }, + { + "author_name": "Zheng-he Wang", + "author_inst": "Department of Epidemiology, School of Public Health, Southern Medical University" + }, + { + "author_name": "Xi-ru Zhang", + "author_inst": "Department of Epidemiology, School of Public Health, Southern Medical University" + }, + { + "author_name": "Pei-liang Chen", + "author_inst": "Department of Epidemiology, School of Public Health, Southern Medical University" + }, + { + "author_name": "Hua-min Liu", + "author_inst": "Department of Epidemiology, School of Public Health, Southern Medical University" + }, + { + "author_name": "Xin Cheng", + "author_inst": "Department of Epidemiology, School of Public Health, Southern Medical University" + }, + { + "author_name": "Miao-chun Cai", + "author_inst": "Department of Epidemiology, School of Public Health, Southern Medical University" + }, + { + "author_name": "Qing-mei Huang", + "author_inst": "Department of Epidemiology, School of Public Health, Southern Medical University" + }, + { + "author_name": "Pei Yang", + "author_inst": "Department of Epidemiology, School of Public Health, Southern Medical University" + }, + { + "author_name": "Xin-fen Yang", + "author_inst": "School of Public Health, Southern Medical University" + }, + { + "author_name": "Zhi-gang Huang", + "author_inst": "Guangzhou Center for Disease Control and Prevention" + }, + { + "author_name": "Jin-ling Tang", + "author_inst": "Guangzhou Women and Children's Medical Center" + }, + { + "author_name": "Yu Ma", + "author_inst": "Guangzhou Center for Disease Control and Prevention" + }, + { + "author_name": "Chen Mao", + "author_inst": "Department of Epidemiology, School of Public Health, Southern Medical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.24.20042218", "rel_title": "Estimating the ascertainment rate of SARS-CoV-2 infection in Wuhan, China: implications for management of the global outbreak", @@ -1592248,53 +1594415,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.24.004655", - "rel_title": "SARS-CoV-2 launches a unique transcriptional signature from in vitro, ex vivo, and in vivo systems", - "rel_date": "2020-03-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.24.004655", - "rel_abs": "One of the greatest threats to humanity is the emergence of a pandemic virus. Among those with the greatest potential for such an event include influenza viruses and coronaviruses. In the last century alone, we have observed four major influenza A virus pandemics as well as the emergence of three highly pathogenic coronaviruses including SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic. As no effective antiviral treatments or vaccines are presently available against SARS-CoV-2, it is important to understand the host response to this virus as this may guide the efforts in development towards novel therapeutics. Here, we offer the first in-depth characterization of the host transcriptional response to SARS-CoV-2 and other respiratory infections through in vitro, ex vivo, and in vivo model systems. Our data demonstrate the each virus elicits both core antiviral components as well as unique transcriptional footprints. Compared to the response to influenza A virus and respiratory syncytial virus, SARS-CoV-2 elicits a muted response that lacks robust induction of a subset of cytokines including the Type I and Type III interferons as well as a numerous chemokines. Taken together, these data suggest that the unique transcriptional signature of this virus may be responsible for the development of COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Daniel Blanco-Melo", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Benjamin Nilsson-Payant", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Wen-Chun Liu", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Rasmus Moeller", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Maryline Panis", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "David Sachs", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Randy Albrecht", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Benjamin R. tenOever", - "author_inst": "Icahn School of Medicine at Mount Sinai" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.03.21.20040691", "rel_title": "Meplazumab treats COVID-19 pneumonia: an open-labelled, concurrent controlled add-on clinical trial", @@ -1592544,6 +1594664,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, + { + "rel_doi": "10.1101/2020.03.19.20039354", + "rel_title": "AI-assisted CT imaging analysis for COVID-19 screening: Building and deploying a medical AI system in four weeks", + "rel_date": "2020-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.19.20039354", + "rel_abs": "The sudden outbreak of novel coronavirus 2019 (COVID-19) increased the diagnostic burden of radiologists. In the time of an epidemic crisis, we hoped artificial intelligence (AI) to help reduce physician workload in regions with the outbreak, and improve the diagnosis accuracy for physicians before they could acquire enough experience with the new disease. Here, we present our experience in building and deploying an AI system that automatically analyzes CT images to detect COVID-19 pneumonia features. Different from conventional medical AI, we were dealing with an epidemic crisis. Working in an interdisciplinary team of over 30 people with medical and / or AI background, geographically distributed in Beijing and Wuhan, we were able to overcome a series of challenges in this particular situation and deploy the system in four weeks. Using 1,136 training cases (723 positives for COVID-19) from five hospitals, we were able to achieve a sensitivity of 0.974 and specificity of 0.922 on the test dataset, which included a variety of pulmonary diseases. Besides, the system automatically highlighted all lesion regions for faster examination. As of today, we have deployed the system in 16 hospitals, and it is performing over 1,300 screenings per day.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Shuo Jin", + "author_inst": "Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China" + }, + { + "author_name": "Bo Wang", + "author_inst": "State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China" + }, + { + "author_name": "Haibo Xu", + "author_inst": "Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan, China" + }, + { + "author_name": "Chuan Luo", + "author_inst": "State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China" + }, + { + "author_name": "Lai Wei", + "author_inst": "Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China" + }, + { + "author_name": "Wei Zhao", + "author_inst": "Beijing Jingzhen Medical Technology Ltd., Beijing, China" + }, + { + "author_name": "Xuexue Hou", + "author_inst": "Beijing Jingzhen Medical Technology Ltd., Beijing, China" + }, + { + "author_name": "Wenshuo Ma", + "author_inst": "Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China" + }, + { + "author_name": "Zhengqing Xu", + "author_inst": "Beijing Jingzhen Medical Technology Ltd., Beijing, China" + }, + { + "author_name": "Zhuozhao Zheng", + "author_inst": "Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China" + }, + { + "author_name": "Wenbo Sun", + "author_inst": "Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan, China" + }, + { + "author_name": "Lan Lan", + "author_inst": "Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan, China" + }, + { + "author_name": "Wei Zhang", + "author_inst": "Beijing Jingzhen Medical Technology Ltd., Beijing, China" + }, + { + "author_name": "Xiangdong Mu", + "author_inst": "Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China" + }, + { + "author_name": "Chenxi Shi", + "author_inst": "Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China" + }, + { + "author_name": "Zhongxiao Wang", + "author_inst": "Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China" + }, + { + "author_name": "Jihae Lee", + "author_inst": "Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China" + }, + { + "author_name": "Zijian Jin", + "author_inst": "Beijing Jingzhen Medical Technology Ltd., Beijing, China" + }, + { + "author_name": "Minggui Lin", + "author_inst": "Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China" + }, + { + "author_name": "Hongbo Jin", + "author_inst": "Beijing Jingzhen Medical Technology Ltd., Beijing, China" + }, + { + "author_name": "Liang Zhang", + "author_inst": "School of Computer Science and Technology, Xidian University, Xi'an, China" + }, + { + "author_name": "Jun Guo", + "author_inst": "Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China" + }, + { + "author_name": "Benqi Zhao", + "author_inst": "Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China" + }, + { + "author_name": "Zhizhong Ren", + "author_inst": "Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China" + }, + { + "author_name": "Shuhao Wang", + "author_inst": "Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China" + }, + { + "author_name": "Zheng You", + "author_inst": "State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China" + }, + { + "author_name": "Jiahong Dong", + "author_inst": "Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China" + }, + { + "author_name": "Xinghuan Wang", + "author_inst": "Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China" + }, + { + "author_name": "Jianming Wang", + "author_inst": "Department of Biliary and Pancreatic Surgery/Cancer Research Center Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Techn" + }, + { + "author_name": "Wei Xu", + "author_inst": "Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.03.19.20038984", "rel_title": "An exploratory randomized, controlled study on the efficacy and safety of lopinavir/ritonavir or arbidol treating adult patients hospitalized with mild/moderate COVID-19 (ELACOI)", @@ -1593778,33 +1596033,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.21.20040444", - "rel_title": "From a single host to global spread. The global mobility based modelling of the COVID-19 pandemic implies higher infection and lower detection rates than current estimates.", - "rel_date": "2020-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.21.20040444", - "rel_abs": "BackgroundSince the outbreak of the COVID-19 pandemic, multiple efforts of modelling of the geo-temporal transmissibility of the virus have been undertaken, but none describes the pandemic spread at the global level. The aim of this research is to provide a high-resolution global model of the pandemic that overcomes the problem of biased country-level data on the number of infected cases. To achieve this we propose a novel SIR-type metapopulation transmission model and a set of analytically derived model parameters. We used them to perform a simulation of the disease spread with help of the Global Epidemic and Mobility (GLEAM) framework embedding actual population densities, commute patterns and long-range travel networks. The simulation starts on Nov 17th, 2019 with just a single pre-symptomatic, yet infectious, case in Wuhan, China, and results in an accurate prediction of the number of diagnosed cases after 154 days in multiple countries across five continents. In addition, the model outcome shows high compliance with the results of a random screening test conducted on pregnant women in the New York area.\n\nMethodsWe have built a modified SIR metapopulation transmission model and parameterized it analytically either by setting the values of the parameters based on the literature, or by assuming their plausible values. We compared our results with the number of diagnosed cases in twenty selected countries which provide reliable statistics but differ substantially in terms of strength and speed of undertaken Non-Drug Interventions. The obtained 95% confidence intervals for the predictions are in agreement with the empirical data.\n\nResultsThe parameters that successfully model the pandemic are: the basic reproduction number R0, 4.4; a latent non-infectious period of 1.1. days followed by 4.6 days of the presymptomatic infectious period; the probability of developing severe symptoms, 0.01; the probability of being diagnosed when presenting severe symptoms of 0.6; the probability of diagnosis for cases with mild symptoms or asymptomatic, 0.001.\n\nDiscussionParameters that successfully reproduce the observed number of cases indicate that both R0 and the prevalence of the virus might be underestimated. This is in concordance with the newest research on undocumented COVID-19 cases. Consequently, the actual mortality rate is putatively lower than estimated. Confirmation of the pandemic characteristic by further refinement of the model and screening tests is crucial for developing an effective strategy for the global epidemiological crisis.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Marlena M Siwiak", - "author_inst": "Data 3.0" - }, - { - "author_name": "Pawel Szczesny", - "author_inst": "Data 3.0" - }, - { - "author_name": "Marian P Siwiak", - "author_inst": "Data 3.0" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.20.20038422", "rel_title": "Estimating the reproduction number of COVID-19 in Iran using epidemic modeling", @@ -1593994,6 +1596222,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.19.20039008", + "rel_title": "Effectiveness and safety of antiviral or antibody treatments for coronavirus", + "rel_date": "2020-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.19.20039008", + "rel_abs": "BackgroundTo identify safe and effective medical countermeasures (e.g., antivirals/antibodies) to address the current outbreak of a novel coronavirus (COVID-19)\n\nMethodsComprehensive literature searches were developed by an experienced librarian for MEDLINE, EMBASE, the Cochrane Library, and biorxiv.org/medrxiv.org; additional searches for ongoing trials and unpublished studies were conducted in clinicaltrials.gov and the Global Infectious Diseases and Epidemiology Network (GIDEON). Title/abstract and full-text screening, data abstraction, and risk of bias appraisal were carried out by single reviewers.\n\nResults54 studies were included in the review: three controlled trials, 10 cohort studies, seven retrospective medical record/database studies, and 34 case reports or series. These studies included patients with severe acute respiratory syndrome (SARs, n=33), middle east respiratory syndrome (MERS, n=16), COVID-19 (n=3), and unspecified coronavirus (n=2). The most common treatment was ribavirin (n=41), followed by oseltamivir (n=10) and the combination of lopinavir/ritonavir (n=7). Additional therapies included broad spectrum antibiotics (n=30), steroids (n=39) or various interferons (n=12). No eligible studies examining monoclonal antibodies for COVID-19 were identified. One trial found that ribavirin prophylactic treatment statistically significantly reduced risk of MERS infection in people who had been exposed to the virus. Of the 21 studies reporting rates of ICU admission in hospitalized SARS or MERS patients, none reported statistically significant results in favour of or against antiviral therapies. Of the 40 studies reporting mortality rates in hospitalized SARS or MERS patients, one cohort study (MERS) and one retrospective study (SARS) found a statistically significant increase in the mortality rate for patients treated with ribavirin. Eighteen studies reported potential drug-related adverse effects including gastrointestinal symptoms, anemia, and altered liver function in patients receiving ribavirin.\n\nConclusionThe current evidence for the effectiveness and safety of antiviral therapies for coronavirus is inconclusive and suffers from a lack of well-designed prospective trials or observational studies, preventing any treatment recommendations from being made. However, it is clear that the existing body of evidence is weighted heavily towards ribavirin (41/54 studies), which has not shown conclusive evidence of effectiveness and may cause harmful adverse events so future investigations may consider focusing on other candidates for antiviral therapy.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Patricia Rios", + "author_inst": "Li Ka Shing Research Institute, Knowledge Translation Program, St. Michael's Hospital, Unity Health Toronto" + }, + { + "author_name": "Amruta Radhakrishnan", + "author_inst": "Li Ka Shing Research Institute, Knowledge Translation Program, St. Michael's Hospital, Unity Health Toronto" + }, + { + "author_name": "Jesmin Antony", + "author_inst": "Li Ka Shing Research Institute, Knowledge Translation Program, St. Michael's Hospital, Unity Health Toronto" + }, + { + "author_name": "Sonia M. Thomas", + "author_inst": "Li Ka Shing Research Institute, Knowledge Translation Program, St. Michael's Hospital, Unity Health Toronto" + }, + { + "author_name": "Mathew Muller", + "author_inst": "Li Ka Shing Research Institute, Knowledge Translation Program, St. Michael's Hospital, Unity Health Toronto" + }, + { + "author_name": "Sharon E. Straus", + "author_inst": "Li Ka Shing Research Institute, Knowledge Translation Program, St. Michael's Hospital, Unity Health Toronto and Department of Medicine, University of Toronto" + }, + { + "author_name": "Andrea C. Tricco", + "author_inst": "Li Ka Shing Research Institute, Knowledge Translation Program, St. Michael's Hospital, Unity Health Toronto and Dalla Lana School of Public Health & Institute o" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.18.20037473", "rel_title": "Now-casting the COVID-19 epidemic: The use case of Japan, March 2020", @@ -1595652,37 +1597923,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.03.21.001586", - "rel_title": "Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis", - "rel_date": "2020-03-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.21.001586", - "rel_abs": "The ongoing pandemic of the coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV2). We have performed an integrated sequence-based analysis of SARS-CoV2 genomes from different geographical locations in order to identify its unique features absent in SARS-CoV and other related coronavirus family genomes, conferring unique infection, facilitation of transmission, virulence and immunogenic features to the virus. The phylogeny of the genomes yields some interesting results. Systematic gene level mutational analysis of the genomes has enabled us to identify several unique features of the SARS-CoV2 genome, which includes a unique mutation in the spike surface glycoprotein (A930V (24351C>T)) in the Indian SARS-CoV2, absent in other strains studied here. We have also predicted the impact of the mutations in the spike glycoprotein function and stability, using computational approach. To gain further insights into host responses to viral infection, we predict that antiviral host-miRNAs may be controlling the viral pathogenesis. Our analysis reveals nine host miRNAs which can potentially target SARS-CoV2 genes. Interestingly, the nine miRNAs do not have targets in SARS and MERS genomes. Also, hsa-miR-27b is the only unique miRNA which has a target gene in the Indian SARS-CoV2 genome. We also predicted immune epitopes in the genomes", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Rahila Sardar", - "author_inst": "International Centre for Genetic Engineering and Biotechnology (ICGEB) and Jamia Hamdard, India" - }, - { - "author_name": "Deepshikha Satish", - "author_inst": "International Centre for Genetic Engineering and Biotechnology (ICGEB), India" - }, - { - "author_name": "Shweta Birla", - "author_inst": "International Centre for Genetic Engineering and Biotechnology (ICGEB), India" - }, - { - "author_name": "Dinesh Gupta", - "author_inst": "International Centre for Genetic Engineering and Biotechnology (ICGEB), India" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.03.19.998724", "rel_title": "All-in-One Dual CRISPR-Cas12a (AIOD-CRISPR) Assay: A Case for Rapid, Ultrasensitive and Visual Detection of Novel Coronavirus SARS-CoV-2 and HIV virus", @@ -1595868,6 +1598108,37 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.03.20.000141", + "rel_title": "COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning", + "rel_date": "2020-03-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.20.000141", + "rel_abs": "To ultimately combat the emerging COVID-19 pandemic, it is desired to develop an effective and safe vaccine against this highly contagious disease caused by the SARS-CoV-2 coronavirus. Our literature and clinical trial survey showed that the whole virus, as well as the spike (S) protein, nucleocapsid (N) protein, and membrane protein, have been tested for vaccine development against SARS and MERS. We further used the Vaxign reverse vaccinology tool and the newly developed Vaxign-ML machine learning tool to predict COVID-19 vaccine candidates. The N protein was found to be conserved in the more pathogenic strains (SARS/MERS/COVID-19), but not in the other human coronaviruses that mostly cause mild symptoms. By investigating the entire proteome of SARS-CoV-2, six proteins, including the S protein and five non-structural proteins (nsp3, 3CL-pro, and nsp8-10) were predicted to be adhesins, which are crucial to the viral adhering and host invasion. The S, nsp3, and nsp8 proteins were also predicted by Vaxign-ML to induce high protective antigenicity. Besides the commonly used S protein, the nsp3 protein has not been tested in any coronavirus vaccine studies and was selected for further investigation. The nsp3 was found to be more conserved among SARS-CoV-2, SARS-CoV, and MERS-CoV than among 15 coronaviruses infecting human and other animals. The protein was also predicted to contain promiscuous MHC-I and MHC-II T-cell epitopes, and linear B-cell epitopes localized in specific locations and functional domains of the protein. Our predicted vaccine targets provide new strategies for effective and safe COVID-19 vaccine development.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Edison Ong", + "author_inst": "University of Michigan" + }, + { + "author_name": "Mei U Wong", + "author_inst": "University of Michigan" + }, + { + "author_name": "Anthony Huffman", + "author_inst": "University of Michigan" + }, + { + "author_name": "Yongqun He", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.03.18.20035816", "rel_title": "Development and utilization of an intelligent application for aiding COVID-19 diagnosis", @@ -1597034,77 +1599305,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.17.20037432", - "rel_title": "Favipiravir versus Arbidol for COVID-19: A Randomized Clinical Trial", - "rel_date": "2020-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.17.20037432", - "rel_abs": "BackgroundNo clinically proven effective antiviral strategy exists for the epidemic Coronavirus Disease 2019 (COVID-19).\n\nMethodsWe conducted a prospective, randomized, controlled, open-label multicenter trial involving adult patients with COVID-19. Patients were randomly assigned in a 1:1 ratio to receive conventional therapy plus Umifenovir (Arbidol) (200mg*3/day) or Favipiravir (1600mg*2/first day followed by 600mg*2/day) for 10 days. The primary outcome was clinical recovery rate of Day 7. Latency to relief for pyrexia and cough, the rate of auxiliary oxygen therapy (AOT) or noninvasive mechanical ventilation (NMV) were the secondary outcomes. Safety data were collected for 17 days.\n\nResults240 enrolled COVID-19 patients underwent randomization; 120 patients were assigned to receive Favipiravir (116 assessed), and 120 to receive Arbidol (120 assessed). Clinical recovery rate of Day 7 does not significantly differ between Favipiravir group (71/116) and Arbidol group (62/120) (P=0.1396, difference of recovery rate: 0.0954; 95% CI: -0.0305 to 0.2213). Favipiravir led to shorter latencies to relief for both pyrexia (difference: 1.70 days, P<0.0001) and cough (difference: 1.75 days, P<0.0001). No difference was observed of AOT or NMV rate (both P>0.05). The most frequently observed Favipiravir-associated adverse event was raised serum uric acid (16/116, OR: 5.52, P=0.0014).\n\nConclusionsAmong patients with COVID-19, Favipiravir, compared to Arbidol, did not significantly improve the clinically recovery rate at Day 7. Favipiravir significantly improved the latency to relief for pyrexia and cough. Adverse effects caused Favipiravir are mild and manageable. This trial is registered with Chictr.org.cn (ChiCTR2000030254).", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Chang Chen", - "author_inst": "Clinical Trial Center, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Yi Zhang", - "author_inst": "Center for Life Sciences, Peking University" - }, - { - "author_name": "Jianying Huang", - "author_inst": "Clinical Trial Center, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Ping Yin", - "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Zhenshun Cheng", - "author_inst": "Department of Respiratory Medicine, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Jianyuan Wu", - "author_inst": "Clinical Trial Center, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Song Chen", - "author_inst": "Department of Urology, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Yongxi Zhang", - "author_inst": "Department of Infectious Diseases, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Bo Chen", - "author_inst": "Clinical Trial Center, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Mengxin Lu", - "author_inst": "Department of Urology, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Yongwen Luo", - "author_inst": "Department of Urology, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Lingao Ju", - "author_inst": "Department of Urology, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Jingyi Zhang", - "author_inst": "Department of Cardiology, The Third People Hospital of Hubei Province" - }, - { - "author_name": "Xinghuan Wang", - "author_inst": "Clinical Trial Center, Zhongnan Hospital of Wuhan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.17.20036640", "rel_title": "Characterization of anti-viral immunity in recovered individuals infected by SARS-CoV-2", @@ -1597294,6 +1599494,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.18.20038133", + "rel_title": "Comparison of the coronavirus pandemic dynamics in Europe, USA and South Korea", + "rel_date": "2020-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.18.20038133", + "rel_abs": "The pandemic cased by coronavirus COVID-19 is of great concern. A detailed scientific analysis of this phenomenon is still to come, but now it is urgently needed to evaluate the disease dynamics in order to organize the appropriate quarantine activities, to estimate the required number of places in hospitals, the level of individual protection, the rate of isolation of infected persons, etc. South Korea has achieved the stabilization of the number of cases at rather low level. The epidemic dynamics there can be compared with its development in other countries to make some preliminary, but very important conclusions. Here we provide a simple method of data comparison that can be useful for both governmental organizations and anyone.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Igor Nesteruk", + "author_inst": "Institute of Hydromechanics National Academy of sciences of Ukraine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.19.20038182", "rel_title": "A prospect on the use of antiviral drugs to control local outbreaks of COVID-19", @@ -1598428,25 +1600647,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2020.03.17.20037838", - "rel_title": "AAEDM: Theoretical Dynamic Epidemic Diffusion Model and Covid-19 Korea Pandemic Cases", - "rel_date": "2020-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.17.20037838", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThis paper deals with an advanced analytical epidemic diffusion model which is capable to predict the status of epidemic impacts. This newly propose model well describes an epidemic growth and it could be widely applied into various topics including pathology, epidemiology, business and data sciences. The Advanced Analytical Epidemic Diffusion Model (AAEDM) is a dynamic diffusion prediction model which is theoretically intuitive and its tractable closed formula could be easily adapted into versatile Bigdata driven analytics including the machine learning system. This dynamic model is still an analytical model but the periods of prediction are segmented for adapting the values from the dataset when the data is available. The epidemiologically vital parameters which effect on the AAEDM are also introduced in this paper. The evaluation of this theoretical model based on the Covid-19 data in Korea has been accomplished with relative fair future prediction accuracies. Although this analytical model has been designed from a basic exponential growth model, the performance of the AAEDM is competitive with other Bigdata based simulation models. Since the AAEDM is relatively simple and handy, anyone can use this model into analyzing outbreak situations in his daily life.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Song-Kyoo Kim", - "author_inst": "Macao Polytechnic Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.03.17.20037788", "rel_title": "Intensive Care Unit Resource Planning During COVID-19 Emergency at the Regional Level: the Italian case.", @@ -1598536,6 +1600736,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.18.20038059", + "rel_title": "SARS-CoV-2 specific antibody responses in COVID-19 patients", + "rel_date": "2020-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.18.20038059", + "rel_abs": "A new coronavirus, SARS-CoV-2, has recently emerged to cause a human pandemic. Whereas molecular diagnostic tests were rapidly developed, serologic assays are still lacking, yet urgently needed. Validated serologic assays are important for contact tracing, identifying the viral reservoir and epidemiological studies. Here, we developed serological assays for the detection of SARS-CoV-2 neutralizing, spike- and nucleocapsid-specific antibodies. Using serum samples from patients with PCR-confirmed infections of SARS-CoV-2, other coronaviruses, or other respiratory pathogenic infections, we validated and tested various antigens in different in-house and commercial ELISAs. We demonstrate that most PCR-confirmed SARS-CoV-2 infected individuals seroconverted, as revealed by sensitive and specific in-house ELISAs. We found that commercial S1 IgG or IgA ELISAs were of lower specificity while sensitivity varied between the two, with IgA showing higher sensitivity. Overall, the validated assays described here can be instrumental for the detection of SARS-CoV-2-specific antibodies for diagnostic, seroepidemiological and vaccine evaluation studies.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "NISREEN M.A. OKBA", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Marcel A Muller", + "author_inst": "Charite Universitatsmedizin" + }, + { + "author_name": "Wentao Li", + "author_inst": "Utrecht University" + }, + { + "author_name": "Chunyan Wang", + "author_inst": "Utrecht University" + }, + { + "author_name": "Corine H. GeurtsvanKessel", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Victor M. Corman", + "author_inst": "Charite Universitatsmedizin" + }, + { + "author_name": "Mart M. Lamers", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Reina S. Sikkema", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Erwin de Bruin", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Felicity D. Chandler", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Yazdan Yazdanpanah", + "author_inst": "Universite de Paris" + }, + { + "author_name": "Quentin Le Hingrat", + "author_inst": "Universite de Paris" + }, + { + "author_name": "Diane Descamps", + "author_inst": "Universite de Paris" + }, + { + "author_name": "Nadhira Houhou-Fidouh", + "author_inst": "Hopital Bichat-Claude Bernard" + }, + { + "author_name": "Chantal B. E. M. Reusken", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Berend-Jan Bosch", + "author_inst": "Utrecht University" + }, + { + "author_name": "Christian Drosten", + "author_inst": "Charite-Universitatsmedizin" + }, + { + "author_name": "Marion P.G. Koopmans", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Bart L. Haagmans", + "author_inst": "Erasmus Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.18.20038018", "rel_title": "Antibody responses to SARS-CoV-2 in COVID-19 patients: the perspective application of serological tests in clinical practice", @@ -1599962,73 +1602253,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.15.991844", - "rel_title": "RBD mutations from circulating SARS-CoV-2 strains enhance the structure stability and infectivity of the spike protein", - "rel_date": "2020-03-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.15.991844", - "rel_abs": "The current global pandemic of COVID-19 is caused by a novel coronavirus SARS-CoV-2. The SARS-CoV-2 spike protein receptor-binding domain (RBD) is the critical determinant of viral tropism and infectivity. To investigate whether naturally occurring mutations in the RBD during the early transmission phase have altered the receptor binding affinity and infectivity, firstly we analyzed in silico the binding dynamics between mutated SARS-CoV-2 RBDs and the human ACE2 receptor. Among 32,123 genomes of SARS-CoV-2 isolates (January through March, 2020), 302 non-synonymous RBD mutants were identified and clustered into 96 mutant types. The six dominant mutations were analyzed applying molecular dynamics simulations. The mutant type V367F continuously circulating worldwide displayed higher binding affinity to human ACE2 due to the enhanced structural stabilization of the RBD beta-sheet scaffold. The increased infectivity of V367 mutants was further validated by performing receptor-ligand binding ELISA, surface plasmon resonance, and pseudotyped virus assays. Genome phylogenetic analysis of V367F mutants showed that during the early transmission phase, most V367F mutants clustered more closely with the SARS-CoV-2 prototype strain than the dual-mutation variants (V367F + D614G) which emerged later and formed a distinct sub-cluster. The analysis of critical RBD mutations provides further insights into the evolutionary trajectory of SARS-CoV-2 under negative selection pressure and supports the continuing surveillance of spike mutations to aid in the development of new COVID-19 drugs and vaccines.\n\nImportanceA novel coronavirus SARS-CoV-2 has caused the pandemic of COVID-19. The origin of SARS-CoV-2 was associated with zoonotic infections. The spike protein receptor-binding domain (RBD) is identified as the critical determinant of viral tropism and infectivity. Thus, whether the mutations in the RBD of the circulating SARS-CoV-2 isolates have altered the receptor binding affinity and caused them more infectious, should be paid more attentions to. Given that SARS-CoV-2 is a novel coronavirus, the significance of our research is in identifying and validating the RBD mutant types emerging during the early transmission phase that have increased human ACE2 receptor binding affinity and infectivity. The RBD mutation analysis provides insights into SARS-CoV-2 evolution. The continuous surveillance of RBD mutations with increased human ACE2 affinity in human or other animals is important and necessary, particularly when the direct correlation between the virus variations and vaccine effectiveness is underdetermined during the sustained COVID-19 pandemic.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Junxian Ou", - "author_inst": "Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, China" - }, - { - "author_name": "Zhonghua Zhou", - "author_inst": "Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Te" - }, - { - "author_name": "Ruixue Dai", - "author_inst": "Fudan University Department of Environmental Science and Engineering" - }, - { - "author_name": "Shan Zhao", - "author_inst": "Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, China" - }, - { - "author_name": "Xiaowei Wu", - "author_inst": "Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University" - }, - { - "author_name": "Jing Zhang", - "author_inst": "Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdong 510632, China" - }, - { - "author_name": "Wendong Lan", - "author_inst": "Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, China" - }, - { - "author_name": "Lilian Cui", - "author_inst": "Novoprotein Scientific Inc" - }, - { - "author_name": "Jianguo Wu", - "author_inst": "Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdong 510632, China" - }, - { - "author_name": "Donald Seto", - "author_inst": "Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA 20110, USA" - }, - { - "author_name": "James Chodosh", - "author_inst": "Department of Ophthalmology, Howe Laboratory Massachusetts Eye and Ear Infirmary Harvard Medical School" - }, - { - "author_name": "Gong Zhang", - "author_inst": "Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Te" - }, - { - "author_name": "Qiwei Zhang", - "author_inst": "Southern Medical University" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.03.12.20027185", "rel_title": "Deep Learning-based Detection for COVID-19 from Chest CT using Weak Label", @@ -1600218,6 +1602442,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.15.993097", + "rel_title": "Cross-reactive antibody response between SARS-CoV-2 and SARS-CoV infections", + "rel_date": "2020-03-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.15.993097", + "rel_abs": "The World Health Organization has recently declared the ongoing outbreak of COVID-19, which is caused by a novel coronavirus SARS-CoV-2, as pandemic. There is currently a lack of knowledge in the antibody response elicited from SARS-CoV-2 infection. One major immunological question is concerning the antigenic differences between SARS-CoV-2 and SARS-CoV. We address this question by using plasma from patients infected by SARS-CoV-2 or SARS-CoV, and plasma obtained from infected or immunized mice. Our results show that while cross-reactivity in antibody binding to the spike protein is common, cross-neutralization of the live viruses is rare, indicating the presence of non-neutralizing antibody response to conserved epitopes in the spike. Whether these non-neutralizing antibody responses will lead to antibody-dependent disease enhancement needs to be addressed in the future. Overall, this study not only addresses a fundamental question regarding the antigenicity differences between SARS-CoV-2 and SARS-CoV, but also has important implications in vaccine development.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Huibin Lv", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Nicholas C. Wu", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Owen Tak-Yin Tsang", + "author_inst": "Hospital Authority of Hong Kong" + }, + { + "author_name": "Meng Yuan", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Ranawaka A. P. M. Perera", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Wai Shing Leung", + "author_inst": "Hospital Authority of Hong Kong" + }, + { + "author_name": "Ray T. Y. So", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Jacky Man Chun Chan", + "author_inst": "Hospital Authority of Hong Kong" + }, + { + "author_name": "Garrick K. Yip", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Thomas Shiu Hong Chik", + "author_inst": "Hospital Authority of Hong Kong" + }, + { + "author_name": "Yiquan Wang", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Chris Yau Chung Choi", + "author_inst": "Hospital Authority of Hong Kong" + }, + { + "author_name": "Yihan Lin", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Wilson W. Ng", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Jincun Zhao", + "author_inst": "The First Affiliated Hospital of Guangzhou Medical University" + }, + { + "author_name": "Leo L. M. Poon", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "J. S. Malik Peiris", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Ian A. Wilson", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Chris K. P. Mok", + "author_inst": "The University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.03.13.20035485", "rel_title": "Impact of the contact and exclusion rates on the spread of COVID-19 pandemic", @@ -1601640,45 +1603955,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.13.20035642", - "rel_title": "Epidemiological Trends of Coronavirus Disease 2019 in China", - "rel_date": "2020-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.13.20035642", - "rel_abs": "BackgroundThe Coronavirus Disease 2019 (COVID-19) epidemic broke out in Wuhan, China, and it spread rapidly. Since January 23, 2020, China has launched a series of unusual and strict measures, including the lockdown of Wuhan city to contain this highly contagious disease. We collected the epidemiological data to analyze the trend of this epidemic in China.\n\nMethodsWe closely tracked the Chinese and global official websites to collect the epidemiological information about COVID-19. The number of total and daily new confirmed cases of COVID-19 in China was presented to illustrate the trend of this epidemic.\n\nResultsOn January 23, 2020, 835 confirmed COVID-19 cases were reported in China. On February 6, 2020, there were 31211 cases. By February 20, 2020, the number reached as high as 75,993. Most cases were distributed in and around Wuhan, Hubei province. Since January 23, 2020, the number of daily new cases in China except Hubei province reached a peak of 890 on the eleventh day and then it declined to a low level of 34 within two full-length incubation periods (28 days), and the number of daily new cases in Hubei also started to decrease on the twelfth day, from 3156 on February 4, 2020 to 955 on February 15, 2020.\n\nConclusionThe COVID-19 epidemic has been primarily contained in China. The battle against this epidemic in China has provided valuable experiences for the rest of the world. Strict measures need to be taken as earlier as possible to prevent its spread.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Bilin Chen", - "author_inst": "Jinling Hospital, Medical School of Nanjing University" - }, - { - "author_name": "Huanhuan Zhong", - "author_inst": "Jinling Hospital, Medical School of Nanjing University" - }, - { - "author_name": "Yueyan Ni", - "author_inst": "Jinling, Hospital, Nanjing Medical University" - }, - { - "author_name": "Lulu Liu", - "author_inst": "Jinling Hospital, Medical School of Nanjing University" - }, - { - "author_name": "Jinjin Zhong", - "author_inst": "Jinling Hospital, Medical School of Nanjing University" - }, - { - "author_name": "Xin Su", - "author_inst": "Jinling Hospital, Medical School of Nanjing University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.14.20035741", "rel_title": "Excess cases of Influenza like illnesses in France synchronous with COVID19 invasion.", @@ -1601780,6 +1604056,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.03.13.20035618", + "rel_title": "Comparative Performance of SARS-CoV-2 Detection Assays using Seven Different Primer/Probe Sets and One Assay Kit", + "rel_date": "2020-03-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.13.20035618", + "rel_abs": "More than 100,000 people worldwide are known to have been infected with SARS-CoV-2 beginning in December 2019. The virus has now spread to over 93 countries including the United States, with the largest cluster of US cases to date in the Seattle metropolitan area in Washington. Given the rapid increase in the number of local cases, the availability of accurate, high-throughput SARS-CoV-2 testing is vital to efforts to manage the current public health crisis. In the course of optimizing SARS-CoV-2 testing performed by the University of Washington Clinical Virology Lab (UW Virology Lab), we tested assays using seven different primer/probe sets and one assay kit. We found that the most sensitive assays were those the used the E-gene primer/probe set described by Corman et al. (Eurosurveillance 25(3), 2020, https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045) and the N2 set described by the CDC (Division of Viral Diseases, Centers for Disease Control and Prevention, 2020, https://www.cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel-primer-probes.pdf). All assays tested were found to be highly specific for SARS-CoV-2, with no cross-reactivity with other respiratory viruses observed in our analyses regardless of the primer/probe set or kit used. These results will provide invaluable information to other clinical laboratories who are actively developing SARS-CoV-2 testing protocols at a time when increased testing capacity is urgently needed worldwide.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Amanda M. Casto", + "author_inst": "University of Washington" + }, + { + "author_name": "Meei-Li Huang", + "author_inst": "University of Washington" + }, + { + "author_name": "Arun Nalla", + "author_inst": "University of Washington" + }, + { + "author_name": "Garrett A. Perchetti", + "author_inst": "University of Washington" + }, + { + "author_name": "Reigran Sampoleo", + "author_inst": "University of Washington" + }, + { + "author_name": "Lasata Shrestha", + "author_inst": "University of Washington" + }, + { + "author_name": "Yulun Wei", + "author_inst": "University of Washington" + }, + { + "author_name": "Haiying Zhu", + "author_inst": "University of Washington" + }, + { + "author_name": "Alexander L. Greninger", + "author_inst": "University of Washington" + }, + { + "author_name": "Keith R. Jerome", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.12.20034686", "rel_title": "Clinical Characteristics of 34 Children with Coronavirus Disease-2019 in the West of China: a Multiple-center Case Series", @@ -1603117,53 +1605448,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2020.03.13.991083", - "rel_title": "Structural and functional conservation of the programmed -1 ribosomal frameshift signal of SARS-CoV-2", - "rel_date": "2020-03-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.13.991083", - "rel_abs": "17 years after the SARS-CoV epidemic, the world is facing the COVID-19 pandemic. COVID-19 is caused by a coronavirus named SARS-CoV-2. Given the most optimistic projections estimating that it will take over a year to develop a vaccine, the best short-term strategy may lie in identifying virus-specific targets for small molecule interventions. All coronaviruses utilize a molecular mechanism called -1 PRF to control the relative expression of their proteins. Prior analyses of SARS-CoV revealed that it employs a structurally unique three-stemmed mRNA pseudoknot to stimulate high rates of -1 PRF, and that it also harbors a -1 PRF attenuation element. Altering -1 PRF activity negatively impacts virus replication, suggesting that this molecular mechanism may be therapeutically targeted. Here we present a comparative analysis of the original SARS-CoV and SARS-CoV-2 frameshift signals. Structural and functional analyses revealed that both elements promote similar rates of -1 PRF and that silent coding mutations in the slippery sites and in all three stems of the pseudoknot strongly ablated -1 PRF activity. The upstream attenuator hairpin activity has also been functionally retained. Small-angle x-ray scattering indicated that the pseudoknots in SARS-CoV and SARS-CoV-2 had the same conformation. Finally, a small molecule previously shown to bind the SARS-CoV pseudoknot and inhibit -1 PRF was similarly effective against -1 PRF in SARS-CoV-2, suggesting that such frameshift inhibitors may provide promising lead compounds to counter the current pandemic.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Jamie A. Kelly", - "author_inst": "University of Maryland" - }, - { - "author_name": "Alexandra N Olson", - "author_inst": "University of Maryland" - }, - { - "author_name": "Krishna Neupane", - "author_inst": "University of Alberta" - }, - { - "author_name": "Sneha Munshi", - "author_inst": "University of Alberta" - }, - { - "author_name": "Josue San Emerterio", - "author_inst": "Cornell University" - }, - { - "author_name": "Lois Pollack", - "author_inst": "Cornell University" - }, - { - "author_name": "Michael T. Woodside", - "author_inst": "University of Alberta" - }, - { - "author_name": "Jonathan D. Dinman", - "author_inst": "University of Maryland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.03.12.988246", "rel_title": "High sensitivity detection of SARS-CoV-2 using multiplex PCR and a multiplex-PCR-based metagenomic method", @@ -1603389,6 +1605673,45 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.03.12.988865", + "rel_title": "The architecture of SARS-CoV-2 transcriptome", + "rel_date": "2020-03-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.12.988865", + "rel_abs": "SARS-CoV-2 is a betacoronavirus that is responsible for the COVID-19 pandemic. The genome of SARS-CoV-2 was reported recently, but its transcriptomic architecture is unknown. Utilizing two complementary sequencing techniques, we here present a high-resolution map of the SARS-CoV-2 transcriptome and epitranscriptome. DNA nanoball sequencing shows that the transcriptome is highly complex owing to numerous recombination events, both canonical and noncanonical. In addition to the genomic RNA and subgenomic RNAs common in all coronaviruses, SARS-CoV-2 produces a large number of transcripts encoding unknown ORFs with fusion, deletion, and/or frameshift. Using nanopore direct RNA sequencing, we further find at least 41 RNA modification sites on viral transcripts, with the most frequent motif being AAGAA. Modified RNAs have shorter poly(A) tails than unmodified RNAs, suggesting a link between the internal modification and the 3' tail. Functional investigation of the unknown ORFs and RNA modifications discovered in this study will open new directions to our understanding of the life cycle and pathogenicity of SARS-CoV-2.\n\nHighlightsO_LIWe provide a high-resolution map of SARS-CoV-2 transcriptome and epitranscriptome using nanopore direct RNA sequencing and DNA nanoball sequencing.\nC_LIO_LIThe transcriptome is highly complex owing to numerous recombination events, both canonical and noncanonical.\nC_LIO_LIIn addition to the genomic and subgenomic RNAs common in all coronaviruses, SARS-CoV-2 produces transcripts encoding unknown ORFs.\nC_LIO_LIWe discover at least 41 potential RNA modification sites with an AAGAA motif.\nC_LI", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Dongwan Kim", + "author_inst": "Institute for Basic Science" + }, + { + "author_name": "Joo-Yeon Lee", + "author_inst": "Korea National Institute of Health" + }, + { + "author_name": "Jeong-Sun Yang", + "author_inst": "Korea National Institute of Health" + }, + { + "author_name": "Jun Won Kim", + "author_inst": "Korea National Institute of Health" + }, + { + "author_name": "V. Narry Kim", + "author_inst": "Institute for Basic Science" + }, + { + "author_name": "Hyeshik Chang", + "author_inst": "Institute for Basic Science" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.03.13.991570", "rel_title": "A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV", @@ -1604869,37 +1607192,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.10.20033613", - "rel_title": "Analysis clinical features of COVID-19 infection in secondary epidemic area and report potential biomarkers in evaluation", - "rel_date": "2020-03-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.10.20033613", - "rel_abs": "ObjectiveBased on the clinical characteristics of infected patients with novel coronavirus in secondary epidemic areas, we aimed to identify potential biomarkers for the evaluation of novel coronavirus-infected patients, guide the diagnosis and treatment of this disease in secondary epidemic areas and provide a reference for the clinical prevention and control of this epidemic situation.\n\nMethodsThe clinical data of 33 patients with respiratory symptoms caused by the novel coronavirus in Wenzhou city from January 15 to February 12, 2020, were thoroughly reviewed. At the onset of the disease, we found that the primary symptoms were fever, cough, fatigue, chest tightness, chest pain and specific blood test results. According to the patients histories, the patients were divided into two groups: those who spent time in the main epidemic area and those who did not spend time in the main epidemic area. The differences in the clinical manifestations between these two groups were analyzed.\n\nResultsThe main clinical symptoms of patients infected with novel coronavirus in the secondary epidemic area were respiratory tract ailments and systemic symptoms. After grouping patients based on the presence or absence of residency in or travel history to the main epidemic area, there was no significant difference between the baseline data of these two groups, and there were no significant differences in symptoms and signs between the two groups (P>0.05). Some patients had abnormally increased serum amyloid protein A (SAA). There were statistically significant differences in the leukocyte count/C-reactive protein, monocyte ratio/C-reactive protein, neutrophil count/C-reactive protein, monocyte count/C-reactive protein and hemoglobin/C-reactive protein values between the two groups (P < 0.05).\n\nConclusionRespiratory tract ailments and systemic symptoms were the primary symptoms of novel coronavirus infection in the secondary epidemic area; these symptoms are not typical. The abnormal increase in serum amyloid protein (SAA) may be used as an auxiliary index for diagnosis and treatment. CRP changes before other blood parameters and thus may be an effective evaluation index for patients with COVID-19 infection.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Weiping Ji", - "author_inst": "wenzhou medical university" - }, - { - "author_name": "Gautam Bishnu", - "author_inst": "wenzhou medical university" - }, - { - "author_name": "Zhenzhai Cai", - "author_inst": "wenzhou medical university" - }, - { - "author_name": "Xian Shen", - "author_inst": "wenzhou medical university" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.10.20033605", "rel_title": "Maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia: a case-control study", @@ -1605061,6 +1607353,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.03.09.20033530", + "rel_title": "Protocol of a randomized controlled trial testing inhaled Nitric Oxide in mechanically ventilated patients with severe acute respiratory syndrome in COVID-19 (SARS-CoV-2).", + "rel_date": "2020-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.09.20033530", + "rel_abs": "IntroductionSevere acute respiratory syndrome due to novel Coronavirus (SARS-CoV-2) related infection (COVID-19) is characterized by severe ventilation perfusion mismatch leading to refractory hypoxemia. To date, there is no specific treatment available for COVID-19. Nitric oxide is a selective pulmonary vasodilator gas used as a rescue therapy in refractory hypoxemia due to acute respiratory distress syndrome (ARDS). In has also shown invitro and clinical evidence that inhaled nitric oxide gas (iNO) has antiviral activity against other strains of coronavirus. The primary aim of this study is to determine whether inhaled NO improves oxygenation in patients with hypoxic COVID-19. This is a multicenter randomized controlled trial with 1:1 individual allocation. Patients will be blinded to the treatment.\n\nMethods and analysisIntubated patients admitted to the intensive care unit with confirmed SARS-CoV-2 infection and severe hypoxemia will be randomized to receive inhalation of NO (treatment group) or not (control group). Treatment will be stopped when patients are free from hypoxemia for more than 24 hours. The primary outcome evaluates levels of oxygenation between the two groups at 48 hours. Secondary outcomes include rate of survival rate at 28 and 90 days in the two groups, time to resolution of severe hypoxemia, time to achieve negativity of SARS-CoV-2 RT-PCR tests.\n\nEthics and disseminationThe study protocol has been approved by the Investigational Review Board of Xijing Hospital (Xian, China) and by the Partners Human Research Committee (Boston, USA). Recruitment will start after approval of both IRBs and local IRBs at other enrolling centers. Results of this study will be published in scientific journals, presented at scientific meetings, reported through flyers and posters, and published on related website or media in combating against this widespread contagious disease.\n\nTrial registrationClinicaltrials.gov. NCT04306393\n\nStrengths and limitations of this study-- Supplementation with nitric oxide (NO) might improve oxygenation and survival of SARS-CoV-2-infected patients.\n-- The antiviral activity of NO inhalation will be explored by measuring the time difference between the two groups to reach SARS-CoV-2 rt-PCR negativity.\n-- The spread of the disease worldwide determines the geographic areas of study and the recruitment rate of patients.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Chong Lei", + "author_inst": "Xijing Hospital, Xi'an, China" + }, + { + "author_name": "Binxiao Su", + "author_inst": "Xijing Hospital, Xi'an China" + }, + { + "author_name": "Hailong Dong", + "author_inst": "Xijing Hospital, Xi'an, China" + }, + { + "author_name": "Andrea Bellavia", + "author_inst": "Harvard T.H. Chan School of Public Health, Boston, MA, USA" + }, + { + "author_name": "Raffaele Di Fenza", + "author_inst": "Massachusetts General Hospital, Boston, MA, USA; University of Milan-Bicocca, Milan, Italy" + }, + { + "author_name": "Bijan Safaee Fakhr", + "author_inst": "Massachusetts General Hospital, Boston, MA, USA" + }, + { + "author_name": "Stefano Gianni", + "author_inst": "Massachusetts General Hospital, Boston, MA, USA" + }, + { + "author_name": "Luigi Giuseppe Grassi", + "author_inst": "Massachusetts General Hospital, Boston, MA, USA" + }, + { + "author_name": "Robert Kacmarek", + "author_inst": "Massachusetts General Hospital, Boston, MA, USA" + }, + { + "author_name": "Caio Cesar Araujo Morais", + "author_inst": "Massachusetts General Hospital, Boston, MA, USA" + }, + { + "author_name": "Riccardo Pinciroli", + "author_inst": "Massachusetts General Hospital, Boston, MA, USA" + }, + { + "author_name": "Emanuele Vassena", + "author_inst": "Massachusetts General Hospital, Boston, MA, USA" + }, + { + "author_name": "Lorenzo Berra", + "author_inst": "Massachusetts General Hospital, Harvard Medical School, Boston MA, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.03.09.983247", "rel_title": "Inhibition of SARS-CoV-2 infection (previously 2019-nCoV) by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion", @@ -1607146,45 +1609505,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.06.20031377", - "rel_title": "Clinical Characteristics on 25 Discharged Patients with COVID-19 Virus Returning", - "rel_date": "2020-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.06.20031377", - "rel_abs": "Here we report the clinical features of 25 discharged patients with COVID-19 recovery. Our analysis indicated that there was a significant inverse correlation existed between serum D-Dimer level and the duration of antiviral treatment, while lymphocyte concentration significantly positively correlated with the duration of virus reversal.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Jing Yuan", - "author_inst": "Diagnosis and Treatment of Infectious Diseases Research Laboratory, Shenzhen Third People's Hospital, Shenzhen 518112, China." - }, - { - "author_name": "Shanglong Kou", - "author_inst": "Diagnosis and Treatment of Infectious Diseases Research Laboratory, Shenzhen Third People's Hospital, Shenzhen 518112, China." - }, - { - "author_name": "Yanhua Liang", - "author_inst": "Diagnosis and Treatment of Infectious Diseases Research Laboratory, Shenzhen Third People's Hospital, Shenzhen 518112, China." - }, - { - "author_name": "Jianfeng Zeng", - "author_inst": "Diagnosis and Treatment of Infectious Diseases Research Laboratory, Shenzhen Third People's Hospital, Shenzhen 518112, China." - }, - { - "author_name": "Yanchao Pan", - "author_inst": "Diagnosis and Treatment of Infectious Diseases Research Laboratory, Shenzhen Third People's Hospital, Shenzhen 518112, China." - }, - { - "author_name": "Lei Liu", - "author_inst": "Diagnosis and Treatment of Infectious Diseases Research Laboratory, Shenzhen Third People's Hospital, Shenzhen 518112, China." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.07.20031393", "rel_title": "The epidemiological characteristics of 2019 novel coronavirus diseases (COVID-19) in Jingmen,Hubei,China", @@ -1607306,6 +1609626,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.06.20032334", + "rel_title": "Rapid Detection of 2019 Novel Coronavirus SARS-CoV-2 Using a CRISPR-based DETECTR Lateral Flow Assay", + "rel_date": "2020-03-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.06.20032334", + "rel_abs": "An outbreak of novel betacoronavirus, SARS-CoV-2 (formerly named 2019-nCoV), began in Wuhan, China in December 2019 and the COVID-19 disease associated with infection has since spread rapidly to multiple countries. Here we report the development of SARS-CoV-2 DETECTR, a rapid ([~]30 min), low-cost, and accurate CRISPR-Cas12 based lateral flow assay for detection of SARS-CoV-2 from respiratory swab RNA extracts. We validated this method using contrived reference samples and clinical samples from infected US patients and demonstrated comparable performance to the US CDC SARS-CoV-2 real-time RT-PCR assay.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "James P Broughton", + "author_inst": "Mammoth Biosciences, Inc." + }, + { + "author_name": "Xianding Deng", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Guixia Yu", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Clare L Fasching", + "author_inst": "Mammoth Biosciences, Inc." + }, + { + "author_name": "Jasmeet Singh", + "author_inst": "Mammoth Biosciences, Inc." + }, + { + "author_name": "Jessica Streithorst", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Andrea Granados", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Alicia Sotomayor-Gonzalez", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kelsey Zorn", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Allan Gopez", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Elaine Hsu", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Wei Gu", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Steven Miller", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Chao-Yang Pan", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Hugo Guevara", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Debra Wadford", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Janice Chen", + "author_inst": "Mammoth Biosciences, Inc." + }, + { + "author_name": "Charles Y Chiu", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.08.20032847", "rel_title": "Prediction of COVID-19 Spreading Profiles in South Korea, Italy and Iran by Data-Driven Coding", @@ -1608584,93 +1610991,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.05.20031849", - "rel_title": "A mathematical model for estimating the age-specific transmissibility of a novel coronavirus", - "rel_date": "2020-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.05.20031849", - "rel_abs": "BackgroundA novel coronavirus named as \"SARS-CoV-2\" has spread widely in many countries since December 2019, especially in China. This study aimed to quantify the age-specific transmissibility by using a mathematical model.\n\nMethodsAn age-specific susceptible - exposed - symptomatic - asymptomatic - recovered - seafood market (SEIARW) model was developed based on two suspected transmission routes (from market to person and person to person). The susceptible people from Wuhan City were divided into different age groups. We used the subscript i and j to represent age group 1 to 4 (i = j; 1: [≤] 14 years; 2: 15-44 years; 3: 45-64 years; 4: [≥] 65 years) and 1 to 5 (i = j; 1: [≤] 5 years; 2: 6-14 years; 3: 15-24 years; 4: 25-59 years; 4: [≥] 60 years), respectively. Data of reported COVID-19 cases were collected from one published literature from 26 November to 22 December, 2019 in Wuhan City, China. The age-specific transmissibility of the virus was estimated accordingly secondary attack rate (SAR).\n\nResultsThe age-specific SEIARW model fitted with the reported data well by dividing the population into four age groups ({chi}2 = 4.99 x 10-6, P > 0.999), and five age groups ({chi}2 = 4.85 x 10-6, P > 0.999). Based on the four-age-group SEIARW model, the highest transmissibility occurred from age group 2 to 3 (SAR23 = 17.56 per 10 million persons), followed by from age group 3 to 2 (SAR32 = 10.17 per 10 million persons). The lowest transmissibility occurred from age group 1 to 2 (SAR12 = 0.002 per 10 million persons). Based on the five-age-group SEIARW model, the highest transmissibility occurred from age group 4 to 5 (SAR45 = 12.40 per 10 million persons), followed by from age group 5 to 4 (SAR54 = 6.61 per 10 million persons). The lowest transmissibility occurred from age group 3 to 4 (SAR34 = 0.0002 per 10 million persons).\n\nConclusionsSARS-CoV-2 has high transmissibility among adults and elder people but low transmissibility among children and young people.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Zeyu Zhao", - "author_inst": "Xiamen University" - }, - { - "author_name": "Yuan-Zhao Zhu", - "author_inst": "Xiamen University" - }, - { - "author_name": "Jing-Wen Xu", - "author_inst": "Xiamen University" - }, - { - "author_name": "Qing-Qing Hu", - "author_inst": "University of Utah" - }, - { - "author_name": "Zhao Lei", - "author_inst": "Xiamen University" - }, - { - "author_name": "Jia Rui", - "author_inst": "Xiamen University" - }, - { - "author_name": "Xingchun Liu", - "author_inst": "Xiamen University" - }, - { - "author_name": "Yao Wang", - "author_inst": "Xiamen University" - }, - { - "author_name": "Li Luo", - "author_inst": "Xiamen University" - }, - { - "author_name": "Shan-Shan Yu", - "author_inst": "Xiamen University" - }, - { - "author_name": "Jia Li", - "author_inst": "Xiamen University" - }, - { - "author_name": "Ruo-Yun Liu", - "author_inst": "Xiamen University" - }, - { - "author_name": "Fang Xie", - "author_inst": "Xiamen University" - }, - { - "author_name": "Ying-Ying Su", - "author_inst": "Xiamen University" - }, - { - "author_name": "Yi-Chen Chiang", - "author_inst": "Xiamen University" - }, - { - "author_name": "Yanhua Su", - "author_inst": "Xiamen University" - }, - { - "author_name": "Benhua Zhao", - "author_inst": "Xiamen University" - }, - { - "author_name": "Tianmu Chen", - "author_inst": "Xiamen University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.06.20031880", "rel_title": "Estimating the scale of COVID-19 Epidemic in the United States: Simulations Based on Air Traffic directly from Wuhan, China", @@ -1608868,6 +1611188,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.03.04.20031237", + "rel_title": "Exploring diseases/traits and blood proteins causally related to expression of ACE2, the putative receptor of 2019-nCov: A Mendelian Randomization analysis", + "rel_date": "2020-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.04.20031237", + "rel_abs": "ObjectivesCOVID-19 has become a major public health problem. There is good evidence that ACE2 is a receptor for SARS-CoV-2, and high expression of ACE2 may increase susceptibility to infection. We aimed to explore risk factors affecting susceptibility to infection and prioritize drug repositioning candidates, based on Mendelian randomization (MR) studies on ACE2 lung expression.\n\nMethodsWe conducted a phenome-wide MR study to prioritize diseases/traits and blood proteins causally linked to ACE2 lung expression in GTEx. We also explored drug candidates whose targets overlapped with the top-ranked proteins in MR, as these drugs may alter ACE2 expression and may be clinically relevant.\n\nResultsThe most consistent finding was tentative evidence of an association between diabetes-related traits and increased ACE2 expression. Based on one of the largest GWAS on type 2 diabetes (T2DM) to date (N=898,130), T2DM was causally linked to raised ACE2 expression(p=2.91E-03;MR-IVW). Significant associations(at nominal level; p<0.05) with ACE2 expression was observed across multiple DM datasets and analytic methods, for type 1 and 2 diabetes and related traits including early start of insulin. Other diseases/traits having nominal significant associations with increased expression included inflammatory bowel disease, (ER+)breast and lung cancers, asthma, smoking and elevated ALT. We also identified drugs that may target the top-ranked proteins in MR, such as fostamatinib and zinc.\n\nConclusionsOur analysis suggested that diabetes and related traits may increase ACE2 expression, which may influence susceptibility to infection (or more severe infection). However, none of these findings withstood rigorous multiple testing corrections (at FDR<0.05). Proteome-wide MR analyses might help uncover mechanisms underlying ACE2 expression and guide drug repositioning. Further studies are required to verify our findings.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Shitao Rao", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Alexandria Lau", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Hon-Cheong So", + "author_inst": "The Chinese University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.05.20031518", "rel_title": "Clinical characterization and chest CT findings in laboratory-confirmed COVID-19: a systematic review and meta-analysis", @@ -1610265,41 +1612612,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.04.20030973", - "rel_title": "Study of the mental health status of medical personnel dealing with new coronavirus pneumonia", - "rel_date": "2020-03-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.04.20030973", - "rel_abs": "ObjectiveThis paper studied the relationship between personality traits and mental health conditions of medical personnel to provide a basis and reference for the implementation of targeted education on mental health.\n\nMethodsA self-report inventory, the Symptom Checklist-90 (SCL-90), was used to investigate the mental health status of 548 medical personnel dealing with the new coronavirus pneumonia in eight provinces and cities of China.\n\nResultsThe overall mean SCL-90 score and mean values of factors (somatization, obsessive-compulsive, anxiety, phobic anxiety, and psychoticism) of the medical personnel were significantly higher than in the norm group (p < 0.05), while their average interpersonal sensitivity score was significantly lower (p < 0.01). In addition, personal factors affecting the mental health status of medical personnel were identified. ( all p < 0.05).\n\nConclusionThe overall mental health status of medical personnel responding to new coronavirus pneumonia is generally higher than that of the norm group in China. The results of this study should contribute to measures to alleviate the psychological pressures on medical personnel dealing with the new coronavirus epidemic in China.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "ning sun", - "author_inst": "ningbo college of health sciences" - }, - { - "author_name": "jun xing", - "author_inst": "The Second Affiliated Hospital of Harbin Medical University" - }, - { - "author_name": "jun xu", - "author_inst": "The Second Affiliated Hospital of Harbin Medical" - }, - { - "author_name": "ling shu geng", - "author_inst": "The Second Affiliated Hospital of Harbin Medical" - }, - { - "author_name": "qian yu li", - "author_inst": "The Second Affiliated Hospital of Harbin Medical" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.03.03.20030775", "rel_title": "Key Points of Clinical and CT Imaging Features of 2019 Novel Coronavirus (2019-nCoV) Imported Pneumonia Based On 21 Cases Analysis", @@ -1610401,6 +1612713,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.03.20030874", + "rel_title": "Psychological impact of the coronavirus disease 2019 (COVID-19) outbreak on healthcare workers in China", + "rel_date": "2020-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.03.20030874", + "rel_abs": "IntroductionSince the outbreak of coronavirus disease 2019 (COVID-19), more than 3000 (including clinical diagnosis) healthcare workers (HCWs) have been infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China. This study is aimed to investigate the risk perception and immediate psychological state of HCWs in the early stage of the COVID-19 epidemic.\n\nMethodsThis study utilized a cross-sectional survey designed on a convenient sample of 4357 HCWs in China. Its data were collected using anonymous structured questionnaires distributed through social software. 6 questions were set to evaluate the participants risk perception of COVID-19, and a General Health Questionnaire was used to identify the participants immediate psychological status. Descriptive statistics were used for data analysis. Risk perception and psychological status were compared by demographic characteristics and COVID-19 exposure experiences.\n\nResultA total of 4,600 questionnaires were distributed, and 4,357 qualified ones (94.7%) were collected. The main concerns of HCWs are: infection of colleagues (72.5%), infection of family members (63.9%), protective measures (52.3%) and medical violence (48.5%). And 39.1% of the HCWs had psychological distress, especially working in Wuhan, participating in frontline treatments, having been isolated and having family members or colleagues infected.\n\nConclusionsThe finding indicating that, faced with the COVID-19 epidemic, HCWs, especially in Wuhan, were worried about the risks of infection and protective measures, resulting in psychological distress, so further actions should be taken.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Yuhong Dai", + "author_inst": "Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Guangyuan Hu", + "author_inst": "Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Huihua Xiong", + "author_inst": "Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Hong Qiu", + "author_inst": "Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Xianglin Yuan", + "author_inst": "Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.02.20030312", "rel_title": "Preliminary estimating the reproduction number of the coronavirus disease (COVID-19) outbreak in Republic of Korea from 31 January to 1 March 2020", @@ -1611927,97 +1614274,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.02.20026708", - "rel_title": "The effect of human mobility and control measures on the COVID-19 epidemic in China", - "rel_date": "2020-03-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.02.20026708", - "rel_abs": "The ongoing COVID-19 outbreak has expanded rapidly throughout China. Major behavioral, clinical, and state interventions are underway currently to mitigate the epidemic and prevent the persistence of the virus in human populations in China and worldwide. It remains unclear how these unprecedented interventions, including travel restrictions, have affected COVID-19 spread in China. We use real-time mobility data from Wuhan and detailed case data including travel history to elucidate the role of case importation on transmission in cities across China and ascertain the impact of control measures. Early on, the spatial distribution of COVID-19 cases in China was well explained by human mobility data. Following the implementation of control measures, this correlation dropped and growth rates became negative in most locations, although shifts in the demographics of reported cases are still indicative of local chains of transmission outside Wuhan. This study shows that the drastic control measures implemented in China have substantially mitigated the spread of COVID-19.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Moritz U.G. Kraemer", - "author_inst": "Department of Zoology, University of Oxford, United Kingdom" - }, - { - "author_name": "Chia-Hung Yang", - "author_inst": "Network Science Institute, Northeastern University, Boston, United States" - }, - { - "author_name": "Bernardo Gutierrez", - "author_inst": "Department of Zoology, University of Oxford, United Kingdom" - }, - { - "author_name": "Chieh-Hsi Wu", - "author_inst": "Mathematical Sciences, University of Southampton, Southampton, United Kingdom" - }, - { - "author_name": "Brennan Klein", - "author_inst": "Network Science Institute, Northeastern University, Boston, United States" - }, - { - "author_name": "David M. Pigott", - "author_inst": "Institute for Health Metrics and Evaluation, Department of Health Metrics, University of Washington, Seattle, United States" - }, - { - "author_name": "- open COVID-19 data working group", - "author_inst": "see manuscript" - }, - { - "author_name": "Louis du Plessis", - "author_inst": "Department of Zoology, University of Oxford, United Kingdom" - }, - { - "author_name": "Nuno R Faria", - "author_inst": "Department of Zoology, University of Oxford, United Kingdom" - }, - { - "author_name": "Ruoran Li", - "author_inst": "Harvard T.H. Chan School of Public Health, Boston, United States" - }, - { - "author_name": "William P. Hanage", - "author_inst": "Harvard T.H. Chan School of Public Health, Boston, United States" - }, - { - "author_name": "John S Brownstein", - "author_inst": "Harvard Medical School, Harvard University, Boston, United States" - }, - { - "author_name": "Maylis Layan", - "author_inst": "Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France" - }, - { - "author_name": "Alessandro Vespignani", - "author_inst": "Network Science Institute, Northeastern University, Boston, United States" - }, - { - "author_name": "Huaiyu Tian", - "author_inst": "State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China" - }, - { - "author_name": "Christopher Dye", - "author_inst": "Department of Zoology, University of Oxford, United Kingdom" - }, - { - "author_name": "Simon Cauchemez", - "author_inst": "Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France" - }, - { - "author_name": "Oliver Pybus", - "author_inst": "University of Oxford" - }, - { - "author_name": "Samuel V Scarpino", - "author_inst": "Northeastern University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.01.20029801", "rel_title": "Evaluation of the incidence of COVID-19 and of the efficacy of contention measures in Spain: a data-driven approach.", @@ -1612175,6 +1614431,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.02.974311", + "rel_title": "Partial RdRp sequences offer a robust method for Coronavirus subgenus classification", + "rel_date": "2020-03-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.02.974311", + "rel_abs": "The recent reclassification of the Riboviria, and the introduction of multiple new taxonomic categories including both subfamilies and subgenera for coronaviruses (family Coronaviridae, subfamily Orthocoronavirinae) represents a major shift in how official classifications are used to designate specific viral lineages. While the newly defined subgenera provide much-needed standardisation for commonly cited viruses of public health importance, no method has been proposed for the assignment of subgenus based on partial sequence data, or for sequences that are divergent from the designated holotype reference genomes. Here, we describe the genetic variation of a partial region of the coronavirus RNA-dependent RNA polymerase (RdRp), which is one of the most used partial sequence loci for both detection and classification of coronaviruses in molecular epidemiology. We infer Bayesian phylogenies from more than 7000 publicly available coronavirus sequences and examine clade groupings relative to all subgenus holotype sequences. Our phylogenetic analyses are largely coherent with genome-scale analyses based on designated holotype members for each subgenus. Distance measures between sequences form discrete clusters between taxa, offering logical threshold boundaries that can attribute subgenus or indicate sequences that are likely to belong to unclassified subgenera both accurately and robustly. We thus propose that partial RdRp sequence data of coronaviruses is sufficient for the attribution of subgenus-level taxonomic classifications and we supply the R package, \"MyCoV\", which provides a method for attributing subgenus and assessing the reliability of the attribution.\n\nImportance StatementThe analysis of polymerase chain reaction amplicons derived from biological samples is the most common modern method for detection and classification of infecting viral agents, such as Coronaviruses. Recent updates to the official standard for taxonomic classification of Coronaviruses, however, may leave researchers unsure as to whether the viral sequences they obtain by these methods can be classified into specific viral taxa due to variations in the sequences when compared to type strains. Here, we present a plausible method for defining genetic dissimilarity cut-offs that will allow researchers to state which taxon their virus belongs to and with what level of certainty. To assist in this, we also provide the R package MyCoV which classifies user generated sequences.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "David Arthur Wilkinson", + "author_inst": "UMR Processus Infectieux en Milieu Insulaire Tropical" + }, + { + "author_name": "L\u00e9a Joffrin", + "author_inst": "University of Reunion Island UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical) INSERM 1187, CNRS 9192, IRD 249;" + }, + { + "author_name": "Camille Lebarbenchon", + "author_inst": "University of Reunion Island" + }, + { + "author_name": "Patrick Mavingui", + "author_inst": "Universit\u00e9 de La R\u00e9union. Unit\u00e9 Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT)" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.03.02.20028704", "rel_title": "Monitoring Disease Transmissibility of 2019 Novel Coronavirus Disease in Zhejiang, China", @@ -1613852,93 +1616139,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.02.20027599", - "rel_title": "Effects of weather-related social distancing on city-scale transmission of respiratory viruses", - "rel_date": "2020-03-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.02.20027599", - "rel_abs": "BACKGROUNDUnusually high snowfall in western Washington State in February 2019 led to widespread school and workplace closures. We assessed the impact of social distancing caused by this extreme weather event on the transmission of respiratory viruses.\n\nMETHODSResidual specimens from patients evaluated for acute respiratory illness at hospitals in the Seattle metropolitan area were screened for a panel of respiratory viruses. Transmission models were fit to each virus, with disruption of contact rates and care-seeking informed by data on local traffic volumes and hospital admissions.\n\nRESULTSDisruption in contact patterns reduced effective contact rates during the intervention period by 16% to 95%, and cumulative disease incidence through the remainder of the season by 3% to 9%. Incidence reductions were greatest for viruses that were peaking when the disruption occurred and least for viruses in early epidemic phase.\n\nCONCLUSIONHigh-intensity, short-duration social distancing measures may substantially reduce total incidence in a respiratory virus epidemic if implemented near the epidemic peak.\n\nOne sentence summaryDisruptions of school and work due to heavy snowfall in the Seattle metro area reduced the total size of respiratory virus epidemics by up to 9%.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Michael L Jackson", - "author_inst": "Kaiser Permanente Washington Health Research Institute, Seattle WA" - }, - { - "author_name": "Gregory R Hart", - "author_inst": "Institute for Disease Modeling, Bellevue WA" - }, - { - "author_name": "Denise J McCulloch", - "author_inst": "Department of Medicine, University of Washington School of Medicine, Seattle WA" - }, - { - "author_name": "Amanda Adler", - "author_inst": "Seattle Children's Research Institute, Seattle WA" - }, - { - "author_name": "Elisabeth Brandstetter", - "author_inst": "Department of Medicine, University of Washington School of Medicine, Seattle WA" - }, - { - "author_name": "Kairsten Fay", - "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA" - }, - { - "author_name": "Peter Han", - "author_inst": "Brotman Baty Institute for Precision Medicine, Seattle WA" - }, - { - "author_name": "Kirsten Lacombe", - "author_inst": "Seattle Children's Research Institute, Seattle WA" - }, - { - "author_name": "Jover Lee", - "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA" - }, - { - "author_name": "Thomas Sibley", - "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA" - }, - { - "author_name": "Deborah A Nickerson", - "author_inst": "Department of Genome Sciences, University of Washington, Seattle WA" - }, - { - "author_name": "Mark Rieder", - "author_inst": "Brotman Baty Institute for Precision Medicine, Seattle WA" - }, - { - "author_name": "Lea Starita", - "author_inst": "Department of Genome Sciences, University of Washington, Seattle WA" - }, - { - "author_name": "Janet A Englund", - "author_inst": "Seattle Children's Research Institute, Seattle WA" - }, - { - "author_name": "Trevor Bedford", - "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA" - }, - { - "author_name": "Helen Chu", - "author_inst": "Department of Medicine, University of Washington School of Medicine, Seattle WA" - }, - { - "author_name": "Michael Famulare", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "the Seattle Flu Study Investigators", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.28.20029272", "rel_title": "Closed environments facilitate secondary transmission of coronavirus disease 2019 (COVID-19)", @@ -1614068,6 +1616268,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.03.01.20029397", + "rel_title": "Epidemiological and clinical features of 2019-nCoV acute respiratory disease cases in Chongqing municipality, China: a retrospective, descriptive, multiple-center study", + "rel_date": "2020-03-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.01.20029397", + "rel_abs": "BackgroundIn January 19, 2020, first case of 2019 novel coronavirus (2019-nCoV) pneumonia (COVID-19) was confirmed in Chongqing municipality, China.\n\nMethodsIn this retrospective, descriptive, multiple-center study, total of 267 patients with COVID-19 confirmed by real-time RT-PCR in Chongqing from Jan 19 to Feb 16, 2020 were recruited. Epidemiological, demographic, clinical, radiological characteristics, laboratory examinations, and treatment regimens were collected on admission. Clinical outcomes were followed up until Feb 16, 2020.\n\nResults267 laboratory-confirmed COVID-19 patients admitted to 3 designated-hospitals in Chongqing provincial municipality from January 19 to February 16, 2020 were enrolled and categorized on admission. 217 (81.27%) and 50 (18.73%) patients were categorized into non-severe and severe subgroups, respectively. The median age of patients was 48.0 years (IQR, 35.0-65.0), with 129 (48.3%) of the patients were more than 50 years of age. 149 (55.8%) patients were men. Severe patients were significantly older (median age, 71.5 years [IQR, 65.8-77.0] vs 43.0 years [IQR, 32.5-57.0]) and more likely to be male (110 [50.7%] vs 39 [78.0%]) and have coexisting disorders (15 [30.0%] vs 26 [12.0%]). 41 (15.4%) patients had a recent travel to Hubei province, and 139 (52.1%) patients had a history of contact with patients from Hubei. On admission, the most common symptoms of COVID-19 were fever 225(84.3%), fatigue (208 [77.9%]), dry cough (189 [70.8%]), myalgia or arthralgia (136 [50.9%]). Severe patients were more likely to present dyspnea (17 [34.0%] vs 26 [12.0%]) and confusion (10 [20.0%] vs 15 [6.9%]). Rales (32 [12.0%]) and wheezes (20 [7.5%]) are not common noted for COVID-19 patients, especially for the non-severe (11 [5.1%], 10 [4.6%]). 118 (44.2%). Most severe patients demonstrated more laboratory abnormalities. 231 (86.5%), 61 (22.8%) patients had lymphopenia, leukopenia and thrombocytopenia, respectively. CD4+T cell counts decrease was observed in 77.1 % of cases, especially in the severe patients (45, 100%). 53.1% patients had decreased CD+3 T cell counts, count of CD8+T cells was lower than the normal range in part of patients (34.4%). More severe patients had lower level of CD4+ T cells and CD+3 T cells (45 [100.0%] vs 29[56.9%], 31 [68.9%] vs 20 [39.2%]). Most patients had normal level of IL-2, IL-4, TNF- and INF-{gamma}, while high level of IL-6 and IL-17A was common in COVID-19 patients (47 [70.1%], 35 [52.2%]). Level of IL-6, IL-17A and TNF- was remarkably elevated in severe patients (32 [84.2%] vs 15 [51.7%], 25 [65.8%] vs 10 [34.5%], 17 [44.7%] vs 5 [17.2%]). All patients received antiviral therapy (267, 100%). A portion of severe patients (38, 76.0%) received systemic corticosteroid therapy. Invasive mechanical ventilation in prone position, non-invasive mechanical ventilation, high-flow nasal cannula oxygen therapy was adopted only in severe patients with respiratory failure (5[10.0%], 35[70.0%], 12[24.0%]). Traditional Chinese medicine was adopted to most of severe patients (43,86.0%).\n\nConclusionOur study firstly demonstrated the regional disparity of COVID-19 in Chongqing municipality and further thoroughly compared the differences between severe and non-severe patients. The 28-day mortality of COVID-19 patients from 3 designed hospitals of Chongqing is 1.5%, lower than that of Hubei province and mainland China including Hubei province. However, the 28-mortality of severe patients was relatively high, with much higher when complications occurred. Notably, the 28-mortality of critically severe patients complicated with severe ARDS is considerably as high as 44.4%. Therefore, early diagnosis and intensive care of critically severe COVID-19 cases, especially those combined with ARDS, will be considerably essential to reduce mortality.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Di Qi", + "author_inst": "The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China" + }, + { + "author_name": "Xiaofeng Yan", + "author_inst": "Chongqing Public Health Medical Center, Chongqing, China." + }, + { + "author_name": "Xumao Tang", + "author_inst": "The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China." + }, + { + "author_name": "Junnan Peng", + "author_inst": "The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China" + }, + { + "author_name": "Qian Yu", + "author_inst": "The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China." + }, + { + "author_name": "Longhua Feng", + "author_inst": "Qianjiang Central Hospital of Chongqing, Chongqing, China." + }, + { + "author_name": "Guodan Yuan", + "author_inst": "Chongqing Public Health Medical Center, Chongqing, China." + }, + { + "author_name": "An Zhang", + "author_inst": "the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China." + }, + { + "author_name": "Yaokai Chen", + "author_inst": "Chongqing Public Health Medical Center, Chongqing, China" + }, + { + "author_name": "Jing Yuan", + "author_inst": "Chongqing Public Health Medical Center, Chongqing, China" + }, + { + "author_name": "Xia Huang", + "author_inst": "Chongqing Three Gorges Central Hospital, Chongqing, China;Chonqing University Three Gorges Hospital, Chongqing, China." + }, + { + "author_name": "Xianxiang Zhang", + "author_inst": "Chonqing University Three Gorges Hospital, Chongqing, China; Chonqing Three Gorges Central Hospital, Chongqing, China." + }, + { + "author_name": "Peng Hu", + "author_inst": "the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China" + }, + { + "author_name": "Yuyan Song", + "author_inst": "Chongqing Public Health Medical Center, Chongqing, China." + }, + { + "author_name": "Chunfang Qian", + "author_inst": "Chongqing Public Health Medical Center, Chongqing, China." + }, + { + "author_name": "Qiangzhong Sun", + "author_inst": "Chongqing Public Health Medical Center, Chongqing, China." + }, + { + "author_name": "Daoxin Wang", + "author_inst": "The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China" + }, + { + "author_name": "Jin Tong", + "author_inst": "the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China." + }, + { + "author_name": "Jianglin Xiang", + "author_inst": "Chonqing University Three Gorges Hospital, Chongqing, China;Chonqing Three Gorges Central Hospital, Chongqing, China." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.02.26.20027797", "rel_title": "Relations of parameters for describing the epidemic of COVID-19 by the Kermack-McKendrick model", @@ -1615217,41 +1617508,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.27.20028829", - "rel_title": "Transmission potential of COVID-19 in South Korea", - "rel_date": "2020-02-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.27.20028829", - "rel_abs": "Since the first identified individual of 2019 novel coronavirus (COVID-19) infection on Jan 20, 2020 in South Korea, the number of confirmed cases rapidly increased. As of Feb 26, 2020, 1,261 cases of COVID-19 including 12 deaths were confirmed in South Korea. Using the incidence data of COVID-19, we estimate the reproduction number at 1.5 (95% CI: 1.4-1.6), which indicates sustained transmission and support the implementation of social distancing measures to rapidly control the outbreak.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Eunha Shim", - "author_inst": "Soongsil University" - }, - { - "author_name": "Amna Tariq", - "author_inst": "Georgia State University" - }, - { - "author_name": "Wongyeong Choi", - "author_inst": "Soongsil University" - }, - { - "author_name": "Yiseul Lee", - "author_inst": "Georgia State University" - }, - { - "author_name": "Gerardo Chowell", - "author_inst": "Georgia State University School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.27.20028928", "rel_title": "A simple ecological model captures the transmission pattern of the coronavirus COVID-19 outbreak in China", @@ -1615429,6 +1617685,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.02.27.20027557", + "rel_title": "Therapeutic effects of dipyridamole on COVID-19 patients with coagulation dysfunction", + "rel_date": "2020-02-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.27.20027557", + "rel_abs": "The human coronavirus HCoV-19 infection can cause acute respiratory distress syndrome (ARDS), hypercoagulability, hypertension, extrapulmonary multiorgan dysfunction. Effective antiviral and anti-coagulation agents with safe clinical profiles are urgently needed to improve the overall prognosis. We screened an FDA approved drug library and found that an anticoagulant agent dipyridamole (DIP) suppressed HCoV-19 replication at an EC50 of 100 nM in vitro. It also elicited potent type I interferon responses and ameliorated lung pathology in a viral pneumonia model. In analysis of twelve HCoV-19 infected patients with prophylactic anti-coagulation therapy, we found that DIP supplementation was associated with significantly increased platelet and lymphocyte counts and decreased D-dimer levels in comparison to control patients. Two weeks after initiation of DIP treatment, 3 of the 6 severe cases (60%) and all 4 of the mild cases (100%) were discharged from the hospital. One critically ill patient with extremely high levels of D-dimer and lymphopenia at the time of receiving DIP passed away. All other patients were in clinical remission. In summary, HCoV-19 infected patients could potentially benefit from DIP adjunctive therapy by reducing viral replication, suppressing hypercoagulability and enhancing immune recovery. Larger scale clinical trials of DIP are needed to validate these therapeutic effects.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Xiaoyan Liu", + "author_inst": "Department of Hematology, Zhongnan Hospital of Wuhan University" + }, + { + "author_name": "Zhe Li", + "author_inst": "School of Pharmaceutical Sciences, Sun Yat-sen University" + }, + { + "author_name": "Shuai Liu", + "author_inst": "Department of Hematology, Zhongnan Hospital of Wuhan University; Dawu County People's Hospital, Xiaogan City;" + }, + { + "author_name": "Zhanghua Chen", + "author_inst": "Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University; Bi" + }, + { + "author_name": "Zhiyao Zhao", + "author_inst": "Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University" + }, + { + "author_name": "Yi-you Huang", + "author_inst": "School of Pharmaceutical Sciences, Sun Yat-sen University" + }, + { + "author_name": "Qingling Zhang", + "author_inst": "Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzho" + }, + { + "author_name": "Jun Wang", + "author_inst": "Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University" + }, + { + "author_name": "Yinyi Shi", + "author_inst": "Dawu County People's Hospital, Xiaogan City" + }, + { + "author_name": "Yanhui Xu", + "author_inst": "Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University" + }, + { + "author_name": "Jing Sun", + "author_inst": "Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzho" + }, + { + "author_name": "Huifang Xian", + "author_inst": "Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University" + }, + { + "author_name": "Rongli Fang", + "author_inst": "Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University" + }, + { + "author_name": "Fan Bai", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University" + }, + { + "author_name": "Changxing Ou", + "author_inst": "Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzho" + }, + { + "author_name": "Bei Xiong", + "author_inst": "Department of Hematology, Zhongnan Hospital of Wuhan University" + }, + { + "author_name": "Andrew M Lew", + "author_inst": "Walter and Eliza Hall Institute of Medical Research and Department of Microbiology & Immunology, University of Melbourne" + }, + { + "author_name": "Jun Cui", + "author_inst": "School of Life Sciences, Sun Yat-sen University" + }, + { + "author_name": "Hui Huang", + "author_inst": "Cardiovascular Department, The Eighth Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Jincun Zhao", + "author_inst": "Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzho" + }, + { + "author_name": "Xuechuan Hong", + "author_inst": "State Key Laboratory of Virology, College of Science, Innovation Center for Traditional Tibetan Medicine Modernization and Quality Control, Medical College, Tib" + }, + { + "author_name": "Yuxia Zhang", + "author_inst": "Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University" + }, + { + "author_name": "Fulin Zhou", + "author_inst": "Department of Hematology, Zhongnan Hospital of Wuhan University" + }, + { + "author_name": "Hai-Bin Luo", + "author_inst": "School of Pharmaceutical Sciences, Sun Yat-sen University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.25.20027615", "rel_title": "Stochastic discrete epidemic modeling of COVID-19 transmission in the Province of Shaanxi incorporating public health intervention and case importation", @@ -1616931,37 +1619298,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.25.20027433", - "rel_title": "An R package and a website with real-time data on the COVID-19 coronavirus outbreak", - "rel_date": "2020-02-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.25.20027433", - "rel_abs": "The COVID-19 outbreak originated at the end of 2019 from Wuhan [1, 2], a city in Hubei province in central China. According to the World Health Organization (WHO), there were 88,948 confirmed cases and 3,043 deaths from 65 countries as of March 2, 2020. In China, the outbreak has effectively confined over 1 billion people to their apartments and homes since the end of January 2020 and continues to disrupt healthcare, wellbeing, and the economy. As the situation in China appears to be stabilizing, sharp increases in confirmed cases are being reported in South Korea, Italy, Japan, and Iran.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Tianzhi Wu", - "author_inst": "Southern Medical University" - }, - { - "author_name": "Xijin Ge", - "author_inst": "South Dakota State University" - }, - { - "author_name": "Guangchuang Yu", - "author_inst": "Southern Medical University" - }, - { - "author_name": "Erqiang Hu", - "author_inst": "Southern Medical University, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.22.951178", "rel_title": "Spike protein binding prediction with neutralizing antibodies of SARS-CoV-2", @@ -1617135,6 +1619471,25 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.02.24.963348", + "rel_title": "Increasing Host Cellular Receptor--Angiotensin-Converting Enzyme 2 (ACE2) Expression by Coronavirus may Facilitate 2019-nCoV Infection", + "rel_date": "2020-02-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.24.963348", + "rel_abs": "The ongoing outbreak of a new coronavirus (2019-nCoV) causes an epidemic of acute respiratory syndrome in humans. 2019-nCoV rapidly spread to national regions and multiple other countries, thus, pose a serious threat to public health. Recent studies show that spike (S) proteins of 2019-nCoV and SARS-CoV may use the same host cell receptor called angiotensin-converting enzyme 2 (ACE2) for entering into host cells. The affinity between ACE2 and 2019-nCoV S is much higher than ACE2 binding to SARS-CoV S protein, explaining that why 2019-nCoV seems to be more readily transmitted from the human to human. Here, we reported that ACE2 can be significantly upregulated after infection of various viruses including SARS-CoV and MERS-CoV. Basing on findings here, we propose that coronavirus infection can positively induce its cellular entry receptor to accelerate their replication and spread, thus drugs targeting ACE2 expression may be prepared for the future emerging infectious diseases caused by this cluster of viruses.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Pei-Hui Wang", + "author_inst": "The University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.02.26.964882", "rel_title": "Structure-based drug design, virtual screening and high-throughput screening rapidly identify antiviral leads targeting COVID-19", @@ -1618625,73 +1620980,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.21.20026559", - "rel_title": "Estimating the serial interval of the novel coronavirus disease (COVID-19): A statistical analysis using the public data in Hong Kong from January 16 to February 15, 2020", - "rel_date": "2020-02-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.21.20026559", - "rel_abs": "BackgroundsThe emerging virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a large outbreak of novel coronavirus disease (COVID-19) in Wuhan, China since December 2019. Based on the publicly available surveillance data, we identified 21 transmission chains in Hong Kong and estimated the serial interval (SI) of COVID-19.\n\nMethodsIndex cases were identified and reported after symptoms onset, and contact tracing was conducted to collect the data of the associated secondary cases. An interval censored likelihood framework is adopted to fit a Gamma distribution function to govern the SI of COVID-19.\n\nFindingsAssuming a Gamma distributed model, we estimated the mean of SI at 4.4 days (95%CI: 2.9-6.7) and SD of SI at 3.0 days (95%CI: 1.8-5.8) by using the information of all 21 transmission chains in Hong Kong.\n\nConclusionThe SI of COVID-19 may be shorter than the preliminary estimates in previous works. Given the likelihood that SI could be shorter than the incubation period, pre-symptomatic transmission may occur, and extra efforts on timely contact tracing and quarantine are recommended in combating the COVID-19 outbreak.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Shi Zhao", - "author_inst": "Chinese University of Hong Kong" - }, - { - "author_name": "Daozhou Gao", - "author_inst": "Shanghai Normal University" - }, - { - "author_name": "Zian Zhuang", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Marc Chong", - "author_inst": "Chinese University of Hong Kong" - }, - { - "author_name": "Yongli Cai", - "author_inst": "Huaiyin Normal University" - }, - { - "author_name": "Jinjun Ran", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Peihua Cao", - "author_inst": "Southern Medical University" - }, - { - "author_name": "Kai Wang", - "author_inst": "Xinjiang Medical University" - }, - { - "author_name": "Yijun Lou", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Weiming Wang", - "author_inst": "Huaiyin Normal University" - }, - { - "author_name": "Lin Yang", - "author_inst": "The Hong Kong Polytechnic University" - }, - { - "author_name": "Daihai He", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Maggie Wang", - "author_inst": "Chinese University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.23.20024802", "rel_title": "Intrinsic growth rules of patients infected, dead and cured with 2019 novel coronavirus in mainland China", @@ -1618793,6 +1621081,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.02.21.20026435", + "rel_title": "Real-time monitoring the transmission potential of COVID-19 in Singapore, February 2020", + "rel_date": "2020-02-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.21.20026435", + "rel_abs": "BackgroundThe ongoing COVID-19 epidemic that spread widely in China since December 2019 is now generating local transmission in multiple countries including Singapore as of February 27, 2020. This highlights the need to monitor in real time the transmission potential of COVID-19. In Singapore, four major COVID-19 case clusters have emerged thus far.\n\nMethodsHere we estimate the effective reproduction number, Rt, of COVID-19 in Singapore from the publicly available daily case series of imported and autochthonous cases by date of symptoms onset, after adjusting the local cases for reporting delays. We also derive the reproduction number from the distribution of cluster sizes using a branching process analysis.\n\nResultsThe effective reproduction number peaked with a mean value [~]1.1 around February 2nd, 2020 and declined thereafter. As of February 27th, 2020, our most recent estimate of Rt is at 0.5 (95% CI: 0.2,0.7) while an estimate of the overall R based on cluster size distribution is at 0.7 (95% CI: 0.5, 0.9).\n\nConclusionThe trajectory of the reproduction number in Singapore underscore the significant effects of containment efforts in Singapore while at the same time suggest the need to sustain social distancing and active case finding efforts to stomp out all active chains of transmission.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Amna Tariq", + "author_inst": "Georgia State University School of Public Health" + }, + { + "author_name": "Yiseul Lee", + "author_inst": "Georgia State University School of Public Health" + }, + { + "author_name": "Kimberlyn Roosa", + "author_inst": "Georgia State University School of Public Health" + }, + { + "author_name": "Seth Blumberg", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Ping Yan", + "author_inst": "Infectious Disease Prevention and Control Branch, Public Health Agency of Canada, Ottawa, Canada" + }, + { + "author_name": "Stefan Ma", + "author_inst": "Epidemiology and Disease Control Division, Public Health Group, Ministry of Health Singapore" + }, + { + "author_name": "Gerardo Chowell", + "author_inst": "Georgia State University School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.24.20027268", "rel_title": "Estimation of risk factors for COVID-19 mortality - preliminary results", @@ -1620331,73 +1622662,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.20.20025841", - "rel_title": "Breadth of concomitant immune responses underpinning viral clearance and patient recovery in a non-severe case of COVID-19", - "rel_date": "2020-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.20.20025841", - "rel_abs": "We report the kinetics of the immune response in relation to clinical and virological features of a patient with mild-to-moderate coronavirus disease-19 (COVID-19) requiring hospitalisation. Increased antibody-secreting cells, follicular T-helper cells, activated CD4+ and CD8+ T-cells and IgM/IgG SARS-CoV-2-binding antibodies were detected in blood, prior to symptomatic recovery. These immunological changes persisted for at least 7 days following full resolution of symptoms, indicating substantial anti-viral immunity in this non-severe COVID-19.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Irani Thevarajan", - "author_inst": "VIDS/Doherty Institute" - }, - { - "author_name": "Thi HO Nguyen", - "author_inst": "University of Melbourne/Doherty Institute" - }, - { - "author_name": "Marios Koutsakos", - "author_inst": "University of Melbourne/Doherty Institute" - }, - { - "author_name": "Julian Druce", - "author_inst": "VIDRL/Doherty Institute" - }, - { - "author_name": "Leon Caly", - "author_inst": "VIDRL/Doherty Institute" - }, - { - "author_name": "Carolien E van de Sandt", - "author_inst": "University of Melbourne/Doherty Institute" - }, - { - "author_name": "Xiaoxiao Jia", - "author_inst": "University of Melbourne/Doherty Institute" - }, - { - "author_name": "Suellen Nicholson", - "author_inst": "VIDRL/Doherty Institute" - }, - { - "author_name": "Mike Catton", - "author_inst": "VIDRL/Doherty Institute" - }, - { - "author_name": "Benjamin Cowie", - "author_inst": "VIDS/Doherty Institute" - }, - { - "author_name": "Steven Tong", - "author_inst": "VIDS/Doherty Institute" - }, - { - "author_name": "Sharon Lewin", - "author_inst": "Doherty Institute" - }, - { - "author_name": "Katherine Kedzierska", - "author_inst": "University of Melbourne/Doherty Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.20.20025619", "rel_title": "Clinical Characteristics of 24 Asymptomatic Infections with COVID-19 Screened among Close Contacts in Nanjing, China", @@ -1620579,6 +1622843,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.02.20.20023572", + "rel_title": "Novel Coronavirus 2019 (Covid-19) epidemic scale estimation: topological network-based infection dynamic model", + "rel_date": "2020-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.20.20023572", + "rel_abs": "BackgroundsAn ongoing outbreak of novel coronavirus pneumonia (Covid-19) hit Wuhan and hundreds of cities, 29 territories in global. We present a method for scale estimation in dynamic while most of the researchers used static parameters.\n\nMethodsWe use historical data and SEIR model for important parameters assumption. And according to the time line, we use dynamic parameters for infection topology network building. Also, the migration data is used for Non-Wuhan area estimation which can be cross validated for Wuhan model. All data are from public.\n\nResultsThe estimated number of infections is 61,596 (95%CI: 58,344.02-64,847.98) by 25 Jan in Wuhan. And the estimation number of the imported cases from Wuhan of Guangzhou was 170 (95%CI: 161.27-179.26), infections scale in Guangzhou is 315 (95%CI: 109.20-520.79), while the imported cases is 168 and the infections scale is 339 published by authority.\n\nConclusionsUsing dynamic network model and dynamic parameters for different time periods is an effective way for infections scale modeling.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Keke Tang", + "author_inst": "Shenyang institute of computing technology, Chinese academy of sciences" + }, + { + "author_name": "Yining Huang", + "author_inst": "Sinohealth research institution" + }, + { + "author_name": "Meilian Chen", + "author_inst": "Sinohealth research institution" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.18.20024539", "rel_title": "Clinical characteristics of 50404 patients with 2019-nCoV infection", @@ -1621948,45 +1624239,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.02.19.956581", - "rel_title": "Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein", - "rel_date": "2020-02-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.19.956581", - "rel_abs": "The recent emergence of a novel coronavirus associated with an ongoing outbreak of pneumonia (Covid-2019) resulted in infections of more than 72,000 people and claimed over 1,800 lives. Coronavirus spike (S) glycoprotein trimers promote entry into cells and are the main target of the humoral immune response. We show here that SARS-CoV-2 S mediates entry in VeroE6 cells and in BHK cells transiently transfected with human ACE2, establishing ACE2 as a functional receptor for this novel coronavirus. We further demonstrate that the receptor-binding domains of SARS-CoV-2 S and SARS-CoV S bind with similar affinities to human ACE2, which correlates with the efficient spread of SARS-CoV-2 among humans. We found that the SARS-CoV-2 S glycoprotein harbors a furin cleavage site at the boundary between the S1/S2 subunits, which is processed during biogenesis and sets this virus apart from SARS-CoV and other SARS-related CoVs. We determined a cryo-electron microscopy structure of the SARS-CoV-2 S ectodomain trimer, demonstrating spontaneous opening of the receptor-binding domain, and providing a blueprint for the design of vaccines and inhibitors of viral entry. Finally, we demonstrate that SARS-CoV S murine polyclonal sera potently inhibited SARS-CoV-2 S-mediated entry into target cells, thereby indicating that cross-neutralizing antibodies targeting conserved S epitopes can be elicited upon vaccination.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Alexandra C Walls", - "author_inst": "University of Washington" - }, - { - "author_name": "Young-Jun Park", - "author_inst": "University of Washington" - }, - { - "author_name": "M. Alexandra Tortorici", - "author_inst": "University of Washington" - }, - { - "author_name": "Abigail Wall", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Andrew T McGuire", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "David Veesler", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.02.19.957118", "rel_title": "Mucin 4 Protects Female Mice from Coronavirus Pathogenesis", @@ -1622124,6 +1624376,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.02.17.952879", + "rel_title": "X-ray Structure of Main Protease of the Novel Coronavirus SARS-CoV-2 Enables Design of \u03b1-Ketoamide Inhibitors", + "rel_date": "2020-02-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.17.952879", + "rel_abs": "A novel coronavirus has been identified as the causative agent of a massive outbreak of atypical pneumonia originating at Wuhan, Hubei province, China. Involved in the formation of the coronavirus replication complex, the viral main protease (Mpro, also called 3CLpro) represents an attractive target for therapy. We determined the crystal structure of the unliganded Mpro at 1.75 [A] resolution and used this structure to guide optimization of a series of alpha-ketoamide inhibitors. The main goal of the optimization efforts was improvement of the pharmacokinetic properties of the compounds. We further describe 1.95- and 2.20-[A] crystal structures of the complex between the enzyme and the most potent alpha-ketoamide optimized this way. These structures will form the basis for further development of these compounds to antiviral drugs.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Linlin Zhang", + "author_inst": "Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany." + }, + { + "author_name": "Daizong Lin", + "author_inst": "Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany." + }, + { + "author_name": "Xinyuanyuan Sun", + "author_inst": "Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany." + }, + { + "author_name": "Katharina Rox", + "author_inst": "Department of Chemical Biology, Helmholtz Center for Infection Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany." + }, + { + "author_name": "Rolf Hilgenfeld", + "author_inst": "Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.02.19.956946", "rel_title": "Structural basis for the recognition of the 2019-nCoV by human ACE2", @@ -1623386,77 +1625673,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.02.13.945485", - "rel_title": "Identification of 2019-nCoV related coronaviruses in Malayan pangolins in southern China", - "rel_date": "2020-02-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.13.945485", - "rel_abs": "The ongoing outbreak of viral pneumonia in China and beyond is associated with a novel coronavirus, provisionally termed 2019-nCoV. This outbreak has been tentatively associated with a seafood market in Wuhan, China, where the sale of wild animals may be the source of zoonotic infection. Although bats are likely reservoir hosts for 2019-nCoV, the identity of any intermediate host facilitating transfer to humans is unknown. Here, we report the identification of 2019-nCoV related coronaviruses in pangolins (Manis javanica) seized in anti-smuggling operations in southern China. Metagenomic sequencing identified pangolin associated CoVs that belong to two sub-lineages of 2019-nCoV related coronaviruses, including one very closely related to 2019-nCoV in the receptor-binding domain. The discovery of multiple lineages of pangolin coronavirus and their similarity to 2019-nCoV suggests that pangolins should be considered as possible intermediate hosts for this novel human virus and should be removed from wet markets to prevent zoonotic transmission.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Tommy Tsan-Yuk Lam", - "author_inst": "The University of Hong Kong, Shantou University" - }, - { - "author_name": "Marcus Ho-Hin Shum", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Hua-Chen Zhu", - "author_inst": "The University of Hong Kong, Shantou University" - }, - { - "author_name": "Yi-Gang Tong", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Xue-Bing Ni", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Yun-Shi Liao", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Wei Wei", - "author_inst": "Guangxi Medical University" - }, - { - "author_name": "William Yiu-Man Cheung", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Wen-Juan Li", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Lian-Feng Li", - "author_inst": "Guangxi Medical University" - }, - { - "author_name": "Gabriel M Leung", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Edward C Holmes", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Yan-Ling Hu", - "author_inst": "Guangxi Medical University" - }, - { - "author_name": "Yi Guan", - "author_inst": "The University of Hong Kong, Shantou University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.02.10.942748", "rel_title": "Recombination and convergent evolution led to the emergence of 2019 Wuhan coronavirus", @@ -1623578,6 +1625794,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.12.20022400", + "rel_title": "Can Search Query Forecast successfully in China's 2019-nCov pneumonia?", + "rel_date": "2020-02-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.12.20022400", + "rel_abs": "Recently the novel coronavirus (2019-nCov) pneumonia outbreak in China then the world, and the Number of infections and death continues to increases. Search Query performs well in forecasting the epidemics. It is still a question whether search engine data can forecast the drift and the inflexion in 2019-nCov pneumonia. Based on the Baidu Search Index, we propose three prediction models: composite Index, composite Index with filtering and suspected NCP(Novel Coronavirus Pneumonia). The result demonstrates that the predictive model of composite index with filtering performs the best while the model of suspected NCP has the highest forecast error. We further predict the out-of-the-set NCP confirmed cases and monitor that the next peak of new diagnoses will occur on February 16th and 17th.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Li Xiaoxuan", + "author_inst": "Fuyang Normal University, China" + }, + { + "author_name": "Wu Qi", + "author_inst": "Fuyang Normal University" + }, + { + "author_name": "Lv Benfu", + "author_inst": "University of the Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.13.20022822", "rel_title": "Estimating the distribution of the incubation period of 2019 novel coronavirus (COVID-19) infection between travelers to Hubei, China and non-travelers", @@ -1624740,37 +1626983,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.02.13.20022707", - "rel_title": "Estimating underdetection of internationally imported COVID-19 cases", - "rel_date": "2020-02-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.13.20022707", - "rel_abs": "Risk of COVID-19 infection in Wuhan has been estimated using imported case counts of international travelers, often under the assumption that all cases in travelers are ascertained. Recent work indicates variation among countries in detection capacity for imported cases. Singapore has historically had very strong epidemiological surveillance and contact-tracing capacity and has shown in the COVID-19 epidemic evidence of a high sensitivity of case detection. We therefore used a Bayesian modeling approach to estimate the relative imported case detection capacity for other countries compared to that of Singapore.We estimate that the global ability to detect imported cases is 38% (95% HPDI 22% - 64%) of Singapores capacity. Equivalently, an estimate of 2.8 (95% HPDI 1.5 - 4.4) times the current number of imported cases, could have been detected, if all countries had had the same detection capacity as Singapore. Using the second component of the Global Health Security index to stratify likely case-detection capacities, we found that the ability to detect imported cases relative to Singapore among high surveillance locations is 40% (95% HPDI 22% - 67%), among intermediate surveillance locations it is 37% (95% HPDI 18% - 68%), and among low surveillance locations it is 11% (95% HPDI 0% - 42%). Using a simple mathematical model, we further find that treating all travelers as if they were residents (rather than accounting for the brief stay of some of these travelers in Wuhan) can modestly contribute to underestimation of prevalence as well. We conclude that estimates of case counts in Wuhan based on assumptions of perfect detection in travelers may be underestimated by several fold, and severity correspondingly overestimated by several fold. Undetected cases are likely in countries around the world, with greater risk in countries of low detection capacity and high connectivity to the epicenter of the outbreak.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Rene Niehus", - "author_inst": "Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America" - }, - { - "author_name": "Pablo M De Salazar", - "author_inst": "Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America" - }, - { - "author_name": "Aimee Taylor", - "author_inst": "Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America" - }, - { - "author_name": "Marc Lipsitch", - "author_inst": "Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.13.20022251", "rel_title": "Understanding the present status and forecasting of COVID-19 in Wuhan", @@ -1624868,6 +1627080,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.02.05.936013", + "rel_title": "Potentially highly potent drugs for 2019-nCoV", + "rel_date": "2020-02-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.05.936013", + "rel_abs": "The World Health Organization (WHO) has declared the 2019 novel coronavirus (2019-nCoV) infection outbreak a global health emergency. Currently, there is no effective anti-2019-nCoV medication. The sequence identity of the 3CL proteases of 2019-nCoV and SARS is 96%, which provides a sound foundation for structural-based drug repositioning (SBDR). Based on a SARS 3CL protease X-ray crystal structure, we construct a 3D homology structure of 2019-nCoV 3CL protease. Based on this structure and existing experimental datasets for SARS 3CL protease inhibitors, we develop an SBDR model based on machine learning and mathematics to screen 1465 drugs in the DrugBank that have been approved by the U.S. Food and Drug Administration (FDA). We found that many FDA approved drugs are potentially highly potent to 2019-nCoV.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Duc Nguyen", + "author_inst": "Michigan State" + }, + { + "author_name": "Kaifu Gao", + "author_inst": "Michigan State" + }, + { + "author_name": "Jiahui Chen", + "author_inst": "Michigan State University" + }, + { + "author_name": "Rui Wang", + "author_inst": "Michigan State University" + }, + { + "author_name": "Guewei Wei", + "author_inst": "Michigan State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.02.07.939207", "rel_title": "Evidence of recombination in coronaviruses implicating pangolin origins of nCoV-2019", @@ -1626070,121 +1628317,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.08.20021212", - "rel_title": "Caution on Kidney Dysfunctions of 2019-nCoV Patients", - "rel_date": "2020-02-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.08.20021212", - "rel_abs": "BackgroundTo date, large amounts of epidemiological and case study data have been available for the Coronavirus Disease 2019 (COVID-19), which suggested that the mortality was related to not just respiratory complications. Here, we specifically analyzed kidney functions in COVID-19 patients and their relations to mortality.\n\nMethodIn this multi-centered, retrospective, observational study, we included 193 adult patients with laboratory-confirmed COVID-19 from 2 hospitals in Wuhan, 1 hospital in Huangshi (Hubei province, 83 km from Wuhan) and 1 hospital in Chongqing (754 km from Wuhan). Demographic data, symptoms, laboratory values, comorbidities, treatments, and clinical outcomes were all collected, including data regarding to kidney functions. Data were compared among three groups: non-severe COVID-19 patients (128), severe COVID-19 patients (65) and a control group of other pneumonia (28). For the data from computed tomographic (CT) scans, we also included a control group of healthy subjects (110 cases, without abnormalities in the lung and without kidney diseases). The primary outcome was a common presence of kidney dysfunctions in COVID-19 patients and the occurrence of acute kidney injury (AKI) in a fraction of COVID-19 patients. Secondary outcomes included a survival analysis of COVID-19 patients in conditions of AKI or comorbid chronic illnesses.\n\nFindingsWe included 193 COVID-19 patients (128 non-severe, 65 severe (including 32 non-survivors), between January 6th and February 21th,2020; the final date of follow-up was March 4th, 2020) and 28 patients of other pneumonia (15 of viral pneumonia, 13 of mycoplasma pneumonia) before the COVID-19 outbreak. On hospitaladmission, a remarkable fraction of patients had signs of kidney dysfunctions, including 59% with proteinuria, 44% with hematuria, 14% with increased levels of blood urea nitrogen, and 10% with increased levels of serum creatinine, although mild but worse than that in cases with other pneumonia. While these kidney dysfunctions might not be readily diagnosed as AKI at admission, over the progress during hospitalization they could be gradually worsened and diagnosed as AKI. A univariate Cox regression analysis showed that proteinuria, hematuria, and elevated levels of blood urea nitrogen, serum creatinine, uric acid as well as D-dimer were significantly associated with the death of COVID-19 patients respectively. Importantly, the Cox regression analysis also suggested that COVID-19 patients that developed AKI had a [~]5.3-times mortality risk of those without AKI, much higher than that of comorbid chronic illnesses ([~]1.5 times risk of those without comorbid chronic illnesses).\n\nInterpretationTo prevent fatality in such conditions, we suggested a high degree of caution in monitoring the kidney functions of severe COVID-19 patients regardless of the past disease history. In addition, upon day-by-day monitoring, clinicians should consider any potential interventions to protect kidney functions at the early stage of the disease and renal replacement therapies in severely ill patients, particularly for those with strong inflammatory reactions or a cytokine storm.\n\nFundingNone.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "- Anti-2019-nCoV Volunteers", - "author_inst": "-" - }, - { - "author_name": "Zhen Li", - "author_inst": "Department of Radiology, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China" - }, - { - "author_name": "Ming Wu", - "author_inst": "Department of Critical Care Medicine, the General Hospital of Central Theater Command and Department of Critical Care Medicine, Wuhan Pulmonary Hospital, Wuhan " - }, - { - "author_name": "Jiwei Yao", - "author_inst": "Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing 400038, China." - }, - { - "author_name": "Jie Guo", - "author_inst": "Department of Gastrointestinal Endoscopy, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Edong Healthcare Group, Huangshi 43500" - }, - { - "author_name": "Xiang Liao", - "author_inst": "Center for Neurointelligence, Chongqing University, Chongqing 400030, China." - }, - { - "author_name": "Siji Song", - "author_inst": "Department of Urology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China." - }, - { - "author_name": "Jiali Li", - "author_inst": "Department of Radiology, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China." - }, - { - "author_name": "Guangjie Duan", - "author_inst": "Department of Pathology, Southwest Hospital, Third Military Medical University, Chongqing 400038,China." - }, - { - "author_name": "Yuanxiu Zhou", - "author_inst": "Department of Urology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China." - }, - { - "author_name": "Xiaojun Wu", - "author_inst": "Department of Urology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China." - }, - { - "author_name": "Zhansong Zhou", - "author_inst": "Department of Urology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China." - }, - { - "author_name": "Taojiao Wang", - "author_inst": "Department of Otolaryngology, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Edong Healthcare Group, Huangshi 435000, China." - }, - { - "author_name": "Ming Hu", - "author_inst": "Department of Critical Care Medicine, Wuhan Pulmonary Hospital, Wuhan 430030, China." - }, - { - "author_name": "Xianxiang Chen", - "author_inst": "Department of Critical Care Medicine, Wuhan Pulmonary Hospital, Wuhan 430030, China." - }, - { - "author_name": "Yu Fu", - "author_inst": "Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597 and Singapore Bioimaging Consortium, Agency for Sc" - }, - { - "author_name": "Chong Lei", - "author_inst": "Department of Anesthesiology and Perioprative Medicine, Xijing Hospital, Fourth Military Medical University, Xi an 710032, China." - }, - { - "author_name": "Hailong Dong", - "author_inst": "Department of Anesthesiology and Perioprative Medicine, Xijing Hospital, Fourth Military Medical University, Xi an 710032, China." - }, - { - "author_name": "Chuou Xu", - "author_inst": "Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan 430030, China" - }, - { - "author_name": "Yahua Hu", - "author_inst": "Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Edong Healthcare Group, Huangshi, 435000, China." - }, - { - "author_name": "Min Han", - "author_inst": "Division of Nephrology, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China." - }, - { - "author_name": "Yi Zhou", - "author_inst": "Department of Neurobiology, Chongqing Key Laboratory of Neurobiology, Third Military Medical University, Chongqing 400038, China." - }, - { - "author_name": "Hongbo Jia", - "author_inst": "Department of Neurobiology, Chongqing Key Laboratory of Neurobiology, Third Military Medical University, Chongqing 400038, China." - }, - { - "author_name": "Xiaowei Chen", - "author_inst": "Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing 400038, China." - }, - { - "author_name": "Junan Yan", - "author_inst": "Department of Urology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.05.20020107", "rel_title": "Tobacco-use disparity in gene expression of ACE2, the receptor of 2019-nCov", @@ -1626270,6 +1628402,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.02.07.20021139", + "rel_title": "Networks of information token recurrences derived from genomic sequences may reveal hidden patterns in epidemic outbreaks: A case study of the 2019-nCoV coronavirus.", + "rel_date": "2020-02-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.07.20021139", + "rel_abs": "Profiling the genetic evolution and dynamic spreading of viruses is a crucial task when responding to epidemic outbreaks. We aim to devise novel ways to model, visualise and analyse the temporal dynamics of epidemic outbreaks in order to help researchers and other people involved in crisis response to make well-informed and targeted decisions about from which geographical locations and time periods more genetic samples may be required to fully understand the outbreak. Our approach relies on the application of Transcendental Information Cascades to a set of temporally ordered nucleotide sequences, and we apply it to real-world data that was collected during the currently ongoing outbreak of the novel 2019-nCoV coronavirus. We assess information-theoretic and network-theoretic measures that characterise the resulting complex network and identify touching points and temporal pathways that are candidates for deeper investigation by geneticists and epidemiologists.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Markus Luczak-Roesch", + "author_inst": "Victoria University of Wellington" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.03.20020248", "rel_title": "Estimation of the asymptomatic ratio of novel coronavirus (2019-nCoV) infections among passengers on evacuation flights", @@ -1627844,41 +1629995,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.04.20020495", - "rel_title": "Using predicted imports of 2019-nCoV cases to determine locations that may not be identifying all imported cases", - "rel_date": "2020-02-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.04.20020495", - "rel_abs": "Cases from the ongoing outbreak of atypical pneumonia caused by the 2019 novel coronavirus (2019-nCoV) exported from mainland China can lead to self-sustained outbreaks in other populations. Internationally imported cases are currently being reported in several different locations. Early detection of imported cases is critical for containment of the virus. Based on air travel volume estimates from Wuhan to international destinations and using a generalized linear regression model we identify locations which may potentially have undetected internationally imported cases.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Pablo M De Salazar", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Rene Niehus", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Aimee Taylor", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Caroline O Buckee", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Marc Lipsitch", - "author_inst": "Harvard T.H. Chan School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.04.20020503", "rel_title": "Risk assessment of novel coronavirus 2019-nCoVoutbreaks outside China", @@ -1627988,6 +1630104,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.03.20020206", + "rel_title": "Integrative Bioinformatics Analysis Provides Insight into the Molecular Mechanisms of 2019-nCoV", + "rel_date": "2020-02-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.03.20020206", + "rel_abs": "The 2019-nCoV is reported to share the same entry (ACE2) as SARS-CoV according to the updated findings. Analyzing the distribution and expression level of the route of coronavirus may help reveal underlying mechanisms of viral susceptibility and post-infection modulation. In this study, we found that the expression of ACE2 in healthy populations and patients with underlying diseases was not significantly different, suggesting relatively similar susceptibility. Besides, based on the expression of ACE2 in smoking individuals, we inferred that long-term smoking might be a risk factor for 2019-nCoV. Analyzing the ACE2 in SARS-CoV infected cells suggested that ACE2 was more than just a receptor but also participated in post-infection regulation, including immune response, cytokine secretion, and viral genome replication. Moreover, we also constructed Protein-protein interaction (PPI) networks and identified hub genes in viral activity and cytokine secretion. Our findings may explain the clinical symptoms so far and help clinicians and researchers understand the pathogenesis and design therapeutic strategies for 2019-nCoV.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Xiang He", + "author_inst": "Chengdu Institute of Respiratory Health" + }, + { + "author_name": "Lei Zhang", + "author_inst": "Chengdu Institute of Respiratory Health" + }, + { + "author_name": "Qin Ran", + "author_inst": "Chengdu Institute of Respiratory Health" + }, + { + "author_name": "Anying Xiong", + "author_inst": "Chengdu Institute of Respiratory Health" + }, + { + "author_name": "Junyi Wang", + "author_inst": "Chengdu Institute of Respiratory Health" + }, + { + "author_name": "Dehong Wu", + "author_inst": "Chengdu Institute of Respiratory Health" + }, + { + "author_name": "Feng Chen", + "author_inst": "Chengdu Institute of Respiratory Health" + }, + { + "author_name": "Guoping Li", + "author_inst": "Chengdu Institute of Respiratory Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.04.20020479", "rel_title": "Assessing spread risk of Wuhan novel coronavirus within and beyond China, January-April 2020: a travel network-based modelling study", @@ -1629134,49 +1631297,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.02.01.929976", - "rel_title": "Potent neutralization of 2019 novel coronavirus by recombinant ACE2-Ig", - "rel_date": "2020-02-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.01.929976", - "rel_abs": "2019-nCoV, which is a novel coronavirus emerged in Wuhan, China, at the end of 2019, has caused at least infected 11,844 as of Feb 1, 2020. However, there is no specific antiviral treatment or vaccine currently. Very recently report had suggested that novel CoV would use the same cell entry receptor, ACE2, as the SARS-CoV. In this report, we generated a novel recombinant protein by connecting the extracellular domain of human ACE2 to the Fc region of the human immunoglobulin IgG1. An ACE2 mutant with low catalytic activity was also used in the study. The fusion proteins were then characterized. Both fusion proteins has high affinity binding to the receptor-binding domain (RBD) of SARS-CoV and 2019-nCoV and exerted desired pharmacological properties. Moreover, fusion proteins potently neutralized SARS-CoV and 2019-nCoV in vitro. As these fusion proteins exhibit cross-reactivity against coronaviruses, they could have potential applications for diagnosis, prophylaxis, and treatment of 2019-nCoV.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Changhai Lei", - "author_inst": "Second Military Medical University" - }, - { - "author_name": "Wenyan Fu", - "author_inst": "Shanghai Jiao Tong University School of Medicine" - }, - { - "author_name": "Kewen Qian", - "author_inst": "Second Military Medical University" - }, - { - "author_name": "Tian Li", - "author_inst": "Second Military Medical University" - }, - { - "author_name": "Sheng Zhang", - "author_inst": "Shanghai Jiao Tong University School of Medicine" - }, - { - "author_name": "Min Ding", - "author_inst": "Pharchoice Therapeutics Inc" - }, - { - "author_name": "Shi Hu", - "author_inst": "Second Militarily Medical University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2020.01.31.929497", "rel_title": "Highly Distinguished Amino Acid Sequences of 2019-nCoV (Wuhan Coronavirus)", @@ -1629314,6 +1631434,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.01.31.929042", + "rel_title": "The novel coronavirus 2019 (2019-nCoV) uses the SARS-coronavirus receptor ACE2 and the cellular protease TMPRSS2 for entry into target cells", + "rel_date": "2020-01-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.31.929042", + "rel_abs": "The emergence of a novel, highly pathogenic coronavirus, 2019-nCoV, in China, and its rapid national and international spread pose a global health emergency. Coronaviruses use their spike proteins to select and enter target cells and insights into nCoV-2019 spike (S)-driven entry might facilitate assessment of pandemic potential and reveal therapeutic targets. Here, we demonstrate that 2019-nCoV-S uses the SARS-coronavirus receptor, ACE2, for entry and the cellular protease TMPRSS2 for 2019-nCoV-S priming. A TMPRSS2 inhibitor blocked entry and might constitute a treatment option. Finally, we show that the serum form a convalescent SARS patient neutralized 2019-nCoV-S-driven entry. Our results reveal important commonalities between 2019-nCoV and SARS-coronavirus infection, which might translate into similar transmissibility and disease pathogenesis. Moreover, they identify a target for antiviral intervention.\n\nOne sentence summaryThe novel 2019 coronavirus and the SARS-coronavirus share central biological properties which can guide risk assessment and intervention.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Markus Hoffmann", + "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" + }, + { + "author_name": "Hannah Kleine-Weber", + "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" + }, + { + "author_name": "Nadine Krueger", + "author_inst": "University of Veterinary Medicine Hannover, Hannover, Germany" + }, + { + "author_name": "Marcel A Mueller", + "author_inst": "Charite Universitaetsmedizin" + }, + { + "author_name": "Christian Drosten", + "author_inst": "Charite Universitaetsmedizin" + }, + { + "author_name": "Stefan Poehlmann", + "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.01.30.927574", "rel_title": "Nucleotide Analogues as Inhibitors of Viral Polymerases", @@ -1630371,65 +1632530,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.01.23.916395", - "rel_title": "Preliminary estimation of the basic reproduction number of novel coronavirus (2019-nCoV) in China, from 2019 to 2020: A data-driven analysis in the early phase of the outbreak", - "rel_date": "2020-01-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.23.916395", - "rel_abs": "BackgroundsAn ongoing outbreak of a novel coronavirus (2019-nCoV) pneumonia hit a major city of China, Wuhan, December 2019 and subsequently reached other provinces/regions of China and countries. We present estimates of the basic reproduction number, R0, of 2019-nCoV in the early phase of the outbreak.\n\nMethodsAccounting for the impact of the variations in disease reporting rate, we modelled the epidemic curve of 2019-nCoV cases time series, in mainland China from January 10 to January 24, 2020, through the exponential growth. With the estimated intrinsic growth rate ({gamma}), we estimated R0 by using the serial intervals (SI) of two other well-known coronavirus diseases, MERS and SARS, as approximations for the true unknown SI.\n\nFindingsThe early outbreak data largely follows the exponential growth. We estimated that the mean R0 ranges from 2.24 (95%CI: 1.96-2.55) to 3.58 (95%CI: 2.89-4.39) associated with 8-fold to 2-fold increase in the reporting rate. We demonstrated that changes in reporting rate substantially affect estimates of R0.\n\nConclusionThe mean estimate of R0 for the 2019-nCoV ranges from 2.24 to 3.58, and significantly larger than 1. Our findings indicate the potential of 2019-nCoV to cause outbreaks.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Shi Zhao", - "author_inst": "Chinese University of Hong Kong" - }, - { - "author_name": "Qianying Lin", - "author_inst": "Michigan Institute for Data Science, University of Michigan, Ann Arbor, Michigan, USA" - }, - { - "author_name": "Jinjun Ran", - "author_inst": "School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong" - }, - { - "author_name": "Salihu Sabiu MUSA", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Guangpu Yang", - "author_inst": "Chinese University of Hong Kong" - }, - { - "author_name": "Weiming Wang", - "author_inst": "Huaiyin Normal University" - }, - { - "author_name": "Yijun Lou", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Daozhou Gao", - "author_inst": "Shanghai Normal University, Shanghai, China" - }, - { - "author_name": "Lin Yang", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Daihai He", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Maggie H Wang", - "author_inst": "Chinese University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "ecology" - }, { "rel_doi": "10.1101/2020.01.23.917351", "rel_title": "Pattern of early human-to-human transmission of Wuhan 2019-nCoV", @@ -1630635,6 +1632735,37 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.01.21.914929", + "rel_title": "Novel ionophores active against La Crosse virus identified through rapid antiviral screening", + "rel_date": "2020-01-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.21.914929", + "rel_abs": "Bunyaviruses are significant human pathogens, causing diseases ranging from hemorrhagic fevers to encephalitis. Among these viruses, La Crosse virus (LACV), a member of the California serogroup, circulates in the eastern and midwestern United States. While LACV infection is often asymptomatic, dozens of cases of encephalitis are reported yearly. Unfortunately, no antivirals have been approved to treat LACV infection. Here, we developed a method to rapidly test potential antivirals against LACV infection. From this screen, we identified several potential antiviral molecules, including known antivirals. Additionally, we identified many novel antivirals that exhibited antiviral activity without affecting cellular viability. Valinomycin, a potassium ionophore, was among our top targets. We found that valinomycin exhibited potent anti-LACV activity in multiple cell types in a dose-dependent manner. Valinomycin did not affect particle stability or infectivity, suggesting that it may preclude virus replication by altering cellular potassium ions, a known determinant of LACV entry. We extended these results to other ionophores and found that the antiviral activity of valinomycin extended to other viral families including bunyaviruses (Rift Valley fever virus, Keystone virus), enteroviruses (Coxsackievirus, rhinovirus), flavirivuses (Zika), and coronaviruses (229E and MERS-CoV). In all viral infections, we observed significant reductions in virus titer in valinomycin-treated cells. In sum, we demonstrate the importance of potassium ions to virus infection, suggesting a potential therapeutic target to disrupt virus replication.\n\nImportanceNo antivirals are approved for the treatment of bunyavirus infection. The ability to rapidly screen compounds and identify novel antivirals is one means to accelerate drug discovery for viruses with no approved treatments. We used this approach to screen hundreds of compounds against La Crosse virus, an emerging bunyavirus that causes significant disease, including encephalitis. We identified several known and previously unidentified antivirals. We focused on a potassium ionophore, valinomycin, due to its promising in vitro antiviral activity. We demonstrate that valinomycin, as well as a selection of other ionophores, exhibits activity against La Crosse virus as well as several other distantly related bunyaviruses. We finally observe that valinomycin has activity against a wide array of human viral pathogens, suggesting that disrupting potassium ion homeostasis with valinomycin may be a potent host pathway to target to quell virus infection.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Zachary J Sandler", + "author_inst": "Loyola University Chicago" + }, + { + "author_name": "Michelle N Vu", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Vineet D. Menachery", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Bryan C. Mounce", + "author_inst": "Loyola University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.01.22.915660", "rel_title": "Functional assessment of cell entry and receptor usage for lineage B \u03b2-coronaviruses, including 2019-nCoV",